Research Elements: new article types by Elsevier to facilitate reproducibility in science

NASA Astrophysics Data System (ADS)

Zudilova-Seinstra, Elena; van Hensbergen, Kitty; Wacek, Bart

2016-04-01

When researchers start to make plans for new experiments, this is the beginning of a whole cycle of work, including experimental designs, tweaking of existing methods, developing protocols, writing code, collecting and processing experimental data, etc. A large part of this very useful information rarely gets published, which makes experiments difficult to reproduce. The same holds for experimental data, which is not always provided in a reusable format and lacks descriptive information. Furthermore, many types of data, such as a replication data, negative datasets or data from "intermediate experiments" often don't get published because they have no place in a research journal. To address this concern, Elsevier launched a series of peer-reviewed journal titles grouped under the umbrella of Research Elements (https://www.elsevier.com/books-and-journals/research-elements) that allow researchers to publish their data, software, materials and methods and other elements of the research cycle in a brief article format. To facilitate reproducibility, Research Elements have thoroughly thought out submission templates that include all necessary information and metadata as well as peer-review criteria defined per article type. Research Elements can be applicable to multiple research areas; for example, a number of multidisciplinary journals (Data in Brief, SoftwareX, MethodsX) welcome submissions from a large number of subject areas. At other times, these elements are better served within a single field; therefore, a number of domain-specific journals (e.g.: Genomics Data, Chemical Data Collections, Neurocomputing) support the new article formats, too. Upon publication, all Research Elements are assigned with persistent identifiers for direct citation and easy discoverability. Persistent identifiers are also used for interlinking Research Elements and relevant research papers published in traditional journals. Some Research Elements allow post-publication article updates. In the presentation, we will share our experiences and summarize lessons learned during the last two years. We will focus on three types of novel research publications: data articles, software articles and lab resources. We will also present two very recent developments targeting researchers working in Earth and Observational Sciences. And finally, we will illustrate how Research Elements fit in the Research Data Management landscape of a rich variety of services developed at Elsevier to assist researchers in sharing, finding, accessing, linking together and analyzing relevant research data.

Author Correction: Time-dependent memory transformation along the hippocampal anterior-posterior axis.

PubMed

Dandolo, Lisa C; Schwabe, Lars

2018-05-24

In the originally published version of this Article, the rightmost graph in Fig. 2c was inadvertently replaced with a duplicate of the central panel. This has now been corrected in both the PDF and HTML versions of the Article.

Publisher Correction: Anderson light localization in biological nanostructures of native silk.

PubMed

Choi, Seung Ho; Kim, Seong-Wan; Ku, Zahyun; Visbal-Onufrak, Michelle A; Kim, Seong-Ryul; Choi, Kwang-Ho; Ko, Hakseok; Choi, Wonshik; Urbas, Augustine M; Goo, Tae-Won; Kim, Young L

2018-03-19

The original PDF version of this Article contained errors in Equations 1 and 2. Both equations omitted all Γ terms. This has been corrected in the PDF version of the Article. The HTML version was correct from the time of publication.

Microform Resources on the Internet Project.

ERIC Educational Resources Information Center

Eichhorn, Sara J.; Yonezawa, Michael

1998-01-01

Summarizes information that will be used to describe microform sets on the University of California, Irvine's World Wide Web site for microform resources, including title, publisher, price, contents, index/bibliography, reviewed in, location/holdings, and Webpac site. Discusses staff/network resources, HTML/UNIX editors, and indexing/search…

Sinclair and Dyes Inlets Toxicity Study: An Assessment of Copper Bioavailability and Toxicity in Surface Waters Adjacent to the Puget Sound Naval Shipyard and Intermediate Maintenance Facility

DTIC Science & Technology

2009-12-01

biblio /92109.html WEF 2004a. “Proposed Research for Developing the Biotic Ligand Model for Establishing Water Quality Criteria. Water Environment...Systems Center, Bremerton, WA. August 2006. Ecology Publication Number 06-10-54 http://www.ecy.wa.gov/ biblio /0610054.html Eriksen, R.S., Mackey

Visual DMDX: A web-based authoring tool for DMDX, a Windows display program with millisecond accuracy.

PubMed

Garaizar, Pablo; Reips, Ulf-Dietrich

2015-09-01

DMDX is a software package for the experimental control and timing of stimulus display for Microsoft Windows systems. DMDX is reliable, flexible, millisecond accurate, and can be downloaded free of charge; therefore it has become very popular among experimental researchers. However, setting up a DMDX-based experiment is burdensome because of its command-based interface. Further, DMDX relies on RTF files in which parts of the stimuli, design, and procedure of an experiment are defined in a complicated (DMASTR-compatible) syntax. Other experiment software, such as E-Prime, Psychopy, and WEXTOR, became successful as a result of integrated visual authoring tools. Such an intuitive interface was lacking for DMDX. We therefore created and present here Visual DMDX (http://visualdmdx.com/), a HTML5-based web interface to set up experiments and export them to DMDX item files format in RTF. Visual DMDX offers most of the features available from the rich DMDX/DMASTR syntax, and it is a useful tool to support researchers who are new to DMDX. Both old and modern versions of DMDX syntax are supported. Further, with Visual DMDX, we go beyond DMDX by having added export to JSON (a versatile web format), easy backup, and a preview option for experiments. In two examples, one experiment each on lexical decision making and affective priming, we explain in a step-by-step fashion how to create experiments using Visual DMDX. We release Visual DMDX under an open-source license to foster collaboration in its continuous improvement.

An observational examination of the literature in diagnostic anatomic pathology.

PubMed

Foucar, Elliott; Wick, Mark R

2005-05-01

Original research published in the medical literature confronts the reader with three very basic and closely linked questions--are the authors' conclusions true in the contextual setting in which the work was performed (internally valid); if so, are the conclusions also applicable in other practice settings (externally valid); and, if the conclusions of the study are bona fide, do they represent an important contribution to medical practice or are they true-but-insignificant? Most publications attempt to convince readers that the researchers' conclusions are both internally valid and important, and occasionally papers also directly address external validity. Developing standardized methods to facilitate the prospective determination of research importance would be useful to both journals and their readers, but has proven difficult. In contrast, the evidence-based medicine (EBM) movement has had more success with understanding and codifying factors thought to promote research validity. Of the many variables that can influence research validity, research design is the one that has received the most attention. The present paper reviews the contributions of EBM to understanding research validity, looking for areas where EBM's body of knowledge is applicable to the anatomic pathology (AP) literature. As part of this project, the authors performed a pilot observational analysis of a representative sample of the current pertinent literature on diagnostic tissue pathology. The results of that review showed that most of the latter publications employ one of the four categories of "observational" research design that have been delineated by the EBM movement, and that the most common of these observational designs is a "cross-sectional" comparison. Pathologists do not presently use the "experimental" research designs so admired by advocates of EBM. Slightly > 50% of AP observational studies employed statistical evaluations to support their final conclusions. Comparison of the current AP literature with a selected group of papers published in 1977 shows a discernible change over that period that has affected not just technological procedures, but also research design and use of statistics. Although we feel that advocates of EBM deserve credit for bringing attention to the close link between research design and research validity, much of the EBM effort has centered on refining "experimental" methodology, and the complexities of observational research have often been treated in an inappropriately dismissive manner. For advocates of EBM, an observational study is what you are relegated to as a second choice when you are unable to do an experimental study. The latter viewpoint may be true for evaluating new chemotherapeutic agents, but is unacceptable to pathologists, whose research advances are currently completely dependent on well-conducted observational research. Rather than succumb to randomization envy and accept EBM's assertion that observational research is second best, the challenge to AP is to develop and adhere to standards for observational research that will allow our patients to benefit from the full potential of this time tested approach to developing valid insights into disease.

Hybrid Particle-Element Simulation of Impact on Composite Orbital Debris Shields

NASA Technical Reports Server (NTRS)

Fahrenthold, Eric P.

2004-01-01

This report describes the development of new numerical methods and new constitutive models for the simulation of hypervelocity impact effects on spacecraft. The research has included parallel implementation of the numerical methods and material models developed under the project. Validation work has included both one dimensional simulations, for comparison with exact solutions, and three dimensional simulations of published hypervelocity impact experiments. The validated formulations have been applied to simulate impact effects in a velocity and kinetic energy regime outside the capabilities of current experimental methods. The research results presented here allow for the expanded use of numerical simulation, as a complement to experimental work, in future design of spacecraft for hypervelocity impact effects.

Designing a Relational Database for the Basic School; Schools Command Web Enabled Officer and Enlisted Database (Sword)

DTIC Science & Technology

2002-06-01

Student memo for personnel MCLLS . . . . . . . . . . . . . . 75 i. Migrate data to SQL Server...The Web Server is on the same server as the SWORD database in the current version. 4: results set 5: dynamic HTML page 6: dynamic HTML page 3: SQL ...still be supported by Access. SQL Server would be a more viable tool for a fully developed application based on the number of potential users and

Implementing Clinical Research Using Factorial Designs: A Primer.

PubMed

Baker, Timothy B; Smith, Stevens S; Bolt, Daniel M; Loh, Wei-Yin; Mermelstein, Robin; Fiore, Michael C; Piper, Megan E; Collins, Linda M

2017-07-01

Factorial experiments have rarely been used in the development or evaluation of clinical interventions. However, factorial designs offer advantages over randomized controlled trial designs, the latter being much more frequently used in such research. Factorial designs are highly efficient (permitting evaluation of multiple intervention components with good statistical power) and present the opportunity to detect interactions amongst intervention components. Such advantages have led methodologists to advocate for the greater use of factorial designs in research on clinical interventions (Collins, Dziak, & Li, 2009). However, researchers considering the use of such designs in clinical research face a series of choices that have consequential implications for the interpretability and value of the experimental results. These choices include: whether to use a factorial design, selection of the number and type of factors to include, how to address the compatibility of the different factors included, whether and how to avoid confounds between the type and number of interventions a participant receives, and how to interpret interactions. The use of factorial designs in clinical intervention research poses choices that differ from those typically considered in randomized clinical trial designs. However, the great information yield of the former encourages clinical researchers' increased and careful execution of such designs. Copyright © 2017. Published by Elsevier Ltd.

Molecular anions.

PubMed

Simons, Jack

2008-07-24

The experimental and theoretical study of molecular anions has undergone explosive growth over the past 40 years. Advances in techniques used to generate anions in appreciable numbers as well as new ion-storage, ion-optics, and laser spectroscopic tools have been key on the experimental front. Theoretical developments on the electronic structure and molecular dynamics fronts now allow one to achieve higher accuracy and to study electronically metastable states, thus bringing theory in close collaboration with experiment in this field. In this article, many of the experimental and theoretical challenges specific to studying molecular anions are discussed. Results from many research groups on several classes of molecular anions are overviewed, and both literature citations and active (in online html and pdf versions) links to numerous contributing scientists' Web sites are provided. Specific focus is made on the following families of anions: dipole-bound, zwitterion-bound, double-Rydberg, multiply charged, metastable, cluster-based, and biological anions. In discussing each kind of anion, emphasis is placed on the structural, energetic, spectroscopic, and chemical-reactivity characteristics that make these anions novel, interesting, and important.

Establishment of expanded and streamlined pipeline of PITCh knock-in – a web-based design tool for MMEJ-mediated gene knock-in, PITCh designer, and the variations of PITCh, PITCh-TG and PITCh-KIKO

PubMed Central

Nakamae, Kazuki; Nishimura, Yuki; Takenaga, Mitsumasa; Sakamoto, Naoaki; Ide, Hiroshi; Sakuma, Tetsushi; Yamamoto, Takashi

2017-01-01

ABSTRACT The emerging genome editing technology has enabled the creation of gene knock-in cells easily, efficiently, and rapidly, which has dramatically accelerated research in the field of mammalian functional genomics, including in humans. We recently developed a microhomology-mediated end-joining-based gene knock-in method, termed the PITCh system, and presented various examples of its application. Since the PITCh system only requires very short microhomologies (up to 40 bp) and single-guide RNA target sites on the donor vector, the targeting construct can be rapidly prepared compared with the conventional targeting vector for homologous recombination-based knock-in. Here, we established a streamlined pipeline to design and perform PITCh knock-in to further expand the availability of this method by creating web-based design software, PITCh designer (http://www.mls.sci.hiroshima-u.ac.jp/smg/PITChdesigner/index.html), as well as presenting an experimental example of versatile gene cassette knock-in. PITCh designer can automatically design not only the appropriate microhomologies but also the primers to construct locus-specific donor vectors for PITCh knock-in. By using our newly established pipeline, a reporter cell line for monitoring endogenous gene expression, and transgenesis (TG) or knock-in/knockout (KIKO) cell line can be produced systematically. Using these new variations of PITCh, an exogenous promoter-driven gene cassette expressing fluorescent protein gene and drug resistance gene can be integrated into a safe harbor or a specific gene locus to create transgenic reporter cells (PITCh-TG) or knockout cells with reporter knock-in (PITCh-KIKO), respectively. PMID:28453368

Establishment of expanded and streamlined pipeline of PITCh knock-in - a web-based design tool for MMEJ-mediated gene knock-in, PITCh designer, and the variations of PITCh, PITCh-TG and PITCh-KIKO.

PubMed

Nakamae, Kazuki; Nishimura, Yuki; Takenaga, Mitsumasa; Nakade, Shota; Sakamoto, Naoaki; Ide, Hiroshi; Sakuma, Tetsushi; Yamamoto, Takashi

2017-05-04

The emerging genome editing technology has enabled the creation of gene knock-in cells easily, efficiently, and rapidly, which has dramatically accelerated research in the field of mammalian functional genomics, including in humans. We recently developed a microhomology-mediated end-joining-based gene knock-in method, termed the PITCh system, and presented various examples of its application. Since the PITCh system only requires very short microhomologies (up to 40 bp) and single-guide RNA target sites on the donor vector, the targeting construct can be rapidly prepared compared with the conventional targeting vector for homologous recombination-based knock-in. Here, we established a streamlined pipeline to design and perform PITCh knock-in to further expand the availability of this method by creating web-based design software, PITCh designer ( http://www.mls.sci.hiroshima-u.ac.jp/smg/PITChdesigner/index.html ), as well as presenting an experimental example of versatile gene cassette knock-in. PITCh designer can automatically design not only the appropriate microhomologies but also the primers to construct locus-specific donor vectors for PITCh knock-in. By using our newly established pipeline, a reporter cell line for monitoring endogenous gene expression, and transgenesis (TG) or knock-in/knockout (KIKO) cell line can be produced systematically. Using these new variations of PITCh, an exogenous promoter-driven gene cassette expressing fluorescent protein gene and drug resistance gene can be integrated into a safe harbor or a specific gene locus to create transgenic reporter cells (PITCh-TG) or knockout cells with reporter knock-in (PITCh-KIKO), respectively.

DIME Students Witness Test Drop

NASA Technical Reports Server (NTRS)

2002-01-01

Students watch a test run on their experiment before the actual drop. They designed and built their apparatus to fit within a NASA-provided drop structure. This was part of the second Dropping in a Microgravity Environment (DIME) competition held April 23-25, 2002, at NASA's Glenn Research Center. Competitors included two teams from Sycamore High School, Cincinnati, OH, and one each from Bay High School, Bay Village, OH, and COSI Academy, Columbus, OH. DIME is part of NASA's education and outreach activities. Details are on line at http://microgravity.grc.nasa.gov/DIME_2002.html.

DIME Students Show Off their Lego(TM) Challenge Creation

NASA Technical Reports Server (NTRS)

2002-01-01

Two students show the Lego (TM) Challenge device they designed and built to operate in the portable drop tower demonstrator as part of the second Dropping in a Microgravity Environment (DIME) competition held April 23-25, 2002, at NASA's Glenn Research Center. Competitors included two teams from Sycamore High School, Cincinnati, OH, and one each from Bay High School, Bay Village, OH, and COSI Academy, Columbus, OH. DIME is part of NASA's education and outreach activities. Details are on line at http://microgravity.grc.nasa.gov/DIME_2002.html.

Publisher Correction: Sumatran tiger survival threatened by deforestation despite increasing densities in parks.

PubMed

Luskin, Matthew Scott; Albert, Wido Rizki; Tobler, Mathias W

2018-02-12

In the original version of the Article, reference 18 was incorrectly numbered as reference 30, and references 19 to 30 were incorrectly numbered as 18 to 29. These errors have now been corrected in the PDF and HTML versions of the manuscript.

Publisher Correction: Recent progress and perspectives of space electric propulsion systems based on smart nanomaterials.

PubMed

Levchenko, I; Xu, S; Teel, G; Mariotti, D; Walker, M L R; Keidar, M

2018-04-10

The original PDF version of this Article had an incorrect volume number of '8'; it should have been '9'. This has been corrected in the PDF version of the Article. The HTML version was correct from the time of publication.

Interval-level measurement with visual analogue scales in Internet-based research: VAS Generator.

PubMed

Reips, Ulf-Dietrich; Funke, Frederik

2008-08-01

The present article describes VAS Generator (www.vasgenerator.net), a free Web service for creating a wide range of visual analogue scales that can be used as measurement devices in Web surveys and Web experimentation, as well as for local computerized assessment. A step-by-step example for creating and implementing a visual analogue scale with visual feedback is given. VAS Generator and the scales it generates work independently of platforms and use the underlying languages HTML and JavaScript. Results from a validation study with 355 participants are reported and show that the scales generated with VAS Generator approximate an interval-scale level. In light of previous research on visual analogue versus categorical (e.g., radio button) scales in Internet-based research, we conclude that categorical scales only reach ordinal-scale level, and thus visual analogue scales are to be preferred whenever possible.

How to successfully implement E-learning for both students and teachers.

PubMed

Gotthardt, Martin; Siegert, Maria J; Schlieck, Anja; Schneider, Stefan; Kohnert, Alfred; Gross, Markus W; Schäfer, Christine; Wagner, Richard; Hörmann, Stefan; Behr, Thomas M; Engenhart-Cabillic, Rita; Klose, Klaus J; Jungclas, Hartmut; Glowalla, Ulrich

2006-03-01

Electronic learning (e-learning) may provide a means to enhance learning efficacy. However, introduction of e-learning often fails. We describe a strategy of how an e-learning curriculum was successfully implemented. The curriculum was designed based on published evidence. It consists of self-directed learning, an online discussion forum, and discussion rounds. The e-content in nuclear medicine and radiotherapy was produced by the k-MED team of medical authors, web designers, and psychologists. The online courses were delivered via a dedicated learning management system. The e-content for diagnostic radiology and physics was provided as PDF/HTML script by the respective teachers who objected to participate in the k-MED project. The exam was taken online. Online evaluation of the curriculum by the students was taken at the end of the course. The new curriculum proved very effective. The time for the preparation for the clinical part of the radiology course could be reduced from 4 to 2 weeks. The students particularly enjoyed the self-directed learning. Although the material provided by k-MED received 90%-99% positive scores, the HTML and PDF scripts scored worse (13%-67% positive ratings). The positive results of the evaluation convinced the teachers responsible for physics and diagnostic radiology to participate in k-MED. As our example shows, new e-learning curricula can successfully be introduced. The strategy of implementation should be based on the existing evidence from the literature. The new curriculum helped to increase the efficacy of teaching and save time as the duration of the respective part of the course could be reduced by half.

A systematic review of the evidence concerning the economic impact of employee-focused health promotion and wellness programs.

PubMed

Lerner, Debra; Rodday, Angie Mae; Cohen, Joshua T; Rogers, William H

2013-02-01

To assess the evidence regarding the economic impact of worker health promotion programs. Peer-reviewed research articles were identified from a database search. Included articles were published between January 2000 and May 2010, described a study conducted in the United States that used an experimental or quasi-experimental study design and analyzed medical, pharmacy (direct), and/or work productivity (indirect) costs. A multidisciplinary review team, following specific criteria, assessed research quality. Of 2030 retrieved articles, 44 met study inclusion criteria. Of these, 10 were of sufficient quality to be considered evidentiary. Only three analyzed direct and indirect costs. Evidence regarding economic impact is limited and inconsistent. Higher-quality research is needed to demonstrate the value of specific programs.

Advanced Data Visualization in Astrophysics: The X3D Pathway

NASA Astrophysics Data System (ADS)

Vogt, Frédéric P. A.; Owen, Chris I.; Verdes-Montenegro, Lourdes; Borthakur, Sanchayeeta

2016-02-01

Most modern astrophysical data sets are multi-dimensional; a characteristic that can nowadays generally be conserved and exploited scientifically during the data reduction/simulation and analysis cascades. However, the same multi-dimensional data sets are systematically cropped, sliced, and/or projected to printable two-dimensional diagrams at the publication stage. In this article, we introduce the concept of the “X3D pathway” as a mean of simplifying and easing the access to data visualization and publication via three-dimensional (3D) diagrams. The X3D pathway exploits the facts that (1) the X3D 3D file format lies at the center of a product tree that includes interactive HTML documents, 3D printing, and high-end animations, and (2) all high-impact-factor and peer-reviewed journals in astrophysics are now published (some exclusively) online. We argue that the X3D standard is an ideal vector for sharing multi-dimensional data sets because it provides direct access to a range of different data visualization techniques, is fully open source, and is a well-defined standard from the International Organization for Standardization. Unlike other earlier propositions to publish multi-dimensional data sets via 3D diagrams, the X3D pathway is not tied to specific software (prone to rapid and unexpected evolution), but instead is compatible with a range of open-source software already in use by our community. The interactive HTML branch of the X3D pathway is also actively supported by leading peer-reviewed journals in the field of astrophysics. Finally, this article provides interested readers with a detailed set of practical astrophysical examples designed to act as a stepping stone toward the implementation of the X3D pathway for any other data set.

Solar Photovoltaic and Liquid Natural Gas Opportunities for Command Naval Region Hawaii

DTIC Science & Technology

2014-12-01

Utilities Commission xii PV Photovoltaic Pwr Power RE Renewable Energy Re-gas Regasification RFP Request For Proposal RMI Rocky... forecasted LS diesel price and the forecasted LNG delivered-to-the- power -plant cost. The forecast for LS diesel by FGE from year 2020–2030 is seen...annual/html/epa_08_01.html Electric Power Research Institute. (July, 2010). Addressing solar photovoltaic operations and maintenance challenges: A

Pre-clinical research in small animals using radiotherapy technology--a bidirectional translational approach.

PubMed

Tillner, Falk; Thute, Prasad; Bütof, Rebecca; Krause, Mechthild; Enghardt, Wolfgang

2014-12-01

For translational cancer research, pre-clinical in-vivo studies using small animals have become indispensable in bridging the gap between in-vitro cell experiments and clinical implementation. When setting up such small animal experiments, various biological, technical and methodical aspects have to be considered. In this work we present a comprehensive topical review based on relevant publications on irradiation techniques used for pre-clinical cancer research in mice and rats. Clinical radiotherapy treatment devices for the application of external beam radiotherapy and brachytherapy as well as dedicated research irradiation devices are feasible for small animal irradiation depending on the animal model and the experimental goals. In this work, appropriate solutions for the technological transfer of human radiation oncology to small animal radiation research are summarised. Additionally, important information concerning the experimental design is provided such that reliable and clinically relevant results can be attained. Copyright © 2014. Published by Elsevier GmbH.

Oral Health

MedlinePlus

... gov/widgets/fahc.html" width="243" height="179" title="Find a Health Center Widget" ... Atkinson, D.D.S., Chief, Center for Clinical Research, Division of Extramural Research, National Institute of Dental ...

The G3 Experience with Electronic Publishing: An Editor's Perspective

NASA Astrophysics Data System (ADS)

White, W. M.

2003-12-01

G3 (Geochemistry, Geophysics, Geosystems) is an all-electronic journal published jointly by the AGU, the Geochemical Society, and the European Association of Geochemistry. G3 publishes original scientific contributions pertaining to understanding the Earth as a system, including relevant observational, experimental, and theoretical investigations of the solid Earth, hydrosphere, atmosphere, and biosphere. The journal was initiated as a result of a grass roots effort with the following goals in mind: a copyright policy designed to enhance, rather than inhibit, the dissemination of scientific information (for example, allowing authors to post electronic reprints on their web sites), provide a means of publishing, in immediately useable formats, large data sets, provide a means for ready dissemination of computer modeling and analysis tools, and provide a forum where authors could use novel ways of illustrating both data and models (e.g., formats such as movies, virtual reality images, sound, mathematical models, etc.), and finally to reduce costs and speed publication. In most respects, G3 has been enormously successful and has met most of its goals. G3 began publishing in December of 1999; in the subsequent 3 1/2 years 625 papers have been submitted to it and 325 have been published. It currently has over 600 institutional and personal subscribers. Papers are submitted through the web (a variety of formats are accepted, however, Microsoft Word is most common) and are converted to Adobe pdf format for peer review. Except that it is fully electronic using the web and e-mail, the peer review process is traditional, which insures the quality of the papers published. Accepted papers are copyedited and converted to SGML for archival purposes. HTML and Acrobat pdf versions are then generated from the SGML and published as they are ready on the G3 web site (www.g-cubed.org). Large data sets are routinely published in digital formats that can be readily downloaded by readers and immediately imported into programs such as Excel. Numerous animations and movies have been published in animated GIF, Apple Quicktime, Macromedia Flash, and Wolfram Research Mathreader formats. Computer models and tools have been published as Excel Macros and MATLAB Scripts. Full color, high resolution images allow superior publication of detailed maps and photographs. While G3 is a success by most measures, the process of pioneering electronic publication has at times been painful and frustrating. Early on, there were problems and delays in converting files, particularly graphics, to pdf format for both review and final publication. Costs have been higher than anticipated - primarily due to the cost of file conversion and formatting. The time from acceptance to publication (currently 10 weeks), although improving, it still longer than the goal, again because of the time required for copy-editing and formatting. Automation of this process in the future is the primary opportunity to both reduce cost and further speed publication. Authors have been slow to take advantage of the new illustration formats, with most relying on tradition figures instead. This will likely change slowly in the future, as these new formats, and the software tools to create them, become more familiar.

NASAwide electronic publishing system: Prototype STI electronic document distribution, stage-4 evaluation report

NASA Technical Reports Server (NTRS)

Tuey, Richard C.; Collins, Mary; Caswell, Pamela; Haynes, Bob; Nelson, Michael L.; Holm, Jeanne; Buquo, Lynn; Tingle, Annette; Cooper, Bill; Stiltner, Roy

1996-01-01

This evaluation report contains an introduction, seven chapters, and five appendices. The Introduction describes the purpose, conceptual frame work, functional description, and technical report server of the STI Electronic Document Distribution (EDD) project. Chapter 1 documents the results of the prototype STI EDD in actual operation. Chapter 2 documents each NASA center's post processing publication processes. Chapter 3 documents each center's STI software, hardware, and communications configurations. Chapter 7 documents STI EDD policy, practices, and procedures. The appendices, which arc contained in Part 2 of this document, consist of (1) STI EDD Project Plan, (2) Team members, (3) Phasing Schedules, (4) Accessing On-line Reports, and (5) Creating an HTML File and Setting Up an xTRS. In summary, Stage 4 of the NASAwide Electronic Publishing System is the final phase of its implementation through the prototyping and gradual integration of each NASA center's electronic printing systems, desktop publishing systems, and technical report servers to be able to provide to NASA's engineers, researchers, scientists, and external users the widest practicable and appropriate dissemination of information concerning its activities and the result thereof to their work stations.

NASAwide electronic publishing system-prototype STI electronic document distribution: Stage-4 evaluation report. Part 2; Appendices

NASA Technical Reports Server (NTRS)

Tuey, Richard C.; Collins, Mary; Caswell, Pamela; Haynes, Bob; Nelson, Michael L.; Holm, Jeanne; Buquo, Lynn; Tingle, Annette; Cooper, Bill; Stiltner, Roy

1996-01-01

This evaluation report contains an introduction, seven chapters, and five appendices. The Introduction describes the purpose, conceptual framework, functional description, and technical report server of the Scientific and Technical Information (STI) Electronic Document Distribution (EDD) project. Chapter 1 documents the results of the prototype STI EDD in actual operation. Chapter 2 documents each NASA center's post processing publication processes. Chapter 3 documents each center's STI software, hardware. and communications configurations. Chapter 7 documents STI EDD policy, practices, and procedures. The appendices consist of (A) the STI EDD Project Plan, (B) Team members, (C) Phasing Schedules, (D) Accessing On-line Reports, and (E) Creating an HTML File and Setting Up an xTRS. In summary, Stage 4 of the NASAwide Electronic Publishing System is the final phase of its implementation through the prototyping and gradual integration of each NASA center's electronic printing systems, desk top publishing systems, and technical report servers, to be able to provide to NASA's engineers, researchers, scientists, and external users, the widest practicable and appropriate dissemination of information concerning its activities and the result thereof to their work stations.

Fire-induced water-repellent soils, an annotated bibliography

USGS Publications Warehouse

Kalendovsky, M.A.; Cannon, S.H.

1997-01-01

The development and nature of water-repellent, or hydrophobic, soils are important issues in evaluating hillslope response to fire. The following annotated bibliography was compiled to consolidate existing published research on the topic. Emphasis was placed on the types, causes, effects and measurement techniques of water repellency, particularly with respect to wildfires and prescribed burns. Each annotation includes a general summary of the respective publication, as well as highlights of interest to this focus. Although some references on the development of water repellency without fires, the chemistry of hydrophobic substances, and remediation of water-repellent conditions are included, coverage of these topics is not intended to be comprehensive. To develop this database, the GeoRef, Agricola, and Water Resources Abstracts databases were searched for appropriate references, and the bibliographies of each reference were then reviewed for additional entries. Additional references will be added to this bibliography as they become available. The annotated bibliography can be accessed on the Web at http://geohazards.cr.usgs.gov/html_files/landslides/ofr97-720/biblio.html. A database consisting of the references and keywords is available through a link at the above address. This database was compiled using EndNote2 plus software by Niles and Associates, and is necessary to search the database.

A review of temporomandibular joint-related papers published between 2014-2015.

PubMed

Singh, Vaibhav; Sudhakar, K N V; Mallela, Kiran Kumar; Mohanty, Rajat

2017-12-01

We conducted a retrospective study and reviewed the temporomandibular joint (TMJ)-related papers published in a leading international journal, Journal of Oral and Maxillofacial Surgery , between January 2014 and December 2015. The study was conducted to ascertain and compare the trends of articles being published in the years 2014 and 2015. A total of 28 articles were reviewed, of which most of the full-length articles were on clinical management and outcomes and the role of radiology. The bulk of the studies were prospective, and less interest was shown in experimental research. A thorough review and analysis thus gives the impression that there is a great need for well-designed clinical studies on TMJ.

Publisher Correction: Selective enhancement of optical nonlinearity in two-dimensional organic-inorganic lead iodide perovskites.

PubMed

Saouma, F O; Stoumpos, C C; Wong, J; Kanatzidis, M G; Jang, J I

2017-11-23

In the PDF version of this article, Eq. 5 is missing all elements after the equals sign. The correct version of Eq. 5 is given below. The HTML version of the paper was correct from the time of publication.[Formula: see text].

Author Correction: Smac mimetics and oncolytic viruses synergize in driving anticancer T-cell responses through complementary mechanisms.

PubMed

Kim, Dae-Sun; Dastidar, Himika; Zhang, Chunfen; Zemp, Franz J; Lau, Keith; Ernst, Matthias; Rakic, Andrea; Sikdar, Saif; Rajwani, Jahanara; Naumenko, Victor; Balce, Dale R; Ewanchuk, Ben W; Tailor, Pankaj; Yates, Robin M; Jenne, Craig; Gafuik, Chris; Mahoney, Douglas J

2018-05-24

The originally published version of this article contained an error in the spelling of the author Pankaj Tailor, which was incorrectly given as Pankaj Taylor. This has now been corrected in both the PDF and HTML versions of the article.

76 FR 68438 - Environmental Impacts Statements; Notice of Availability

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-04

... Los Angeles River between Mateo and Mill Streets, Los Angeles County, CA, Review Period Ends: 12/05..., USFWS, CA, Southern Sea Otters (Enhydra lutris nereis) Translocation Program, Updated Information to the.../species_information/so_sea_otter/index.html . Revision of FR Notice Published 08/26/2011: Reopening...

Author Correction: Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation.

PubMed

Preissl, Sebastian; Fang, Rongxin; Huang, Hui; Zhao, Yuan; Raviram, Ramya; Gorkin, David U; Zhang, Yanxiao; Sos, Brandon C; Afzal, Veena; Dickel, Diane E; Kuan, Samantha; Visel, Axel; Pennacchio, Len A; Zhang, Kun; Ren, Bing

2018-03-01

In the version of this article initially published online, the accession code was given as GSE1000333. The correct code is GSE100033. The error has been corrected in the print, HTML and PDF versions of the article.

XML: A Publisher's Perspective.

ERIC Educational Resources Information Center

Andrews, Timothy M.

1999-01-01

Explains eXtensible Markup Language (XML) and describes how Dow Jones Interactive is using it to improve the news-gathering and dissemination process through intranets and the World Wide Web. Discusses benefits of using XML, the relationship to HyperText Markup Language (HTML), lack of available software tools and industry support, and future…

78 FR 12801 - Advisory Committee on Reactor Safeguards; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-25

... meetings were published in the Federal Register on October 18, 2012, (77 FR 64146-64147). In accordance.../reading-rm/adams.html or http://www.nrc.gov/reading-rm/doc-collections/ACRS/ . Video teleconferencing... providing the equipment and facilities that they use to establish the video teleconferencing link. The...

Maximum unbiased validation (MUV) data sets for virtual screening based on PubChem bioactivity data.

PubMed

Rohrer, Sebastian G; Baumann, Knut

2009-02-01

Refined nearest neighbor analysis was recently introduced for the analysis of virtual screening benchmark data sets. It constitutes a technique from the field of spatial statistics and provides a mathematical framework for the nonparametric analysis of mapped point patterns. Here, refined nearest neighbor analysis is used to design benchmark data sets for virtual screening based on PubChem bioactivity data. A workflow is devised that purges data sets of compounds active against pharmaceutically relevant targets from unselective hits. Topological optimization using experimental design strategies monitored by refined nearest neighbor analysis functions is applied to generate corresponding data sets of actives and decoys that are unbiased with regard to analogue bias and artificial enrichment. These data sets provide a tool for Maximum Unbiased Validation (MUV) of virtual screening methods. The data sets and a software package implementing the MUV design workflow are freely available at http://www.pharmchem.tu-bs.de/lehre/baumann/MUV.html.

Demonstrating S-NPP VIIRS Products with the Naval Research Laboratory R&D Websites

NASA Astrophysics Data System (ADS)

Kuciauskas, A. P.; Hawkins, J.; Solbrig, J.; Bankert, R.; Richardson, K.; Surratt, M.; Miller, S. D.; Kent, J.

2014-12-01

The Naval Research Laboratory, Marine Meteorology Division in Monterey, CA (NRL-MRY) has been developing and providing the global community with VIIRS-derived state of the art image products on three operational websites: · NexSat: www.nrlmry.navy.mil/NEXSAT.html · VIIRS Page: www.nrlmry.navy.mil/VIIRS.html · Tropical Cyclone Page: www.nrlmry.navy.mil/TC.html These user-friendly websites are accessed by the global public with a daily average of 250,000 and 310,000 web hits for NexSat and Tropical Cyclone websites, respectively. Users consist of operational, research, scientific field campaigns, academia, and weather enthusiasts. The websites also contain ancillary products from 5 geostationary and 27 low earth orbiting sensors, ranging from visible through microwave channels. NRL-MRY also leverages the NRL global and regional numerical weather prediction (NWP) models for assessing cloud top measurements and synoptic overlays. With collaborations at CIMSS' Direct Readout site along with the AFWA IDPS-FNMOC and NOAA IDPS portals, a robust component to our websites are product latencies that typically satisfy operational time constraints necessary for planning purposes. Given these resources, NRL-MRY acquires ~2TBytes of data and produces 100,000 image products on a daily basis. In partnership with the COMET program, our product tutorials contain simple and graphically enhanced descriptions that accommodate users ranging from basic to advanced understanding of satellite meteorology. This presentation will provide an overview of our website functionality: animations, co-registered formats, and Google Earth viewing. Through imagery, we will also demonstrate the superiority of VIIRS against its heritage sensor counterparts. A focal aspect will be the demonstration of the VIIRS Day Night Band (DNB) in detecting nighttime features such as wildfires, volcanic ash, Arctic sea ice, and tropical cyclones. We also plan to illustrate how NexSat and VIIRS websites demonstrate CAL/VAL ocean color activity. We will also discuss outreach and training efforts designed for research and operational applications. Our goal is to encourage the audience to add our URLs into their suite of web-based satellite resources.

Heterogeneous Biomedical Database Integration Using a Hybrid Strategy: A p53 Cantcer Research Database

PubMed Central

Bichutskiy, Vadim Y.; Colman, Richard; Brachmann, Rainer K.; Lathrop, Richard H.

2006-01-01

Complex problems in life science research give rise to multidisciplinary collaboration, and hence, to the need for heterogeneous database integration. The tumor suppressor p53 is mutated in close to 50% of human cancers, and a small drug-like molecule with the ability to restore native function to cancerous p53 mutants is a long-held medical goal of cancer treatment. The Cancer Research DataBase (CRDB) was designed in support of a project to find such small molecules. As a cancer informatics project, the CRDB involved small molecule data, computational docking results, functional assays, and protein structure data. As an example of the hybrid strategy for data integration, it combined the mediation and data warehousing approaches. This paper uses the CRDB to illustrate the hybrid strategy as a viable approach to heterogeneous data integration in biomedicine, and provides a design method for those considering similar systems. More efficient data sharing implies increased productivity, and, hopefully, improved chances of success in cancer research. (Code and database schemas are freely downloadable, http://www.igb.uci.edu/research/research.html.) PMID:19458771

Informatics in radiology (infoRAD): HTML and Web site design for the radiologist: a primer.

PubMed

Ryan, Anthony G; Louis, Luck J; Yee, William C

2005-01-01

A Web site has enormous potential as a medium for the radiologist to store, present, and share information in the form of text, images, and video clips. With a modest amount of tutoring and effort, designing a site can be as painless as preparing a Microsoft PowerPoint presentation. The site can then be used as a hub for the development of further offshoots (eg, Web-based tutorials, storage for a teaching library, publication of information about one's practice, and information gathering from a wide variety of sources). By learning the basics of hypertext markup language (HTML), the reader will be able to produce a simple and effective Web page that permits display of text, images, and multimedia files. The process of constructing a Web page can be divided into five steps: (a) creating a basic template with formatted text, (b) adding color, (c) importing images and multimedia files, (d) creating hyperlinks, and (e) uploading one's page to the Internet. This Web page may be used as the basis for a Web-based tutorial comprising text documents and image files already in one's possession. Finally, there are many commercially available packages for Web page design that require no knowledge of HTML.

Optimal design of stimulus experiments for robust discrimination of biochemical reaction networks.

PubMed

Flassig, R J; Sundmacher, K

2012-12-01

Biochemical reaction networks in the form of coupled ordinary differential equations (ODEs) provide a powerful modeling tool for understanding the dynamics of biochemical processes. During the early phase of modeling, scientists have to deal with a large pool of competing nonlinear models. At this point, discrimination experiments can be designed and conducted to obtain optimal data for selecting the most plausible model. Since biological ODE models have widely distributed parameters due to, e.g. biologic variability or experimental variations, model responses become distributed. Therefore, a robust optimal experimental design (OED) for model discrimination can be used to discriminate models based on their response probability distribution functions (PDFs). In this work, we present an optimal control-based methodology for designing optimal stimulus experiments aimed at robust model discrimination. For estimating the time-varying model response PDF, which results from the nonlinear propagation of the parameter PDF under the ODE dynamics, we suggest using the sigma-point approach. Using the model overlap (expected likelihood) as a robust discrimination criterion to measure dissimilarities between expected model response PDFs, we benchmark the proposed nonlinear design approach against linearization with respect to prediction accuracy and design quality for two nonlinear biological reaction networks. As shown, the sigma-point outperforms the linearization approach in the case of widely distributed parameter sets and/or existing multiple steady states. Since the sigma-point approach scales linearly with the number of model parameter, it can be applied to large systems for robust experimental planning. An implementation of the method in MATLAB/AMPL is available at http://www.uni-magdeburg.de/ivt/svt/person/rf/roed.html. flassig@mpi-magdeburg.mpg.de Supplementary data are are available at Bioinformatics online.

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

Carnes, E.T.; Truett, D.F.; Truett, L.F.

In the handful of years since the World Wide Web (WWW or Web) came into being, Web sites have developed at an astonishing rate. With the influx of Web pages comes a disparity of site types, including personal homepages, commercial sales sites, and educational data. The variety of sites and the deluge of information contained on the Web exemplify the individual nature of the WWW. Whereas some people argue that it is this eclecticism which gives the Web its charm, we propose that sites which are repositories of technical data would benefit from standardization. This paper proffers a methodology formore » publishing ecological research on the Web. The template we describe uses capabilities of HTML (the HyperText Markup Language) to enhance the value of the traditional scientific paper.« less

Design standards for experimental and field studies to evaluate diagnostic accuracy of tests for infectious diseases in aquatic animals.

PubMed

Laurin, E; Thakur, K K; Gardner, I A; Hick, P; Moody, N J G; Crane, M S J; Ernst, I

2018-05-01

Design and reporting quality of diagnostic accuracy studies (DAS) are important metrics for assessing utility of tests used in animal and human health. Following standards for designing DAS will assist in appropriate test selection for specific testing purposes and minimize the risk of reporting biased sensitivity and specificity estimates. To examine the benefits of recommending standards, design information from published DAS literature was assessed for 10 finfish, seven mollusc, nine crustacean and two amphibian diseases listed in the 2017 OIE Manual of Diagnostic Tests for Aquatic Animals. Of the 56 DAS identified, 41 were based on field testing, eight on experimental challenge studies and seven on both. Also, we adapted human and terrestrial-animal standards and guidelines for DAS structure for use in aquatic animal diagnostic research. Through this process, we identified and addressed important metrics for consideration at the design phase: study purpose, targeted disease state, selection of appropriate samples and specimens, laboratory analytical methods, statistical methods and data interpretation. These recommended design standards for DAS are presented as a checklist including risk-of-failure points and actions to mitigate bias at each critical step. Adherence to standards when designing DAS will also facilitate future systematic review and meta-analyses of DAS research literature. © 2018 John Wiley & Sons Ltd.

Where We Have Been and Where We Are Going: A Content Analysis of Articles Published in the Journal of Women's Health Physical Therapy From 2005 to 2015

PubMed Central

Coronado, Rogelio A.; Hill, Alexandra D.; Alappattu, Meryl J.

2018-01-01

Objective The objective of this study was to examine the type and content of Journal of Women’s Health Physical Therapy (JWHPT) publications over the last decade. Study Design Content and bibliometric analysis of published literature Background Component sections, such as the Section on Women’s Health (SoWH) of the American Physical Therapy Association provide content expertise to areas of specialty physical therapist practice, thereby supporting the dissemination of evidence for physical therapists to use. Closely aligned with the mission of the SoWH, JWHPT provides evidence reflecting this practice area. The purpose of our analysis was to examine publications within JWHPT to determine how closely JWHPT is meeting the mission and focus of section members. Methods and Measures We used established bibliographic methodology to code and review manuscripts published online between 2005 and 2015 in JWHPT using established domains (article type, participant type, research design, study purpose, and area of focus). Total publications and proportion of publications based on domain were described. Impact by citation and author was examined using bibliometric software. Results Eighteen percent of the items published in JWHPT were original research papers submitted for the first time. Of those papers, the primary study design was cross-sectional experimental research, most commonly studying interventions. The primary practice area reported was management of incontinence. Conclusions We suggest that a continued need to increase efforts for the submission and publication of a greater proportion of randomized controlled trials and metric articles. PMID:29375281

Military Personnel Attrition and Retention: Research in Progress

DTIC Science & Technology

1981-10-01

designed to assess the relative risks of attrition among non -h.gh. school graduate Army enlistees. As a group, these individuals historically...this methodology see the Majcýhrzak paper in this volume) Research in the PlanningStaaqe Stage ’TV: Administrative Experimentation In order to derive...different research designs : 1. True experimental designs ; 2. Correlational research designs ; 3. Quasi- experimental research designs . We rejected the idea

Improving planning, design, reporting and scientific quality of animal experiments by using the Gold Standard Publication Checklist, in addition to the ARRIVE guidelines.

PubMed

Hooijmans, Carlijn R; de Vries, Rob; Leenaars, Marlies; Curfs, Jo; Ritskes-Hoitinga, Merel

2011-03-01

Several studies have demonstrated serious omissions in the way research that use animals is reported. In order to improve the quality of reporting of animal experiments, the Animals in research: reporting in vivo experiments (ARRIVE) Guidelines were published in the British Journal of Pharmacology in August 2010. However, not only the quality of reporting of completed animal studies needs to be improved, but also the design and execution of new experiments. With both these goals in mind, we published the Gold Standard Publication Checklist (GSPC) in May 2010, a few months before the ARRIVE guidelines appeared. In this letter, we compare the GSPC checklist with the ARRIVE Guidelines. The GSPC describes certain items in more detail, which makes it both easier to use when designing and conducting an experiment and particularly suitable for making systematic reviews of animal studies more feasible. In order to improve not only the reporting but also the planning, design, execution and thereby, the scientific quality of animal experiments, we strongly recommend to all scientists involved in animal experimentation and to editors of journals publishing animal studies to take a closer look at the contents of both the ARRIVE guidelines and GSPC, and select the set of guidelines which is most appropriate for their particular situation. © 2011 The Authors. British Journal of Pharmacology © 2011 The British Pharmacological Society.

Documenting the Emergence of Electronic Nicotine Delivery Systems as a Disruptive Technology in Nicotine and Tobacco Science

PubMed Central

Correa, John B.; Ariel, Idan; Menzie, Nicole S.; Brandon, Thomas H.

2016-01-01

Background The emergence of the electronic nicotine delivery systems (ENDS, or “e-cigarettes”) has resulted in nicotine and tobacco scientists committing increased resources to studying these products. Despite this surge of research on various topics related to e-cigarettes, it is important to characterize the evolving e-cigarette research landscape as a way to identify important future research directions. The purpose of this review was to broadly categorize published scholarly work on e-cigarettes using a structured, multi-level coding scheme. Methods A systematic literature search was conducted to collect articles on e-cigarettes that were published in peer-reviewed journals from 2006 through 2014. Studies were classified through 3 coding waves. Articles were first divided into research reports, literature reviews and opinions/editorials. Research reports were further categorized to determine the proportion of these studies using human participants. Finally, human studies were classified based on their methodologies: descriptive, predictive, explanatory, and intervention. Results Research reports (n = 224) and opinions/editorials (n = 248) were published at similar rates during this time period. All types of articles showed exponential rates of increase in more recent years. 76.3% of human research studies tended to be descriptive in nature, with very little research employing experimental (6.8%) or intervention-based methodologies (5.4%). Conclusions This review reinforces the idea that e-cigarettes are a disruptive technology exerting substantial influence on nicotine and tobacco science. This review also suggests that opinions on e-cigarettes may be outpacing our scientific understanding of these devices. Our findings highlight the need for more e-cigarette research involving experimental, intervention, and longitudinal designs. PMID:27816664

Documenting the emergence of electronic nicotine delivery systems as a disruptive technology in nicotine and tobacco science.

PubMed

Correa, John B; Ariel, Idan; Menzie, Nicole S; Brandon, Thomas H

2017-02-01

The emergence of electronic nicotine delivery systems (ENDS, or "e-cigarettes") has resulted in nicotine and tobacco scientists committing increased resources to studying these products. Despite this surge of research on various topics related to e-cigarettes, it is important to characterize the evolving e-cigarette research landscape as a way to identify important future research directions. The purpose of this review was to broadly categorize published scholarly work on e-cigarettes using a structured, multi-level coding scheme. A systematic literature search was conducted to collect articles on e-cigarettes that were published in peer-reviewed journals from 2006 through 2014. Studies were classified through 3 coding waves. Articles were first divided into research reports, literature reviews and opinions/editorials. Research reports were further categorized to determine the proportion of these studies using human participants. Finally, human studies were classified based on their methodologies: descriptive, predictive, explanatory, and intervention. Research reports (n=224) and opinions/editorials (n=248) were published at similar rates during this time period. All types of articles showed exponential rates of increase in more recent years. 76.4% of human research studies were descriptive in nature, with very little research employing experimental (6.8%) or intervention-based methodologies (5.4%). This review reinforces the idea that e-cigarettes are a disruptive technology exerting substantial influence on nicotine and tobacco science. This review also suggests that opinions on e-cigarettes may be outpacing our scientific understanding of these devices. Our findings highlight the need for more e-cigarette research involving experimental, intervention, and longitudinal designs. Copyright © 2016 Elsevier Ltd. All rights reserved.

Signaling network of dendritic cells in response to pathogens: a community-input supported knowledgebase.

PubMed

Patil, Sonali; Pincas, Hanna; Seto, Jeremy; Nudelman, German; Nudelman, Irina; Sealfon, Stuart C

2010-10-07

Dendritic cells are antigen-presenting cells that play an essential role in linking the innate and adaptive immune systems. Much research has focused on the signaling pathways triggered upon infection of dendritic cells by various pathogens. The high level of activity in the field makes it desirable to have a pathway-based resource to access the information in the literature. Current pathway diagrams lack either comprehensiveness, or an open-access editorial interface. Hence, there is a need for a dependable, expertly curated knowledgebase that integrates this information into a map of signaling networks. We have built a detailed diagram of the dendritic cell signaling network, with the goal of providing researchers with a valuable resource and a facile method for community input. Network construction has relied on comprehensive review of the literature and regular updates. The diagram includes detailed depictions of pathways activated downstream of different pathogen recognition receptors such as Toll-like receptors, retinoic acid-inducible gene-I-like receptors, C-type lectin receptors and nucleotide-binding oligomerization domain-like receptors. Initially assembled using CellDesigner software, it provides an annotated graphical representation of interactions stored in Systems Biology Mark-up Language. The network, which comprises 249 nodes and 213 edges, has been web-published through the Biological Pathway Publisher software suite. Nodes are annotated with PubMed references and gene-related information, and linked to a public wiki, providing a discussion forum for updates and corrections. To gain more insight into regulatory patterns of dendritic cell signaling, we analyzed the network using graph-theory methods: bifan, feedforward and multi-input convergence motifs were enriched. This emphasis on activating control mechanisms is consonant with a network that subserves persistent and coordinated responses to pathogen detection. This map represents a navigable aid for presenting a consensus view of the current knowledge on dendritic cell signaling that can be continuously improved through contributions of research community experts. Because the map is available in a machine readable format, it can be edited and may assist researchers in data analysis. Furthermore, the availability of a comprehensive knowledgebase might help further research in this area such as vaccine development. The dendritic cell signaling knowledgebase is accessible at http://tsb.mssm.edu/pathwayPublisher/DC_pathway/DC_pathway_index.html.

Utah Virtual Lab: JAVA interactivity for teaching science and statistics on line.

PubMed

Malloy, T E; Jensen, G C

2001-05-01

The Utah on-line Virtual Lab is a JAVA program run dynamically off a database. It is embedded in StatCenter (www.psych.utah.edu/learn/statsampler.html), an on-line collection of tools and text for teaching and learning statistics. Instructors author a statistical virtual reality that simulates theories and data in a specific research focus area by defining independent, predictor, and dependent variables and the relations among them. Students work in an on-line virtual environment to discover the principles of this simulated reality: They go to a library, read theoretical overviews and scientific puzzles, and then go to a lab, design a study, collect and analyze data, and write a report. Each student's design and data analysis decisions are computer-graded and recorded in a database; the written research report can be read by the instructor or by other students in peer groups simulating scientific conventions.

Astrophysical blast wave data

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

Riley, Nathan; Geissel, Matthias; Lewis, Sean M

2015-03-01

The data described in this document consist of image files of shadowgraphs of astrophysically relevant laser driven blast waves. Supporting files include Mathematica notebooks containing design calculations, tabulated experimental data and notes, and relevant publications from the open research literature. The data was obtained on the Z-Beamlet laser from July to September 2014. Selected images and calculations will be published as part of a PhD dissertation and in associated publications in the open research literature, with Sandia credited as appropriate. The authors are not aware of any restrictions that could affect the release of the data.

A review on human reinstatement studies: an overview and methodological challenges

PubMed Central

Haaker, Jan; Golkar, Armita; Hermans, Dirk

2014-01-01

In human research, studies of return of fear (ROF) phenomena, and reinstatement in particular, began only a decade ago and recently are more widely used, e.g., as outcome measures for fear/extinction memory manipulations (e.g., reconsolidation). As reinstatement research in humans is still in its infancy, providing an overview of its stability and boundary conditions and summarizing methodological challenges is timely to foster fruitful future research. As a translational endeavor, clarifying the circumstances under which (experimental) reinstatement occurs may offer a first step toward understanding relapse as a clinical phenomenon and pave the way for the development of new pharmacological or behavioral ways to prevent ROF. The current state of research does not yet allow pinpointing these circumstances in detail and we hope this review will aid the research field to advance in this direction. As an introduction, we begin with a synopsis of rodent work on reinstatement and theories that have been proposed to explain the findings. The review however mainly focuses on reinstatement in humans. We first describe details and variations of the experimental setup in reinstatement studies in humans and give a general overview of results. We continue with a compilation of possible experimental boundary conditions and end with the role of individual differences and behavioral and/or pharmacological manipulations. Furthermore, we compile important methodological and design details on the published studies in humans and end with open research questions and some important methodological and design recommendations as a guide for future research. PMID:25128533

75 FR 36374 - Privacy Act of 1974; System of Records

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-25

... this document is the document published in the Federal Register. Free Internet access to the official... the deaf (TDD), call the Federal Relay Service (FRS), toll free, at 1-800-877-8339. Accessible Format... the Internet at the following site: http:// www.ed.gov/news/fedregister/index.html . To use PDF you...

76 FR 27309 - Committee on Measures of Student Success

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-11

... version of this document is the document published in the Federal Register. Free Internet access to the... text or Adobe Portable Document Format (PDF) on the Internet at the following site: http://www.ed.gov/news/fed-register/index.html . To use PDF you must have Adobe Acrobat Reader, which is available free...

Erratum: Erratum: Annealing effect of fluorine-doped SnO2/WO3 core-shell inverse opal nanoarchitecture for photoelectrochemical water splitting

NASA Astrophysics Data System (ADS)

Cho, Seo Yoon; Kang, Soon Hyung; Yun, Gun; Balamurugan, Maheswari; Ahn, Kwang-Soon

2018-03-01

In the version of this article initially published, the name of co- author Maheswari was incorrect. The correct name is Maheswari Arunachalam. The error has been corrected in the HTML and PDF versions of the article.

Enhanced Cyberspace Defense through Covert Publish-Subscribe Broker Pattern Communications

DTIC Science & Technology

2008-06-01

http://www.cnn.com/TECH/computing/9902/26/t_t/internet.time/, accessed June 2008. [3] C. V. Clausewitz, On War, 1st ed.. London, England: Kegan ...34 2003. [17] T. Greene . (2008 , Apr.) Network World. [Online]. http://www.networkworld.com/news/2008/040908-rsa-hack-power-grid.html, accessed

21 CFR 184.1259 - Cocoa butter substitute.

Code of Federal Regulations, 2013 CFR

2013-04-01

..._locations.html. (9) Hexane—not more than 5 parts per million as determined by the method of Dupuy et al., “Rapid Quantitative Determination of Residual Hexane in Oils by Direct Gas Chromatography,” published in... good manufacturing practice: Confections and frostings as defined in § 170.3(n)(9) of this chapter...

21 CFR 184.1259 - Cocoa butter substitute.

Code of Federal Regulations, 2012 CFR

2012-04-01

..._locations.html. (9) Hexane—not more than 5 parts per million as determined by the method of Dupuy et al., “Rapid Quantitative Determination of Residual Hexane in Oils by Direct Gas Chromatography,” published in... good manufacturing practice: Confections and frostings as defined in § 170.3(n)(9) of this chapter...

75 FR 20040 - Waiver Extension Request

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-16

... equipment and testing, commencing in the summer of 2011, for a period of 39 months, or approval of a..., etc.). You may review the DOT's complete Privacy Act Statement in the Federal Register published on April 11, 2000 (Volume 65, Number 70; Pages 19477-78) or at http://dot.gov/privacy.html . Issued in...

Workshop on quantum stochastic differential equations for the quantum simulation of physical systems

DTIC Science & Technology

2016-09-22

University of Tennessee. The web site for the Workshop is http://aesop.phys.utk.edu/QI/Workshop.html. (a) Papers published in peer-reviewed journals ( N ...List the papers, including journal references, in the following categories: (b) Papers published in non-peer-reviewed journals ( N /A for none) (c...Lomonaco, A. Spörl, N . Pomplun, J. Myers, and S. J. Glaser, NMR Quantum Calculations of the Jones Polynomial, Phys. Rev. A 81, 032319 (2010). [13] S. J

Effect of Simulation on Undergraduate Nursing Students' Knowledge of Nursing Ethics Principles.

PubMed

Donnelly, Mary Broderick; Horsley, Trisha Leann; Adams, William H; Gallagher, Peggy; Zibricky, C Dawn

2017-12-01

Background Undergraduate nursing education standards include acquisition of knowledge of ethics principles and the prevalence of health-care ethical dilemmas mandates that nursing students study ethics. However, little research has been published to support best practices for teaching/learning ethics principles. Purpose This study sought to determine if participation in an ethics consultation simulation increased nursing students' knowledge of nursing ethics principles compared to students who were taught ethics principles in the traditional didactic format. Methods This quasi-experimental study utilized a pre-test/post-test design with randomized assignment of students at three universities into both control and experimental groups. Results Nursing students' knowledge of nursing ethics principles significantly improved from pre-test to post-test ( p = .002); however, there was no significant difference between the experimental and control groups knowledge scores ( p = .13). Conclusion Further research into use of simulation to teach ethics principles is indicated.

Assessment & Commitment Tracking System (ACTS)

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

Bryant, Robert A.; Childs, Teresa A.; Miller, Michael A.

2004-12-20

The ACTS computer code provides a centralized tool for planning and scheduling assessments, tracking and managing actions associated with assessments or that result from an event or condition, and "mining" data for reporting and analyzing information for improving performance. The ACTS application is designed to work with the MS SQL database management system. All database interfaces are written in SQL. The following software is used to develop and support the ACTS application: Cold Fusion HTML JavaScript Quest TOAD Microsoft Visual Source Safe (VSS) HTML Mailer for sending email Microsoft SQL Microsoft Internet Information Server

Exercise genomics--a paradigm shift is needed: a commentary.

PubMed

Bouchard, Claude

2015-12-01

The overarching goal of exercise genomics is to illuminate exercise biology and behaviour in order to better understand the preventive and therapeutic values of exercise. An ancillary aim is to understand the role of genomic variation in human physical attributes and sports performance. The aim of this report is to briefly comment on the current status of exercise genetics and genomics and to suggest potential improvements to the research agenda and translational activities. First, the genomic features of interest to the biology of exercise are defined. Then, the limit of the current focus on common variants and their implications for exercise genomics is highlighted. The need for a major paradigm shift in exercise genomics research is discussed with an emphasis on study designs and appropriately powered studies as well as on more mechanistic and functional research. Finally, a summary of current practices in translational activities compared with what best practice demands is introduced. One suggestion is that the research portfolio of exercise genomics be composed of a larger fraction of experimental and mechanistic investigations and a smaller fraction of observational studies. It is also recommended that research should shift to unbiased exploration of the genome using all the power of genomics, epigenomics and transcriptomics in combination with large observational but preferably experimental study designs, including Mendelian randomisation. In all cases, emphasis on replications is of paramount importance. This represents an extraordinary challenge that can only be met with large-scale collaborative and multicentre research programmes. 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/

Comparison of Controlled Field Test Aerosol Generation Devices to a Laboratory Device

DTIC Science & Technology

2013-11-01

detector, and it allows airflow through the region between its exhaust tube and the detector inlet tube. 2 The atomizer (Aerogen; Dangan, Galway ...Aerogen; Dangan, Galway , Ireland. http://www.aerogen.com/ aeroneb-go.html (accessed October 2013). Byron, P. Dosing Reproducibility from Experimental

[Radiotherapy phase I trials' methodology: Features].

PubMed

Rivoirard, R; Vallard, A; Langrand-Escure, J; Guy, J-B; Ben Mrad, M; Yaoxiong, X; Diao, P; Méry, B; Pigne, G; Rancoule, C; Magné, N

2016-12-01

In clinical research, biostatistical methods allow the rigorous analysis of data collection and should be defined from the trial design to obtain the appropriate experimental approach. Thus, if the main purpose of phase I is to determine the dose to use during phase II, methodology should be finely adjusted to experimental treatment(s). Today, the methodology for chemotherapy and targeted therapy is well known. For radiotherapy and chemoradiotherapy phase I trials, the primary endpoint must reflect both effectiveness and potential treatment toxicities. Methodology should probably be complex to limit failures in the following phases. However, there are very few data about methodology design in the literature. The present study focuses on these particular trials and their characteristics. It should help to raise existing methodological patterns shortcomings in order to propose new and better-suited designs. Copyright © 2016 Société française de radiothérapie oncologique (SFRO). Published by Elsevier SAS. All rights reserved.

[Basic science and applied science].

PubMed

Pérez-Tamayo, R

2001-01-01

A lecture was presented by the author at the Democratic Opinion Forum on Health Teaching and Research, organized by Mexico's National Health Institutes Coordinating Office, at National Cardiology Institute "Ignacio Chavez", where he presented a critical review of the conventional classification of basic and applied science, as well as his personal view on health science teaching and research. According to the author, "well-conducted science" is that "generating reality-checked knowledge" and "mis-conducted science" is that "unproductive or producing 'just lies' and 'non-fundable'. To support his views, the author reviews utilitarian and pejorative definitions of science, as well as those of committed and pure science, useful and useless science, and practical and esoterical science, as synonyms of applied and basic science. He also asserts that, in Mexico, "this classification has been used in the past to justify federal funding cutbacks to basic science, allegedly because it is not targeted at solving 'national problems' or because it was not relevant to priorities set in a given six-year political administration period". Regarding health education and research, the author asserts that the current academic programs are inefficient and ineffective; his proposal to tackle these problems is to carry out a solid scientific study, conducted by a multidisciplinary team of experts, "to design the scientific researcher curricula from recruitment of intelligent young people to retirement or death". Performance assessment of researchers would not be restricted to publication of papers, since "the quality of scientific work and contribution to the development of science is not reflected by the number of published papers". The English version of this paper is available at: http://www.insp.mx/salud/index.html

PCPPI: a comprehensive database for the prediction of Penicillium-crop protein-protein interactions.

PubMed

Yue, Junyang; Zhang, Danfeng; Ban, Rongjun; Ma, Xiaojing; Chen, Danyang; Li, Guangwei; Liu, Jia; Wisniewski, Michael; Droby, Samir; Liu, Yongsheng

2017-01-01

Penicillium expansum , the causal agent of blue mold, is one of the most prevalent post-harvest pathogens, infecting a wide range of crops after harvest. In response, crops have evolved various defense systems to protect themselves against this and other pathogens. Penicillium -crop interaction is a multifaceted process and mediated by pathogen- and host-derived proteins. Identification and characterization of the inter-species protein-protein interactions (PPIs) are fundamental to elucidating the molecular mechanisms underlying infection processes between P. expansum and plant crops. Here, we have developed PCPPI, the Penicillium -Crop Protein-Protein Interactions database, which is constructed based on the experimentally determined orthologous interactions in pathogen-plant systems and available domain-domain interactions (DDIs) in each PPI. Thus far, it stores information on 9911 proteins, 439 904 interactions and seven host species, including apple, kiwifruit, maize, pear, rice, strawberry and tomato. Further analysis through the gene ontology (GO) annotation indicated that proteins with more interacting partners tend to execute the essential function. Significantly, semantic statistics of the GO terms also provided strong support for the accuracy of our predicted interactions in PCPPI. We believe that all the PCPPI datasets are helpful to facilitate the study of pathogen-crop interactions and freely available to the research community. : http://bdg.hfut.edu.cn/pcppi/index.html. © The Author(s) 2017. Published by Oxford University Press.

ChAMP: updated methylation analysis pipeline for Illumina BeadChips.

PubMed

Tian, Yuan; Morris, Tiffany J; Webster, Amy P; Yang, Zhen; Beck, Stephan; Feber, Andrew; Teschendorff, Andrew E

2017-12-15

The Illumina Infinium HumanMethylationEPIC BeadChip is the new platform for high-throughput DNA methylation analysis, effectively doubling the coverage compared to the older 450 K array. Here we present a significantly updated and improved version of the Bioconductor package ChAMP, which can be used to analyze EPIC and 450k data. Many enhanced functionalities have been added, including correction for cell-type heterogeneity, network analysis and a series of interactive graphical user interfaces. ChAMP is a BioC package available from https://bioconductor.org/packages/release/bioc/html/ChAMP.html. a.teschendorff@ucl.ac.uk or s.beck@ucl.ac.uk or a.feber@ucl.ac.uk. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Raising the bar for reproducible science at the U.S. Environmental Protection Agency Office of Research and Development.

PubMed

George, Barbara Jane; Sobus, Jon R; Phelps, Lara P; Rashleigh, Brenda; Simmons, Jane Ellen; Hines, Ronald N

2015-05-01

Considerable concern has been raised regarding research reproducibility both within and outside the scientific community. Several factors possibly contribute to a lack of reproducibility, including a failure to adequately employ statistical considerations during study design, bias in sample selection or subject recruitment, errors in developing data inclusion/exclusion criteria, and flawed statistical analysis. To address some of these issues, several publishers have developed checklists that authors must complete. Others have either enhanced statistical expertise on existing editorial boards, or formed distinct statistics editorial boards. Although the U.S. Environmental Protection Agency, Office of Research and Development, already has a strong Quality Assurance Program, an initiative was undertaken to further strengthen statistics consideration and other factors in study design and also to ensure these same factors are evaluated during the review and approval of study protocols. To raise awareness of the importance of statistical issues and provide a forum for robust discussion, a Community of Practice for Statistics was formed in January 2014. In addition, three working groups were established to develop a series of questions or criteria that should be considered when designing or reviewing experimental, observational, or modeling focused research. This article describes the process used to develop these study design guidance documents, their contents, how they are being employed by the Agency's research enterprise, and expected benefits to Agency science. The process and guidance documents presented here may be of utility for any research enterprise interested in enhancing the reproducibility of its science. © The Author 2015. Published by Oxford University Press on behalf of the Society of Toxicology.

75 FR 7573 - Office of Safe and Drug-Free Schools; Overview Information; Models of Exemplary, Effective, and...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-22

... to the research, then a quasi- experimental evaluation of the program's implementation on the... experimental or quasi- experimental research design, with the evaluation results suggesting effectiveness in... this grant competition, a research design of the highest quality means an experimental design in which...

A DVE Time Management Simulation and Verification Platform Based on Causality Consistency Middleware

NASA Astrophysics Data System (ADS)

Zhou, Hangjun; Zhang, Wei; Peng, Yuxing; Li, Sikun

During the course of designing a time management algorithm for DVEs, the researchers always become inefficiency for the distraction from the realization of the trivial and fundamental details of simulation and verification. Therefore, a platform having realized theses details is desirable. However, this has not been achieved in any published work to our knowledge. In this paper, we are the first to design and realize a DVE time management simulation and verification platform providing exactly the same interfaces as those defined by the HLA Interface Specification. Moreover, our platform is based on a new designed causality consistency middleware and might offer the comparison of three kinds of time management services: CO, RO and TSO. The experimental results show that the implementation of the platform only costs small overhead, and that the efficient performance of it is highly effective for the researchers to merely focus on the improvement of designing algorithms.

JERHRE's New Web Pages.

PubMed

2006-06-01

JERHRE'S WEBSITE, www.csueastbay.edu/JERHRE/ has two new pages. One of those pages is devoted to curriculum that may be used to educate students, investigators and ethics committee members about issues in the ethics of human subjects research, and to evaluate their learning. It appears at www.csueastbay.edu/JERHRE/cur.html. The other is devoted to emailed letters from readers. Appropriate letters will be posted as soon as they are received by the editor. Letters from readers appear at www.csueastbay.edu/JERHRE/let.html.

An interactive HTML ocean nowcast GUI based on Perl and JavaScript

NASA Astrophysics Data System (ADS)

Sakalaukus, Peter J.; Fox, Daniel N.; Louise Perkins, A.; Smedstad, Lucy F.

1999-02-01

We describe the use of Hyper Text Markup Language (HTML), JavaScript code, and Perl I/O to create and validate forms in an Internet-based graphical user interface (GUI) for the Naval Research Laboratory (NRL) Ocean models and Assimilation Demonstration System (NOMADS). The resulting nowcast system can be operated from any compatible browser across the Internet, for although the GUI was prepared in a Netscape browser, it used no Netscape extensions. Code available at: http://www.iamg.org/CGEditor/index.htm

Reaction time effects in lab- versus Web-based research: Experimental evidence.

PubMed

Hilbig, Benjamin E

2016-12-01

Although Web-based research is now commonplace, it continues to spur skepticism from reviewers and editors, especially whenever reaction times are of primary interest. Such persistent preconceptions are based on arguments referring to increased variation, the limits of certain software and technologies, and a noteworthy lack of comparisons (between Web and lab) in fully randomized experiments. To provide a critical test, participants were randomly assigned to complete a lexical decision task either (a) in the lab using standard experimental software (E-Prime), (b) in the lab using a browser-based version (written in HTML and JavaScript), or (c) via the Web using the same browser-based version. The classical word frequency effect was typical in size and corresponded to a very large effect in all three conditions. There was no indication that the Web- or browser-based data collection was in any way inferior. In fact, if anything, a larger effect was obtained in the browser-based conditions than in the condition relying on standard experimental software. No differences between Web and lab (within the browser-based conditions) could be observed, thus disconfirming any substantial influence of increased technical or situational variation. In summary, the present experiment contradicts the still common preconception that reaction time effects of only a few hundred milliseconds cannot be detected in Web experiments.

fastBMA: scalable network inference and transitive reduction.

PubMed

Hung, Ling-Hong; Shi, Kaiyuan; Wu, Migao; Young, William Chad; Raftery, Adrian E; Yeung, Ka Yee

2017-10-01

Inferring genetic networks from genome-wide expression data is extremely demanding computationally. We have developed fastBMA, a distributed, parallel, and scalable implementation of Bayesian model averaging (BMA) for this purpose. fastBMA also includes a computationally efficient module for eliminating redundant indirect edges in the network by mapping the transitive reduction to an easily solved shortest-path problem. We evaluated the performance of fastBMA on synthetic data and experimental genome-wide time series yeast and human datasets. When using a single CPU core, fastBMA is up to 100 times faster than the next fastest method, LASSO, with increased accuracy. It is a memory-efficient, parallel, and distributed application that scales to human genome-wide expression data. A 10 000-gene regulation network can be obtained in a matter of hours using a 32-core cloud cluster (2 nodes of 16 cores). fastBMA is a significant improvement over its predecessor ScanBMA. It is more accurate and orders of magnitude faster than other fast network inference methods such as the 1 based on LASSO. The improved scalability allows it to calculate networks from genome scale data in a reasonable time frame. The transitive reduction method can improve accuracy in denser networks. fastBMA is available as code (M.I.T. license) from GitHub (https://github.com/lhhunghimself/fastBMA), as part of the updated networkBMA Bioconductor package (https://www.bioconductor.org/packages/release/bioc/html/networkBMA.html) and as ready-to-deploy Docker images (https://hub.docker.com/r/biodepot/fastbma/). © The Authors 2017. Published by Oxford University Press.

Quasi experimental designs in pharmacist intervention research.

PubMed

Krass, Ines

2016-06-01

Background In the field of pharmacist intervention research it is often difficult to conform to the rigorous requirements of the "true experimental" models, especially the requirement of randomization. When randomization is not feasible, a practice based researcher can choose from a range of "quasi-experimental designs" i.e., non-randomised and at time non controlled. Objective The aim of this article was to provide an overview of quasi-experimental designs, discuss their strengths and weaknesses and to investigate their application in pharmacist intervention research over the previous decade. Results In the literature quasi experimental studies may be classified into five broad categories: quasi-experimental design without control groups; quasi-experimental design that use control groups with no pre-test; quasi-experimental design that use control groups and pre-tests; interrupted time series and stepped wedge designs. Quasi-experimental study design has consistently featured in the evolution of pharmacist intervention research. The most commonly applied of all quasi experimental designs in the practice based research literature are the one group pre-post-test design and the non-equivalent control group design i.e., (untreated control group with dependent pre-tests and post-tests) and have been used to test the impact of pharmacist interventions in general medications management as well as in specific disease states. Conclusion Quasi experimental studies have a role to play as proof of concept, in the pilot phases of interventions when testing different intervention components, especially in complex interventions. They serve to develop an understanding of possible intervention effects: while in isolation they yield weak evidence of clinical efficacy, taken collectively, they help build a body of evidence in support of the value of pharmacist interventions across different practice settings and countries. However, when a traditional RCT is not feasible for logistical and/or ethical reasons researchers should endeavour to use the more robust of the quasi experimental designs.

Designing and Managing Your Digital Library.

ERIC Educational Resources Information Center

Guenther, Kim

2000-01-01

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

Cognitive, Behavioral, and Functional Consequences of Inadequate Sleep in Children and Adolescents

PubMed Central

Beebe, Dean W.

2011-01-01

Synopsis During the past few decades, studies using multiple research designs have examined whether sleep during childhood and adolescence is related to cognition, behavior, and other aspects of daytime functioning. This paper summarizes recent correlational, case-control, quasi-experimental, and experimental studies, highlighting how the strengths and limitations of each research design are complementary, thereby allowing one to more confidently draw conclusions when viewing the research literature as a whole. Viewed in this manner, published findings suggest that inadequate sleep quality and/or quantity can cause sleepiness, inattention and, very likely, other cognitive and behavioral deficits that significantly impact children and adolescents in important functional settings (e.g., school). This paper then integrates findings from longitudinal studies within a developmental psychopathology model. In this model, inadequate sleep is viewed as a noxious exposure that can, over time, fundamentally alter a child or adolescent's development, resulting in poorer long-term outcomes. Important research questions remain, but the available evidence supports the integration of sleep screening and interventions into routine clinical care and also supports advocacy for public policy changes to improve the sleep of children and adolescents. PMID:21600347

The Influence of Scientific Research and Evaluation on Publishing Educational Curriculum

ERIC Educational Resources Information Center

Baughman, Marcy

2008-01-01

Prior to the No Child Left Behind (NCLB) Act, scientific research to support development of curriculum materials or to demonstrate curricular efficacy was not required. NCLB transformed the development and publishing process for K-12 educational materials by prompting publishers to increase funding for experimentally based research on educational…

Using NetCloak to develop server-side Web-based experiments without writing CGI programs.

PubMed

Wolfe, Christopher R; Reyna, Valerie F

2002-05-01

Server-side experiments use the Web server, rather than the participant's browser, to handle tasks such as random assignment, eliminating inconsistencies with JAVA and other client-side applications. Heretofore, experimenters wishing to create server-side experiments have had to write programs to create common gateway interface (CGI) scripts in programming languages such as Perl and C++. NetCloak uses simple, HTML-like commands to create CGIs. We used NetCloak to implement an experiment on probability estimation. Measurements of time on task and participants' IP addresses assisted quality control. Without prior training, in less than 1 month, we were able to use NetCloak to design and create a Web-based experiment and to help graduate students create three Web-based experiments of their own.

Stroke Rehabilitation: What Research is Being Done?

MedlinePlus

... of this page please turn Javascript on. Feature: Stroke Rehabilitation What Research is Being Done? Past Issues / ... Table of Contents To Find Out More MedlinePlus: Stroke Rehabilitation medlineplus.gov/strokerehabilitation.html National Institute of ...

2017 Technology Showcase Presentations | NCI Technology Transfer Center | TTC

Cancer.gov

Presentations from the 2017 Technology Showcase by NIH Intramural Research Program scientists held at Frederick National Laboratories for Cancer Research on June 7, 2017. | [google6f4cd5334ac394ab.html

Multimodal communication in animals, humans and robots: an introduction to perspectives in brain-inspired informatics.

PubMed

Wermter, S; Page, M; Knowles, M; Gallese, V; Pulvermüller, F; Taylor, J

2009-03-01

Recent years have seen convergence in research on brain mechanisms and neurocomputational approaches, culminating in the creation of a new generation of robots whose artificial "brains" respect neuroscience principles and whose "cognitive" systems venture into higher cognitive domains such as planning and action sequencing, complex object and concept processing, and language. The present article gives an overview of selected projects in this general multidisciplinary field. The work reviewed centres on research funded by the EU in the context of the New and Emergent Science and Technology, NEST, funding scheme highlighting the topic "What it means to be human". Examples of such projects include learning by imitation (Edici project), examining the origin of human rule-based reasoning (Far), studying the neural origins of language (Neurocom), exploring the evolutionary origins of the human mind (Pkb140404), researching into verbal and non-verbal communication (Refcom), using and interpreting signs (Sedsu), characterising human language by structural complexity (Chlasc), and representing abstract concepts (Abstract). Each of the communication-centred research projects revealed individual insights; however, there had been little overall analysis of results and hypotheses. In the Specific Support Action Nestcom, we proposed to analyse some NEST projects focusing on the central question "What it means to communicate" and to review, understand and integrate the results of previous communication-related research, in order to develop and communicate multimodal experimental hypotheses for investigation by future projects. The present special issue includes a range of papers on the interplay between neuroinformatics, brain science and robotics in the general area of higher cognitive functions and multimodal communication. These papers extend talks given at the NESTCOM workshops, at ICANN (http://www.his.sunderland.ac.uk/nestcom/workshop/icann.html) in Porto and at the first meeting of the Federation of the European Societies of Neuropsychology in Edinburgh in 2008 (http://www.his.sunderland.ac.uk/nestcom/workshop/esn.html). We hope that the collection will give a vivid insight into current trends in the field.

Where We Have Been and Where We Are Going: A Content Analysis of Articles Published in the Journal of Women's Health Physical Therapy From 2005 to 2015.

PubMed

Bishop, Mark D; Coronado, Rogelio A; Hill, Alexandra D; Alappattu, Meryl J

2017-05-01

The objective of this study was to examine the type and content of Journal of Women's Health Physical Therapy (JWHPT) publications over the last decade. Content and bibliometric analysis of published literature. Component sections, such as the Section on Women's Health (SoWH) of the American Physical Therapy Association provide content expertise to areas of specialty physical therapist practice, thereby supporting the dissemination of evidence for physical therapists to use. Closely aligned with the mission of the SoWH, JWHPT provides evidence reflecting this practice area. The purpose of our analysis was to examine publications within JWHPT to determine how closely JWHPT is meeting the mission and focus of section members. We used established bibliographic methodology to code and review manuscripts published online between 2005 and 2015 in JWHPT using established domains (article type, participant type, research design, study purpose, and area of focus). Total publications and proportion of publications based on domain were described. Impact by citation and author was examined using bibliometric software. Eighteen percent of the items published in JWHPT were original research papers submitted for the first time. Of those papers, the primary study design was cross-sectional experimental research, most commonly studying interventions. The primary practice area reported was management of incontinence. We suggest that a continued need to increase efforts for the submission and publication of a greater proportion of randomized controlled trials and metric articles.

Erratum: Erratum: Dual roles of a flouride-doped SnO2/TiO2 bilayer based on inverse opal/nanoparticle structure for water oxidation

NASA Astrophysics Data System (ADS)

Yun, Gun; Balamurugan, Maheswari; Ahn, Kwang-Soon; Lee, Sang-Kwon; Kang, Soon Hyung; Lim, Dong-Ha

2018-03-01

In the version of this article initially published, the name of co- author Maheswari was incorrect. The correct name is Maheswari Arunachalam. The error has been corrected in the HTML and PDF versions of the article.

Author Correction: The F-box protein FKF1 inhibits dimerization of COP1 in the control of photoperiodic flowering.

PubMed

Lee, Byoung-Doo; Kim, Mi Ri; Kang, Min-Young; Cha, Joon-Yung; Han, Su-Hyun; Nawkar, Ganesh M; Sakuraba, Yasuhito; Lee, Sang Yeol; Imaizumi, Takato; McClung, C Robertson; Kim, Woe-Yeon; Paek, Nam-Chon

2018-02-02

The previously published version of this Article contained errors in Figure 5. In panel c, the second and fourth blot images were incorrectly labeled 'α-Myc' and should have been labelled 'α-HA'. These errors have been corrected in both the PDF and HTML versions of the Article.

Military Innovation in the New Normal

DTIC Science & Technology

2015-04-13

fundamentally flawed. Having Soldiers with regional affiliation, cultural appreciation, and language proficiency makes sense . The concept simply fails in...36 Recognizing the urgency of this training deficiency, both First and Second Marine Divisions published their respective...Witch Hunt,” http://www.huffingtonpost.com/ sen -barbara- boxer/the-gops-benghazi-witch-h_b_5315857.html (accessed 28 Jan 2015). Military Innovation in

76 FR 2309 - Consumer Information Regulations; Fees for Use of Traction Skid Pads

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-13

....regulations.gov , including any personal information provided. Privacy Act: Anyone is able to search the....). You may review DOT's complete Privacy Act Statement in the Federal Register published on April 11, 2000 (65 FR 19477-78) or you may visit http://www.dot.gov/privacy.html . Docket: For access to the...

Author Correction: Circuit dissection of the role of somatostatin in itch and pain.

PubMed

Huang, Jing; Polgár, Erika; Solinski, Hans Jürgen; Mishra, Santosh K; Tseng, Pang-Yen; Iwagaki, Noboru; Boyle, Kieran A; Dickie, Allen C; Kriegbaum, Mette C; Wildner, Hendrik; Zeilhofer, Hanns Ulrich; Watanabe, Masahiko; Riddell, John S; Todd, Andrew J; Hoon, Mark A

2018-06-01

In the version of this article initially published online, the labels were switched for the right-hand pair of bars in Fig. 4e. The left one of the two should be Chloroquine + veh, the right one Chloroquine + CNO. The error has been corrected in the print, HTML and PDF versions of the article.

Physics for Teachers: Understanding Physics: David Cassidy, Gerald Holton, & James Rutherford

NASA Astrophysics Data System (ADS)

Hubisz, John L.

2009-11-01

Physics for Teachers: Understanding Physics, by David Cassidy, Gerald Holton, & James Rutherford and published by Springer Verlag, New York, NY 10010 (2002), pp. xxiii + 851 80.00 hardback. ISBN 0-387-98756-8. Student Guide & Instructor Guide are also available. The text and Instructor Guide are available online at http://www.dcassidybooks.com/up.html

HTML5: a new standard for the Web.

PubMed

Hoy, Matthew B

2011-01-01

HTML5 is the newest revision of the HTML standard developed by the World Wide Web Consortium (W3C). This new standard adds several exciting news features and capabilities to HTML. This article will briefly discuss the history of HTML standards, explore what changes are in the new HTML5 standard, and what implications it has for information professionals. A list of HTML5 resources and examples will also be provided.

Evidence-based practice: a quality indicator analysis of peer-tutoring in adapted physical education.

PubMed

Kalef, Laura; Reid, Greg; Macdonald, Cathy

2013-09-01

The purpose of the research was to conduct a quality indicator analysis of studies investigating peer-tutoring for students with a disability in adapted physical education. An electronic search was conducted among English journals published from 1960 to November 2012. Databases included ERIC, PsycINFO, and SPORTDiscus. Fifteen research studies employing group-experimental (Gersten et al., 2005) or single-subject designs (Horner et al., 2005) met inclusion criteria. Each study was assessed for the presence and clarity of quality indicators. Group designs met an average of 62.5% essential and 69% desirable indicators. An average of 80% of indicators was present for single-subject designs. Results suggest claims of peer-tutoring being an evidence-based practice are premature. Recommendations for clarifying and applying the quality indicators are offered. Copyright © 2013 Elsevier Ltd. All rights reserved.

EDITORIAL: Plasma Surface Interactions for Fusion

NASA Astrophysics Data System (ADS)

2006-05-01

Because plasma-boundary physics encompasses some of the most important unresolved issues for both the International Thermonuclear Experimental Reactor (ITER) project and future fusion power reactors, there is a strong interest in the fusion community for better understanding and characterization of plasma wall interactions. Chemical and physical sputtering cause the erosion of the limiters/divertor plates and vacuum vessel walls (made of C, Be and W, for example) and degrade fusion performance by diluting the fusion fuel and excessively cooling the core, while carbon redeposition could produce long-term in-vessel tritium retention, degrading the superior thermo-mechanical properties of the carbon materials. Mixed plasma-facing materials are proposed, requiring optimization for different power and particle flux characteristics. Knowledge of material properties as well as characteristics of the plasma material interaction are prerequisites for such optimizations. Computational power will soon reach hundreds of teraflops, so that theoretical and plasma science expertise can be matched with new experimental capabilities in order to mount a strong response to these challenges. To begin to address such questions, a Workshop on New Directions for Advanced Computer Simulations and Experiments in Fusion-Related Plasma Surface Interactions for Fusion (PSIF) was held at the Oak Ridge National Laboratory from 21 to 23 March, 2005. The purpose of the workshop was to bring together researchers in fusion related plasma wall interactions in order to address these topics and to identify the most needed and promising directions for study, to exchange opinions on the present depth of knowledge of surface properties for the main fusion-related materials, e.g., C, Be and W, especially for sputtering, reflection, and deuterium (tritium) retention properties. The goal was to suggest the most important next steps needed for such basic computational and experimental work to be facilitated by researchers in fusion, material, and physical sciences. Representatives from many fusion research laboratories attended, and 25 talks were given, the majority of them making up the content of these Workshop proceedings. The presentations of all talks and further information on the Workshop are available at http://www-cfadc.phy.ornl.gov/psif/home.html. The workshop talks dealt with identification of needs from the perspective of integrated fusion simulation and ITER design, recent developments and perspectives on computation of plasma-facing surface properties using the current and expected new generation of computation capability, and with the status of dedicated laboratory experiments which characterize the underlying processes of PSIF. The Workshop summary and conclusions are being published in Nuclear Fusion 45 (2005). We are indebted to Lynda Saddiq and Fay Ownby, secretaries in the Physics Division of ORNL, whose special efforts, devotion, and expertise made possible both the Workshop and these Proceedings. J T Hogan, P S Krstic and F W Meyer Physics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6372, USA

E-RNAi: a web application for the multi-species design of RNAi reagents—2010 update

PubMed Central

Horn, Thomas; Boutros, Michael

2010-01-01

The design of RNA interference (RNAi) reagents is an essential step for performing loss-of-function studies in many experimental systems. The availability of sequenced and annotated genomes greatly facilitates RNAi experiments in an increasing number of organisms that were previously not genetically tractable. The E-RNAi web-service, accessible at http://www.e-rnai.org/, provides a computational resource for the optimized design and evaluation of RNAi reagents. The 2010 update of E-RNAi now covers 12 genomes, including Drosophila, Caenorhabditis elegans, human, emerging model organisms such as Schmidtea mediterranea and Acyrthosiphon pisum, as well as the medically relevant vectors Anopheles gambiae and Aedes aegypti. The web service calculates RNAi reagents based on the input of target sequences, sequence identifiers or by visual selection of target regions through a genome browser interface. It identifies optimized RNAi target-sites by ranking sequences according to their predicted specificity, efficiency and complexity. E-RNAi also facilitates the design of secondary RNAi reagents for validation experiments, evaluation of pooled siRNA reagents and batch design. Results are presented online, as a downloadable HTML report and as tab-delimited files. PMID:20444868

Clinical trials transparency and the Trial and Experimental Studies Transparency (TEST) act.

PubMed

Logvinov, Ilana

2014-03-01

Clinical trial research is the cornerstone for successful advancement of medicine that provides hope for millions of people in the future. Full transparency in clinical trials may allow independent investigators to evaluate study designs, perform additional analysis of data, and potentially eliminate duplicate studies. Current regulatory system and publishers rely on investigators and pharmaceutical industries for complete and accurate reporting of results from completed clinical trials. Legislation seems to be the only way to enforce mandatory disclosure of results. The Trial and Experimental Studies Transparency (TEST) Act of 2012 was introduced to the legislators in the United States to promote greater transparency in research industry. Public safety and advancement of science are the driving forces for the proposed policy change. The TEST Act may benefit the society and researchers; however, there are major concerns with participants' privacy and intellectual property protection. Copyright © 2014 Elsevier Inc. All rights reserved.

Invited review: Experimental design, data reporting, and sharing in support of animal systems modeling research.

PubMed

McNamara, J P; Hanigan, M D; White, R R

2016-12-01

The National Animal Nutrition Program "National Research Support Project 9" supports efforts in livestock nutrition, including the National Research Council's committees on the nutrient requirements of animals. Our objective was to review the status of experimentation and data reporting in animal nutrition literature and to provide suggestions for the advancement of animal nutrition research and the ongoing improvement of field-applied nutrient requirement models. Improved data reporting consistency and completeness represent a substantial opportunity to improve nutrition-related mathematical models. We reviewed a body of nutrition research; recorded common phrases used to describe diets, animals, housing, and environmental conditions; and proposed equivalent numerical data that could be reported. With the increasing availability of online supplementary material sections in journals, we developed a comprehensive checklist of data that should be included in publications. To continue to improve our research effectiveness, studies utilizing multiple research methodologies to address complex systems and measure multiple variables will be necessary. From the current body of animal nutrition literature, we identified a series of opportunities to integrate research focuses (nutrition, reproduction and genetics) to advance the development of nutrient requirement models. From our survey of current experimentation and data reporting in animal nutrition, we identified 4 key opportunities to advance animal nutrition knowledge: (1) coordinated experiments should be designed to employ multiple research methodologies; (2) systems-oriented research approaches should be encouraged and supported; (3) publication guidelines should be updated to encourage and support sharing of more complete data sets; and (4) new experiments should be more rapidly integrated into our knowledge bases, research programs and practical applications. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Water-Quality and Lake-Stage Data for Wisconsin Lakes, Water Year 2006

USGS Publications Warehouse

Rose, W.J.; Garn, H.S.; Goddard, G.L.; Marsh, S.B.; Olson, D.L.; Robertson, Dale M.

2007-01-01

The U.S. Geological Survey (USGS), in cooperation with local and other agencies, collects data at selected lakes throughout Wisconsin. These data, accumulated over many years, provide a data base for developing an improved understanding of the water quality of lakes. To make these data available to interested parties outside the USGS, the data are published annually in this report series. The locations of water-quality and lake-stage stations in Wisconsin for water year 2006 are shown in figure 1. A water year is the 12-month period from October 1 through September 30. It is designated by the calendar year in which it ends. Thus, the period October 1, 2005 through September 30, 2006 is called 'water year 2006.' The purpose of this report is to provide information about the chemical and physical characteristics of Wisconsin lakes. Data that have been collected at specific lakes, and information to aid in the interpretation of those data, are included in this report. Data collected include measurements of in-lake water quality and lake stage. Time series of Secchi depths, surface total phosphorus and chlorophyll a concentrations collected during non-frozen periods are included for all lakes. Graphs of vertical profiles of temperature, dissolved oxygen, pH, and specific conductance are included for sites where these parameters were measured. Descriptive information for each lake includes: location of the lake, area of the lake's watershed, period for which data are available, revisions to previously published records, and pertinent remarks. Additional data, such as streamflow and water quality in tributary and outlet streams of some of the lakes, are published in another volume: 'Water Resources Data-Wisconsin, 2006.' Water-resources data, including stage and discharge data at most streamflow-gaging stations, are available through the World Wide Web on the Internet. The Wisconsin Water Science Center's home page is at http://wi.water.usgs.gov/. Information on the Wisconsin Water Science Center's Lakes Program is found at http://wi.water.usgs.gov/lake/index.html and http://wi.water.usgs.gov/projects/index.html.

Water-quality and Llake-stage data for Wisconsin Lakes, Water Year 2004

USGS Publications Warehouse

Rose, W.J.; Garn, H.S.; Goddard, G.L.; Marsh, S.B.; Olson, D.L.; Robertson, Dale M.

2005-01-01

The U.S. Geological Survey (USGS), in cooperation with local and other agencies, collects data at selected lakes throughout Wisconsin. These data, accumulated over many years, provide a data base for developing an improved understanding of the water quality of lakes. To make these data available to interested parties outside the USGS, the data are published annually in this report series. The locations of water-quality and lake-stage stations in Wisconsin for water year 2004 are shown in figure 1. A water year is the 12-month period from October 1 through September 30. It is designated by the calendar year in which it ends. Thus, the period October 1, 2003 through September 30, 2004 is called 'water year 2004.' The purpose of this report is to provide information about the chemical and physical characteristics of Wisconsin lakes. Data that have been collected at specific lakes, and information to aid in the interpretation of those data, are included in this report. Data collected include measurements of in-lake water quality and lake stage. Time series of Secchi depths, surface total phosphorus and chlorophyll a concentrations collected during non-frozen periods are included for all lakes. Graphs of vertical profiles of temperature, dissolved oxygen, pH, and specific conductance are included for sites where these parameters were measured. Descriptive information for each lake includes: location of the lake, area of the lake's watershed, period for which data are available, revisions to previously published records, and pertinent remarks. Additional data, such as streamflow and water quality in tributary and outlet streams of some of the lakes, are published in another volume: 'Water Resources Data-Wisconsin, 2004.' Water-resources data, including stage and discharge data at most streamflow-gaging stations, are available throught the World Wide Web on the Internet. The Wisconsin Water Science Center's home page is at http://wi.water.usgs.gov/. Information on the Wisconsin Water Science Center's Lakes Program is found at wi.water.usgs.gov/lake/index.html and wi.water.usgs.gov/projects/index.html

Water-quality and lake-stage data for Wisconsin lakes, water year 2014

USGS Publications Warehouse

Manteufel, S. Bridgett; Robertson, Dale M.

2017-05-25

IntroductionThe U.S. Geological Survey (USGS), in cooperation with local and other agencies, collects data at selected lakes throughout Wisconsin. These data, accumulated over many years, provide a database for developing an improved understanding of the water quality of lakes. To make these data available to interested parties outside the USGS, the data are published annually in this report series. The locations of water-quality and lake-stage stations in Wisconsin for water year 2014 are shown in figure 1. A water year is the 12-month period from October 1 through September 30. It is designated by the calendar year in which it ends. Thus, the periodOctober 1, 2013, through September 30, 2014, is called “water year 2014.”The purpose of this report is to provide information about the chemical and physical characteristics of Wisconsin lakes. Data that have been collected at specific lakes, and information to aid in the interpretation of those data, are included in this report. Data collected include measurements of in-lake water quality and lake stage. Time series of Secchi depths, surface total phosphorus, and chlorophyll a concentrations collected during nonfrozen periods are included for many lakes. Graphs of vertical profiles of temperature, dissolved oxygen, pH, and specific conductance are included for sites where these parameters were measured. Descriptive information for each lake includes the location of the lake, area of the lake’s watershed, period for which data are available, revisions to previously published records, and pertinent remarks. Additional data, such as streamflow and water quality in tributary and outlet streams of some of the lakes, are published online at http://nwis.waterdata.usgs.gov/wi/nwis.Water-resources data, including stage and discharge data at most streamflow-gaging stations, are available online. The Wisconsin Water Science Center’s home page is at https://www.usgs.gov/centers/wisconsin-water-science-center. Information about the Wisconsin Water Science Center’s Lakes Program is found at http://wi.water.usgs.gov/lakes/index.html and http://wi.water.usgs.gov/projects/index.html.

Water-quality and lake-stage data for Wisconsin lakes, water years 2012–2013

USGS Publications Warehouse

Manteufel, S. Bridgett; Robertson, Dale M.

2017-05-25

IntroductionThe U.S. Geological Survey (USGS), in cooperation with local and other agencies, collects data at selected lakes throughout Wisconsin. These data, accumulated over many years, provide a data base for developing an improved understanding of the water quality of lakes. To make these data available to interested parties outside the USGS, the data are published annually in this report series. The locations of water-quality and lake-stage stations in Wisconsin for water year 2012 are shown in figure 1. A water year is the 12-month period from October 1 through September 30. It is designated by the calendar year in which it ends. Thus, the period October 1, 2011 through September 30, 2012, is called “water year 2012.”The purpose of this report is to provide information about the chemical and physical characteristics of Wisconsin lakes. Data that have been collected at specific lakes, and information to aid in the interpretation of those data, are included in this report. Data collected include measurements of in-lake water quality and lake stage. Time series of Secchi depths, surface total phosphorus and chlorophyll a concentrations collected during non-frozen periods are included for all lakes. Graphs of vertical profiles of temperature, dissolved oxygen, pH, and specific conductance are included for sites where these parameters were measured. Descriptive information for each lake includes: location of the lake, area of the lake’s watershed, period for which data are available, revisions to previously published records, and pertinent remarks. Additional data, such as streamflow and water quality in tributary and outlet streams of some of the lakes, are published online at http://nwis.waterdata.usgs.gov/wi/nwis.Water-resources data, including stage and discharge data at most streamflow-gaging stations, are available online. The Wisconsin Water Science Center’s home page is at https://www.usgs.gov/centers/wisconsin-water-science-center. Information on the Wisconsin Water Science Center’s Lakes Program is found at http://wi.water.usgs.gov/lakes/index.html and http://wi.water.usgs.gov/projects/index.html.

Data standards can boost metabolomics research, and if there is a will, there is a way.

PubMed

Rocca-Serra, Philippe; Salek, Reza M; Arita, Masanori; Correa, Elon; Dayalan, Saravanan; Gonzalez-Beltran, Alejandra; Ebbels, Tim; Goodacre, Royston; Hastings, Janna; Haug, Kenneth; Koulman, Albert; Nikolski, Macha; Oresic, Matej; Sansone, Susanna-Assunta; Schober, Daniel; Smith, James; Steinbeck, Christoph; Viant, Mark R; Neumann, Steffen

2016-01-01

Thousands of articles using metabolomics approaches are published every year. With the increasing amounts of data being produced, mere description of investigations as text in manuscripts is not sufficient to enable re-use anymore: the underlying data needs to be published together with the findings in the literature to maximise the benefit from public and private expenditure and to take advantage of an enormous opportunity to improve scientific reproducibility in metabolomics and cognate disciplines. Reporting recommendations in metabolomics started to emerge about a decade ago and were mostly concerned with inventories of the information that had to be reported in the literature for consistency. In recent years, metabolomics data standards have developed extensively, to include the primary research data, derived results and the experimental description and importantly the metadata in a machine-readable way. This includes vendor independent data standards such as mzML for mass spectrometry and nmrML for NMR raw data that have both enabled the development of advanced data processing algorithms by the scientific community. Standards such as ISA-Tab cover essential metadata, including the experimental design, the applied protocols, association between samples, data files and the experimental factors for further statistical analysis. Altogether, they pave the way for both reproducible research and data reuse, including meta-analyses. Further incentives to prepare standards compliant data sets include new opportunities to publish data sets, but also require a little "arm twisting" in the author guidelines of scientific journals to submit the data sets to public repositories such as the NIH Metabolomics Workbench or MetaboLights at EMBL-EBI. In the present article, we look at standards for data sharing, investigate their impact in metabolomics and give suggestions to improve their adoption.

The design, implementation, and evaluation of online credit nutrition courses: a systematic review.

PubMed

Cohen, Nancy L; Carbone, Elena T; Beffa-Negrini, Patricia A

2011-01-01

To assess how postsecondary online nutrition education courses (ONEC) are delivered, determine ONEC effectiveness, identify theoretical models used, and identify future research needs. Systematic search of database literature. Postsecondary education. Nine research articles evaluating postsecondary ONEC. Knowledge/performance outcomes and student satisfaction, motivation, or perceptions. Systematic search of 922 articles and review of 9 articles meeting search criteria. Little research regarding ONEC marketing/management existed. Studies primarily evaluated introductory courses using email/websites (before 2000), or course management systems (after 2002). None used true experimental designs; just 3 addressed validity or reliability of measures or pilot-tested instruments. Three articles used theoretical models in course design; few used theories to guide evaluations. Four quasi-experimental studies indicated no differences in nutrition knowledge/performance between online and face-to-face learners. Results were inconclusive regarding student satisfaction, motivation, or perceptions. Students can gain knowledge in online as well as in face-to-face nutrition courses, but satisfaction was mixed. More up-to-date investigations on effective practices are warranted, using theories to identify factors that enhance student outcomes, addressing emerging technologies, and documenting ONEC marketing, management, and delivery. Adequate training/support for faculty is needed to improve student experiences and faculty time management. Copyright © 2011 Society for Nutrition Education. Published by Elsevier Inc. All rights reserved.

NORSTAR Project: Norfolk public schools student team for acoustical research

NASA Technical Reports Server (NTRS)

Fortunato, Ronald C.

1987-01-01

Development of the NORSTAR (Norfolk Public Student Team for Acoustical Research) Project includes the definition, design, fabrication, testing, analysis, and publishing the results of an acoustical experiment. The student-run program is based on a space flight organization similar to the Viking Project. The experiment will measure the scattering transfer of momentum from a sound field to spheres in a liquid medium. It is hoped that the experimental results will shed light on a difficult physics problem - the difference in scattering cross section (the overall effect of the sound wave scattering) for solid spheres and hollow spheres of differing wall thicknesses.

Design and Development of a Virtual Facility Tour Using iPIX(TM) Technology

NASA Technical Reports Server (NTRS)

Farley, Douglas L.

2002-01-01

The capabilities of the iPIX virtual tour software, in conjunction with a web-based interface create a unique and valuable system that provides users with an efficient virtual capability to tour facilities while being able to acquire the necessary technical content is demonstrated. A users guide to the Mechanics and Durability Branch's virtual tour is presented. The guide provides the user with instruction on operating both scripted and unscripted tours as well as a discussion of the tours for Buildings 1148, 1205 and 1256 and NASA Langley Research Center. Furthermore, an indepth discussion has been presented on how to develop a virtual tour using the iPIX software interface with conventional html and JavaScript. The main aspects for discussion are on network and computing issues associated with using this capability. A discussion of how to take the iPIX pictures, manipulate them and bond them together to form hemispherical images is also presented. Linking of images with additional multimedia content is discussed. Finally, a method to integrate the iPIX software with conventional HTML and JavaScript to facilitate linking with multi-media is presented.

Using Propensity Scores in Quasi-Experimental Designs to Equate Groups

ERIC Educational Resources Information Center

Lane, Forrest C.; Henson, Robin K.

2010-01-01

Education research rarely lends itself to large scale experimental research and true randomization, leaving the researcher to quasi-experimental designs. The problem with quasi-experimental research is that underlying factors may impact group selection and lead to potentially biased results. One way to minimize the impact of non-randomization is…

Designing Multimedia for the Hypertext Markup Language.

ERIC Educational Resources Information Center

Schwier, Richard A.; Misanchuk, Earl R.

Dynamic discussions have begun to emerge concerning style of presentation on world wide web sites. Some hypertext markup language (HTML) designers seek an intimate and chatty ambience, while others want to project a more professional image. Evaluators see many sites as overdecorated and indecipherable. This paper offers suggestions on selecting…

Washington Public Libraries Online: Collaborating in Cyberspace.

ERIC Educational Resources Information Center

Wildin, Nancy

1997-01-01

Discussion of public libraries, the Internet, and the World Wide Web focuses on development of a Web site in Washington. Highlights include access to the Internet through online public access catalogs; partnerships between various types of libraries; hardware and software; HTML training; content design; graphics design; marketing; evaluation; and…

ABAEnrichment: an R package to test for gene set expression enrichment in the adult and developing human brain.

PubMed

Grote, Steffi; Prüfer, Kay; Kelso, Janet; Dannemann, Michael

2016-10-15

We present ABAEnrichment, an R package that tests for expression enrichment in specific brain regions at different developmental stages using expression information gathered from multiple regions of the adult and developing human brain, together with ontologically organized structural information about the brain, both provided by the Allen Brain Atlas. We validate ABAEnrichment by successfully recovering the origin of gene sets identified in specific brain cell-types and developmental stages. ABAEnrichment was implemented as an R package and is available under GPL (≥ 2) from the Bioconductor website (http://bioconductor.org/packages/3.3/bioc/html/ABAEnrichment.html). steffi_grote@eva.mpg.de, kelso@eva.mpg.de or michael_dannemann@eva.mpg.deSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Quasi-experimental Studies in the Fields of Infection Control and Antibiotic Resistance, Ten Years Later: A Systematic Review.

PubMed

Alsaggaf, Rotana; O'Hara, Lyndsay M; Stafford, Kristen A; Leekha, Surbhi; Harris, Anthony D

2018-02-01

OBJECTIVE A systematic review of quasi-experimental studies in the field of infectious diseases was published in 2005. The aim of this study was to assess improvements in the design and reporting of quasi-experiments 10 years after the initial review. We also aimed to report the statistical methods used to analyze quasi-experimental data. DESIGN Systematic review of articles published from January 1, 2013, to December 31, 2014, in 4 major infectious disease journals. METHODS Quasi-experimental studies focused on infection control and antibiotic resistance were identified and classified based on 4 criteria: (1) type of quasi-experimental design used, (2) justification of the use of the design, (3) use of correct nomenclature to describe the design, and (4) statistical methods used. RESULTS Of 2,600 articles, 173 (7%) featured a quasi-experimental design, compared to 73 of 2,320 articles (3%) in the previous review (P<.01). Moreover, 21 articles (12%) utilized a study design with a control group; 6 (3.5%) justified the use of a quasi-experimental design; and 68 (39%) identified their design using the correct nomenclature. In addition, 2-group statistical tests were used in 75 studies (43%); 58 studies (34%) used standard regression analysis; 18 (10%) used segmented regression analysis; 7 (4%) used standard time-series analysis; 5 (3%) used segmented time-series analysis; and 10 (6%) did not utilize statistical methods for comparisons. CONCLUSIONS While some progress occurred over the decade, it is crucial to continue improving the design and reporting of quasi-experimental studies in the fields of infection control and antibiotic resistance to better evaluate the effectiveness of important interventions. Infect Control Hosp Epidemiol 2018;39:170-176.

A novel statistical method for quantitative comparison of multiple ChIP-seq datasets.

PubMed

Chen, Li; Wang, Chi; Qin, Zhaohui S; Wu, Hao

2015-06-15

ChIP-seq is a powerful technology to measure the protein binding or histone modification strength in the whole genome scale. Although there are a number of methods available for single ChIP-seq data analysis (e.g. 'peak detection'), rigorous statistical method for quantitative comparison of multiple ChIP-seq datasets with the considerations of data from control experiment, signal to noise ratios, biological variations and multiple-factor experimental designs is under-developed. In this work, we develop a statistical method to perform quantitative comparison of multiple ChIP-seq datasets and detect genomic regions showing differential protein binding or histone modification. We first detect peaks from all datasets and then union them to form a single set of candidate regions. The read counts from IP experiment at the candidate regions are assumed to follow Poisson distribution. The underlying Poisson rates are modeled as an experiment-specific function of artifacts and biological signals. We then obtain the estimated biological signals and compare them through the hypothesis testing procedure in a linear model framework. Simulations and real data analyses demonstrate that the proposed method provides more accurate and robust results compared with existing ones. An R software package ChIPComp is freely available at http://web1.sph.emory.edu/users/hwu30/software/ChIPComp.html. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Mammograms

MedlinePlus

... gov/widgets/fahc.html" width="243" height="179" title="Find a Health Center Widget" ... M.D., Community Oncology and Prevention Trials Research Group, Division of Cancer Prevention, National Cancer Institute, ...

ggCyto: Next Generation Open-Source Visualization Software for Cytometry.

PubMed

Van, Phu; Jiang, Wenxin; Gottardo, Raphael; Finak, Greg

2018-06-01

Open source software for computational cytometry has gained in popularity over the past few years. Efforts such as FlowCAP, the Lyoplate and Euroflow projects have highlighted the importance of efforts to standardize both experimental and computational aspects of cytometry data analysis. The R/BioConductor platform hosts the largest collection of open source cytometry software covering all aspects of data analysis and providing infrastructure to represent and analyze cytometry data with all relevant experimental, gating, and cell population annotations enabling fully reproducible data analysis. Data visualization frameworks to support this infrastructure have lagged behind. ggCyto is a new open-source BioConductor software package for cytometry data visualization built on ggplot2 that enables ggplot-like functionality with the core BioConductor flow cytometry data structures. Amongst its features are the ability to transform data and axes on-the-fly using cytometry-specific transformations, plot faceting by experimental meta-data variables, and partial matching of channel, marker and cell populations names to the contents of the BioConductor cytometry data structures. We demonstrate the salient features of the package using publicly available cytometry data with complete reproducible examples in a supplementary material vignette. https://bioconductor.org/packages/devel/bioc/html/ggcyto.html. gfinak@fredhutch.org. Supplementary data are available at Bioinformatics online and at http://rglab.org/ggcyto/.

Ethical use of animal models in musculoskeletal research.

PubMed

Allen, Matthew J; Hankenson, Kurt D; Goodrich, Laurie; Boivin, Gregory P; von Rechenberg, Brigitte

2017-04-01

The use of animals in research is under increasing scrutiny from the general public, funding agencies, and regulatory authorities. Our ability to continue to perform in-vivo studies in laboratory animals will be critically determined by how researchers respond to this new reality. This Perspectives article summarizes recent and ongoing initiatives within ORS and allied organizations to ensure that musculoskeletal research is performed to the highest ethical standards. It goes on to present an overview of the practical application of the 3Rs (reduction, refinement, and replacement) into experimental design and execution, and discusses recent guidance with regard to improvements in the way in which animal data are reported in publications. The overarching goal of this review is to challenge the status quo, to highlight the absolute interdependence between animal welfare and rigorous science, and to provide practical recommendations and resources to allow clinicians and scientists to optimize the ways in which they undertake preclinical studies involving animals. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:740-751, 2017. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

Analysis of the Effect of Environmental Conditions in Conducting Amphibious Assaults Using a Ship Simulator/Vessel-Response Model Proof-of-Concept Study

DTIC Science & Technology

2017-05-01

Center ESRI Environmental Systems Research Institute GIS Geographic Information System HTML Hyper -Text Markup Language LCAC Landing Craft Air... loop .” The ship simulator bridge is generic in that its layout is similar to that found in a variety of ships. As shown in Figures 17 and 18, the...information stored in the geodatabases. The Hyper -Text Markup Language (HTML) capability built into ArcMap permits a planner to click on a vessel track and

Erratum to "Combustion oscillation study in a kerosene fueled rocket-based combined-cycle engine combustor" [Acta Astronaut. 129 (2016) 260-270

NASA Astrophysics Data System (ADS)

Huang, Zhi-Wei; He, Guo-Qiang; Qin, Fei; Xue, Rui; Wei, Xiang-Geng; Shi, Lei

2017-03-01

The publisher regrets that in the above article we found that Table 1 is present online, in the html version in ScienceDirect, but has been omitted in error from the final version of the PDF online and in the print version. The table can be found below:

Author Correction: RNA cytosine methylation and methyltransferases mediate chromatin organization and 5-azacytidine response and resistance in leukaemia.

PubMed

Cheng, Jason X; Chen, Li; Li, Yuan; Cloe, Adam; Yue, Ming; Wei, Jiangbo; Watanabe, Kenneth A; Shammo, Jamile M; Anastasi, John; Shen, Qingxi J; Larson, Richard A; He, Chuan; Le Beau, Michelle M; Vardiman, James W

2018-06-06

In the originally published version of this Article, the GAPDH loading control blot in Fig. 1a was inadvertently replaced with a duplicate of the DNMT2 blot in the same panel during assembly of the figure. This has now been corrected in both the PDF and HTML versions of the Article.

Publisher Correction: Role of outer surface probes for regulating ion gating of nanochannels.

PubMed

Li, Xinchun; Zhai, Tianyou; Gao, Pengcheng; Cheng, Hongli; Hou, Ruizuo; Lou, Xiaoding; Xia, Fan

2018-02-08

The original version of this Article contained an error in Fig. 3. The scale bars in Figs 3c and 3d were incorrectly labelled as 50 μA. In the correct version, the scale bars are labelled as 0.5 μA. This has now been corrected in both the PDF and HTML versions of the Article.

Key and Driving Requirements for the Juno Payload of Instruments

NASA Technical Reports Server (NTRS)

Dodge, Randy; Boyles, Mark A.; Rasbach, Chuck E.

2007-01-01

The Juno Mission was selected in the summer of 2005 via NASA's New Frontiers competitive AO process (refer to http://www.nasa.gov/home/hqnews/2005/jun/HQ_05138_New_Frontiers_2.html). The Juno project is led by a Principle Investigator based at Southwest Research Institute [SwRI] in San Antonio, Texas, with project management based at the Jet Propulsion Laboratory [JPL] in Pasadena, California, while the Spacecraft design and Flight System Integration are under contract to Lockheed Martin Space Systems Company [LM-SSC] in Denver, Colorado. the payload suite consists of a large number of instruments covering a wide spectrum of experimentation. The science team includes a lead Co-investigator for each one of the following experiments: A Magnetometer experiment (consisting of both a FluxGate Magnetometer (FGM) built at Goddard Space Flight Center GSFC] and a Scalar Helium Magnetometer (SHM) built at JPL, a MicroWave Radiometer (MWR) also built at JPL, a Gravity Science experiment (GS) implemented via the telecom subsystem, two complementary particle instruments (Jovian Auroral Distribution Experiment, JADE developed by SwRI and Juno Energetic-particle Detector Instrument, JEDI from the Applied Physics Lab (APL)--JEDI and JADE both measure electrons and ions), an Ultraviolet Spectrometer (UVS) also developed at SwRI, and a radio and plasma (WAVES) experiment (from the University of Iowa). In addition, a visible camera (JunoCam) is included in the payload to facilitate education and public outreach (designed & fabricated by Malin Space Science Systems [MSSS]).

Cycle time reduction by Html report in mask checking flow

NASA Astrophysics Data System (ADS)

Chen, Jian-Cheng; Lu, Min-Ying; Fang, Xiang; Shen, Ming-Feng; Ma, Shou-Yuan; Yang, Chuen-Huei; Tsai, Joe; Lee, Rachel; Deng, Erwin; Lin, Ling-Chieh; Liao, Hung-Yueh; Tsai, Jenny; Bowhill, Amanda; Vu, Hien; Russell, Gordon

2017-07-01

The Mask Data Correctness Check (MDCC) is a reticle-level, multi-layer DRC-like check evolved from mask rule check (MRC). The MDCC uses extended job deck (EJB) to achieve mask composition and to perform a detailed check for positioning and integrity of each component of the reticle. Different design patterns on the mask will be mapped to different layers. Therefore, users may be able to review the whole reticle and check the interactions between different designs before the final mask pattern file is available. However, many types of MDCC check results, such as errors from overlapping patterns usually have very large and complex-shaped highlighted areas covering the boundary of the design. Users have to load the result OASIS file and overlap it to the original database that was assembled in MDCC process on a layout viewer, then search for the details of the check results. We introduce a quick result-reviewing method based on an html format report generated by Calibre® RVE. In the report generation process, we analyze and extract the essential part of result OASIS file to a result database (RDB) file by standard verification rule format (SVRF) commands. Calibre® RVE automatically loads the assembled reticle pattern and generates screen shots of these check results. All the processes are automatically triggered just after the MDCC process finishes. Users just have to open the html report to get the information they need: for example, check summary, captured images of results and their coordinates.

What's in a Name? The Incorrect Use of Case Series as a Study Design Label in Studies Involving Dogs and Cats.

PubMed

Sargeant, J M; O'Connor, A M; Cullen, J N; Makielski, K M; Jones-Bitton, A

2017-07-01

Study design labels are used to identify relevant literature to address specific clinical and research questions and to aid in evaluating the evidentiary value of research. Evidence from the human healthcare literature indicates that the label "case series" may be used inconsistently and inappropriately. Our primary objective was to determine the proportion of studies in the canine and feline veterinary literature labeled as case series that actually corresponded to descriptive cohort studies, population-based cohort studies, or other study designs. Our secondary objective was to identify the proportion of case series in which potentially inappropriate inferential statements were made. Descriptive evaluation of published literature. One-hundred published studies (from 19 journals) labeled as case series. Studies were identified by a structured literature search, with random selection of 100 studies from the relevant citations. Two reviewers independently characterized each study, with disagreements resolved by consensus. Of the 100 studies, 16 were case series. The remaining studies were descriptive cohort studies (35), population-based cohort studies (36), or other observational or experimental study designs (13). Almost half (48.8%) of the case series or descriptive cohort studies, with no control group and no formal statistical analysis, included inferential statements about the efficacy of treatment or statistical significance of potential risk factors. Authors, peer-reviewers, and editors should carefully consider the design elements of a study to accurately identify and label the study design. Doing so will facilitate an understanding of the evidentiary value of the results. Copyright © 2017 The Authors. Journal of Veterinary Internal Medicine published by Wiley Periodicals, Inc. on behalf of the American College of Veterinary Internal Medicine.

Using Multiple Dialog Modes in a User-System Interface to Accomodate Different Levels of User Experience: An Experimental Study.

DTIC Science & Technology

1986-01-01

Chapter it Research Methodology This chapter describes the methodology and the experimental design used for this research. Prior to discussing the...50 Experimental Design ............................... 50 Task/Treatm ent ................................... 55 Task Design ...Figure 3.3 Interface Experiment Elements ............... 54 Figure 3.4 Experimental Design ....................... 55 Figure 3.5 Subject Assignment

Submersible Aircraft Concept Design Study - Amendment 1. Additional Assessment of Design Risks & Sensitivities within the Original Study, and an Initial Assessment of Key Control Aspects

DTIC Science & Technology

2011-02-01

http://www.redhammer.se/tornado/index.html (3) Aircraft Design: A Conceptual Approach, Daniel P. Raymer , AIAA, 1992 (4) (5) Moran, J., Computational...Fluid Dynamics, Wiley & Sons, 1984. Notes on the Stability and Control of Tailless Airplanes, Robert T. Jones, NACA Technical Note No.837, December

The ElderSmile TimeMap: Benefits of Connecting Statistics With Time and Place.

PubMed

Kum, Susan S; Wang, Hua; Wang, Peng; Jin, Zhu; De La Cruz, Leydis; Northridge, Mary E; Kunzel, Carol; Marshall, Stephen E; Metcalf, Sara S

2015-09-01

Community-based programs are critical for locally targeted public health education and accessible service delivery. Deriving useful information from such programs is important for their own evaluation and improvement and may facilitate research collaboration with partners and experts. Here we present an interactive Web-based application designed for a community-based oral health outreach program called ElderSmile to demonstrate how data can be summarized, filtered, compared, and visualized by time and place to inform program planning, evaluation, and research. The ElderSmile TimeMap ( http://www.acsu.buffalo.edu/∼smetcalf/resources/timemap.html ) is an emergent product of a US National Institutes of Health-funded collaboration of knowledge sharing among multidisciplinary team members at the University at Buffalo, Columbia University, and New York University.

DTMiner: identification of potential disease targets through biomedical literature mining.

PubMed

Xu, Dong; Zhang, Meizhuo; Xie, Yanping; Wang, Fan; Chen, Ming; Zhu, Kenny Q; Wei, Jia

2016-12-01

Biomedical researchers often search through massive catalogues of literature to look for potential relationships between genes and diseases. Given the rapid growth of biomedical literature, automatic relation extraction, a crucial technology in biomedical literature mining, has shown great potential to support research of gene-related diseases. Existing work in this field has produced datasets that are limited both in scale and accuracy. In this study, we propose a reliable and efficient framework that takes large biomedical literature repositories as inputs, identifies credible relationships between diseases and genes, and presents possible genes related to a given disease and possible diseases related to a given gene. The framework incorporates name entity recognition (NER), which identifies occurrences of genes and diseases in texts, association detection whereby we extract and evaluate features from gene-disease pairs, and ranking algorithms that estimate how closely the pairs are related. The F1-score of the NER phase is 0.87, which is higher than existing studies. The association detection phase takes drastically less time than previous work while maintaining a comparable F1-score of 0.86. The end-to-end result achieves a 0.259 F1-score for the top 50 genes associated with a disease, which performs better than previous work. In addition, we released a web service for public use of the dataset. The implementation of the proposed algorithms is publicly available at http://gdr-web.rwebox.com/public_html/index.php?page=download.php The web service is available at http://gdr-web.rwebox.com/public_html/index.php CONTACT: jenny.wei@astrazeneca.com or kzhu@cs.sjtu.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Inquiry-based Science Activities Using The Infrared Zoo and Infrared Yellowstone Resources at Cool Cosmos

NASA Astrophysics Data System (ADS)

Daou, D.; Gauthier, A.

2003-12-01

Inquiry-based activities that utilize the Cool Cosmos image galleries have been designed and developed by K12 teachers enrolled in The Invisible Universe Online for Teachers course. The exploration activities integrate the Our Infrared World Gallery (http://coolcosmos.ipac.caltech.edu/image_galleries/our_ir_world_gallery.html) with either the Infrared Zoo gallery (http://coolcosmos.ipac.caltech.edu/image_galleries/ir_zoo/index.html) or the Infrared Yellowstone image http://coolcosmos.ipac.caltech.edu/image_galleries/ir_yellowstone/index.html) and video (http://coolcosmos.ipac.caltech.edu/videos/ir_yellowstone/index.html) galleries. Complete instructor guides have been developed for the activities and will be presented by the authors in poster and CD form. Although the activities are written for middle and highschool learners, they can easily be adapted for college audiences. The Our Infrared World Gallery exploration helps learners think critically about visible light and infrared light as they compare sets of images (IR and visible light) of known objects. For example: by taking a regular photograph of a running faucet, can you tell if it is running hot or cold water? What new information does the IR image give you? The Infrared Zoo activities encourage learners to investigate the differences between warm and cold blooded animals by comparing sets of IR and visible images. In one activity, learners take on the role of a pit viper seeking prey in various desert and woodland settings. The main activities are extended into the real world by discussing and researching industrial, medical, and societal applications of infrared technologies. The Infrared Yellowstone lessons give learners a unique perspective on Yellowstone National Park and it's spectacular geologic and geothermal features. Infrared video technology is highlighted as learners make detailed observations about the visible and infrared views of the natural phenomena. The "Cool Cosmos" EPO activities are coordinated and managed by the SIRTF Science Center, based at the Infrared Processing and Analysis Center on the campus of the California Institute of Technology in Pasadena. You can find Cool Cosmos at http://coolcosmos.ipac.caltech.edu/

A Response to Paul Stapleton's "Critiquing Research Methodology"

ERIC Educational Resources Information Center

Ross, Steven J.

2006-01-01

Paul Stapleton's (2006) critique of quantitative research brings to the surface some common interpretive problems arising when experimental and quasi-experimental research designs are compared. While Stapleton may be correct in pointing out the superiority of experimental research designs because they best eliminate the influence of extraneous…

The state of RT-quantitative PCR: firsthand observations of implementation of minimum information for the publication of quantitative real-time PCR experiments (MIQE).

PubMed

Taylor, Sean C; Mrkusich, Eli M

2014-01-01

In the past decade, the techniques of quantitative PCR (qPCR) and reverse transcription (RT)-qPCR have become accessible to virtually all research labs, producing valuable data for peer-reviewed publications and supporting exciting research conclusions. However, the experimental design and validation processes applied to the associated projects are the result of historical biases adopted by individual labs that have evolved and changed since the inception of the techniques and associated technologies. This has resulted in wide variability in the quality, reproducibility and interpretability of published data as a direct result of how each lab has designed their RT-qPCR experiments. The 'minimum information for the publication of quantitative real-time PCR experiments' (MIQE) was published to provide the scientific community with a consistent workflow and key considerations to perform qPCR experiments. We use specific examples to highlight the serious negative ramifications for data quality when the MIQE guidelines are not applied and include a summary of good and poor practices for RT-qPCR. © 2013 S. Karger AG, Basel.

75 FR 4173 - Water Quality Standards for the State of Florida's Lakes and Flowing Waters

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-26

.... 2009. What Is in Our Drinking Water. United States Environmental Protection Agency, Office of Research and Development. http://www.epa.gov/extrmurl/research/process/drinkingwater.html . Accessed December... and fauna.\\7\\ \\7\\ National Research Council, 2000. Clean Coastal Waters: Understanding and Reducing...

Design Issues and Inference in Experimental L2 Research

ERIC Educational Resources Information Center

Hudson, Thom; Llosa, Lorena

2015-01-01

Explicit attention to research design issues is essential in experimental second language (L2) research. Too often, however, such careful attention is not paid. This article examines some of the issues surrounding experimental L2 research and its relationships to causal inferences. It discusses the place of research questions and hypotheses,…

Presentation and response timing accuracy in Adobe Flash and HTML5/JavaScript Web experiments.

PubMed

Reimers, Stian; Stewart, Neil

2015-06-01

Web-based research is becoming ubiquitous in the behavioral sciences, facilitated by convenient, readily available participant pools and relatively straightforward ways of running experiments: most recently, through the development of the HTML5 standard. Although in most studies participants give untimed responses, there is a growing interest in being able to record response times online. Existing data on the accuracy and cross-machine variability of online timing measures are limited, and generally they have compared behavioral data gathered on the Web with similar data gathered in the lab. For this article, we took a more direct approach, examining two ways of running experiments online-Adobe Flash and HTML5 with CSS3 and JavaScript-across 19 different computer systems. We used specialist hardware to measure stimulus display durations and to generate precise response times to visual stimuli in order to assess measurement accuracy, examining effects of duration, browser, and system-to-system variability (such as across different Windows versions), as well as effects of processing power and graphics capability. We found that (a) Flash and JavaScript's presentation and response time measurement accuracy are similar; (b) within-system variability is generally small, even in low-powered machines under high load; (c) the variability of measured response times across systems is somewhat larger; and (d) browser type and system hardware appear to have relatively small effects on measured response times. Modeling of the effects of this technical variability suggests that for most within- and between-subjects experiments, Flash and JavaScript can both be used to accurately detect differences in response times across conditions. Concerns are, however, noted about using some correlational or longitudinal designs online.

Design and evaluation of web-based image transmission and display with different protocols

NASA Astrophysics Data System (ADS)

Tan, Bin; Chen, Kuangyi; Zheng, Xichuan; Zhang, Jianguo

2011-03-01

There are many Web-based image accessing technologies used in medical imaging area, such as component-based (ActiveX Control) thick client Web display, Zerofootprint thin client Web viewer (or called server side processing Web viewer), Flash Rich Internet Application(RIA) ,or HTML5 based Web display. Different Web display methods have different peformance in different network environment. In this presenation, we give an evaluation on two developed Web based image display systems. The first one is used for thin client Web display. It works between a PACS Web server with WADO interface and thin client. The PACS Web server provides JPEG format images to HTML pages. The second one is for thick client Web display. It works between a PACS Web server with WADO interface and thick client running in browsers containing ActiveX control, Flash RIA program or HTML5 scripts. The PACS Web server provides native DICOM format images or JPIP stream for theses clients.

LIFE CYCLE ASSESSMENT IN MANAGEMENT, PRODUCT AND PROCESS DESIGN, AND POLICY DECISION MAKING: A CONFERENCE REPORT

EPA Science Inventory

On 24 September 2003, life cycle assessment (LCA) practitioners and decision makers gathered at the InLCA/LCM Conference in Seattle, Washington, USA (see http://www.lcacenter.org/InLCA-LCM03/index.html) to discuss the role of LCA in management, product design, process development...

Description of research design of articles published in four Brazilian physical therapy journals

PubMed Central

Saragiotto, Bruno T.; Costa, Lucíola C. M.; Oliveira, Ronaldo F.; Lopes, Alexandre D.; Moseley, Anne M.; Costa, Leonardo O. P.

2014-01-01

Background While the research design of articles published in medical journals and in some physical therapy journals has already been evaluated, this has not been investigated in Brazilian physical therapy journals. Objective To describe the research design used in all articles published in Brazilian scientific journals that are freely available, have high Qualis rankings, and are relevant to physical therapy over a 7-year period. Method We extracted the bibliometric data, research design, research type (human or animal), and clinical area for all articles published. The articles were grouped into their level of evidence, and descriptive analyses were performed. We calculated the frequency, proportions of articles, and 95% confidence interval of these proportions with each research design in each journal. We cross-tabulated the clinical areas with research designs (expressed as number and percentages). Results A total of 1,458 articles from four Brazilian journals were found: Revista Brasileira de Fisioterapia, Revista Fisioterapia em Movimento, Revista Fisioterapia e Pesquisa, and Revista Acta Fisiátrica. The majority of articles were classified as level II of evidence (60%), followed by level III (29%) and level I (10%). The most prevalent research designs were cross-sectional studies (38%), single-case or case-series studies, and narrative reviews. Most articles reported human research and were in the musculoskeletal, neurologic, and cardiothoracic areas. Conclusions Most of the research published in Brazilian physical therapy journals used levels II and III of evidence. Increasing the publication rate of systematic reviews and randomized controlled trials would provide more high-quality evidence to guide evidence-based physical therapy practice. PMID:24675913

Description of research design of articles published in four Brazilian physical therapy journals.

PubMed

Saragiotto, Bruno T; Costa, Lucíola C M; Oliveira, Ronaldo F; Lopes, Alexandre D; Moseley, Anne M; Costa, Leonardo O P

2014-01-01

While the research design of articles published in medical journals and in some physical therapy journals has already been evaluated, this has not been investigated in Brazilian physical therapy journals. Objective : To describe the research design used in all articles published in Brazilian scientific journals that are freely available, have high Qualis rankings, and are relevant to physical therapy over a 7-year period. We extracted the bibliometric data, research design, research type (human or animal), and clinical area for all articles published. The articles were grouped into their level of evidence, and descriptive analyses were performed. We calculated the frequency, proportions of articles, and 95% confidence interval of these proportions with each research design in each journal. We cross-tabulated the clinical areas with research designs (expressed as number and percentages). A total of 1,458 articles from four Brazilian journals were found: Revista Brasileira de Fisioterapia, Revista Fisioterapia em Movimento, Revista Fisioterapia e Pesquisa, and Revista Acta Fisiátrica. The majority of articles were classified as level II of evidence (60%), followed by level III (29%) and level I (10%). The most prevalent research designs were cross-sectional studies (38%), single-case or case-series studies, and narrative reviews. Most articles reported human research and were in the musculoskeletal, neurologic, and cardiothoracic areas. Most of the research published in Brazilian physical therapy journals used levels II and III of evidence. Increasing the publication rate of systematic reviews and randomized controlled trials would provide more high-quality evidence to guide evidence-based physical therapy practice.

NGS Catalog: A Database of Next Generation Sequencing Studies in Humans

PubMed Central

Xia, Junfeng; Wang, Qingguo; Jia, Peilin; Wang, Bing; Pao, William; Zhao, Zhongming

2015-01-01

Next generation sequencing (NGS) technologies have been rapidly applied in biomedical and biological research since its advent only a few years ago, and they are expected to advance at an unprecedented pace in the following years. To provide the research community with a comprehensive NGS resource, we have developed the database Next Generation Sequencing Catalog (NGS Catalog, http://bioinfo.mc.vanderbilt.edu/NGS/index.html), a continually updated database that collects, curates and manages available human NGS data obtained from published literature. NGS Catalog deposits publication information of NGS studies and their mutation characteristics (SNVs, small insertions/deletions, copy number variations, and structural variants), as well as mutated genes and gene fusions detected by NGS. Other functions include user data upload, NGS general analysis pipelines, and NGS software. NGS Catalog is particularly useful for investigators who are new to NGS but would like to take advantage of these powerful technologies for their own research. Finally, based on the data deposited in NGS Catalog, we summarized features and findings from whole exome sequencing, whole genome sequencing, and transcriptome sequencing studies for human diseases or traits. PMID:22517761

Analysis of a spacecraft life support system for a Mars mission.

PubMed

Czupalla, M; Aponte, V; Chappell, S; Klaus, D

2004-01-01

This report summarizes a trade study conducted as part of the Fall 2002 semester Spacecraft Life Support System Design course (ASEN 5116) in the Aerospace Engineering Sciences Department at the University of Colorado. It presents an analysis of current life support system technologies and a preliminary design of an integrated system for supporting humans during transit to and on the surface of the planet Mars. This effort was based on the NASA Design Reference Mission (DRM) for the human exploration of Mars [NASA Design Reference Mission (DRM) for Mars, Addendum 3.0, from the world wide web: http://exploration.jsc.nasa.gov/marsref/contents.html.]. The integrated design was broken into four subsystems: Water Management, Atmosphere Management, Waste Processing, and Food Supply. The process started with the derivation of top-level requirements from the DRM. Additional system and subsystem level assumptions were added where clarification was needed. Candidate technologies were identified and characterized based on performance factors. Trade studies were then conducted for each subsystem. The resulting technologies were integrated into an overall design solution using mass flow relationships. The system level trade study yielded two different configurations--one for the transit to Mars and another for the surface habitat, which included in situ resource utilization. Equivalent System Mass analyses were used to compare each design against an open-loop (non-regenerable) baseline system. c2003 International Astronautical Federation. Published by Elsevier Ltd. All rights reserved.

Good experimental design and statistics can save animals, but how can it be promoted?

PubMed

Festing, Michael F W

2004-06-01

Surveys of published papers show that there are many errors both in the design of the experiments and in the statistical analysis of the resulting data. This must result in a waste of animals and scientific resources, and it is surely unethical. Scientific quality might be improved, to some extent, by journal editors, but they are constrained by lack of statistical referees and inadequate statistical training of those referees that they do use. Other parties, such as welfare regulators, ethical review committees and individual scientists also have an interest in scientific quality, but they do not seem to be well placed to make the required changes. However, those who fund research would have the power to do something if they could be convinced that it is in their best interests to do so. More examples of the way in which better experimental design has led to improved experiments would be helpful in persuading these funding organisations to take further action.

Efficient preliminary floating offshore wind turbine design and testing methodologies and application to a concrete spar design.

PubMed

Matha, Denis; Sandner, Frank; Molins, Climent; Campos, Alexis; Cheng, Po Wen

2015-02-28

The current key challenge in the floating offshore wind turbine industry and research is on designing economic floating systems that can compete with fixed-bottom offshore turbines in terms of levelized cost of energy. The preliminary platform design, as well as early experimental design assessments, are critical elements in the overall design process. In this contribution, a brief review of current floating offshore wind turbine platform pre-design and scaled testing methodologies is provided, with a focus on their ability to accommodate the coupled dynamic behaviour of floating offshore wind systems. The exemplary design and testing methodology for a monolithic concrete spar platform as performed within the European KIC AFOSP project is presented. Results from the experimental tests compared to numerical simulations are presented and analysed and show very good agreement for relevant basic dynamic platform properties. Extreme and fatigue loads and cost analysis of the AFOSP system confirm the viability of the presented design process. In summary, the exemplary application of the reduced design and testing methodology for AFOSP confirms that it represents a viable procedure during pre-design of floating offshore wind turbine platforms. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

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

ClassLess: A Comprehensive Database of Young Stellar Objects

NASA Astrophysics Data System (ADS)

Hillenbrand, Lynne; Baliber, Nairn

2015-01-01

We have designed and constructed a database housing published measurements of Young Stellar Objects (YSOs) within ~1 kpc of the Sun. ClassLess, so called because it includes YSOs in all stages of evolution, is a relational database in which user interaction is conducted via HTML web browsers, queries are performed in scientific language, and all data are linked to the sources of publication. Each star is associated with a cluster (or clusters), and both spatially resolved and unresolved measurements are stored, allowing proper use of data from multiple star systems. With this fully searchable tool, myriad ground- and space-based instruments and surveys across wavelength regimes can be exploited. In addition to primary measurements, the database self consistently calculates and serves higher level data products such as extinction, luminosity, and mass. As a result, searches for young stars with specific physical characteristics can be completed with just a few mouse clicks.

An Investigation of Momentum Exchange Parameterizations and Atmospheric Forcing for the Coastal Mixing and Optics Program

DTIC Science & Technology

1998-09-01

Stenner , 1996.] Figure 2.2. Coastal Mixing and Optics central 3 m discus buoy. [From Baumgartner and Anderson, 1997 (Figure 4).] 12 2.2.2. SoNIC...Meteorology, 78, 247-290. Stenner , R., 1996: Coastal Mixing and Optics Experimental Site (http://wavelet.apl.washington.edu/CMO/CMO_bath.html). Thiermann

Calibrated dilatometer exercise to probe thermoplastic properties of coal in pressurized CO 2

DOE PAGES

Romanov, Vyacheslav N.; Lynn, Ronald J.; Warzinski, Robert P.

2017-07-03

This research was aimed at testing a hypothesis, that at elevated CO 2 pressure coal can soften at temperatures well below those obtained in the presence of other gases. That could have serious negative implications for injection of CO 2 into deep coal seams. Here, we have examined the experimental design issues and procedures used in the previously published studies, and experimentally investigated the physical behavior of a similar coal in the presence of CO 2 as a function of pressure and temperature, using the same high-pressure micro-dilatometer refurbished and carefully calibrated for this purpose. No notable reduction in coalmore » softening temperature was observed in this study.« less

Calibrated dilatometer exercise to probe thermoplastic properties of coal in pressurized CO 2

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

Romanov, Vyacheslav N.; Lynn, Ronald J.; Warzinski, Robert P.

This research was aimed at testing a hypothesis, that at elevated CO 2 pressure coal can soften at temperatures well below those obtained in the presence of other gases. That could have serious negative implications for injection of CO 2 into deep coal seams. Here, we have examined the experimental design issues and procedures used in the previously published studies, and experimentally investigated the physical behavior of a similar coal in the presence of CO 2 as a function of pressure and temperature, using the same high-pressure micro-dilatometer refurbished and carefully calibrated for this purpose. No notable reduction in coalmore » softening temperature was observed in this study.« less

The effect of integrating constructivist and evidence-based practice on baccalaureate nursing student's cognitive load and learning performance in a research course.

PubMed

Hsieh, Suh-Ing; Hsu, Li-Ling; Huang, Tzu-Hsin

2016-07-01

Baccalaureate nursing students perceive research as unattractive, doubt the value of nursing research, and do not appreciate the link of research with practice. No studies have examined students' cognitive load during an evidence-based practice research course versus a traditional research course. To assess the effect of integrating constructivist theories and evidence-based practice on student cognitive load and learning performance in a research course. A true experimental study. A Registered Nurse-to-Bachelor of Science in Nursing program. Six classes of second-year students. Students were randomly allocated to the control group (two classes) or the experimental group (two classes) using cluster randomization. The control group underwent "traditional research"; the experimental group experienced "integrating evidence-based practice into research." Instruments for outcome assessment include the Cognitive Load Scale, cognitive test, team critique paper, and qualitative feedback on course satisfaction. The between-subjects effects were compared by Analysis of Covariance. The experimental group had significantly higher mental load (8.74 vs. 7.27, p<.001), mental effort (11.07 vs. 10.07, p=.009), mental efficiency (0.33 vs. -0.31, p<.001), and research knowledge (70.61 vs. 44.92, p<.001) than the control group. The experimental group had better critique paper scores in introduction (92.80%), literature review (91.70%), and assignment requirement and writing (89.40%). Some experimental learners expressed satisfaction with learning evidence-based practice (17.78%) and critiquing a research article (7.78%). Integrating evidence-based practice into a research course not only improved the research knowledge of baccalaureate nursing students, but also increased their mental load, mental effort, and mental efficiency. Additional studies may track learners' responses to different learning systems using the developed instrument to measure the three types of cognitive load. These findings may help educators design more effective and interesting curricula for integrating research and evidence-based practice into the studies of student nurses. Copyright © 2016. Published by Elsevier Ltd.

City Connects: Building an Argument for Effects on Student Achievement with a Quasi-Experimental Design

ERIC Educational Resources Information Center

Walsh, Mary; Raczek, Anastasia; Sibley, Erin; Lee-St. John, Terrence; An, Chen; Akbayin, Bercem; Dearing, Eric; Foley, Claire

2015-01-01

While randomized experimental designs are the gold standard in education research concerned with causal inference, non-experimental designs are ubiquitous. For researchers who work with non-experimental data and are no less concerned for causal inference, the major problem is potential omitted variable bias. In this presentation, the authors…

diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data.

PubMed

Lareau, Caleb A; Aryee, Martin J; Berger, Bonnie

2018-02-15

The 3D architecture of DNA within the nucleus is a key determinant of interactions between genes, regulatory elements, and transcriptional machinery. As a result, differences in DNA looping structure are associated with variation in gene expression and cell state. To systematically assess changes in DNA looping architecture between samples, we introduce diffloop, an R/Bioconductor package that provides a suite of functions for the quality control, statistical testing, annotation, and visualization of DNA loops. We demonstrate this functionality by detecting differences between ENCODE ChIA-PET samples and relate looping to variability in epigenetic state. Diffloop is implemented as an R/Bioconductor package available at https://bioconductor.org/packages/release/bioc/html/diffloop.html. aryee.martin@mgh.harvard.edu. 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

HDF-EOS Web Server

NASA Technical Reports Server (NTRS)

Ullman, Richard; Bane, Bob; Yang, Jingli

2008-01-01

A shell script has been written as a means of automatically making HDF-EOS-formatted data sets available via the World Wide Web. ("HDF-EOS" and variants thereof are defined in the first of the two immediately preceding articles.) The shell script chains together some software tools developed by the Data Usability Group at Goddard Space Flight Center to perform the following actions: Extract metadata in Object Definition Language (ODL) from an HDF-EOS file, Convert the metadata from ODL to Extensible Markup Language (XML), Reformat the XML metadata into human-readable Hypertext Markup Language (HTML), Publish the HTML metadata and the original HDF-EOS file to a Web server and an Open-source Project for a Network Data Access Protocol (OPeN-DAP) server computer, and Reformat the XML metadata and submit the resulting file to the EOS Clearinghouse, which is a Web-based metadata clearinghouse that facilitates searching for, and exchange of, Earth-Science data.

The Experimental Design Assistant.

PubMed

Percie du Sert, Nathalie; Bamsey, Ian; Bate, Simon T; Berdoy, Manuel; Clark, Robin A; Cuthill, Innes; Fry, Derek; Karp, Natasha A; Macleod, Malcolm; Moon, Lawrence; Stanford, S Clare; Lings, Brian

2017-09-01

Addressing the common problems that researchers encounter when designing and analysing animal experiments will improve the reliability of in vivo research. In this article, the Experimental Design Assistant (EDA) is introduced. The EDA is a web-based tool that guides the in vivo researcher through the experimental design and analysis process, providing automated feedback on the proposed design and generating a graphical summary that aids communication with colleagues, funders, regulatory authorities, and the wider scientific community. It will have an important role in addressing causes of irreproducibility.

The Experimental Design Assistant

PubMed Central

Bamsey, Ian; Bate, Simon T.; Berdoy, Manuel; Clark, Robin A.; Cuthill, Innes; Fry, Derek; Karp, Natasha A.; Macleod, Malcolm; Moon, Lawrence; Stanford, S. Clare; Lings, Brian

2017-01-01

Addressing the common problems that researchers encounter when designing and analysing animal experiments will improve the reliability of in vivo research. In this article, the Experimental Design Assistant (EDA) is introduced. The EDA is a web-based tool that guides the in vivo researcher through the experimental design and analysis process, providing automated feedback on the proposed design and generating a graphical summary that aids communication with colleagues, funders, regulatory authorities, and the wider scientific community. It will have an important role in addressing causes of irreproducibility. PMID:28957312

Publisher Correction: Random access quantum information processors using multimode circuit quantum electrodynamics.

PubMed

Naik, R K; Leung, N; Chakram, S; Groszkowski, Peter; Lu, Y; Earnest, N; McKay, D C; Koch, Jens; Schuster, D I

2018-01-09

In the original version of this Article, the affiliation details for Peter Groszkowski and Jens Koch were incorrectly given as 'Department of Physics, University of Chicago, Chicago, IL, 60637, USA', instead of the correct 'Department of Physics and Astronomy, Northwestern University, Evanston, Illinois 60208, USA'. This has now been corrected in both the PDF and HTML versions of the Article.

The Fraser Experimental Forest, Colorado: Research program and published research 1937-1985

Treesearch

Robert R. Alexander; Charles A. Troendle; Merrill R. Kaufmann; Wayne D. Shepperd; Glenn L. Crouch; Ross K. Watkins

1985-01-01

This report provides an overview of the research done on the Fraser Experimental Forest. It replaces GTR's no. 40 and 40A by Robert R. Alexander and Ross K. Watkins in 1977. Included are descriptions of physical features and resources, highlights of past and current research, and the publications derived from that research.

PC-based web authoring: How to learn as little unix as possible while getting on the Web

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

Gennari, L.T.; Breaux, M.; Minton, S.

1996-09-01

This document is a general guide for creating Web pages, using commonly available word processing and file transfer applications. It is not a full guide to HTML, nor does it provide an introduction to the many WYSIWYG HTML editors available. The viability of the authoring method it describes will not be affected by changes in the HTML specification or the rapid release-and-obsolescence cycles of commercial WYSIWYG HTML editors. This document provides a gentle introduction to HTML for the beginner, and as the user gains confidence and experience, encourages greater familiarity with HTML through continued exposure to and hands-on usage ofmore » HTML code.« less

Mac-based Web authoring: How to learn as little Unix as possible while getting on the Web.

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

Gennari, L.T.

1996-06-01

This document is a general guide for creating Web pages, using commonly available word processing and file transfer applications. It is not a full guide to HTML, nor does it provide an introduction to the many WYSIWYG HTML editors available. The viability of the authoring method it describes will not be affected by changes in the HTML specification or the rapid release-and-obsolescence cycles of commercial WYSIWYG HTML editors. This document provides a gentle introduction to HTML for the beginner and as the user gains confidence and experience, encourages greater familiarity with HTML through continued exposure to and hands-on usage ofmore » HTML code.« less

RESEARCH DESIGNS IN SPORTS PHYSICAL THERAPY

PubMed Central

2012-01-01

Research is designed to answer a question or to describe a phenomenon in a scientific process. Sports physical therapists must understand the different research methods, types, and designs in order to implement evidence‐based practice. The purpose of this article is to describe the most common research designs used in sports physical therapy research and practice. Both experimental and non‐experimental methods will be discussed. PMID:23091780

Bromamine Decomposition Revisited: A Holistic Approach for Analyzing Acid and Base Catalysis Kinetics.

PubMed

Wahman, David G; Speitel, Gerald E; Katz, Lynn E

2017-11-21

Chloramine chemistry is complex, with a variety of reactions occurring in series and parallel and many that are acid or base catalyzed, resulting in numerous rate constants. Bromide presence increases system complexity even further with possible bromamine and bromochloramine formation. Therefore, techniques for parameter estimation must address this complexity through thoughtful experimental design and robust data analysis approaches. The current research outlines a rational basis for constrained data fitting using Brønsted theory, application of the microscopic reversibility principle to reversible acid or base catalyzed reactions, and characterization of the relative significance of parallel reactions using fictive product tracking. This holistic approach was used on a comprehensive and well-documented data set for bromamine decomposition, allowing new interpretations of existing data by revealing that a previously published reaction scheme was not robust; it was not able to describe monobromamine or dibromamine decay outside of the conditions for which it was calibrated. The current research's simplified model (3 reactions, 17 constants) represented the experimental data better than the previously published model (4 reactions, 28 constants). A final model evaluation was conducted based on representative drinking water conditions to determine a minimal model (3 reactions, 8 constants) applicable for drinking water conditions.

Conducting Research in Technical Communication: The Application of True Experimental Designs.

ERIC Educational Resources Information Center

Spyridakis, Jan H.

1992-01-01

Explains the use of true experimental designs in technical communication research, lists the eight steps in the research process, and concludes with the hope that practitioners should now be able to read research studies critically and perhaps design empirical studies of their own after further reading. (SR)

Publisher Correction: Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity.

PubMed

Turcot, Valérie; Lu, Yingchang; Highland, Heather M; Schurmann, Claudia; Justice, Anne E; Fine, Rebecca S; Bradfield, Jonathan P; Esko, Tõnu; Giri, Ayush; Graff, Mariaelisa; Guo, Xiuqing; Hendricks, Audrey E; Karaderi, Tugce; Lempradl, Adelheid; Locke, Adam E; Mahajan, Anubha; Marouli, Eirini; Sivapalaratnam, Suthesh; Young, Kristin L; Alfred, Tamuno; Feitosa, Mary F; Masca, Nicholas G D; Manning, Alisa K; Medina-Gomez, Carolina; Mudgal, Poorva; Ng, Maggie C Y; Reiner, Alex P; Vedantam, Sailaja; Willems, Sara M; Winkler, Thomas W; Abecasis, Gonçalo; Aben, Katja K; Alam, Dewan S; Alharthi, Sameer E; Allison, Matthew; Amouyel, Philippe; Asselbergs, Folkert W; Auer, Paul L; Balkau, Beverley; Bang, Lia E; Barroso, Inês; Bastarache, Lisa; Benn, Marianne; Bergmann, Sven; Bielak, Lawrence F; Blüher, Matthias; Boehnke, Michael; Boeing, Heiner; Boerwinkle, Eric; Böger, Carsten A; Bork-Jensen, Jette; Bots, Michiel L; Bottinger, Erwin P; Bowden, Donald W; Brandslund, Ivan; Breen, Gerome; Brilliant, Murray H; Broer, Linda; Brumat, Marco; Burt, Amber A; Butterworth, Adam S; Campbell, Peter T; Cappellani, Stefania; Carey, David J; Catamo, Eulalia; Caulfield, Mark J; Chambers, John C; Chasman, Daniel I; Chen, Yii-Der I; Chowdhury, Rajiv; Christensen, Cramer; Chu, Audrey Y; Cocca, Massimiliano; Collins, Francis S; Cook, James P; Corley, Janie; Corominas Galbany, Jordi; Cox, Amanda J; Crosslin, David S; Cuellar-Partida, Gabriel; D'Eustacchio, Angela; Danesh, John; Davies, Gail; Bakker, Paul I W; Groot, Mark C H; Mutsert, Renée; Deary, Ian J; Dedoussis, George; Demerath, Ellen W; Heijer, Martin; Hollander, Anneke I; Ruijter, Hester M; Dennis, Joe G; Denny, Josh C; Di Angelantonio, Emanuele; Drenos, Fotios; Du, Mengmeng; Dubé, Marie-Pierre; Dunning, Alison M; Easton, Douglas F; Edwards, Todd L; Ellinghaus, David; Ellinor, Patrick T; Elliott, Paul; Evangelou, Evangelos; Farmaki, Aliki-Eleni; Farooqi, I Sadaf; Faul, Jessica D; Fauser, Sascha; Feng, Shuang; Ferrannini, Ele; Ferrieres, Jean; Florez, Jose C; Ford, Ian; Fornage, Myriam; Franco, Oscar H; Franke, Andre; Franks, Paul W; Friedrich, Nele; Frikke-Schmidt, Ruth; Galesloot, Tessel E; Gan, Wei; Gandin, Ilaria; Gasparini, Paolo; Gibson, Jane; Giedraitis, Vilmantas; Gjesing, Anette P; Gordon-Larsen, Penny; Gorski, Mathias; Grabe, Hans-Jörgen; Grant, Struan F A; Grarup, Niels; Griffiths, Helen L; Grove, Megan L; Gudnason, Vilmundur; Gustafsson, Stefan; Haessler, Jeff; Hakonarson, Hakon; Hammerschlag, Anke R; Hansen, Torben; Harris, Kathleen Mullan; Harris, Tamara B; Hattersley, Andrew T; Have, Christian T; Hayward, Caroline; He, Liang; Heard-Costa, Nancy L; Heath, Andrew C; Heid, Iris M; Helgeland, Øyvind; Hernesniemi, Jussi; Hewitt, Alex W; Holmen, Oddgeir L; Hovingh, G Kees; Howson, Joanna M M; Hu, Yao; Huang, Paul L; Huffman, Jennifer E; Ikram, M Arfan; Ingelsson, Erik; Jackson, Anne U; Jansson, Jan-Håkan; Jarvik, Gail P; Jensen, Gorm B; Jia, Yucheng; Johansson, Stefan; Jørgensen, Marit E; Jørgensen, Torben; Jukema, J Wouter; Kahali, Bratati; Kahn, René S; Kähönen, Mika; Kamstrup, Pia R; Kanoni, Stavroula; Kaprio, Jaakko; Karaleftheri, Maria; Kardia, Sharon L R; Karpe, Fredrik; Kathiresan, Sekar; Kee, Frank; Kiemeney, Lambertus A; Kim, Eric; Kitajima, Hidetoshi; Komulainen, Pirjo; Kooner, Jaspal S; Kooperberg, Charles; Korhonen, Tellervo; Kovacs, Peter; Kuivaniemi, Helena; Kutalik, Zoltán; Kuulasmaa, Kari; Kuusisto, Johanna; Laakso, Markku; Lakka, Timo A; Lamparter, David; Lange, Ethan M; Lange, Leslie A; Langenberg, Claudia; Larson, Eric B; Lee, Nanette R; Lehtimäki, Terho; Lewis, Cora E; Li, Huaixing; Li, Jin; Li-Gao, Ruifang; Lin, Honghuang; Lin, Keng-Hung; Lin, Li-An; Lin, Xu; Lind, Lars; Lindström, Jaana; Linneberg, Allan; Liu, Ching-Ti; Liu, Dajiang J; Liu, Yongmei; Lo, Ken S; Lophatananon, Artitaya; Lotery, Andrew J; Loukola, Anu; Luan, Jian'an; Lubitz, Steven A; Lyytikäinen, Leo-Pekka; Männistö, Satu; Marenne, Gaëlle; Mazul, Angela L; McCarthy, Mark I; McKean-Cowdin, Roberta; Medland, Sarah E; Meidtner, Karina; Milani, Lili; Mistry, Vanisha; Mitchell, Paul; Mohlke, Karen L; Moilanen, Leena; Moitry, Marie; Montgomery, Grant W; Mook-Kanamori, Dennis O; Moore, Carmel; Mori, Trevor A; Morris, Andrew D; Morris, Andrew P; Müller-Nurasyid, Martina; Munroe, Patricia B; Nalls, Mike A; Narisu, Narisu; Nelson, Christopher P; Neville, Matt; Nielsen, Sune F; Nikus, Kjell; Njølstad, Pål R; Nordestgaard, Børge G; Nyholt, Dale R; O'Connel, Jeffrey R; O'Donoghue, Michelle L; Olde Loohuis, Loes M; Ophoff, Roel A; Owen, Katharine R; Packard, Chris J; Padmanabhan, Sandosh; Palmer, Colin N A; Palmer, Nicholette D; Pasterkamp, Gerard; Patel, Aniruddh P; Pattie, Alison; Pedersen, Oluf; Peissig, Peggy L; Peloso, Gina M; Pennell, Craig E; Perola, Markus; Perry, James A; Perry, John R B; Pers, Tune H; Person, Thomas N; Peters, Annette; Petersen, Eva R B; Peyser, Patricia A; Pirie, Ailith; Polasek, Ozren; Polderman, Tinca J; Puolijoki, Hannu; Raitakari, Olli T; Rasheed, Asif; Rauramaa, Rainer; Reilly, Dermot F; Renström, Frida; Rheinberger, Myriam; Ridker, Paul M; Rioux, John D; Rivas, Manuel A; Roberts, David J; Robertson, Neil R; Robino, Antonietta; Rolandsson, Olov; Rudan, Igor; Ruth, Katherine S; Saleheen, Danish; Salomaa, Veikko; Samani, Nilesh J; Sapkota, Yadav; Sattar, Naveed; Schoen, Robert E; Schreiner, Pamela J; Schulze, Matthias B; Scott, Robert A; Segura-Lepe, Marcelo P; Shah, Svati H; Sheu, Wayne H-H; Sim, Xueling; Slater, Andrew J; Small, Kerrin S; Smith, Albert V; Southam, Lorraine; Spector, Timothy D; Speliotes, Elizabeth K; Starr, John M; Stefansson, Kari; Steinthorsdottir, Valgerdur; Stirrups, Kathleen E; Strauch, Konstantin; Stringham, Heather M; Stumvoll, Michael; Sun, Liang; Surendran, Praveen; Swift, Amy J; Tada, Hayato; Tansey, Katherine E; Tardif, Jean-Claude; Taylor, Kent D; Teumer, Alexander; Thompson, Deborah J; Thorleifsson, Gudmar; Thorsteinsdottir, Unnur; Thuesen, Betina H; Tönjes, Anke; Tromp, Gerard; Trompet, Stella; Tsafantakis, Emmanouil; Tuomilehto, Jaakko; Tybjaerg-Hansen, Anne; Tyrer, Jonathan P; Uher, Rudolf; Uitterlinden, André G; Uusitupa, Matti; Laan, Sander W; Duijn, Cornelia M; Leeuwen, Nienke; van Setten, Jessica; Vanhala, Mauno; Varbo, Anette; Varga, Tibor V; Varma, Rohit; Velez Edwards, Digna R; Vermeulen, Sita H; Veronesi, Giovanni; Vestergaard, Henrik; Vitart, Veronique; Vogt, Thomas F; Völker, Uwe; Vuckovic, Dragana; Wagenknecht, Lynne E; Walker, Mark; Wallentin, Lars; Wang, Feijie; Wang, Carol A; Wang, Shuai; Wang, Yiqin; Ware, Erin B; Wareham, Nicholas J; Warren, Helen R; Waterworth, Dawn M; Wessel, Jennifer; White, Harvey D; Willer, Cristen J; Wilson, James G; Witte, Daniel R; Wood, Andrew R; Wu, Ying; Yaghootkar, Hanieh; Yao, Jie; Yao, Pang; Yerges-Armstrong, Laura M; Young, Robin; Zeggini, Eleftheria; Zhan, Xiaowei; Zhang, Weihua; Zhao, Jing Hua; Zhao, Wei; Zhao, Wei; Zhou, Wei; Zondervan, Krina T; Rotter, Jerome I; Pospisilik, John A; Rivadeneira, Fernando; Borecki, Ingrid B; Deloukas, Panos; Frayling, Timothy M; Lettre, Guillaume; North, Kari E; Lindgren, Cecilia M; Hirschhorn, Joel N; Loos, Ruth J F

2018-05-01

In the version of this article originally published, one of the two authors with the name Wei Zhao was omitted from the author list and the affiliations for both authors were assigned to the single Wei Zhao in the author list. In addition, the ORCID for Wei Zhao (Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA) was incorrectly assigned to author Wei Zhou. The errors have been corrected in the HTML and PDF versions of the article.

Publisher Correction: RING tetramerization is required for nuclear body biogenesis and PML sumoylation.

PubMed

Wang, Pengran; Benhenda, Shirine; Wu, Haiyan; Lallemand-Breitenbach, Valérie; Zhen, Tao; Jollivet, Florence; Peres, Laurent; Li, Yuwen; Chen, Sai-Juan; Chen, Zhu; de Thé, Hugues; Meng, Guoyu

2018-05-04

In the originally published version of this Article, the authors Sai-Juan Chen and Zhu Chen were incorrectly listed as being affiliated with 'University Paris Diderot, Sorbonne Paris Cité, INSERM U944, CNRS UMR7212, Equipe labellisée LNCC, Hôpital St. Louis 1, Paris 75475, France', and the affiliation 'Institute of Health Sciences, Shanghai Institutes for Biological Sciences and Graduate School, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China' was inadvertently omitted. These errors have now been corrected in both the PDF and HTML versions of the Article.

Experimental design and reporting standards for improving the internal validity of pre-clinical studies in the field of pain: Consensus of the IMI-Europain consortium.

PubMed

Knopp, K L; Stenfors, C; Baastrup, C; Bannon, A W; Calvo, M; Caspani, O; Currie, G; Finnerup, N B; Huang, W; Kennedy, J D; Lefevre, I; Machin, I; Macleod, M; Rees, H; Rice, A S C; Rutten, K; Segerdahl, M; Serra, J; Wodarski, R; Berge, O-G; Treedef, R-D

2017-12-29

Background and aims Pain is a subjective experience, and as such, pre-clinical models of human pain are highly simplified representations of clinical features. These models are nevertheless critical for the delivery of novel analgesics for human pain, providing pharmacodynamic measurements of activity and, where possible, on-target confirmation of that activity. It has, however, been suggested that at least 50% of all pre-clinical data, independent of discipline, cannot be replicated. Additionally, the paucity of "negative" data in the public domain indicates a publication bias, and significantly impacts the interpretation of failed attempts to replicate published findings. Evidence suggests that systematic biases in experimental design and conduct and insufficiencies in reporting play significant roles in poor reproducibility across pre-clinical studies. It then follows that recommendations on how to improve these factors are warranted. Methods Members of Europain, a pain research consortium funded by the European Innovative Medicines Initiative (IMI), developed internal recommendations on how to improve the reliability of pre-clinical studies between laboratories. This guidance is focused on two aspects: experimental design and conduct, and study reporting. Results Minimum requirements for experimental design and conduct were agreed upon across the dimensions of animal characteristics, sample size calculations, inclusion and exclusion criteria, random allocation to groups, allocation concealment, and blinded assessment of outcome. Building upon the Animals in Research: Reportingin vivo Experiments (ARRIVE) guidelines, reporting standards were developed for pre-clinical studies of pain. These include specific recommendations for reporting on ethical issues, experimental design and conduct, and data analysis and interpretation. Key principles such as sample size calculation, a priori definition of a primary efficacy measure, randomization, allocation concealments, and blinding are discussed. In addition, considerations of how stress and normal rodent physiology impact outcome of analgesic drug studies are considered. Flow diagrams are standard requirements in all clinical trials, and flow diagrams for preclinical trials, which describe number of animals included/excluded, and reasons for exclusion are proposed. Creation of a trial registry for pre-clinical studies focused on drug development in order to estimate possible publication bias is discussed. Conclusions More systematic research is needed to analyze how inadequate internal validity and/or experimental bias may impact reproducibility across pre-clinical pain studies. Addressing the potential threats to internal validity and the sources of experimental biases, as well as increasing the transparency in reporting, are likely to improve preclinical research broadly by ensuring relevant progress is made in advancing the knowledge of chronic pain pathophysiology and identifying novel analgesics. Implications We are now disseminating these Europain processes for discussion in the wider pain research community. Any benefit from these guidelines will be dependent on acceptance and disciplined implementation across pre-clinical laboratories, funding agencies and journal editors, but it is anticipated that these guidelines will be a first step towards improving scientific rigor across the field of pre-clinical pain research.

Generalized empirical Bayesian methods for discovery of differential data in high-throughput biology.

PubMed

Hardcastle, Thomas J

2016-01-15

High-throughput data are now commonplace in biological research. Rapidly changing technologies and application mean that novel methods for detecting differential behaviour that account for a 'large P, small n' setting are required at an increasing rate. The development of such methods is, in general, being done on an ad hoc basis, requiring further development cycles and a lack of standardization between analyses. We present here a generalized method for identifying differential behaviour within high-throughput biological data through empirical Bayesian methods. This approach is based on our baySeq algorithm for identification of differential expression in RNA-seq data based on a negative binomial distribution, and in paired data based on a beta-binomial distribution. Here we show how the same empirical Bayesian approach can be applied to any parametric distribution, removing the need for lengthy development of novel methods for differently distributed data. Comparisons with existing methods developed to address specific problems in high-throughput biological data show that these generic methods can achieve equivalent or better performance. A number of enhancements to the basic algorithm are also presented to increase flexibility and reduce computational costs. The methods are implemented in the R baySeq (v2) package, available on Bioconductor http://www.bioconductor.org/packages/release/bioc/html/baySeq.html. tjh48@cam.ac.uk 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.

Learning Experimental Design through Targeted Student-Centric Journal Club with Screencasting.

PubMed

Carter, Bradley S; Hamilton, David E; Thompson, Robert C

2017-01-01

Knowledge and application of experimental design principles are essential components of scientific methodology, and experience with these skills is fundamental for participating in scientific research. However, undergraduates often enter the research laboratory with little training in designing and interpreting their own experiments. In the context of a research university laboratory, we designed a journal club training exercise to address this need. Students were instructed on methods for interpreting scientific literature using a screencast, a digital recording of a slide presentation narrated by an instructor. Students subsequently examined a series of research publications with a focus on the experimental designs and data interpretation in a two-session group discussion journal club format. We have found this approach to be an efficient and productive method for engaging students in learning about principles of experimental design and further preparing them for success in laboratory research.

Design and Implementation of an Experimental Cataloging Advisor--Mapper.

ERIC Educational Resources Information Center

Ercegovac, Zorana; Borko, Harold

1992-01-01

Describes the design of an experimental computer-aided cataloging advisor, Mapper, that was developed to help novice users with the descriptive cataloging of single-sheet maps from U.S. publishers. The human-computer interface is considered, the use of HyperCard is discussed, the knowledge base is explained, and assistance screens are described.…

Segmented Polynomial Models in Quasi-Experimental Research.

ERIC Educational Resources Information Center

Wasik, John L.

1981-01-01

The use of segmented polynomial models is explained. Examples of design matrices of dummy variables are given for the least squares analyses of time series and discontinuity quasi-experimental research designs. Linear combinations of dummy variable vectors appear to provide tests of effects in the two quasi-experimental designs. (Author/BW)

Teaching Experimental Design to Elementary School Pupils in Greece

ERIC Educational Resources Information Center

Karampelas, Konstantinos

2016-01-01

This research is a study about the possibility to promote experimental design skills to elementary school pupils. Experimental design and the experiment process are foundational elements in current approaches to Science Teaching, as they provide learners with profound understanding about knowledge construction and science inquiry. The research was…

The Impact on Education of the World Wide Web.

ERIC Educational Resources Information Center

Hobbs, D. J.; Taylor, R. J.

This paper describes a project which created a set of World Wide Web (WWW) pages documenting the state of the art in educational multimedia design; a prototype WWW-based multimedia teaching tool--a podiatry test using HTML forms, 24-bit color images and MPEG video--was also designed, developed, and evaluated. The project was conducted between…

Shared Modular Build of Warships: How a Shared Build Can Support Future Shipbuilding

DTIC Science & Technology

2011-01-01

design (CAD) files used for the design were not shared through this environment (Tang and Molas -Gillart, 2009). As the case studies show, shipyards...undated web page. As of December 20, 2010: http://www.fas.org/programs/ssp/man/uswpns/navy/submarines/ssn774_virginia.html Tang, Puay, and Jordi Molas

PHYSICS EDUCATION AND THE INTERNET: A beginner's guide to a physicist starting out on an Internet journey

NASA Astrophysics Data System (ADS)

Burton, Paul

1998-05-01

Thirty useful physics-related sites are listed to help get you started. I hope you will find some of the following sites of use in your teaching or good for pointing your pupils in the right direction when doing research. I have not attempted to rank or sort them in any order. However, by the time you read this issue of Physics Education some of the sites may not be available; this is the nature of the net. Those not wishing to retype each address can access them from my school's physics page (http://www.bootham.demon.co.uk/physics/links.html) or e-mail me at pkb@bootham.demon.co.uk and I can send you a document with the hypertext live links in. The new IOP sponsored 16-19 Physics project is promising great things with its own Internet site. You will be able to download information, updates, worksheets etc. Any queries about the development of this project at present can be sent to Evelyn van Dyk at: 16-19project@iop.org Engineering and Physical Sciences Research Councilhttp://www.epsrc.ac.uk Particle Physics and Astronomy Research Councilhttp://www.pparc.ac.uk American Institute of Physicshttp://www.aip.org Usenet Physics FAQ (frequently asked questions)http://www.weburbia.demon.co.uk/physics/faq.html CERNhttp://www.cern.ch/ BBC Educationhttp://www.bbc.co.uk/education/ Useful data on the Periodic Tablehttp://www.shef.ac.uk/chemistry/web-elements/ JET WWW index page:http://www.jet.uk NERC satellite station, Dundee Universityhttp://www.sat.dundee.ac.uk/ The Meteorological Officehttp://www.meto.govt.uk/ The Smithsonian Institute, Washington, DChttp://www.si.edu/newstart.htm Frequently asked questions on time and frequencyhttp://www.boulder.nist.gov/timefreq/faq/faq.htm Physics newshttp://www.het.brown.edu/news/index.html TIPTOP: The Internet Pilot to Physicshttp://www.tp.umu.se/TIPTOP/ A Dictionary of Scientific Quotationshttp://naturalscience.com/dsqhome.html ScI-Journal: an on-line publication for science studentshttp://www.soton.ac.uk/~plf/ScI-Journal/ Science On-linehttp://www.shu.ac.uk/schools/sci/sol/contents.htm Physics humourhttp://quark.physics.uwo.ca/~harwood/humor12.htm Searching for someone's e-mail address?http://www.four11.com SKY publicationshttp://www.skypub.com Planet Sciencehttp://www.keysites.com New Scientisthttp://www.newscientist.com NASA links to the American space programhttp://www.nasa.gov NASA Jet Propulsion Laboratoryhttp://www.jpl.nasa.gov Hewlett-Packardhttp://www.hp.com The Bradford Schools Telescope Projecthttp://www.telescope.org/rti/nuffield/ To contact a professional societyhttp://www.lib.uwaterloo.ca/society/overview.html The Schools' Physics Group: post-16 issueshttp://diana.ecs.soton.ac.uk/~pm/Physics/post16.html Sleuth search for physics and chemistryhttp://www.isleuth.com/index.shtml The Particle Adventurehttp://pdg.lbl.gov/cpep/adventure_home.html Acknowledgments I thank colleagues David Robinson and Robin Peach for their help in selecting and validating these sites and William Try, pupil at Bootham School, for preparing and maintaining the department's homepage with hypertext links. Received 21 January 1998

A Primer on Experimental and Quasi-experimental Design.

ERIC Educational Resources Information Center

Dawson, Thomas E.

Counseling psychology is a relatively new field that is gaining autonomy and respect. Unfortunately, research efforts in the field may lack an appropriate research design. This paper considers some of the more common types of research design and the associated threats to their validity. An example of each design type is drawn from the counseling…

A methodological analysis of chaplaincy research: 2000-2009.

PubMed

Galek, Kathleen; Flannelly, Kevin J; Jankowski, Katherine R B; Handzo, George F

2011-01-01

The present article presents a comprehensive review and analysis of quantitative research conducted in the United States on chaplaincy and closely related topics published between 2000 and 2009. A combined search strategy identified 49 quantitative studies in 13 journals. The analysis focuses on the methodological sophistication of the studies, compared to earlier research on chaplaincy and pastoral care. Cross-sectional surveys of convenience samples still dominate the field, but sample sizes have increased somewhat over the past three decades. Reporting of the validity and reliability of measures continues to be low, although reporting of response rates has improved. Improvements in the use of inferential statistics and statistical controls were also observed, compared to previous research. The authors conclude that more experimental research is needed on chaplaincy, along with an increased use of hypothesis testing, regardless of the research designs that are used.

Effect of Operating Conditions and Design on Afterburner Performance

NASA Technical Reports Server (NTRS)

Fleming, W. A.; Gabriel, D. S.; Lundin, B. T.

1956-01-01

Afterburners for turbojet engines have, within the past decade, found increasing application in service aircraft. Practically all engines manufactured today are equipped with some form of afterburner, and its use has increased from what was originally a short-period thrust-augmentation application to an essential feature of the turbojet propulsion system for flight at supersonic speeds. The design of these afterburners has been based on extensive research and development effort in expanded laboratory facilities by both the NACA and the American engine industry. Most of the work of the engine industry, however, has either not been published or is not generally available owing to its proprietary nature. Consequently, the main bulk of research information available for summary and discussion is of NACA origin. However, because industrial afterburner development has closely followed NACA research, the omission is more one of technical detail than method or concept. One principal difficulty encountered in summarizing the work in this field is that sufficient knowledge does not yet exist to rationally or directly integrate the available background of basic combustion principles into combustor design. A further difficulty is that most of the experimental investigations that have been conducted were directed chiefly toward the development of specific afterburners for various engines rather than to the accumulation of systematic data. This work has, nonetheless, provided not only substantial improvements in the performance of afterburners but also a large fund of experimental data and an extensive background of experience in the field. Consequently, it is the purpose of the present chapter to summarize the many, and frequently unrelated, experimental investigations that have been conducted rather than to formulate a set of design rules. In the treatment of this material an effort has been made, however, to convey to the reader the "know how" acquired by research engineers in the course of afterburner studies.

From proteomics to systems biology: MAPA, MASS WESTERN, PROMEX, and COVAIN as a user-oriented platform.

PubMed

Weckwerth, Wolfram; Wienkoop, Stefanie; Hoehenwarter, Wolfgang; Egelhofer, Volker; Sun, Xiaoliang

2014-01-01

Genome sequencing and systems biology are revolutionizing life sciences. Proteomics emerged as a fundamental technique of this novel research area as it is the basis for gene function analysis and modeling of dynamic protein networks. Here a complete proteomics platform suited for functional genomics and systems biology is presented. The strategy includes MAPA (mass accuracy precursor alignment; http://www.univie.ac.at/mosys/software.html ) as a rapid exploratory analysis step; MASS WESTERN for targeted proteomics; COVAIN ( http://www.univie.ac.at/mosys/software.html ) for multivariate statistical analysis, data integration, and data mining; and PROMEX ( http://www.univie.ac.at/mosys/databases.html ) as a database module for proteogenomics and proteotypic peptides for targeted analysis. Moreover, the presented platform can also be utilized to integrate metabolomics and transcriptomics data for the analysis of metabolite-protein-transcript correlations and time course analysis using COVAIN. Examples for the integration of MAPA and MASS WESTERN data, proteogenomic and metabolic modeling approaches for functional genomics, phosphoproteomics by integration of MOAC (metal-oxide affinity chromatography) with MAPA, and the integration of metabolomics, transcriptomics, proteomics, and physiological data using this platform are presented. All software and step-by-step tutorials for data processing and data mining can be downloaded from http://www.univie.ac.at/mosys/software.html.

TOPS On-Line: Automating the Construction and Maintenance of HTML Pages

NASA Technical Reports Server (NTRS)

Jones, Kennie H.

1994-01-01

After the Technology Opportunities Showcase (TOPS), in October, 1993, Langley Research Center's (LaRC) Information Systems Division (ISD) accepted the challenge to preserve the investment in information assembled in the TOPS exhibits by establishing a data base. Following the lead of several people at LaRC and others around the world, the HyperText Transport Protocol (HTTP) server and Mosaic were the obvious tools of choice for implementation. Initially, some TOPS exhibitors began the conventional approach of constructing HyperText Markup Language (HTML) pages of their exhibits as input to Mosaic. Considering the number of pages to construct, a better approach was conceived that would automate the construction of pages. This approach allowed completion of the data base construction in a shorter period of time using fewer resources than would have been possible with the conventional approach. It also provided flexibility for the maintenance and enhancement of the data base. Since that time, this approach has been used to automate construction of other HTML data bases. Through these experiences, it is concluded that the most effective use of the HTTP/Mosaic technology will require better tools and techniques for creating, maintaining and managing the HTML pages. The development and use of these tools and techniques are the subject of this document.

Automated generation of a World Wide Web-based data entry and check program for medical applications.

PubMed

Kiuchi, T; Kaihara, S

1997-02-01

The World Wide Web-based form is a promising method for the construction of an on-line data collection system for clinical and epidemiological research. It is, however, laborious to prepare a common gateway interface (CGI) program for each project, which the World Wide Web server needs to handle the submitted data. In medicine, it is even more laborious because the CGI program must check deficits, type, ranges, and logical errors (bad combination of data) of entered data for quality assurance as well as data length and meta-characters of the entered data to enhance the security of the server. We have extended the specification of the hypertext markup language (HTML) form to accommodate information necessary for such data checking and we have developed software named AUTOFORM for this purpose. The software automatically analyzes the extended HTML form and generates the corresponding ordinary HTML form, 'Makefile', and C source of CGI programs. The resultant CGI program checks the entered data through the HTML form, records them in a computer, and returns them to the end-user. AUTOFORM drastically reduces the burden of development of the World Wide Web-based data entry system and allows the CGI programs to be more securely and reliably prepared than had they been written from scratch.

Guidelines for Initiating a Research Agenda: Research Design and Dissemination of Results.

PubMed

Delost, Maria E; Nadder, Teresa S

2014-01-01

Successful research outcomes require selection and implementation of the appropriate research design. A realistic sampling plan appropriate for the design is essential. Qualitative or quantitative methodology may be utilized, depending on the research question and goals. Quantitative research may be experimental where there is an intervention, or nonexperimental, if no intervention is included in the design. Causation can only be established with experimental research. Popular types of nonexperimental research include descriptive and survey research. Research findings may be disseminated via presentations, posters, and publications, such as abstracts and manuscripts.

A Visual Galaxy Classification Interface and its Classroom Application

NASA Astrophysics Data System (ADS)

Kautsch, Stefan J.; Phung, Chau; VanHilst, Michael; Castro, Victor H

2014-06-01

Galaxy morphology is an important topic in modern astronomy to understand questions concerning the evolution and formation of galaxies and their dark matter content. In order to engage students in exploring galaxy morphology, we developed a web-based, graphical interface that allows students to visually classify galaxy images according to various morphological types. The website is designed with HTML5, JavaScript, PHP, and a MySQL database. The classification interface provides hands-on research experience and training for students and interested clients, and allows them to contribute to studies of galaxy morphology. We present the first results of a pilot study and compare the visually classified types using our interface with that from automated classification routines.

MortalityPredictors.org: a manually-curated database of published biomarkers of human all-cause mortality

PubMed Central

Winslow, Ksenia; Ho, Andrew; Fortney, Kristen; Morgen, Eric

2017-01-01

Biomarkers of all-cause mortality are of tremendous clinical and research interest. Because of the long potential duration of prospective human lifespan studies, such biomarkers can play a key role in quantifying human aging and quickly evaluating any potential therapies. Decades of research into mortality biomarkers have resulted in numerous associations documented across hundreds of publications. Here, we present MortalityPredictors.org, a manually-curated, publicly accessible database, housing published, statistically-significant relationships between biomarkers and all-cause mortality in population-based or generally healthy samples. To gather the information for this database, we searched PubMed for appropriate research papers and then manually curated relevant data from each paper. We manually curated 1,576 biomarker associations, involving 471 distinct biomarkers. Biomarkers ranged in type from hematologic (red blood cell distribution width) to molecular (DNA methylation changes) to physical (grip strength). Via the web interface, the resulting data can be easily browsed, searched, and downloaded for further analysis. MortalityPredictors.org provides comprehensive results on published biomarkers of human all-cause mortality that can be used to compare biomarkers, facilitate meta-analysis, assist with the experimental design of aging studies, and serve as a central resource for analysis. We hope that it will facilitate future research into human mortality and aging. PMID:28858850

MortalityPredictors.org: a manually-curated database of published biomarkers of human all-cause mortality.

PubMed

Peto, Maximus V; De la Guardia, Carlos; Winslow, Ksenia; Ho, Andrew; Fortney, Kristen; Morgen, Eric

2017-08-31

Biomarkers of all-cause mortality are of tremendous clinical and research interest. Because of the long potential duration of prospective human lifespan studies, such biomarkers can play a key role in quantifying human aging and quickly evaluating any potential therapies. Decades of research into mortality biomarkers have resulted in numerous associations documented across hundreds of publications. Here, we present MortalityPredictors.org , a manually-curated, publicly accessible database, housing published, statistically-significant relationships between biomarkers and all-cause mortality in population-based or generally healthy samples. To gather the information for this database, we searched PubMed for appropriate research papers and then manually curated relevant data from each paper. We manually curated 1,576 biomarker associations, involving 471 distinct biomarkers. Biomarkers ranged in type from hematologic (red blood cell distribution width) to molecular (DNA methylation changes) to physical (grip strength). Via the web interface, the resulting data can be easily browsed, searched, and downloaded for further analysis. MortalityPredictors.org provides comprehensive results on published biomarkers of human all-cause mortality that can be used to compare biomarkers, facilitate meta-analysis, assist with the experimental design of aging studies, and serve as a central resource for analysis. We hope that it will facilitate future research into human mortality and aging.

The research evidence published in high impact nursing journals between 2000 and 2006: a quantitative content analysis.

PubMed

Mantzoukas, Stefanos

2009-04-01

Evidence-based practice has become an imperative for efficient, effective and safe practice. Furthermore, evidences emerging from published research are considered as valid knowledge sources to guiding practice. The aim of this paper is to review all research articles published in the top 10 general nursing journals for the years 2000-2006 to identify the methodologies used, the types of evidence these studies produced and the issues upon which they endeavored. Quantitative content analysis was implemented to study all published research papers of the top 10 general nursing journals for the years 2000-2006. The top 10 general nursing journals were included in the study. The abstracts of all research articles were analysed with regards the methodologies of enquiry, the types of evidence produced and the issues of study they endeavored upon. Percentages were developed as to enable conclusions to be drawn. The results for the category methodologies used were 7% experimental, 6% quasi-experimental, 39% non-experimental, 2% ethnographical studies, 7% phenomenological, 4% grounded theory, 1% action research, 1% case study, 15% unspecified, 5.5% other, 0.5% meta-synthesis, 2% meta-analysis, 5% literature reviews and 3% secondary analysis. For the category types of evidence were 4% hypothesis/theory testing, 11% evaluative, 5% comparative, 2% correlational, 46% descriptive, 5% interpretative and 27% exploratory. For the category issues of study were 45% practice/clinical, 8% educational, 11% professional, 3% spiritual/ethical/metaphysical, 26% health promotion and 7% managerial/policy. Published studies can provide adequate evidences for practice if nursing journals conceptualise evidence emerging from non-experimental and qualitative studies as relevant types of evidences for practice and develop appropriate mechanisms for assessing their validity. Also, nursing journals need to increase and encourage the publication of studies that implement RCT methodology, systematic reviews, meta-synthesis and meta-analysis methodologies. Finally, nursing journals need to encourage more high quality research evidence that derive from interpretative, theory testing and evaluative types of studies that are practice relevant.

A perinatal signature of light on chronobiology? If so, numerous questions arise and experimental animal research must provide more information.

PubMed

Erren, Thomas C; Reiter, Russel J; Meyer-Rochow, V Benno

2012-01-01

That light and melatonin rhythms provide both clock and calendar information in humans and numerous other species is beyond dispute; this holds true for all stages of life, including the very early ones. Experimental evidence elucidates that exposure to light and melatonin titres are keys for the very development of circadian and seasonal rhythms. As evinced by a 2011 publication in Nature Neuroscience such awareness could impact considerably on the design and conduct of experimental studies as well as their subsequent analyses, interpretations and comparisons. Therefore "when and how experimental animals were bred, developed and raised" may be critical when experimenting with animals generally, and not just rodents. As long as the suggested imprinting of circadian system stability via light cues is not falsified, the perinatal season or perinatal experimental light:dark [L:D] conditions that an animal was kept under should be routinely recorded, published and considered in analysing and interpreting study data.

A survey of publication practices of single-case design researchers when treatments have small or large effects.

PubMed

Shadish, William R; Zelinsky, Nicole A M; Vevea, Jack L; Kratochwill, Thomas R

2016-09-01

The published literature often underrepresents studies that do not find evidence for a treatment effect; this is often called publication bias. Literature reviews that fail to include such studies may overestimate the size of an effect. Only a few studies have examined publication bias in single-case design (SCD) research, but those studies suggest that publication bias may occur. This study surveyed SCD researchers about publication preferences in response to simulated SCD results that show a range of small to large effects. Results suggest that SCD researchers are more likely to submit manuscripts that show large effects for publication and are more likely to recommend acceptance of manuscripts that show large effects when they act as a reviewer. A nontrivial minority of SCD researchers (4% to 15%) would drop 1 or 2 cases from the study if the effect size is small and then submit for publication. This article ends with a discussion of implications for publication practices in SCD research. © 2016 Society for the Experimental Analysis of Behavior.

From 'just the facts' to 'more theory and methods, please': The evolution of the research article in Administrative Science Quarterly, 1956-2008.

PubMed

Strang, David; Siler, Kyle

2017-08-01

This paper analyzes the surface structure of research articles published in Administrative Science Quarterly between 1956 and 2008. The period is marked by a shift from essays that interweave theory, methods and results to experimental reports that separate them. There is dramatic growth in the size of theory, methods and discussion sections, accompanied by a shrinking results section. Bibliographic references and hypotheses expand in number and become concentrated in theory sections. Article structure varies primarily with historical time and also with research design (broadly, quantitative vs. qualitative) and the author's background. We link trends in article structure to the disciplinary development of organization studies and consider its distinctive trajectory relative to physical science.

Publisher Correction: Rotating robots move collectively and self-organize.

PubMed

Scholz, Christian; Engel, Michael; Pöschel, Thorsten

2018-04-11

The original version of this Article contained an error in Fig. 5. In Fig. 5e, the scale on the y-axis originally incorrectly went from '0' to '1.10 -4 '. The correct scale goes from '0' to '0.4'. In Fig 5f, the x-axis labels were incorrectly shifted to the right. This has been corrected in both the PDF and HTML versions of the Article.

VizieR Online Data Catalog: Spectroscopically identified white dwarfs (McCook+, 2014)

NASA Astrophysics Data System (ADS)

McCook, G. P.; Sion, E. M.

2016-10-01

This is an update of the Villanova catalog published in the ApJS paper, corresponding to the Web version of the catalog in Apr 2014 (see http://www.astronomy.villanova.edu/WDCatalog/index.html). The introduction to the 1999 catalog is in the file "preface.tex". This updated version lists 14294 unique white dwarfs for a total of 27975 rows (multiple observations). (5 data files).

Teaching Structure from Motion to Undergraduates: New Learning Module for Field Geoscience Courses

NASA Astrophysics Data System (ADS)

Pratt-Sitaula, B. A.; Shervais, K.; Crosby, C. J.; Douglas, B. J.; Crosby, B. T.; Charlevoix, D. J.

2016-12-01

With photogrammetry use expanding rapidly, it is essential to integrate these methods into undergraduate geosciences courses. The NSF-funded "GEodetic Tools for Societal Issues" (GETSI) project has recently published a module for field geoscience courses called "Analyzing High Resolution Topography with TLS and SfM" (serc.carleton.edu/getsi/teaching_materials/high-rez-topo/index.html). Structure from motion (SfM) and terrestrial laser scanning (TLS) are two valuable methods for generating high-resolution topographic landscape models. In addition to teaching the basic surveying methods, the module includes several specific applications that are tied to societally important geoscience research questions. The module goals are that students will be able to: 1) design and conduct a complex TLS and/or SfM survey to address a geologic research question; 2) articulate the societal impetus for answering a given research question; and 3) justify why TLS and/or SfM is the appropriate method in some circumstances. The module includes 6 units: Unit 1-TLS Introduction, Unit 1-SfM Introduction, Unit 2 Stratigraphic Section Survey, Unit 3 Fault Scarp Survey, Unit 4 Geomorphic Change Detection Survey, and Unit 5 Summative Assessment. One or both survey methods can be taught. Instructors choose which application/s to use from Units 2-4. Unit 5 Summative Assessment is flexibly written and can be used to assess any of the learned applications or others such as dinosaur tracks or seismic trench photomosaics. Prepared data sets are also provided for courses unable to visit the field. The included SfM learning manuals may also be of interest to researchers seeking to start with SfM; these are "SfM Guide of Instructors and Investigators" and "SfM Data Exploration and Processing Manual (Agisoft)". The module is appropriate for geoscience courses with field components such as field methods, geomorphology, geophysics, tectonics, and structural geology. All GETSI modules are designed and developed by teams of faculty and content experts and undergo rigorous review and classroom testing. GETSI is a collaborative project by UNAVCO (which runs NSF's Geodetic Facility), Indiana University, and Idaho State University. The Science Education Resource Center (SERC) provides assessment and evaluation expertise and webhosting.

oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language.

PubMed

Sanges, Remo; Cordero, Francesca; Calogero, Raffaele A

2007-12-15

OneChannelGUI is an add-on Bioconductor package providing a new set of functions extending the capability of the affylmGUI package. This library provides a graphical interface (GUI) for Bioconductor libraries to be used for quality control, normalization, filtering, statistical validation and data mining for single channel microarrays. Affymetrix 3' expression (IVT) arrays as well as the new whole transcript expression arrays, i.e. gene/exon 1.0 ST, are actually implemented. oneChannelGUI is available for most platforms on which R runs, i.e. Windows and Unix-like machines. http://www.bioconductor.org/packages/2.0/bioc/html/oneChannelGUI.html

RAPID and HTML5's potential

NASA Technical Reports Server (NTRS)

Torosyan, David

2012-01-01

Just as important as the engineering that goes into building a robot is the method of interaction, or how human users will use the machine. As part of the Human-System Interactions group (Conductor) at JPL, I explored using a web interface to interact with ATHLETE, a prototype lunar rover. I investigated the usefulness of HTML 5 and Javascript as a telemetry viewer as well as the feasibility of having a rover communicate with a web server. To test my ideas I built a mobile-compatible website and designed primarily for an Android tablet. The website took input from ATHLETE engineers, and upon its completion I conducted a user test to assess its effectiveness.

Impact of care pathways for in-hospital management of COPD exacerbation: a systematic review.

PubMed

Lodewijckx, C; Sermeus, W; Panella, M; Deneckere, S; Leigheb, F; Decramer, M; Vanhaecht, K

2011-11-01

In-hospital management of COPD exacerbation is suboptimal, and outcomes are poor. Care pathways are a possible strategy for optimizing care processes and outcomes. The aim of the literature review was to explore characteristics of existing care pathways for in-hospital management of COPD exacerbations and to address their impact on performance of care processes, clinical outcomes, and team functioning. A literature search was conducted for articles published between 1990 and 2010 in the electronic databases of Medline, CINAHL, EMBASE, and Cochrane Library. Main inclusion criteria were (I) patients hospitalized for a COPD exacerbation; (II) implementation and evaluation of a care pathway; (III) report of original research, including experimental and quasi experimental designs, variance analysis, and interviews of professionals and patients about their perception on pathway effectiveness. Four studies with a quasi experimental design were included. Three studies used a pre-post test design; the fourth study was a non randomized controlled trial comparing an experimental group where patients were treated according to a care pathway with a control group where usual care was provided. The four studied care pathways were multidisciplinary structured care plans, outlining time-specific clinical interventions and responsibilities by discipline. Statistic analyses were rarely performed, and the trials used very divergent indicators to evaluate the impact of the care pathways. The studies described positive effects on blood sampling, daily weight measurement, arterial blood gas measurement, referral to rehabilitation, feelings of anxiety, length of stay, readmission, and in-hospital mortality. Research on COPD care pathways is very limited. The studies described few positive effects of the care pathways on diagnostic processes and on clinical outcomes. Though due to limited statistical analysis and weak design of the studies, the internal validity of results is limited. Therefore, based on these studies the impact of care pathways on COPD exacerbation is inconclusive. These findings indicate the need for properly designed research like a cluster randomized controlled trial to evaluate the impact of COPD care pathways on performance of care processes, clinical outcomes, and teamwork. Copyright © 2011 Elsevier Ltd. All rights reserved.

Red Blood Cell Antibody Identification

MedlinePlus

... cause a transfusion reaction (is not clinically significant). Examples of RBC antibodies and their clinical significance are ... online at http://chapters.redcross.org/ca/socal/research/circular.html. Accessed June 2009. Oren, E. and ...

77 FR 55856 - Proposed Flood Hazard Determinations

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-11

... resolution process. SRPs are independent panels of experts in hydrology, hydraulics, and other pertinent... Inspection Online at: http://www.dnr.sc.gov/water/flood/comaps.html City of Florence Planning, Research and...

Designing microarray and RNA-Seq experiments for greater systems biology discovery in modern plant genomics.

PubMed

Yang, Chuanping; Wei, Hairong

2015-02-01

Microarray and RNA-seq experiments have become an important part of modern genomics and systems biology. Obtaining meaningful biological data from these experiments is an arduous task that demands close attention to many details. Negligence at any step can lead to gene expression data containing inadequate or composite information that is recalcitrant for pattern extraction. Therefore, it is imperative to carefully consider experimental design before launching a time-consuming and costly experiment. Contemporarily, most genomics experiments have two objectives: (1) to generate two or more groups of comparable data for identifying differentially expressed genes, gene families, biological processes, or metabolic pathways under experimental conditions; (2) to build local gene regulatory networks and identify hierarchically important regulators governing biological processes and pathways of interest. Since the first objective aims to identify the active molecular identities and the second provides a basis for understanding the underlying molecular mechanisms through inferring causality relationships mediated by treatment, an optimal experiment is to produce biologically relevant and extractable data to meet both objectives without substantially increasing the cost. This review discusses the major issues that researchers commonly face when embarking on microarray or RNA-seq experiments and summarizes important aspects of experimental design, which aim to help researchers deliberate how to generate gene expression profiles with low background noise but with more interaction to facilitate novel biological discoveries in modern plant genomics. Copyright © 2015 The Author. Published by Elsevier Inc. All rights reserved.

GenoGAM: genome-wide generalized additive models for ChIP-Seq analysis.

PubMed

Stricker, Georg; Engelhardt, Alexander; Schulz, Daniel; Schmid, Matthias; Tresch, Achim; Gagneur, Julien

2017-08-01

Chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) is a widely used approach to study protein-DNA interactions. Often, the quantities of interest are the differential occupancies relative to controls, between genetic backgrounds, treatments, or combinations thereof. Current methods for differential occupancy of ChIP-Seq data rely however on binning or sliding window techniques, for which the choice of the window and bin sizes are subjective. Here, we present GenoGAM (Genome-wide Generalized Additive Model), which brings the well-established and flexible generalized additive models framework to genomic applications using a data parallelism strategy. We model ChIP-Seq read count frequencies as products of smooth functions along chromosomes. Smoothing parameters are objectively estimated from the data by cross-validation, eliminating ad hoc binning and windowing needed by current approaches. GenoGAM provides base-level and region-level significance testing for full factorial designs. Application to a ChIP-Seq dataset in yeast showed increased sensitivity over existing differential occupancy methods while controlling for type I error rate. By analyzing a set of DNA methylation data and illustrating an extension to a peak caller, we further demonstrate the potential of GenoGAM as a generic statistical modeling tool for genome-wide assays. Software is available from Bioconductor: https://www.bioconductor.org/packages/release/bioc/html/GenoGAM.html . gagneur@in.tum.de. Supplementary information is available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

SMART-1 Technology and Science Experiments in Preparation of Future Missions and ESA Cornerstones

NASA Astrophysics Data System (ADS)

Marini, A. E.; Racca, G. D.; Foing, B. H.; SMART-1 Project

1999-12-01

SMART-1 is the first ESA Small Mission for Advanced Research in Technology, aimed at the demonstration of enabling technologies for future scientific missions. SMART-1's prime technology objective is the demonstration of the solar primary electric propulsion, a key for future interplanetary missions. SMART-1 will use a Stationary Plasma Thruster engine, cruising 15 months to capture a Moon polar orbit. A gallery of images of the spacecraft is available at the web site: http://www.estec.esa.nl/spdwww/smart1/html/11742.html SMART-1 payload aims at monitoring the electric propulsion and its spacecraft environment and to test novel instrument technologies. The Diagnostic Instruments include SPEDE, a spacecraft potential plasma and charged particles detector, to characterise both spacecraft and planetary environment, together with EPDP, a suite of sensors monitoring secondary thrust-ions, charging and deposition effects. Innovative spacecraft technologies will be tested on SMART-1 : Lithium batteries and KATE, an experimental X/Ka-band deep-space transponder, to support radio-science, to monitor the accelerations of the electric propulsion and to test turbo-code technique, enhancing the return of scientific data. The scientific instruments for imaging and spectrometry are: \\begin{itemize} D-CIXS, a compact X-ray spectrometer based on novel SCD detectors and micro-structure optics, to observe X-ray celectial objects and to perform lunar chemistry measurements. SIR, a miniaturised quasi-monolithic point-spectrometer, operating in the Near-IR (0.9 ÷ 2.4 micron), to survey the lunar crust in previously uncovered optical regions. AMIE, a miniature camera based on 3-D integrated electronics, imaging the Moon, and other bodies and supporting LASER-LINK and RSIS. RSIS and LASER-LINK are investigations performed with the SMART-1 Payload: \\begin{itemize} RSIS: A radio-science Experiment to validate in-orbit determination of the libration of the celestial target, based on high-accuracy tracking in Ka-band and imaging of a surface landmark LASER-LINK: a demonstration of acquisition of a deep-space laser-link from the ESA Optical Ground Station at Tenerife, validating also the novel sub-apertured telescope designed for the mitigation of atmospheric scintillation disturbances.

78 FR 5162 - Designation of a Nonessential Experimental Population of Central Valley Spring-Run Chinook Salmon...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-24

... Director, Office of Protected Resources, National Marine Fisheries Service. [FR Doc. 2013-01343 Filed 1-23.... SUMMARY: On January 16, 2013, we, NMFS, published a proposed rule to designate a nonessential experimental... January 29, 2013, at the Fresno Metropolitan Flood Control District, Board Meeting Room, 5469 E. Olive...

Klusters, NeuroScope, NDManager: a free software suite for neurophysiological data processing and visualization.

PubMed

Hazan, Lynn; Zugaro, Michaël; Buzsáki, György

2006-09-15

Recent technological advances now allow for simultaneous recording of large populations of anatomically distributed neurons in behaving animals. The free software package described here was designed to help neurophysiologists process and view recorded data in an efficient and user-friendly manner. This package consists of several well-integrated applications, including NeuroScope (http://neuroscope.sourceforce.net), an advanced viewer for electrophysiological and behavioral data with limited editing capabilities, Klusters (http://klusters.sourceforge.net), a graphical cluster cutting application for manual and semi-automatic spike sorting, NDManager (GPL,see http://www.gnu.org/licenses/gpl.html), an experimental parameter and data processing manager. All of these programs are distributed under the GNU General Public License (GPL, see ), which gives its users legal permission to copy, distribute and/or modify the software. Also included are extensive user manuals and sample data, as well as source code and documentation.

A Bright Future for Evolutionary Methods in Drug Design.

PubMed

Le, Tu C; Winkler, David A

2015-08-01

Most medicinal chemists understand that chemical space is extremely large, essentially infinite. Although high-throughput experimental methods allow exploration of drug-like space more rapidly, they are still insufficient to fully exploit the opportunities that such large chemical space offers. Evolutionary methods can synergistically blend automated synthesis and characterization methods with computational design to identify promising regions of chemical space more efficiently. We describe how evolutionary methods are implemented, and provide examples of published drug development research in which these methods have generated molecules with increased efficacy. We anticipate that evolutionary methods will play an important role in future drug discovery. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

[Research-oriented experimental course of plant cell and gene engineering for undergraduates].

PubMed

Xiaofei, Lin; Rong, Zheng; Morigen, Morigen

2015-04-01

Research-oriented comprehensive experimental course for undergraduates is an important part for their training of innovation. We established an optional course of plant cell and gene engineering for undergraduates using our research platform. The course is designed to study the cellular and molecular basis and experimental techniques for plant tissue culture, isolation and culture of protoplast, genetic transformation, and screening and identification of transgenic plants. To develop undergraduates' ability in experimental design and operation, and inspire their interest in scientific research and innovation consciousness, we integrated experimental teaching and practice in plant genetic engineering on the tissue, cellular, and molecular levels. Students in the course practiced an experimental teaching model featured by two-week teaching of principles, independent experimental design and bench work, and ready-to-access laboratory. In this paper, we describe the contents, methods, evaluation system and a few issues to be solved in this course, as well as the general application and significance of the research-oriented experimental course in reforming undergraduates' teaching and training innovative talents.

May 2012 DMM Podcast: an interview with Mark Fishman

PubMed Central

2012-01-01

SUMMARY Mark Fishman, President of the Novartis Institutes for BioMedical Research, discusses developing the zebrafish as a research tool, academia-industry collaborations and perspectives on the future of drug development. Narrated by Sarah E. Allan. To listen to this podcast, visit http://www.biologists.com/DMM/podcasts/index.html.

75 FR 39054 - Agency Information Collection Activities: Submission for the Office of Management and Budget (OMB...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-07

... feedback to the industry. These forms are designed to provide the information necessary for engineering... the NRC worldwide Web site: http://www.nrc.gov/public-involve/doc-comment/omb/index.html . The...

Immigration Policies in Europe: Impact on Crime -- A Case Study of Germany

DTIC Science & Technology

2008-06-01

2180188,00.html? maca =en-bulletin- 433-html. Accessed 24 Feb 2008. 51 448,000 illegal immigrants up until September 2006 without EU assistance.168 The...asylum. 168 Your Link to Germany. http://www.dw-world.de/dw/article/0,,2180188,00.html? maca =en...for a European Response to Illegal Immigration" 21 September 2006. .http://www.dw- world.de/dw/article/0,,2180188,00.html? maca =en-bulletin-433-html

Measuring and Advancing Experimental Design Ability in an Introductory Course without Altering Existing Lab Curriculum.

PubMed

Shanks, Ryan A; Robertson, Chuck L; Haygood, Christian S; Herdliksa, Anna M; Herdliska, Heather R; Lloyd, Steven A

2017-01-01

Introductory biology courses provide an important opportunity to prepare students for future courses, yet existing cookbook labs, although important in their own way, fail to provide many of the advantages of semester-long research experiences. Engaging, authentic research experiences aid biology students in meeting many learning goals. Therefore, overlaying a research experience onto the existing lab structure allows faculty to overcome barriers involving curricular change. Here we propose a working model for this overlay design in an introductory biology course and detail a means to conduct this lab with minimal increases in student and faculty workloads. Furthermore, we conducted exploratory factor analysis of the Experimental Design Ability Test (EDAT) and uncovered two latent factors which provide valid means to assess this overlay model's ability to increase advanced experimental design abilities. In a pre-test/post-test design, we demonstrate significant increases in both basic and advanced experimental design abilities in an experimental and comparison group. We measured significantly higher gains in advanced experimental design understanding in students in the experimental group. We believe this overlay model and EDAT factor analysis contribute a novel means to conduct and assess the effectiveness of authentic research experiences in an introductory course without major changes to the course curriculum and with minimal increases in faculty and student workloads.

Why and how to use virtual reality to study human social interaction: The challenges of exploring a new research landscape.

PubMed

Pan, Xueni; Hamilton, Antonia F de C

2018-03-05

As virtual reality (VR) technology and systems become more commercially available and accessible, more and more psychologists are starting to integrate VR as part of their methods. This approach offers major advantages in experimental control, reproducibility, and ecological validity, but also has limitations and hidden pitfalls which may distract the novice user. This study aimed to guide the psychologist into the novel world of VR, reviewing available instrumentation and mapping the landscape of possible systems. We use examples of state-of-the-art research to describe challenges which research is now solving, including embodiment, uncanny valley, simulation sickness, presence, ethics, and experimental design. Finally, we propose that the biggest challenge for the field would be to build a fully interactive virtual human who can pass a VR Turing test - and that this could only be achieved if psychologists, VR technologists, and AI researchers work together. © 2018 The Authors British Journal of Psychology published by John Wiley & Sons Ltd on behalf of British Psychological Society.

Autonomy @ Ames

NASA Technical Reports Server (NTRS)

Van Dalsem, William; Krishnakumar, Kalmanje Srinivas

2016-01-01

This is a powerpoint presentation that highlights autonomy across the 15 NASA technology roadmaps, including specific examples of projects (past and present) at NASA Ames Research Center. The NASA technology roadmaps are located here: http:www.nasa.govofficesocthomeroadmapsindex.html

jsNMR: an embedded platform-independent NMR spectrum viewer.

PubMed

Vosegaard, Thomas

2015-04-01

jsNMR is a lightweight NMR spectrum viewer written in JavaScript/HyperText Markup Language (HTML), which provides a cross-platform spectrum visualizer that runs on all computer architectures including mobile devices. Experimental (and simulated) datasets are easily opened in jsNMR by (i) drag and drop on a jsNMR browser window, (ii) by preparing a jsNMR file from the jsNMR web site, or (iii) by mailing the raw data to the jsNMR web portal. jsNMR embeds the original data in the HTML file, so a jsNMR file is a self-transforming dataset that may be exported to various formats, e.g. comma-separated values. The main applications of jsNMR are to provide easy access to NMR data without the need for dedicated software installed and to provide the possibility to visualize NMR spectra on web sites. Copyright © 2015 John Wiley & Sons, Ltd.

esATAC: An Easy-to-use Systematic pipeline for ATAC-seq data analysis.

PubMed

Wei, Zheng; Zhang, Wei; Fang, Huan; Li, Yanda; Wang, Xiaowo

2018-03-07

ATAC-seq is rapidly emerging as one of the major experimental approaches to probe chromatin accessibility genome-wide. Here, we present "esATAC", a highly integrated easy-to-use R/Bioconductor package, for systematic ATAC-seq data analysis. It covers essential steps for full analyzing procedure, including raw data processing, quality control and downstream statistical analysis such as peak calling, enrichment analysis and transcription factor footprinting. esATAC supports one command line execution for preset pipelines, and provides flexible interfaces for building customized pipelines. esATAC package is open source under the GPL-3.0 license. It is implemented in R and C ++. Source code and binaries for Linux, MAC OS X and Windows are available through Bioconductor https://www.bioconductor.org/packages/release/bioc/html/esATAC.html). xwwang@tsinghua.edu.cn. Supplementary data are available at Bioinformatics online.

deltaGseg: macrostate estimation via molecular dynamics simulations and multiscale time series analysis.

PubMed

Low, Diana H P; Motakis, Efthymios

2013-10-01

Binding free energy calculations obtained through molecular dynamics simulations reflect intermolecular interaction states through a series of independent snapshots. Typically, the free energies of multiple simulated series (each with slightly different starting conditions) need to be estimated. Previous approaches carry out this task by moving averages at certain decorrelation times, assuming that the system comes from a single conformation description of binding events. Here, we discuss a more general approach that uses statistical modeling, wavelets denoising and hierarchical clustering to estimate the significance of multiple statistically distinct subpopulations, reflecting potential macrostates of the system. We present the deltaGseg R package that performs macrostate estimation from multiple replicated series and allows molecular biologists/chemists to gain physical insight into the molecular details that are not easily accessible by experimental techniques. deltaGseg is a Bioconductor R package available at http://bioconductor.org/packages/release/bioc/html/deltaGseg.html.

Encouraging planetary sciences students at the Master level with observations using small telescopes that lead to their publication

NASA Astrophysics Data System (ADS)

Sanchez-Lavega, A.; Ordoñez-Etxeberria, I.; del Rio Gaztelurrutia, T.; Illarramendi, M. A.; Perez-Hoyos, S.; Hueso, R.; Rojas, J. F.

2017-12-01

We present a set of practical experiments carried out with the students of the Master in Space Science and Technology of the University of the Basque Country (A. Sanchez-Lavega et al., Eur. J. of Eng. Education. 2014) using small telescopes that have been published in refereed journals. The telescopes (from 15 to 50 cm in aperture) and instruments pertain to the Aula EspaZio Gela Observatory (http://www.ehu.eus/aula-espazio/presentacion.html). The students have participated in some cases as co-authors of the publications or in presentations at meetings which encourages them to continue their scientific career towards PhD studies. Dedicated observations with these small telescopes with the participation of the planetary amateur community have also been employed in scientific research and publications. A series of examples are presented.

MOCCASIN: converting MATLAB ODE models to SBML.

PubMed

Gómez, Harold F; Hucka, Michael; Keating, Sarah M; Nudelman, German; Iber, Dagmar; Sealfon, Stuart C

2016-06-15

MATLAB is popular in biological research for creating and simulating models that use ordinary differential equations (ODEs). However, sharing or using these models outside of MATLAB is often problematic. A community standard such as Systems Biology Markup Language (SBML) can serve as a neutral exchange format, but translating models from MATLAB to SBML can be challenging-especially for legacy models not written with translation in mind. We developed MOCCASIN (Model ODE Converter for Creating Automated SBML INteroperability) to help. MOCCASIN can convert ODE-based MATLAB models of biochemical reaction networks into the SBML format. MOCCASIN is available under the terms of the LGPL 2.1 license (http://www.gnu.org/licenses/lgpl-2.1.html). Source code, binaries and test cases can be freely obtained from https://github.com/sbmlteam/moccasin : mhucka@caltech.edu More information is available at https://github.com/sbmlteam/moccasin. © The Author 2016. Published by Oxford University Press.

TCIApathfinder: an R client for The Cancer Imaging Archive REST API.

PubMed

Russell, Pamela; Fountain, Kelly; Wolverton, Dulcy; Ghosh, Debashis

2018-06-05

The Cancer Imaging Archive (TCIA) hosts publicly available de-identified medical images of cancer from over 25 body sites and over 30,000 patients. Over 400 published studies have utilized freely available TCIA images. Images and metadata are available for download through a web interface or a REST API. Here we present TCIApathfinder, an R client for the TCIA REST API. TCIApathfinder wraps API access in user-friendly R functions that can be called interactively within an R session or easily incorporated into scripts. Functions are provided to explore the contents of the large database and to download image files. TCIApathfinder provides easy access to TCIA resources in the highly popular R programming environment. TCIApathfinder is freely available under the MIT license as a package on CRAN (https://cran.r-project.org/web/packages/TCIApathfinder/index.html) and at https://github.com/pamelarussell/TCIApathfinder. Copyright ©2018, American Association for Cancer Research.

Trends analysis on research articles in the korean journal of medical education.

PubMed

Lee, Young Hee; Lee, Young-Mee; Kwon, Hyojin

2012-12-01

The purpose of this study was to examine the chronological changes and progress in medical education research in Korea and to identify the less investigated topics that need further study and improvement with regard to methodological quality. Of the 590 articles that were published from 1989 to 2010 in the Korean Journal of Medical Education, 386 original research papers were extracted for the analysis. The extracted papers were systematically reviewed using 2 analysis schemes that we developed: one scheme was designed to classify research topics, and the other determined the methodology that was used. The main results were as follows: The most popular research areas were curriculum, educational method, and evaluation in basic medical education; in contrast, studies that addressed postgraduate education, continuous professional development, and educational administration were less frequent; The most frequently studied topics were clinical performance/skills evaluation, clerkship, curriculum development, and problem-based learning, Quantitative studies predominated over qualitative studies and mixed methods (265 vs. 95 vs. 26). Two hundred forty papers were descriptive, cross-sectional studies, and 17 were experimental studies. Most qualitative studies were non-participation observational studies. In conclusion, there has been dramatic growth in the extent of medical education research in Korea in the past two decades. However, more studies that investigate the graduate medical education and the continuous professional development should be performed. Moreover, robust experimental designs and methods should be applied to provide stronger evidence that can practice best-evidence medical education.

An activist's argument that participant values should guide risk-benefit ratio calculations in HIV cure research.

PubMed

Evans, David

2017-02-01

The patient empowerment movement, spurred by AIDS activism in the 1980s, quickly evolved to encompass how study participants are considered and treated in clinical research. Initially, people fearing death of AIDS sought early access to experimental medications that had not undergone rigorous testing in hopes of extending their lives. Thirty years on, scientists are asking a different set of ethical questions about clinical research, this time in the pursuit of either a sterilising cure or long-term remission for HIV. Instead of hastening access to experimental drugs for the sickest, researchers are now testing interventions for eradicating or controlling the virus in typically very healthy HIV-positive individuals who have the most to lose from such interventions if something goes wrong. While clinical researchers and ethicists debate the merits and limits of this type of research they should avoid discounting altruistic motivations as a powerful factor in a prospective study participant's decisions to assume risks. My conversations with four men who participated in HIV cure studies confirmed the capacity of these people to make carefully considered decisions about risks and the sometimes substantial influence/sway of non-clinical benefits that may come from participation in cure-oriented research. Studies must undergo ethical and clinical review before proceeding, and not all participants of such studies will be able to weigh or understand risks and benefits as those profiled here. But respecting the self-agency of people living with HIV should be a goal in the design and conduct of cure research. 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/.

Learning Compositional Simulation Models

DTIC Science & Technology

2010-01-01

techniques developed by social scientists, economists, and medical researchers over the past four decades. Quasi-experimental designs (QEDs) are...statistical techniques from the social sciences known as quasi- experimental design (QED). QEDs allow a researcher to exploit unique characteristics...can be grouped under the rubric “quasi-experimental design ” (QED), and they attempt to exploit inherent characteristics of observational data sets

TU-H-BRA-07: Design, Construction, and Installation of An Experimental Beam Line for the Development of MRI-Linac Compatible Electron Accelerator

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

Whelan, B; Keall, P; Holloway, L

Purpose: MRI guided radiation therapy (MRIgRT) is a rapidly growing field; however, Linac operation in MRI fringe fields represents an ongoing challenge. We have previously shown in-silico that Linacs could be redesigned to function in the in-line orientation with no magnetic shielding by adopting an RF-gun configuration. Other authors have also published insilico studies of Linac operation in magnetic fields; however to date no experimental validation data is published. This work details the design, construction, and installation of an experimental beam line to validate our in-silico results. Methods: An RF-gun comprising 1.5 accelerating cells and capable of generating electron energiesmore » up to 3.2MeV is used. The experimental apparatus was designed to monitor both beam current (toroid current monitor), spot size (two phosphor screens with viewports), and generate peak magnetic fields of at least 1000G (three variable current electromagnetic coils). Thermal FEM simulations were developed to ensure coil temperature remained within 100degC. Other design considerations included beam disposal, vacuum maintenance, radiation shielding, earthquake safety, and machine protection interlocks. Results: The beam line has been designed, built, and installed in a radiation shielded bunker. Water cooling, power supplies, thermo-couples, cameras, and radiation shielding have been successfully connected and tested. Interlock testing, vacuum processing, and RF processing have been successfully completed. The first beam on is expected within weeks. The coil heating simulations show that with care, peak fields of up to 1200G (320G at cathode) can be produced using 40A current, which is well within the fields expected for MRI-Linac systems. The maximum coil temperature at this current was 84degC after 6 minutes. Conclusion: An experimental beam line has been constructed and installed at SLAC in order to experimentally characterise RF gun performance in in-line magnetic fields, validate in-silico design work, and provide the first published experimental data relating to accelerator functionality for MRIgRT.« less

New Issues for New Methods: Ethical and Editorial Challenges for an Experimental Philosophy.

PubMed

Polonioli, Andrea

2017-08-01

This paper examines a constellation of ethical and editorial issues that have arisen since philosophers started to conduct, submit and publish empirical research. These issues encompass concerns over responsible authorship, fair treatment of human subjects, ethicality of experimental procedures, availability of data, unselective reporting and publishability of research findings. This study aims to assess whether the philosophical community has as yet successfully addressed such issues. To do so, the instructions for authors, submission process and published research papers of 29 main journals in philosophy have been considered and analyzed. In light of the evidence reported here, it is argued that the philosophical community has as yet failed to properly tackle such issues. The paper also delivers some recommendations for authors, reviewers and editors in the field.

Evaluation and comparison of classical interatomic potentials through a user-friendly interactive web-interface

NASA Astrophysics Data System (ADS)

Choudhary, Kamal; Congo, Faical Yannick P.; Liang, Tao; Becker, Chandler; Hennig, Richard G.; Tavazza, Francesca

2017-01-01

Classical empirical potentials/force-fields (FF) provide atomistic insights into material phenomena through molecular dynamics and Monte Carlo simulations. Despite their wide applicability, a systematic evaluation of materials properties using such potentials and, especially, an easy-to-use user-interface for their comparison is still lacking. To address this deficiency, we computed energetics and elastic properties of variety of materials such as metals and ceramics using a wide range of empirical potentials and compared them to density functional theory (DFT) as well as to experimental data, where available. The database currently consists of 3248 entries including energetics and elastic property calculations, and it is still increasing. We also include computational tools for convex-hull plots for DFT and FF calculations. The data covers 1471 materials and 116 force-fields. In addition, both the complete database and the software coding used in the process have been released for public use online (presently at http://www.ctcms.nist.gov/˜knc6/periodic.html) in a user-friendly way designed to enable further material design and discovery.

Evaluation and comparison of classical interatomic potentials through a user-friendly interactive web-interface

PubMed Central

Choudhary, Kamal; Congo, Faical Yannick P.; Liang, Tao; Becker, Chandler; Hennig, Richard G.; Tavazza, Francesca

2017-01-01

Classical empirical potentials/force-fields (FF) provide atomistic insights into material phenomena through molecular dynamics and Monte Carlo simulations. Despite their wide applicability, a systematic evaluation of materials properties using such potentials and, especially, an easy-to-use user-interface for their comparison is still lacking. To address this deficiency, we computed energetics and elastic properties of variety of materials such as metals and ceramics using a wide range of empirical potentials and compared them to density functional theory (DFT) as well as to experimental data, where available. The database currently consists of 3248 entries including energetics and elastic property calculations, and it is still increasing. We also include computational tools for convex-hull plots for DFT and FF calculations. The data covers 1471 materials and 116 force-fields. In addition, both the complete database and the software coding used in the process have been released for public use online (presently at http://www.ctcms.nist.gov/∼knc6/periodic.html) in a user-friendly way designed to enable further material design and discovery. PMID:28140407

MelanomaDB: A Web Tool for Integrative Analysis of Melanoma Genomic Information to Identify Disease-Associated Molecular Pathways

PubMed Central

Trevarton, Alexander J.; Mann, Michael B.; Knapp, Christoph; Araki, Hiromitsu; Wren, Jonathan D.; Stones-Havas, Steven; Black, Michael A.; Print, Cristin G.

2013-01-01

Despite on-going research, metastatic melanoma survival rates remain low and treatment options are limited. Researchers can now access a rapidly growing amount of molecular and clinical information about melanoma. This information is becoming difficult to assemble and interpret due to its dispersed nature, yet as it grows it becomes increasingly valuable for understanding melanoma. Integration of this information into a comprehensive resource to aid rational experimental design and patient stratification is needed. As an initial step in this direction, we have assembled a web-accessible melanoma database, MelanomaDB, which incorporates clinical and molecular data from publically available sources, which will be regularly updated as new information becomes available. This database allows complex links to be drawn between many different aspects of melanoma biology: genetic changes (e.g., mutations) in individual melanomas revealed by DNA sequencing, associations between gene expression and patient survival, data concerning drug targets, biomarkers, druggability, and clinical trials, as well as our own statistical analysis of relationships between molecular pathways and clinical parameters that have been produced using these data sets. The database is freely available at http://genesetdb.auckland.ac.nz/melanomadb/about.html. A subset of the information in the database can also be accessed through a freely available web application in the Illumina genomic cloud computing platform BaseSpace at http://www.biomatters.com/apps/melanoma-profiler-for-research. The MelanomaDB database illustrates dysregulation of specific signaling pathways across 310 exome-sequenced melanomas and in individual tumors and identifies the distribution of somatic variants in melanoma. We suggest that MelanomaDB can provide a context in which to interpret the tumor molecular profiles of individual melanoma patients relative to biological information and available drug therapies. PMID:23875173

A Decade of Literacy Research in the "Journal of Experimental Education."

ERIC Educational Resources Information Center

Knudson, Ruth E.; Theurer, Joan Leikam; Onofrey, Karen A.

This study examined various trends that exist among the 246 refereed articles published in the "Journal of Experimental Education" between 1990 and 1999. The study's results showed that 39 (16%) of the Journal articles published during this 9-year span focused on literacy. Information was categorized for each article with respect to authors'…

Use of a bibliometric literature review to assess medical research capacity in post-conflict and developing countries: Somaliland 1991-2013.

PubMed

Boyce, Ross; Rosch, Richard; Finlayson, Alexander; Handuleh, Djibril; Walhad, Said Ahmed; Whitwell, Susannah; Leather, Andy

2015-11-01

Effective healthcare systems require high-quality research to guide evidence-based interventions and strategic planning. In low- and middle-income countries, especially those emerging from violent conflict, research capacity often lags behind other aspects of health system development. Here, we sought to bibliometrically review health-related research output in Somaliland, a post-conflict self-declared, autonomous nation on the Horn of Africa, as a means of assessing research capacity. We reviewed articles on health-related research conducted in Somaliland between 1991 and 2013 that included a description of the experimental design, and articles were published in either a peer-reviewed journal or as part of a scholarly programme receiving formal review. We did not include policy or social science research that did not enrol or interact with subjects from Somaliland. Using online databases, all studies meeting minimum eligibility criteria were reviewed in regard to Somaliland-based co-authorship, topic of research and specific measures of quality. A total of 37 studies were included in this review. Of these, only 19 (51%) included co-authorship by Somaliland-based researchers. Of the 21 studies reporting ethical approval, 16 (64%) received approval from the Somalia or Somaliland Ministry of Health, while five received approval from a university or national commission. More than two-thirds of published research was limited to a few areas of investigation with most (19, 51%) following basic cross-sectional study designs. The number of articles published per year increased from 0 to 1 in the years 1991-2007 to a maximum of 8 in 2013. Research activity in Somaliland is extremely limited. Investigators from high-income countries have largely directed the research agenda in Somaliland; only half of the included studies list co-authors from institutions in Somaliland. Leadership and governance of health research in Somaliland is required to define national priorities, promote scholarly activity and guide the responsible conduct of research. The methods used here to assess research capacity may be generalisable to other low- and middle-income countries and post-conflict settings to measure the impact of research capacity-building efforts. © 2015 John Wiley & Sons Ltd.

Obesity interventions for people with a learning disability: an integrative literature review.

PubMed

Jinks, Annette; Cotton, Angela; Rylance, Rebecca

2011-03-01

This paper is a review of the effectiveness of non-surgical, non-pharmaceutical interventions designed to promote weight loss in people with a learning disability and how qualitative evidence on people's experiences and motivations can help understanding of the quantitative research outcomes. The health risks of obesity underline the importance of effective evidence-based weight loss interventions for people with learning disabilities as they are at increased risk of being overweight. Papers published from 1998 to 2009 were identified through searches of the Cumulative Index for Nursing and Allied Health Literature, Proquest, Medline (PubMed), PSYCHINFO databases, and the Cochrane Library. An integrative review method was used. Studies included were non-surgical or non-pharmaceutical interventions aimed at weight reduction for people with a learning disability. Synthesis of the findings related to study design, participants, types of interventions, outcome measures and participant perspectives. Twelve studies met the inclusion criteria. The most common research design was quasi-experimental pretest and post-test. Few researchers used a clinical trial approach, and there was only one predominantly qualitative study. Interventions were mainly focused on energy intake, energy expenditure or health promotion. Only a few studies incorporated behaviour modification approaches. Nurses who work with clients with learning disabilities have a key role to play in the management of obesity. Future research needs to focus on qualitative studies of the perceptions of clients and their families, controlled trials investigating the effectiveness of interventions and their costs and sustainability, and longitudinal studies examining weight loss over time. © 2010 Blackwell Publishing Ltd.

Assessment of Department of Defense Basic Research

DTIC Science & Technology

2005-01-01

Sciences, the National Academy of Engineering, the Institute of Medicine, and the National Research Council: • Download hundreds of free books in PDF...with our innovative research tools Thank you for downloading this free PDF. If you have comments, questions or just want more information... downloaded from: http://www.nap.edu/catalog/11177.html Assessment of Department of Defense Basic Research Committee on Department of Defense Basic

The Federal Networking and Information Technology Research and Development Program: Funding Issues and Activities

DTIC Science & Technology

2009-05-14

11 Next Generation Internet Research Act of 1998...performance computing R&D and called for increased interagency planning and coordination. The second, the Next Generation Internet Research Act of...law is available at http://www.nitrd.gov/congressional/laws/pl_102-194.html. 19 Next Generation Internet Research Act of 1998, P.L. 105-305, 15 U.S.C

NASA Space Biology Plant Research for 2010-2020

NASA Technical Reports Server (NTRS)

Levine, H. G.; Tomko, D. L.; Porterfield, D. M.

2012-01-01

The U.S. National Research Council (NRC) recently published "Recapturing a Future for Space Exploration: Life and Physical Sciences Research for a New Era" (http://www.nap.edu/catalog.php?record id=13048), and NASA completed a Space Biology Science Plan to develop a strategy for implementing its recommendations ( http://www.nasa.gov/exploration/library/esmd documents.html). The most important recommendations of the NRC report on plant biology in space were that NASA should: (1) investigate the roles of microbial-plant systems in long-term bioregenerative life support systems, and (2) establish a robust spaceflight program of research analyzing plant growth and physiological responses to the multiple stimuli encountered in spaceflight environments. These efforts should take advantage of recently emerged analytical technologies (genomics, transcriptomics, proteomics, metabolomics) and apply modern cellular and molecular approaches in the development of a vigorous flight-based and ground-based research program. This talk will describe NASA's strategy and plans for implementing these NRC Plant Space Biology recommendations. New research capabilities for Plant Biology, optimized by providing state-of-the-art automated technology and analytical techniques to maximize scientific return, will be described. Flight experiments will use the most appropriate platform to achieve science results (e.g., ISS, free flyers, sub-orbital flights) and NASA will work closely with its international partners and other U.S. agencies to achieve its objectives. One of NASA's highest priorities in Space Biology is the development research capabilities for use on the International Space Station and other flight platforms for studying multiple generations of large plants. NASA will issue recurring NASA Research Announcements (NRAs) that include a rapid turn-around model to more fully engage the biology community in designing experiments to respond to the NRC recommendations. In doing so, NASA's Space Biology research will optimize ISS research utilization, develop and demonstrate technology and hardware that will enable new science, and contribute to the base of fundamental knowledge that will facilitate development of new tools for human space exploration and Earth applications. By taking these steps, NASA will energize the Space Biology user community and advance our knowledge of the effect of the space flight environment on living systems.

Development of a Model for Measuring Scientific Processing Skills Based on Brain-Imaging Technology: Focused on the Experimental Design Process

ERIC Educational Resources Information Center

Lee, Il-Sun; Byeon, Jung-Ho; Kim, Young-shin; Kwon, Yong-Ju

2014-01-01

The purpose of this study was to develop a model for measuring experimental design ability based on functional magnetic resonance imaging (fMRI) during biological inquiry. More specifically, the researchers developed an experimental design task that measures experimental design ability. Using the developed experimental design task, they measured…

Reconciling research and implementation in micro health insurance experiments in India: study protocol for a randomized controlled trial

PubMed Central

2011-01-01

Background Microinsurance or Community-Based Health Insurance is a promising healthcare financing mechanism, which is increasingly applied to aid rural poor persons in low-income countries. Robust empirical evidence on the causal relations between Community-Based Health Insurance and healthcare utilisation, financial protection and other areas is scarce and necessary. This paper contains a discussion of the research design of three Cluster Randomised Controlled Trials in India to measure the impact of Community-Based Health Insurance on several outcomes. Methods/Design Each trial sets up a Community-Based Health Insurance scheme among a group of micro-finance affiliate families. Villages are grouped into clusters which are congruous with pre-existing social groupings. These clusters are randomly assigned to one of three waves of implementation, ensuring the entire population is offered Community-Based Health Insurance by the end of the experiment. Each wave of treatment is preceded by a round of mixed methods evaluation, with quantitative, qualitative and spatial evidence on impact collected. Improving upon practices in published Cluster Randomised Controlled Trial literature, we detail how research design decisions have ensured that both the households offered insurance and the implementers of the Community-Based Health Insurance scheme operate in an environment replicating a non-experimental implementation. Discussion When a Cluster Randomised Controlled Trial involves randomizing within a community, generating adequate and valid conclusions requires that the research design must be made congruous with social structures within the target population, to ensure that such trials are conducted in an implementing environment which is a suitable analogue to that of a non-experimental implementing environment. PMID:21988774

ExportAid: database of RNA elements regulating nuclear RNA export in mammals.

PubMed

Giulietti, Matteo; Milantoni, Sara Armida; Armeni, Tatiana; Principato, Giovanni; Piva, Francesco

2015-01-15

Regulation of nuclear mRNA export or retention is carried out by RNA elements but the mechanism is not yet well understood. To understand the mRNA export process, it is important to collect all the involved RNA elements and their trans-acting factors. By hand-curated literature screening we collected, in ExportAid database, experimentally assessed data about RNA elements regulating nuclear export or retention of endogenous, heterologous or artificial RNAs in mammalian cells. This database could help to understand the RNA export language and to study the possible export efficiency alterations owing to mutations or polymorphisms. Currently, ExportAid stores 235 and 96 RNA elements, respectively, increasing and decreasing export efficiency, and 98 neutral assessed sequences. Freely accessible without registration at http://www.introni.it/ExportAid/ExportAid.html. Database and web interface are implemented in Perl, MySQL, Apache and JavaScript with all major browsers supported. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Biotool2Web: creating simple Web interfaces for bioinformatics applications.

PubMed

Shahid, Mohammad; Alam, Intikhab; Fuellen, Georg

2006-01-01

Currently there are many bioinformatics applications being developed, but there is no easy way to publish them on the World Wide Web. We have developed a Perl script, called Biotool2Web, which makes the task of creating web interfaces for simple ('home-made') bioinformatics applications quick and easy. Biotool2Web uses an XML document containing the parameters to run the tool on the Web, and generates the corresponding HTML and common gateway interface (CGI) files ready to be published on a web server. This tool is available for download at URL http://www.uni-muenster.de/Bioinformatics/services/biotool2web/ Georg Fuellen (fuellen@alum.mit.edu).

Publisher Correction: N6-methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications.

PubMed

Wang, Yang; Li, Yue; Yue, Minghui; Wang, Jun; Kumar, Sandeep; Wechsler-Reya, Robert J; Zhang, Zhaolei; Ogawa, Yuya; Kellis, Manolis; Duester, Gregg; Zhao, Jing Crystal

2018-06-07

In the version of this article initially published online, there were errors in URLs for www.southernbiotech.com, appearing in Methods sections "m6A dot-blot" and "Western blot analysis." The first two URLs should be https://www.southernbiotech.com/?catno=4030-05&type=Polyclonal#&panel1-1 and the third should be https://www.southernbiotech.com/?catno=6170-05&type=Polyclonal. In addition, some Methods URLs for bioz.com, www.abcam.com and www.sysy.com were printed correctly but not properly linked. The errors have been corrected in the PDF and HTML versions of this article.

So You Wanna Be a Web Author?

ERIC Educational Resources Information Center

Buchanan, Larry

1996-01-01

Defines HyperText Markup Language (HTML) as it relates to the World Wide Web (WWW). Describes steps needed to create HTML files on a UNIX system and to make them accessible via the WWW. Presents a list of basic HTML formatting codes and explains the coding used in the author's personal HTML file. (JMV)

A More Rigorous Quasi-Experimental Alternative to the One-Group Pretest-Posttest Design.

ERIC Educational Resources Information Center

Johnson, Craig W.

1986-01-01

A simple quasi-experimental design is described which may have utility in a variety of applied and laboratory research settings where ordinarily the one-group pretest-posttest pre-experimental design might otherwise be the procedure of choice. The design approaches the internal validity of true experimental designs while optimizing external…

XML: An Introduction.

ERIC Educational Resources Information Center

Lewis, John D.

1998-01-01

Describes XML (extensible markup language), a new language classification submitted to the World Wide Web Consortium that is defined in terms of both SGML (Standard Generalized Markup Language) and HTML (Hypertext Markup Language), specifically designed for the Internet. Limitations of PDF (Portable Document Format) files for electronic journals…

Nutrition: ethical issues and challenges.

PubMed

Rucker, Robert B; Rucker, Michael R

2016-11-01

For nutrition and its associated disciplines, ethical considerations related to research are often complicated by factors that range from the use of experimental research designs that are overly holistic to inextricable links between nutrition research and marketing. As a consequence, there is the need for constant vigilance to assess and deal with apparent conflicts of interest. Also, there are few scientific disciplines that are defined by cultural, religious, or political codifications as is nutrition. Accordingly, examples of historical, cultural, and political events are described that have influenced ethical approaches related to nutrition research. Furthermore, nutrition research questions are often multifaceted and require dealing with complex variables. In this regard, ethical principles and perspectives that have relevance to data acquisition, the publication and translation of nutrition research, and the marketing of nutritional products and concepts are highlighted. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Case study and case-based research in emergency nursing and care: Theoretical foundations and practical application in paramedic pre-hospital clinical judgment and decision-making of patients with mental illness.

PubMed

Shaban, Ramon Z; Considine, Julie; Fry, Margaret; Curtis, Kate

2017-02-01

Generating knowledge through quality research is fundamental to the advancement of professional practice in emergency nursing and care. There are multiple paradigms, designs and methods available to researchers to respond to challenges in clinical practice. Systematic reviews, randomised control trials and other forms of experimental research are deemed the gold standard of evidence, but there are comparatively few such trials in emergency care. In some instances it is not possible or appropriate to undertake experimental research. When exploring new or emerging problems where there is limited evidence available, non-experimental methods are required and appropriate. This paper provides the theoretical foundations and an exemplar of the use of case study and case-based research to explore a new and emerging problem in the context of emergency care. It examines pre-hospital clinical judgement and decision-making of mental illness by paramedics. Using an exemplar the paper explores the theoretical foundations and conceptual frameworks of case study, it explains how cases are defined and the role researcher in this form of inquiry, it details important principles and the procedures for data gathering and analysis, and it demonstrates techniques to enhance trustworthiness and credibility of the research. Moreover, it provides theoretically and practical insights into using case study in emergency care. Copyright © 2017 College of Emergency Nursing Australasia. Published by Elsevier Ltd. All rights reserved.

How to design a single-cell RNA-sequencing experiment: pitfalls, challenges and perspectives.

PubMed

Dal Molin, Alessandra; Di Camillo, Barbara

2018-01-31

The sequencing of the transcriptome of single cells, or single-cell RNA-sequencing, has now become the dominant technology for the identification of novel cell types in heterogeneous cell populations or for the study of stochastic gene expression. In recent years, various experimental methods and computational tools for analysing single-cell RNA-sequencing data have been proposed. However, most of them are tailored to different experimental designs or biological questions, and in many cases, their performance has not been benchmarked yet, thus increasing the difficulty for a researcher to choose the optimal single-cell transcriptome sequencing (scRNA-seq) experiment and analysis workflow. In this review, we aim to provide an overview of the current available experimental and computational methods developed to handle single-cell RNA-sequencing data and, based on their peculiarities, we suggest possible analysis frameworks depending on specific experimental designs. Together, we propose an evaluation of challenges and open questions and future perspectives in the field. In particular, we go through the different steps of scRNA-seq experimental protocols such as cell isolation, messenger RNA capture, reverse transcription, amplification and use of quantitative standards such as spike-ins and Unique Molecular Identifiers (UMIs). We then analyse the current methodological challenges related to preprocessing, alignment, quantification, normalization, batch effect correction and methods to control for confounding effects. © The Author(s) 2018. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Publisher Correction: Precisely printable and biocompatible silk fibroin bioink for digital light processing 3D printing.

PubMed

Kim, Soon Hee; Yeon, Yeung Kyu; Lee, Jung Min; Chao, Janet Ren; Lee, Young Jin; Seo, Ye Been; Sultan, Md Tipu; Lee, Ok Joo; Lee, Ji Seung; Yoon, Sung-Il; Hong, In-Sun; Khang, Gilson; Lee, Sang Jin; Yoo, James J; Park, Chan Hum

2018-06-11

The original version of this Article contained errors in Figs. 5 and 6. In Fig. 5b, the second panel on the bottom row was stretched out of proportion. In Fig. 6d, the first panel was also stretched out of proportion. In Fig. 6f, the fifth panel inadvertently repeated the fourth. This has been corrected in both the PDF and HTML versions of the Article.

Case Study: Accelerating Process Improvement by Integrating the TSP and CMMI

DTIC Science & Technology

2005-12-01

improve their work? Watts S . Humphrey , a founder of the process improvement initiative at the SEI, de- cided to apply SW-CMM principles to the...authorized PSP instructor. At Schwalb’s urging, Watts Humphrey briefed the SLT on the PSP and TSP, and after the briefing, the team understood...hefley.html. [ Humphrey 96] Humphrey , Watts S . Introduction to the Personal Software Process. Boston, MA: Addison-Wesley Publishing Company, Inc., 1996

First Nuclear DNA Amounts in more than 300 Angiosperms

PubMed Central

ZONNEVELD, B. J. M.; LEITCH, I. J.; BENNETT, M. D.

2005-01-01

• Background and Aims Genome size (DNA C-value) data are key biodiversity characters of fundamental significance used in a wide variety of biological fields. Since 1976, Bennett and colleagues have made scattered published and unpublished genome size data more widely accessible by assembling them into user-friendly compilations. Initially these were published as hard copy lists, but since 1997 they have also been made available electronically (see the Plant DNA C-values database www.kew.org/cval/homepage.html). Nevertheless, at the Second Plant Genome Size Meeting in 2003, Bennett noted that as many as 1000 DNA C-value estimates were still unpublished and hence unavailable. Scientists were strongly encouraged to communicate such unpublished data. The present work combines the databasing experience of the Kew-based authors with the unpublished C-values produced by Zonneveld to make a large body of valuable genome size data available to the scientific community. • Methods C-values for angiosperm species, selected primarily for their horticultural interest, were estimated by flow cytometry using the fluorochrome propidium iodide. The data were compiled into a table whose form is similar to previously published lists of DNA amounts by Bennett and colleagues. • Key Results and Conclusions The present work contains C-values for 411 taxa including first values for 308 species not listed previously by Bennett and colleagues. Based on a recent estimate of the global published output of angiosperm DNA C-value data (i.e. 200 first C-value estimates per annum) the present work equals 1·5 years of average global published output; and constitutes over 12 % of the latest 5-year global target set by the Second Plant Genome Size Workshop (see www.kew.org/cval/workshopreport.html). Hopefully, the present example will encourage others to unveil further valuable data which otherwise may lie forever unpublished and unavailable for comparative analyses. PMID:15905300

Bibliometric Analysis of Journal of Clinical and Diagnostic Research (Dentistry Section; 2007-2014)

PubMed Central

Basavaraj, P; Singla, Ashish; Singh, Khushboo; Kundu, Hansa; Vashishtha, Vaibhav; Pandita, Venisha; Malhi, Ravneet

2015-01-01

Background: The role of scientific journals in diffusion of data concerning researches in the field of Public Health Dentistry is of premier importance. Bibliometric analysis involves analysis of publications reflecting the type of research work. Aim: The present study was conducted with an aim to determine the number and trends of published articles in Journal of Clinical and Diagnostic Research (JCDR) from Feb. 2007 to Oct.2014. Settings and Design: A retrospective observational study was conducted for JCDR. Materials and Methods: All issues of JCDR were electronically searched for the parameters : study design, area of interest of research, state /college where research was conducted, authorship pattern, source of articles published each year, changing study trends, disease under study and publication bias. Statistical Analysis used: The data was organized and analyzed using software SPSS - version 21.0; descriptive statistics was used. Results: Bibliometric analysis was done for 601 articles of JCDR published from Feb. 2007 to Oct. 2014. The total number of articles published under Dentistry section have tremendously increased from mere 2 articles in 2007 to 328 articles in 2014.Majority of the study designs published in both the journal were case reports (42.6%) followed by cross sectional studies (24.8%). 96.3% of the articles were from India. Majority of the articles published were of multi authors (65.2%) and from Educational institutes (98.4%). The trends of the articles published indicated that the case reports/series formed the major bulk (others=59.1%) followed by research studies (21.3%). Conclusion: It was concluded that most articles published were case reports followed by researches indicating an inclination towards better quality methodology. The SJR and the citation count of the articles published also indicated the quality of the scientific articles published. PMID:26023643

New Media for Instruction: Survey of Educational Media Research in the Far East. Instructional Uses and Research Direction. Bulletin, 1963, No. 40. OE-34025

ERIC Educational Resources Information Center

Duke, Benjamin C., Ed.

1963-01-01

The primary purpose of this project was to compile, translate, and publish educational media research material from the major Asian countries and to make that information available in the United States. Educational media research and experimentation is interpreted to include experimental programming, testing, evaluation, and use of all the newer…

Upper surface blowing noise of the NASA-Ames quiet short-haul research aircraft

NASA Technical Reports Server (NTRS)

Bohn, A. J.; Shovlin, M. D.

1980-01-01

An experimental study of the propulsive-lift noise of the NASA-Ames quiet short-haul research aircraft (QSRA) is described. Comparisons are made of measured QSRA flyover noise and model propulsive-lift noise data available in references. Developmental tests of trailing-edge treatments were conducted using sawtooth-shaped and porous USB flap trailing-edge extensions. Small scale parametric tests were conducted to determine noise reduction/design relationships. Full-scale static tests were conducted with the QSRA preparatory to the selection of edge treatment designs for flight testing. QSRA flight and published model propulsive-lift noise data have similar characteristics. Noise reductions of 2 to 3 dB were achieved over a wide range of frequency and directivity angles in static tests of the QSRA. These noise reductions are expected to be achieved or surpassed in flight tests planned by NASA in 1980.

Current and Future Research in Active Control of Lightweight, Flexible Structures Using the X-56 Aircraft

NASA Technical Reports Server (NTRS)

Ryan, John J.; Bosworth, John T.; Burken, John J.; Suh, Peter M.

2014-01-01

The X-56 Multi-Utility Technology Testbed aircraft system is a versatile experimental research flight platform. The system was primarily designed to investigate active control of lightweight flexible structures, but is reconfigurable and capable of hosting a wide breadth of research. Current research includes flight experimentation of a Lockheed Martin designed active control flutter suppression system. Future research plans continue experimentation with alternative control systems, explore the use of novel sensor systems, and experiments with the use of novel control effectors. This paper describes the aircraft system, current research efforts designed around the system, and future planned research efforts that will be hosted on the aircraft system.

Evaluating the design and reporting of pragmatic trials in osteoarthritis research.

PubMed

Ali, Shabana Amanda; Kloseck, Marita; Lee, Karen; Walsh, Kathleen Ellen; MacDermid, Joy C; Fitzsimmons, Deborah

2018-01-01

Among the challenges in health research is translating interventions from controlled experimental settings to clinical and community settings where chronic disease is managed daily. Pragmatic trials offer a method for testing interventions in real-world settings but are seldom used in OA research. The aim of this study was to evaluate the literature on pragmatic trials in OA research up to August 2016 in order to identify strengths and weaknesses in the design and reporting of these trials. We used established guidelines to assess the degree to which 61 OA studies complied with pragmatic trial design and reporting. We assessed design according to the pragmatic-explanatory continuum indicator summary and reporting according to the pragmatic trials extension of the CONsolidated Standards of Reporting Trials guidelines. None of the pragmatic trials met all 11 criteria evaluated and most of the trials met between 5 and 8 of the criteria. Criteria most often unmet pertained to practitioner expertise (by requiring specialists) and criteria most often met pertained to primary outcome analysis (by using intention-to-treat analysis). Our results suggest a lack of highly pragmatic trials in OA research. We identify this as a point of opportunity to improve research translation, since optimizing the design and reporting of pragmatic trials can facilitate implementation of evidence-based interventions for OA care. © The Author 2017. Published by Oxford University Press on behalf of the British Society for Rheumatology. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Evaluating statistical and clinical significance of intervention effects in single-case experimental designs: an SPSS method to analyze univariate data.

PubMed

Maric, Marija; de Haan, Else; Hogendoorn, Sanne M; Wolters, Lidewij H; Huizenga, Hilde M

2015-03-01

Single-case experimental designs are useful methods in clinical research practice to investigate individual client progress. Their proliferation might have been hampered by methodological challenges such as the difficulty applying existing statistical procedures. In this article, we describe a data-analytic method to analyze univariate (i.e., one symptom) single-case data using the common package SPSS. This method can help the clinical researcher to investigate whether an intervention works as compared with a baseline period or another intervention type, and to determine whether symptom improvement is clinically significant. First, we describe the statistical method in a conceptual way and show how it can be implemented in SPSS. Simulation studies were performed to determine the number of observation points required per intervention phase. Second, to illustrate this method and its implications, we present a case study of an adolescent with anxiety disorders treated with cognitive-behavioral therapy techniques in an outpatient psychotherapy clinic, whose symptoms were regularly assessed before each session. We provide a description of the data analyses and results of this case study. Finally, we discuss the advantages and shortcomings of the proposed method. Copyright © 2014. Published by Elsevier Ltd.

Masculinity, Racism, Social Support, and Colorectal Cancer Screening Uptake Among African American Men: A Systematic Review.

PubMed

Rogers, Charles R; Mitchell, Jamie A; Franta, Gabriel J; Foster, Margaret J; Shires, Deirdre

2017-09-01

Colorectal cancer (CRC) is highly preventable when CRC screening is utilized, yet CRC screening completion among African American men is relatively low and their mortality rates remain 50% higher juxtaposed to their White counterparts. Since a growing body of literature indicates masculinity, racism, and social support each have strong influences on CRC screening uptake, this systematic review examined the connections between these three sociocultural factors and CRC screening uptake among African American men. Potential studies were retrieved from MEDLINE, CINAHL, EMBASE, and PsycINFO. Cited reference searching for the final sample was employed to identify and assess additional studies for inclusion using Scopus. The methodological quality of the reviewed evidence was also evaluated. Nineteen studies met inclusion/exclusion criteria. Thirteen studies employed nonexperimental research designs; a quasi-experimental design was present in four, and two utilized experimental designs. Studies were published between 2000 and 2014; the majority between 2009 and 2013. Social support was most frequently addressed (84%) while masculinity and racism were equally studied with paucity (11%) for their influence on CRC screening. After evaluating conceptual and methodological characteristics of the studies, 42% fell below average in quality and rigor. The need for increased attention to the sociocultural correlates of CRC screening for African American men are highlighted in this systematic review, and important recommendations for research and practice are provided. Alongside a call for more rigorous research, further research examining the influence of masculinity and racism on CRC screening completion among African American men is warranted.

Measuring and Advancing Experimental Design Ability in an Introductory Course without Altering Existing Lab Curriculum†

PubMed Central

Shanks, Ryan A.; Robertson, Chuck L.; Haygood, Christian S.; Herdliksa, Anna M.; Herdliska, Heather R.; Lloyd, Steven A.

2017-01-01

Introductory biology courses provide an important opportunity to prepare students for future courses, yet existing cookbook labs, although important in their own way, fail to provide many of the advantages of semester-long research experiences. Engaging, authentic research experiences aid biology students in meeting many learning goals. Therefore, overlaying a research experience onto the existing lab structure allows faculty to overcome barriers involving curricular change. Here we propose a working model for this overlay design in an introductory biology course and detail a means to conduct this lab with minimal increases in student and faculty workloads. Furthermore, we conducted exploratory factor analysis of the Experimental Design Ability Test (EDAT) and uncovered two latent factors which provide valid means to assess this overlay model’s ability to increase advanced experimental design abilities. In a pre-test/post-test design, we demonstrate significant increases in both basic and advanced experimental design abilities in an experimental and comparison group. We measured significantly higher gains in advanced experimental design understanding in students in the experimental group. We believe this overlay model and EDAT factor analysis contribute a novel means to conduct and assess the effectiveness of authentic research experiences in an introductory course without major changes to the course curriculum and with minimal increases in faculty and student workloads. PMID:28904647

Estimating the Impact of the PROMISE Scholarship Using Propensity Score Weighted Frontier Fuzzy Regression Discontinuity Design

ERIC Educational Resources Information Center

Shobo, Yetty; Wong, Jen D.; Bell, Angie

2014-01-01

Regression discontinuity (RD), an "as good as randomized," research design is increasingly prominent in education research in recent years; the design gets eligible quasi-experimental designs as close as possible to experimental designs by using a stated threshold on a continuous baseline variable to assign individuals to a…

76 FR 55390 - Guidance on Exculpatory Language in Informed Consent, Draft

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-07

...://www.fda.gov/ScienceResearch/SpecialTopics/RunningClinicalTrials/default.htm , is intended to assist... , http://www.hhs.gov/ohrp/newsroom/rfc/index.html , or http://www.fda.gov/ScienceResearch/SpecialTopics/RunningClinicalTrials/default.htm . III. Request for Comments OHRP and FDA are making their joint draft...

Wetlands postcard

USGS Publications Warehouse

Ball, Lianne C.

2016-05-25

Research conducted by scientists at the U.S. Geological Survey provides reliable scientific information for the management of wetlands ranging from small freshwater alpine lakes in the Western United States to coastal wetlands of the Great Lakes and salt marshes along the Southeastern coast. Learn more about USGS wetlands research at: http://www.usgs.gov/ecosystems/environments/wetlands.html.

A Meta-Analysis of Empirical Research on Teaching Students with Mathematics Learning Difficulties

ERIC Educational Resources Information Center

Dennis, Minyi Shih; Sharp, Emily; Chovanes, Jacquelyn; Thomas, Amanda; Burns, Raquel M.; Custer, Beth; Park, Junkoung

2016-01-01

This article quantitatively summarizes experimental and quasi-experimental studies on teaching students with mathematics difficulties (MD) published between 2000 and 2014, research that was available following earlier syntheses. It reports the analysis of effect sizes of 25 intervention studies on participant characteristics, intervention…

Privacy-preserving microbiome analysis using secure computation.

PubMed

Wagner, Justin; Paulson, Joseph N; Wang, Xiao; Bhattacharjee, Bobby; Corrada Bravo, Héctor

2016-06-15

Developing targeted therapeutics and identifying biomarkers relies on large amounts of research participant data. Beyond human DNA, scientists now investigate the DNA of micro-organisms inhabiting the human body. Recent work shows that an individual's collection of microbial DNA consistently identifies that person and could be used to link a real-world identity to a sensitive attribute in a research dataset. Unfortunately, the current suite of DNA-specific privacy-preserving analysis tools does not meet the requirements for microbiome sequencing studies. To address privacy concerns around microbiome sequencing, we implement metagenomic analyses using secure computation. Our implementation allows comparative analysis over combined data without revealing the feature counts for any individual sample. We focus on three analyses and perform an evaluation on datasets currently used by the microbiome research community. We use our implementation to simulate sharing data between four policy-domains. Additionally, we describe an application of our implementation for patients to combine data that allows drug developers to query against and compensate patients for the analysis. The software is freely available for download at: http://cbcb.umd.edu/∼hcorrada/projects/secureseq.html Supplementary data are available at Bioinformatics online. hcorrada@umiacs.umd.edu. © The Author 2016. Published by Oxford University Press.

Local CD-ROM in interaction with HTML documents over the Internet.

PubMed

Mattheos, N; Nattestad, A; Attström, R

2000-08-01

The internet and computer assisted learning have enhanced the possibilities of providing quality distance learning in dentistry. The use of multimedia material is an essential part of such distance learning courses. However the Internet technology available has limitations regarding transmission of large multimedia files. Therefore especially when addressing undergraduate students or geographically isolated professionals, large download times make distance learning unattractive. This problem was technically solved in a distance learning course for undergraduate students from all over Europe. The present communication describes a method to bypass the problem of transmitting large multimedia files by the use of a specially designed CD-ROM. This CD-ROM was run locally on the students' PC interacting with HTML documents sent over the Internet.

Monte Carlo generator ELRADGEN 2.0 for simulation of radiative events in elastic ep-scattering of polarized particles

NASA Astrophysics Data System (ADS)

Akushevich, I.; Filoti, O. F.; Ilyichev, A.; Shumeiko, N.

2012-07-01

The structure and algorithms of the Monte Carlo generator ELRADGEN 2.0 designed to simulate radiative events in polarized ep-scattering are presented. The full set of analytical expressions for the QED radiative corrections is presented and discussed in detail. Algorithmic improvements implemented to provide faster simulation of hard real photon events are described. Numerical tests show high quality of generation of photonic variables and radiatively corrected cross section. The comparison of the elastic radiative tail simulated within the kinematical conditions of the BLAST experiment at MIT BATES shows a good agreement with experimental data. Catalogue identifier: AELO_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AELO_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC license, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 1299 No. of bytes in distributed program, including test data, etc.: 11 348 Distribution format: tar.gz Programming language: FORTRAN 77 Computer: All Operating system: Any RAM: 1 MB Classification: 11.2, 11.4 Nature of problem: Simulation of radiative events in polarized ep-scattering. Solution method: Monte Carlo simulation according to the distributions of the real photon kinematic variables that are calculated by the covariant method of QED radiative correction estimation. The approach provides rather fast and accurate generation. Running time: The simulation of 108 radiative events for itest:=1 takes up to 52 seconds on Pentium(R) Dual-Core 2.00 GHz processor.

Youths Teaching Youths: Learning to Code as an Example of Interest-Driven Learning

ERIC Educational Resources Information Center

Vickery, Jacqueline

2014-01-01

This column examines a case study focusing on web design as an example of interest-driven learning and the acquisition of (digital media) literacies. A summer workshop was offered at a working-class public library, led by a self-taught seventeen year old girl. Nine students (ages 8-16) learned basic HTML and CSS and designed their own websites in…

Survey of basic medical researchers on the awareness of animal experimental designs and reporting standards in China.

PubMed

Ma, Bin; Xu, Jia-Ke; Wu, Wen-Jing; Liu, Hong-Yan; Kou, Cheng-Kun; Liu, Na; Zhao, Lulu

2017-01-01

To investigate the awareness and use of the Systematic Review Center for Laboratory Animal Experimentation's (SYRCLE) risk-of-bias tool, the Animal Research: Reporting of In Vivo Experiments (ARRIVE) reporting guidelines, and Gold Standard Publication Checklist (GSPC) in China in basic medical researchers of animal experimental studies. A national questionnaire-based survey targeting basic medical researchers was carried in China to investigate the basic information and awareness of SYRCLE's risk of bias tool, ARRIVE guidelines, GSPC, and animal experimental bias risk control factors. The EpiData3.1 software was used for data entry, and Microsoft Excel 2013 was used for statistical analysis in this study. The number of cases (n) and percentage (%) of classified information were statistically described, and the comparison between groups (i.e., current students vs. research staff) was performed using chi-square test. A total of 298 questionnaires were distributed, and 272 responses were received, which included 266 valid questionnaires (from 118 current students and 148 research staff). Among the 266 survey participants, only 15.8% was aware of the SYRCLE's risk of bias tool, with significant difference between the two groups (P = 0.003), and the awareness rates of ARRIVE guidelines and GSPC were only 9.4% and 9.0%, respectively; 58.6% survey participants believed that the reports of animal experimental studies in Chinese literature were inadequate, with significant difference between the two groups (P = 0.004). In addition, only approximately 1/3 of the survey participants had read systematic reviews and meta-analysis reports of animal experimental studies; only 16/266 (6.0%) had carried out/participated in and 11/266 (4.1%) had published systematic reviews/meta-analysis of animal experimental studies. The awareness and use rates of SYRCLE's risk-of-bias tool, the ARRIVE guidelines, and the GSPC were low among Chinese basic medical researchers. Therefore, specific measures are necessary to promote and popularize these standards and specifications and to introduce these standards into guidelines of Chinese domestic journals as soon as possible to raise awareness and increase use rates of researchers and journal editors, thereby improving the quality of animal experimental methods and reports.

Lateral Coordination of Interdependent U.S. Army Information Tasks

DTIC Science & Technology

2008-12-01

83 Galbraith, Designing Complex Organizations, p. 2. 84 Richard M. Burton and Børge Obel, Strategic Organizational Diagnosis and...professionalwriting/volumes/volume4 /july_2006/7_06_3.html (accessed 6/17/2008). Burton, Richard M. and Børge Obel. Strategic Organizational Diagnosis and

OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes in asexual populations.

PubMed

Diaz-Uriarte, Ramon

2017-06-15

OncoSimulR implements forward-time genetic simulations of biallelic loci in asexual populations with special focus on cancer progression. Fitness can be defined as an arbitrary function of genetic interactions between multiple genes or modules of genes, including epistasis, restrictions in the order of accumulation of mutations, and order effects. Mutation rates can differ among genes, and can be affected by (anti)mutator genes. Also available are sampling from simulations (including single-cell sampling), plotting the genealogical relationships of clones and generating and plotting fitness landscapes. Implemented in R and C ++, freely available from BioConductor for Linux, Mac and Windows under the GNU GPL license. Version 2.5.9 or higher available from: http://www.bioconductor.org/packages/devel/bioc/html/OncoSimulR.html . GitHub repository at: https://github.com/rdiaz02/OncoSimul. ramon.diaz@iib.uam.es. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Gateway Architecture: A Major "Flexible Path" Step to the Moon and Mars After the International Space Station?

NASA Technical Reports Server (NTRS)

Thronson, Harley; Talay, Ted

2010-01-01

With NASA's commitment to the International Space Station (ISS) now all but certain for at least through the coming decade, serious consideration may be given to extended US in-space operations in the 2020s, when presumably the ISS will exceed its sell by date. Indeed, both ESA and Roscosmos, in addition to their unambiguous current commitment to ISS, have published early concept studies for extended post-ISS habitation (e.g., http://www.esa.int/esaHS/index.html, http://www.russianspaceweb.com/opsek.html and references therein). In the US, engineers and scientists have for a decade been working both within and outside NASA to assess one consistent candidate for long-term post-ISS habitation and operations, although interrupted by changing priorities for human space flight, Congressional direction, and constrained budgets. The evolving work of these groups is described here, which may have renewed relevance with the recent completion of a major review of the nation s human space flight program.

DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis.

PubMed

Yu, Guangchuang; Wang, Li-Gen; Yan, Guang-Rong; He, Qing-Yu

2015-02-15

Disease ontology (DO) annotates human genes in the context of disease. DO is important annotation in translating molecular findings from high-throughput data to clinical relevance. DOSE is an R package providing semantic similarity computations among DO terms and genes which allows biologists to explore the similarities of diseases and of gene functions in disease perspective. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented to support discovering disease associations of high-throughput biological data. This allows biologists to verify disease relevance in a biological experiment and identify unexpected disease associations. Comparison among gene clusters is also supported. DOSE is released under Artistic-2.0 License. The source code and documents are freely available through Bioconductor (http://www.bioconductor.org/packages/release/bioc/html/DOSE.html). Supplementary data are available at Bioinformatics online. gcyu@connect.hku.hk or tqyhe@jnu.edu.cn. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Different Types of Sounds and Their Relationship With the Electrocardiographic Signals and the Cardiovascular System – Review

PubMed Central

Idrobo-Ávila, Ennio H.; Loaiza-Correa, Humberto; van Noorden, Leon; Muñoz-Bolaños, Flavio G.; Vargas-Cañas, Rubiel

2018-01-01

Background: For some time now, the effects of sound, noise, and music on the human body have been studied. However, despite research done through time, it is still not completely clear what influence, interaction, and effects sounds have on human body. That is why it is necessary to conduct new research on this topic. Thus, in this paper, a systematic review is undertaken in order to integrate research related to several types of sound, both pleasant and unpleasant, specifically noise and music. In addition, it includes as much research as possible to give stakeholders a more general vision about relevant elements regarding methodologies, study subjects, stimulus, analysis, and experimental designs in general. This study has been conducted in order to make a genuine contribution to this area and to perhaps to raise the quality of future research about sound and its effects over ECG signals. Methods: This review was carried out by independent researchers, through three search equations, in four different databases, including: engineering, medicine, and psychology. Inclusion and exclusion criteria were applied and studies published between 1999 and 2017 were considered. The selected documents were read and analyzed independently by each group of researchers and subsequently conclusions were established between all of them. Results: Despite the differences between the outcomes of selected studies, some common factors were found among them. Thus, in noise studies where both BP and HR increased or tended to increase, it was noted that HRV (HF and LF/HF) changes with both sound and noise stimuli, whereas GSR changes with sound and musical stimuli. Furthermore, LF also showed changes with exposure to noise. Conclusion: In many cases, samples displayed a limitation in experimental design, and in diverse studies, there was a lack of a control group. There was a lot of variability in the presented stimuli providing a wide overview of the effects they could produce in humans. In the listening sessions, there were numerous examples of good practice in experimental design, such as the use of headphones and comfortable positions for study subjects, while the listening sessions lasted 20 min in most of the studies. PMID:29872400

Different Types of Sounds and Their Relationship With the Electrocardiographic Signals and the Cardiovascular System - Review.

PubMed

Idrobo-Ávila, Ennio H; Loaiza-Correa, Humberto; van Noorden, Leon; Muñoz-Bolaños, Flavio G; Vargas-Cañas, Rubiel

2018-01-01

Background: For some time now, the effects of sound, noise, and music on the human body have been studied. However, despite research done through time, it is still not completely clear what influence, interaction, and effects sounds have on human body. That is why it is necessary to conduct new research on this topic. Thus, in this paper, a systematic review is undertaken in order to integrate research related to several types of sound, both pleasant and unpleasant, specifically noise and music. In addition, it includes as much research as possible to give stakeholders a more general vision about relevant elements regarding methodologies, study subjects, stimulus, analysis, and experimental designs in general. This study has been conducted in order to make a genuine contribution to this area and to perhaps to raise the quality of future research about sound and its effects over ECG signals. Methods: This review was carried out by independent researchers, through three search equations, in four different databases, including: engineering, medicine, and psychology. Inclusion and exclusion criteria were applied and studies published between 1999 and 2017 were considered. The selected documents were read and analyzed independently by each group of researchers and subsequently conclusions were established between all of them. Results: Despite the differences between the outcomes of selected studies, some common factors were found among them. Thus, in noise studies where both BP and HR increased or tended to increase, it was noted that HRV (HF and LF/HF) changes with both sound and noise stimuli, whereas GSR changes with sound and musical stimuli. Furthermore, LF also showed changes with exposure to noise. Conclusion: In many cases, samples displayed a limitation in experimental design, and in diverse studies, there was a lack of a control group. There was a lot of variability in the presented stimuli providing a wide overview of the effects they could produce in humans. In the listening sessions, there were numerous examples of good practice in experimental design, such as the use of headphones and comfortable positions for study subjects, while the listening sessions lasted 20 min in most of the studies.

Prevalence of Recommendations Made Within Dental Research Articles Using Uncontrolled Intervention or Observational Study Designs.

PubMed

Wilson, M K; Chestnutt, I G

2016-03-01

Evidence to inform clinical practice is reliant on research carried out using appropriate study design. The objectives of this work were to (i) identify the prevalence of articles reporting on human studies using uncontrolled intervention or observational research designs published in peer-reviewed dental journals and (ii) determine the nature of recommendations made by these articles. Six peer-reviewed dental journals were selected. Issues published in January to June 2013 were examined and the types of articles published categorized. Following pre-defined inclusion/exclusion criteria, human studies classified as using uncontrolled intervention or observational research designs were subject to detailed review by two independent investigators, to examine if they presented clinical, policy or research recommendations and if these recommendations were supported by the data presented. 52.9% (n = 156) of studies published during the time period met the inclusion criteria. Studies with uncontrolled intervention or observational research designs comprised a larger proportion of the primary research studies published in the journals with lower impact factors (73.3%; n = 107) compared to the high impact journals (38.9%; n = 49). Analysis showed that 60.9% (n = 95) of the included studies made recommendations for clinical practice/dental policy. In 28.2% (n = 44) of studies, the clinical/policy recommendations made were judged to not be fully supported by the data presented. Many studies published in the current dental literature, which are not considered to produce strong evidence, make recommendations for clinical practice or policy. There were some cases when the recommendations were not fully supported by the data presented. Copyright © 2016 Elsevier Inc. All rights reserved.

Drug Use Normalization: A Systematic and Critical Mixed-Methods Review.

PubMed

Sznitman, Sharon R; Taubman, Danielle S

2016-09-01

Drug use normalization, which is a process whereby drug use becomes less stigmatized and more accepted as normative behavior, provides a conceptual framework for understanding contemporary drug issues and changes in drug use trends. Through a mixed-methods systematic review of the normalization literature, this article seeks to (a) critically examine how the normalization framework has been applied in empirical research and (b) make recommendations for future research in this area. Twenty quantitative, 26 qualitative, and 4 mixed-methods studies were identified through five electronic databases and reference lists of published studies. Studies were assessed for relevance, study characteristics, quality, and aspects of normalization examined. None of the studies applied the most rigorous research design (experiments) or examined all of the originally proposed normalization dimensions. The most commonly assessed dimension of drug use normalization was "experimentation." In addition to the original dimensions, the review identified the following new normalization dimensions in the literature: (a) breakdown of demographic boundaries and other risk factors in relation to drug use; (b) de-normalization; (c) drug use as a means to achieve normal goals; and (d) two broad forms of micro-politics associated with managing the stigma of illicit drug use: assimilative and transformational normalization. Further development in normalization theory and methodology promises to provide researchers with a novel framework for improving our understanding of drug use in contemporary society. Specifically, quasi-experimental designs that are currently being made feasible by swift changes in cannabis policy provide researchers with new and improved opportunities to examine normalization processes.

Monitoring of small laboratory animal experiments by a designated web-based database.

PubMed

Frenzel, T; Grohmann, C; Schumacher, U; Krüll, A

2015-10-01

Multiple-parametric small animal experiments require, by their very nature, a sufficient number of animals which may need to be large to obtain statistically significant results.(1) For this reason database-related systems are required to collect the experimental data as well as to support the later (re-) analysis of the information gained during the experiments. In particular, the monitoring of animal welfare is simplified by the inclusion of warning signals (for instance, loss in body weight >20%). Digital patient charts have been developed for human patients but are usually not able to fulfill the specific needs of animal experimentation. To address this problem a unique web-based monitoring system using standard MySQL, PHP, and nginx has been created. PHP was used to create the HTML-based user interface and outputs in a variety of proprietary file formats, namely portable document format (PDF) or spreadsheet files. This article demonstrates its fundamental features and the easy and secure access it offers to the data from any place using a web browser. This information will help other researchers create their own individual databases in a similar way. The use of QR-codes plays an important role for stress-free use of the database. We demonstrate a way to easily identify all animals and samples and data collected during the experiments. Specific ways to record animal irradiations and chemotherapy applications are shown. This new analysis tool allows the effective and detailed analysis of huge amounts of data collected through small animal experiments. It supports proper statistical evaluation of the data and provides excellent retrievable data storage. © The Author(s) 2015.

Parametric Design and Mechanical Analysis of Beams based on SINOVATION

NASA Astrophysics Data System (ADS)

Xu, Z. G.; Shen, W. D.; Yang, D. Y.; Liu, W. M.

2017-07-01

In engineering practice, engineer needs to carry out complicated calculation when the loads on the beam are complex. The processes of analysis and calculation take a lot of time and the results are unreliable. So VS2005 and ADK are used to develop a software for beams design based on the 3D CAD software SINOVATION with C ++ programming language. The software can realize the mechanical analysis and parameterized design of various types of beams and output the report of design in HTML format. Efficiency and reliability of design of beams are improved.

A python module to normalize microarray data by the quantile adjustment method.

PubMed

Baber, Ibrahima; Tamby, Jean Philippe; Manoukis, Nicholas C; Sangaré, Djibril; Doumbia, Seydou; Traoré, Sekou F; Maiga, Mohamed S; Dembélé, Doulaye

2011-06-01

Microarray technology is widely used for gene expression research targeting the development of new drug treatments. In the case of a two-color microarray, the process starts with labeling DNA samples with fluorescent markers (cyanine 635 or Cy5 and cyanine 532 or Cy3), then mixing and hybridizing them on a chemically treated glass printed with probes, or fragments of genes. The level of hybridization between a strand of labeled DNA and a probe present on the array is measured by scanning the fluorescence of spots in order to quantify the expression based on the quality and number of pixels for each spot. The intensity data generated from these scans are subject to errors due to differences in fluorescence efficiency between Cy5 and Cy3, as well as variation in human handling and quality of the sample. Consequently, data have to be normalized to correct for variations which are not related to the biological phenomena under investigation. Among many existing normalization procedures, we have implemented the quantile adjustment method using the python computer language, and produced a module which can be run via an HTML dynamic form. This module is composed of different functions for data files reading, intensity and ratio computations and visualization. The current version of the HTML form allows the user to visualize the data before and after normalization. It also gives the option to subtract background noise before normalizing the data. The output results of this module are in agreement with the results of other normalization tools. Published by Elsevier B.V.

Skin Microbiome Surveys Are Strongly Influenced by Experimental Design.

PubMed

Meisel, Jacquelyn S; Hannigan, Geoffrey D; Tyldsley, Amanda S; SanMiguel, Adam J; Hodkinson, Brendan P; Zheng, Qi; Grice, Elizabeth A

2016-05-01

Culture-independent studies to characterize skin microbiota are increasingly common, due in part to affordable and accessible sequencing and analysis platforms. Compared to culture-based techniques, DNA sequencing of the bacterial 16S ribosomal RNA (rRNA) gene or whole metagenome shotgun (WMS) sequencing provides more precise microbial community characterizations. Most widely used protocols were developed to characterize microbiota of other habitats (i.e., gastrointestinal) and have not been systematically compared for their utility in skin microbiome surveys. Here we establish a resource for the cutaneous research community to guide experimental design in characterizing skin microbiota. We compare two widely sequenced regions of the 16S rRNA gene to WMS sequencing for recapitulating skin microbiome community composition, diversity, and genetic functional enrichment. We show that WMS sequencing most accurately recapitulates microbial communities, but sequencing of hypervariable regions 1-3 of the 16S rRNA gene provides highly similar results. Sequencing of hypervariable region 4 poorly captures skin commensal microbiota, especially Propionibacterium. WMS sequencing, which is resource and cost intensive, provides evidence of a community's functional potential; however, metagenome predictions based on 16S rRNA sequence tags closely approximate WMS genetic functional profiles. This study highlights the importance of experimental design for downstream results in skin microbiome surveys. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Benefits and Pitfalls of Using HTML as a CD-ROM Development Tool.

ERIC Educational Resources Information Center

Misanchuk, Earl R.; Schwier, Richard A.

The hypertext markup language (HTML) used to develop pages for the world wide web also has potential for use in creating some types of multimedia instruction destined for CD-ROMs. After providing a brief overview of HTML, this document presents pros and cons relevant to CD-ROM production. HTML can offer compatibility to both Windows and Macintosh…

The EnzymeTracker: an open-source laboratory information management system for sample tracking.

PubMed

Triplet, Thomas; Butler, Gregory

2012-01-26

In many laboratories, researchers store experimental data on their own workstation using spreadsheets. However, this approach poses a number of problems, ranging from sharing issues to inefficient data-mining. Standard spreadsheets are also error-prone, as data do not undergo any validation process. To overcome spreadsheets inherent limitations, a number of proprietary systems have been developed, which laboratories need to pay expensive license fees for. Those costs are usually prohibitive for most laboratories and prevent scientists from benefiting from more sophisticated data management systems. In this paper, we propose the EnzymeTracker, a web-based laboratory information management system for sample tracking, as an open-source and flexible alternative that aims at facilitating entry, mining and sharing of experimental biological data. The EnzymeTracker features online spreadsheets and tools for monitoring numerous experiments conducted by several collaborators to identify and characterize samples. It also provides libraries of shared data such as protocols, and administration tools for data access control using OpenID and user/team management. Our system relies on a database management system for efficient data indexing and management and a user-friendly AJAX interface that can be accessed over the Internet. The EnzymeTracker facilitates data entry by dynamically suggesting entries and providing smart data-mining tools to effectively retrieve data. Our system features a number of tools to visualize and annotate experimental data, and export highly customizable reports. It also supports QR matrix barcoding to facilitate sample tracking. The EnzymeTracker was designed to be easy to use and offers many benefits over spreadsheets, thus presenting the characteristics required to facilitate acceptance by the scientific community. It has been successfully used for 20 months on a daily basis by over 50 scientists. The EnzymeTracker is freely available online at http://cubique.fungalgenomics.ca/enzymedb/index.html under the GNU GPLv3 license.

The EnzymeTracker: an open-source laboratory information management system for sample tracking

PubMed Central

2012-01-01

Background In many laboratories, researchers store experimental data on their own workstation using spreadsheets. However, this approach poses a number of problems, ranging from sharing issues to inefficient data-mining. Standard spreadsheets are also error-prone, as data do not undergo any validation process. To overcome spreadsheets inherent limitations, a number of proprietary systems have been developed, which laboratories need to pay expensive license fees for. Those costs are usually prohibitive for most laboratories and prevent scientists from benefiting from more sophisticated data management systems. Results In this paper, we propose the EnzymeTracker, a web-based laboratory information management system for sample tracking, as an open-source and flexible alternative that aims at facilitating entry, mining and sharing of experimental biological data. The EnzymeTracker features online spreadsheets and tools for monitoring numerous experiments conducted by several collaborators to identify and characterize samples. It also provides libraries of shared data such as protocols, and administration tools for data access control using OpenID and user/team management. Our system relies on a database management system for efficient data indexing and management and a user-friendly AJAX interface that can be accessed over the Internet. The EnzymeTracker facilitates data entry by dynamically suggesting entries and providing smart data-mining tools to effectively retrieve data. Our system features a number of tools to visualize and annotate experimental data, and export highly customizable reports. It also supports QR matrix barcoding to facilitate sample tracking. Conclusions The EnzymeTracker was designed to be easy to use and offers many benefits over spreadsheets, thus presenting the characteristics required to facilitate acceptance by the scientific community. It has been successfully used for 20 months on a daily basis by over 50 scientists. The EnzymeTracker is freely available online at http://cubique.fungalgenomics.ca/enzymedb/index.html under the GNU GPLv3 license. PMID:22280360

77 FR 61375 - Endangered and Threatened Wildlife and Plants; 12-Month Finding on Petitions To List the Mexican...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-09

... 15915). We published a final rule, ``Establishment of a Nonessential Experimental Population of the... Mexican Wolf Experimental Population Area in central Arizona and New Mexico and designated the reintroduced population as a nonessential experimental population under section 10(j) of the Act. In March of...

Work Program. Fiscal Year 1972 for The Department of the Army. Research and Development in Training, Motivation, and Leadership

DTIC Science & Technology

1971-07-01

itself. IlumRRO assistance was requested by the Infantry School both for design of experimental tests and for analysis and interpretation of the data from...of Research. To develop an experimental Army literacy training program designed to provide a level of functional literacy appropriate to present...assigned under the provisions of a long- range program (up to two years in duration) designed by tlumRRO. Specially designed experimental

Fast access to the CMS detector condition data employing HTML5 technologies

NASA Astrophysics Data System (ADS)

Pierro, Giuseppe Antonio; Cavallari, Francesca; Di Guida, Salvatore; Innocente, Vincenzo

2011-12-01

This paper focuses on using HTML version 5 (HTML5) for accessing condition data for the CMS experiment, evaluating the benefits and risks posed by the use of this technology. According to the authors of HTML5, this technology attempts to solve issues found in previous iterations of HTML and addresses the needs of web applications, an area previously not adequately covered by HTML. We demonstrate that employing HTML5 brings important benefits in terms of access performance to the CMS condition data. The combined use of web storage and web sockets allows increasing the performance and reducing the costs in term of computation power, memory usage and network bandwidth for client and server. Above all, the web workers allow creating different scripts that can be executed using multi-thread mode, exploiting multi-core microprocessors. Web workers have been employed in order to substantially decrease the web page rendering time to display the condition data stored in the CMS condition database.

Launching an Academic Career: On the Cutting Edge Resources for Geoscience Graduate Students, Post-doctoral Fellows, and Early Career Faculty

NASA Astrophysics Data System (ADS)

Richardson, R. M.; Ormand, C. J.; MacDonald, H.; Dunbar, R. W.; Allen-King, R. M.; Manduca, C. A.

2010-12-01

Launching an academic career presents a number of challenges. A recent article in the Chronicle of Higher Education depicts academia as an “ivory sweatshop,” citing rising standards for tenure. Most graduate programs provide minimal training for life beyond graduate school. The professional development program “On the Cutting Edge” fills this gap by providing workshops and web resources on academic careers for graduate students, postdoctoral fellows, and early career faculty. These workshops and web resources address a wide range of topics related to teaching, research, and managing one’s career, tailored for each group. The Preparing for an Academic Career in the Geosciences workshop to help graduate students and postdoctoral fellows make the transition into an academic career has been offered annually since 2003. It provides a panel on academic careers in different institutional settings, sessions on research on learning, various teaching strategies, design of effective teaching activities, moving research forward to new settings, effective teaching and research statements, the job search process, negotiation, and presenting oneself to others. Complementary online resources (http://serc.carleton.edu/NAGTWorkshops/careerprep/index.html) focus on these topics. The workshops and web resources offer guidance for each step of the job search process, for developing and teaching one’s own courses, and for making the transition from being a research student to being in charge of a research program. Online resources also include case studies of successful dual career couples, documenting their job search strategies. A four-day workshop for Early Career Geoscience Faculty: Teaching, Research, and Managing Your Career, offered annually since 1999, provides sessions on teaching strategies, course design, developing a strategic plan for research, supervising student researchers, navigating departmental and institutional politics, preparing for tenure, time and task management, and more. Complementary online resources (http://serc.carleton.edu/NAGTWorkshops/earlycareer/index.html) also address these topics. The workshops and web resources offer guidance for becoming an efficient and effective teacher, for developing a thriving research program, for staying on track for tenure, and for managing a balance of one’s personal and professional lives. Online resources feature a collection of successful grant proposals, profiles of successful researchers and their collaborations with their students, and profiles of geoscience faculty from a variety of institutions describing how they achieve balance in their lives. Participants in both workshops overwhelmingly report that the workshop met or exceeded their expectations, that they feel much better prepared to move forward in their careers as a result of the workshops, and that they will use the website in the future. The two sets of web pages receive more than 7,000 visitors each month.

See Also:Mechanics of Cohesive-frictional MaterialsCopyright © 2004 John Wiley & Sons, Ltd.Get Sample Copy