Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis.

PubMed

Yang, Chao; He, Zengyou; Yu, Weichuan

2009-01-06

In mass spectrometry (MS) based proteomic data analysis, peak detection is an essential step for subsequent analysis. Recently, there has been significant progress in the development of various peak detection algorithms. However, neither a comprehensive survey nor an experimental comparison of these algorithms is yet available. The main objective of this paper is to provide such a survey and to compare the performance of single spectrum based peak detection methods. In general, we can decompose a peak detection procedure into three consequent parts: smoothing, baseline correction and peak finding. We first categorize existing peak detection algorithms according to the techniques used in different phases. Such a categorization reveals the differences and similarities among existing peak detection algorithms. Then, we choose five typical peak detection algorithms to conduct a comprehensive experimental study using both simulation data and real MALDI MS data. The results of comparison show that the continuous wavelet-based algorithm provides the best average performance.

Analytical and Experimental Vibration Analysis of a Faulty Gear System.

DTIC Science & Technology

1994-10-01

Wigner - Ville Distribution ( WVD ) was used to give a comprehensive comparison of the predicted and...experimental results. The WVD method applied to the experimental results were also compared to other fault detection techniques to verify the WVD’s ability to...of the damaged test gear and the predicted vibration from the model with simulated gear tooth pitting damage. Results also verified that the WVD method can successfully detect and locate gear tooth wear and pitting damage.

Study of Thermodynamic Vent and Screen Baffle Integration for Orbital Storage and Transfer of Liquid Hydrogen

NASA Technical Reports Server (NTRS)

Cady, E. C.

1973-01-01

A comprehensive analytical and experimental program was performed to determine the feasibility of integrating an internal thermodynamic vent system and a full wall-screen liner for the orbital storage and transfer of liquid hydrogen (LH2). Ten screens were selected from a comprehensive screen survey. The experimental study determined the screen bubble point, flow-through pressure loss, and pressure loss along rectangular channels lined with screen on one side, for the 10 screens using LH2 saturated at 34.5 N/cm2 (50 psia). The correlated experimental data were used in an analysis to determine the optimum system characteristics in terms of minimum weight for 6 tanks ranging from 141.6 m3 (5,000 ft3) to 1.416 m3 (50 ft3) for orbital storage times of 30 and 300 days.

Modelling and simulation of complex sociotechnical systems: envisioning and analysing work environments

PubMed Central

Hettinger, Lawrence J.; Kirlik, Alex; Goh, Yang Miang; Buckle, Peter

2015-01-01

Accurate comprehension and analysis of complex sociotechnical systems is a daunting task. Empirically examining, or simply envisioning the structure and behaviour of such systems challenges traditional analytic and experimental approaches as well as our everyday cognitive capabilities. Computer-based models and simulations afford potentially useful means of accomplishing sociotechnical system design and analysis objectives. From a design perspective, they can provide a basis for a common mental model among stakeholders, thereby facilitating accurate comprehension of factors impacting system performance and potential effects of system modifications. From a research perspective, models and simulations afford the means to study aspects of sociotechnical system design and operation, including the potential impact of modifications to structural and dynamic system properties, in ways not feasible with traditional experimental approaches. This paper describes issues involved in the design and use of such models and simulations and describes a proposed path forward to their development and implementation. Practitioner Summary: The size and complexity of real-world sociotechnical systems can present significant barriers to their design, comprehension and empirical analysis. This article describes the potential advantages of computer-based models and simulations for understanding factors that impact sociotechnical system design and operation, particularly with respect to process and occupational safety. PMID:25761227

The Effects of ABRACADABRA on Reading Outcomes: A Meta-Analysis of Applied Field Research

ERIC Educational Resources Information Center

Abrami, Philip; Borohkovski, Eugene; Lysenko, Larysa

2015-01-01

This meta-analysis summarizes research on the effects of a comprehensive, interactive web-based software (AXXX) on the development of reading competencies among kindergarteners and elementary students. Findings from seven randomized control trials and quasi-experimental studies undertaken in a variety of contexts across Canada, Australia and Kenya…

Expanding the Scope of Organizational Behavior Management: Relational Frame Theory and the Experimental Analysis of Complex Human Behavior

ERIC Educational Resources Information Center

Hayes, Steven C.; Bunting, Kara; Herbst, Scott; Bond, Frank W.; Barnes-Holmes, Dermot

2006-01-01

Behavior analysis in general and applied behavior analysis in particular requires a well developed, empirically supported, and useful approach to human language and cognition in order to fulfill its mission of providing a relatively adequate comprehensive account of complex human behavior. This article introduces a series of articles in which the…

Advanced technology airfoil research, volume 2. [conferences

NASA Technical Reports Server (NTRS)

1979-01-01

A comprehensive review of airfoil research is presented. The major thrust of the research is in three areas: development of computational aerodynamic codes for airfoil analysis and design, development of experimental facilities and test techniques, and all types of airfoil applications.

An Analysis of Listening Skill Development Using the Midwest Program on Airborne Television Instruction.

ERIC Educational Resources Information Center

Purdom, Boyd Andra

One experimental and three varied control groups (a total of 340 fourth graders) were used to investigate the effectiveness of a listening skill developmental unit produced by the Midwest Program on Airborne Television Instruction (MPATI). Results from an analysis of the effectiveness of the unit in developing skills of listening comprehension,…

A Pilot Study of Biomedical Text Comprehension using an Attention-Based Deep Neural Reader: Design and Experimental Analysis

PubMed Central

Lee, Kyubum; Kim, Byounggun; Jeon, Minji; Kim, Jihye; Tan, Aik Choon

2018-01-01

Background With the development of artificial intelligence (AI) technology centered on deep-learning, the computer has evolved to a point where it can read a given text and answer a question based on the context of the text. Such a specific task is known as the task of machine comprehension. Existing machine comprehension tasks mostly use datasets of general texts, such as news articles or elementary school-level storybooks. However, no attempt has been made to determine whether an up-to-date deep learning-based machine comprehension model can also process scientific literature containing expert-level knowledge, especially in the biomedical domain. Objective This study aims to investigate whether a machine comprehension model can process biomedical articles as well as general texts. Since there is no dataset for the biomedical literature comprehension task, our work includes generating a large-scale question answering dataset using PubMed and manually evaluating the generated dataset. Methods We present an attention-based deep neural model tailored to the biomedical domain. To further enhance the performance of our model, we used a pretrained word vector and biomedical entity type embedding. We also developed an ensemble method of combining the results of several independent models to reduce the variance of the answers from the models. Results The experimental results showed that our proposed deep neural network model outperformed the baseline model by more than 7% on the new dataset. We also evaluated human performance on the new dataset. The human evaluation result showed that our deep neural model outperformed humans in comprehension by 22% on average. Conclusions In this work, we introduced a new task of machine comprehension in the biomedical domain using a deep neural model. Since there was no large-scale dataset for training deep neural models in the biomedical domain, we created the new cloze-style datasets Biomedical Knowledge Comprehension Title (BMKC_T) and Biomedical Knowledge Comprehension Last Sentence (BMKC_LS) (together referred to as BioMedical Knowledge Comprehension) using the PubMed corpus. The experimental results showed that the performance of our model is much higher than that of humans. We observed that our model performed consistently better regardless of the degree of difficulty of a text, whereas humans have difficulty when performing biomedical literature comprehension tasks that require expert level knowledge. PMID:29305341

Versatile Analysis of Single-Molecule Tracking Data by Comprehensive Testing against Monte Carlo Simulations

PubMed Central

Wieser, Stefan; Axmann, Markus; Schütz, Gerhard J.

2008-01-01

We propose here an approach for the analysis of single-molecule trajectories which is based on a comprehensive comparison of an experimental data set with multiple Monte Carlo simulations of the diffusion process. It allows quantitative data analysis, particularly whenever analytical treatment of a model is infeasible. Simulations are performed on a discrete parameter space and compared with the experimental results by a nonparametric statistical test. The method provides a matrix of p-values that assess the probability for having observed the experimental data at each setting of the model parameters. We show the testing approach for three typical situations observed in the cellular plasma membrane: i), free Brownian motion of the tracer, ii), hop diffusion of the tracer in a periodic meshwork of squares, and iii), transient binding of the tracer to slowly diffusing structures. By plotting the p-value as a function of the model parameters, one can easily identify the most consistent parameter settings but also recover mutual dependencies and ambiguities which are difficult to determine by standard fitting routines. Finally, we used the test to reanalyze previous data obtained on the diffusion of the glycosylphosphatidylinositol-protein CD59 in the plasma membrane of the human T24 cell line. PMID:18805933

Computational Fluid Dynamics Uncertainty Analysis Applied to Heat Transfer over a Flat Plate

NASA Technical Reports Server (NTRS)

Groves, Curtis Edward; Ilie, Marcel; Schallhorn, Paul A.

2013-01-01

There have been few discussions on using Computational Fluid Dynamics (CFD) without experimental validation. Pairing experimental data, uncertainty analysis, and analytical predictions provides a comprehensive approach to verification and is the current state of the art. With pressed budgets, collecting experimental data is rare or non-existent. This paper investigates and proposes a method to perform CFD uncertainty analysis only from computational data. The method uses current CFD uncertainty techniques coupled with the Student-T distribution to predict the heat transfer coefficient over a at plate. The inputs to the CFD model are varied from a specified tolerance or bias error and the difference in the results are used to estimate the uncertainty. The variation in each input is ranked from least to greatest to determine the order of importance. The results are compared to heat transfer correlations and conclusions drawn about the feasibility of using CFD without experimental data. The results provide a tactic to analytically estimate the uncertainty in a CFD model when experimental data is unavailable

Experimental Approaches to Microarray Analysis of Tumor Samples

ERIC Educational Resources Information Center

Furge, Laura Lowe; Winter, Michael B.; Meyers, Jacob I.; Furge, Kyle A.

2008-01-01

Comprehensive measurement of gene expression using high-density nucleic acid arrays (i.e. microarrays) has become an important tool for investigating the molecular differences in clinical and research samples. Consequently, inclusion of discussion in biochemistry, molecular biology, or other appropriate courses of microarray technologies has…

Detailed Measurements of the Aeroelastic Response of a Rigid Coaxial Rotor in Hover

DTIC Science & Technology

2017-08-11

included: hover testing of single and CCR rotors (Year 1), deformation measurement and modal identification of rotor blades in the non -rotating and...the rotor blades, as well as the detailed experimental data were shared with Dr. Rajneesh Singh and Dr. Hao Kang at Vehicle Technology Directorate...VTD), Aberdeen Proving Grounds, MD. In this way, the experimental data could be used to validate US Army comprehensive analysis tools, specifically

Comparative Analysis of Mass Spectral Similarity Measures on Peak Alignment for Comprehensive Two-Dimensional Gas Chromatography Mass Spectrometry

PubMed Central

2013-01-01

Peak alignment is a critical procedure in mass spectrometry-based biomarker discovery in metabolomics. One of peak alignment approaches to comprehensive two-dimensional gas chromatography mass spectrometry (GC×GC-MS) data is peak matching-based alignment. A key to the peak matching-based alignment is the calculation of mass spectral similarity scores. Various mass spectral similarity measures have been developed mainly for compound identification, but the effect of these spectral similarity measures on the performance of peak matching-based alignment still remains unknown. Therefore, we selected five mass spectral similarity measures, cosine correlation, Pearson's correlation, Spearman's correlation, partial correlation, and part correlation, and examined their effects on peak alignment using two sets of experimental GC×GC-MS data. The results show that the spectral similarity measure does not affect the alignment accuracy significantly in analysis of data from less complex samples, while the partial correlation performs much better than other spectral similarity measures when analyzing experimental data acquired from complex biological samples. PMID:24151524

On Design Experiment Teaching in Engineering Quality Cultivation

ERIC Educational Resources Information Center

Chen, Xiao

2008-01-01

Design experiment refers to that designed and conducted by students independently and is surely an important method to cultivate students' comprehensive quality. According to the development and requirements of experimental teaching, this article carries out a study and analysis on the purpose, significance, denotation, connotation and…

A Pilot Study of Biomedical Text Comprehension using an Attention-Based Deep Neural Reader: Design and Experimental Analysis.

PubMed

Kim, Seongsoon; Park, Donghyeon; Choi, Yonghwa; Lee, Kyubum; Kim, Byounggun; Jeon, Minji; Kim, Jihye; Tan, Aik Choon; Kang, Jaewoo

2018-01-05

With the development of artificial intelligence (AI) technology centered on deep-learning, the computer has evolved to a point where it can read a given text and answer a question based on the context of the text. Such a specific task is known as the task of machine comprehension. Existing machine comprehension tasks mostly use datasets of general texts, such as news articles or elementary school-level storybooks. However, no attempt has been made to determine whether an up-to-date deep learning-based machine comprehension model can also process scientific literature containing expert-level knowledge, especially in the biomedical domain. This study aims to investigate whether a machine comprehension model can process biomedical articles as well as general texts. Since there is no dataset for the biomedical literature comprehension task, our work includes generating a large-scale question answering dataset using PubMed and manually evaluating the generated dataset. We present an attention-based deep neural model tailored to the biomedical domain. To further enhance the performance of our model, we used a pretrained word vector and biomedical entity type embedding. We also developed an ensemble method of combining the results of several independent models to reduce the variance of the answers from the models. The experimental results showed that our proposed deep neural network model outperformed the baseline model by more than 7% on the new dataset. We also evaluated human performance on the new dataset. The human evaluation result showed that our deep neural model outperformed humans in comprehension by 22% on average. In this work, we introduced a new task of machine comprehension in the biomedical domain using a deep neural model. Since there was no large-scale dataset for training deep neural models in the biomedical domain, we created the new cloze-style datasets Biomedical Knowledge Comprehension Title (BMKC_T) and Biomedical Knowledge Comprehension Last Sentence (BMKC_LS) (together referred to as BioMedical Knowledge Comprehension) using the PubMed corpus. The experimental results showed that the performance of our model is much higher than that of humans. We observed that our model performed consistently better regardless of the degree of difficulty of a text, whereas humans have difficulty when performing biomedical literature comprehension tasks that require expert level knowledge. ©Seongsoon Kim, Donghyeon Park, Yonghwa Choi, Kyubum Lee, Byounggun Kim, Minji Jeon, Jihye Kim, Aik Choon Tan, Jaewoo Kang. Originally published in JMIR Medical Informatics (http://medinform.jmir.org), 05.01.2018.

Relationship Between Speech Intelligibility and Speech Comprehension in Babble Noise.

PubMed

Fontan, Lionel; Tardieu, Julien; Gaillard, Pascal; Woisard, Virginie; Ruiz, Robert

2015-06-01

The authors investigated the relationship between the intelligibility and comprehension of speech presented in babble noise. Forty participants listened to French imperative sentences (commands for moving objects) in a multitalker babble background for which intensity was experimentally controlled. Participants were instructed to transcribe what they heard and obey the commands in an interactive environment set up for this purpose. The former test provided intelligibility scores and the latter provided comprehension scores. Collected data revealed a globally weak correlation between intelligibility and comprehension scores (r = .35, p < .001). The discrepancy tended to grow as noise level increased. An analysis of standard deviations showed that variability in comprehension scores increased linearly with noise level, whereas higher variability in intelligibility scores was found for moderate noise level conditions. These results support the hypothesis that intelligibility scores are poor predictors of listeners' comprehension in real communication situations. Intelligibility and comprehension scores appear to provide different insights, the first measure being centered on speech signal transfer and the second on communicative performance. Both theoretical and practical implications for the use of speech intelligibility tests as indicators of speakers' performances are discussed.

An interactive web-based application for Comprehensive Analysis of RNAi-screen Data.

PubMed

Dutta, Bhaskar; Azhir, Alaleh; Merino, Louis-Henri; Guo, Yongjian; Revanur, Swetha; Madhamshettiwar, Piyush B; Germain, Ronald N; Smith, Jennifer A; Simpson, Kaylene J; Martin, Scott E; Buehler, Eugen; Beuhler, Eugen; Fraser, Iain D C

2016-02-23

RNAi screens are widely used in functional genomics. Although the screen data can be susceptible to a number of experimental biases, many of these can be corrected by computational analysis. For this purpose, here we have developed a web-based platform for integrated analysis and visualization of RNAi screen data named CARD (for Comprehensive Analysis of RNAi Data; available at https://card.niaid.nih.gov). CARD allows the user to seamlessly carry out sequential steps in a rigorous data analysis workflow, including normalization, off-target analysis, integration of gene expression data, optimal thresholds for hit selection and network/pathway analysis. To evaluate the utility of CARD, we describe analysis of three genome-scale siRNA screens and demonstrate: (i) a significant increase both in selection of subsequently validated hits and in rejection of false positives, (ii) an increased overlap of hits from independent screens of the same biology and (iii) insight to microRNA (miRNA) activity based on siRNA seed enrichment.

An interactive web-based application for Comprehensive Analysis of RNAi-screen Data

PubMed Central

Dutta, Bhaskar; Azhir, Alaleh; Merino, Louis-Henri; Guo, Yongjian; Revanur, Swetha; Madhamshettiwar, Piyush B.; Germain, Ronald N.; Smith, Jennifer A.; Simpson, Kaylene J.; Martin, Scott E.; Beuhler, Eugen; Fraser, Iain D. C.

2016-01-01

RNAi screens are widely used in functional genomics. Although the screen data can be susceptible to a number of experimental biases, many of these can be corrected by computational analysis. For this purpose, here we have developed a web-based platform for integrated analysis and visualization of RNAi screen data named CARD (for Comprehensive Analysis of RNAi Data; available at https://card.niaid.nih.gov). CARD allows the user to seamlessly carry out sequential steps in a rigorous data analysis workflow, including normalization, off-target analysis, integration of gene expression data, optimal thresholds for hit selection and network/pathway analysis. To evaluate the utility of CARD, we describe analysis of three genome-scale siRNA screens and demonstrate: (i) a significant increase both in selection of subsequently validated hits and in rejection of false positives, (ii) an increased overlap of hits from independent screens of the same biology and (iii) insight to microRNA (miRNA) activity based on siRNA seed enrichment. PMID:26902267

Comprehension and retrieval of failure cases in airborne observatories

NASA Technical Reports Server (NTRS)

Alvarado, Sergio J.; Mock, Kenrick J.

1995-01-01

This paper describes research dealing with the computational problem of analyzing and repairing failures of electronic and mechanical systems of telescopes in NASA's airborne observatories, such as KAO (Kuiper Airborne Observatory) and SOFIA (Stratospheric Observatory for Infrared Astronomy). The research has resulted in the development of an experimental system that acquires knowledge of failure analysis from input text, and answers questions regarding failure detection and correction. The system's design builds upon previous work on text comprehension and question answering, including: knowledge representation for conceptual analysis of failure descriptions, strategies for mapping natural language into conceptual representations, case-based reasoning strategies for memory organization and indexing, and strategies for memory search and retrieval. These techniques have been combined into a model that accounts for: (a) how to build a knowledge base of system failures and repair procedures from descriptions that appear in telescope-operators' logbooks and FMEA (failure modes and effects analysis) manuals; and (b) how to use that knowledge base to search and retrieve answers to questions about causes and effects of failures, as well as diagnosis and repair procedures. This model has been implemented in FANSYS (Failure ANalysis SYStem), a prototype text comprehension and question answering program for failure analysis.

Comprehension and retrieval of failure cases in airborne observatories

NASA Astrophysics Data System (ADS)

Alvarado, Sergio J.; Mock, Kenrick J.

1995-05-01

This paper describes research dealing with the computational problem of analyzing and repairing failures of electronic and mechanical systems of telescopes in NASA's airborne observatories, such as KAO (Kuiper Airborne Observatory) and SOFIA (Stratospheric Observatory for Infrared Astronomy). The research has resulted in the development of an experimental system that acquires knowledge of failure analysis from input text, and answers questions regarding failure detection and correction. The system's design builds upon previous work on text comprehension and question answering, including: knowledge representation for conceptual analysis of failure descriptions, strategies for mapping natural language into conceptual representations, case-based reasoning strategies for memory organization and indexing, and strategies for memory search and retrieval. These techniques have been combined into a model that accounts for: (a) how to build a knowledge base of system failures and repair procedures from descriptions that appear in telescope-operators' logbooks and FMEA (failure modes and effects analysis) manuals; and (b) how to use that knowledge base to search and retrieve answers to questions about causes and effects of failures, as well as diagnosis and repair procedures. This model has been implemented in FANSYS (Failure ANalysis SYStem), a prototype text comprehension and question answering program for failure analysis.

Experimental confirmation of long-memory correlations in star-wander data.

PubMed

Zunino, Luciano; Gulich, Damián; Funes, Gustavo; Ziad, Aziz

2014-07-01

In this Letter we have analyzed the temporal correlations of the angle-of-arrival fluctuations of stellar images. Experimentally measured data were carefully examined by implementing multifractal detrended fluctuation analysis. This algorithm is able to discriminate the presence of fractal and multifractal structures in recorded time sequences. We have confirmed that turbulence-degraded stellar wavefronts are compatible with a long-memory correlated monofractal process. This experimental result is quite significant for the accurate comprehension and modeling of the atmospheric turbulence effects on the stellar images. It can also be of great utility within the adaptive optics field.

A Comprehensive Database and Analysis Framework To Incorporate Multiscale Data Types and Enable Integrated Analysis of Bioactive Polyphenols.

PubMed

Ho, Lap; Cheng, Haoxiang; Wang, Jun; Simon, James E; Wu, Qingli; Zhao, Danyue; Carry, Eileen; Ferruzzi, Mario G; Faith, Jeremiah; Valcarcel, Breanna; Hao, Ke; Pasinetti, Giulio M

2018-03-05

The development of a given botanical preparation for eventual clinical application requires extensive, detailed characterizations of the chemical composition, as well as the biological availability, biological activity, and safety profiles of the botanical. These issues are typically addressed using diverse experimental protocols and model systems. Based on this consideration, in this study we established a comprehensive database and analysis framework for the collection, collation, and integrative analysis of diverse, multiscale data sets. Using this framework, we conducted an integrative analysis of heterogeneous data from in vivo and in vitro investigation of a complex bioactive dietary polyphenol-rich preparation (BDPP) and built an integrated network linking data sets generated from this multitude of diverse experimental paradigms. We established a comprehensive database and analysis framework as well as a systematic and logical means to catalogue and collate the diverse array of information gathered, which is securely stored and added to in a standardized manner to enable fast query. We demonstrated the utility of the database in (1) a statistical ranking scheme to prioritize response to treatments and (2) in depth reconstruction of functionality studies. By examination of these data sets, the system allows analytical querying of heterogeneous data and the access of information related to interactions, mechanism of actions, functions, etc., which ultimately provide a global overview of complex biological responses. Collectively, we present an integrative analysis framework that leads to novel insights on the biological activities of a complex botanical such as BDPP that is based on data-driven characterizations of interactions between BDPP-derived phenolic metabolites and their mechanisms of action, as well as synergism and/or potential cancellation of biological functions. Out integrative analytical approach provides novel means for a systematic integrative analysis of heterogeneous data types in the development of complex botanicals such as polyphenols for eventual clinical and translational applications.

The Respective Advantages and Disadvantages of Different Ways of Measuring the Instructional Sensitivity of Reading Comprehension Test Items.

ERIC Educational Resources Information Center

Perkins, Kyle

In this paper four classes of procedures for measuring the instructional sensitivity of reading comprehension test items are reviewed. True experimental designs are not recommended because some of the most important reading comprehension variables do not lend themselves to experimental manipulation. "Ex post facto" factorial designs are…

Attention Process Training-3 to improve reading comprehension in mild aphasia: A single-case experimental design study.

PubMed

Lee, Jaime B; Sohlberg, McKay Moore; Harn, Beth; Horner, Robert; Cherney, Leora R

2018-06-04

People with aphasia frequently present with nonlinguistic deficits, in addition to their compromised language abilities, which may contribute to their problems with reading comprehension. Treatment of attention, working memory and executive control may improve reading comprehension in individuals with aphasia, particularly those with mild reading problems. This single-case experimental design study evaluated the efficacy of Attention Process Training-3, an intervention combining direct attention training and metacognitive facilitation, for improving reading comprehension in individuals with mild aphasia. A multiple baseline design across six participants was used to evaluate treatment effects. The primary outcome measure was a maze reading task. Cognitive measures were administered pre- and post-treatment. Visual inspection of graphed maze reading performance data indicated a basic effect between APT-3 and improved maze reading for three of the six participants. Quantitative analyses, using Tau-U, corroborated findings identified through visual analysis. The overall effect size was significant (Tau = .48, p = .01). Results suggest that APT-3 has the potential to improve reading in individuals with aphasia, but that it may be more efficacious under certain conditions. Treatment and participant variables, including intensity of treatment and metacognitive strategy usage, are discussed as potential influences on participants' responsiveness to APT-3.

Meta-T: TetrisⓇ as an experimental paradigm for cognitive skills research.

PubMed

Lindstedt, John K; Gray, Wayne D

2015-12-01

Studies of human performance in complex tasks using video games are an attractive prospect, but many existing games lack a comprehensive way to modify the game and track performance beyond basic levels of analysis. Meta-T provides experimenters a tool to study behavior in a dynamic task environment with time-stressed decision-making and strong perceptual-motor elements, offering a host of experimental manipulations with a robust and detailed logging system for all user events, system events, and screen objects. Its experimenter-friendly interface provides control over detailed parameters of the task environment without need for programming expertise. Support for eye-tracking and computational cognitive modeling extend the paradigm's scope.

EVALUATION OF VADOSE ZONE AND SORUCE MODULES FOR MULTI-MEDIA, MULTI-PATHWAY, AND MULTI-RECEPTOR RISK ASSESSMENT USING LARGE-SOIL-COLUMN EXPERIMENTAL DATA

EPA Science Inventory

The United States Environmental Protection Agency (EPA) is developing a comprehensive environmental exposure and risk analysis software system for agency-wide application using the methodology of a Multi-media, Multi-pathway, Multi-receptor Risk Assessment (3MRA) model. This sof...

Large size crystalline vs. co-sintered ceramic Yb(3+):YAG disk performance in diode pumped amplifiers.

PubMed

Albach, Daniel; Chanteloup, Jean-Christophe

2015-01-12

A comprehensive experimental benchmarking of Yb(3+):YAG crystalline and co-sintered ceramic disks of similar thickness and doping level is presented in the context of high average power laser amplifier operation. Comparison is performed considering gain, depolarization and wave front deformation quantitative measurements and analysis.

EMOTIONS AND IMAGES IN LANGUAGE--A LEARNING ANALYSIS OF THEIR ACQUISITION AND FUNCTION.

ERIC Educational Resources Information Center

STAATS, ARTHUR W.

THIS ARTICLE PRESENTED THEORETICAL AND EXPERIMENTAL ANALYSES CONCERNING IMPORTANT ASPECTS OF LANGUAGE. IT WAS SUGGESTED THAT A LEARNING THEORY WHICH INEGRATES INSTRUMENTAL AND CLASSICAL CONDITIONING, CUTTING ACROSS THEORETICAL LINES, COULD SERVE AS THE BASIS FOR A COMPREHENSIVE THEORY OF LANGUAGE ACQUISITION AND FUNCTION. THE PAPER ILLUSTRATED THE…

Intelligence and Personality Revisited: An Experimental Approach.

ERIC Educational Resources Information Center

Goh, David S. J.; And Others

The history of attempts by psychologists to determine the contribution of personality to intelligence has not been one of unqualified success. Part of the problem may be in the balance of granularity of analyses on the intelligence side and the personality side. A comprehensive analysis of the contributions of extraversion and neuroticism to…

A Dynamic Calibration Method for Experimental and Analytical Hub Load Comparison

NASA Technical Reports Server (NTRS)

Kreshock, Andrew R.; Thornburgh, Robert P.; Wilbur, Matthew L.

2017-01-01

This paper presents the results from an ongoing effort to produce improved correlation between analytical hub force and moment prediction and those measured during wind-tunnel testing on the Aeroelastic Rotor Experimental System (ARES), a conventional rotor testbed commonly used at the Langley Transonic Dynamics Tunnel (TDT). A frequency-dependent transformation between loads at the rotor hub and outputs of the testbed balance is produced from frequency response functions measured during vibration testing of the system. The resulting transformation is used as a dynamic calibration of the balance to transform hub loads predicted by comprehensive analysis into predicted balance outputs. In addition to detailing the transformation process, this paper also presents a set of wind-tunnel test cases, with comparisons between the measured balance outputs and transformed predictions from the comprehensive analysis code CAMRAD II. The modal response of the testbed is discussed and compared to a detailed finite-element model. Results reveal that the modal response of the testbed exhibits a number of characteristics that make accurate dynamic balance predictions challenging, even with the use of the balance transformation.

Metacognitive reading strategies of children with learning disabilities.

PubMed

Nicolielo-Carrilho, Ana Paola; Hage, Simone Rocha de Vasconcellos

2017-05-15

to check the use of metacognitive reading strategies in children with learning disabilities and determine whether there is a relationship between their use and text comprehension. the study was conducted on 30 children, aged 8 to 12 years, of both genders, divided into experimental group (EG) - 15 children with learning disabilities; and control group (CG) - 15 children without disability. All children were submitted to the Reading Strategies Scale and Prolec text comprehension subtest. The sample was described in mean, median, minimum and maximum values. Comparative analysis was performed between the groups using the Mann-Whitney test. The degree of correlation between variables was verified by Spearman Correlation Analysis. The significance level was set at 5%. across the total scores of the scale, EG performance was lower in all descriptive measures, with a significant difference compared to CG. The EG achieved a performance close to children without difficulties only in global strategies. The correlation between the use of metacognitive strategies and reading comprehension was positive. children with learning disabilities showed deficits in the use of metacognitive reading strategies when compared to children without learning disabilities. The better the performance in reading strategies, the better textual comprehension was and vice versa, suggesting that metacognitive reading skills contribute to reading comprehension.

Analytical and experimental vibration analysis of a faulty gear system

NASA Astrophysics Data System (ADS)

Choy, F. K.; Braun, M. J.; Polyshchuk, V.; Zakrajsek, J. J.; Townsend, D. P.; Handschuh, R. F.

1994-10-01

A comprehensive analytical procedure was developed for predicting faults in gear transmission systems under normal operating conditions. A gear tooth fault model is developed to simulate the effects of pitting and wear on the vibration signal under normal operating conditions. The model uses changes in the gear mesh stiffness to simulate the effects of gear tooth faults. The overall dynamics of the gear transmission system is evaluated by coupling the dynamics of each individual gear-rotor system through gear mesh forces generated between each gear-rotor system and the bearing forces generated between the rotor and the gearbox structures. The predicted results were compared with experimental results obtained from a spiral bevel gear fatigue test rig at NASA Lewis Research Center. The Wigner-Ville Distribution (WVD) was used to give a comprehensive comparison of the predicted and experimental results. The WVD method applied to the experimental results were also compared to other fault detection techniques to verify the WVD's ability to detect the pitting damage, and to determine its relative performance. Overall results show good correlation between the experimental vibration data of the damaged test gear and the predicted vibration from the model with simulated gear tooth pitting damage. Results also verified that the WVD method can successfully detect and locate gear tooth wear and pitting damage.

Analytical and experimental vibration analysis of a faulty gear system

NASA Astrophysics Data System (ADS)

Choy, F. K.; Braun, M. J.; Polyshchuk, V.; Zakrajsek, J. J.; Townsend, D. P.; Handschuh, R. F.

1994-10-01

A comprehensive analytical procedure was developed for predicting faults in gear transmission systems under normal operating conditions. A gear tooth fault model is developed to simulate the effects of pitting and wear on the vibration signal under normal operating conditions. The model uses changes in the gear mesh stiffness to simulate the effects of gear tooth faults. The overall dynamics of the gear transmission system is evaluated by coupling the dynamics of each individual gear-rotor system through gear mesh forces generated between each gear-rotor system and the bearing forces generated between the rotor and the gearbox structure. The predicted results were compared with experimental results obtained from a spiral bevel gear fatigue test rig at NASA Lewis Research Center. The Wigner-Ville distribution (WVD) was used to give a comprehensive comparison of the predicted and experimental results. The WVD method applied to the experimental results were also compared to other fault detection techniques to verify the WVD's ability to detect the pitting damage, and to determine its relative performance. Overall results show good correlation between the experimental vibration data of the damaged test gear and the predicted vibration from the model with simulated gear tooth pitting damage. Results also verified that the WVD method can successfully detect and locate gear tooth wear and pitting damage.

Analytical and Experimental Vibration Analysis of a Faulty Gear System

NASA Technical Reports Server (NTRS)

Choy, F. K.; Braun, M. J.; Polyshchuk, V.; Zakrajsek, J. J.; Townsend, D. P.; Handschuh, R. F.

1994-01-01

A comprehensive analytical procedure was developed for predicting faults in gear transmission systems under normal operating conditions. A gear tooth fault model is developed to simulate the effects of pitting and wear on the vibration signal under normal operating conditions. The model uses changes in the gear mesh stiffness to simulate the effects of gear tooth faults. The overall dynamics of the gear transmission system is evaluated by coupling the dynamics of each individual gear-rotor system through gear mesh forces generated between each gear-rotor system and the bearing forces generated between the rotor and the gearbox structure. The predicted results were compared with experimental results obtained from a spiral bevel gear fatigue test rig at NASA Lewis Research Center. The Wigner-Ville distribution (WVD) was used to give a comprehensive comparison of the predicted and experimental results. The WVD method applied to the experimental results were also compared to other fault detection techniques to verify the WVD's ability to detect the pitting damage, and to determine its relative performance. Overall results show good correlation between the experimental vibration data of the damaged test gear and the predicted vibration from the model with simulated gear tooth pitting damage. Results also verified that the WVD method can successfully detect and locate gear tooth wear and pitting damage.

A Computational Clonal Analysis of the Developing Mouse Limb Bud

PubMed Central

Marcon, Luciano; Arqués, Carlos G.; Torres, Miguel S.; Sharpe, James

2011-01-01

A comprehensive spatio-temporal description of the tissue movements underlying organogenesis would be an extremely useful resource to developmental biology. Clonal analysis and fate mappings are popular experiments to study tissue movement during morphogenesis. Such experiments allow cell populations to be labeled at an early stage of development and to follow their spatial evolution over time. However, disentangling the cumulative effects of the multiple events responsible for the expansion of the labeled cell population is not always straightforward. To overcome this problem, we develop a novel computational method that combines accurate quantification of 2D limb bud morphologies and growth modeling to analyze mouse clonal data of early limb development. Firstly, we explore various tissue movements that match experimental limb bud shape changes. Secondly, by comparing computational clones with newly generated mouse clonal data we are able to choose and characterize the tissue movement map that better matches experimental data. Our computational analysis produces for the first time a two dimensional model of limb growth based on experimental data that can be used to better characterize limb tissue movement in space and time. The model shows that the distribution and shapes of clones can be described as a combination of anisotropic growth with isotropic cell mixing, without the need for lineage compartmentalization along the AP and PD axis. Lastly, we show that this comprehensive description can be used to reassess spatio-temporal gene regulations taking tissue movement into account and to investigate PD patterning hypothesis. PMID:21347315

Highly oxygenated ent-pimarane-type diterpenoids from the Chinese liverwort Pedinophyllum interruptum and their allelopathic activities.

PubMed

Liu, Na; Li, Rui-Juan; Wang, Xiao-Ning; Zhu, Rong-Xiu; Wang, Lei; Lin, Zhao-Min; Zhao, Yu; Lou, Hong-Xiang

2013-09-27

Ten highly oxygenated ent-pimarane-type diterpenoids, pedinophyllols A-J (1-10), were isolated from the Chinese liverwort Pedinophyllum interruptum. Their structures were determined by comprehensive analysis of spectroscopic data together with single-crystal X-ray diffraction analysis. The absolute configurations were elucidated by comparison of experimental and theoretically calculated electronic circular dichroism spectra. Allelopathic testing showed that several new diterpenoids inhibited germination of Arabidopsis thaliana seeds.

Asymmetric transmission and reflection spectra of FBG in single-multi-single mode fiber structure.

PubMed

Chai, Quan; Liu, Yanlei; Zhang, Jianzhong; Yang, Jun; Chen, Yujin; Yuan, Libo; Peng, Gang-Ding

2015-05-04

We give a comprehensive theoretical analysis and simulation of a FBG in single-multi-single mode fiber structure (FBG-in-SMS), based on the coupled mode analysis and the mode interference analysis. This enables us to explain the experimental observations, its asymmetric transmission and reflection spectra with the similar temperature responses near the spectral range of Bragg wavelengths. The transmission spectrum shift during FBG written-in process is observed and discussed. The analysis results are useful in the design of the SMS structure based sensors and filters.

PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens.

PubMed

Spahn, Philipp N; Bath, Tyler; Weiss, Ryan J; Kim, Jihoon; Esko, Jeffrey D; Lewis, Nathan E; Harismendy, Olivier

2017-11-20

Large-scale genetic screens using CRISPR/Cas9 technology have emerged as a major tool for functional genomics. With its increased popularity, experimental biologists frequently acquire large sequencing datasets for which they often do not have an easy analysis option. While a few bioinformatic tools have been developed for this purpose, their utility is still hindered either due to limited functionality or the requirement of bioinformatic expertise. To make sequencing data analysis of CRISPR/Cas9 screens more accessible to a wide range of scientists, we developed a Platform-independent Analysis of Pooled Screens using Python (PinAPL-Py), which is operated as an intuitive web-service. PinAPL-Py implements state-of-the-art tools and statistical models, assembled in a comprehensive workflow covering sequence quality control, automated sgRNA sequence extraction, alignment, sgRNA enrichment/depletion analysis and gene ranking. The workflow is set up to use a variety of popular sgRNA libraries as well as custom libraries that can be easily uploaded. Various analysis options are offered, suitable to analyze a large variety of CRISPR/Cas9 screening experiments. Analysis output includes ranked lists of sgRNAs and genes, and publication-ready plots. PinAPL-Py helps to advance genome-wide screening efforts by combining comprehensive functionality with user-friendly implementation. PinAPL-Py is freely accessible at http://pinapl-py.ucsd.edu with instructions and test datasets.

Modeling Criminal Activity in Urban Landscapes

NASA Astrophysics Data System (ADS)

Brantingham, Patricia; Glässer, Uwe; Jackson, Piper; Vajihollahi, Mona

Computational and mathematical methods arguably have an enormous potential for serving practical needs in crime analysis and prevention by offering novel tools for crime investigations and experimental platforms for evidence-based policy making. We present a comprehensive formal framework and tool support for mathematical and computational modeling of criminal behavior to facilitate systematic experimental studies of a wide range of criminal activities in urban environments. The focus is on spatial and temporal aspects of different forms of crime, including opportunistic and serial violent crimes. However, the proposed framework provides a basis to push beyond conventional empirical research and engage the use of computational thinking and social simulations in the analysis of terrorism and counter-terrorism.

Comprehensive analysis of the optical Kerr coefficient of graphene

DOE PAGES

Soh, Daniel B. S.; Hamerly, Ryan; Mabuchi, Hideo

2016-08-25

We present a comprehensive analysis of the nonlinear optical Kerr effect in graphene. We directly solve the S-matrix element to calculate the absorption rate, utilizing the Volkov-Keldysh-type crystal wave functions. We then convert to the nonlinear refractive index coefficients through the Kramers-Kronig relation. In this formalism, the source of Kerr nonlinearity is the interplay of optical fields that cooperatively drive the transition from valence to conduction band. This formalism makes it possible to identify and compute the rates of distinct nonlinear processes that contribute to the Kerr nonlinear refractive index coefficient. The four identified mechanisms are two-photon absorption, Raman transition,more » self-coupling, and quadratic ac Stark effect. As a result, we present a comparison of our theory with recent experimental and theoretical results.« less

Teaching practice and experiences of verifying the three laws of genetics based on the SSLP marker analysis.

PubMed

Huang, Xue-Ying; Fan, Kai; Ye, Yan-Fang; Wang, Bin; Wu, Wei-Ren; Lan, Tao

2017-09-20

We explored the practical effect of the genetic analysis of simple sequence length polymorphism (SSLP) molecular markers in rice in the genetics lab course. Two parents and their F 2 population were analyzed and detected with three SSLP molecular markers that located on two chromosomes of the rice genome. The markers' genotype data were used to verify the three laws of genetics, including segregation, independent assortment and linkage and crossing-over. Our practice has proved not only beneficial to deepen students' understandings about the three laws of genetics, but also conducive to cultivate students' interests in research and innovation and improve their skills and comprehensive analysis abilities. At the same time, the application scope of the experiment was discussed. This comprehensive experiment is also useful for the transformation of scientific research achievements into undergraduate experimental teaching.

Comprehensive detection of genes causing a phenotype using phenotype sequencing and pathway analysis.

PubMed

Harper, Marc; Gronenberg, Luisa; Liao, James; Lee, Christopher

2014-01-01

Discovering all the genetic causes of a phenotype is an important goal in functional genomics. We combine an experimental design for detecting independent genetic causes of a phenotype with a high-throughput sequencing analysis that maximizes sensitivity for comprehensively identifying them. Testing this approach on a set of 24 mutant strains generated for a metabolic phenotype with many known genetic causes, we show that this pathway-based phenotype sequencing analysis greatly improves sensitivity of detection compared with previous methods, and reveals a wide range of pathways that can cause this phenotype. We demonstrate our approach on a metabolic re-engineering phenotype, the PEP/OAA metabolic node in E. coli, which is crucial to a substantial number of metabolic pathways and under renewed interest for biofuel research. Out of 2157 mutations in these strains, pathway-phenoseq discriminated just five gene groups (12 genes) as statistically significant causes of the phenotype. Experimentally, these five gene groups, and the next two high-scoring pathway-phenoseq groups, either have a clear connection to the PEP metabolite level or offer an alternative path of producing oxaloacetate (OAA), and thus clearly explain the phenotype. These high-scoring gene groups also show strong evidence of positive selection pressure, compared with strictly neutral selection in the rest of the genome.

Effect of attention therapy on reading comprehension.

PubMed

Solan, Harold A; Shelley-Tremblay, John; Ficarra, Anthony; Silverman, Michael; Larson, Steven

2003-01-01

This study quantified the influence of visual attention therapy on the reading comprehension of Grade 6 children with moderate reading disabilities (RD) in the absence of specific reading remediation. Thirty students with below-average reading scores were identified using standardized reading comprehension tests. Fifteen children were placed randomly in the experimental group and 15 in the control group. The Attention Battery of the Cognitive Assessment System was administered to all participants. The experimental group received 12 one-hour sessions of individually monitored, computer-based attention therapy programs; the control group received no therapy during their 12-week period. Each group was retested on attention and reading comprehension measures. In order to stimulate selective and sustained visual attention, the vision therapy stressed various aspects of arousal, activation, and vigilance. At the completion of attention therapy, the mean standard attention and reading comprehension scores of the experimental group had improved significantly. The control group, however, showed no significant improvement in reading comprehension scores after 12 weeks. Although uncertainties still exist, this investigation supports the notion that visual attention is malleable and that attention therapy has a significant effect on reading comprehension in this often neglected population.

L'Apport des Faits Phonetiques au Developpement de la Comprehension Auditive en Langue Seconde (The Influence of Phonetic Skills on the Development of Listening Comprehension in a Second Language).

ERIC Educational Resources Information Center

Champagne-Muzar, Cecile

1996-01-01

Ascertains the influence of the development of receptive phonetic skills on the level of listening comprehension of adults learning French as a second language in a formal setting. Test results indicate substantial gains in phonetics by the experimental group and a significant difference between the performance of experimental and control groups.…

Comprehensive Analysis of Transport Proteins Encoded Within the Genome of Bdellovibrio bacteriovorus

PubMed Central

Barabote, Ravi D.; Rendulic, Snjezana; Schuster, Stephan C.; Saier, Milton H.

2012-01-01

Bdellovibrio bacteriovorus is a bacterial parasite with an unusual lifestyle. It grows and reproduces in the periplasm of a host prey bacterium. The complete genome sequence of B. bacteriovorus has recently been reported. We have reanalyzed the transport proteins encoded within the B. bacteriovorus genome according to the current content of the transporter classification database (TCDB). A comprehensive analysis is given on the types and numbers of transport systems that B. bacteriovorus has. In this regard, the potential protein secretory capabilities of at least 4 types of inner membrane secretion systems and 5 types for outer membrane secretion are described. Surprisingly, B. bacteriovorus has a disproportionate percentage of cytoplasmic membrane channels and outer membrane porins. It has far more TonB/ExbBD-type systems and MotAB-type systems for energizing outer membrane transport and motility than does E. coli. Analysis of probable substrate specificities of its transporters provides clues to its metabolic preferences. Interesting examples of gene fusions and of potentially overlapping genes were also noted. Our analyses provide a comprehensive, detailed appreciation of the transport capabilities of B. bacteriovorus. They should serve as a guide for functional experimental analyses. PMID:17706914

Emotional state talk and emotion understanding: a training study with preschool children.

PubMed

Gavazzi, Ilaria Grazzani; Ornaghi, Veronica

2011-11-01

ABSTRACTThe present study investigates whether training preschool children in the active use of emotional state talk plays a significant role in bringing about greater understanding of emotion terms and improved emotion comprehension. Participants were 100 preschool children (M=52 months; SD=9·9; range: 35-70 months), randomly assigned to experimental or control conditions. They were pre- and post-tested to assess their language comprehension, metacognitive language comprehension and emotion understanding. Analyses of pre-test data did not show any significant differences between experimental and control groups. During the intervention phase, the children were read stories enriched with emotional lexicon. After listening to the stories, children in the experimental group took part in conversational language games designed to stimulate use of the selected emotional terms. In contrast, the control group children did not take part in any special linguistic activities after the story readings. Analyses revealed that the experimental group outperformed the control group in the understanding of inner state language and in the comprehension of emotion.

Navigating freely-available software tools for metabolomics analysis.

PubMed

Spicer, Rachel; Salek, Reza M; Moreno, Pablo; Cañueto, Daniel; Steinbeck, Christoph

2017-01-01

The field of metabolomics has expanded greatly over the past two decades, both as an experimental science with applications in many areas, as well as in regards to data standards and bioinformatics software tools. The diversity of experimental designs and instrumental technologies used for metabolomics has led to the need for distinct data analysis methods and the development of many software tools. To compile a comprehensive list of the most widely used freely available software and tools that are used primarily in metabolomics. The most widely used tools were selected for inclusion in the review by either ≥ 50 citations on Web of Science (as of 08/09/16) or the use of the tool being reported in the recent Metabolomics Society survey. Tools were then categorised by the type of instrumental data (i.e. LC-MS, GC-MS or NMR) and the functionality (i.e. pre- and post-processing, statistical analysis, workflow and other functions) they are designed for. A comprehensive list of the most used tools was compiled. Each tool is discussed within the context of its application domain and in relation to comparable tools of the same domain. An extended list including additional tools is available at https://github.com/RASpicer/MetabolomicsTools which is classified and searchable via a simple controlled vocabulary. This review presents the most widely used tools for metabolomics analysis, categorised based on their main functionality. As future work, we suggest a direct comparison of tools' abilities to perform specific data analysis tasks e.g. peak picking.

Retrieval, automaticity, vocabulary elaboration, orthography (RAVE-O): a comprehensive, fluency-based reading intervention program.

PubMed

Wolf, M; Miller, L; Donnelly, K

2000-01-01

The most important implication of the double-deficit hypothesis (Wolf & Bowers, in this issue) concerns a new emphasis on fluency and automaticity in intervention for children with developmental reading disabilities. The RAVE-O (Retrieval, Automaticity, Vocabulary Elaboration, Orthography) program is an experimental, fluency-based approach to reading intervention that is designed to accompany a phonological analysis program. In an effort to address multiple possible sources of dysfluency in readers with disabilities, the program involves comprehensive emphases both on fluency in word attack, word identification, and comprehension and on automaticity in underlying componential processes (e.g., phonological, orthographic, semantic, and lexical retrieval skills). The goals, theoretical principles, and applied activities of the RAVE-O curriculum are described with particular stress on facilitating the development of rapid orthographic pattern recognition and on changing children's attitudes toward language.

Effects of Classroom Practices on Reading Comprehension, Engagement, and Motivations for Adolescents

PubMed Central

Guthrie, John T.; Klauda, Susan Lutz

2014-01-01

We investigated the roles of classroom supports for multiple motivations and engagement in students’ informational text comprehension, motivation, and engagement. A composite of classroom contextual variables consisting of instructional support for choice, importance, collaboration, and competence, accompanied by cognitive scaffolding for informational text comprehension, was provided in four-week instructional units for 615 grade 7 students. These classroom motivational-engagement supports were implemented within integrated literacy/history instruction in the Concept-Oriented Reading Instruction (CORI) framework. CORI increased informational text comprehension compared with traditional instruction (TI) in a switching replications experimental design. Students’ perceptions of the motivational-engagement supports were associated with increases in students’ intrinsic motivation, value, perceived competence, and increased positive engagement (dedication) more markedly in CORI than in TI, according to multiple regression analyses. Results extended the evidence for the effectiveness of CORI to literacy/history subject matter and informational text comprehension among middle school students. The experimental effects in classroom contexts confirmed effects from task-specific, situated experimental studies in the literature. PMID:25506087

Effects of Classroom Practices on Reading Comprehension, Engagement, and Motivations for Adolescents.

PubMed

Guthrie, John T; Klauda, Susan Lutz

2014-10-01

We investigated the roles of classroom supports for multiple motivations and engagement in students' informational text comprehension, motivation, and engagement. A composite of classroom contextual variables consisting of instructional support for choice, importance, collaboration, and competence, accompanied by cognitive scaffolding for informational text comprehension, was provided in four-week instructional units for 615 grade 7 students. These classroom motivational-engagement supports were implemented within integrated literacy/history instruction in the Concept-Oriented Reading Instruction (CORI) framework. CORI increased informational text comprehension compared with traditional instruction (TI) in a switching replications experimental design. Students' perceptions of the motivational-engagement supports were associated with increases in students' intrinsic motivation, value, perceived competence, and increased positive engagement (dedication) more markedly in CORI than in TI, according to multiple regression analyses. Results extended the evidence for the effectiveness of CORI to literacy/history subject matter and informational text comprehension among middle school students. The experimental effects in classroom contexts confirmed effects from task-specific, situated experimental studies in the literature.

ANALYSIS OF MATERIALS IN AN EXPERIMENTAL TESTING PIPE SYSTEM FOR AN INHIBITOR OF MUSSEL KILL

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

Daniel P. Molloy

2003-06-04

A comprehensive series of 16 laboratory experiments demonstrated that the presence of vinyl tubing within a recirculating pipe system was responsible for lowering zebra mussel kill following treatment with the bacterium Pseudomonas fluorescens. All vinyl tubing was replaced in all testing units with silicone tubing, and high mussel kill (>95%) was then obtained.

Comprehensive School Counseling Programs and Student Achievement Outcomes: A Comparative Analysis of Ramp versus Non-Ramp Schools

ERIC Educational Resources Information Center

Wilkerson, Kevin; Perusse, Rachelle; Hughes, Ashley

2013-01-01

This study compares school-wide Annual Yearly Progress (AYP) results in Indiana schools earning the Recognized ASCA Model Program (RAMP) designation (n = 75) with a sample of control schools stratified by level and locale (n = 226). K-12 schools earning the RAMP designation in 2007, 2008, and 2009 comprise the experimental group. Findings indicate…

Joint Services Electronics Program.

DTIC Science & Technology

1985-12-31

year a comprehensive experimental study of the collision- enhanced Hanle-type resonances in Na vapor with various buffer gases has been completed...demonstrated theoretically that the collision-enhanced Hanle resonances are equivalent to the phenomenon of collision-induced transverse optical pumping. The...for the sensitivity of the mean sojourn times. We also developed a set of new equations based on perturbation analysis which calculates theoretically

The Problem of Size in Robust Design

NASA Technical Reports Server (NTRS)

Koch, Patrick N.; Allen, Janet K.; Mistree, Farrokh; Mavris, Dimitri

1997-01-01

To facilitate the effective solution of multidisciplinary, multiobjective complex design problems, a departure from the traditional parametric design analysis and single objective optimization approaches is necessary in the preliminary stages of design. A necessary tradeoff becomes one of efficiency vs. accuracy as approximate models are sought to allow fast analysis and effective exploration of a preliminary design space. In this paper we apply a general robust design approach for efficient and comprehensive preliminary design to a large complex system: a high speed civil transport (HSCT) aircraft. Specifically, we investigate the HSCT wing configuration design, incorporating life cycle economic uncertainties to identify economically robust solutions. The approach is built on the foundation of statistical experimentation and modeling techniques and robust design principles, and is specialized through incorporation of the compromise Decision Support Problem for multiobjective design. For large problems however, as in the HSCT example, this robust design approach developed for efficient and comprehensive design breaks down with the problem of size - combinatorial explosion in experimentation and model building with number of variables -and both efficiency and accuracy are sacrificed. Our focus in this paper is on identifying and discussing the implications and open issues associated with the problem of size for the preliminary design of large complex systems.

Analysis of the interaction between experimental and applied behavior analysis.

PubMed

Virues-Ortega, Javier; Hurtado-Parrado, Camilo; Cox, Alison D; Pear, Joseph J

2014-01-01

To study the influences between basic and applied research in behavior analysis, we analyzed the coauthorship interactions of authors who published in JABA and JEAB from 1980 to 2010. We paid particular attention to authors who published in both JABA and JEAB (dual authors) as potential agents of cross-field interactions. We present a comprehensive analysis of dual authors' coauthorship interactions using social networks methodology and key word analysis. The number of dual authors more than doubled (26 to 67) and their productivity tripled (7% to 26% of JABA and JEAB articles) between 1980 and 2010. Dual authors stood out in terms of number of collaborators, number of publications, and ability to interact with multiple groups within the field. The steady increase in JEAB and JABA interactions through coauthors and the increasing range of topics covered by dual authors provide a basis for optimism regarding the progressive integration of basic and applied behavior analysis. © Society for the Experimental Analysis of Behavior.

Quantitative characterization of galectin-3-C affinity mass spectrometry measurements: Comprehensive data analysis, obstacles, shortcuts and robustness.

PubMed

Haramija, Marko; Peter-Katalinić, Jasna

2017-10-30

Affinity mass spectrometry (AMS) is an emerging tool in the field of the study of protein•carbohydrate complexes. However, experimental obstacles and data analysis are preventing faster integration of AMS methods into the glycoscience field. Here we show how analysis of direct electrospray ionization mass spectrometry (ESI-MS) AMS data can be simplified for screening purposes, even for complex AMS spectra. A direct ESI-MS assay was tested in this study and binding data for the galectin-3C•lactose complex were analyzed using a comprehensive and simplified data analysis approach. In the comprehensive data analysis approach, noise, all protein charge states, alkali ion adducts and signal overlap were taken into account. In a simplified approach, only the intensities of the fully protonated free protein and the protein•carbohydrate complex for the main protein charge state were taken into account. In our study, for high intensity signals, noise was negligible, sodiated protein and sodiated complex signals cancelled each other out when calculating the K d value, and signal overlap influenced the Kd value only to a minor extent. Influence of these parameters on low intensity signals was much higher. However, low intensity protein charge states should be avoided in quantitative AMS analyses due to poor ion statistics. The results indicate that noise, alkali ion adducts, signal overlap, as well as low intensity protein charge states, can be neglected for preliminary experiments, as well as in screening assays. One comprehensive data analysis performed as a control should be sufficient to validate this hypothesis for other binding systems as well. Copyright © 2017 John Wiley & Sons, Ltd.

Metal fires and their implications for advanced reactors.

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

Nowlen, Steven Patrick; Figueroa, Victor G.; Olivier, Tara Jean

This report details the primary results of the Laboratory Directed Research and Development project (LDRD 08-0857) Metal Fires and Their Implications for Advance Reactors. Advanced reactors may employ liquid metal coolants, typically sodium, because of their many desirable qualities. This project addressed some of the significant challenges associated with the use of liquid metal coolants, primary among these being the extremely rapid oxidation (combustion) that occurs at the high operating temperatures in reactors. The project has identified a number of areas for which gaps existed in knowledge pertinent to reactor safety analyses. Experimental and analysis capabilities were developed in thesemore » areas to varying degrees. In conjunction with team participation in a DOE gap analysis panel, focus was on the oxidation of spilled sodium on thermally massive surfaces. These are spills onto surfaces that substantially cool the sodium during the oxidation process, and they are relevant because standard risk mitigation procedures seek to move spill environments into this regime through rapid draining of spilled sodium. While the spilled sodium is not quenched, the burning mode is different in that there is a transition to a smoldering mode that has not been comprehensively described previously. Prior work has described spilled sodium as a pool fire, but there is a crucial, experimentally-observed transition to a smoldering mode of oxidation. A series of experimental measurements have comprehensively described the thermal evolution of this type of sodium fire for the first time. A new physics-based model has been developed that also predicts the thermal evolution of this type of sodium fire for the first time. The model introduces smoldering oxidation through porous oxide layers to go beyond traditional pool fire analyses that have been carried out previously in order to predict experimentally observed trends. Combined, these developments add significantly to the safety analysis capabilities of the advanced-reactor community for directly relevant scenarios. Beyond the focus on the thermally-interacting and smoldering sodium pool fires, experimental and analysis capabilities for sodium spray fires have also been developed in this project.« less

Effects of an intervention in active strategies for text comprehension and recall.

PubMed

Elosúa, M Rosa; García-Madruga, Juan A; Gutiérrez, Francisco; Luque, Juan Luis; Gárate, Milagros

2002-11-01

The aim of this study was to investigate the effects of an intervention program to promote active text-processing strategies (main-idea identification and summarization) at two developmental levels (12- and 16-year-olds). The independent variables were training condition (experimental and control) and school level (7th and 10th grades). Several measures were taken as dependent variables: reading span, reading time, construction of macrostructure, and structural recall. The hypothesis claimed that training would increase comprehension and recall significantly. Furthermore, as a result of the training program, a reduction in developmental differences in the experimental groups at posttest was also expected. Results supported the predictions, showing a significant improvement in the experimental groups' reading comprehension and recall. These results are discussed in terms of the importance of active and self-controlled strategies for text comprehension and recall.

Comprehensive DFT study on molecular structures of Lewisites in support of the Chemical Weapons Convention

NASA Astrophysics Data System (ADS)

Saeidian, Hamid; Sahandi, Morteza

2015-11-01

The structure of all of Lewisite's stereoisomers has been examined by B3LYP/6-311++G(3df,3pd) calculations. The geometry analysis for trans Lewisite L1-1 shows that the calculated bond angles, bond distances and dipole moment have a satisfactory relation compared with experimental values. HOMO-LUMO analysis of Lewisites reveals that L1-2 and L3-7 have the maximum and minimum electrophilicity index, respectively. The calculated chemical shifts were compared with experimental data, showing a very good agreement both for 1H and 13C. The vibrational and Raman frequencies of Lewisites have been precisely assigned and theoretical data were compared with the experimental vibrations. The bonding trends and Mulliken and atomic polar tensor charge distribution in Lewisites can be explained by the Bent's rule and the donor-acceptor interaction, respectively.

Tables of E2 transition probabilities from the first 2 + states in even-even nuclei [B(E2) evaluation for 0 + 1 → 2 + 1 transitions in even-even nuclei

DOE PAGES

Pritychenko, B.; Birch, M.; Singh, B.; ...

2015-11-03

A complete B(E2)↑ evaluation and compilation for even-even nuclei has been presented. The present paper is a continuation of P.H. Stelson and L. Grodzins, and S. Raman et al. nuclear data evaluations and was motivated by a large number of new measurements. It extends the list of evaluated nuclides from 328 to 452, includes an extended list of nuclear reaction kinematics parameters and comprehensive shell model analysis. Evaluation policies for analysis of experimental data have been discussed and conclusions are given. Moreover, future plans for B(E2)↑ systematics and experimental technique analyses of even-even nuclei are outlined.

Data consistency checks for Jefferson Lab Experiment E00-002

NASA Astrophysics Data System (ADS)

Telfeyan, John; Niculescu, Gabriel; Niculescu, Ioana

2006-10-01

Jefferson Lab experiment E00-002 aims to measure inclusive electron-proton and electron-deuteron scattering cross section at low Q squared and moderately low Bjorken x. Data in this kinematic region will further our understanding of the transition between the perturbative and non-perturbative regimes of Quantum Chromodynamics (QCD). As part of the data analysis effort underway at James Madison University (JMU) a comprehensive set of checks and tests was implemented. These tests ensure the quality and consistency of the experimental data, as well as providing, where appropriate, correction factors between the experimental apparatus as used and its idealized computer-simulated representation. This contribution will outline this testing procedure as implemented in the JMU analysis, highlighting the most important features/results.

Abbreviations: Their Effects on Comprehension of Classified Advertisements.

ERIC Educational Resources Information Center

Sokol, Kirstin R.

Two experimental designs were used to test the hypothesis that abbreviations in classified advertisements decrease the reader's comprehension of such ads. In the first experimental design, 73 high school students read four ads (for employment, used cars, apartments for rent, and articles for sale) either with abbreviations or with all…

Effects of Note-Taking Training on Reading Comprehension and Recall

ERIC Educational Resources Information Center

Rahmani, Mina; Sadeghi, Karim

2011-01-01

The present study examined the process and product effects of note-taking strategy training on Iranian EFL learners' comprehension and retention of written material, with gender as a moderating variable. Intermediate undergraduate EFL learners (N = 108) were assigned to experimental and control groups. The Experimental (intervention) Group…

The Effect of Screen Size on Mobile Phone User Comprehension of Health Information and Application Structure: An Experimental Approach.

PubMed

Al Ghamdi, Ebtisam; Yunus, Faisal; Da'ar, Omar; El-Metwally, Ashraf; Khalifa, Mohamed; Aldossari, Bakheet; Househ, Mowafa

2016-01-01

This research analyzes the impact of mobile phone screen size on user comprehension of health information and application structure. Applying experimental approach, we asked randomly selected users to read content and conduct tasks on a commonly used diabetes mobile application using three different mobile phone screen sizes. We timed and tracked a number of parameters, including correctness, effectiveness of completing tasks, content ease of reading, clarity of information organization, and comprehension. The impact of screen size on user comprehension/retention, clarity of information organization, and reading time were mixed. It is assumed on first glance that mobile screen size would affect all qualities of information reading and comprehension, including clarity of displayed information organization, reading time and user comprehension/retention of displayed information, but actually the screen size, in this experimental research, did not have significant impact on user comprehension/retention of the content or on understanding the application structure. However, it did have significant impact on clarity of information organization and reading time. Participants with larger screen size took shorter time reading the content with a significant difference in the ease of reading. While there was no significant difference in the comprehension of information or the application structures, there were a higher task completion rate and a lower number of errors with the bigger screen size. Screen size does not directly affect user comprehension of health information. However, it does affect clarity of information organization, reading time and user's ability to recall information.

THE EFFECT OF PLAUSIBILITY ON SENTENCE COMPREHENSION AMONG OLDER ADULTS AND ITS RELATION TO COGNITIVE FUNCTIONS

PubMed Central

Yoon, Jungmee; Campanelli, Luca; Goral, Mira; Marton, Klara; Eichorn, Naomi; Obler, Loraine K.

2016-01-01

Background/Study Context Older adults show age-related decline in complex-sentence comprehension. This has been attributed to a decrease in cognitive abilities that may support language processing, such as working memory (e.g., Caplan, DeDe, Waters, & Michaud, 2011,Psychology and Aging, 26, 439–450). The authors examined whether older adults have difficulty comprehending semantically implausible sentences and whether specific executive functions contribute to their comprehension performance. Methods Forty-two younger adults (aged 18–35) and 42 older adults (aged 55–75) were tested on two experimental tasks: a multiple negative comprehension task and an information processing battery. Results Both groups, older and younger adults, showed poorer performance for implausible sentences than for plausible sentences; however, no interaction was found between plausibility and age group. A regression analysis revealed that inhibition efficiency, as measured by a task that required resistance to proactive interference, predicted comprehension of implausible sentences in older adults only. Consistent with the compensation hypothesis, the older adults with better inhibition skills showed better comprehension than those with poor inhibition skills. Conclusion The findings suggest that semantic implausibility, along with syntactic complexity, increases linguistic and cognitive processing loads on auditory sentence comprehension. Moreover, the contribution of inhibitory control to the processing of semantic plausibility, particularly among older adults, suggests that the relationship between cognitive ability and language comprehension is strongly influenced by age. PMID:25978447

The effect of plausibility on sentence comprehension among older adults and its relation to cognitive functions.

PubMed

Yoon, Jungmee; Campanelli, Luca; Goral, Mira; Marton, Klara; Eichorn, Naomi; Obler, Loraine K

2015-01-01

BACKGROUND/STUDY CONTEXT: Older adults show age-related decline in complex-sentence comprehension. This has been attributed to a decrease in cognitive abilities that may support language processing, such as working memory (e.g., Caplan, DeDe, Waters, & Michaud, 2011,Psychology and Aging, 26, 439-450). The authors examined whether older adults have difficulty comprehending semantically implausible sentences and whether specific executive functions contribute to their comprehension performance. Forty-two younger adults (aged 18-35) and 42 older adults (aged 55-75) were tested on two experimental tasks: a multiple negative comprehension task and an information processing battery. Both groups, older and younger adults, showed poorer performance for implausible sentences than for plausible sentences; however, no interaction was found between plausibility and age group. A regression analysis revealed that inhibition efficiency, as measured by a task that required resistance to proactive interference, predicted comprehension of implausible sentences in older adults only. Consistent with the compensation hypothesis, the older adults with better inhibition skills showed better comprehension than those with poor inhibition skills. The findings suggest that semantic implausibility, along with syntactic complexity, increases linguistic and cognitive processing loads on auditory sentence comprehension. Moreover, the contribution of inhibitory control to the processing of semantic plausibility, particularly among older adults, suggests that the relationship between cognitive ability and language comprehension is strongly influenced by age.

A Temperature Sensor Based on a Polymer Optical Fiber Macro-Bend

PubMed Central

Moraleda, Alberto Tapetado; García, Carmen Vázquez; Zaballa, Joseba Zubia; Arrue, Jon

2013-01-01

The design and development of a plastic optical fiber (POF) macrobend temperature sensor is presented. The sensor has a linear response versus temperature at a fixed bend radius, with a sensitivity of 1.92·10−3 (°C)−1. The sensor system used a dummy fiber-optic sensor for reference purposes having a resolution below 0.3 °C. A comprehensive experimental analysis was carried out to provide insight into the effect of different surrounding media on practical macro-bend POF sensor implementation. Experimental results are successfully compared with bend loss calculations. PMID:24077323

CHESS (CgHExpreSS): a comprehensive analysis tool for the analysis of genomic alterations and their effects on the expression profile of the genome.

PubMed

Lee, Mikyung; Kim, Yangseok

2009-12-16

Genomic alterations frequently occur in many cancer patients and play important mechanistic roles in the pathogenesis of cancer. Furthermore, they can modify the expression level of genes due to altered copy number in the corresponding region of the chromosome. An accumulating body of evidence supports the possibility that strong genome-wide correlation exists between DNA content and gene expression. Therefore, more comprehensive analysis is needed to quantify the relationship between genomic alteration and gene expression. A well-designed bioinformatics tool is essential to perform this kind of integrative analysis. A few programs have already been introduced for integrative analysis. However, there are many limitations in their performance of comprehensive integrated analysis using published software because of limitations in implemented algorithms and visualization modules. To address this issue, we have implemented the Java-based program CHESS to allow integrative analysis of two experimental data sets: genomic alteration and genome-wide expression profile. CHESS is composed of a genomic alteration analysis module and an integrative analysis module. The genomic alteration analysis module detects genomic alteration by applying a threshold based method or SW-ARRAY algorithm and investigates whether the detected alteration is phenotype specific or not. On the other hand, the integrative analysis module measures the genomic alteration's influence on gene expression. It is divided into two separate parts. The first part calculates overall correlation between comparative genomic hybridization ratio and gene expression level by applying following three statistical methods: simple linear regression, Spearman rank correlation and Pearson's correlation. In the second part, CHESS detects the genes that are differentially expressed according to the genomic alteration pattern with three alternative statistical approaches: Student's t-test, Fisher's exact test and Chi square test. By successive operations of two modules, users can clarify how gene expression levels are affected by the phenotype specific genomic alterations. As CHESS was developed in both Java application and web environments, it can be run on a web browser or a local machine. It also supports all experimental platforms if a properly formatted text file is provided to include the chromosomal position of probes and their gene identifiers. CHESS is a user-friendly tool for investigating disease specific genomic alterations and quantitative relationships between those genomic alterations and genome-wide gene expression profiling.

The Effects of Advance Organizers and Subtitles on EFL Learners' Listening Comprehension Skills

ERIC Educational Resources Information Center

Yang, Hui-Yu

2014-01-01

The present research reports the findings of three experiments which explore how subtitles and advance organizers affect EFL learners' listening comprehension of authentic videos. EFL learners are randomly assigned to one of two groups. The control group receives no treatment and the experimental group receives the experimental conditions of one…

Strategies Training in the Teaching of Reading Comprehension for EFL Learners in Indonesia

ERIC Educational Resources Information Center

Mistar, Junaidi; Zuhairi, Alfan; Yanti, Nofita

2016-01-01

This study investigated the effect of reading strategies training on the students' literal and inferential reading comprehension. The training involved three concrete strategies: predicting, text mapping, and summarizing. To achieve the purpose of this study, a quasi experimental design was selected with the experimental group being given reading…

Capturing the Cumulative Effects of School Reform: An 11-Year Study of the Impacts of America's Choice on Student Achievement

ERIC Educational Resources Information Center

May, Henry; Supovitz, Jonathan A.

2006-01-01

This article presents the results of an 11-year longitudinal study of the impact of America's Choice comprehensive school reform (CSR) design on student learning gains in Rochester, New York. A quasi-experimental interrupted time-series approach using Bayesian hierarchical growth curve analysis with crossed random effects is used to compare the…

An Analysis of the Tasks in School Social Work as a Basis for Improved Use of Staff. Final Report.

ERIC Educational Resources Information Center

Costin, Lela B.

The two basic questions investigated in this study were: (1) the function of school social work and its relative importance as defined by social workers, and (2) whether this definition provides a basis for experimentation in assigning responsibilities to social work staff with different levels of training. A comprehensive list of the school…

Eye-Tracking Evidence that Happy Faces Impair Verbal Message Comprehension: The Case of Health Warnings in Direct-to-Consumer Pharmaceutical Television Commercials

PubMed Central

Russell, Cristel Antonia; Swasy, John L.; Russell, Dale Wesley; Engel, Larry

2017-01-01

Risk warning or disclosure information in advertising is only effective in correcting consumers’ judgments if enough cognitive capacity is available to process that information. Hence, comprehension of verbal warnings in TV commercials may suffer if accompanied by positive visual elements. This research addresses this concern about cross-modality interference in the context of direct-to-consumer (DTC) pharmaceutical commercials in the United States by experimentally testing whether positive facial expressions reduce consumers’ understanding of the mandated health warning. A content analysis of a sample of DTC commercials reveals that positive facial expressions are more prevalent during the verbal warning act of the commercials than during the other acts. An eye-tracking experiment conducted with specially produced DTC commercials, which vary the valence of characters’ facial expressions during the health warning, provides evidence that happy faces reduce objective comprehension of the warning. PMID:29269979

Study of the structure of 3-D composites based on carbon nanotubes in bovine serum albumin matrix by X-ray microtomography

NASA Astrophysics Data System (ADS)

Ignatov, D.; Zhurbina, N.; Gerasimenko, A.

2017-01-01

3-D composites are widely used in tissue engineering. A comprehensive analysis by X-ray microtomography was conducted to study the structure of the 3-D composites. Comprehensive analysis of the structure of the 3-D composites consisted of scanning, image reconstruction of shadow projections, two-dimensional and three-dimensional visualization of the reconstructed images and quantitative analysis of the samples. Experimental samples of composites were formed by laser vaporization of the aqueous dispersion BSA and single-walled (SWCNTs) and multi-layer (MWCNTs) carbon nanotubes. The samples have a homogeneous structure over the entire volume, the percentage of porosity of 3-D composites based on SWCNTs and MWCNTs - 16.44%, 28.31%, respectively. An average pore diameter of 3-D composites based on SWCNTs and MWCNTs - 45 μm 93 μm. 3-D composites based on carbon nanotubes in bovine serum albumin matrix can be used in tissue engineering of bone and cartilage, providing cell proliferation and blood vessel sprouting.

Comprehensive multilevel in vivo and in vitro analysis of heart rate fluctuations in mice by ECG telemetry and electrophysiology.

PubMed

Fenske, Stefanie; Pröbstle, Rasmus; Auer, Franziska; Hassan, Sami; Marks, Vanessa; Pauza, Danius H; Biel, Martin; Wahl-Schott, Christian

2016-01-01

The normal heartbeat slightly fluctuates around a mean value; this phenomenon is called physiological heart rate variability (HRV). It is well known that altered HRV is a risk factor for sudden cardiac death. The availability of genetic mouse models makes it possible to experimentally dissect the mechanism of pathological changes in HRV and its relation to sudden cardiac death. Here we provide a protocol that allows for a comprehensive multilevel analysis of heart rate (HR) fluctuations. The protocol comprises a set of techniques that include in vivo telemetry and in vitro electrophysiology of intact sinoatrial network preparations or isolated single sinoatrial node (SAN) cells. In vitro preparations can be completed within a few hours, with data acquisition within 1 d. In vivo telemetric ECG requires 1 h for surgery and several weeks for data acquisition and analysis. This protocol is of interest to researchers investigating cardiovascular physiology and the pathophysiology of sudden cardiac death.

Comprehensive Analysis of Immunological Synapse Phenotypes Using Supported Lipid Bilayers.

PubMed

Valvo, Salvatore; Mayya, Viveka; Seraia, Elena; Afrose, Jehan; Novak-Kotzer, Hila; Ebner, Daniel; Dustin, Michael L

2017-01-01

Supported lipid bilayers (SLB) formed on glass substrates have been a useful tool for study of immune cell signaling since the early 1980s. The mobility of lipid-anchored proteins in the system, first described for antibodies binding to synthetic phospholipid head groups, allows for the measurement of two-dimensional binding reactions and signaling processes in a single imaging plane over time or for fixed samples. The fragility of SLB and the challenges of building and validating individual substrates limit most experimenters to ~10 samples per day, perhaps increasing this few-fold when examining fixed samples. Successful experiments might then require further days to fully analyze. We present methods for automation of many steps in SLB formation, imaging in 96-well glass bottom plates, and analysis that enables >100-fold increase in throughput for fixed samples and wide-field fluorescence. This increased throughput will allow better coverage of relevant parameters and more comprehensive analysis of aspects of the immunological synapse that are well reconstituted by SLB.

Methods for heat transfer and temperature field analysis of the insulated diesel

NASA Technical Reports Server (NTRS)

Morel, T.; Blumberg, P. N.; Fort, E. F.; Keribar, R.

1984-01-01

Work done during phase 1 of a three-year program aimed at developing a comprehensive heat transfer and thermal analysis methodology oriented specifically to the design requirements of insulated diesel engines is reported. The technology developed in this program makes possible a quantitative analysis of the low heat rejection concept. The program is comprehensive in that it addresses all the heat transfer issues that are critical to the successful development of the low heat rejection diesel engine: (1) in-cylinder convective and radiative heat transfer; (2) cyclic transient heat transfer in thin solid layers at component surfaces adjacent to the combustion chamber; and (3) steady-state heat conduction in the overall engine structure. The Integral Technologies, Inc. (ITI) program is comprised of a set of integrated analytical and experimental tasks. A detailed review of the ITI program approach is provided, including the technical issues which underlie it and a summay of the methods that were developed.

[The development and effects of a comprehensive communication course for nursing students].

PubMed

Kim, Sunah; Park, Jung-Hwa; Lee, Hyun-Hwa

2004-06-01

The purposes of this study were to: (a) develop a comprehensive communication course combined with a group program for improving communication skills; and (b) examine the effects of the comprehensive communication course on interpersonal communication, relationship change, self-esteem, and depression in nursing students. The experimental group consisted of 82 nursing students, and the control group, 108 nursing students. Both groups each took communication courses from March to June, 2002 and 2003. A group program for improving communication skills was conducted for each 8 subgroups of the experimental group for 90 minutes once a week during the 6 weeks, while the existing communication lecture was conducted for the control group. Both groups were post-tested after the intervention for verifying the difference of variables between the two groups, and the experimental group was also pre-tested for verifying the difference between before and after the treatment. Interpersonal communication score of the post-test in the experimental group was significantly higher than in the control group and the depression score of the post-test in the experimental group was significantly lower than in the control group. Interpersonal communication, relationship change and self-esteem scores were significantly increased and the depression score was significantly decreased in experimental group after the treatment. In conclusion, the comprehensive communication course that was developed in this study had positive effects on communication skills in nursing students.

Analysis of drugs by microcalorimetry Isothermal power-conduction calorimetry and thermometric titrimetry.

PubMed

Chowdhry, B Z; Beezer, A E; Greenhow, E J

1983-04-01

Microcalorimetric analysis has been the subject of a few review's in recent years, but these reviews have mainly dealt with the wide-ranging capabilities of calorimetric assay. This review, however, discusses the experimental basis and practical exploitation of the method in the particularly important area of pharmaceuticals. This field of analysis embraces both conventional chemical assays and bioassays which involve living microbial species. The review highlights the design of calorimetric instruments appropriate for study of microbial metabolism and interaction with drug substances. For comprehensiveness, both microcalorimetric and thermometric assay systems are discussed and critically assessed.

A Meta-Analysis of the Long-Term Effects of Phonemic Awareness, Phonics, Fluency, and Reading Comprehension Interventions.

PubMed

Suggate, Sebastian P

2016-01-01

Much is known about short-term--but very little about the long-term--effects of reading interventions. To rectify this, a detailed analysis of follow-up effects as a function of intervention, sample, and methodological variables was conducted. A total of 71 intervention-control groups were selected (N = 8,161 at posttest) from studies reporting posttest and follow-up data (M = 11.17 months) for previously established reading interventions. The posttest effect sizes indicated effects (dw = 0.37) that decreased to follow-up (dw = 0.22). Overall, comprehension and phonemic awareness interventions showed good maintenance of effect that transferred to nontargeted skills, whereas phonics and fluency interventions, and those for preschool and kindergarten children, tended not to. Several methodological features also related to effect sizes at follow-up, namely experimental design and dosage, and sample attrition, risk status, and gender balance. © Hammill Institute on Disabilities 2014.

Comprehensive Quantitative Analysis on Privacy Leak Behavior

PubMed Central

Fan, Lejun; Wang, Yuanzhuo; Jin, Xiaolong; Li, Jingyuan; Cheng, Xueqi; Jin, Shuyuan

2013-01-01

Privacy information is prone to be leaked by illegal software providers with various motivations. Privacy leak behavior has thus become an important research issue of cyber security. However, existing approaches can only qualitatively analyze privacy leak behavior of software applications. No quantitative approach, to the best of our knowledge, has been developed in the open literature. To fill this gap, in this paper we propose for the first time four quantitative metrics, namely, possibility, severity, crypticity, and manipulability, for privacy leak behavior analysis based on Privacy Petri Net (PPN). In order to compare the privacy leak behavior among different software, we further propose a comprehensive metric, namely, overall leak degree, based on these four metrics. Finally, we validate the effectiveness of the proposed approach using real-world software applications. The experimental results demonstrate that our approach can quantitatively analyze the privacy leak behaviors of various software types and reveal their characteristics from different aspects. PMID:24066046

Comprehensive quantitative analysis on privacy leak behavior.

PubMed

Fan, Lejun; Wang, Yuanzhuo; Jin, Xiaolong; Li, Jingyuan; Cheng, Xueqi; Jin, Shuyuan

2013-01-01

Privacy information is prone to be leaked by illegal software providers with various motivations. Privacy leak behavior has thus become an important research issue of cyber security. However, existing approaches can only qualitatively analyze privacy leak behavior of software applications. No quantitative approach, to the best of our knowledge, has been developed in the open literature. To fill this gap, in this paper we propose for the first time four quantitative metrics, namely, possibility, severity, crypticity, and manipulability, for privacy leak behavior analysis based on Privacy Petri Net (PPN). In order to compare the privacy leak behavior among different software, we further propose a comprehensive metric, namely, overall leak degree, based on these four metrics. Finally, we validate the effectiveness of the proposed approach using real-world software applications. The experimental results demonstrate that our approach can quantitatively analyze the privacy leak behaviors of various software types and reveal their characteristics from different aspects.

dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins.

PubMed

Huang, Kai-Yao; Su, Min-Gang; Kao, Hui-Ju; Hsieh, Yun-Chung; Jhong, Jhih-Hua; Cheng, Kuang-Hao; Huang, Hsien-Da; Lee, Tzong-Yi

2016-01-04

Owing to the importance of the post-translational modifications (PTMs) of proteins in regulating biological processes, the dbPTM (http://dbPTM.mbc.nctu.edu.tw/) was developed as a comprehensive database of experimentally verified PTMs from several databases with annotations of potential PTMs for all UniProtKB protein entries. For this 10th anniversary of dbPTM, the updated resource provides not only a comprehensive dataset of experimentally verified PTMs, supported by the literature, but also an integrative interface for accessing all available databases and tools that are associated with PTM analysis. As well as collecting experimental PTM data from 14 public databases, this update manually curates over 12 000 modified peptides, including the emerging S-nitrosylation, S-glutathionylation and succinylation, from approximately 500 research articles, which were retrieved by text mining. As the number of available PTM prediction methods increases, this work compiles a non-homologous benchmark dataset to evaluate the predictive power of online PTM prediction tools. An increasing interest in the structural investigation of PTM substrate sites motivated the mapping of all experimental PTM peptides to protein entries of Protein Data Bank (PDB) based on database identifier and sequence identity, which enables users to examine spatially neighboring amino acids, solvent-accessible surface area and side-chain orientations for PTM substrate sites on tertiary structures. Since drug binding in PDB is annotated, this update identified over 1100 PTM sites that are associated with drug binding. The update also integrates metabolic pathways and protein-protein interactions to support the PTM network analysis for a group of proteins. Finally, the web interface is redesigned and enhanced to facilitate access to this resource. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

miRNet - dissecting miRNA-target interactions and functional associations through network-based visual analysis

PubMed Central

Fan, Yannan; Siklenka, Keith; Arora, Simran K.; Ribeiro, Paula; Kimmins, Sarah; Xia, Jianguo

2016-01-01

MicroRNAs (miRNAs) can regulate nearly all biological processes and their dysregulation is implicated in various complex diseases and pathological conditions. Recent years have seen a growing number of functional studies of miRNAs using high-throughput experimental technologies, which have produced a large amount of high-quality data regarding miRNA target genes and their interactions with small molecules, long non-coding RNAs, epigenetic modifiers, disease associations, etc. These rich sets of information have enabled the creation of comprehensive networks linking miRNAs with various biologically important entities to shed light on their collective functions and regulatory mechanisms. Here, we introduce miRNet, an easy-to-use web-based tool that offers statistical, visual and network-based approaches to help researchers understand miRNAs functions and regulatory mechanisms. The key features of miRNet include: (i) a comprehensive knowledge base integrating high-quality miRNA-target interaction data from 11 databases; (ii) support for differential expression analysis of data from microarray, RNA-seq and quantitative PCR; (iii) implementation of a flexible interface for data filtering, refinement and customization during network creation; (iv) a powerful fully featured network visualization system coupled with enrichment analysis. miRNet offers a comprehensive tool suite to enable statistical analysis and functional interpretation of various data generated from current miRNA studies. miRNet is freely available at http://www.mirnet.ca. PMID:27105848

TranslatomeDB: a comprehensive database and cloud-based analysis platform for translatome sequencing data

PubMed Central

Liu, Wanting; Xiang, Lunping; Zheng, Tingkai; Jin, Jingjie

2018-01-01

Abstract Translation is a key regulatory step, linking transcriptome and proteome. Two major methods of translatome investigations are RNC-seq (sequencing of translating mRNA) and Ribo-seq (ribosome profiling). To facilitate the investigation of translation, we built a comprehensive database TranslatomeDB (http://www.translatomedb.net/) which provides collection and integrated analysis of published and user-generated translatome sequencing data. The current version includes 2453 Ribo-seq, 10 RNC-seq and their 1394 corresponding mRNA-seq datasets in 13 species. The database emphasizes the analysis functions in addition to the dataset collections. Differential gene expression (DGE) analysis can be performed between any two datasets of same species and type, both on transcriptome and translatome levels. The translation indices translation ratios, elongation velocity index and translational efficiency can be calculated to quantitatively evaluate translational initiation efficiency and elongation velocity, respectively. All datasets were analyzed using a unified, robust, accurate and experimentally-verifiable pipeline based on the FANSe3 mapping algorithm and edgeR for DGE analyzes. TranslatomeDB also allows users to upload their own datasets and utilize the identical unified pipeline to analyze their data. We believe that our TranslatomeDB is a comprehensive platform and knowledgebase on translatome and proteome research, releasing the biologists from complex searching, analyzing and comparing huge sequencing data without needing local computational power. PMID:29106630

Associating Animations with Concrete Models to Enhance Students' Comprehension of Different Visual Representations in Organic Chemistry

ERIC Educational Resources Information Center

Al-Balushi, Sulaiman M.; Al-Hajri, Sheikha H.

2014-01-01

The purpose of the current study is to explore the impact of associating animations with concrete models on eleventh-grade students' comprehension of different visual representations in organic chemistry. The study used a post-test control group quasi-experimental design. The experimental group (N = 28) used concrete models, submicroscopic…

Morphological Instructional Packages as Determinants of Inferring Word Meanings in Reading Comprehension among Secondary School Students

ERIC Educational Resources Information Center

Akinwumi, Julius Olaitan; Olubunmi, Olagundoye Christanah

2017-01-01

This study investigated the effects of morphological instructional packages as determinants of inferring word meanings in reading comprehension among secondary school students in Ekiti State. The study adopted pre-test, post-test and control quasi-experimental research using two experimental groups and one control group with a sample of 270 Senior…

Using Different Types of Dictionaries for Improving EFL Reading Comprehension and Vocabulary Learning

ERIC Educational Resources Information Center

Alharbi, Majed A.

2016-01-01

This study investigated the effects of monolingual book dictionaries, popup dictionaries, and type-in dictionaries on improving reading comprehension and vocabulary learning in an EFL program. An experimental design involving four groups and a post-test was chosen for the experiment: (1) pop-up dictionary (experimental group 1); (2) type-in…

Vibration and noise analysis of a gear transmission system

NASA Technical Reports Server (NTRS)

Choy, F. K.; Qian, W.; Zakrajsek, J. J.; Oswald, F. B.

1993-01-01

This paper presents a comprehensive procedure to predict both the vibration and noise generated by a gear transmission system under normal operating conditions. The gearbox vibrations were obtained from both numerical simulation and experimental studies using a gear noise test rig. In addition, the noise generated by the gearbox vibrations was recorded during the experimental testing. A numerical method was used to develop linear relationships between the gearbox vibration and the generated noise. The hypercoherence function is introduced to correlate the nonlinear relationship between the fundamental noise frequency and its harmonics. A numerical procedure was developed using both the linear and nonlinear relationships generated from the experimental data to predict noise resulting from the gearbox vibrations. The application of this methodology is demonstrated by comparing the numerical and experimental results from the gear noise test rig.

Advanced Technology Airfoil Research, volume 1, part 1. [conference on development of computational codes and test facilities

NASA Technical Reports Server (NTRS)

1979-01-01

A comprehensive review of all NASA airfoil research, conducted both in-house and under grant and contract, as well as a broad spectrum of airfoil research outside of NASA is presented. Emphasis is placed on the development of computational aerodynamic codes for airfoil analysis and design, the development of experimental facilities and test techniques, and all types of airfoil applications.

Thermochemical Stability Study of Alkyl-Tethered Quaternary Ammonium Cations for Anion Exchange Membrane Fuel Cells

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

Mohanty, Angela D.; Tignor, Steven E.; Sturgeon, Matthew R.

2017-01-01

The increased interest in the use of anion exchange membranes (AEMs) for applications in electrochemical devices has prompted significant efforts in designing materials with robust stability in alkaline media. Most reported AEMs suffer from polymer backbone degradation as well as cation functional group degradation. In this report, we provide comprehensive experimental investigations for the analysis of cation functional group stability under alkaline media. A silver oxide-mediated ion exchange method and an accelerated stability test in aqueous KOH solutions at elevated temperatures using a Parr reactor were used to evaluate a broad scope of quaternary ammonium (QA) cationic model compound structures,more » particularly focusing on alkyl-tethered cations. Additionally, byproduct analysis was employed to gain better understanding of degradation pathways and trends of alkaline stability. Experimental results under different conditions gave consistent trends in the order of cation stability of various QA small molecule model compounds. Overall, cations that are benzyl-substituted or that are near to electronegative atoms (such as oxygen) degrade faster in alkaline media in comparison to alkyl-tethered QAs. These comprehensive model compound stability studies provide valuable information regarding the relative stability of various cation structures and can help guide researchers towards designing new and promising candidates for AEM materials.« less

The Effects of Self-Regulation Strategies on Reading Comprehension, Motivation for Learning, and Self-Efficacy with Struggling Readers

ERIC Educational Resources Information Center

Cosentino, Cassandra L.

2017-01-01

The purpose of this quasi-experimental study was to investigate the effect of a self-regulation treatment on sixth grade students' reading comprehension, motivation for learning, and self-efficacy perceptions. The research took place in three urban schools in the northeast United States in the winter of 2016. The study's quasi-experimental design…

The Impact of Cross-Age Peer Tutoring on Third and Sixth Graders' Reading Strategy Awareness, Reading Strategy Use, and Reading Comprehension

ERIC Educational Resources Information Center

Van Keer, Hilde; Vanderlinde, Ruben

2010-01-01

The present study explores the impact of an experimental reading intervention focusing on explicit reading strategy instruction and cross-age peer tutoring on third and sixth graders' reading strategy awareness, cognitive and metacognitive reading strategy use, and reading comprehension achievement. A quasi-experimental pretest-posttest design was…

Electrostimulation mapping of comprehension of auditory and visual words.

PubMed

Roux, Franck-Emmanuel; Miskin, Krasimir; Durand, Jean-Baptiste; Sacko, Oumar; Réhault, Emilie; Tanova, Rositsa; Démonet, Jean-François

2015-10-01

In order to spare functional areas during the removal of brain tumours, electrical stimulation mapping was used in 90 patients (77 in the left hemisphere and 13 in the right; 2754 cortical sites tested). Language functions were studied with a special focus on comprehension of auditory and visual words and the semantic system. In addition to naming, patients were asked to perform pointing tasks from auditory and visual stimuli (using sets of 4 different images controlled for familiarity), and also auditory object (sound recognition) and Token test tasks. Ninety-two auditory comprehension interference sites were observed. We found that the process of auditory comprehension involved a few, fine-grained, sub-centimetre cortical territories. Early stages of speech comprehension seem to relate to two posterior regions in the left superior temporal gyrus. Downstream lexical-semantic speech processing and sound analysis involved 2 pathways, along the anterior part of the left superior temporal gyrus, and posteriorly around the supramarginal and middle temporal gyri. Electrostimulation experimentally dissociated perceptual consciousness attached to speech comprehension. The initial word discrimination process can be considered as an "automatic" stage, the attention feedback not being impaired by stimulation as would be the case at the lexical-semantic stage. Multimodal organization of the superior temporal gyrus was also detected since some neurones could be involved in comprehension of visual material and naming. These findings demonstrate a fine graded, sub-centimetre, cortical representation of speech comprehension processing mainly in the left superior temporal gyrus and are in line with those described in dual stream models of language comprehension processing. Copyright © 2015 Elsevier Ltd. All rights reserved.

A vibrational study of inulin by means of experimental and theoretical methods

NASA Astrophysics Data System (ADS)

Balan, C.; Chis, M. I.; Rachisan, A. L.; Baia, M.

2018-07-01

Inulin, a natural polymer formed by several units of fructose and just one unit of glucose, is found in different plants or directly in some fruits or vegetables. Due to its structure it has been used in many applications from medicine, pharmacology or food industry. In spite of this, a complete vibrational analysis of the molecule is missing in the literature. Moreover, there are contradictory results regarding the assignment of certain vibrational modes. Therefore, the aim of this study was to obtain a comprehensive vibrational investigation of inulin by means of experimental (FT-IR and Raman spectroscopy) and theoretical (density functional theory -DFT simulations) methods.

Exploring Valid Reference Genes for Quantitative Real-time PCR Analysis in Plutella xylostella (Lepidoptera: Plutellidae)

PubMed Central

Fu, Wei; Xie, Wen; Zhang, Zhuo; Wang, Shaoli; Wu, Qingjun; Liu, Yong; Zhou, Xiaomao; Zhou, Xuguo; Zhang, Youjun

2013-01-01

Abstract: Quantitative real-time PCR (qRT-PCR), a primary tool in gene expression analysis, requires an appropriate normalization strategy to control for variation among samples. The best option is to compare the mRNA level of a target gene with that of reference gene(s) whose expression level is stable across various experimental conditions. In this study, expression profiles of eight candidate reference genes from the diamondback moth, Plutella xylostella, were evaluated under diverse experimental conditions. RefFinder, a web-based analysis tool, integrates four major computational programs including geNorm, Normfinder, BestKeeper, and the comparative ΔCt method to comprehensively rank the tested candidate genes. Elongation factor 1 (EF1) was the most suited reference gene for the biotic factors (development stage, tissue, and strain). In contrast, although appropriate reference gene(s) do exist for several abiotic factors (temperature, photoperiod, insecticide, and mechanical injury), we were not able to identify a single universal reference gene. Nevertheless, a suite of candidate reference genes were specifically recommended for selected experimental conditions. Our finding is the first step toward establishing a standardized qRT-PCR analysis of this agriculturally important insect pest. PMID:23983612

Image analysis technique as a tool to identify morphological changes in Trametes versicolor pellets according to exopolysaccharide or laccase production.

PubMed

Tavares, Ana P M; Silva, Rui P; Amaral, António L; Ferreira, Eugénio C; Xavier, Ana M R B

2014-02-01

Image analysis technique was applied to identify morphological changes of pellets from white-rot fungus Trametes versicolor on agitated submerged cultures during the production of exopolysaccharide (EPS) or ligninolytic enzymes. Batch tests with four different experimental conditions were carried out. Two different culture media were used, namely yeast medium or Trametes defined medium and the addition of lignolytic inducers as xylidine or pulp and paper industrial effluent were evaluated. Laccase activity, EPS production, and final biomass contents were determined for batch assays and the pellets morphology was assessed by image analysis techniques. The obtained data allowed establishing the choice of the metabolic pathways according to the experimental conditions, either for laccase enzymatic production in the Trametes defined medium, or for EPS production in the rich Yeast Medium experiments. Furthermore, the image processing and analysis methodology allowed for a better comprehension of the physiological phenomena with respect to the corresponding pellets morphological stages.

Comprehensive silicon solar cell computer modeling

NASA Technical Reports Server (NTRS)

Lamorte, M. F.

1984-01-01

The development of an efficient, comprehensive Si solar cell modeling program that has the capability of simulation accuracy of 5 percent or less is examined. A general investigation of computerized simulation is provided. Computer simulation programs are subdivided into a number of major tasks: (1) analytical method used to represent the physical system; (2) phenomena submodels that comprise the simulation of the system; (3) coding of the analysis and the phenomena submodels; (4) coding scheme that results in efficient use of the CPU so that CPU costs are low; and (5) modularized simulation program with respect to structures that may be analyzed, addition and/or modification of phenomena submodels as new experimental data become available, and the addition of other photovoltaic materials.

Evidence Base Update for Autism Spectrum Disorder.

PubMed

Smith, Tristram; Iadarola, Suzannah

2015-01-01

This evidence base update examines the level of empirical support for interventions for children with autism spectrum disorder (ASD) younger than 5 years old. It focuses on research published since a previous review in this journal (Rogers & Vismara, 2008 ). We identified psychological or behavioral interventions that had been manualized and evaluated in either (a) experimental or quasi-experimental group studies or (b) systematic reviews of single-subject studies. We extracted data from all studies that met these criteria and were published after the previous review. Interventions were categorized across two dimensions. First, primary theoretical principles included applied behavior analysis (ABA), developmental social-pragmatic (DSP), or both. Second, practice elements included scope (comprehensive or focused), modality (individual intervention with the child, parent training, or classrooms), and intervention targets (e.g., spoken language or alternative and augmentative communication). We classified two interventions as well-established (individual, comprehensive ABA and teacher-implemented, focused ABA + DSP), 3 as probably efficacious (individual, focused ABA for augmentative and alternative communication; individual, focused ABA + DSP; and focused DSP parent training), and 5 as possibly efficacious (individual, comprehensive ABA + DSP; comprehensive ABA classrooms; focused ABA for spoken communication; focused ABA parent training; and teacher-implemented, focused DSP). The evidence base for ASD interventions has grown substantially since 2008. An increasing number of interventions have some empirical support; others are emerging as potentially efficacious. Priorities for future research include improving outcome measures, developing interventions for understudied ASD symptoms (e.g., repetitive behaviors), pinpointing mechanisms of action in interventions, and adapting interventions for implementation with fidelity by community providers.

Identification of reference genes for quantitative expression analysis using large-scale RNA-seq data of Arabidopsis thaliana and model crop plants.

PubMed

Kudo, Toru; Sasaki, Yohei; Terashima, Shin; Matsuda-Imai, Noriko; Takano, Tomoyuki; Saito, Misa; Kanno, Maasa; Ozaki, Soichi; Suwabe, Keita; Suzuki, Go; Watanabe, Masao; Matsuoka, Makoto; Takayama, Seiji; Yano, Kentaro

2016-10-13

In quantitative gene expression analysis, normalization using a reference gene as an internal control is frequently performed for appropriate interpretation of the results. Efforts have been devoted to exploring superior novel reference genes using microarray transcriptomic data and to evaluating commonly used reference genes by targeting analysis. However, because the number of specifically detectable genes is totally dependent on probe design in the microarray analysis, exploration using microarray data may miss some of the best choices for the reference genes. Recently emerging RNA sequencing (RNA-seq) provides an ideal resource for comprehensive exploration of reference genes since this method is capable of detecting all expressed genes, in principle including even unknown genes. We report the results of a comprehensive exploration of reference genes using public RNA-seq data from plants such as Arabidopsis thaliana (Arabidopsis), Glycine max (soybean), Solanum lycopersicum (tomato) and Oryza sativa (rice). To select reference genes suitable for the broadest experimental conditions possible, candidates were surveyed by the following four steps: (1) evaluation of the basal expression level of each gene in each experiment; (2) evaluation of the expression stability of each gene in each experiment; (3) evaluation of the expression stability of each gene across the experiments; and (4) selection of top-ranked genes, after ranking according to the number of experiments in which the gene was expressed stably. Employing this procedure, 13, 10, 12 and 21 top candidates for reference genes were proposed in Arabidopsis, soybean, tomato and rice, respectively. Microarray expression data confirmed that the expression of the proposed reference genes under broad experimental conditions was more stable than that of commonly used reference genes. These novel reference genes will be useful for analyzing gene expression profiles across experiments carried out under various experimental conditions.

Experimental Study on Permeability of Concrete

NASA Astrophysics Data System (ADS)

Yang, Honglu; Liu, Rentai; Zheng, Zhuo; Liu, Haojie; Gao, Yan; Liu, Yankai

2018-01-01

To study the influencing factors on permeability of pervious concrete, by adding inorganic organic composite materials obtained experimental results show that different aggregate size, aggregate cement ratio of different, different water cement ratio on the permeability performance. The permeability of the concrete was tested by using the self - made permeable device. The experimental results showed that the permeation coefficient of the experiment was obtained and the factors influencing the permeability of the concrete were compared and analyzed. At the same time, the porosity of pervious concrete was measured, the influence of various variables on porosity was studied, and the influence of various factors on the permeability of voids was found. Finally, through comprehensive analysis of a variety of factors, the optimal water cement ratio is 0.28. At this time, the pervious performance of concrete is optimal.

Effects of Gender and School Location on the Ekiti State Secondary Schools Students' Achievement in Reading Comprehension in English Language

ERIC Educational Resources Information Center

Akinwumi, Julius Olaitan

2017-01-01

The purpose of this study was to find out the effects of gender and school location on the Ekiti State secondary school students achievement in reading comprehension in English language. The study adopted pre-test, post-test and control quasi-experimental research using two experimental groups and one control group. The sample for the study…

Improving Language-Focused Comprehension Instruction in Primary-Grade Classrooms: Impacts of the "Let's Know!" Experimental Curriculum

ERIC Educational Resources Information Center

Justice, Laura M.; Pratt, Amy; Logan, Jessica; Gray, Shelley

2014-01-01

This quasi-experimental study was designed to test the impacts of a curriculum supplement, "Let's Know!", on the quantity and quality of language-focused comprehension instruction in pre-kindergarten to third grade classrooms. Sixty classrooms (12 per each of pre-K to grade 3) were enrolled in the study, with 40 teachers assigned to…

The Effects of Phonological Short-Term Memory and Speech Perception on Spoken Sentence Comprehension in Children: Simulating Deficits in an Experimental Design

ERIC Educational Resources Information Center

Higgins, Meaghan C.; Penney, Sarah B.; Robertson, Erin K.

2017-01-01

The roles of phonological short-term memory (pSTM) and speech perception in spoken sentence comprehension were examined in an experimental design. Deficits in pSTM and speech perception were simulated through task demands while typically-developing children (N = 71) completed a sentence-picture matching task. Children performed the control,…

Aqua-vanadyl ion interaction with Nafion® membranes

DOE PAGES

Vijayakumar, Murugesan; Govind, Niranjan; Li, Bin; ...

2015-03-23

Lack of comprehensive understanding about the interactions between Nafion membrane and battery electrolytes prevents the straightforward tailoring of optimal materials for redox flow battery applications. In this work, we analyzed the interaction between aqua-vanadyl cation and sulfonic sites within the pores of Nafion membranes using combined theoretical and experimental X-ray spectroscopic methods. Molecular level interactions, namely, solvent share and contact pair mechanisms are discussed based on Vanadium and Sulfur K-edge spectroscopic analysis.

Scenario Generation and Assessment Framework Solution in Support of the Comprehensive Approach

DTIC Science & Technology

2010-04-01

attention, stress, fatigue etc.) and neurofeedback tracking for evaluation in a qualitative manner the real involvement of the trained participants in CAX...Series, Softrade, 2006 (in Bulgarian). [11] Minchev Z., Dukov G., Georgiev S. EEG Spectral Analysis in Serious Gaming: An Ad Hoc Experimental...Nonlinear and linear forecasting of the EEG time series, Biological Cybernetics, 66, 221-259, 1991. [20] Schubert, J., Svenson, P., and Mårtenson, Ch

Impact of a Technology-Mediated Reading Intervention on Adolescents' Reading Comprehension

ERIC Educational Resources Information Center

Fogarty, Melissa; Clemens, Nathan; Simmons, Deborah; Anderson, Leah; Davis, John; Smith, Ashley; Wang, Huan; Kwok, Oi-man; Simmons, Leslie E.; Oslund, Eric

2017-01-01

In this experimental study we examined the effects of a technology-mediated, multicomponent reading comprehension intervention, Comprehension Circuit Training (CCT), for middle school students, the majority of whom were struggling readers. The study was conducted in three schools, involving three teachers and 228 students. Using a within-teacher…

Genome analysis of Excretory/Secretory proteins in Taenia solium reveals their Abundance of Antigenic Regions (AAR).

PubMed

Gomez, Sandra; Adalid-Peralta, Laura; Palafox-Fonseca, Hector; Cantu-Robles, Vito Adrian; Soberón, Xavier; Sciutto, Edda; Fragoso, Gladis; Bobes, Raúl J; Laclette, Juan P; Yauner, Luis del Pozo; Ochoa-Leyva, Adrián

2015-05-19

Excretory/Secretory (ES) proteins play an important role in the host-parasite interactions. Experimental identification of ES proteins is time-consuming and expensive. Alternative bioinformatics approaches are cost-effective and can be used to prioritize the experimental analysis of therapeutic targets for parasitic diseases. Here we predicted and functionally annotated the ES proteins in T. solium genome using an integration of bioinformatics tools. Additionally, we developed a novel measurement to evaluate the potential antigenicity of T. solium secretome using sequence length and number of antigenic regions of ES proteins. This measurement was formalized as the Abundance of Antigenic Regions (AAR) value. AAR value for secretome showed a similar value to that obtained for a set of experimentally determined antigenic proteins and was different to the calculated value for the non-ES proteins of T. solium genome. Furthermore, we calculated the AAR values for known helminth secretomes and they were similar to that obtained for T. solium. The results reveal the utility of AAR value as a novel genomic measurement to evaluate the potential antigenicity of secretomes. This comprehensive analysis of T. solium secretome provides functional information for future experimental studies, including the identification of novel ES proteins of therapeutic, diagnosis and immunological interest.

Genome analysis of Excretory/Secretory proteins in Taenia solium reveals their Abundance of Antigenic Regions (AAR)

PubMed Central

Gomez, Sandra; Adalid-Peralta, Laura; Palafox-Fonseca, Hector; Cantu-Robles, Vito Adrian; Soberón, Xavier; Sciutto, Edda; Fragoso, Gladis; Bobes, Raúl J.; Laclette, Juan P.; Yauner, Luis del Pozo; Ochoa-Leyva, Adrián

2015-01-01

Excretory/Secretory (ES) proteins play an important role in the host-parasite interactions. Experimental identification of ES proteins is time-consuming and expensive. Alternative bioinformatics approaches are cost-effective and can be used to prioritize the experimental analysis of therapeutic targets for parasitic diseases. Here we predicted and functionally annotated the ES proteins in T. solium genome using an integration of bioinformatics tools. Additionally, we developed a novel measurement to evaluate the potential antigenicity of T. solium secretome using sequence length and number of antigenic regions of ES proteins. This measurement was formalized as the Abundance of Antigenic Regions (AAR) value. AAR value for secretome showed a similar value to that obtained for a set of experimentally determined antigenic proteins and was different to the calculated value for the non-ES proteins of T. solium genome. Furthermore, we calculated the AAR values for known helminth secretomes and they were similar to that obtained for T. solium. The results reveal the utility of AAR value as a novel genomic measurement to evaluate the potential antigenicity of secretomes. This comprehensive analysis of T. solium secretome provides functional information for future experimental studies, including the identification of novel ES proteins of therapeutic, diagnosis and immunological interest. PMID:25989346

Sentence Comprehension in Adolescents with down Syndrome and Typically Developing Children: Role of Sentence Voice, Visual Context, and Auditory-Verbal Short-Term Memory.

ERIC Educational Resources Information Center

Miolo, Giuliana; Chapman, Robins S.; Sindberg, Heidi A.

2005-01-01

The authors evaluated the roles of auditory-verbal short-term memory, visual short-term memory, and group membership in predicting language comprehension, as measured by an experimental sentence comprehension task (SCT) and the Test for Auditory Comprehension of Language--Third Edition (TACL-3; E. Carrow-Woolfolk, 1999) in 38 participants: 19 with…

TranslatomeDB: a comprehensive database and cloud-based analysis platform for translatome sequencing data.

PubMed

Liu, Wanting; Xiang, Lunping; Zheng, Tingkai; Jin, Jingjie; Zhang, Gong

2018-01-04

Translation is a key regulatory step, linking transcriptome and proteome. Two major methods of translatome investigations are RNC-seq (sequencing of translating mRNA) and Ribo-seq (ribosome profiling). To facilitate the investigation of translation, we built a comprehensive database TranslatomeDB (http://www.translatomedb.net/) which provides collection and integrated analysis of published and user-generated translatome sequencing data. The current version includes 2453 Ribo-seq, 10 RNC-seq and their 1394 corresponding mRNA-seq datasets in 13 species. The database emphasizes the analysis functions in addition to the dataset collections. Differential gene expression (DGE) analysis can be performed between any two datasets of same species and type, both on transcriptome and translatome levels. The translation indices translation ratios, elongation velocity index and translational efficiency can be calculated to quantitatively evaluate translational initiation efficiency and elongation velocity, respectively. All datasets were analyzed using a unified, robust, accurate and experimentally-verifiable pipeline based on the FANSe3 mapping algorithm and edgeR for DGE analyzes. TranslatomeDB also allows users to upload their own datasets and utilize the identical unified pipeline to analyze their data. We believe that our TranslatomeDB is a comprehensive platform and knowledgebase on translatome and proteome research, releasing the biologists from complex searching, analyzing and comparing huge sequencing data without needing local computational power. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Transitioning from Targeted to Comprehensive Mass Spectrometry Using Genetic Algorithms.

PubMed

Jaffe, Jacob D; Feeney, Caitlin M; Patel, Jinal; Lu, Xiaodong; Mani, D R

2016-11-01

Targeted proteomic assays are becoming increasingly popular because of their robust quantitative applications enabled by internal standardization, and they can be routinely executed on high performance mass spectrometry instrumentation. However, these assays are typically limited to 100s of analytes per experiment. Considerable time and effort are often expended in obtaining and preparing samples prior to targeted analyses. It would be highly desirable to detect and quantify 1000s of analytes in such samples using comprehensive mass spectrometry techniques (e.g., SWATH and DIA) while retaining a high degree of quantitative rigor for analytes with matched internal standards. Experimentally, it is facile to port a targeted assay to a comprehensive data acquisition technique. However, data analysis challenges arise from this strategy concerning agreement of results from the targeted and comprehensive approaches. Here, we present the use of genetic algorithms to overcome these challenges in order to configure hybrid targeted/comprehensive MS assays. The genetic algorithms are used to select precursor-to-fragment transitions that maximize the agreement in quantification between the targeted and the comprehensive methods. We find that the algorithm we used provided across-the-board improvement in the quantitative agreement between the targeted assay data and the hybrid comprehensive/targeted assay that we developed, as measured by parameters of linear models fitted to the results. We also found that the algorithm could perform at least as well as an independently-trained mass spectrometrist in accomplishing this task. We hope that this approach will be a useful tool in the development of quantitative approaches for comprehensive proteomics techniques. Graphical Abstract ᅟ.

Transitioning from Targeted to Comprehensive Mass Spectrometry Using Genetic Algorithms

NASA Astrophysics Data System (ADS)

Jaffe, Jacob D.; Feeney, Caitlin M.; Patel, Jinal; Lu, Xiaodong; Mani, D. R.

2016-11-01

Targeted proteomic assays are becoming increasingly popular because of their robust quantitative applications enabled by internal standardization, and they can be routinely executed on high performance mass spectrometry instrumentation. However, these assays are typically limited to 100s of analytes per experiment. Considerable time and effort are often expended in obtaining and preparing samples prior to targeted analyses. It would be highly desirable to detect and quantify 1000s of analytes in such samples using comprehensive mass spectrometry techniques (e.g., SWATH and DIA) while retaining a high degree of quantitative rigor for analytes with matched internal standards. Experimentally, it is facile to port a targeted assay to a comprehensive data acquisition technique. However, data analysis challenges arise from this strategy concerning agreement of results from the targeted and comprehensive approaches. Here, we present the use of genetic algorithms to overcome these challenges in order to configure hybrid targeted/comprehensive MS assays. The genetic algorithms are used to select precursor-to-fragment transitions that maximize the agreement in quantification between the targeted and the comprehensive methods. We find that the algorithm we used provided across-the-board improvement in the quantitative agreement between the targeted assay data and the hybrid comprehensive/targeted assay that we developed, as measured by parameters of linear models fitted to the results. We also found that the algorithm could perform at least as well as an independently-trained mass spectrometrist in accomplishing this task. We hope that this approach will be a useful tool in the development of quantitative approaches for comprehensive proteomics techniques.

The Attitudinal and Cognitive Effects of Planetarium Integration in Teaching Selected Astronomical Concepts to Fourth, Fifth, and Sixth-Grade Students

NASA Astrophysics Data System (ADS)

Twiest, Mark Gilbert

The purpose of this study was to investigate the attitudinal and cognitive differences among students in an astronomy curriculum which utilizes a planetarium in comparison to an astronomy curriculum which is presented solely in the classroom. The specific attitudes of interest in this study are those student attitudes toward science as a whole and toward astronomy in particular. Researcher developed attitude and astronomy achievement measures were developed and administered to 423 fourth, fifth, and sixth grade students in three schools. Pre and post test data were collected from students in this quasi-experimental design. Two way analysis of covariance techniques were used to analyze the independent variables of gender and treatment. Results revealed significant differences (p < .05) in student attitudes toward astronomy in the fourth grade favoring the control school students. No other significant differences in student attitudes were found with respect to treatment or gender. Achievement was analyzed at both the knowledge and comprehension levels. Significant differences (p <.05) in student achievement were found fourth and fifth grades with respect to knowledge level questions. In both instances these differences favored the control school setting. Significant differences (p <.05) in student achievement were found for comprehension level questions at every grade level. In this case the control school outperformed the experimental setting in the fourth and sixth grades. Fifth grade experimental setting students had significantly higher achievement on comprehension level questions. A significant interaction occurred between treatment and gender with respect to student attitudes toward astronomy in the fifth grade. A second significant interaction occurred between treatment and gender for knowledge level questions for sixth grade students. No other significant interactions were found between treatment and gender. Correlations between post test attitudes and achievement were also calculated for each grade level in both the control and experimental settings. Correlations remained below.2 in every instance except one. Post test correlations between attitudes overall and achievement in the control school's sixth grade were.54.

Modeling and analysis of a resonant nanosystem

NASA Astrophysics Data System (ADS)

Calvert, Scott L.

The majority of investigations into nanoelectromechanical resonators focus on a single area of the resonator's function. This focus varies from the development of a model for a beam's vibration, to the modeling of electrostatic forces, to a qualitative explanation of experimentally-obtained currents. Despite these efforts, there remains a gap between these works, and the level of sophistication needed to truly design nanoresonant systems for efficient commercial use. Towards this end, a comprehensive system model for both a nanobeam resonator and its related experimental setup is proposed. Furthermore, a simulation arrangement is suggested as a method for facilitating the study of the system-level behavior of these devices in a variety of cases that could not be easily obtained experimentally or analytically. The dynamics driving the nanoresonator's motion, as well as the electrical interactions influencing the forcing and output of the system, are modeled, experimentally validated, and studied. The model seeks to develop both a simple circuit representation of the nanoresonator, and to create a mathematical system that can be used to predict and interpret the observed behavior. Due to the assumptions used to simplify the model to a point of reasonable comprehension, the model is most accurate for small beam deflections near the first eigenmode of the beam. The process and results of an experimental investigation are documented, and compared with a circuit simulation modeling the full test system. The comparison qualitatively proves the functionality of the model, while a numerical analysis serves to validate the functionality and setup of the circuit simulation. The use of the simulation enables a much broader investigation of both the electrical behavior and the physical device's dynamics. It is used to complement an assessment of the tuning behavior of the system's linear natural frequency by demonstrating the tuning behavior of the full nonlinear response. The simulation is used to demonstrate the difficulties with the contemporary mixing approach to experimental data collection and to complete a variety of case studies investigating the use of the nanoresonator systems in practical applications, such as signal filtering. Many of these case studies would be difficult to complete analytically, but results are quickly achieved through the use of the simulation.

An Effect Analysis of Comprehensive Treatment of Groundwater Over-Exploitation in Cheng’an County, Hebei Province, China

PubMed Central

Shao, Weiwei; Zhou, Jinjun; Liu, Jiahong; Zhang, Haixing; Wang, Jianhua; Xiang, Chenyao; Yang, Guiyu; Tang, Yun

2017-01-01

The comprehensive treatment project of groundwater over-exploitation in Hebei Province has been implemented for more than a year, and the effect of exploitation restriction is in urgent need of evaluation. This paper deals with Cheng’an County of Hebei Province as the research subject. Based on collected hydro-meteorological, socioeconomic, groundwater, and other related data, together with typical regional experimental research, this study generates the effective precipitation–groundwater exploitation (P-W) curve and accompanying research methods, and calculates the quantity of groundwater exploitation restriction. It analyzes the target completion status of groundwater exploitation restriction through water conservancy measures and agricultural practices of the groundwater over-exploitation comprehensive treatment project that was implemented in Cheng’an County in 2014. The paper evaluates the treatment effect of groundwater over-exploitation, as well as provides technical support for the effect evaluation of groundwater exploitation restriction of agricultural irrigation in Cheng’an County and relevant areas. PMID:28054979

An Effect Analysis of Comprehensive Treatment of Groundwater Over-Exploitation in Cheng'an County, Hebei Province, China.

PubMed

Shao, Weiwei; Zhou, Jinjun; Liu, Jiahong; Zhang, Haixing; Wang, Jianhua; Xiang, Chenyao; Yang, Guiyu; Tang, Yun

2017-01-04

The comprehensive treatment project of groundwater over-exploitation in Hebei Province has been implemented for more than a year, and the effect of exploitation restriction is in urgent need of evaluation. This paper deals with Cheng'an County of Hebei Province as the research subject. Based on collected hydro-meteorological, socioeconomic, groundwater, and other related data, together with typical regional experimental research, this study generates the effective precipitation-groundwater exploitation (P-W) curve and accompanying research methods, and calculates the quantity of groundwater exploitation restriction. It analyzes the target completion status of groundwater exploitation restriction through water conservancy measures and agricultural practices of the groundwater over-exploitation comprehensive treatment project that was implemented in Cheng'an County in 2014. The paper evaluates the treatment effect of groundwater over-exploitation, as well as provides technical support for the effect evaluation of groundwater exploitation restriction of agricultural irrigation in Cheng'an County and relevant areas.

Mechanisms underlying syntactic comprehension deficits in vascular aphasia: new evidence from self-paced listening.

PubMed

Caplan, David; Michaud, Jennifer; Hufford, Rebecca

2015-01-01

Sixty-one people with aphasia (pwa) and 41 matched controls were tested for the ability to understand sentences that required the ability to process particular syntactic elements and assign particular syntactic structures. Participants paced themselves word-by-word through 20 examples of 11 spoken sentence types and indicated which of two pictures corresponded to the meaning of each sentence. Sentences were developed in pairs such that comprehension of the experimental version of a pair required an aspect of syntactic processing not required in the corresponding baseline sentence. The need for the syntactic operations required only in the experimental version was triggered at a "critical word" in the experimental sentence. Listening times for critical words in experimental sentences were compared to those for corresponding words in the corresponding baseline sentences. The results were consistent with several models of syntactic comprehension deficits in pwa: resource reduction, slowed lexical and/or syntactic processing, abnormal susceptibility to interference from thematic roles generated non-syntactically. They suggest that a previously unidentified disturbance limiting the duration of parsing and interpretation may lead to these deficits, and that this mechanism may lead to structure-specific deficits in pwa. The results thus point to more than one mechanism underlying syntactic comprehension disorders both across and within pwa.

Method Improving Reading Comprehension In Primary Education Program Students

NASA Astrophysics Data System (ADS)

Rohana

2018-01-01

This study aims to determine the influence of reading comprehension skills of English for PGSD students through the application of SQ3R learning method. The type of this research is Pre-Experimental research because it is not yet a real experiment, there are external variables that influence the formation of a dependent variable, this is because there is no control variable and the sample is not chosen randomly. The research design is used is one-group pretest-post-test design involving one group that is an experimental group. In this design, the observation is done twice before and after the experiment. Observations made before the experiment (O1) are called pretests and the post-experimental observation (O2) is called posttest. The difference between O1 and O2 ie O2 - O1 is the effect of the treatment. The results showed that there was an improvement in reading comprehension skills of PGSD students in Class M.4.3 using SQ3R method, and better SQ3R enabling SQ3R to improve English comprehension skills.

EFL Learners' Reading Comprehension Development through MALL: Telegram Groups in Focus

ERIC Educational Resources Information Center

Naderi, Naderi; Akrami, Azam

2018-01-01

The study aimed at investigating the effect of instruction through telegram groups on the learners' reading comprehension. Moreover, it investigated that whether there is any difference between two genders of the experimental groups in reading comprehension ability. For this purpose, 147 subjects were selected. To homogenize them, a standard…

Students' Reading Comprehension Performance with Emotional Literacy-Based Strategy Intervention

ERIC Educational Resources Information Center

Yussof, Yusfarina Mohd; Jamian, Abdul Rasid; Hamzah, Zaitul Azma Zainon; Roslan, Samsilah

2013-01-01

An effective reading comprehension process demands a strategy to enhance the cognitive ability to digest text information in the effort to elicit meaning contextually. In addition, the role of emotions also influences the efficacy of this process, especially in narrative text comprehension. This quasi-experimental study aims to observe students'…

The Effects of Self-Questioning on Reading Comprehension: A Literature Review

ERIC Educational Resources Information Center

Joseph, Laurice M.; Alber-Morgan, Sheila; Cullen, Jennifer; Rouse, Christina

2016-01-01

The ability to monitor one's own reading comprehension is a critical skill for deriving meaning from text. Self-questioning during reading is a strategy that enables students to monitor their reading comprehension and increases their ability to learn independently. The purpose of this article was to review experimental research studies that…

Classroom Simulation to Prepare Teachers to Use Evidence-Based Comprehension Practices

ERIC Educational Resources Information Center

Ely, Emily; Alves, Kat D.; Dolenc, Nathan R.; Sebolt, Stephanie; Walton, Emily A.

2018-01-01

Reading comprehension is an area of weakness for many students, including those with disabilities. Innovative technology methods may play a role in improving teacher readiness to use evidence-based comprehension practices for all students. In this experimental study, researchers examined a classroom simulation (TLE TeachLivE™) to improve…

Navier-Stokes and Comprehensive Analysis Performance Predictions of the NREL Phase VI Experiment

NASA Technical Reports Server (NTRS)

Duque, Earl P. N.; Burklund, Michael D.; Johnson, Wayne

2003-01-01

A vortex lattice code, CAMRAD II, and a Reynolds-Averaged Navier-Stoke code, OVERFLOW-D2, were used to predict the aerodynamic performance of a two-bladed horizontal axis wind turbine. All computations were compared with experimental data that was collected at the NASA Ames Research Center 80- by 120-Foot Wind Tunnel. Computations were performed for both axial as well as yawed operating conditions. Various stall delay models and dynamics stall models were used by the CAMRAD II code. Comparisons between the experimental data and computed aerodynamic loads show that the OVERFLOW-D2 code can accurately predict the power and spanwise loading of a wind turbine rotor.

Oxidation Mechanisms of Toluene and Benzene

NASA Technical Reports Server (NTRS)

Bittker, David A.

1995-01-01

An expanded and improved version of a previously published benzene oxidation mechanism is presented and shown to model published experimental data fairly successfully. This benzene submodel is coupled to a modified version of a toluene oxidation submodel from the recent literature. This complete mechanism is shown to successfully model published experimental toluene oxidation data for a highly mixed flow reactor and for higher temperature ignition delay times in a shock tube. A comprehensive sensitivity analysis showing the most important reactions is presented for both the benzene and toluene reacting systems. The NASA Lewis toluene mechanism's modeling capability is found to be equivalent to that of the previously published mechanism which contains a somewhat different benzene submodel.

Coupled CFD/CSD Analysis of an Active-Twist Rotor in a Wind Tunnel with Experimental Validation

NASA Technical Reports Server (NTRS)

Massey, Steven J.; Kreshock, Andrew R.; Sekula, Martin K.

2015-01-01

An unsteady Reynolds averaged Navier-Stokes analysis loosely coupled with a comprehensive rotorcraft code is presented for a second-generation active-twist rotor. High fidelity Navier-Stokes results for three configurations: an isolated rotor, a rotor with fuselage, and a rotor with fuselage mounted in a wind tunnel, are compared to lifting-line theory based comprehensive rotorcraft code calculations and wind tunnel data. Results indicate that CFD/CSD predictions of flapwise bending moments are in good agreement with wind tunnel measurements for configurations with a fuselage, and that modeling the wind tunnel environment does not significantly enhance computed results. Actuated rotor results for the rotor with fuselage configuration are also validated for predictions of vibratory blade loads and fixed-system vibratory loads. Varying levels of agreement with wind tunnel measurements are observed for blade vibratory loads, depending on the load component (flap, lag, or torsion) and the harmonic being examined. Predicted trends in fixed-system vibratory loads are in good agreement with wind tunnel measurements.

Systems cell biology

PubMed Central

Mast, Fred D.; Ratushny, Alexander V.

2014-01-01

Systems cell biology melds high-throughput experimentation with quantitative analysis and modeling to understand many critical processes that contribute to cellular organization and dynamics. Recently, there have been several advances in technology and in the application of modeling approaches that enable the exploration of the dynamic properties of cells. Merging technology and computation offers an opportunity to objectively address unsolved cellular mechanisms, and has revealed emergent properties and helped to gain a more comprehensive and fundamental understanding of cell biology. PMID:25225336

PeTTSy: a computational tool for perturbation analysis of complex systems biology models.

PubMed

Domijan, Mirela; Brown, Paul E; Shulgin, Boris V; Rand, David A

2016-03-10

Over the last decade sensitivity analysis techniques have been shown to be very useful to analyse complex and high dimensional Systems Biology models. However, many of the currently available toolboxes have either used parameter sampling, been focused on a restricted set of model observables of interest, studied optimisation of a objective function, or have not dealt with multiple simultaneous model parameter changes where the changes can be permanent or temporary. Here we introduce our new, freely downloadable toolbox, PeTTSy (Perturbation Theory Toolbox for Systems). PeTTSy is a package for MATLAB which implements a wide array of techniques for the perturbation theory and sensitivity analysis of large and complex ordinary differential equation (ODE) based models. PeTTSy is a comprehensive modelling framework that introduces a number of new approaches and that fully addresses analysis of oscillatory systems. It examines sensitivity analysis of the models to perturbations of parameters, where the perturbation timing, strength, length and overall shape can be controlled by the user. This can be done in a system-global setting, namely, the user can determine how many parameters to perturb, by how much and for how long. PeTTSy also offers the user the ability to explore the effect of the parameter perturbations on many different types of outputs: period, phase (timing of peak) and model solutions. PeTTSy can be employed on a wide range of mathematical models including free-running and forced oscillators and signalling systems. To enable experimental optimisation using the Fisher Information Matrix it efficiently allows one to combine multiple variants of a model (i.e. a model with multiple experimental conditions) in order to determine the value of new experiments. It is especially useful in the analysis of large and complex models involving many variables and parameters. PeTTSy is a comprehensive tool for analysing large and complex models of regulatory and signalling systems. It allows for simulation and analysis of models under a variety of environmental conditions and for experimental optimisation of complex combined experiments. With its unique set of tools it makes a valuable addition to the current library of sensitivity analysis toolboxes. We believe that this software will be of great use to the wider biological, systems biology and modelling communities.

Comprehension and Motivation Levels in Conjunction with the Use of eBooks with Audio: A Quasi-Experimental Study of Post-Secondary Remedial Reading Students

ERIC Educational Resources Information Center

Wheeler, Kimberly W.

2014-01-01

This quasi-experimental pretest, posttest nonequivalent control group study investigated the comprehension scores and motivation levels of post-secondary remedial reading students in a two-year technical college in Northwest Georgia using an eBook, an eBook with audio, and a print book. After reading a module on Purpose and Tone in the three book…

Turbulence-induced persistence in laser beam wandering.

PubMed

Zunino, Luciano; Gulich, Damián; Funes, Gustavo; Pérez, Darío G

2015-07-01

We have experimentally confirmed the presence of long-memory correlations in the wandering of a thin Gaussian laser beam over a screen after propagating through a turbulent medium. A laboratory-controlled experiment was conducted in which coordinate fluctuations of the laser beam were recorded at a sufficiently high sampling rate for a wide range of turbulent conditions. Horizontal and vertical displacements of the laser beam centroid were subsequently analyzed by implementing detrended fluctuation analysis. This is a very well-known and widely used methodology to unveil memory effects from time series. Results obtained from this experimental analysis allow us to confirm that both coordinates behave as highly persistent signals for strong turbulent intensities. This finding is relevant for a better comprehension and modeling of the turbulence effects in free-space optical communication systems and other applications related to propagation of optical signals in the atmosphere.

Analysis of natural convection in nanofluid-filled H-shaped cavity by entropy generation and heatline visualization using lattice Boltzmann method

NASA Astrophysics Data System (ADS)

Rahimi, Alireza; Sepehr, Mohammad; Lariche, Milad Janghorban; Mesbah, Mohammad; Kasaeipoor, Abbas; Malekshah, Emad Hasani

2018-03-01

The lattice Boltzmann simulation of natural convection in H-shaped cavity filled with nanofluid is performed. The entropy generation analysis and heatline visualization are employed to analyze the considered problem comprehensively. The produced nanofluid is SiO2-TiO2/Water-EG (60:40) hybrid nanofluid, and the thermal conductivity and dynamic viscosity of used nanofluid are measured experimentally. To use the experimental data of thermal conductivity and dynamic viscosity, two sets of correlations based on temperature for six different solid volume fractions of 0.5, 1, 1.5, 2, 2.5 and 3 vol% are derived. The influences of different governing parameters such different aspect ratio, solid volume fractions of nanofluid and Rayleigh numbers on the fluid flow, temperature filed, average/local Nusselt number, total/local entropy generation and heatlines are presented.

Knowledge-based analysis of microarrays for the discovery of transcriptional regulation relationships

PubMed Central

2010-01-01

Background The large amount of high-throughput genomic data has facilitated the discovery of the regulatory relationships between transcription factors and their target genes. While early methods for discovery of transcriptional regulation relationships from microarray data often focused on the high-throughput experimental data alone, more recent approaches have explored the integration of external knowledge bases of gene interactions. Results In this work, we develop an algorithm that provides improved performance in the prediction of transcriptional regulatory relationships by supplementing the analysis of microarray data with a new method of integrating information from an existing knowledge base. Using a well-known dataset of yeast microarrays and the Yeast Proteome Database, a comprehensive collection of known information of yeast genes, we show that knowledge-based predictions demonstrate better sensitivity and specificity in inferring new transcriptional interactions than predictions from microarray data alone. We also show that comprehensive, direct and high-quality knowledge bases provide better prediction performance. Comparison of our results with ChIP-chip data and growth fitness data suggests that our predicted genome-wide regulatory pairs in yeast are reasonable candidates for follow-up biological verification. Conclusion High quality, comprehensive, and direct knowledge bases, when combined with appropriate bioinformatic algorithms, can significantly improve the discovery of gene regulatory relationships from high throughput gene expression data. PMID:20122245

Performance Evaluation and Online Realization of Data-driven Normalization Methods Used in LC/MS based Untargeted Metabolomics Analysis.

PubMed

Li, Bo; Tang, Jing; Yang, Qingxia; Cui, Xuejiao; Li, Shuang; Chen, Sijie; Cao, Quanxing; Xue, Weiwei; Chen, Na; Zhu, Feng

2016-12-13

In untargeted metabolomics analysis, several factors (e.g., unwanted experimental &biological variations and technical errors) may hamper the identification of differential metabolic features, which requires the data-driven normalization approaches before feature selection. So far, ≥16 normalization methods have been widely applied for processing the LC/MS based metabolomics data. However, the performance and the sample size dependence of those methods have not yet been exhaustively compared and no online tool for comparatively and comprehensively evaluating the performance of all 16 normalization methods has been provided. In this study, a comprehensive comparison on these methods was conducted. As a result, 16 methods were categorized into three groups based on their normalization performances across various sample sizes. The VSN, the Log Transformation and the PQN were identified as methods of the best normalization performance, while the Contrast consistently underperformed across all sub-datasets of different benchmark data. Moreover, an interactive web tool comprehensively evaluating the performance of 16 methods specifically for normalizing LC/MS based metabolomics data was constructed and hosted at http://server.idrb.cqu.edu.cn/MetaPre/. In summary, this study could serve as a useful guidance to the selection of suitable normalization methods in analyzing the LC/MS based metabolomics data.

Performance Evaluation and Online Realization of Data-driven Normalization Methods Used in LC/MS based Untargeted Metabolomics Analysis

PubMed Central

Li, Bo; Tang, Jing; Yang, Qingxia; Cui, Xuejiao; Li, Shuang; Chen, Sijie; Cao, Quanxing; Xue, Weiwei; Chen, Na; Zhu, Feng

2016-01-01

In untargeted metabolomics analysis, several factors (e.g., unwanted experimental & biological variations and technical errors) may hamper the identification of differential metabolic features, which requires the data-driven normalization approaches before feature selection. So far, ≥16 normalization methods have been widely applied for processing the LC/MS based metabolomics data. However, the performance and the sample size dependence of those methods have not yet been exhaustively compared and no online tool for comparatively and comprehensively evaluating the performance of all 16 normalization methods has been provided. In this study, a comprehensive comparison on these methods was conducted. As a result, 16 methods were categorized into three groups based on their normalization performances across various sample sizes. The VSN, the Log Transformation and the PQN were identified as methods of the best normalization performance, while the Contrast consistently underperformed across all sub-datasets of different benchmark data. Moreover, an interactive web tool comprehensively evaluating the performance of 16 methods specifically for normalizing LC/MS based metabolomics data was constructed and hosted at http://server.idrb.cqu.edu.cn/MetaPre/. In summary, this study could serve as a useful guidance to the selection of suitable normalization methods in analyzing the LC/MS based metabolomics data. PMID:27958387

Knowledge-based analysis of microarrays for the discovery of transcriptional regulation relationships.

PubMed

Seok, Junhee; Kaushal, Amit; Davis, Ronald W; Xiao, Wenzhong

2010-01-18

The large amount of high-throughput genomic data has facilitated the discovery of the regulatory relationships between transcription factors and their target genes. While early methods for discovery of transcriptional regulation relationships from microarray data often focused on the high-throughput experimental data alone, more recent approaches have explored the integration of external knowledge bases of gene interactions. In this work, we develop an algorithm that provides improved performance in the prediction of transcriptional regulatory relationships by supplementing the analysis of microarray data with a new method of integrating information from an existing knowledge base. Using a well-known dataset of yeast microarrays and the Yeast Proteome Database, a comprehensive collection of known information of yeast genes, we show that knowledge-based predictions demonstrate better sensitivity and specificity in inferring new transcriptional interactions than predictions from microarray data alone. We also show that comprehensive, direct and high-quality knowledge bases provide better prediction performance. Comparison of our results with ChIP-chip data and growth fitness data suggests that our predicted genome-wide regulatory pairs in yeast are reasonable candidates for follow-up biological verification. High quality, comprehensive, and direct knowledge bases, when combined with appropriate bioinformatic algorithms, can significantly improve the discovery of gene regulatory relationships from high throughput gene expression data.

The Comprehension Problems of Children with Poor Reading Comprehension Despite Adequate Decoding: A Meta-Analysis

ERIC Educational Resources Information Center

Spencer, Mercedes; Wagner, Richard K.

2018-01-01

The purpose of this meta-analysis was to examine the comprehension problems of children who have a specific reading comprehension deficit (SCD), which is characterized by poor reading comprehension despite adequate decoding. The meta-analysis included 86 studies of children with SCD who were assessed in reading comprehension and oral language…

Teaching Genetics with Multimedia Results in Better Acquisition of Knowledge and Improvement in Comprehension

ERIC Educational Resources Information Center

Starbek, P.; Erjavec, M. Starcic; Peklaj, C.

2010-01-01

The main goal of this study was to explore whether the use of multimedia in genetics instruction contributes more to students' knowledge and comprehension than other instructional modes. We were also concerned with the influence of different instructional modes on the retention of knowledge and comprehension. In a quasi-experimental design, four…

Acquisition of Prosodic Focus Marking by English, French, and German Three-, Four-, Five- and Six-Year-Olds

ERIC Educational Resources Information Center

Szendroi, Kriszta; Bernard, Carline; Berger, Frauke; Gervain, Judit; Hohle, Barbara

2018-01-01

Previous research on young children's knowledge of prosodic focus marking has revealed an apparent paradox, with comprehension appearing to lag behind production. Comprehension of prosodic focus is difficult to study experimentally due to its subtle and ambiguous contribution to pragmatic meaning. We designed a novel comprehension task, which…

The Effects of an Intensive Reading Intervention for Ninth Graders with Very Low Reading Comprehension

ERIC Educational Resources Information Center

Solís, Michael; Vaughn, Sharon; Scammacca, Nancy

2015-01-01

This experimental study examined the efficacy of a multicomponent reading intervention compared to a control condition on the reading comprehension of adolescent students with low reading comprehension (more than 1½ standard deviations below normative sample). Ninth-grade students were randomly assigned to treatment (n = 25) and comparison (n =…

Can Cloze Tests Really Improve Second Language Learners' Reading Comprehension Skills?

ERIC Educational Resources Information Center

Ren, Guanxin

2011-01-01

Cloze testing is a widely-used procedure to test learners' reading comprehension in learning a language, but little is known if it can really improve learners' reading comprehension skills. This paper attempts to seek answers to this question by comparing the cloze test scores of two groups of students (Experimental versus Control) undertaking…

The Effect of Text Typographical Features on Legibility, Comprehension, and Retrieval of EFL Learners

ERIC Educational Resources Information Center

Soleimani, Hassan; Mohammadi, Elham

2012-01-01

This experimental study investigated the relationship between font type, font size, and line spacing and legibility, as measured by speed of reading, comprehension, and recalling. Instruments for testing legibility and reading comprehension were presented in eight typographical styles in print. The study tested 90 students for legibility and 76…

Bringing Together Reading and Writing: An Experimental Study of Writing Intensive Reading Comprehension in Low-Performing Urban Elementary Schools

ERIC Educational Resources Information Center

Collins, James L.; Lee, Jaekyung; Fox, Jeffery D.; Madigan, Timothy P.

2017-01-01

This study examined the hypothesis that assisted writing during reading improves reading comprehension. The hypothesis was derived from sociocognitive and constructivist theory and research and implemented in the form of a curricular intervention called Writing Intensive Reading Comprehension after its main feature of bringing together reading…

Enhancing Literacy Skills of Students with Congenital and Profound Hearing Impairment in Nigeria Using Babudoh's Comprehension Therapy

ERIC Educational Resources Information Center

Babudoh, Gladys B.

2014-01-01

This study reports the effect of a treatment tool called "Babudoh's comprehension therapy" in enhancing the comprehension and writing skills of 10 junior secondary school students with congenital and profound hearing impairment in Plateau State, Nigeria. The study adopted the single group pretest-posttest quasi-experimental research…

Comprehensive Experimental and Computational Analysis of Binding Energy Hot Spots at the NF-κB Essential Modulator (NEMO)/IKKβ Protein-Protein Interface

PubMed Central

Golden, Mary S.; Cote, Shaun M.; Sayeg, Marianna; Zerbe, Brandon S.; Villar, Elizabeth A.; Beglov, Dmitri; Sazinsky, Stephen L.; Georgiadis, Rosina M.; Vajda, Sandor; Kozakov, Dima; Whitty, Adrian

2013-01-01

We report a comprehensive analysis of binding energy hot spots at the protein-protein interaction (PPI) interface between NF-κB Essential Modulator (NEMO) and IκB kinase subunit β (IKKβ), an interaction that is critical for NF-κB pathway signaling, using experimental alanine scanning mutagenesis and also the FTMap method for computational fragment screening. The experimental results confirm that the previously identified NBD region of IKKβ contains the highest concentration of hot spot residues, the strongest of which are W739, W741 and L742 (ΔΔG = 4.3, 3.5 and 3.2 kcal/mol, respectively). The region occupied by these residues defines a potentially druggable binding site on NEMO that extends for ~16 Å to additionally include the regions that bind IKKβ L737 and F734. NBD residues D738 and S740 are also important for binding but do not make direct contact with NEMO, instead likely acting to stabilize the active conformation of surrounding residues. We additionally found two previously unknown hot spot regions centered on IKKβ residues L708/V709 and L719/I723. The computational approach successfully identified all three hot spot regions on IKKβ. Moreover, the method was able to accurately quantify the energetic importance of all hot spots residues involving direct contact with NEMO. Our results provide new information to guide the discovery of small molecule inhibitors that target the NEMO/IKKβ interaction. They additionally clarify the structural and energetic complementarity between “pocket-forming” and “pocket occupying” hot spot residues, and further validate computational fragment mapping as a method for identifying hot spots at PPI interfaces. PMID:23506214

Plant Architecture: A Dynamic, Multilevel and Comprehensive Approach to Plant Form, Structure and Ontogeny

PubMed Central

Barthélémy, Daniel; Caraglio, Yves

2007-01-01

Background and Aims The architecture of a plant depends on the nature and relative arrangement of each of its parts; it is, at any given time, the expression of an equilibrium between endogenous growth processes and exogenous constraints exerted by the environment. The aim of architectural analysis is, by means of observation and sometimes experimentation, to identify and understand these endogenous processes and to separate them from the plasticity of their expression resulting from external influences. Scope Using the identification of several morphological criteria and considering the plant as a whole, from germination to death, architectural analysis is essentially a detailed, multilevel, comprehensive and dynamic approach to plant development. Despite their recent origin, architectural concepts and analysis methods provide a powerful tool for studying plant form and ontogeny. Completed by precise morphological observations and appropriated quantitative methods of analysis, recent researches in this field have greatly increased our understanding of plant structure and development and have led to the establishment of a real conceptual and methodological framework for plant form and structure analysis and representation. This paper is a summarized update of current knowledge on plant architecture and morphology; its implication and possible role in various aspects of modern plant biology is also discussed. PMID:17218346

Comprehensive analysis of ß-lactam antibiotics including penicillins, cephalosporins, and carbapenems in poultry muscle using liquid chromatography coupled to tandem mass spectrometry.

PubMed

Berendsen, Bjorn J A; Gerritsen, Henk W; Wegh, Robin S; Lameris, Steven; van Sebille, Ralph; Stolker, Alida A M; Nielen, Michel W F

2013-09-01

A comprehensive method for the quantitative residue analysis of trace levels of 22 ß-lactam antibiotics, including penicillins, cephalosporins, and carbapenems, in poultry muscle by liquid chromatography in combination with tandem mass spectrometric detection is reported. The samples analyzed for ß-lactam residues are hydrolyzed using piperidine in order to improve compound stability and to include the total residue content of the cephalosporin ceftifour. The reaction procedure was optimized using a full experimental design. Following detailed isotope labeling, tandem mass spectrometry studies and exact mass measurements using high-resolution mass spectrometry reaction schemes could be proposed for all ß-lactams studied. The main reaction occurring is the hydrolysis of the ß-lactam ring under formation of the piperidine substituted amide. For some ß-lactams, multiple isobaric hydrolysis reaction products are obtained, in accordance with expectations, but this did not hamper quantitative analysis. The final method was fully validated as a quantitative confirmatory residue analysis method according to Commission Decision 2002/657/EC and showed satisfactory quantitative performance for all compounds with trueness between 80 and 110% and within-laboratory reproducibility below 22% at target level, except for biapenem. For biapenem, the method proved to be suitable for qualitative analysis only.

CalFitter: a web server for analysis of protein thermal denaturation data.

PubMed

Mazurenko, Stanislav; Stourac, Jan; Kunka, Antonin; Nedeljkovic, Sava; Bednar, David; Prokop, Zbynek; Damborsky, Jiri

2018-05-14

Despite significant advances in the understanding of protein structure-function relationships, revealing protein folding pathways still poses a challenge due to a limited number of relevant experimental tools. Widely-used experimental techniques, such as calorimetry or spectroscopy, critically depend on a proper data analysis. Currently, there are only separate data analysis tools available for each type of experiment with a limited model selection. To address this problem, we have developed the CalFitter web server to be a unified platform for comprehensive data fitting and analysis of protein thermal denaturation data. The server allows simultaneous global data fitting using any combination of input data types and offers 12 protein unfolding pathway models for selection, including irreversible transitions often missing from other tools. The data fitting produces optimal parameter values, their confidence intervals, and statistical information to define unfolding pathways. The server provides an interactive and easy-to-use interface that allows users to directly analyse input datasets and simulate modelled output based on the model parameters. CalFitter web server is available free at https://loschmidt.chemi.muni.cz/calfitter/.

BFDCA: A Comprehensive Tool of Using Bayes Factor for Differential Co-Expression Analysis.

PubMed

Wang, Duolin; Wang, Juexin; Jiang, Yuexu; Liang, Yanchun; Xu, Dong

2017-02-03

Comparing the gene-expression profiles between biological conditions is useful for understanding gene regulation underlying complex phenotypes. Along this line, analysis of differential co-expression (DC) has gained attention in the recent years, where genes under one condition have different co-expression patterns compared with another. We developed an R package Bayes Factor approach for Differential Co-expression Analysis (BFDCA) for DC analysis. BFDCA is unique in integrating various aspects of DC patterns (including Shift, Cross, and Re-wiring) into one uniform Bayes factor. We tested BFDCA using simulation data and experimental data. Simulation results indicate that BFDCA outperforms existing methods in accuracy and robustness of detecting DC pairs and DC modules. Results of using experimental data suggest that BFDCA can cluster disease-related genes into functional DC subunits and estimate the regulatory impact of disease-related genes well. BFDCA also achieves high accuracy in predicting case-control phenotypes by using significant DC gene pairs as markers. BFDCA is publicly available at http://dx.doi.org/10.17632/jdz4vtvnm3.1. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evaluation of a long-term home care program.

PubMed

Hughes, S L; Cordray, D S; Spiker, V A

1984-05-01

This article reports the outcomes of a 9-month evaluation of the Five Hospital Homebound Elderly Program ( FHHEP ), a model long-term, comprehensive, coordinated home care program in Chicago. Outcomes assessed include the mortality, comprehensive functional status, and rates of hospitalization and of institutionalization of the elderly (mean age, 80.4 years), chronically impaired population served by the FHHEP . The evaluation utilized a quasi-experimental, preposttest design with a nonequivalent control group consisting of similarly elderly and impaired subjects who received OAA Title III-c home-delivered meals. Consecutively accepted experimental (n = 122) and control group clients (n = 123) were interviewed using the Duke/ OARS Multi-dimensional Functional Assessment Questionnaire at the time of acceptance to service and 9 months later. Service utilization data were also obtained for both groups to correlate client outcomes and characteristics with level and type of services used. Data collection took place over a 31-month period. Posttest functional status measures were obtained for 83% of experimental and 81% of control subjects. Multivariate analysis was used to control measured pretest differences. Major findings include a significant reduction in the nursing home admissions (16 vs. 28) and nursing home days (including sheltered care) of experimental group clients. The reported analyses also show an increase in experimental clients' sense of physical health well-being and a decrease in their number of previously unmet needs for community services. Somewhat paradoxically, the experimental sample also demonstrated a decrease in physical activities of daily living ( PADL ) functioning. The mortality and hospitalization rate were equal for both groups. Despite savings in nursing home days of care, average per-capita costs for experimental group clients were 19% higher than for controls. However, this additional cost was accompanied by an increase in quality of life. Longer-range cost and outcomes are being assessed through a 4-year follow-up study currently in progress.

Comprehensive Modeling and Analysis of Rotorcraft Variable Speed Propulsion System With Coupled Engine/Transmission/Rotor Dynamics

NASA Technical Reports Server (NTRS)

DeSmidt, Hans A.; Smith, Edward C.; Bill, Robert C.; Wang, Kon-Well

2013-01-01

This project develops comprehensive modeling and simulation tools for analysis of variable rotor speed helicopter propulsion system dynamics. The Comprehensive Variable-Speed Rotorcraft Propulsion Modeling (CVSRPM) tool developed in this research is used to investigate coupled rotor/engine/fuel control/gearbox/shaft/clutch/flight control system dynamic interactions for several variable rotor speed mission scenarios. In this investigation, a prototypical two-speed Dual-Clutch Transmission (DCT) is proposed and designed to achieve 50 percent rotor speed variation. The comprehensive modeling tool developed in this study is utilized to analyze the two-speed shift response of both a conventional single rotor helicopter and a tiltrotor drive system. In the tiltrotor system, both a Parallel Shift Control (PSC) strategy and a Sequential Shift Control (SSC) strategy for constant and variable forward speed mission profiles are analyzed. Under the PSC strategy, selecting clutch shift-rate results in a design tradeoff between transient engine surge margins and clutch frictional power dissipation. In the case of SSC, clutch power dissipation is drastically reduced in exchange for the necessity to disengage one engine at a time which requires a multi-DCT drive system topology. In addition to comprehensive simulations, several sections are dedicated to detailed analysis of driveline subsystem components under variable speed operation. In particular an aeroelastic simulation of a stiff in-plane rotor using nonlinear quasi-steady blade element theory was conducted to investigate variable speed rotor dynamics. It was found that 2/rev and 4/rev flap and lag vibrations were significant during resonance crossings with 4/rev lagwise loads being directly transferred into drive-system torque disturbances. To capture the clutch engagement dynamics, a nonlinear stick-slip clutch torque model is developed. Also, a transient gas-turbine engine model based on first principles mean-line compressor and turbine approximations is developed. Finally an analysis of high frequency gear dynamics including the effect of tooth mesh stiffness variation under variable speed operation is conducted including experimental validation. Through exploring the interactions between the various subsystems, this investigation provides important insights into the continuing development of variable-speed rotorcraft propulsion systems.

Elbow stress indices using finite element analysis

NASA Astrophysics Data System (ADS)

Yu, Lixin

Section III of the ASME Boiler and Pressure Vessel Code (the Code) specifies rules for the design of nuclear power plant components. NB-3600 of the Code presents a simplified design method using stress indices---Scalar Coefficients used the modify straight pipe stress equations so that they can be applied to elbows, tees and other piping components. The stress indices of piping components are allowed to be determined both analytically and experimentally. This study concentrates on the determination of B2 stress indices for elbow components using finite element analysis (FEA). First, the previous theoretical, numerical and experimental investigations on elbow behavior were comprehensively reviewed, as was the philosophy behind the use of stress indices. The areas of further research was defined. Then, a comprehensive investigation was carried out to determine how the finite element method should be used to correctly simulate an elbow's structural behavior. This investigation included choice of element type, convergence of mesh density, use of boundary restraint and a reconciliation study between FEA and laboratory experiments or other theoretical formulations in both elastic and elasto-plastic domain. Results from different computer programs were also compared. Reasonably good reconciliation was obtained. Appendix II of the Code describes the experimental method to determine B2 stress indices based on load-deflection curves. This procedure was used to compute the B2 stress indices for various loading modes on one particular elbow configuration. The B2 stress indices thus determined were found to be about half of the value calculated from the Code equation. Then the effect on B2 stress indices of those factors such as internal pressure and flange attachments were studied. Finally, the investigation was extended to other configurations of elbow components. A parametric study was conducted on different elbow sizes and schedules. Regression analysis was then used to obtain a modified coefficient and exponent for the Code equation used to calculate B2 index for elbows.

Thermomagnetic convective flows in a vertical layer of ferrocolloid: perturbation energy analysis and experimental study.

PubMed

Suslov, Sergey A; Bozhko, Alexandra A; Sidorov, Alexander S; Putin, Gennady F

2012-07-01

Flow patterns arising in a vertical differentially heated layer of nonconducting ferromagnetic fluid placed in an external uniform transverse magnetic field are studied experimentally and discussed from the point of view of the perturbation energy balance. A quantitative criterion for detecting the parametric point where the dominant role in generating a flow instability is transferred between the thermogravitational and thermomagnetic mechanisms is suggested, based on the disturbance energy balance analysis. A comprehensive experimental study of various flow patterns is undertaken, and the existence is demonstrated of oblique thermomagnetic waves theoretically predicted by Suslov [Phys. Fluids 20, 084101 (2008)] and superposed onto the stationary magnetoconvective pattern known previously. It is found that the wave number of the detected convection patterns depends sensitively on the temperature difference across the layer and on the applied magnetic field. In unsteady regimes its value varies periodically by a factor of almost 2, indicating the appearance of two different competing wave modes. The wave numbers and spatial orientation of the observed dominant flow patterns are found to be in good agreement with theoretical predictions.

Experimental and operational modal analysis of a laboratory scale model of a tripod support structure.

NASA Astrophysics Data System (ADS)

Luczak, M. M.; Mucchi, E.; Telega, J.

2016-09-01

The goal of the research is to develop a vibration-based procedure for the identification of structural failures in a laboratory scale model of a tripod supporting structure of an offshore wind turbine. In particular, this paper presents an experimental campaign on the scale model tested in two stages. Stage one encompassed the model tripod structure tested in air. The second stage was done in water. The tripod model structure allows to investigate the propagation of a circumferential representative crack of a cylindrical upper brace. The in-water test configuration included the tower with three bladed rotor. The response of the structure to the different waves loads were measured with accelerometers. Experimental and operational modal analysis was applied to identify the dynamic properties of the investigated scale model for intact and damaged state with different excitations and wave patterns. A comprehensive test matrix allows to assess the differences in estimated modal parameters due to damage or as potentially introduced by nonlinear structural response. The presented technique proves to be effective for detecting and assessing the presence of representative cracks.

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

Shi, J.; Xue, X.

A comprehensive 3D CFD model is developed for a bi-electrode supported cell (BSC) SOFC. The model includes complicated transport phenomena of mass/heat transfer, charge (electron and ion) migration, and electrochemical reaction. The uniqueness of the modeling study is that functionally graded porous electrode property is taken into account, including not only linear but nonlinear porosity distributions. Extensive numerical analysis is performed to elucidate the effects of both porous microstructure distributions and operating condition on cell performance. Results indicate that cell performance is strongly dependent on both operating conditions and porous microstructure distributions of electrodes. Using the proposed fuel/gas feeding design,more » the uniform hydrogen distribution within porous anode is achieved; the oxygen distribution within the cathode is dependent on porous microstructure distributions as well as pressure loss conditions. Simulation results show that fairly uniform temperature distribution can be obtained with the proposed fuel/gas feeding design. The modeling results can be employed to guide experimental design of BSC test and provide pre-experimental analysis, as a result, to circumvent high cost associated with try-and-error experimental design and setup.« less

MetaGenyo: a web tool for meta-analysis of genetic association studies.

PubMed

Martorell-Marugan, Jordi; Toro-Dominguez, Daniel; Alarcon-Riquelme, Marta E; Carmona-Saez, Pedro

2017-12-16

Genetic association studies (GAS) aims to evaluate the association between genetic variants and phenotypes. In the last few years, the number of this type of study has increased exponentially, but the results are not always reproducible due to experimental designs, low sample sizes and other methodological errors. In this field, meta-analysis techniques are becoming very popular tools to combine results across studies to increase statistical power and to resolve discrepancies in genetic association studies. A meta-analysis summarizes research findings, increases statistical power and enables the identification of genuine associations between genotypes and phenotypes. Meta-analysis techniques are increasingly used in GAS, but it is also increasing the amount of published meta-analysis containing different errors. Although there are several software packages that implement meta-analysis, none of them are specifically designed for genetic association studies and in most cases their use requires advanced programming or scripting expertise. We have developed MetaGenyo, a web tool for meta-analysis in GAS. MetaGenyo implements a complete and comprehensive workflow that can be executed in an easy-to-use environment without programming knowledge. MetaGenyo has been developed to guide users through the main steps of a GAS meta-analysis, covering Hardy-Weinberg test, statistical association for different genetic models, analysis of heterogeneity, testing for publication bias, subgroup analysis and robustness testing of the results. MetaGenyo is a useful tool to conduct comprehensive genetic association meta-analysis. The application is freely available at http://bioinfo.genyo.es/metagenyo/ .

Application of a novel metabolomic approach based on atmospheric pressure photoionization mass spectrometry using flow injection analysis for the study of Alzheimer's disease.

PubMed

González-Domínguez, Raúl; García-Barrera, Tamara; Gómez-Ariza, José Luis

2015-01-01

The use of atmospheric pressure photoionization is not widespread in metabolomics, despite its considerable potential for the simultaneous analysis of compounds with diverse polarities. This work considers the development of a novel analytical approach based on flow injection analysis and atmospheric pressure photoionization mass spectrometry for rapid metabolic screening of serum samples. Several experimental parameters were optimized, such as type of dopant, flow injection solvent, and their flows, given that a careful selection of these variables is mandatory for a comprehensive analysis of metabolites. Toluene and methanol were the most suitable dopant and flow injection solvent, respectively. Moreover, analysis in negative mode required higher solvent and dopant flows (100 µl min(-1) and 40 µl min(-1), respectively) compared to positive mode (50 µl min(-1) and 20 µl min(-1)). Then, the optimized approach was used to elucidate metabolic alterations associated with Alzheimer's disease. Thereby, results confirm the increase of diacylglycerols, ceramides, ceramide-1-phosphate and free fatty acids, indicating membrane destabilization processes, and reduction of fatty acid amides and several neurotransmitters related to impairments in neuronal transmission, among others. Therefore, it could be concluded that this metabolomic tool presents a great potential for analysis of biological samples, considering its high-throughput screening capability, fast analysis and comprehensive metabolite coverage. Copyright © 2014 Elsevier B.V. All rights reserved.

Analysis of honeybush tea (Cyclopia spp.) volatiles by comprehensive two-dimensional gas chromatography using a single-stage thermal modulator.

PubMed

Ntlhokwe, Gaalebalwe; Tredoux, Andreas G J; Górecki, Tadeusz; Edwards, Matthew; Vestner, Jochen; Muller, Magdalena; Erasmus, Lené; Joubert, Elizabeth; Christel Cronje, J; de Villiers, André

2017-07-01

The applicability of comprehensive two-dimensional gas chromatography (GC×GC) using a single-stage thermal modulator was explored for the analysis of honeybush tea (Cyclopia spp.) volatile compounds. Headspace solid phase micro-extraction (HS-SPME) was used in combination with GC×GC separation on a non-polar × polar column set with flame ionisation (FID) detection for the analysis of fermented Cyclopia maculata, Cyclopia subternata and Cyclopia genistoides tea infusions of a single harvest season. Method optimisation entailed evaluation of the effects of several experimental parameters on the performance of the modulator, the choice of columns in both dimensions, as well as the HS-SPME extraction fibre. Eighty-four volatile compounds were identified by co-injection of reference standards. Principal component analysis (PCA) showed clear differentiation between the species based on their volatile profiles. Due to the highly reproducible separations obtained using the single-stage thermal modulator, multivariate data analysis was simplified. The results demonstrate both the complexity of honeybush volatile profiles and the potential of GC×GC separation in combination with suitable data analysis techniques for the investigation of the relationship between sensory properties and volatile composition of these products. The developed method therefore offers a fast and inexpensive methodology for the profiling of honeybush tea volatiles. Graphical abstract Surface plot obtained for the GC×GC-FID analysis of honeybush tea volatiles.

Shared Decision-Making for Nursing Practice: An Integrative Review.

PubMed

Truglio-Londrigan, Marie; Slyer, Jason T

2018-01-01

Shared decision-making has received national and international interest by providers, educators, researchers, and policy makers. The literature on shared decision-making is extensive, dealing with the individual components of shared decision-making rather than a comprehensive process. This view of shared decision-making leaves healthcare providers to wonder how to integrate shared decision-making into practice. To understand shared decision-making as a comprehensive process from the perspective of the patient and provider in all healthcare settings. An integrative review was conducted applying a systematic approach involving a literature search, data evaluation, and data analysis. The search included articles from PubMed, CINAHL, the Cochrane Central Register of Controlled Trials, and PsycINFO from 1970 through 2016. Articles included quantitative experimental and non-experimental designs, qualitative, and theoretical articles about shared decision-making between all healthcare providers and patients in all healthcare settings. Fifty-two papers were included in this integrative review. Three categories emerged from the synthesis: (a) communication/ relationship building; (b) working towards a shared decision; and (c) action for shared decision-making. Each major theme contained sub-themes represented in the proposed visual representation for shared decision-making. A comprehensive understanding of shared decision-making between the nurse and the patient was identified. A visual representation offers a guide that depicts shared decision-making as a process taking place during a healthcare encounter with implications for the continuation of shared decisions over time offering patients an opportunity to return to the nurse for reconsiderations of past shared decisions.

Systems cell biology.

PubMed

Mast, Fred D; Ratushny, Alexander V; Aitchison, John D

2014-09-15

Systems cell biology melds high-throughput experimentation with quantitative analysis and modeling to understand many critical processes that contribute to cellular organization and dynamics. Recently, there have been several advances in technology and in the application of modeling approaches that enable the exploration of the dynamic properties of cells. Merging technology and computation offers an opportunity to objectively address unsolved cellular mechanisms, and has revealed emergent properties and helped to gain a more comprehensive and fundamental understanding of cell biology. © 2014 Mast et al.

Mathematical Modeling Approaches in Plant Metabolomics.

PubMed

Fürtauer, Lisa; Weiszmann, Jakob; Weckwerth, Wolfram; Nägele, Thomas

2018-01-01

The experimental analysis of a plant metabolome typically results in a comprehensive and multidimensional data set. To interpret metabolomics data in the context of biochemical regulation and environmental fluctuation, various approaches of mathematical modeling have been developed and have proven useful. In this chapter, a general introduction to mathematical modeling is presented and discussed in context of plant metabolism. A particular focus is laid on the suitability of mathematical approaches to functionally integrate plant metabolomics data in a metabolic network and combine it with other biochemical or physiological parameters.

Energy landscape in frustrated systems: Cation hopping in pyrochlores

NASA Astrophysics Data System (ADS)

Brooks Hinojosa, Beverly; Asthagiri, Aravind; Nino, Juan C.

2013-07-01

We investigate the dynamics of the local environment and electronic structure in inherently dipolar frustrated pyrochlore compounds to help identify the fundamental nature of dipolar disorder in pyrochlore systems and determine the necessary and sufficient conditions for dielectric relaxation. We map out the energy landscape associated with cation hopping events in three compounds and correlate the hopping pathway with experimental dielectric response. Comprehensive analysis of the calculations allows us to postulate rules to predict the occurrence of relaxation and cation hopping pathways.

The Comparative Effects of Comprehensible Input, Output and Corrective Feedback on the Receptive Acquisition of L2 Vocabulary Items

ERIC Educational Resources Information Center

Nowbakht, Mohammad; Shahnazari, Mohammadtaghi

2015-01-01

In the present study, the comparative effects of comprehensible input, output and corrective feedback on the receptive acquisition of L2 vocabulary items were investigated. Two groups of beginning EFL learners participated in the study. The control group received comprehensible input only, while the experimental group received input and was…

A thorough experimental study of CH/π interactions in water: quantitative structure-stability relationships for carbohydrate/aromatic complexes.

PubMed

Jiménez-Moreno, Ester; Jiménez-Osés, Gonzalo; Gómez, Ana M; Santana, Andrés G; Corzana, Francisco; Bastida, Agatha; Jiménez-Barbero, Jesus; Asensio, Juan Luis

2015-11-13

CH/π interactions play a key role in a large variety of molecular recognition processes of biological relevance. However, their origins and structural determinants in water remain poorly understood. In order to improve our comprehension of these important interaction modes, we have performed a quantitative experimental analysis of a large data set comprising 117 chemically diverse carbohydrate/aromatic stacking complexes, prepared through a dynamic combinatorial approach recently developed by our group. The obtained free energies provide a detailed picture of the structure-stability relationships that govern the association process, opening the door to the rational design of improved carbohydrate-based ligands or carbohydrate receptors. Moreover, this experimental data set, supported by quantum mechanical calculations, has contributed to the understanding of the main driving forces that promote complex formation, underlining the key role played by coulombic and solvophobic forces on the stabilization of these complexes. This represents the most quantitative and extensive experimental study reported so far for CH/π complexes in water.

CFD Validation Experiment of a Mach 2.5 Axisymmetric Shock-Wave/Boundary-Layer Interaction

NASA Technical Reports Server (NTRS)

Davis, David O.

2015-01-01

Experimental investigations of specific flow phenomena, e.g., Shock Wave Boundary-Layer Interactions (SWBLI), provide great insight to the flow behavior but often lack the necessary details to be useful as CFD validation experiments. Reasons include: 1.Undefined boundary conditions Inconsistent results 2.Undocumented 3D effects (CL only measurements) 3.Lack of uncertainty analysis While there are a number of good subsonic experimental investigations that are sufficiently documented to be considered test cases for CFD and turbulence model validation, the number of supersonic and hypersonic cases is much less. This was highlighted by Settles and Dodsons [1] comprehensive review of available supersonic and hypersonic experimental studies. In all, several hundred studies were considered for their database.Of these, over a hundred were subjected to rigorous acceptance criteria. Based on their criteria, only 19 (12 supersonic, 7 hypersonic) were considered of sufficient quality to be used for validation purposes. Aeschliman and Oberkampf [2] recognized the need to develop a specific methodology for experimental studies intended specifically for validation purposes.

Improving text comprehension strategies in upper primary school children: a design experiment.

PubMed

De Corte, E; Verschaffel, L; Van De Ven, A

2001-12-01

With respect to the acquisition of competence in reading, new standards for primary education stress more than before the importance of learning and teaching cognitive and metacognitive strategies that facilitate text comprehension. Therefore, there is a need to design a research-based instructional approach to strategic reading comprehension. The design experiment aimed at developing, implementing and evaluating a research-based, but also practically applicable learning environment for enhancing skilled strategy use in upper primary school children when reading a text. Four text comprehension strategies (activating prior knowledge, clarifying difficult words, making a schematic representation of the text, and formulating the main idea) and a metacognitive strategy (regulating one's own reading process) were trained through a variety of highly interactive instructional techniques, namely modelling, whole class discussion, and small group work in the format of reciprocal teaching. Participants in the study were four experimental 5th grade classes (79 children) and eight comparable control classes (149 pupils). The effects of the learning environment were measured using a pretest-post-test-retention design. Multilevel hierarchical linear regression models were used to analyse the quantitative data of a Reading Strategy Test, a standardised Reading Comprehension Test, a Reading Attitude Scale, a Transfer Test and an interview about strategy use during reading. The data of the Reading Strategy Test, the Transfer Test and the interviews about strategy use showed that the experimental group out-performed the control group in terms of the strategy adoption and application during text reading. Whilst the experimental group also scored higher on the Reading Comprehension Test than the control group, the difference was not significant. This design experiment shows that it is possible to foster pupils' use and transfer of strategic reading comprehension skills in regular classrooms by immersing them in a powerful learning environment. But this intervention does not automatically result in improvement of performance on a standardised reading comprehension test.

Failure analysis of energy storage spring in automobile composite brake chamber

NASA Astrophysics Data System (ADS)

Luo, Zai; Wei, Qing; Hu, Xiaofeng

2015-02-01

This paper set energy storage spring of parking brake cavity, part of automobile composite brake chamber, as the research object. And constructed the fault tree model of energy storage spring which caused parking brake failure based on the fault tree analysis method. Next, the parking brake failure model of energy storage spring was established by analyzing the working principle of composite brake chamber. Finally, the data of working load and the push rod stroke measured by comprehensive test-bed valve was used to validate the failure model above. The experimental result shows that the failure model can distinguish whether the energy storage spring is faulted.

The Fulde–Ferrell–Larkin–Ovchinnikov state for ultracold fermions in lattice and harmonic potentials: a review

NASA Astrophysics Data System (ADS)

Kinnunen, Jami J.; Baarsma, Jildou E.; Martikainen, Jani-Petri; Törmä, Päivi

2018-04-01

We review the concepts and the present state of theoretical studies of spin-imbalanced superfluidity, in particular the elusive Fulde–Ferrell–Larkin–Ovchinnikov (FFLO) state, in the context of ultracold quantum gases. The comprehensive presentation of the theoretical basis for the FFLO state that we provide is useful also for research on the interplay between magnetism and superconductivity in other physical systems. We focus on settings that have been predicted to be favourable for the FFLO state, such as optical lattices in various dimensions and spin–orbit coupled systems. These are also the most likely systems for near-future experimental observation of the FFLO state. Theoretical bounds, such as Bloch’s and Luttinger’s theorems, and experimentally important limitations, such as finite-size effects and trapping potentials, are considered. In addition, we provide a comprehensive review of the various ideas presented for the observation of the FFLO state. We conclude our review with an analysis of the open questions related to the FFLO state, such as its stability, superfluid density, collective modes and extending the FFLO superfluid concept to new types of lattice systems.

A review of the effects of nicotine on social functioning.

PubMed

Martin, Lea M; Sayette, Michael A

2018-06-28

Many smokers are aware that smoking is a dangerous health behavior and eventually try to quit smoking. Unfortunately, most quit attempts end in failure. Traditionally, the addictive nature of smoking has been attributed to the pharmacologic effects of nicotine. In an effort to offer a more comprehensive, biobehavioral analysis of smoking behavior and motivation, some researchers have begun to consider the role of social factors in smoking. In line with recent recommendations to integrate social and pharmacological analyses of smoking, we reviewed the experimental literature examining the effects of nicotine and nicotine withdrawal on social functioning. The review identified 13 studies that experimentally manipulated nicotine and assessed social functioning, 12 of which found support for nicotine's enhancement of social functioning. Although few experiments have investigated social functioning, they nevertheless offer compelling evidence that nicotine enhances social functioning in smokers and suggest that nicotine deprivation may hamper social functioning in those dependent on nicotine. Future directions for investigating social outcomes and context in those who use nicotine products are discussed with a focus on leveraging advances in social and developmental psychology, animal research, sociology, and neuroimaging to more comprehensively understand smoking behavior. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Multi-fracture response of cross-ply ceramic composites

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

Erdman, D.L.; Weitsman, Y.J.

1996-12-31

Ceramic matrix composites are candidate materials for high temperature applications due to their ability to retain mechanical properties. However, in view of the relatively low transverse strength and ductility associated with unidirectional ceramic matrix lay-ups, it is necessary to consider multi-directional reinforcement for any practical structural application. The simplest laminate that would provide multi-directional toughness would be the cross-ply lay-up. Although there are numerous publications concerned with modeling of the stress-strain response of unidirectional ceramic matrix laminates, there are relatively few investigations in the current literature which deal with laminates such as the cross-ply lay-up. Additionally, the aforementioned publications aremore » often incomplete since they fail to address the failure mechanisms associated with this lay-up in a comprehensive manner and consequently have limited success in correlating experimental stress-strain response with mechanical test results. Furthermore, many current experimental investigations fail to report the details of damage evolution and stress-strain response which are required for correlation with analyses. This investigation presents a comprehensive extended shear-lag type analysis that considers transverse matrix cracking in the 90{degree} plies, the non-linearity of the 0{degree} plies, and slip at the 0/90 ply interface.« less

Confocal fluorescence techniques in industrial application

NASA Astrophysics Data System (ADS)

Eggeling, Christian; Gall, Karsten; Palo, Kaupo; Kask, Peet; Brand, Leif

2003-06-01

The FCS+plus family of evaluation tools for confocal fluorescence spectroscopy, which was developed during recent years, offers a comprehensive view to a series of fluorescence properties. Originating in fluorescence correlation spectroscopy (FCS) and using similar experimental equipment, a system of signal processing methods such as fluorescence intensity distribution analysis (FIDA) was created to analyze in detail the fluctuation behavior of fluorescent particles within a small area of detection. Giving simultaneous access to molecular parameters like concentration, translational and rotational diffusion, molecular brightness, and multicolor coincidence, this portfolio was enhanced by more traditional techniques of fluorescence lifetime as well as time-resolved anisotropy determination. The cornerstones of the FCS+plus methodology will be shortly described. The inhibition of a phosphatase enzyme activity gives a comprehensive industrial application that demonstrates FCS+plus' versatility and its potential for pharmaceutical drug discovery.

The measurement of bacterial translation by photon correlation spectroscopy.

PubMed Central

Stock, G B; Jenkins, T C

1978-01-01

Photon correlation spectroscopy is shown to be a practical technique for the accurate determination of translational speeds of bacteria. Though other attempts have been made to use light scattering as a probe of various aspects of bacterial motility, no other comprehensive studies to establish firmly the basic capabilities and limitations of the technique have been published. The intrinsic accuracy of the assay of translational speeds by photon correlation spectroscopy is investigated by analysis of synthetic autocorrelation data; consistently accurate estimates of the mean and second moment of the speed distribution can be calculated. Extensive analyses of experimental preparations of Salmonella typhimurium examine the possible sources of experimental difficulty with the assay. Cinematography confirms the bacterial speed estimates obtained by photon correlation techniques. PMID:346073

Mechanisms of carbon dimer formation in colliding laser-produced carbon plasmas

NASA Astrophysics Data System (ADS)

Sizyuk, Tatyana; Oliver, John; Diwakar, Prasoon K.

2017-07-01

It has been demonstrated that the hot stagnation region formed during the collision of laser-produced carbon plasmas is rich with carbon dimers which have been shown to be synthesized into large carbon macromolecules such as carbon fullerene onions and nanotubes. In this study, we developed and integrated experimental and multidimensional modeling techniques to access the temporal and spatial resolution of colliding plasma characteristics that elucidated the mechanism for early carbon dimer formation. Plume evolution imaging, monochromatic imaging, and optical emission spectroscopy of graphite-produced, carbon plasmas were performed. Experimental results were compared with the results of the 3D comprehensive modeling using our HEIGHTS simulation package. The results are explained based on a fundamental analysis of plasma evolution, colliding layer formation, stagnation, and expansion. The precise mechanisms of the plasma collision, plume propagation, and particle formation are discussed based on the experimental and modeling results.

Harmony of computational quantum chemistry and experimental chemistry: Comprehensive DFT studies, microsynthesis, and characterization of mustard gas polysulfide analogues

NASA Astrophysics Data System (ADS)

Saeidian, Hamid; Faraz, Sajjad Mousavi; Mirjafary, Zohreh; Babri, Mehran

2018-05-01

After microsynthesis, structures of mustard gas polysulfide analogues were characterized using electron impact (EI) mass spectrometry. General EI fragmentation pathways for such compounds are proposed. The structure of sulfur mustard (HD) and its two other polysulfide analogues have been examined through B3LYP/6-311++G(2d, 2p) calculations. Geometrical analysis of HD shows that the calculated bond distances are satisfactorily comparable with experimental results. Calculated NMR chemical shifts for HD also were compared with experimental data, indicating good agreement both for 1H and 13C atoms. The vibrational frequencies of HD and polysulfide analogues have been precisely assigned. At the end, based on visual inspection of lowest unoccupied molecular orbitals and the relative difference in the total energies of their episulfonium ions, relative reactivity of HD and its polysulfide analogues were investigated.

An experimentally validated network of nine haematopoietic transcription factors reveals mechanisms of cell state stability

PubMed Central

Schütte, Judith; Wang, Huange; Antoniou, Stella; Jarratt, Andrew; Wilson, Nicola K; Riepsaame, Joey; Calero-Nieto, Fernando J; Moignard, Victoria; Basilico, Silvia; Kinston, Sarah J; Hannah, Rebecca L; Chan, Mun Chiang; Nürnberg, Sylvia T; Ouwehand, Willem H; Bonzanni, Nicola; de Bruijn, Marella FTR; Göttgens, Berthold

2016-01-01

Transcription factor (TF) networks determine cell-type identity by establishing and maintaining lineage-specific expression profiles, yet reconstruction of mammalian regulatory network models has been hampered by a lack of comprehensive functional validation of regulatory interactions. Here, we report comprehensive ChIP-Seq, transgenic and reporter gene experimental data that have allowed us to construct an experimentally validated regulatory network model for haematopoietic stem/progenitor cells (HSPCs). Model simulation coupled with subsequent experimental validation using single cell expression profiling revealed potential mechanisms for cell state stabilisation, and also how a leukaemogenic TF fusion protein perturbs key HSPC regulators. The approach presented here should help to improve our understanding of both normal physiological and disease processes. DOI: http://dx.doi.org/10.7554/eLife.11469.001 PMID:26901438

Assessment of analytical and experimental techniques utilized in conducting plume technology tests 575 and 593. [exhaust flow simulation (wind tunnel tests) of scale model Space Shuttle Orbiter

NASA Technical Reports Server (NTRS)

Baker, L. R.; Sulyma, P. R.; Tevepaugh, J. A.; Penny, M. M.

1976-01-01

Since exhaust plumes affect vehicle base environment (pressure and heat loads) and the orbiter vehicle aerodynamic control surface effectiveness, an intensive program involving detailed analytical and experimental investigations of the exhaust plume/vehicle interaction was undertaken as a pertinent part of the overall space shuttle development program. The program, called the Plume Technology program, has as its objective the determination of the criteria for simulating rocket engine (in particular, space shuttle propulsion system) plume-induced aerodynamic effects in a wind tunnel environment. The comprehensive experimental program was conducted using test facilities at NASA's Marshall Space Flight Center and Ames Research Center. A post-test examination of some of the experimental results obtained from NASA-MSFC's 14 x 14-inch trisonic wind tunnel is presented. A description is given of the test facility, simulant gas supply system, nozzle hardware, test procedure and test matrix. Analysis of exhaust plume flow fields and comparison of analytical and experimental exhaust plume data are presented.

Space shuttle booster multi-engine base flow analysis

NASA Technical Reports Server (NTRS)

Tang, H. H.; Gardiner, C. R.; Anderson, W. A.; Navickas, J.

1972-01-01

A comprehensive review of currently available techniques pertinent to several prominent aspects of the base thermal problem of the space shuttle booster is given along with a brief review of experimental results. A tractable engineering analysis, capable of predicting the power-on base pressure, base heating, and other base thermal environmental conditions, such as base gas temperature, is presented and used for an analysis of various space shuttle booster configurations. The analysis consists of a rational combination of theoretical treatments of the prominent flow interaction phenomena in the base region. These theories consider jet mixing, plume flow, axisymmetric flow effects, base injection, recirculating flow dynamics, and various modes of heat transfer. Such effects as initial boundary layer expansion at the nozzle lip, reattachment, recompression, choked vent flow, and nonisoenergetic mixing processes are included in the analysis. A unified method was developed and programmed to numerically obtain compatible solutions for the various flow field components in both flight and ground test conditions. Preliminary prediction for a 12-engine space shuttle booster base thermal environment was obtained for a typical trajectory history. Theoretical predictions were also obtained for some clustered-engine experimental conditions. Results indicate good agreement between the data and theoretical predicitons.

A NEW METHOD OF PEAK DETECTION FOR ANALYSIS OF COMPREHENSIVE TWO-DIMENSIONAL GAS CHROMATOGRAPHY MASS SPECTROMETRY DATA.

PubMed

Kim, Seongho; Ouyang, Ming; Jeong, Jaesik; Shen, Changyu; Zhang, Xiang

2014-06-01

We develop a novel peak detection algorithm for the analysis of comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GC×GC-TOF MS) data using normal-exponential-Bernoulli (NEB) and mixture probability models. The algorithm first performs baseline correction and denoising simultaneously using the NEB model, which also defines peak regions. Peaks are then picked using a mixture of probability distribution to deal with the co-eluting peaks. Peak merging is further carried out based on the mass spectral similarities among the peaks within the same peak group. The algorithm is evaluated using experimental data to study the effect of different cut-offs of the conditional Bayes factors and the effect of different mixture models including Poisson, truncated Gaussian, Gaussian, Gamma, and exponentially modified Gaussian (EMG) distributions, and the optimal version is introduced using a trial-and-error approach. We then compare the new algorithm with two existing algorithms in terms of compound identification. Data analysis shows that the developed algorithm can detect the peaks with lower false discovery rates than the existing algorithms, and a less complicated peak picking model is a promising alternative to the more complicated and widely used EMG mixture models.

Isotopically Nonstationary Metabolic Flux Analysis (INST-MFA) of Photosynthesis and Photorespiration in Plants.

PubMed

Ma, Fangfang; Jazmin, Lara J; Young, Jamey D; Allen, Doug K

2017-01-01

Photorespiration is a central component of photosynthesis; however to better understand its role it should be viewed in the context of an integrated metabolic network rather than a series of individual reactions that operate independently. Isotopically nonstationary 13 C metabolic flux analysis (INST-MFA), which is based on transient labeling studies at metabolic steady state, offers a comprehensive platform to quantify plant central metabolism. In this chapter, we describe the application of INST-MFA to investigate metabolism in leaves. Leaves are an autotrophic tissue, assimilating CO 2 over a diurnal period implying that the metabolic steady state is limited to less than 12 h and thus requiring an INST-MFA approach. This strategy results in a comprehensive unified description of photorespiration, Calvin cycle, sucrose and starch synthesis, tricarboxylic acid (TCA) cycle, and amino acid biosynthetic fluxes. We present protocols of the experimental aspects for labeling studies: transient 13 CO 2 labeling of leaf tissue, sample quenching and extraction, mass spectrometry (MS) analysis of isotopic labeling data, measurement of sucrose and amino acids in vascular exudates, and provide details on the computational flux estimation using INST-MFA.

MIPS: analysis and annotation of proteins from whole genomes

PubMed Central

Mewes, H. W.; Amid, C.; Arnold, R.; Frishman, D.; Güldener, U.; Mannhaupt, G.; Münsterkötter, M.; Pagel, P.; Strack, N.; Stümpflen, V.; Warfsmann, J.; Ruepp, A.

2004-01-01

The Munich Information Center for Protein Sequences (MIPS-GSF), Neuherberg, Germany, provides protein sequence-related information based on whole-genome analysis. The main focus of the work is directed toward the systematic organization of sequence-related attributes as gathered by a variety of algorithms, primary information from experimental data together with information compiled from the scientific literature. MIPS maintains automatically generated and manually annotated genome-specific databases, develops systematic classification schemes for the functional annotation of protein sequences and provides tools for the comprehensive analysis of protein sequences. This report updates the information on the yeast genome (CYGD), the Neurospora crassa genome (MNCDB), the database of complete cDNAs (German Human Genome Project, NGFN), the database of mammalian protein–protein interactions (MPPI), the database of FASTA homologies (SIMAP), and the interface for the fast retrieval of protein-associated information (QUIPOS). The Arabidopsis thaliana database, the rice database, the plant EST databases (MATDB, MOsDB, SPUTNIK), as well as the databases for the comprehensive set of genomes (PEDANT genomes) are described elsewhere in the 2003 and 2004 NAR database issues, respectively. All databases described, and the detailed descriptions of our projects can be accessed through the MIPS web server (http://mips.gsf.de). PMID:14681354

MIPS: analysis and annotation of proteins from whole genomes.

PubMed

Mewes, H W; Amid, C; Arnold, R; Frishman, D; Güldener, U; Mannhaupt, G; Münsterkötter, M; Pagel, P; Strack, N; Stümpflen, V; Warfsmann, J; Ruepp, A

2004-01-01

The Munich Information Center for Protein Sequences (MIPS-GSF), Neuherberg, Germany, provides protein sequence-related information based on whole-genome analysis. The main focus of the work is directed toward the systematic organization of sequence-related attributes as gathered by a variety of algorithms, primary information from experimental data together with information compiled from the scientific literature. MIPS maintains automatically generated and manually annotated genome-specific databases, develops systematic classification schemes for the functional annotation of protein sequences and provides tools for the comprehensive analysis of protein sequences. This report updates the information on the yeast genome (CYGD), the Neurospora crassa genome (MNCDB), the database of complete cDNAs (German Human Genome Project, NGFN), the database of mammalian protein-protein interactions (MPPI), the database of FASTA homologies (SIMAP), and the interface for the fast retrieval of protein-associated information (QUIPOS). The Arabidopsis thaliana database, the rice database, the plant EST databases (MATDB, MOsDB, SPUTNIK), as well as the databases for the comprehensive set of genomes (PEDANT genomes) are described elsewhere in the 2003 and 2004 NAR database issues, respectively. All databases described, and the detailed descriptions of our projects can be accessed through the MIPS web server (http://mips.gsf.de).

Rapid Fine Conformational Epitope Mapping Using Comprehensive Mutagenesis and Deep Sequencing*

PubMed Central

Kowalsky, Caitlin A.; Faber, Matthew S.; Nath, Aritro; Dann, Hailey E.; Kelly, Vince W.; Liu, Li; Shanker, Purva; Wagner, Ellen K.; Maynard, Jennifer A.; Chan, Christina; Whitehead, Timothy A.

2015-01-01

Knowledge of the fine location of neutralizing and non-neutralizing epitopes on human pathogens affords a better understanding of the structural basis of antibody efficacy, which will expedite rational design of vaccines, prophylactics, and therapeutics. However, full utilization of the wealth of information from single cell techniques and antibody repertoire sequencing awaits the development of a high throughput, inexpensive method to map the conformational epitopes for antibody-antigen interactions. Here we show such an approach that combines comprehensive mutagenesis, cell surface display, and DNA deep sequencing. We develop analytical equations to identify epitope positions and show the method effectiveness by mapping the fine epitope for different antibodies targeting TNF, pertussis toxin, and the cancer target TROP2. In all three cases, the experimentally determined conformational epitope was consistent with previous experimental datasets, confirming the reliability of the experimental pipeline. Once the comprehensive library is generated, fine conformational epitope maps can be prepared at a rate of four per day. PMID:26296891

Can You Read Me Now? Disciplinary Literacy Reading Strategies in the 7th Grade Science Classroom

NASA Astrophysics Data System (ADS)

McQuaid, Kelly Kathleen

Adolescent readers require a broad range of reading skills to deal with the challenges of reading complex text. Some researchers argue for a discipline-specific focus to address the low reading proficiency rates among secondary students. Disciplinary literacy attends to the different ways disciplines, such as science, generate and communicate knowledge. The purpose of this quasi-experimental study was to examine if and to what degree disciplinary literacy reading strategies impact student learning outcomes in reading comprehension and science content knowledge for 132 7th grade science students in five Southern Arizona charter schools and whether reading ability moderates that impact. The theoretical foundation for this study rested on expert-novice theory and Halliday's theory of critical moments of language development. It is not known if and to what degree disciplinary literacy reading strategies impact student learning outcomes in reading comprehension and science content knowledge for 7th grade science students and whether or not reading ability has a moderating effect on those student learning outcomes. The results for MANCOVA did not produce statistically significant results nor did the moderation analysis for the influence of reading ability on reading comprehension in the disciplinary literacy group. However, the moderation analysis for the influence of reading ability on science content knowledge resulted in conditional significant results for low (p < .01) and average readers (p <. 05). Low to average readers in the disciplinary literacy group appeared to benefit the most from reading comprehension instruction focused on learning science content in the science classroom.

The Effect of Stories for Thinking on Reading and Listening Comprehension: A Case Study in Turkey

ERIC Educational Resources Information Center

Tok, Sükran; Mazl, Aysegül

2015-01-01

This study has been conducted in order to examine the effects of the stories for thinking on 5th graders' reading comprehension and listening comprehension. A pretest-post test control group quasi-experimental design was used in the study. The sample of the etstudy was composed of 74 5th graders attending public elementary schools. The data have…

Determination of minor and trace elements concentration in kidney stones using elemental analysis techniques

NASA Astrophysics Data System (ADS)

Srivastava, Anjali

The determination of accurate material composition of a kidney stone is crucial for understanding the formation of the kidney stone as well as for preventive therapeutic strategies. Radiations probing instrumental activation analysis techniques are excellent tools for identification of involved materials present in the kidney stone. The X-ray fluorescence (XRF) and neutron activation analysis (NAA) experiments were performed and different kidney stones were analyzed. The interactions of X-ray photons and neutrons with matter are complementary in nature, resulting in distinctly different materials detection. This is the first approach to utilize combined X-ray fluorescence and neutron activation analysis for a comprehensive analysis of the kideny stones. Presently, experimental studies in conjunction with analytical techniques were used to determine the exact composition of the kidney stone. The use of open source program Python Multi-Channel Analyzer was utilized to unfold the XRF spectrum. A new type of experimental set-up was developed and utilized for XRF and NAA analysis of the kidney stone. To verify the experimental results with analytical calculation, several sets of kidney stones were analyzed using XRF and NAA technique. The elements which were identified from XRF technique are Br, Cu, Ga, Ge, Mo, Nb, Ni, Rb, Se, Sr, Y, Zr. And, by using Neutron Activation Analysis (NAA) are Au, Br, Ca, Er, Hg, I, K, Na, Pm, Sb, Sc, Sm, Tb, Yb, Zn. This thesis presents a new approach for exact detection of accurate material composition of kidney stone materials using XRF and NAA instrumental activation analysis techniques.

Improved Bond Equations for Fiber-Reinforced Polymer Bars in Concrete.

PubMed

Pour, Sadaf Moallemi; Alam, M Shahria; Milani, Abbas S

2016-08-30

This paper explores a set of new equations to predict the bond strength between fiber reinforced polymer (FRP) rebar and concrete. The proposed equations are based on a comprehensive statistical analysis and existing experimental results in the literature. Namely, the most effective parameters on bond behavior of FRP concrete were first identified by applying a factorial analysis on a part of the available database. Then the database that contains 250 pullout tests were divided into four groups based on the concrete compressive strength and the rebar surface. Afterward, nonlinear regression analysis was performed for each study group in order to determine the bond equations. The results show that the proposed equations can predict bond strengths more accurately compared to the other previously reported models.

A comprehensive company database analysis of biological assay variability.

PubMed

Kramer, Christian; Dahl, Göran; Tyrchan, Christian; Ulander, Johan

2016-08-01

Analysis of data from various compounds measured in diverse biological assays is a central part of drug discovery research projects. However, no systematic overview of the variability in biological assays has been published and judgments on assay quality and robustness of data are often based on personal belief and experience within the drug discovery community. To address this we performed a reproducibility analysis of all biological assays at AstraZeneca between 2005 and 2014. We found an average experimental uncertainty of less than a twofold difference and no technologies or assay types had higher variability than others. This work suggests that robust data can be obtained from the most commonly applied biological assays. Copyright © 2016. Published by Elsevier Ltd.

Classification and Quality Evaluation of Tobacco Leaves Based on Image Processing and Fuzzy Comprehensive Evaluation

PubMed Central

Zhang, Fan; Zhang, Xinhong

2011-01-01

Most of classification, quality evaluation or grading of the flue-cured tobacco leaves are manually operated, which relies on the judgmental experience of experts, and inevitably limited by personal, physical and environmental factors. The classification and the quality evaluation are therefore subjective and experientially based. In this paper, an automatic classification method of tobacco leaves based on the digital image processing and the fuzzy sets theory is presented. A grading system based on image processing techniques was developed for automatically inspecting and grading flue-cured tobacco leaves. This system uses machine vision for the extraction and analysis of color, size, shape and surface texture. Fuzzy comprehensive evaluation provides a high level of confidence in decision making based on the fuzzy logic. The neural network is used to estimate and forecast the membership function of the features of tobacco leaves in the fuzzy sets. The experimental results of the two-level fuzzy comprehensive evaluation (FCE) show that the accuracy rate of classification is about 94% for the trained tobacco leaves, and the accuracy rate of the non-trained tobacco leaves is about 72%. We believe that the fuzzy comprehensive evaluation is a viable way for the automatic classification and quality evaluation of the tobacco leaves. PMID:22163744

Effects of reading-oriented tasks on students' reading comprehension of geometry proof

NASA Astrophysics Data System (ADS)

Yang, Kai-Lin; Lin, Fou-Lai

2012-06-01

This study compared the effects of reading-oriented tasks and writing-oriented tasks on students' reading comprehension of geometry proof (RCGP). The reading-oriented tasks were designed with reading strategies and the idea of problem posing. The writing-oriented tasks were consistent with usual proof instruction for writing a proof and applying it. Twenty-two classes of ninth-grade students ( N = 683), aged 14 to 15 years, and 12 mathematics teachers participated in this quasi-experimental classroom study. While the experimental group was instructed to read and discuss the reading tasks in two 45-minute lessons, the control group was instructed to prove and apply the same propositions. Generalised estimating equation (GEE) method was used to compare the scores of the post-test and the delayed post-test with the pre-test scores as covariates. Results showed that the total scores of the delayed post-test of the experimental group were significantly higher than those of the control group. Furthermore, the scores of the experimental group on all facets of reading comprehension except the application facet were significantly higher than those of the control group for both the post-test and delayed post-test.

Universality and diversity of folding mechanics for three-helix bundle proteins.

PubMed

Yang, Jae Shick; Wallin, Stefan; Shakhnovich, Eugene I

2008-01-22

In this study we evaluate, at full atomic detail, the folding processes of two small helical proteins, the B domain of protein A and the Villin headpiece. Folding kinetics are studied by performing a large number of ab initio Monte Carlo folding simulations using a single transferable all-atom potential. Using these trajectories, we examine the relaxation behavior, secondary structure formation, and transition-state ensembles (TSEs) of the two proteins and compare our results with experimental data and previous computational studies. To obtain a detailed structural information on the folding dynamics viewed as an ensemble process, we perform a clustering analysis procedure based on graph theory. Moreover, rigorous p(fold) analysis is used to obtain representative samples of the TSEs and a good quantitative agreement between experimental and simulated Phi values is obtained for protein A. Phi values for Villin also are obtained and left as predictions to be tested by future experiments. Our analysis shows that the two-helix hairpin is a common partially stable structural motif that gets formed before entering the TSE in the studied proteins. These results together with our earlier study of Engrailed Homeodomain and recent experimental studies provide a comprehensive, atomic-level picture of folding mechanics of three-helix bundle proteins.

A DFT-Based Computational-Experimental Methodology for Synthetic Chemistry: Example of Application to the Catalytic Opening of Epoxides by Titanocene.

PubMed

Jaraíz, Martín; Enríquez, Lourdes; Pinacho, Ruth; Rubio, José E; Lesarri, Alberto; López-Pérez, José L

2017-04-07

A novel DFT-based Reaction Kinetics (DFT-RK) simulation approach, employed in combination with real-time data from reaction monitoring instrumentation (like UV-vis, FTIR, Raman, and 2D NMR benchtop spectrometers), is shown to provide a detailed methodology for the analysis and design of complex synthetic chemistry schemes. As an example, it is applied to the opening of epoxides by titanocene in THF, a catalytic system with abundant experimental data available. Through a DFT-RK analysis of real-time IR data, we have developed a comprehensive mechanistic model that opens new perspectives to understand previous experiments. Although derived specifically from the opening of epoxides, the prediction capabilities of the model, built on elementary reactions, together with its practical side (reaction kinetics simulations of real experimental conditions) make it a useful simulation tool for the design of new experiments, as well as for the conception and development of improved versions of the reagents. From the perspective of the methodology employed, because both the computational (DFT-RK) and the experimental (spectroscopic data) components can follow the time evolution of several species simultaneously, it is expected to provide a helpful tool for the study of complex systems in synthetic chemistry.

Emergence of complementarity and the Baconian roots of Niels Bohr's method

NASA Astrophysics Data System (ADS)

Perovic, Slobodan

2013-08-01

I argue that instead of a rather narrow focus on N. Bohr's account of complementarity as a particular and perhaps obscure metaphysical or epistemological concept (or as being motivated by such a concept), we should consider it to result from pursuing a particular method of studying physical phenomena. More precisely, I identify a strong undercurrent of Baconian method of induction in Bohr's work that likely emerged during his experimental training and practice. When its development is analyzed in light of Baconian induction, complementarity emerges as a levelheaded rather than a controversial account, carefully elicited from a comprehensive grasp of the available experimental basis, shunning hasty metaphysically motivated generalizations based on partial experimental evidence. In fact, Bohr's insistence on the "classical" nature of observations in experiments, as well as the counterintuitive synthesis of wave and particle concepts that have puzzled scholars, seem a natural outcome (an updated instance) of the inductive method. Such analysis clarifies the intricacies of early Schrödinger's critique of the account as well as Bohr's response, which have been misinterpreted in the literature. If adequate, the analysis may lend considerable support to the view that Bacon explicated the general terms of an experimentally minded strand of the scientific method, developed and refined by scientists in the following three centuries.

Mass Spectrometry-Based GPCR Proteomics: Comprehensive Characterization of the Human Cannabinoid 1 Receptor

PubMed Central

Zvonok, Nikolai; Xu, Wei; Williams, John; Janero, David R.; Krishnan, Srinivasan C.; Makriyannis, Alexandros

2013-01-01

The human cannabinoid 1 receptor (hCB1), a ubiquitous G protein-coupled receptor (GPCR), transmits cannabinergic signals that participate in diverse (patho)physiological processes. Pharmacotherapeutic hCB1 targeting is considered a tractable approach for treating such prevalent diseases as obesity, mood disorders, and drug addiction. The hydrophobic nature of the transmembrane helices of hCB1 presents a formidable difficulty to its direct structural analysis. Comprehensive experimental characterization of functional hCB1 by mass spectrometry (MS) is essential to the targeting of affinity probes that can be used to define directly hCB1 binding domains using a ligand-assisted experimental approach. Such information would greatly facilitate the rational design of hCB1-selective agonists/antagonists with therapeutic potential. We report the first high-coverage MS analysis of the primary sequence of the functional hCB1 receptor, one of the few such comprehensive MS-based analyses of any GPCR. Recombinant C-terminal hexa-histidine-tagged hCB1 (His6-hCB1) was expressed in cultured insect (Spodoptera frugiperda) cells, solubilized by a procedure devised to enhance receptor purity following metal-affinity chromatography, desalted by buffer exchange, and digested in solution with (chymo)-trypsin. “Bottom-up” nanoLC-MS/MS of the (chymo)tryptic digests afforded a degree of overall hCB1 coverage (>94%) thus far reported for only two other GPCRs. This MS-compatible procedure devised for His6-hCB1 sample preparation, incorporating in-solution (chymo)trypsin digestion in the presence of a low concentration of CYMAL-5 detergent, may be applicable to the MS-based proteomic characterization of other GPCRs. This work should help enable future ligand-assisted structural characterization of hCB1 binding motifs at the amino-acid level using rationally designed and targeted covalent cannabinergic probes. PMID:20131867

Manipulating Google's Knowledge Graph Box to Counter Biased Information Processing During an Online Search on Vaccination: Application of a Technological Debiasing Strategy.

PubMed

Ludolph, Ramona; Allam, Ahmed; Schulz, Peter J

2016-06-02

One of people's major motives for going online is the search for health-related information. Most consumers start their search with a general search engine but are unaware of the fact that its sorting and ranking criteria do not mirror information quality. This misconception can lead to distorted search outcomes, especially when the information processing is characterized by heuristic principles and resulting cognitive biases instead of a systematic elaboration. As vaccination opponents are vocal on the Web, the chance of encountering their non‒evidence-based views on immunization is high. Therefore, biased information processing in this context can cause subsequent impaired judgment and decision making. A technological debiasing strategy could counter this by changing people's search environment. This study aims at testing a technological debiasing strategy to reduce the negative effects of biased information processing when using a general search engine on people's vaccination-related knowledge and attitudes. This strategy is to manipulate the content of Google's knowledge graph box, which is integrated in the search interface and provides basic information about the search topic. A full 3x2 factorial, posttest-only design was employed with availability of basic factual information (comprehensible vs hardly comprehensible vs not present) as the first factor and a warning message as the second factor of experimental manipulation. Outcome variables were the evaluation of the knowledge graph box, vaccination-related knowledge, as well as beliefs and attitudes toward vaccination, as represented by three latent variables emerged from an exploratory factor analysis. Two-way analysis of variance revealed a significant main effect of availability of basic information in the knowledge graph box on participants' vaccination knowledge scores (F2,273=4.86, P=.01), skepticism/fear of vaccination side effects (F2,273=3.5, P=.03), and perceived information quality (F2,273=3.73, P=.02). More specifically, respondents receiving comprehensible information appeared to be more knowledgeable, less skeptical of vaccination, and more critical of information quality compared to participants exposed to hardly comprehensible information. Although, there was no significant interaction effect between the availability of information and the presence of the warning, there was a dominant pattern in which the presence of the warning appeared to have a positive influence on the group receiving comprehensible information while the opposite was true for the groups exposed to hardly comprehensible information and no information at all. Participants evaluated the knowledge graph box as moderately to highly useful, with no significant differences among the experimental groups. Overall, the results suggest that comprehensible information in the knowledge graph box positively affects participants' vaccination-related knowledge and attitudes. A small change in the content retrieval procedure currently used by Google could already make a valuable difference in the pursuit of an unbiased online information search. Further research is needed to gain insights into the knowledge graph box's entire potential.

Comprehensive School Reform: Meta-Analytic Evidence of Black-White Achievement Gap Narrowing.

PubMed

Gorey, Kevin M

2009-12-30

This meta-analysis extends a previous review of the achievement effects of comprehensive school reform (CSR) programs (Borman, Hewes, Overman, & Brown, 2003). That meta-analysis observed significant effects of well endowed and well-researched programs, but it did not account for race/ethnicity. This article synthesizes 34 cohort or quasi-experimental outcomes of studies that incorporated the policy-critical characteristic of race/ethnicity. compared with matched traditional schools, the black-white achievement gap narrowed significantly more among students in CSR schools. In addition, the aggregate effects were large, substantially to completely eliminating the achievement gap between African American and non-Hispanic white students in elementary and middle schools. Title I policies before or after the No Child Left Behind Act of 2001 seem to have had essentially no impact on the black-white achievement gap. Curricular and testing mandates along with the threat of sanctions without concomitant resource supports seem to have failed. This study suggests that educational achievement inequities need not be America's destiny. It seems that they could be eliminated through concerted political will and ample resource commitments to evidence-based educational programs.

Using the QCM Biosensor-Based T7 Phage Display Combined with Bioinformatics Analysis for Target Identification of Bioactive Small Molecule.

PubMed

Takakusagi, Yoichi; Takakusagi, Kaori; Sugawara, Fumio; Sakaguchi, Kengo

2018-01-01

Identification of target proteins that directly bind to bioactive small molecule is of great interest in terms of clarifying the mode of action of the small molecule as well as elucidating the biological phenomena at the molecular level. Of the experimental technologies available, T7 phage display allows comprehensive screening of small molecule-recognizing amino acid sequence from the peptide libraries displayed on the T7 phage capsid. Here, we describe the T7 phage display strategy that is combined with quartz-crystal microbalance (QCM) biosensor for affinity selection platform and bioinformatics analysis for small molecule-recognizing short peptides. This method dramatically enhances efficacy and throughput of the screening for small molecule-recognizing amino acid sequences without repeated rounds of selection. Subsequent execution of bioinformatics programs allows combinatorial and comprehensive target protein discovery of small molecules with its binding site, regardless of protein sample insolubility, instability, or inaccessibility of the fixed small molecules to internally located binding site on larger target proteins when conventional proteomics approaches are used.

The Impact of Comprehensive School Nursing Services on Students' Academic Performance.

PubMed

Kocoglu, Deniz; Emiroglu, Oya Nuran

2017-03-01

Introduction: School nursing services should be evaluated through health and academic outcomes of students; however, it is observed that the number of studies in this field is limited. The aim of this study is to evaluate the impact of comprehensive school nursing services provided to 4th grade primary school students on academic performance of students. Methods: The quasi-experimental study was conducted with 31 students attending a randomly selected school in economic disadvantaged area in Turky. Correlation analysis, repeated measures analyses of variance, multiple regression analysis were used to analyze the data with SPSS software. Results: At the end of school nursing practices, an increase was occurred in students' academic achievement grades whereas a decrease was occurred in absenteeism and academic procrastination behaviors. Whilst it was determined that nursing interventions including treatment/ procedure and surveillance was associated to the decrease of absenteeism, it also was discovered that the change in the health status of the student after nursing interventions was related to the increase of the academic achievement grade and the decrease of the academic procrastination behavior score. Conclusion: In this study, the conclusion that comprehensive school nursing services contributed positively to the academic performance of students has been reached. In addition, it can be suggested that effective school nursing services should include services such as acute-chronic disease treatment, first aid, health screening, health improvement-protection, health education, guidance and counseling and case management.

Experimental Study of Hollow Formation

NASA Astrophysics Data System (ADS)

Parman, S. W.; Orlando, T. M.; Milliken, R. E.; Head, J. W.; Jones, B. M.; Anzures, B. A.

2018-05-01

Hollows are enigmatic features on the surface of Mercury caused by sublimation and/or space weathering. Here we propose a comprehensive experimental study in which candidate hollows materials are exposed to a range of relevant conditions.

Structural Analysis of Single-Point Mutations Given an RNA Sequence: A Case Study with RNAMute

NASA Astrophysics Data System (ADS)

Churkin, Alexander; Barash, Danny

2006-12-01

We introduce here for the first time the RNAMute package, a pattern-recognition-based utility to perform mutational analysis and detect vulnerable spots within an RNA sequence that affect structure. Mutations in these spots may lead to a structural change that directly relates to a change in functionality. Previously, the concept was tried on RNA genetic control elements called "riboswitches" and other known RNA switches, without an organized utility that analyzes all single-point mutations and can be further expanded. The RNAMute package allows a comprehensive categorization, given an RNA sequence that has functional relevance, by exploring the patterns of all single-point mutants. For illustration, we apply the RNAMute package on an RNA transcript for which individual point mutations were shown experimentally to inactivate spectinomycin resistance in Escherichia coli. Functional analysis of mutations on this case study was performed experimentally by creating a library of point mutations using PCR and screening to locate those mutations. With the availability of RNAMute, preanalysis can be performed computationally before conducting an experiment.

Le Facteur d'Adaptation dans la Comprehension de l'Anglais Oral (The Adaptation Factor in the Understanding of Spoken English). Melanges Pedagogiques, 1972.

ERIC Educational Resources Information Center

Roussel, F.

Progress in the teaching of oral comprehension depends partly on the isolation of factors which block comprehension. Research in conjunction with an experimental course in English as a second language led to the definition of errors due to: (1) insufficient knowledge of the language and the cultural context of its use, and (2) a failure to…

[Experimental Methods and Result Analysis of a Variety of Spectral Reflectance Properties of the Thin Oil Film].

PubMed

Ye, Zhou; Liu, Li; Wei, Chuan-xin; Gu, Qun; An, Ping-ao; Zhao, Yue-jiao; Yin, Da-yi

2015-06-01

In order to analysis the oil spill situation based on the obtained data in airborne aerial work, it's needed to get the spectral reflectance characteristics of the oil film of different oils and thickness as support and to select the appropriate operating band. An experiment is set up to measure the reflectance spectroscopy from ultraviolet to near-infrared for the film of five target samples, which means petrol, diesel, lubricating oil, kerosene and fossil, using spectral measurement device. The result is compared with the reflectance spectra of water in the same experimental environment, which shows that the spectral reflection characteristics of the oil film are related to the thickness and the type of the oil film. In case of the same thickness, the spectral reflectance curve of different types of film is far different, and for the same type of film, the spectral reflectance curve changes accordingly with the change of film thickness, therefore in terms of the single film, different film thickness can be distinguished by reflectance curves. It also shows that in terms of the same film thickness, the reflectance of diesel, kerosene, lubricants reaches peak around 380 nm wavelength, obviously different from the reflectance of water, and that the reflectance of crude oil is far less than that of water in more than 340 nm wavelength, and the obtained reflection spectrum can be used to distinguish between different types of oil film to some extent. The experiment covers main types of spilled oil, with data comprehensively covering commonly used detect spectral bands, and quantitative description of the spectral reflectance properties of film. It provides comprehensive theoretical and data support for the selection of airborne oil spill detection working band and the detection and analysis of water-surface oil spill.

MASH Suite Pro: A Comprehensive Software Tool for Top-Down Proteomics*

PubMed Central

Cai, Wenxuan; Guner, Huseyin; Gregorich, Zachery R.; Chen, Albert J.; Ayaz-Guner, Serife; Peng, Ying; Valeja, Santosh G.; Liu, Xiaowen; Ge, Ying

2016-01-01

Top-down mass spectrometry (MS)-based proteomics is arguably a disruptive technology for the comprehensive analysis of all proteoforms arising from genetic variation, alternative splicing, and posttranslational modifications (PTMs). However, the complexity of top-down high-resolution mass spectra presents a significant challenge for data analysis. In contrast to the well-developed software packages available for data analysis in bottom-up proteomics, the data analysis tools in top-down proteomics remain underdeveloped. Moreover, despite recent efforts to develop algorithms and tools for the deconvolution of top-down high-resolution mass spectra and the identification of proteins from complex mixtures, a multifunctional software platform, which allows for the identification, quantitation, and characterization of proteoforms with visual validation, is still lacking. Herein, we have developed MASH Suite Pro, a comprehensive software tool for top-down proteomics with multifaceted functionality. MASH Suite Pro is capable of processing high-resolution MS and tandem MS (MS/MS) data using two deconvolution algorithms to optimize protein identification results. In addition, MASH Suite Pro allows for the characterization of PTMs and sequence variations, as well as the relative quantitation of multiple proteoforms in different experimental conditions. The program also provides visualization components for validation and correction of the computational outputs. Furthermore, MASH Suite Pro facilitates data reporting and presentation via direct output of the graphics. Thus, MASH Suite Pro significantly simplifies and speeds up the interpretation of high-resolution top-down proteomics data by integrating tools for protein identification, quantitation, characterization, and visual validation into a customizable and user-friendly interface. We envision that MASH Suite Pro will play an integral role in advancing the burgeoning field of top-down proteomics. PMID:26598644

VIRmiRNA: a comprehensive resource for experimentally validated viral miRNAs and their targets.

PubMed

Qureshi, Abid; Thakur, Nishant; Monga, Isha; Thakur, Anamika; Kumar, Manoj

2014-01-01

Viral microRNAs (miRNAs) regulate gene expression of viral and/or host genes to benefit the virus. Hence, miRNAs play a key role in host-virus interactions and pathogenesis of viral diseases. Lately, miRNAs have also shown potential as important targets for the development of novel antiviral therapeutics. Although several miRNA and their target repositories are available for human and other organisms in literature, but a dedicated resource on viral miRNAs and their targets are lacking. Therefore, we have developed a comprehensive viral miRNA resource harboring information of 9133 entries in three subdatabases. This includes 1308 experimentally validated miRNA sequences with their isomiRs encoded by 44 viruses in viral miRNA ' VIRMIRNA: ' and 7283 of their target genes in ' VIRMIRTAR': . Additionally, there is information of 542 antiviral miRNAs encoded by the host against 24 viruses in antiviral miRNA ' AVIRMIR': . The web interface was developed using Linux-Apache-MySQL-PHP (LAMP) software bundle. User-friendly browse, search, advanced search and useful analysis tools are also provided on the web interface. VIRmiRNA is the first specialized resource of experimentally proven virus-encoded miRNAs and their associated targets. This database would enhance the understanding of viral/host gene regulation and may also prove beneficial in the development of antiviral therapeutics. Database URL: http://crdd.osdd.net/servers/virmirna. © The Author(s) 2014. Published by Oxford University Press.

Enhancing the educational value of direct-to-consumer advertising of prescription drugs.

PubMed

Hwang, Monica J; Young, Henry N

The educational value of direct-to-consumer advertising (DTCA) of prescription drugs hinges on its ability to convey important benefit and risk information to consumers. However, the literacy level required to understand some of the information presented in print advertisements may hinder DTCA's ability to educate consumers. The objective of this study was to compare the comprehension and retention of benefit and risk information between consumers who viewed an original print DTCA and those who viewed an advertisement modified according to health literacy principles. An experimental design was used to conduct the study. Participants were randomly assigned to view a modified print advertisement (experimental group) or the original print advertisement (control group) for an antidepressant medication. Study participants were recruited from the University of Wisconsin Kidney Clinic. Ten true-false and 10 multiple-choice questions were developed to assess participants' comprehension and retention of benefit and risk information. A total of 120 participants were randomized to view either the original or the modified version of the advertisement. Regarding the comprehension and retention of only the benefit information, no significant differences were observed between the 2 groups. Significant differences were observed for comprehension and retention of only the risk information. The experimental group had significantly higher scores in comprehension (U = 1224; P < 0.01) and retention (U = 965; P < 0.01) of the risk information compared with the control group. These differences were also significant in multivariate analyses controlling for extraneous variables that were found to have associations with comprehension and retention of information. Study results demonstrated that the health literacy techniques used to modify the advertisement were successful in enhancing both consumers' comprehension and their retention of information presented in a print DTCA. This was especially apparent for the risk information. Copyright © 2017 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Investigating the prevention of hospital-acquired infection through standardized teaching ward rounds in clinical nursing.

PubMed

Zhang, R

2015-04-22

This study aimed to explore the effect of standardized teaching ward rounds in clinical nursing on preventing hospital-acquired infection. The experimental group comprised 120 nursing students from our hospital selected between June 2010 and June 2012. The control group consisted of 120 nursing students selected from May 2008 to May 2010. Traditional teaching ward rounds for nursing education were carried out with the control group, while a standardized teaching ward round was carried out with the experimental group. The comprehensive application of nursing abilities and skills, the mastering of situational infection knowledge, and patient satisfaction were compared between the two groups. The applied knowledge of nursing procedures and the pass rate on comprehensive skill tests were significantly higher in the experimental group than in the control group (P < 0.05). The rate of mastery of sterilization and hygiene procedures was also higher in the experimental group than in the control group (P < 0.05). The patient satisfaction rate with infection control procedures in the experimental group time period was 98.09%, which was significantly higher than patient satisfaction in the control group time period (93.05%, P < 0.05). Standardized teaching ward rounds for nursing education expanded the knowledge of the nursing staff in controlling hospital-acquired infection and enhanced the ability of comprehensive application and awareness of infection control procedures.

Shared Decision-Making for Nursing Practice: An Integrative Review

PubMed Central

Truglio-Londrigan, Marie; Slyer, Jason T.

2018-01-01

Background: Shared decision-making has received national and international interest by providers, educators, researchers, and policy makers. The literature on shared decision-making is extensive, dealing with the individual components of shared decision-making rather than a comprehensive process. This view of shared decision-making leaves healthcare providers to wonder how to integrate shared decision-making into practice. Objective: To understand shared decision-making as a comprehensive process from the perspective of the patient and provider in all healthcare settings. Methods: An integrative review was conducted applying a systematic approach involving a literature search, data evaluation, and data analysis. The search included articles from PubMed, CINAHL, the Cochrane Central Register of Controlled Trials, and PsycINFO from 1970 through 2016. Articles included quantitative experimental and non-experimental designs, qualitative, and theoretical articles about shared decision-making between all healthcare providers and patients in all healthcare settings. Results: Fifty-two papers were included in this integrative review. Three categories emerged from the synthesis: (a) communication/ relationship building; (b) working towards a shared decision; and (c) action for shared decision-making. Each major theme contained sub-themes represented in the proposed visual representation for shared decision-making. Conclusion: A comprehensive understanding of shared decision-making between the nurse and the patient was identified. A visual representation offers a guide that depicts shared decision-making as a process taking place during a healthcare encounter with implications for the continuation of shared decisions over time offering patients an opportunity to return to the nurse for reconsiderations of past shared decisions. PMID:29456779

An integrated multiscale river basin observing system in the Heihe River Basin, northwest China

NASA Astrophysics Data System (ADS)

Li, X.; Liu, S.; Xiao, Q.; Ma, M.; Jin, R.; Che, T.

2015-12-01

Using the watershed as the unit to establish an integrated watershed observing system has been an important trend in integrated eco-hydrologic studies in the past ten years. Thus far, a relatively comprehensive watershed observing system has been established in the Heihe River Basin, northwest China. In addition, two comprehensive remote sensing hydrology experiments have been conducted sequentially in the Heihe River Basin, including the Watershed Allied Telemetry Experimental Research (WATER) (2007-2010) and the Heihe Watershed Allied Telemetry Experimental Research (HiWATER) (2012-2015). Among these two experiments, an important result of WATER has been the generation of some multi-scale, high-quality comprehensive datasets, which have greatly supported the development, improvement and validation of a series of ecological, hydrological and quantitative remote-sensing models. The goal of a breakthrough for solving the "data bottleneck" problem has been achieved. HiWATER was initiated in 2012. This project has established a world-class hydrological and meteorological observation network, a flux measurement matrix and an eco-hydrological wireless sensor network. A set of super high-resolution airborne remote-sensing data has also been obtained. In addition, there has been important progress with regard to the scaling research. Furthermore, the automatic acquisition, transmission, quality control and remote control of the observational data has been realized through the use of wireless sensor network technology. The observation and information systems have been highly integrated, which will provide a solid foundation for establishing a research platform that integrates observation, data management, model simulation, scenario analysis and decision-making support to foster 21st-century watershed science in China.

A comprehensive pathway map of epidermal growth factor receptor signaling

PubMed Central

Oda, Kanae; Matsuoka, Yukiko; Funahashi, Akira; Kitano, Hiroaki

2005-01-01

The epidermal growth factor receptor (EGFR) signaling pathway is one of the most important pathways that regulate growth, survival, proliferation, and differentiation in mammalian cells. Reflecting this importance, it is one of the best-investigated signaling systems, both experimentally and computationally, and several computational models have been developed for dynamic analysis. A map of molecular interactions of the EGFR signaling system is a valuable resource for research in this area. In this paper, we present a comprehensive pathway map of EGFR signaling and other related pathways. The map reveals that the overall architecture of the pathway is a bow-tie (or hourglass) structure with several feedback loops. The map is created using CellDesigner software that enables us to graphically represent interactions using a well-defined and consistent graphical notation, and to store it in Systems Biology Markup Language (SBML). PMID:16729045

Communication: Microphase equilibrium and assembly dynamics.

PubMed

Zhuang, Yuan; Charbonneau, Patrick

2017-09-07

Despite many attempts, ordered equilibrium microphases have yet to be obtained in experimental colloidal suspensions. The recent computation of the equilibrium phase diagram of a microscopic, particle-based microphase former [Zhuang et al., Phys. Rev. Lett. 116, 098301 (2016)] has nonetheless found such mesoscale assemblies to be thermodynamically stable. Here, we consider their equilibrium and assembly dynamics. At intermediate densities above the order-disorder transition, we identify four different dynamical regimes and the structural changes that underlie the dynamical crossovers from one disordered regime to the next. Below the order-disorder transition, we also find that periodic lamellae are the most dynamically accessible of the periodic microphases. Our analysis thus offers a comprehensive view of the dynamics of disordered microphases and a route to the assembly of periodic microphases in a putative well-controlled, experimental system.

PANORAMA: An approach to performance modeling and diagnosis of extreme-scale workflows

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

Deelman, Ewa; Carothers, Christopher; Mandal, Anirban

Here we report that computational science is well established as the third pillar of scientific discovery and is on par with experimentation and theory. However, as we move closer toward the ability to execute exascale calculations and process the ensuing extreme-scale amounts of data produced by both experiments and computations alike, the complexity of managing the compute and data analysis tasks has grown beyond the capabilities of domain scientists. Therefore, workflow management systems are absolutely necessary to ensure current and future scientific discoveries. A key research question for these workflow management systems concerns the performance optimization of complex calculation andmore » data analysis tasks. The central contribution of this article is a description of the PANORAMA approach for modeling and diagnosing the run-time performance of complex scientific workflows. This approach integrates extreme-scale systems testbed experimentation, structured analytical modeling, and parallel systems simulation into a comprehensive workflow framework called Pegasus for understanding and improving the overall performance of complex scientific workflows.« less

Coupled thermal-fluid-mechanics analysis of twin roll casting of A7075 aluminum alloy

NASA Astrophysics Data System (ADS)

Lee, Yun-Soo; Kim, Hyoung-Wook; Cho, Jae-Hyung; Chun, Se-Hwan

2017-09-01

Better understanding of temperature distribution and roll separation force during twin roll casting of aluminum alloys is critical to successfully fabricate good quality of aluminum strips. Therefore, the simulation techniques are widely applied to understand the twin roll casting process in a comprehensive way and to reduce the experimental time and cost of trial and error. However, most of the conventional approaches are considered thermally coupled flow, or thermally coupled mechanical behaviors. In this study, a fully coupled thermal-fluid-mechanical analysis of twin roll casting of A7075 aluminum strips was carried out using the finite element method. Temperature profile, liquid fraction and metal flow of aluminum strips with different thickness were predicted. Roll separation force and roll temperatures were experimentally obtained from a pilot-scale twin roll caster, and those results were compared with model predictions. Coupling the fluid of the liquid melt to the thermal and mechanical modeling reasonably predicted roll temperature distribution and roll separation force during twin roll casting.

PANORAMA: An approach to performance modeling and diagnosis of extreme-scale workflows

DOE PAGES

Deelman, Ewa; Carothers, Christopher; Mandal, Anirban; ...

2015-07-14

Here we report that computational science is well established as the third pillar of scientific discovery and is on par with experimentation and theory. However, as we move closer toward the ability to execute exascale calculations and process the ensuing extreme-scale amounts of data produced by both experiments and computations alike, the complexity of managing the compute and data analysis tasks has grown beyond the capabilities of domain scientists. Therefore, workflow management systems are absolutely necessary to ensure current and future scientific discoveries. A key research question for these workflow management systems concerns the performance optimization of complex calculation andmore » data analysis tasks. The central contribution of this article is a description of the PANORAMA approach for modeling and diagnosing the run-time performance of complex scientific workflows. This approach integrates extreme-scale systems testbed experimentation, structured analytical modeling, and parallel systems simulation into a comprehensive workflow framework called Pegasus for understanding and improving the overall performance of complex scientific workflows.« less

High spatial resolution mapping of surface plasmon resonance modes in single and aggregated gold nanoparticles assembled on DNA strands

NASA Astrophysics Data System (ADS)

Diaz-Egea, Carlos; Sigle, Wilfried; van Aken, Peter A.; Molina, Sergio I.

2013-07-01

We present the mapping of the full plasmonic mode spectrum for single and aggregated gold nanoparticles linked through DNA strands to a silicon nitride substrate. A comprehensive analysis of the electron energy loss spectroscopy images maps was performed on nanoparticles standing alone, dimers, and clusters of nanoparticles. The experimental results were confirmed by numerical calculations using the Mie theory and Gans-Mie theory for solving Maxwell's equations. Both bright and dark surface plasmon modes have been unveiled.

Advanced technology airfoil research, volume 1, part 2

NASA Technical Reports Server (NTRS)

1978-01-01

This compilation contains papers presented at the NASA Conference on Advanced Technology Airfoil Research held at Langley Research Center on March 7-9, 1978, which have unlimited distribution. This conference provided a comprehensive review of all NASA airfoil research, conducted in-house and under grant and contract. A broad spectrum of airfoil research outside of NASA was also reviewed. The major thrust of the technical sessions were in three areas: development of computational aerodynamic codes for airfoil analysis and design, development of experimental facilities and test techniques, and all types of airfoil applications.

Computational and Experimental Analysis of the Secretome of Methylococcus capsulatus (Bath)

PubMed Central

Indrelid, Stine; Mathiesen, Geir; Jacobsen, Morten; Lea, Tor; Kleiveland, Charlotte R.

2014-01-01

The Gram-negative methanotroph Methylococcus capsulatus (Bath) was recently demonstrated to abrogate inflammation in a murine model of inflammatory bowel disease, suggesting interactions with cells involved in maintaining mucosal homeostasis and emphasizing the importance of understanding the many properties of M. capsulatus. Secreted proteins determine how bacteria may interact with their environment, and a comprehensive knowledge of such proteins is therefore vital to understand bacterial physiology and behavior. The aim of this study was to systematically analyze protein secretion in M. capsulatus (Bath) by identifying the secretion systems present and the respective secreted substrates. Computational analysis revealed that in addition to previously recognized type II secretion systems and a type VII secretion system, a type Vb (two-partner) secretion system and putative type I secretion systems are present in M. capsulatus (Bath). In silico analysis suggests that the diverse secretion systems in M.capsulatus transport proteins likely to be involved in adhesion, colonization, nutrient acquisition and homeostasis maintenance. Results of the computational analysis was verified and extended by an experimental approach showing that in addition an uncharacterized protein and putative moonlighting proteins are released to the medium during exponential growth of M. capsulatus (Bath). PMID:25479164

Characterizing psychological dimensions in non-pathological subjects through autonomic nervous system dynamics

PubMed Central

Nardelli, Mimma; Valenza, Gaetano; Cristea, Ioana A.; Gentili, Claudio; Cotet, Carmen; David, Daniel; Lanata, Antonio; Scilingo, Enzo P.

2015-01-01

The objective assessment of psychological traits of healthy subjects and psychiatric patients has been growing interest in clinical and bioengineering research fields during the last decade. Several experimental evidences strongly suggest that a link between Autonomic Nervous System (ANS) dynamics and specific dimensions such as anxiety, social phobia, stress, and emotional regulation might exist. Nevertheless, an extensive investigation on a wide range of psycho-cognitive scales and ANS non-invasive markers gathered from standard and non-linear analysis still needs to be addressed. In this study, we analyzed the discerning and correlation capabilities of a comprehensive set of ANS features and psycho-cognitive scales in 29 non-pathological subjects monitored during resting conditions. In particular, the state of the art of standard and non-linear analysis was performed on Heart Rate Variability, InterBreath Interval series, and InterBeat Respiration series, which were considered as monovariate and multivariate measurements. Experimental results show that each ANS feature is linked to specific psychological traits. Moreover, non-linear analysis outperforms the psychological assessment with respect to standard analysis. Considering that the current clinical practice relies only on subjective scores from interviews and questionnaires, this study provides objective tools for the assessment of psychological dimensions. PMID:25859212

Overview of research on Bombyx mori microRNA

PubMed Central

Wang, Xin; Tang, Shun-ming; Shen, Xing-jia

2014-01-01

Abstract MicroRNAs (miRNAs) constitute some of the most significant regulatory factors involved at the post-transcriptional level after gene expression, contributing to the modulation of a large number of physiological processes such as development, metabolism, and disease occurrence. This review comprehensively and retrospectively explores the literature investigating silkworm, Bombyx mori L. (Lepidoptera: Bombicidae), miRNAs published to date, including discovery, identification, expression profiling analysis, target gene prediction, and the functional analysis of both miRNAs and their targets. It may provide experimental considerations and approaches for future study of miRNAs and benefit elucidation of the mechanisms of miRNAs involved in silkworm developmental processes and intracellular activities of other unknown non-coding RNAs. PMID:25368077

Effectiveness of a comprehensive integrated module using interactive lectures and workshops in understanding and knowledge retention about infant feeding practice in fifth year medical students: a quasi-experimental study.

PubMed

Sjarif, Damayanti Rusli; Yuliarti, Klara; Wahyuni, Luh Karunia; Wiguna, Tjhin; Prawitasari, Titis; Devaera, Yoga; Triyuniati, Henni Wahyu; Afriansyah, Andika

2016-08-18

Sixty percent of the 10.9 million under-5 deaths every year are related to malnutrition. More than two thirds of malnutrition is caused by inappropriate infant feeding practice. Only 35 % of mothers worldwide provide 4 months of exclusive breast-feeding, while complementary feeding is often untimely, nutritionally inadequate, hygienically poor, and improperly delivered. The existing pediatric nutrition module in our institution does not include proper delivery of food that involves oral-motor skills and feeding behavior. To scale up the knowledge and skill of medical students regarding evidence-based infant feeding practice, we designed a new module composed of comprehensive and integrated lectures with additional multidisciplinary lectures on oral-motor skill development and feeding behavior. A quasi-experimental study was conducted to evaluate the efficacy of the new module compared to the previous module. Fifth year medical students of Universitas Indonesia were divided into intervention and control groups. The control group received lectures and a paper-based workshop. The intervention group received comprehensive and integrated interactive lectures with additional multidisciplinary lectures on oral-motor skill development and behavioral approaches to feeding problems. A hands-on workshop using real cases shown on recorded video and role-play sessions was also presented to the intervention group. A pre-/post-test, 3-month retention test, and Observed Structured Clinical Examination (OSCE) were performed to evaluate understanding, knowledge retention, and counseling skills. A linear mixed effect model with a random intercept analysis for pre-test, post-test, and retention test scores showed significant higher result for intervention group compared to control group (p < 0.001). Comprehensive knowledge and counselling skills were better in the intervention group than in the control group as shown by the OSCE score (68.6 vs 59.3, p < 0.001). Our comprehensive integrated infant feeding practice module, which incorporates multidisciplinary learning processes and an interactive hands-on workshop with a role-play session yields better knowledge understanding and counseling skills compared with the existing module. Comprehensive knowledge and good counseling skills of medical students as future doctors are a pre-requisite to provide effective education to parents to support successful infant feeding practices.

The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience.

PubMed

Griss, Johannes; Jones, Andrew R; Sachsenberg, Timo; Walzer, Mathias; Gatto, Laurent; Hartler, Jürgen; Thallinger, Gerhard G; Salek, Reza M; Steinbeck, Christoph; Neuhauser, Nadin; Cox, Jürgen; Neumann, Steffen; Fan, Jun; Reisinger, Florian; Xu, Qing-Wei; Del Toro, Noemi; Pérez-Riverol, Yasset; Ghali, Fawaz; Bandeira, Nuno; Xenarios, Ioannis; Kohlbacher, Oliver; Vizcaíno, Juan Antonio; Hermjakob, Henning

2014-10-01

The HUPO Proteomics Standards Initiative has developed several standardized data formats to facilitate data sharing in mass spectrometry (MS)-based proteomics. These allow researchers to report their complete results in a unified way. However, at present, there is no format to describe the final qualitative and quantitative results for proteomics and metabolomics experiments in a simple tabular format. Many downstream analysis use cases are only concerned with the final results of an experiment and require an easily accessible format, compatible with tools such as Microsoft Excel or R. We developed the mzTab file format for MS-based proteomics and metabolomics results to meet this need. mzTab is intended as a lightweight supplement to the existing standard XML-based file formats (mzML, mzIdentML, mzQuantML), providing a comprehensive summary, similar in concept to the supplemental material of a scientific publication. mzTab files can contain protein, peptide, and small molecule identifications together with experimental metadata and basic quantitative information. The format is not intended to store the complete experimental evidence but provides mechanisms to report results at different levels of detail. These range from a simple summary of the final results to a representation of the results including the experimental design. This format is ideally suited to make MS-based proteomics and metabolomics results available to a wider biological community outside the field of MS. Several software tools for proteomics and metabolomics have already adapted the format as an output format. The comprehensive mzTab specification document and extensive additional documentation can be found online. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience*

PubMed Central

Griss, Johannes; Jones, Andrew R.; Sachsenberg, Timo; Walzer, Mathias; Gatto, Laurent; Hartler, Jürgen; Thallinger, Gerhard G.; Salek, Reza M.; Steinbeck, Christoph; Neuhauser, Nadin; Cox, Jürgen; Neumann, Steffen; Fan, Jun; Reisinger, Florian; Xu, Qing-Wei; del Toro, Noemi; Pérez-Riverol, Yasset; Ghali, Fawaz; Bandeira, Nuno; Xenarios, Ioannis; Kohlbacher, Oliver; Vizcaíno, Juan Antonio; Hermjakob, Henning

2014-01-01

The HUPO Proteomics Standards Initiative has developed several standardized data formats to facilitate data sharing in mass spectrometry (MS)-based proteomics. These allow researchers to report their complete results in a unified way. However, at present, there is no format to describe the final qualitative and quantitative results for proteomics and metabolomics experiments in a simple tabular format. Many downstream analysis use cases are only concerned with the final results of an experiment and require an easily accessible format, compatible with tools such as Microsoft Excel or R. We developed the mzTab file format for MS-based proteomics and metabolomics results to meet this need. mzTab is intended as a lightweight supplement to the existing standard XML-based file formats (mzML, mzIdentML, mzQuantML), providing a comprehensive summary, similar in concept to the supplemental material of a scientific publication. mzTab files can contain protein, peptide, and small molecule identifications together with experimental metadata and basic quantitative information. The format is not intended to store the complete experimental evidence but provides mechanisms to report results at different levels of detail. These range from a simple summary of the final results to a representation of the results including the experimental design. This format is ideally suited to make MS-based proteomics and metabolomics results available to a wider biological community outside the field of MS. Several software tools for proteomics and metabolomics have already adapted the format as an output format. The comprehensive mzTab specification document and extensive additional documentation can be found online. PMID:24980485

Effects of Tier I Differentiation and Reading Intervention on Reading Fluency, Comprehension, and High Stakes Measures

ERIC Educational Resources Information Center

Jefferson, Ruth E.; Grant, Christina E.; Sander, Janay B.

2017-01-01

This quasi-experimental study examined differences in student reading outcomes. Participants were third grade non-struggling readers. Intervention classrooms included core curriculum instruction plus evidence-based reading comprehension instruction and differentiated repeated readings. Comparison classrooms provided core curriculum instruction…

Relationship between Speech Intelligibility and Speech Comprehension in Babble Noise

ERIC Educational Resources Information Center

Fontan, Lionel; Tardieu, Julien; Gaillard, Pascal; Woisard, Virginie; Ruiz, Robert

2015-01-01

Purpose: The authors investigated the relationship between the intelligibility and comprehension of speech presented in babble noise. Method: Forty participants listened to French imperative sentences (commands for moving objects) in a multitalker babble background for which intensity was experimentally controlled. Participants were instructed to…

Referential Strategy Training for Second Language Reading Comprehension of Japanese Texts.

ERIC Educational Resources Information Center

Kitajima, Ryu

1997-01-01

Examines whether strategy training orienting second language (L2) students' attention toward referential processes improves their comprehension of Japanese narrative. Findings revealed that experimental students comprehended the story at the macro level significantly better than control students, suggesting that the strategy training is beneficial…

The Effect of the Thinking-Aloud Strategy on the Reading Comprehension Skills of 4th Grade Primary School Students

ERIC Educational Resources Information Center

Sönmez, Yasemin; Sulak, Süleyman Erkam

2018-01-01

The purpose of this study, which is designed in quasi-experimental model, is to examine the effect of the thinking aloud strategy on the reading comprehension skills of the 4th grade primary school students. For this purpose, in the second semester of 2016-2017 academic year, the reading comprehension levels of 26 students in the 4th grade at a…

Novel Metaphors Comprehension in a Child with High-Functioning Autism Spectrum Disorder: A Study on Assessment and Treatment

PubMed Central

Melogno, Sergio; Pinto, Maria A.; Orsolini, Margherita

2017-01-01

Until the first decade of the current millennium, the literature on metaphor comprehension highlighted typical difficulties in children with high-functioning Autism Spectrum Disorder (ASD). More recently, some scholars have devised special programs for enhancing the capability of understanding metaphors in these children. This article presents a case study based on a treatment aiming at enhancing novel metaphor comprehension in a high-functioning child with ASD. M.M., a pseudoacronym for an 8;10 year-old boy, diagnosed with high-functioning ASD, was first assessed with a metaphor comprehension test. This testing (at time T0) highlighted a rigid refusal of metaphors and a marked tendency toward literal interpretation. A baseline treatment (8 sessions of 45–60 min each, twice a week) was implemented, based on a series of recognition, denomination and emotion comprehension activities. M.M.'s metaphor comprehension was assessed a second time (T1), followed by the experimental treatment (same duration and frequency as the first one), specifically focused on metaphor comprehension. Finally, a third assessment of metaphor comprehension took place (T2), followed by a last assessment 4 months later (follow-up, T3). The comparison between the performances at the metaphor comprehension test across the four assessments, from T0 to T3, showed that the baseline treatment produced no effect at all, whereas a significant improvement appeared at T2, just after the experimental treatment, later confirmed at the follow up. Both quantitative and qualitative results showed an evident improvement in the way M.M. handled the semantic issues posed by the metaphors of the test, in line with the strategies he was taught during the treatment. PMID:28101069

A Comprehensive Validation Methodology for Sparse Experimental Data

NASA Technical Reports Server (NTRS)

Norman, Ryan B.; Blattnig, Steve R.

2010-01-01

A comprehensive program of verification and validation has been undertaken to assess the applicability of models to space radiation shielding applications and to track progress as models are developed over time. The models are placed under configuration control, and automated validation tests are used so that comparisons can readily be made as models are improved. Though direct comparisons between theoretical results and experimental data are desired for validation purposes, such comparisons are not always possible due to lack of data. In this work, two uncertainty metrics are introduced that are suitable for validating theoretical models against sparse experimental databases. The nuclear physics models, NUCFRG2 and QMSFRG, are compared to an experimental database consisting of over 3600 experimental cross sections to demonstrate the applicability of the metrics. A cumulative uncertainty metric is applied to the question of overall model accuracy, while a metric based on the median uncertainty is used to analyze the models from the perspective of model development by analyzing subsets of the model parameter space.

QRAC-the-Code: a comprehension monitoring strategy for middle school social studies textbooks.

PubMed

Berkeley, Sheri; Riccomini, Paul J

2013-01-01

Requirements for reading and ascertaining information from text increase as students advance through the educational system, especially in content-rich classes; hence, monitoring comprehension is especially important. However, this is a particularly challenging skill for many students who struggle with reading comprehension, including students with learning disabilities. A randomized pre-post experimental design was employed to investigate the effectiveness of a comprehension monitoring strategy (QRAC-the-Code) for improving the reading comprehension of 323 students in grades 6 and 7 in inclusive social studies classes. Findings indicated that both general education students and students with learning disabilities who were taught a simple comprehension monitoring strategy improved their comprehension of textbook content compared to students who read independently and noted important points. In addition, students in the comprehension monitoring condition reported using more reading strategies after the intervention. Implications for research and practice are discussed.

The Effect of Integrated Instructions on Reading Comprehension, Motivation, and Cognitive Variables

ERIC Educational Resources Information Center

Alhabahba, Mohammad Madallh; Pandian, Ambigapathy; Mahfoodh, Omer Hassan Ali

2016-01-01

This quasi-experimental study examined the contribution of concept-oriented reading instruction (CORI) on fifth grade students' reading comprehension, motivation and metacognition. Participants were sixty-six fifth grade female Jordanian students who matched in gender, socioeconomic status, number of years learning English, and school attended.…

A Comprehensive Multi-Media Program to Prevent Smoking among Black Students.

ERIC Educational Resources Information Center

Kaufman, Joy S.; And Others

1994-01-01

Implemented program to decrease incidence of new smokers among black adolescents. Program combined school-based curriculum with comprehensive media intervention. There were two experimental conditions: one group participated in school-based intervention and was prompted to participate in multimedia intervention; other group had access to…

A Comprehensive Enzyme Kinetic Exercise for Biochemistry

ERIC Educational Resources Information Center

Barton, Janice S.

2011-01-01

This article describes a comprehensive treatment of experimental enzyme kinetics strongly coupled to electronic data acquisition and use of spreadsheets to organize data and perform linear and nonlinear least-squares analyses, all in a manner that promotes development of important reasoning skills. Kinetic parameters are obtained for the stable…

Effect of Hypertextual Reading on Academic Success and Comprehension Skills

ERIC Educational Resources Information Center

Durukan, Erhan

2014-01-01

As computer technology developed, hypertexts emerged as an influential environment for developing language skills. This study aims to evaluate a text prepared in a hypertextual environment and its effects on academic success and comprehension skills. In this study, "preliminary test final test control group experimental pattern" was used…

Captioned Instructional Video: Effects on Content Comprehension, Vocabulary Acquisition and Language Proficiency

ERIC Educational Resources Information Center

BavaHarji, Madhubala; Alavi, Zhinoos Kamal; Letchumanan, Krishnaveni

2014-01-01

This experimental design study examined the effects of viewing captioned instructional videos on EFL learners' content comprehension, vocabulary acquisition and language proficiency. It also examined the participants' perception of viewing the captioned instructional videos. The 92 EFL students in two classes, who were undertaking the "Tape…

Improved Bond Equations for Fiber-Reinforced Polymer Bars in Concrete

PubMed Central

Pour, Sadaf Moallemi; Alam, M. Shahria; Milani, Abbas S.

2016-01-01

This paper explores a set of new equations to predict the bond strength between fiber reinforced polymer (FRP) rebar and concrete. The proposed equations are based on a comprehensive statistical analysis and existing experimental results in the literature. Namely, the most effective parameters on bond behavior of FRP concrete were first identified by applying a factorial analysis on a part of the available database. Then the database that contains 250 pullout tests were divided into four groups based on the concrete compressive strength and the rebar surface. Afterward, nonlinear regression analysis was performed for each study group in order to determine the bond equations. The results show that the proposed equations can predict bond strengths more accurately compared to the other previously reported models. PMID:28773859

Virtual Diagnostic Interface: Aerospace Experimentation in the Synthetic Environment

NASA Technical Reports Server (NTRS)

Schwartz, Richard J.; McCrea, Andrew C.

2009-01-01

The Virtual Diagnostics Interface (ViDI) methodology combines two-dimensional image processing and three-dimensional computer modeling to provide comprehensive in-situ visualizations commonly utilized for in-depth planning of wind tunnel and flight testing, real time data visualization of experimental data, and unique merging of experimental and computational data sets in both real-time and post-test analysis. The preparation of such visualizations encompasses the realm of interactive three-dimensional environments, traditional and state of the art image processing techniques, database management and development of toolsets with user friendly graphical user interfaces. ViDI has been under development at the NASA Langley Research Center for over 15 years, and has a long track record of providing unique and insightful solutions to a wide variety of experimental testing techniques and validation of computational simulations. This report will address the various aspects of ViDI and how it has been applied to test programs as varied as NASCAR race car testing in NASA wind tunnels to real-time operations concerning Space Shuttle aerodynamic flight testing. In addition, future trends and applications will be outlined in the paper.

Virtual Diagnostic Interface: Aerospace Experimentation in the Synthetic Environment

NASA Technical Reports Server (NTRS)

Schwartz, Richard J.; McCrea, Andrew C.

2010-01-01

The Virtual Diagnostics Interface (ViDI) methodology combines two-dimensional image processing and three-dimensional computer modeling to provide comprehensive in-situ visualizations commonly utilized for in-depth planning of wind tunnel and flight testing, real time data visualization of experimental data, and unique merging of experimental and computational data sets in both real-time and post-test analysis. The preparation of such visualizations encompasses the realm of interactive three-dimensional environments, traditional and state of the art image processing techniques, database management and development of toolsets with user friendly graphical user interfaces. ViDI has been under development at the NASA Langley Research Center for over 15 years, and has a long track record of providing unique and insightful solutions to a wide variety of experimental testing techniques and validation of computational simulations. This report will address the various aspects of ViDI and how it has been applied to test programs as varied as NASCAR race car testing in NASA wind tunnels to real-time operations concerning Space Shuttle aerodynamic flight testing. In addition, future trends and applications will be outlined in the paper.

Simulation and experimental research of 1MWe solar tower power plant in China

NASA Astrophysics Data System (ADS)

Yu, Qiang; Wang, Zhifeng; Xu, Ershu

2016-05-01

The establishment of a reliable simulation system for a solar tower power plant can greatly increase the economic and safety performance of the whole system. In this paper, a dynamic model of the 1MWe Solar Tower Power Plant at Badaling in Beijing is developed based on the "STAR-90" simulation platform, including the heliostat field, the central receiver system (water/steam), etc. The dynamic behavior of the global CSP plant can be simulated. In order to verify the validity of simulation system, a complete experimental process was synchronously simulated by repeating the same operating steps based on the simulation platform, including the locations and number of heliostats, the mass flow of the feed water, etc. According to the simulation and experimental results, some important parameters are taken out to make a deep comparison. The results show that there is good alignment between the simulations and the experimental results and that the error range can be acceptable considering the error of the models. In the end, a comprehensive and deep analysis on the error source is carried out according to the comparative results.

microPIR2: a comprehensive database for human–mouse comparative study of microRNA–promoter interactions

PubMed Central

Piriyapongsa, Jittima; Bootchai, Chaiwat; Ngamphiw, Chumpol; Tongsima, Sissades

2014-01-01

microRNA (miRNA)–promoter interaction resource (microPIR) is a public database containing over 15 million predicted miRNA target sites located within human promoter sequences. These predicted targets are presented along with their related genomic and experimental data, making the microPIR database the most comprehensive repository of miRNA promoter target sites. Here, we describe major updates of the microPIR database including new target predictions in the mouse genome and revised human target predictions. The updated database (microPIR2) now provides ∼80 million human and 40 million mouse predicted target sites. In addition to being a reference database, microPIR2 is a tool for comparative analysis of target sites on the promoters of human–mouse orthologous genes. In particular, this new feature was designed to identify potential miRNA–promoter interactions conserved between species that could be stronger candidates for further experimental validation. We also incorporated additional supporting information to microPIR2 such as nuclear and cytoplasmic localization of miRNAs and miRNA–disease association. Extra search features were also implemented to enable various investigations of targets of interest. Database URL: http://www4a.biotec.or.th/micropir2 PMID:25425035

The impact of aircraft noise exposure on South African children's reading comprehension: the moderating effect of home language.

PubMed

Seabi, Joseph; Cockcroft, Kate; Goldschagg, Paul; Greyling, Mike

2012-01-01

Given the limited studies conducted within the African continent, the purpose of this study was to investigate the impact of chronic aircraft noise exposure and the moderating effect of home language on the learners' reading comprehension. The sample comprised 437 (52%) senior primary learners exposed to high levels of aircraft noise (Experimental group) and 337 (48%) learners residing in a quieter area (Control group). Of these, 151 learners in the Experimental group spoke English as a first language (EFL) and 162 spoke English as a second language (ESL). In the Control group, the numbers were similarly divided (EFL n = 191; ESL n = 156). A univariate General Linear Model was used to investigate the effects of aircraft noise exposure and language on reading comprehension, while observing for the possible impact of intellectual ability, gender, and socioeconomic status on the results. A significant difference was observed between ESL and EFL learners in favor of the latter (F 1,419 = 21.95, P =.000). In addition a substantial and significant interaction effect was found between the experimental and control groups for the two language groups. For the EFL speakers there was a strong reduction in reading comprehension in the aircraft noise group. By contrast this difference was not significant for the ESL speakers. Implications of the findings and suggestions for further research are made in the article.

A Comprehensive Analysis on Wearable Acceleration Sensors in Human Activity Recognition.

PubMed

Janidarmian, Majid; Roshan Fekr, Atena; Radecka, Katarzyna; Zilic, Zeljko

2017-03-07

Sensor-based motion recognition integrates the emerging area of wearable sensors with novel machine learning techniques to make sense of low-level sensor data and provide rich contextual information in a real-life application. Although Human Activity Recognition (HAR) problem has been drawing the attention of researchers, it is still a subject of much debate due to the diverse nature of human activities and their tracking methods. Finding the best predictive model in this problem while considering different sources of heterogeneities can be very difficult to analyze theoretically, which stresses the need of an experimental study. Therefore, in this paper, we first create the most complete dataset, focusing on accelerometer sensors, with various sources of heterogeneities. We then conduct an extensive analysis on feature representations and classification techniques (the most comprehensive comparison yet with 293 classifiers) for activity recognition. Principal component analysis is applied to reduce the feature vector dimension while keeping essential information. The average classification accuracy of eight sensor positions is reported to be 96.44% ± 1.62% with 10-fold evaluation, whereas accuracy of 79.92% ± 9.68% is reached in the subject-independent evaluation. This study presents significant evidence that we can build predictive models for HAR problem under more realistic conditions, and still achieve highly accurate results.

Miniaturization of the Clonogenic Assay Using Confluence Measurement

PubMed Central

Mayr, Christian; Beyreis, Marlena; Dobias, Heidemarie; Gaisberger, Martin; Pichler, Martin; Ritter, Markus; Jakab, Martin; Neureiter, Daniel; Kiesslich, Tobias

2018-01-01

The clonogenic assay is a widely used method to study the ability of cells to ‘infinitely’ produce progeny and is, therefore, used as a tool in tumor biology to measure tumor-initiating capacity and stem cell status. However, the standard protocol of using 6-well plates has several disadvantages. By miniaturizing the assay to a 96-well microplate format, as well as by utilizing the confluence detection function of a multimode reader, we here describe a new and modified protocol that allows comprehensive experimental setups and a non-endpoint, label-free semi-automatic analysis. Comparison of bright field images with confluence images demonstrated robust and reproducible detection of clones by the confluence detection function. Moreover, time-resolved non-endpoint confluence measurement of the same well showed that semi-automatic analysis was suitable for determining the mean size and colony number. By treating cells with an inhibitor of clonogenic growth (PTC-209), we show that our modified protocol is suitable for comprehensive (broad concentration range, addition of technical replicates) concentration- and time-resolved analysis of the effect of substances or treatments on clonogenic growth. In summary, this protocol represents a time- and cost-effective alternative to the commonly used 6-well protocol (with endpoint staining) and also provides additional information about the kinetics of clonogenic growth. PMID:29510509

A NEW METHOD OF PEAK DETECTION FOR ANALYSIS OF COMPREHENSIVE TWO-DIMENSIONAL GAS CHROMATOGRAPHY MASS SPECTROMETRY DATA*

PubMed Central

Kim, Seongho; Ouyang, Ming; Jeong, Jaesik; Shen, Changyu; Zhang, Xiang

2014-01-01

We develop a novel peak detection algorithm for the analysis of comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GC×GC-TOF MS) data using normal-exponential-Bernoulli (NEB) and mixture probability models. The algorithm first performs baseline correction and denoising simultaneously using the NEB model, which also defines peak regions. Peaks are then picked using a mixture of probability distribution to deal with the co-eluting peaks. Peak merging is further carried out based on the mass spectral similarities among the peaks within the same peak group. The algorithm is evaluated using experimental data to study the effect of different cut-offs of the conditional Bayes factors and the effect of different mixture models including Poisson, truncated Gaussian, Gaussian, Gamma, and exponentially modified Gaussian (EMG) distributions, and the optimal version is introduced using a trial-and-error approach. We then compare the new algorithm with two existing algorithms in terms of compound identification. Data analysis shows that the developed algorithm can detect the peaks with lower false discovery rates than the existing algorithms, and a less complicated peak picking model is a promising alternative to the more complicated and widely used EMG mixture models. PMID:25264474

PATRIC: the Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species ▿ ‡ #

PubMed Central

Gillespie, Joseph J.; Wattam, Alice R.; Cammer, Stephen A.; Gabbard, Joseph L.; Shukla, Maulik P.; Dalay, Oral; Driscoll, Timothy; Hix, Deborah; Mane, Shrinivasrao P.; Mao, Chunhong; Nordberg, Eric K.; Scott, Mark; Schulman, Julie R.; Snyder, Eric E.; Sullivan, Daniel E.; Wang, Chunxia; Warren, Andrew; Williams, Kelly P.; Xue, Tian; Seung Yoo, Hyun; Zhang, Chengdong; Zhang, Yan; Will, Rebecca; Kenyon, Ronald W.; Sobral, Bruno W.

2011-01-01

Funded by the National Institute of Allergy and Infectious Diseases, the Pathosystems Resource Integration Center (PATRIC) is a genomics-centric relational database and bioinformatics resource designed to assist scientists in infectious-disease research. Specifically, PATRIC provides scientists with (i) a comprehensive bacterial genomics database, (ii) a plethora of associated data relevant to genomic analysis, and (iii) an extensive suite of computational tools and platforms for bioinformatics analysis. While the primary aim of PATRIC is to advance the knowledge underlying the biology of human pathogens, all publicly available genome-scale data for bacteria are compiled and continually updated, thereby enabling comparative analyses to reveal the basis for differences between infectious free-living and commensal species. Herein we summarize the major features available at PATRIC, dividing the resources into two major categories: (i) organisms, genomes, and comparative genomics and (ii) recurrent integration of community-derived associated data. Additionally, we present two experimental designs typical of bacterial genomics research and report on the execution of both projects using only PATRIC data and tools. These applications encompass a broad range of the data and analysis tools available, illustrating practical uses of PATRIC for the biologist. Finally, a summary of PATRIC's outreach activities, collaborative endeavors, and future research directions is provided. PMID:21896772

Advances in metabolome information retrieval: turning chemistry into biology. Part I: analytical chemistry of the metabolome.

PubMed

Tebani, Abdellah; Afonso, Carlos; Bekri, Soumeya

2018-05-01

Metabolites are small molecules produced by enzymatic reactions in a given organism. Metabolomics or metabolic phenotyping is a well-established omics aimed at comprehensively assessing metabolites in biological systems. These comprehensive analyses use analytical platforms, mainly nuclear magnetic resonance spectroscopy and mass spectrometry, along with associated separation methods to gather qualitative and quantitative data. Metabolomics holistically evaluates biological systems in an unbiased, data-driven approach that may ultimately support generation of hypotheses. The approach inherently allows the molecular characterization of a biological sample with regard to both internal (genetics) and environmental (exosome, microbiome) influences. Metabolomics workflows are based on whether the investigator knows a priori what kind of metabolites to assess. Thus, a targeted metabolomics approach is defined as a quantitative analysis (absolute concentrations are determined) or a semiquantitative analysis (relative intensities are determined) of a set of metabolites that are possibly linked to common chemical classes or a selected metabolic pathway. An untargeted metabolomics approach is a semiquantitative analysis of the largest possible number of metabolites contained in a biological sample. This is part I of a review intending to give an overview of the state of the art of major metabolic phenotyping technologies. Furthermore, their inherent analytical advantages and limits regarding experimental design, sample handling, standardization and workflow challenges are discussed.

CANEapp: a user-friendly application for automated next generation transcriptomic data analysis.

PubMed

Velmeshev, Dmitry; Lally, Patrick; Magistri, Marco; Faghihi, Mohammad Ali

2016-01-13

Next generation sequencing (NGS) technologies are indispensable for molecular biology research, but data analysis represents the bottleneck in their application. Users need to be familiar with computer terminal commands, the Linux environment, and various software tools and scripts. Analysis workflows have to be optimized and experimentally validated to extract biologically meaningful data. Moreover, as larger datasets are being generated, their analysis requires use of high-performance servers. To address these needs, we developed CANEapp (application for Comprehensive automated Analysis of Next-generation sequencing Experiments), a unique suite that combines a Graphical User Interface (GUI) and an automated server-side analysis pipeline that is platform-independent, making it suitable for any server architecture. The GUI runs on a PC or Mac and seamlessly connects to the server to provide full GUI control of RNA-sequencing (RNA-seq) project analysis. The server-side analysis pipeline contains a framework that is implemented on a Linux server through completely automated installation of software components and reference files. Analysis with CANEapp is also fully automated and performs differential gene expression analysis and novel noncoding RNA discovery through alternative workflows (Cuffdiff and R packages edgeR and DESeq2). We compared CANEapp to other similar tools, and it significantly improves on previous developments. We experimentally validated CANEapp's performance by applying it to data derived from different experimental paradigms and confirming the results with quantitative real-time PCR (qRT-PCR). CANEapp adapts to any server architecture by effectively using available resources and thus handles large amounts of data efficiently. CANEapp performance has been experimentally validated on various biological datasets. CANEapp is available free of charge at http://psychiatry.med.miami.edu/research/laboratory-of-translational-rna-genomics/CANE-app . We believe that CANEapp will serve both biologists with no computational experience and bioinformaticians as a simple, timesaving but accurate and powerful tool to analyze large RNA-seq datasets and will provide foundations for future development of integrated and automated high-throughput genomics data analysis tools. Due to its inherently standardized pipeline and combination of automated analysis and platform-independence, CANEapp is an ideal for large-scale collaborative RNA-seq projects between different institutions and research groups.

Comprehensive analysis of orthologous protein domains using the HOPS database.

PubMed

Storm, Christian E V; Sonnhammer, Erik L L

2003-10-01

One of the most reliable methods for protein function annotation is to transfer experimentally known functions from orthologous proteins in other organisms. Most methods for identifying orthologs operate on a subset of organisms with a completely sequenced genome, and treat proteins as single-domain units. However, it is well known that proteins are often made up of several independent domains, and there is a wealth of protein sequences from genomes that are not completely sequenced. A comprehensive set of protein domain families is found in the Pfam database. We wanted to apply orthology detection to Pfam families, but first some issues needed to be addressed. First, orthology detection becomes impractical and unreliable when too many species are included. Second, shorter domains contain less information. It is therefore important to assess the quality of the orthology assignment and avoid very short domains altogether. We present a database of orthologous protein domains in Pfam called HOPS: Hierarchical grouping of Orthologous and Paralogous Sequences. Orthology is inferred in a hierarchic system of phylogenetic subgroups using ortholog bootstrapping. To avoid the frequent errors stemming from horizontally transferred genes in bacteria, the analysis is presently limited to eukaryotic genes. The results are accessible in the graphical browser NIFAS, a Java tool originally developed for analyzing phylogenetic relations within Pfam families. The method was tested on a set of curated orthologs with experimentally verified function. In comparison to tree reconciliation with a complete species tree, our approach finds significantly more orthologs in the test set. Examples for investigating gene fusions and domain recombination using HOPS are given.

A study of perceptual and verbal skills of disabled readers in grades 4, 5 and 6.

PubMed

Solan, H A; Ficarra, A P

1990-08-01

This investigation addresses the role of the optometrist in diagnosing and treating children in grades 4, 5, and 6 who have been identified as reading disabled. Fifty-one subjects with average intelligence, but whose reading comprehension skills were below the 31st percentile (mean, 20th percentile), were evaluated using verbal and perceptual tests. When the performance of this experimental group was compared with the mean scores from standardized test norms for each of the various tasks, the disabled readers scored significantly lower in seven of the eight perceptual and five of the six verbal tasks. These results lend support to the hypothesis that both perceptual and verbal deficits are related to reading comprehension. Using step-wise multiple correlation analysis, three perceptual factors; eye-movements, Auditory-Visual Integration Test (AVIT), and grooved peg-board, contributed 38 percent of the variance whereas the addition of two verbal factors (digit span and token test) provided just 2 percent. That is, 38 percent of the variations in reading comprehension could be accounted for by variations in perceptual skills in the disabled readers. The results were interpreted in terms of spatial-simultaneous and verbal-successive processing skills.

Advanced technology development multi-color holography

NASA Technical Reports Server (NTRS)

Vikram, Chandra S.

1993-01-01

This is the final report of the Multi-color Holography project. The comprehensive study considers some strategic aspects of multi-color holography. First, various methods of available techniques for accurate fringe counting are reviewed. These are heterodyne interferometry, quasi-heterodyne interferometry, and phase-shifting interferometry. Phase-shifting interferometry was found to be the most suitable for multi-color holography. Details of experimentation with a sugar solution are also reported where better than 1/200 of a fringe order measurement capability was established. Rotating plate glass phase shifter was used for the experimentation. The report then describes the possible role of using more than two wavelengths with special reference-to-object beam intensity ratio needs in multicolor holography. Some specific two- and three-color cases are also described in detail. Then some new analysis methods of the reconstructed wavefront are considered. These are deflectometry, speckle metrology, confocal optical signal processing, and phase shifting technique related applications. Finally, design aspects of an experimental breadboard are presented.

Platform construction and extraction mechanism study of magnetic mixed hemimicelles solid-phase extraction

NASA Astrophysics Data System (ADS)

Xiao, Deli; Zhang, Chan; He, Jia; Zeng, Rong; Chen, Rong; He, Hua

2016-12-01

Simple, accurate and high-throughput pretreatment method would facilitate large-scale studies of trace analysis in complex samples. Magnetic mixed hemimicelles solid-phase extraction has the power to become a key pretreatment method in biological, environmental and clinical research. However, lacking of experimental predictability and unsharpness of extraction mechanism limit the development of this promising method. Herein, this work tries to establish theoretical-based experimental designs for extraction of trace analytes from complex samples using magnetic mixed hemimicelles solid-phase extraction. We selected three categories and six sub-types of compounds for systematic comparative study of extraction mechanism, and comprehensively illustrated the roles of different force (hydrophobic interaction, π-π stacking interactions, hydrogen-bonding interaction, electrostatic interaction) for the first time. What’s more, the application guidelines for supporting materials, surfactants and sample matrix were also summarized. The extraction mechanism and platform established in the study render its future promising for foreseeable and efficient pretreatment under theoretical based experimental design for trace analytes from environmental, biological and clinical samples.

Treating stimuli as a random factor in social psychology: a new and comprehensive solution to a pervasive but largely ignored problem.

PubMed

Judd, Charles M; Westfall, Jacob; Kenny, David A

2012-07-01

Throughout social and cognitive psychology, participants are routinely asked to respond in some way to experimental stimuli that are thought to represent categories of theoretical interest. For instance, in measures of implicit attitudes, participants are primed with pictures of specific African American and White stimulus persons sampled in some way from possible stimuli that might have been used. Yet seldom is the sampling of stimuli taken into account in the analysis of the resulting data, in spite of numerous warnings about the perils of ignoring stimulus variation (Clark, 1973; Kenny, 1985; Wells & Windschitl, 1999). Part of this failure to attend to stimulus variation is due to the demands imposed by traditional analysis of variance procedures for the analysis of data when both participants and stimuli are treated as random factors. In this article, we present a comprehensive solution using mixed models for the analysis of data with crossed random factors (e.g., participants and stimuli). We show the substantial biases inherent in analyses that ignore one or the other of the random factors, and we illustrate the substantial advantages of the mixed models approach with both hypothetical and actual, well-known data sets in social psychology (Bem, 2011; Blair, Chapleau, & Judd, 2005; Correll, Park, Judd, & Wittenbrink, 2002). PsycINFO Database Record (c) 2012 APA, all rights reserved

Computation and Communication Evaluation of an Authentication Mechanism for Time-Triggered Networked Control Systems

PubMed Central

Martins, Goncalo; Moondra, Arul; Dubey, Abhishek; Bhattacharjee, Anirban; Koutsoukos, Xenofon D.

2016-01-01

In modern networked control applications, confidentiality and integrity are important features to address in order to prevent against attacks. Moreover, network control systems are a fundamental part of the communication components of current cyber-physical systems (e.g., automotive communications). Many networked control systems employ Time-Triggered (TT) architectures that provide mechanisms enabling the exchange of precise and synchronous messages. TT systems have computation and communication constraints, and with the aim to enable secure communications in the network, it is important to evaluate the computational and communication overhead of implementing secure communication mechanisms. This paper presents a comprehensive analysis and evaluation of the effects of adding a Hash-based Message Authentication (HMAC) to TT networked control systems. The contributions of the paper include (1) the analysis and experimental validation of the communication overhead, as well as a scalability analysis that utilizes the experimental result for both wired and wireless platforms and (2) an experimental evaluation of the computational overhead of HMAC based on a kernel-level Linux implementation. An automotive application is used as an example, and the results show that it is feasible to implement a secure communication mechanism without interfering with the existing automotive controller execution times. The methods and results of the paper can be used for evaluating the performance impact of security mechanisms and, thus, for the design of secure wired and wireless TT networked control systems. PMID:27463718

Computation and Communication Evaluation of an Authentication Mechanism for Time-Triggered Networked Control Systems.

PubMed

Martins, Goncalo; Moondra, Arul; Dubey, Abhishek; Bhattacharjee, Anirban; Koutsoukos, Xenofon D

2016-07-25

In modern networked control applications, confidentiality and integrity are important features to address in order to prevent against attacks. Moreover, network control systems are a fundamental part of the communication components of current cyber-physical systems (e.g., automotive communications). Many networked control systems employ Time-Triggered (TT) architectures that provide mechanisms enabling the exchange of precise and synchronous messages. TT systems have computation and communication constraints, and with the aim to enable secure communications in the network, it is important to evaluate the computational and communication overhead of implementing secure communication mechanisms. This paper presents a comprehensive analysis and evaluation of the effects of adding a Hash-based Message Authentication (HMAC) to TT networked control systems. The contributions of the paper include (1) the analysis and experimental validation of the communication overhead, as well as a scalability analysis that utilizes the experimental result for both wired and wireless platforms and (2) an experimental evaluation of the computational overhead of HMAC based on a kernel-level Linux implementation. An automotive application is used as an example, and the results show that it is feasible to implement a secure communication mechanism without interfering with the existing automotive controller execution times. The methods and results of the paper can be used for evaluating the performance impact of security mechanisms and, thus, for the design of secure wired and wireless TT networked control systems.

Impedance analysis of GPCR-mediated changes in endothelial barrier function: overview, and fundamental considerations for stable and reproducible measurements

PubMed Central

Stolwijk, Judith A.; Matrougui, Khalid; Renken, Christian W.; Trebak, Mohamed

2014-01-01

The past 20 years have seen significant growth in using impedance-based assays to understand the molecular underpinning of endothelial and epithelial barrier function in response to physiological agonists, pharmacological and toxicological compounds. Most studies on barrier function use G protein coupled receptor (GPCR) agonists which couple to fast and transient changes in barrier properties. The power of impedance based techniques such as Electric Cell-Substrate Impedance Sensing (ECIS) reside in its ability to detect minute changes in cell layer integrity label-free and in real-time ranging from seconds to days. We provide a comprehensive overview of the biophysical principles, applications and recent developments in impedance-based methodologies. Despite extensive application of impedance analysis in endothelial barrier research little attention has been paid to data analysis and critical experimental variables, which are both essential for signal stability and reproducibility. We describe the rationale behind common ECIS data presentation and interpretation and illustrate practical guidelines to improve signal intensity by adapting technical parameters such as electrode layout, monitoring frequency or parameter (resistance versus impedance magnitude). Moreover, we discuss the impact of experimental parameters, including cell source, liquid handling and agonist preparation on signal intensity and kinetics. Our discussions are supported by experimental data obtained from human microvascular endothelial cells challenged with three GPCR agonists, thrombin, histamine and Sphingosine-1-Phosphate. PMID:25537398

Impedance analysis of GPCR-mediated changes in endothelial barrier function: overview and fundamental considerations for stable and reproducible measurements.

PubMed

Stolwijk, Judith A; Matrougui, Khalid; Renken, Christian W; Trebak, Mohamed

2015-10-01

The past 20 years has seen significant growth in using impedance-based assays to understand the molecular underpinning of endothelial and epithelial barrier function in response to physiological agonists and pharmacological and toxicological compounds. Most studies on barrier function use G protein-coupled receptor (GPCR) agonists which couple to fast and transient changes in barrier properties. The power of impedance-based techniques such as electric cell-substrate impedance sensing (ECIS) resides in its ability to detect minute changes in cell layer integrity label-free and in real-time ranging from seconds to days. We provide a comprehensive overview of the biophysical principles, applications, and recent developments in impedance-based methodologies. Despite extensive application of impedance analysis in endothelial barrier research, little attention has been paid to data analysis and critical experimental variables, which are both essential for signal stability and reproducibility. We describe the rationale behind common ECIS data presentation and interpretation and illustrate practical guidelines to improve signal intensity by adapting technical parameters such as electrode layout, monitoring frequency, or parameter (resistance versus impedance magnitude). Moreover, we discuss the impact of experimental parameters, including cell source, liquid handling, and agonist preparation on signal intensity and kinetics. Our discussions are supported by experimental data obtained from human microvascular endothelial cells challenged with three GPCR agonists, thrombin, histamine, and sphingosine-1-phosphate.

The Effect of Presentation Strategy on Reading Comprehension of Iranian Intermediate EFL Learners

ERIC Educational Resources Information Center

Khoshsima, Hooshang; Rezaeiantiyar, Forouzan

2014-01-01

The present experimental study primarily aimed at examining the effect of presentation strategy on reading comprehension of Iranian intermediate EFL learners. To determine the effect of this strategy, 61 students who enrolled in English Language Center of Chabahar Maritime University were initially selected and then divided randomly into two…

Designating Reader Perspective to Increase Comprehension and Interest

ERIC Educational Resources Information Center

Ramsay, Crystal M.; Sperling, Rayne A.

2010-01-01

In three experiments we examined whether reader perspective on a long expository text could be manipulated such that increased text interest and enhancement of two comprehension outcomes would result. In Experiment 1 we verified the viability of a new text for experimental purposes. We then assigned readers a perspective before reading in…

The Effects of Pre-Reading Activities on Reading Comprehension of Iranian EFL Learners

ERIC Educational Resources Information Center

Moghaddam, Nahid Nemati; Mahmoudi, Asgar

2016-01-01

This study investigated the effects of three types of pre-reading activities (movie-watching, vocabulary presentation, and pre-reading summarization) on the reading comprehension of 76 elementary-level EFL Iranian learners. The participants were randomly assigned to one control and three experimental conditions and then a pretest was given to…

Reading Comprehension to 1970: Its Theoretical and Empirical Bases, and Its Implementation in Secondary Professional Textbooks, Instructional Materials, and Tests.

ERIC Educational Resources Information Center

Harker, William John

This study was designed: (1) to determine current concepts of reading comprehension deriving from experimental investigations and theoretical statements, and (2) to establish whether these concepts are represented consistently in current secondary professional reading textbooks, instructional materials, and published tests. Current knowledge of…

The Effect of Illustrations on Second Graders' Reading Comprehension.

ERIC Educational Resources Information Center

Parisi, Gina

A study investigated whether text illustrations improve the reading comprehension of second graders. Subjects, 14 second-grade students, read five stories from a basal reader. The control group read each story with accompanying illustrations, while the experimental group was exposed to only the written version of the same stories. Questions based…

The Cooperative Learning Effects on English Reading Comprehension and Learning Motivation of EFL Freshmen

ERIC Educational Resources Information Center

Pan, Ching-Ying; Wu, Hui-Yi

2013-01-01

This experimental study aims to investigate the effects of using cooperative learning to enhance the English reading comprehension and learning motivation of EFL freshmen by comparing the cooperative learning instruction and traditional lecture instruction. This experiment was implemented in a Freshman English Reading course, a two credit course,…

Models Matter--The Final Report of the National Longitudinal Evaluation of Comprehensive School Reform

ERIC Educational Resources Information Center

Aladjem, Daniel K.; LeFloch, Kerstin Carlson; Zhang, Yu; Kurki, Anja; Boyle, Andrea; Taylor, James E.; Herrmann, Suzannah; Uekawa, Kazuaki; Thomsen, Kerri; Fashola, Olatokunbo

2006-01-01

The National Longitudinal Evaluation of Comprehensive School Reform (NLECSR) is a quantitative and qualitative study of behavior, decisions, processes, and outcomes. It employs a quasi-experimental design with matched treatment and comparison schools. NLECSR seeks to determine the effects of CSR models on student achievement in about 650…

Media Presentations on the Reading Attention and Comprehension of Taiwanese Elementary School Students

ERIC Educational Resources Information Center

Ku, David Tawei; Cheng, Yu-Mei

2016-01-01

We adopted an experimental design to investigate the effects of various media presentation modes on the reading attention and comprehension of Taiwanese elementary school students. The participants comprised 138 students from 4 classes of third grade elementary school students from New Taipei City, Taiwan. The participants attended 5 short stories…

Impacts of Comprehensive Reading Instruction on Diverse Outcomes of Low- and High-Achieving Readers

ERIC Educational Resources Information Center

Guthrie, John T.; McRae, Angela; Coddington, Cassandra S.; Klauda, Susan Lutz; Wigfield, Allan; Barbosa, Pedro

2009-01-01

Low-achieving readers in Grade 5 often lack comprehension strategies, domain knowledge, word recognition skills, fluency, and motivation to read. Students with such multiple reading needs seem likely to benefit from instruction that supports each of these reading processes. The authors tested this expectation experimentally by comparing the…

Oral Interpretation as a Pedagogical Tool in Teaching Literary Comprehension and Appreciation.

ERIC Educational Resources Information Center

Ford-Brown, Lisa A.

A study investigated whether there was a significant difference in the comprehension and appreciation of literature studied through oral interpretation when compared to silent reading. Two hundred and sixty-three third, fourth, and fifth graders from Terre Haute, Indiana were separated into experimental and control groups, and were given pre- and…

Comprehensible Input and Second Language Acquisition: What Is the Relationship?

ERIC Educational Resources Information Center

Loschky, Lester

1994-01-01

Examined the influence of input and interactional modifications on second-language acquisition, assigning 41 learners of Japanese to 1 of 3 experimental groups: (1) unmodified input with no interaction; (2) premodified input with no interaction; and (3) unmodified input with the chance for negotiated input. Results indicated that comprehension was…

Effect of Focused Vocabulary Instruction on 7th Graders' Reading Comprehension

ERIC Educational Resources Information Center

Horn, Mary; Feng, Jianhua

2012-01-01

This study reports an investigation on the effects of directed vocabulary and whole class instruction on improving students' vocabulary acquisition and reading comprehension. Fifty-eight seventh grade students participated in the study, and a pre-test/post-test experimental design was employed. The results did not indicate any statistically…

Does Multimedia Support Individual Differences?--EFL Learners' Listening Comprehension and Cognitive Load

ERIC Educational Resources Information Center

Yang, Hui-Yu

2014-01-01

The present study examines how display model, English proficiency and cognitive preference affect English as a Foreign Language (EFL) learners' listening comprehension of authentic videos and cognitive load degree. EFL learners were randomly assigned to one of two groups. The control group received single coding and the experimental group received…

The Impact of Mobile Learning on Listening Anxiety and Listening Comprehension

ERIC Educational Resources Information Center

Rahimi, Mehrak; Soleymani, Elham

2015-01-01

This study aimed at investigating the impact of mobile learning on EFL learners' listening anxiety and listening comprehension. Fifty students of two intermediate English courses were selected and sampled as the experimental (n = 25) and control (n = 25) groups. Students' entry level of listening anxiety was assessed by foreign language listening…

A Proof of Concept Study of Function-Based Statistical Analysis of fNIRS Data: Syntax Comprehension in Children with Specific Language Impairment Compared to Typically-Developing Controls.

PubMed

Fu, Guifang; Wan, Nicholas J A; Baker, Joseph M; Montgomery, James W; Evans, Julia L; Gillam, Ronald B

2016-01-01

Functional near infrared spectroscopy (fNIRS) is a neuroimaging technology that enables investigators to indirectly monitor brain activity in vivo through relative changes in the concentration of oxygenated and deoxygenated hemoglobin. One of the key features of fNIRS is its superior temporal resolution, with dense measurements over very short periods of time (100 ms increments). Unfortunately, most statistical analysis approaches in the existing literature have not fully utilized the high temporal resolution of fNIRS. For example, many analysis procedures are based on linearity assumptions that only extract partial information, thereby neglecting the overall dynamic trends in fNIRS trajectories. The main goal of this article is to assess the ability of a functional data analysis (FDA) approach for detecting significant differences in hemodynamic responses recorded by fNIRS. Children with and without SLI wore two, 3 × 5 fNIRS caps situated over the bilateral parasylvian areas as they completed a language comprehension task. FDA was used to decompose the high dimensional hemodynamic curves into the mean function and a few eigenfunctions to represent the overall trend and variation structures over time. Compared to the most popular GLM, we did not assume any parametric structure and let the data speak for itself. This analysis identified significant differences between the case and control groups in the oxygenated hemodynamic mean trends in the bilateral inferior frontal and left inferior posterior parietal brain regions. We also detected significant group differences in the deoxygenated hemodynamic mean trends in the right inferior posterior parietal cortex and left temporal parietal junction. These findings, using dramatically different approaches, experimental designs, data sets, and foci, were consistent with several other reports, confirming group differences in the importance of these two areas for syntax comprehension. The proposed FDA was consistent with the temporal characteristics of fNIRS, thus providing an alternative methodology for fNIRS analyses.

Manipulating Google’s Knowledge Graph Box to Counter Biased Information Processing During an Online Search on Vaccination: Application of a Technological Debiasing Strategy

PubMed Central

Allam, Ahmed; Schulz, Peter J

2016-01-01

Background One of people’s major motives for going online is the search for health-related information. Most consumers start their search with a general search engine but are unaware of the fact that its sorting and ranking criteria do not mirror information quality. This misconception can lead to distorted search outcomes, especially when the information processing is characterized by heuristic principles and resulting cognitive biases instead of a systematic elaboration. As vaccination opponents are vocal on the Web, the chance of encountering their non‒evidence-based views on immunization is high. Therefore, biased information processing in this context can cause subsequent impaired judgment and decision making. A technological debiasing strategy could counter this by changing people’s search environment. Objective This study aims at testing a technological debiasing strategy to reduce the negative effects of biased information processing when using a general search engine on people’s vaccination-related knowledge and attitudes. This strategy is to manipulate the content of Google’s knowledge graph box, which is integrated in the search interface and provides basic information about the search topic. Methods A full 3x2 factorial, posttest-only design was employed with availability of basic factual information (comprehensible vs hardly comprehensible vs not present) as the first factor and a warning message as the second factor of experimental manipulation. Outcome variables were the evaluation of the knowledge graph box, vaccination-related knowledge, as well as beliefs and attitudes toward vaccination, as represented by three latent variables emerged from an exploratory factor analysis. Results Two-way analysis of variance revealed a significant main effect of availability of basic information in the knowledge graph box on participants’ vaccination knowledge scores (F2,273=4.86, P=.01), skepticism/fear of vaccination side effects (F2,273=3.5, P=.03), and perceived information quality (F2,273=3.73, P=.02). More specifically, respondents receiving comprehensible information appeared to be more knowledgeable, less skeptical of vaccination, and more critical of information quality compared to participants exposed to hardly comprehensible information. Although, there was no significant interaction effect between the availability of information and the presence of the warning, there was a dominant pattern in which the presence of the warning appeared to have a positive influence on the group receiving comprehensible information while the opposite was true for the groups exposed to hardly comprehensible information and no information at all. Participants evaluated the knowledge graph box as moderately to highly useful, with no significant differences among the experimental groups. Conclusion Overall, the results suggest that comprehensible information in the knowledge graph box positively affects participants’ vaccination-related knowledge and attitudes. A small change in the content retrieval procedure currently used by Google could already make a valuable difference in the pursuit of an unbiased online information search. Further research is needed to gain insights into the knowledge graph box’s entire potential. PMID:27255736

Time series modeling of human operator dynamics in manual control tasks

NASA Technical Reports Server (NTRS)

Biezad, D. J.; Schmidt, D. K.

1984-01-01

A time-series technique is presented for identifying the dynamic characteristics of the human operator in manual control tasks from relatively short records of experimental data. Control of system excitation signals used in the identification is not required. The approach is a multi-channel identification technique for modeling multi-input/multi-output situations. The method presented includes statistical tests for validity, is designed for digital computation, and yields estimates for the frequency responses of the human operator. A comprehensive relative power analysis may also be performed for validated models. This method is applied to several sets of experimental data; the results are discussed and shown to compare favorably with previous research findings. New results are also presented for a multi-input task that has not been previously modeled to demonstrate the strengths of the method.

Time Series Modeling of Human Operator Dynamics in Manual Control Tasks

NASA Technical Reports Server (NTRS)

Biezad, D. J.; Schmidt, D. K.

1984-01-01

A time-series technique is presented for identifying the dynamic characteristics of the human operator in manual control tasks from relatively short records of experimental data. Control of system excitation signals used in the identification is not required. The approach is a multi-channel identification technique for modeling multi-input/multi-output situations. The method presented includes statistical tests for validity, is designed for digital computation, and yields estimates for the frequency response of the human operator. A comprehensive relative power analysis may also be performed for validated models. This method is applied to several sets of experimental data; the results are discussed and shown to compare favorably with previous research findings. New results are also presented for a multi-input task that was previously modeled to demonstrate the strengths of the method.

Middle Term Achievements of Project 5322: Retrieval Of Key Eco-Hydrological Parameters From Remote Sensing In The Watershed Allied Telemetry Experimental Research (Water)

NASA Astrophysics Data System (ADS)

Li, Xin; Menenti, Massimo

2010-10-01

The general objective of project 5322 in the Dragon 2 programme is to quantitatively retrieve some key eco- hydrological parameters by using remote sensed data, especially from ESA, Chinese, and the Third Party Mission (TPM). To achieve this goal, a comprehensive observation experiment, Watershed Allied Telemetry Experimental Research (WATER) was carried out. WARER is a simultaneously airborne, satellite-borne, and ground-based remote sensing experiment took place in the Heihe River Basin, a typical inland river basin in the northwest of China. This paper introduces the background and implementation of WATER. Data have been obtained so far are described in details. After a period of data analysis for two years, numerous results have also been achieved. This paper presents some early results of WATER as well.

Analysis of underivatised low volatility compounds by comprehensive two-dimensional gas chromatography with a short primary column.

PubMed

Novaes, Fábio Junior Moreira; Kulsing, Chadin; Bizzo, Humberto Ribeiro; de Aquino Neto, Francisco Radler; Rezende, Claudia Moraes; Marriott, Philip John

2018-02-09

Comprehensive two-dimensional gas chromatography (GC×GC) approaches with cryogenic modulation were developed for the qualitative analysis of selected low volatility compounds in raw coffee bean extracts, without derivatisation. The approaches employed short first ( 1 D) and second ( 2 D) dimension columns, specifically a 1 D 65% phenyl methyl siloxane column (11m) and a 2 D 5% phenyl methyl siloxane column (1m), which allowed elution of high molar mass compounds (e.g.>600Da). Solutes included hydrocarbons, fatty acids, diterpenes, tocopherols, sterols, diterpene esters, and di- and triacylglycerides. An oven temperature program up to 370°C was employed. The effects of experimental conditions were investigated, revealing that the GC×GC results strongly depended on the cryogenic trap T, and oven T program. An appropriate condition was selected and further applied for group type analysis of low volatility compounds in green Arabica coffee beans. Retention indices were compiled for 1D GC analysis and were similar for the composite column data in GC×GC. The elution of some compounds was confirmed by use of authentic standards. The approach allowed direct analysis of coffee extract in ethyl acetate solution, with improved analyte peak capacity (approximately 200 compounds were detected) without prior fractionation or pre-treatment of the sample. This avoided potential hydrolysis of high molar mass conjugate esters as well as degradation of thermally labile compounds such as the derivatives of the diterpenes cafestol and kahweol. Copyright © 2017 Elsevier B.V. All rights reserved.

Preliminary design of mesoscale turbocompressor and rotordynamics tests of rotor bearing system

NASA Astrophysics Data System (ADS)

Hossain, Md Saddam

2011-12-01

A mesoscale turbocompressor spinning above 500,000 RPM is evolutionary technology for micro turbochargers, turbo blowers, turbo compressors, micro-gas turbines, auxiliary power units, etc for automotive, aerospace, and fuel cell industries. Objectives of this work are: (1) to evaluate different air foil bearings designed for the intended applications, and (2) to design & perform CFD analysis of a micro-compressor. CFD analysis of shrouded 3-D micro compressor was conducted using Ansys Bladegen as blade generation tool, ICEM CFD as mesh generation tool, and CFX as main solver for different design and off design cases and also for different number of blades. Comprehensive experimental facilities for testing the turbocompressor system have been also designed and proposed for future work.

Experimental analysis of bruises in human volunteers using radiometric depth profiling and diffuse reflectance spectroscopy

NASA Astrophysics Data System (ADS)

Vidovič, Luka; Milanič, Matija; Majaron, Boris

2015-07-01

We combine pulsed photothermal radiometry (PPTR) depth profiling with diffuse reflectance spectroscopy (DRS) measurements for a comprehensive analysis of bruise evolution in vivo. While PPTR enables extraction of detailed depth distribution and concentration profiles of selected absorbers (e.g. melanin, hemoglobin), DRS provides information in a wide range of visible wavelengths and thus offers an additional insight into dynamics of the hemoglobin degradation products. Combining the two approaches enables us to quantitatively characterize bruise evolution dynamics. Our results indicate temporal variations of the bruise evolution parameters in the course of bruise self-healing process. The obtained parameter values and trends represent a basis for a future development of an objective technique for bruise age determination.

ΔΔPT: a comprehensive toolbox for the analysis of protein motion

PubMed Central

2013-01-01

Background Normal Mode Analysis is one of the most successful techniques for studying motions in proteins and macromolecules. It can provide information on the mechanism of protein functions, used to aid crystallography and NMR data reconstruction, and calculate protein free energies. Results ΔΔPT is a toolbox allowing calculation of elastic network models and principle component analysis. It allows the analysis of pdb files or trajectories taken from; Gromacs, Amber, and DL_POLY. As well as calculation of the normal modes it also allows comparison of the modes with experimental protein motion, variation of modes with mutation or ligand binding, and calculation of molecular dynamic entropies. Conclusions This toolbox makes the respective tools available to a wide community of potential NMA users, and allows them unrivalled ability to analyse normal modes using a variety of techniques and current software. PMID:23758746

Comprehensive machine learning analysis of Hydra behavior reveals a stable basal behavioral repertoire

PubMed Central

Taralova, Ekaterina; Dupre, Christophe; Yuste, Rafael

2018-01-01

Animal behavior has been studied for centuries, but few efficient methods are available to automatically identify and classify it. Quantitative behavioral studies have been hindered by the subjective and imprecise nature of human observation, and the slow speed of annotating behavioral data. Here, we developed an automatic behavior analysis pipeline for the cnidarian Hydra vulgaris using machine learning. We imaged freely behaving Hydra, extracted motion and shape features from the videos, and constructed a dictionary of visual features to classify pre-defined behaviors. We also identified unannotated behaviors with unsupervised methods. Using this analysis pipeline, we quantified 6 basic behaviors and found surprisingly similar behavior statistics across animals within the same species, regardless of experimental conditions. Our analysis indicates that the fundamental behavioral repertoire of Hydra is stable. This robustness could reflect a homeostatic neural control of "housekeeping" behaviors which could have been already present in the earliest nervous systems. PMID:29589829

Vibration Signature Analysis of a Faulted Gear Transmission System

NASA Technical Reports Server (NTRS)

Choy, F. K.; Huang, S.; Zakrajsek, J. J.; Handschuh, R. F.; Townsend, D. P.

1994-01-01

A comprehensive procedure in predicting faults in gear transmission systems under normal operating conditions is presented. Experimental data was obtained from a spiral bevel gear fatigue test rig at NASA Lewis Research Center. Time synchronous averaged vibration data was recorded throughout the test as the fault progressed from a small single pit to severe pitting over several teeth, and finally tooth fracture. A numerical procedure based on the Winger-Ville distribution was used to examine the time averaged vibration data. Results from the Wigner-Ville procedure are compared to results from a variety of signal analysis techniques which include time domain analysis methods and frequency analysis methods. Using photographs of the gear tooth at various stages of damage, the limitations and accuracy of the various techniques are compared and discussed. Conclusions are drawn from the comparison of the different approaches as well as the applicability of the Wigner-Ville method in predicting gear faults.

A comprehensive combined experimental and computational framework for pre-clinical wear simulation of total knee replacements.

PubMed

Abdelgaied, A; Fisher, J; Jennings, L M

2018-02-01

A more robust pre-clinical wear simulation framework is required in order to simulate wider and higher ranges of activities, observed in different patient populations such as younger more active patients. Such a framework will help to understand and address the reported higher failure rates for younger and more active patients (National_Joint_Registry, 2016). The current study has developed and validated a comprehensive combined experimental and computational framework for pre-clinical wear simulation of total knee replacements (TKR). The input mechanical (elastic modulus and Poisson's ratio) and wear parameters of the moderately cross-linked ultra-high molecular weight polyethylene (UHMWPE) bearing material were independently measured from experimental studies under realistic test conditions, similar to the loading conditions found in the total knee replacements. The wear predictions from the computational wear simulation were validated against the direct experimental wear measurements for size 3 Sigma curved total knee replacements (DePuy, UK) in an independent experimental wear simulation study under three different daily activities; walking, deep squat, and stairs ascending kinematic conditions. The measured compressive mechanical properties of the moderately cross-linked UHMWPE material were more than 20% lower than that reported in the literature under tensile test conditions. The pin-on-plate wear coefficient of moderately cross-linked UHMWPE was significantly dependant of the contact stress and the degree of cross-shear at the articulating surfaces. The computational wear predictions for the TKR from the current framework were consistent and in a good agreement with the independent full TKR experimental wear simulation measurements, with 0.94 coefficient of determination of the framework. In addition, the comprehensive combined experimental and computational framework was able to explain the complex experimental wear trends from the three different daily activities investigated. Therefore, such a framework can be adopted as a pre-clinical simulation approach to optimise different designs, materials, as well as patient's specific total knee replacements for a range of activities. Copyright © 2017. Published by Elsevier Ltd.

Integrated web visualizations for protein-protein interaction databases.

PubMed

Jeanquartier, Fleur; Jean-Quartier, Claire; Holzinger, Andreas

2015-06-16

Understanding living systems is crucial for curing diseases. To achieve this task we have to understand biological networks based on protein-protein interactions. Bioinformatics has come up with a great amount of databases and tools that support analysts in exploring protein-protein interactions on an integrated level for knowledge discovery. They provide predictions and correlations, indicate possibilities for future experimental research and fill the gaps to complete the picture of biochemical processes. There are numerous and huge databases of protein-protein interactions used to gain insights into answering some of the many questions of systems biology. Many computational resources integrate interaction data with additional information on molecular background. However, the vast number of diverse Bioinformatics resources poses an obstacle to the goal of understanding. We present a survey of databases that enable the visual analysis of protein networks. We selected M=10 out of N=53 resources supporting visualization, and we tested against the following set of criteria: interoperability, data integration, quantity of possible interactions, data visualization quality and data coverage. The study reveals differences in usability, visualization features and quality as well as the quantity of interactions. StringDB is the recommended first choice. CPDB presents a comprehensive dataset and IntAct lets the user change the network layout. A comprehensive comparison table is available via web. The supplementary table can be accessed on http://tinyurl.com/PPI-DB-Comparison-2015. Only some web resources featuring graph visualization can be successfully applied to interactive visual analysis of protein-protein interaction. Study results underline the necessity for further enhancements of visualization integration in biochemical analysis tools. Identified challenges are data comprehensiveness, confidence, interactive feature and visualization maturing.

A comprehensive equivalent circuit model of all-vanadium redox flow battery for power system analysis

NASA Astrophysics Data System (ADS)

Zhang, Yu; Zhao, Jiyun; Wang, Peng; Skyllas-Kazacos, Maria; Xiong, Binyu; Badrinarayanan, Rajagopalan

2015-09-01

Electrical equivalent circuit models demonstrate excellent adaptability and simplicity in predicting the electrical dynamic response of the all-vanadium redox flow battery (VRB) system. However, only a few publications that focus on this topic are available. The paper presents a comprehensive equivalent circuit model of VRB for system level analysis. The least square method is used to identify both steady-state and dynamic characteristics of VRB. The inherent features of the flow battery such as shunt current, ion diffusion and pumping energy consumption are also considered. The proposed model consists of an open-circuit voltage source, two parasitic shunt bypass circuits, a 1st order resistor-capacitor network and a hydraulic circuit model. Validated with experimental data, the proposed model demonstrates excellent accuracy. The mean-error of terminal voltage and pump consumption are 0.09 V and 0.49 W respectively. Based on the proposed model, self-discharge and system efficiency are studied. An optimal flow rate which maximizes the system efficiency is identified. Finally, the dynamic responses of the proposed VRB model under step current profiles are presented. Variables such as SOC and stack terminal voltage can be provided.

Comprehensive School Reform: Meta-Analytic Evidence of Black-White Achievement Gap Narrowing1

PubMed Central

Gorey, Kevin M.

2016-01-01

This meta-analysis extends a previous review of the achievement effects of comprehensive school reform (CSR) programs (Borman, Hewes, Overman, & Brown, 2003). That meta-analysis observed significant effects of well endowed and well-researched programs, but it did not account for race/ethnicity. This article synthesizes 34 cohort or quasi-experimental outcomes of studies that incorporated the policy-critical characteristic of race/ethnicity. Findings: compared with matched traditional schools, the black-white achievement gap narrowed significantly more among students in CSR schools. In addition, the aggregate effects were large, substantially to completely eliminating the achievement gap between African American and non-Hispanic white students in elementary and middle schools. Title I policies before or after the No Child Left Behind Act of 2001 seem to have had essentially no impact on the black-white achievement gap. Curricular and testing mandates along with the threat of sanctions without concomitant resource supports seem to have failed. This study suggests that educational achievement inequities need not be America’s destiny. It seems that they could be eliminated through concerted political will and ample resource commitments to evidence-based educational programs. PMID:27453681

Envelope analysis of rotating machine vibrations in variable speed conditions: A comprehensive treatment

NASA Astrophysics Data System (ADS)

Abboud, D.; Antoni, J.; Sieg-Zieba, S.; Eltabach, M.

2017-02-01

Nowadays, the vibration analysis of rotating machine signals is a well-established methodology, rooted on powerful tools offered, in particular, by the theory of cyclostationary (CS) processes. Among them, the squared envelope spectrum (SES) is probably the most popular to detect random CS components which are typical symptoms, for instance, of rolling element bearing faults. Recent researches are shifted towards the extension of existing CS tools - originally devised in constant speed conditions - to the case of variable speed conditions. Many of these works combine the SES with computed order tracking after some preprocessing steps. The principal object of this paper is to organize these dispersed researches into a structured comprehensive framework. Three original features are furnished. First, a model of rotating machine signals is introduced which sheds light on the various components to be expected in the SES. Second, a critical comparison is made of three sophisticated methods, namely, the improved synchronous average, the cepstrum prewhitening, and the generalized synchronous average, used for suppressing the deterministic part. Also, a general envelope enhancement methodology which combines the latter two techniques with a time-domain filtering operation is revisited. All theoretical findings are experimentally validated on simulated and real-world vibration signals.

Simultaneous analysis of nuclear and mitochondrial DNA, mRNA and miRNA from backspatter from inside parts of firearms generated by shots at "triple contrast" doped ballistic models.

PubMed

Grabmüller, Melanie; Schyma, Christian; Euteneuer, Jan; Madea, Burkhard; Courts, Cornelius

2015-09-01

When a firearm projectile hits a biological target a spray of biological material (e.g., blood and tissue fragments) can be propelled from the entrance wound back towards the firearm. This phenomenon has become known as "backspatter" and if caused by contact shots or shots from short distances traces of backspatter may reach, consolidate on, and be recovered from, the inside surfaces of the firearm. Thus, a comprehensive investigation of firearm-related crimes must not only comprise of wound ballistic assessment but also backspatter analysis, and may even take into account potential correlations between these emergences. The aim of the present study was to evaluate and expand the applicability of the "triple contrast" method by probing its compatibility with forensic analysis of nuclear and mitochondrial DNA and the simultaneous investigation of co-extracted mRNA and miRNA from backspatter collected from internal components of different types of firearms after experimental shootings. We demonstrate that "triple contrast" stained biological samples collected from the inside surfaces of firearms are amenable to forensic co-analysis of DNA and RNA and permit sequence analysis of the entire mtDNA displacement-loop, even for "low template" DNA amounts that preclude standard short tandem repeat DNA analysis. Our findings underscore the "triple contrast" method's usefulness as a research tool in experimental forensic ballistics.

Requirements for Next Generation Comprehensive Analysis of Rotorcraft

NASA Technical Reports Server (NTRS)

Johnson, Wayne; Data, Anubhav

2008-01-01

The unique demands of rotorcraft aeromechanics analysis have led to the development of software tools that are described as comprehensive analyses. The next generation of rotorcraft comprehensive analyses will be driven and enabled by the tremendous capabilities of high performance computing, particularly modular and scaleable software executed on multiple cores. Development of a comprehensive analysis based on high performance computing both demands and permits a new analysis architecture. This paper describes a vision of the requirements for this next generation of comprehensive analyses of rotorcraft. The requirements are described and substantiated for what must be included and justification provided for what should be excluded. With this guide, a path to the next generation code can be found.

CREDO: a structural interactomics database for drug discovery

PubMed Central

Schreyer, Adrian M.; Blundell, Tom L.

2013-01-01

CREDO is a unique relational database storing all pairwise atomic interactions of inter- as well as intra-molecular contacts between small molecules and macromolecules found in experimentally determined structures from the Protein Data Bank. These interactions are integrated with further chemical and biological data. The database implements useful data structures and algorithms such as cheminformatics routines to create a comprehensive analysis platform for drug discovery. The database can be accessed through a web-based interface, downloads of data sets and web services at http://www-cryst.bioc.cam.ac.uk/credo. Database URL: http://www-cryst.bioc.cam.ac.uk/credo PMID:23868908

Social network supported process recommender system.

PubMed

Ye, Yanming; Yin, Jianwei; Xu, Yueshen

2014-01-01

Process recommendation technologies have gained more and more attention in the field of intelligent business process modeling to assist the process modeling. However, most of the existing technologies only use the process structure analysis and do not take the social features of processes into account, while the process modeling is complex and comprehensive in most situations. This paper studies the feasibility of social network research technologies on process recommendation and builds a social network system of processes based on the features similarities. Then, three process matching degree measurements are presented and the system implementation is discussed subsequently. Finally, experimental evaluations and future works are introduced.

Numerical Modeling of Electrode Degradation During Resistance Spot Welding Using CuCrZr Electrodes

NASA Astrophysics Data System (ADS)

Gauthier, Elise; Carron, Denis; Rogeon, Philippe; Pilvin, Philippe; Pouvreau, Cédric; Lety, Thomas; Primaux, François

2014-05-01

Resistance spot welding is a technique widely used by the automotive industry to assemble thin steel sheets. The cyclic thermo-mechanical loading associated with the accumulation of weld spots progressively deteriorates the electrodes. This study addresses the development of a comprehensive multi-physical model that describes the sequential deterioration. Welding tests achieved on uncoated and Zn-coated steel sheets are analyzed. Finite element analysis is performed using an electrical-thermal-metallurgical model. A numerical experimental design is carried out to highlight the main process parameters and boundary conditions which affect electrode degradation.

Calculation of Prestressed Pressure Vessel Taking into Account the Concrete Temperature Inhomogeneity

NASA Astrophysics Data System (ADS)

Andreev, Vladimir

2018-03-01

The paper deals with the problem of determining the stress state of the pressure vessel (PV) with considering the concrete temperature inhomogeneity. Such structures are widely used in heat power engineering, for example, in nuclear power engineering. The structures of such buildings are quite complex and a comprehensive analysis of the stress state in them can be carried out either by numerical or experimental methods. However, a number of fundamental questions can be solved on the basis of simplified models, in particular, studies of the effect on the stressed state of the inhomogeneity caused by the temperature field.

Estimation of Solvation Quantities from Experimental Thermodynamic Data: Development of the Comprehensive CompSol Databank for Pure and Mixed Solutes

NASA Astrophysics Data System (ADS)

Moine, Edouard; Privat, Romain; Sirjean, Baptiste; Jaubert, Jean-Noël

2017-09-01

The Gibbs energy of solvation measures the affinity of a solute for its solvent and is thus a key property for the selection of an appropriate solvent for a chemical synthesis or a separation process. More fundamentally, Gibbs energies of solvation are choice data for developing and benchmarking molecular models predicting solvation effects. The Comprehensive Solvation—CompSol—database was developed with the ambition to propose very large sets of new experimental solvation chemical-potential, solvation entropy, and solvation enthalpy data of pure and mixed components, covering extended temperature ranges. For mixed compounds, the solvation quantities were generated in infinite-dilution conditions by combining experimental values of pure-component and binary-mixture thermodynamic properties. Three types of binary-mixture properties were considered: partition coefficients, activity coefficients at infinite dilution, and Henry's-law constants. A rigorous methodology was implemented with the aim to select data at appropriate conditions of temperature, pressure, and concentration for the estimation of solvation data. Finally, our comprehensive CompSol database contains 21 671 data associated with 1969 pure species and 70 062 data associated with 14 102 binary mixtures (including 760 solvation data related to the ionic-liquid class of solvents). On the basis of the very large amount of experimental data contained in the CompSol database, it is finally discussed how solvation energies are influenced by hydrogen-bonding association effects.

Analysis of high field effects on the steady-state current-voltage response of semi-insulating 4H-SiC for photoconductive switch applications

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

Tiskumara, R.; Joshi, R. P., E-mail: ravi.joshi@ttu.edu; Mauch, D.

A model-based analysis of the steady-state, current-voltage response of semi-insulating 4H-SiC is carried out to probe the internal mechanisms, focusing on electric field driven effects. Relevant physical processes, such as multiple defects, repulsive potential barriers to electron trapping, band-to-trap impact ionization, and field-dependent detrapping, are comprehensively included. Results of our model match the available experimental data fairly well over orders of magnitude variation in the current density. A number of important parameters are also extracted in the process through comparisons with available data. Finally, based on our analysis, the possible presence of holes in the samples can be discounted upmore » to applied fields as high as ∼275 kV/cm.« less

Numerical model of tapered fiber Bragg gratings for comprehensive analysis and optimization of their sensing and strain-induced tunable dispersion properties.

PubMed

Osuch, Tomasz; Markowski, Konrad; Jędrzejewski, Kazimierz

2015-06-10

A versatile numerical model for spectral transmission/reflection, group delay characteristic analysis, and design of tapered fiber Bragg gratings (TFBGs) is presented. This approach ensures flexibility with defining both distribution of refractive index change of the gratings (including apodization) and shape of the taper profile. Additionally, sensing and tunable dispersion properties of the TFBGs were fully examined, considering strain-induced effects. The presented numerical approach, together with Pareto optimization, were also used to design the best tanh apodization profiles of the TFBG in terms of maximizing its spectral width with simultaneous minimization of the group delay oscillations. Experimental verification of the model confirms its correctness. The combination of model versatility and possibility to define the other objective functions of Pareto optimization creates a universal tool for TFBG analysis and design.

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.

Principal Components Analysis on the spectral Bidirectional Reflectance Distribution Function of ceramic colour standards.

PubMed

Ferrero, A; Campos, J; Rabal, A M; Pons, A; Hernanz, M L; Corróns, A

2011-09-26

The Bidirectional Reflectance Distribution Function (BRDF) is essential to characterize an object's reflectance properties. This function depends both on the various illumination-observation geometries as well as on the wavelength. As a result, the comprehensive interpretation of the data becomes rather complex. In this work we assess the use of the multivariable analysis technique of Principal Components Analysis (PCA) applied to the experimental BRDF data of a ceramic colour standard. It will be shown that the result may be linked to the various reflection processes occurring on the surface, assuming that the incoming spectral distribution is affected by each one of these processes in a specific manner. Moreover, this procedure facilitates the task of interpolating a series of BRDF measurements obtained for a particular sample. © 2011 Optical Society of America

The Comprehension Problems of Children with Poor Reading Comprehension despite Adequate Decoding: A Meta-Analysis.

PubMed

Spencer, Mercedes; Wagner, Richard K

2018-06-01

The purpose of this meta-analysis was to examine the comprehension problems of children who have a specific reading comprehension deficit (SCD), which is characterized by poor reading comprehension despite adequate decoding. The meta-analysis included 86 studies of children with SCD who were assessed in reading comprehension and oral language (vocabulary, listening comprehension, storytelling ability, and semantic and syntactic knowledge). Results indicated that children with SCD had deficits in oral language ( d = -0.78, 95% CI [-0.89, -0.68], but these deficits were not as severe as their deficit in reading comprehension ( d = -2.78, 95% CI [-3.01, -2.54]). When compared to reading comprehension age-matched normal readers, the oral language skills of the two groups were comparable ( d = 0.32, 95% CI [-0.49, 1.14]), which suggests that the oral language weaknesses of children with SCD represent a developmental delay rather than developmental deviance. Theoretical and practical implications of these findings are discussed.

Influence of Text Type, Topic Familiarity, and Stuttering Frequency on Listener Recall, Comprehension, and Mental Effort

ERIC Educational Resources Information Center

Panico, James; Healey, E. Charles

2009-01-01

Purpose: To determine how text type, topic familiarity, and stuttering frequency influence listener recall, comprehension, and perceived mental effort. Method: Sixty adults listened to familiar and unfamiliar narrative and expository texts produced with 0%, 5%, 10%, and 15% stuttering. Participants listened to 4 experimental text samples at only 1…

The Effect of Talking Story Books on Saudi Young EFL Learners' Reading Comprehension

ERIC Educational Resources Information Center

Alsamadani, Hashem Ahmed

2017-01-01

The current research study investigated the effects of talking story books on Saudi young EFL learners' reading comprehension skills. A sample of Saudi-young-EFL learners were randomly selected and divided into two groups: an experimental group (40 students) and a control group (39 students). Students of both groups took a pre reading…

Effects of Cloze Instructional Approach on Senior Secondary School Students' Achievement in Igbo Language Reading Comprehension

ERIC Educational Resources Information Center

Eze, Nneka Justina

2015-01-01

This study assessed the effects of cloze instructional approach on senior secondary school students' achievement in Igbo language reading comprehension. The study utilized a quasi experimental research design of the pretest posttest non-equivalent control group design. The study was conducted in Abakaliki education zone of Ebonyi State of Nigeria.…

Graphic Comprehension and Interpretation Skills of Preservice Teachers with Different Learning Approaches in a Technology-Aided Learning Environment

ERIC Educational Resources Information Center

Çelik, Harun; Pektas, Hüseyin Miraç

2017-01-01

A one-group quasi-experimental design and survey methodology were used to investigate the effect of virtual laboratory practices on preservice teachers' (N = 29) graphic comprehension and interpretation skills with different learning approaches. Pretest and posttest data were collected with the Test of Understanding Kinematic Graphs. The Learning…

Effect of Direct Instruction Programs on Teaching Reading Comprehension to Students with Learning Disabilities

ERIC Educational Resources Information Center

Parker, Jennifer Leigh Sarratt

2014-01-01

The purpose of this quasi experimental research study was to examine the effects of two direct instruction programs, SRA Reading Mastery Signature and SRA Reading Success on reading comprehension skill acquisition of middle school students who qualify as a student with a specific learning disability. Furthermore, the study was used to compare the…

The Effect of Note-Taking on University Students' Listening Comprehension of Lectures

ERIC Educational Resources Information Center

Kiliçkaya, Ferit; Çokal Karadas, Derya

2009-01-01

The study investigated the effect of note-taking on comprehension of lectures by 44 undergraduate EFL students who are in the first year of their undergraduate level in the Department of Foreign Language Education in Middle East Technical University. The participants were divided into two groups, namely experimental and control groups. The…

E-Readers and the Effects on Students' Reading Motivation, Attitude and Comprehension during Guided Reading

ERIC Educational Resources Information Center

Long, Deanna; Szabo, Susan

2016-01-01

This quasi-experimental mixed methods study examined the use of e-readers during guided reading instruction and its impact on 5th grade students' reading motivation, attitude toward reading, and reading comprehension. For 10 weeks, 19 students received guided reading instruction by means of the traditional paper/text format, while 16 students…

The Effects of Using WebQuests on Reading Comprehension Performance of Saudi EFL Students

ERIC Educational Resources Information Center

Alshumaimeri, Yousif A.; Almasri, Meshail M.

2012-01-01

This paper is a report on the effects of using WebQuest on Saudi male EFL students reading comprehension performance. WebQuests expose students to several online resources and require them to gather information about a specific topic. The experimental group received traditional teaching plus WebQuests as supplementary activities. The control group…

Improving Second Grade Student's Reading Fluency and Comprehension Using Teacher-Guided iPad® App Instruction

ERIC Educational Resources Information Center

Redcay, Jessica D.; Preston, Sean M.

2016-01-01

Purpose: This study aims to examine the differences in second grade students' reading fluency and comprehension scores when using varying levels of teacher-guided iPad® app instruction to determine effective reading practices. Design/methodology/approach: This study reports the results of the quasi-experimental pre-post study by providing…

The Effect of Gloss Type and Mode on Iranian EFL Learners' Reading Comprehension

ERIC Educational Resources Information Center

Sadeghi, Karim; Ahmadi, Negar

2012-01-01

This study investigated the effects of three kinds of gloss conditions that is traditional non-CALL marginal gloss, computer-based audio gloss, and computer-based extended audio gloss, on reading comprehension of Iranian EFL learners. To this end, three experimental and one control groups, each comprising 15 participants, took part in this study.…

The Effects of Knowledge of Criterion Task on Comprehension and Recall in Normally Achieving and Learning Disabled Children.

ERIC Educational Resources Information Center

Wong, Bernice Y. L.; And Others

1982-01-01

A study investigated the hypothesis that poor comprehension or recall of task demands, rather than a putative lack of goal directedness, is a possible source of learning-disabled children's poor performance of experimental tasks. Clear instructions substantially facilitated performance by both normally achieving and learning disabled children of…

Effect of the Paideia Seminar on the Comprehension of Poetry and Reading Anxiety

ERIC Educational Resources Information Center

Awada, Ghada M.; Ghaith, Ghazi M.

2018-01-01

This article reports the results of an experimental study on the relative effectiveness of the Paideia Seminar in improving the comprehension of poetry and decreasing reading anxiety. The participants (n = 50) were English as a foreign language (EFL) ninth grade learners enrolled in classrooms at a public school in Lebanon. The study employed a…

Comprehensive Instructional Management System (CIMS). A Cyclical Mathematics Curriculum. Workbook Part 2. Experimental. Level K.

ERIC Educational Resources Information Center

New York City Board of Education, Brooklyn, NY. Div. of Curriculum and Instruction.

This document is part 2 of the workbook for kindergarten pupils in the Comprehensive Instructional Management System, a unified mathematics curriculum for kindergarten through grade 7. Each objective is developed by a variety of strategies, with mastery of objectives diagnosed through a testing component. The activities in the student workbook are…

Improving Reading Comprehension of At-Risk High-School Students: The ART of Reading Program

ERIC Educational Resources Information Center

McCallum, R. Steve; Krohn, Katherine R.; Skinner, Christopher H.; Hilton-Prillhart, Angela; Hopkins, Michael; Waller, Steven; Polite, Fritz

2011-01-01

Participants (115 low-socioeconomic-status [SES], inner-city, high-school students) were exposed to three reading conditions: (1) a control condition in which students silently read brief selected passages; (2) an experimental condition in which students were prompted to perform a three-part (Ask, Read, and Tell [ART]) comprehension enhancement…

Effects of Cooperative Learning Method on the Development of Listening Comprehension and Listening Skills

ERIC Educational Resources Information Center

Kirbas, Abdulkadir

2017-01-01

In this study, the effect of the learning together technique, which is one of the cooperative learning methods, on the development of the listening comprehension and listening skills of the secondary school eighth grade students was investigated. Regarding the purpose of the research, experimental and control groups consisting of 75 students from,…

E-Readers and the Effects on Students' Reading Motivation, Attitude, and Comprehension

ERIC Educational Resources Information Center

Long, Deanna

2014-01-01

The purpose of this study was to determine if the use of E-readers during guided reading instruction would affect students' reading motivation, attitude toward reading, and reading comprehension. The study utilized on a quasi-experimental mixed methods research design that involved 35 fifth grade students in two fifth grade reading classes. For 10…

The Effect of Implementation of TBLT in Reading Comprehension Classes of Iranian EFL Learners

ERIC Educational Resources Information Center

Madhkhan, Mozhgan; Mousavi, Seyed Mojtaba

2017-01-01

The present study investigates the impact of Task-Based Language Teaching (TBLT) on Iranian EFL learners' reading comprehension performance. Seventy participants were assigned randomly to the experimental and control groups. Having instructed the two groups with the same texts but different task types and activities (i.e., tasks in 4 types) during…

Adaptive and Maladaptive Strategy Use in Computer-Assisted Language Learning Activities for Listening Comprehension

ERIC Educational Resources Information Center

McBride, Cara

2008-01-01

College students of English as a foreign language (EFL) in Chile participated in an online mini course designed to improve their listening comprehension. There were four experimental conditions: A) one in which participants listened to fast dialogues; B) one in which participants listened to slow dialogues; C) one in which participants were given…

Experimental Evaluation of Computer Assisted Self-Assessment of Reading Comprehension: Effects on Reading Achievement and Attitude.

ERIC Educational Resources Information Center

Vollands, Stacy R.; And Others

A study evaluated the effect software for self-assessment and management of reading practice had on reading achievement and motivation in two primary schools in Aberdeen, Scotland. The program utilized was The Accelerated Reader (AR) which was designed to enable curriculum based assessment of reading comprehension within the classroom. Students…

Investigating the Effects of an Experimental Approach to Comprehension Instruction within a Literacy Clinic

ERIC Educational Resources Information Center

Ortlieb, Evan; McDowell, F. D.

2015-01-01

Reading comprehension levels of elementary students have not significantly improved in the 21st century and as a result, the need for systematic and intensive reading interventions is as high as ever. Literacy clinics are an ideal setting for struggling readers to experience success through the implementation of a cyclical approach to individual…

Information Comprehension from Longhand Notes and Slides in the Language Classroom

ERIC Educational Resources Information Center

Kiliçkaya, Ferit

2016-01-01

The aim of the study presented in this paper was to compare undergraduate students' information comprehension under conditions where they took notes in longhand during traditional lectures and lectures given through slides. A quasi-experimental approach was adopted to collect the data from 42 participants enrolled in a compulsory course at a state…

Inference in Right Hemisphere Damaged Individuals' Comprehension: The Role of Sustained Attention

ERIC Educational Resources Information Center

Saldert, Charlotta; Ahlsen, Elisabeth

2007-01-01

The ability to make inferences for the purposes of comprehension is considered an important factor in pragmatic ability. In this experimental group study with stroke patients, the ability to make inferences and its associations with sustained attention and verbal working memory were explored. A group of 14 left-hemisphere-damaged individuals had…

Reading Comprehension Strategy Instruction and Attribution Retraining for Secondary Students with Learning and Other Mild Disabilities

ERIC Educational Resources Information Center

Berkeley, Sheri; Mastropieri, Margo A.; Scruggs, Thomas E.

2011-01-01

A pre-post experimental design with 6-week delayed posttest was implemented to investigate the effects of reading comprehension strategy (RCS) instruction with and without attribution retraining (AR) on reading outcomes for seventh, eighth, and ninth graders with learning and other mild disabilities. Students were randomly assigned to one of three…

The Effectiveness of Multimedia Application on Students Listening Comprehension

ERIC Educational Resources Information Center

Pangaribuan, Tagor; Sinaga, Andromeda; Sipayung, Kammer Tuahman

2017-01-01

Listening comprehension is a complex skill particulaly in mastered by non-native speaker settings. This research aimed at finding out the effect of multimedia application on students' listening. The research design is experimental, with a t-test. The population is the sixth semester of HKBP Nommensen University at the academic year of 2016/2017,…

Design, development, and evaluation of visual aids for communicating prescription drug instructions to nonliterate patients in rural Cameroon.

PubMed

Ngoh, L N; Shepherd, M D

1997-03-01

In this study, culturally sensitive visual aids designed to help convey drug information to nonliterate female adults who had a prescription for a solid oral dosage form of antibiotic medications were developed and evaluated. The researchers conceptualized the educational messages while a local artist produced the visual aids. Seventy-eight female ambulatory patients were evaluated for comprehension and compliance with antibiotic prescription instructions. The study was conducted in three health centers in Cameroon, West Africa and followed a pre-test, post-test, and follow-up format for three groups: two experimental, and one control. All participants were randomly assigned to either experimental or control groups, 26 patients to each group. Subjects in the experimental groups received visual aids alone or visual aids plus an Advanced Organizer. A comparison of the three groups showed that subjects in the experimental groups scored significantly higher than the control group in both the comprehension and compliance measures.

Structural bioinformatics of the human spliceosomal proteome

PubMed Central

Korneta, Iga; Magnus, Marcin; Bujnicki, Janusz M.

2012-01-01

In this work, we describe the results of a comprehensive structural bioinformatics analysis of the spliceosomal proteome. We used fold recognition analysis to complement prior data on the ordered domains of 252 human splicing proteins. Examples of newly identified domains include a PWI domain in the U5 snRNP protein 200K (hBrr2, residues 258–338), while examples of previously known domains with a newly determined fold include the DUF1115 domain of the U4/U6 di-snRNP protein 90K (hPrp3, residues 540–683). We also established a non-redundant set of experimental models of spliceosomal proteins, as well as constructed in silico models for regions without an experimental structure. The combined set of structural models is available for download. Altogether, over 90% of the ordered regions of the spliceosomal proteome can be represented structurally with a high degree of confidence. We analyzed the reduced spliceosomal proteome of the intron-poor organism Giardia lamblia, and as a result, we proposed a candidate set of ordered structural regions necessary for a functional spliceosome. The results of this work will aid experimental and structural analyses of the spliceosomal proteins and complexes, and can serve as a starting point for multiscale modeling of the structure of the entire spliceosome. PMID:22573172

Study/experimental/research design: much more than statistics.

PubMed

Knight, Kenneth L

2010-01-01

The purpose of study, experimental, or research design in scientific manuscripts has changed significantly over the years. It has evolved from an explanation of the design of the experiment (ie, data gathering or acquisition) to an explanation of the statistical analysis. This practice makes "Methods" sections hard to read and understand. To clarify the difference between study design and statistical analysis, to show the advantages of a properly written study design on article comprehension, and to encourage authors to correctly describe study designs. The role of study design is explored from the introduction of the concept by Fisher through modern-day scientists and the AMA Manual of Style. At one time, when experiments were simpler, the study design and statistical design were identical or very similar. With the complex research that is common today, which often includes manipulating variables to create new variables and the multiple (and different) analyses of a single data set, data collection is very different than statistical design. Thus, both a study design and a statistical design are necessary. Scientific manuscripts will be much easier to read and comprehend. A proper experimental design serves as a road map to the study methods, helping readers to understand more clearly how the data were obtained and, therefore, assisting them in properly analyzing the results.

Examining the Effects of Classroom Discussion on Students' Comprehension of Text: A Meta-Analysis

ERIC Educational Resources Information Center

Murphy, P. Karen; Wilkinson, Ian A. G.; Soter, Anna O.; Hennessey, Maeghan N.; Alexander, John F.

2009-01-01

The role of classroom discussions in comprehension and learning has been the focus of investigations since the early 1960s. Despite this long history, no syntheses have quantitatively reviewed the vast body of literature on classroom discussions for their effects on students' comprehension and learning. This comprehensive meta-analysis of…

The Effects of Meta-Cognitive Instruction on Students' Reading Comprehension in Computerized Reading Contexts: A Quantitative Meta-Analysis

ERIC Educational Resources Information Center

Lan, Yi-Chin; Lo, Yu-Ling; Hsu, Ying-Shao

2014-01-01

Comprehension is the essence of reading. Finding appropriate and effective reading strategies to support students' reading comprehension has always been a critical issue for educators. This article presents findings from a meta-analysis of 17 studies of metacognitive strategy instruction on students' reading comprehension in computerized…

An Electromagnetic/Capacitive Composite Sensor for Testing of Thermal Barrier Coatings

PubMed Central

Ren, Yuan; Pan, Mengchun; Chen, Dixiang; Tian, Wugang

2018-01-01

Thermal barrier coatings (TBCs) can significantly reduce the operating temperature of the aeroengine turbine blade substrate, and their testing technology is very urgently demanded. Due to their complex multi-layer structure, it is hard to evaluate TBCs with a single function sensor. In this paper, an electromagnetic/capacitive composite sensor is proposed for the testing of thermal barrier coatings. The dielectric material is tested with planar capacitor, and the metallic material is tested with electromagnetic coils. Then, the comprehensive test and evaluation of thermal barrier coating system can be realized. The sensor is optimized by means of theoretical and simulation analysis, and the interaction between the planar capacitor and the electromagnetic coil is studied. The experimental system is built based on an impedance analyser and multiplex unit to evaluate the performance of the composite sensor. The transimpedances and capacitances are measured under different coating parameters, such as thickness and permittivity of top coating as well as bond layer conductivity. The experimental results agree with the simulation analysis, and the feasibility of the sensor is proved. PMID:29783746

Comprehensive Characterization of Cancer Driver Genes and Mutations.

PubMed

Bailey, Matthew H; Tokheim, Collin; Porta-Pardo, Eduard; Sengupta, Sohini; Bertrand, Denis; Weerasinghe, Amila; Colaprico, Antonio; Wendl, Michael C; Kim, Jaegil; Reardon, Brendan; Ng, Patrick Kwok-Shing; Jeong, Kang Jin; Cao, Song; Wang, Zixing; Gao, Jianjiong; Gao, Qingsong; Wang, Fang; Liu, Eric Minwei; Mularoni, Loris; Rubio-Perez, Carlota; Nagarajan, Niranjan; Cortés-Ciriano, Isidro; Zhou, Daniel Cui; Liang, Wen-Wei; Hess, Julian M; Yellapantula, Venkata D; Tamborero, David; Gonzalez-Perez, Abel; Suphavilai, Chayaporn; Ko, Jia Yu; Khurana, Ekta; Park, Peter J; Van Allen, Eliezer M; Liang, Han; Lawrence, Michael S; Godzik, Adam; Lopez-Bigas, Nuria; Stuart, Josh; Wheeler, David; Getz, Gad; Chen, Ken; Lazar, Alexander J; Mills, Gordon B; Karchin, Rachel; Ding, Li

2018-04-05

Identifying molecular cancer drivers is critical for precision oncology. Multiple advanced algorithms to identify drivers now exist, but systematic attempts to combine and optimize them on large datasets are few. We report a PanCancer and PanSoftware analysis spanning 9,423 tumor exomes (comprising all 33 of The Cancer Genome Atlas projects) and using 26 computational tools to catalog driver genes and mutations. We identify 299 driver genes with implications regarding their anatomical sites and cancer/cell types. Sequence- and structure-based analyses identified >3,400 putative missense driver mutations supported by multiple lines of evidence. Experimental validation confirmed 60%-85% of predicted mutations as likely drivers. We found that >300 MSI tumors are associated with high PD-1/PD-L1, and 57% of tumors analyzed harbor putative clinically actionable events. Our study represents the most comprehensive discovery of cancer genes and mutations to date and will serve as a blueprint for future biological and clinical endeavors. Published by Elsevier Inc.

Comparison of Computed and Measured Vortex Evolution for a UH-60A Rotor in Forward Flight

NASA Technical Reports Server (NTRS)

Ahmad, Jasim Uddin; Yamauchi, Gloria K.; Kao, David L.

2013-01-01

A Computational Fluid Dynamics (CFD) simulation using the Navier-Stokes equations was performed to determine the evolutionary and dynamical characteristics of the vortex flowfield for a highly flexible aeroelastic UH-60A rotor in forward flight. The experimental wake data were acquired using Particle Image Velocimetry (PIV) during a test of the fullscale UH-60A rotor in the National Full-Scale Aerodynamics Complex 40- by 80-Foot Wind Tunnel. The PIV measurements were made in a stationary cross-flow plane at 90 deg rotor azimuth. The CFD simulation was performed using the OVERFLOW CFD solver loosely coupled with the rotorcraft comprehensive code CAMRAD II. Characteristics of vortices captured in the PIV plane from different blades are compared with CFD calculations. The blade airloads were calculated using two different turbulence models. A limited spatial, temporal, and CFD/comprehensive-code coupling sensitivity analysis was performed in order to verify the unsteady helicopter simulations with a moving rotor grid system.

Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis.

PubMed

Kalendar, Ruslan; Lee, David; Schulman, Alan H

2011-08-01

The polymerase chain reaction is fundamental to molecular biology and is the most important practical molecular technique for the research laboratory. We have developed and tested efficient tools for PCR primer and probe design, which also predict oligonucleotide properties based on experimental studies of PCR efficiency. The tools provide comprehensive facilities for designing primers for most PCR applications and their combinations, including standard, multiplex, long-distance, inverse, real-time, unique, group-specific, bisulphite modification assays, Overlap-Extension PCR Multi-Fragment Assembly, as well as a programme to design oligonucleotide sets for long sequence assembly by ligase chain reaction. The in silico PCR primer or probe search includes comprehensive analyses of individual primers and primer pairs. It calculates the melting temperature for standard and degenerate oligonucleotides including LNA and other modifications, provides analyses for a set of primers with prediction of oligonucleotide properties, dimer and G-quadruplex detection, linguistic complexity, and provides a dilution and resuspension calculator. Copyright © 2011 Elsevier Inc. All rights reserved.

Learning to Listen: Does Intervention Make a Difference?

ERIC Educational Resources Information Center

Lotfi, Ghazal; Maftoon, Parviz; Birjandi, Parviz

2016-01-01

This study explored the impact of listening strategy training conducted within two strategy interventions on pre-intermediate and intermediate EFL learners' comprehension of unidirectional listening. Participants were divided into two experimental groups (n = 156) and a comparison group (n = 50). Each experimental group was trained in eight…

Investigation of interpolation techniques for the reconstruction of the first dimension of comprehensive two-dimensional liquid chromatography-diode array detector data.

PubMed

Allen, Robert C; Rutan, Sarah C

2011-10-31

Simulated and experimental data were used to measure the effectiveness of common interpolation techniques during chromatographic alignment of comprehensive two-dimensional liquid chromatography-diode array detector (LC×LC-DAD) data. Interpolation was used to generate a sufficient number of data points in the sampled first chromatographic dimension to allow for alignment of retention times from different injections. Five different interpolation methods, linear interpolation followed by cross correlation, piecewise cubic Hermite interpolating polynomial, cubic spline, Fourier zero-filling, and Gaussian fitting, were investigated. The fully aligned chromatograms, in both the first and second chromatographic dimensions, were analyzed by parallel factor analysis to determine the relative area for each peak in each injection. A calibration curve was generated for the simulated data set. The standard error of prediction and percent relative standard deviation were calculated for the simulated peak for each technique. The Gaussian fitting interpolation technique resulted in the lowest standard error of prediction and average relative standard deviation for the simulated data. However, upon applying the interpolation techniques to the experimental data, most of the interpolation methods were not found to produce statistically different relative peak areas from each other. While most of the techniques were not statistically different, the performance was improved relative to the PARAFAC results obtained when analyzing the unaligned data. Copyright © 2011 Elsevier B.V. All rights reserved.

Effects of anisotropic interaction-induced properties of hydrogen-rare gas compounds on rototranslational Raman scattering spectra: Comprehensive theoretical and numerical analysis

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

Głaz, Waldemar, E-mail: glaz@kielich.amu.edu.pl; Bancewicz, Tadeusz; Godet, Jean-Luc

2016-07-21

A comprehensive study is presented of many aspects of the depolarized anisotropic collision induced (CI) component of light scattered by weakly bound compounds composed of a dihydrogen molecule and a rare gas (Rg) atom, H{sub 2}–Rg. The work continues a series of earlier projects marking the revival of interest in linear light scattering following the development of new highly advanced tools of quantum chemistry and other theoretical, computational, and experimental means of spectral analyses. Sophisticated ab initio computing procedures are applied in order to obtain the anisotropic polarizability component’s dependence on the H{sub 2}–Rg geometry. These data are then usedmore » to evaluate the CI spectral lines for all types of Rg atoms ranging from He to Xe (Rn excluded). Evolution of the properties of CI spectra with growing polarizability/masses of the complexes studied is observed. Special attention is given to the heaviest, Kr and Xe based, scatterers. The influence of specific factors shaping the spectral lines (e.g., bound and metastable contribution, potential anisotropy) is discussed. Also the share of pressure broadened allowed rotational transitions in the overall spectral profile is taken into account and the extent to which it is separable from the pure CI contribution is discussed. We finish with a brief comparison between the obtained results and available experimental data.« less

Reform of experimental teaching based on quality cultivation

NASA Astrophysics Data System (ADS)

Wang, Wei; Yan, Xingwei; Liu, Wei; Yao, Tianfu; Shi, Jianhua; Lei, Bing; Hu, Haojun

2017-08-01

Experimental teaching plays an import part in quality education which devotes to cultivating students with innovative spirit, strong technological talents and practical ability. However, in the traditional experimental teaching mode, the experiments are treated as a vassal or supplementary mean of theoretical teaching, and students prefer focus on theory to practice. Therefore, the traditional experimental teaching mode is difficult to meet the requirements of quality education. To address this issue, the reform of experimental teaching is introduced in this paper taking the photoelectric detector experiment as the example. The new experimental teaching mode is designed from such aspects as experimental content, teaching method and experimental evaluation. With the purpose of cultivating students' practical ability, two different-level experimental content is designed. Not only the basic experiments used to verify the theory are set to consolidate the students' learned theoretical knowledge, but also comprehensive experiments are designed to encourage the students to apply their learned knowledge to solve practical problems. In the teaching process, heuristic teaching thought is adopt and the traditional `teacher-centered' teaching form is replaced by `student-centered' form, which aims to encourage students to design the experimental systems by their own with the teacher's guidance. In addition to depending on stimulating the students' interest of science research, experimental evaluation is necessary to urge students to complete the experiments efficiently. Multifaceted evaluation method is proposed to test the students' mastery of theoretical knowledge, practice ability, troubleshooting and problem solving skills, and innovation capability comprehensively. Practices demonstrated the satisfying effect of our experimental teaching mode.

Cultivating engineering innovation ability based on optoelectronic experimental platform

NASA Astrophysics Data System (ADS)

Li, Dangjuan; Wu, Shenjiang

2017-08-01

As the supporting experimental platform of the Xi'an Technological University education reform experimental class, "optical technological innovation experimental platform" integrated the design and comprehensive experiments of the optical multi-class courses. On the basis of summing up the past two years teaching experience, platform pilot projects were improve. It has played a good role by making the use of an open teaching model in the cultivating engineering innovation spirit and scientific thinking of the students.

Behavior of Industrial Steel Rack Connections

NASA Astrophysics Data System (ADS)

Shah, S. N. R.; Ramli Sulong, N. H.; Khan, R.; Jumaat, M. Z.; Shariati, M.

2016-03-01

Beam-to-column connections (BCCs) used in steel pallet racks (SPRs) play a significant role to maintain the stability of rack structures in the down-aisle direction. The variety in the geometry of commercially available beam end connectors hampers the development of a generalized analytic design approach for SPR BCCs. The experimental prediction of flexibility in SPR BCCs is prohibitively expensive and difficult for all types of commercially available beam end connectors. A suitable solution to derive a particular uniform M-θ relationship for each connection type in terms of geometric parameters may be achieved through finite element (FE) modeling. This study first presents a comprehensive description of the experimental investigations that were performed and used as the calibration bases for the numerical study that constituted its main contribution. A three dimensioned (3D) non-linear finite element (FE) model was developed and calibrated against the experimental results. The FE model took into account material nonlinearities, geometrical properties and large displacements. Comparisons between numerical and experimental data for observed failure modes and M-θ relationship showed close agreement. The validated FE model was further extended to perform parametric analysis to identify the effects of various parameters which may affect the overall performance of the connection.

ARMOUR - A Rice miRNA: mRNA Interaction Resource.

PubMed

Sanan-Mishra, Neeti; Tripathi, Anita; Goswami, Kavita; Shukla, Rohit N; Vasudevan, Madavan; Goswami, Hitesh

2018-01-01

ARMOUR was developed as A Rice miRNA:mRNA interaction resource. This informative and interactive database includes the experimentally validated expression profiles of miRNAs under different developmental and abiotic stress conditions across seven Indian rice cultivars. This comprehensive database covers 689 known and 1664 predicted novel miRNAs and their expression profiles in more than 38 different tissues or conditions along with their predicted/known target transcripts. The understanding of miRNA:mRNA interactome in regulation of functional cellular machinery is supported by the sequence information of the mature and hairpin structures. ARMOUR provides flexibility to users in querying the database using multiple ways like known gene identifiers, gene ontology identifiers, KEGG identifiers and also allows on the fly fold change analysis and sequence search query with inbuilt BLAST algorithm. ARMOUR database provides a cohesive platform for novel and mature miRNAs and their expression in different experimental conditions and allows searching for their interacting mRNA targets, GO annotation and their involvement in various biological pathways. The ARMOUR database includes a provision for adding more experimental data from users, with an aim to develop it as a platform for sharing and comparing experimental data contributed by research groups working on rice.

Comprehensive Approach to Pupil Planning: Stage I - Classroom Support (Includes Classroom Support Procedures). Experimental Edition.

ERIC Educational Resources Information Center

Mabry, Ann; Kaufman, Martin J.

Presented is Stage I of the Comprehensive Approach to Pupil Planning (CAPP) System, a three-stage model for planning educational interventions in the regular and special education classrooms and for guiding placement decisions. The guide consists of the following: an overview of the CAPP System; an introduction to Stage I on classroom support…

Comprehensive Approach to Pupil Planning: Stage II - Planning and Placement (Includes Planning and Placement Team Meeting Agenda). Experimental Edition.

ERIC Educational Resources Information Center

Vlasak, Frances Stetson; Kaufman, Martin J.

Presented is Stage II of the Comprehensive Approach to Pupil Planning (CAPP) System, a three-stage model for planning educational interventions in the regular and special education classrooms and for guiding placement decisions. The guide focuses on the evaluation services performed by the Planning and Placement Team (PPT) with sections on the…

Improving Reading Comprehension Skills with Children's Books through Metacognitive Strategy: The Turkish Context

ERIC Educational Resources Information Center

Çer, Erkan; Sahin, Ertugrul

2016-01-01

The aim of this study was to explore the effect of metacognitive strategy in improving reading comprehension skills through children's literature of literary quality. A quasi-experimental study was carried out in a private secondary school in a city located Middle Black Sea region of Turkey. Two classes were randomly chosen as the study group, and…

The Effects of Learning-Style Based Activities on Students' Reading Comprehension Skills and Self-Efficacy Perceptions in English Foreign Language Classes

ERIC Educational Resources Information Center

Balci, Özgül

2017-01-01

This study investigated the effects of learning-style based activities on students' reading comprehension skills and self-efficacy perceptions in English foreign language classes. A quasi-experimental, matching-only pretest-posttest control group design was utilized. The study was conducted with freshmen university students majoring in Elementary…

Investigating the Effectiveness of MRM Instruction on Improving Comprehension of Paragraphs.

ERIC Educational Resources Information Center

Dwyer, Edward J.

A study of the effects of using the MRM (message unit--verb unit--message unit) instructional system on reading comprehension was studied using 69 college freshmen, 37 in an experimental group and 32 in a control group. Both groups were engaged in a variety of activities designed to promote greater reading efficiency as a regular part of their…

The Effects of Visual and Textual Annotations on Spanish Listening Comprehension, Vocabulary Acquisition and Cognitive Load

ERIC Educational Resources Information Center

Cottam, Michael Evan

2010-01-01

The purpose of this experimental study was to investigate the effects of textual and visual annotations on Spanish listening comprehension and vocabulary acquisition in the context of an online multimedia listening activity. 95 students who were enrolled in different sections of first year Spanish classes at a community college and a large…

Effects of the Wisconsin Reading Design Comprehension Program on Reading Achievement and Self-Concept of Sixth Grade Students.

ERIC Educational Resources Information Center

Negley, Sandra Anne

The main purpose of this study was to determine and describe the effects of the comprehension component of the criterion-referenced reading program, Wisconsin Design for Reading Skills Development (WDRSD), on reading achievement and self-concept of sixth-grade students. Parametric techniques were employed in a quasi-experimental study involving 44…

Impact of a Teacher-Led Intervention on Preference for Self-Regulated Learning, Finding Main Ideas in Expository Texts, and Reading Comprehension

ERIC Educational Resources Information Center

Stoeger, Heidrun; Sontag, Christine; Ziegler, Albert

2014-01-01

We examined the impact of a teacher-led intervention, implemented during regular classroom instruction and homework, on fourth-grade students' preference for self-regulated learning, finding main ideas in expository texts, and reading comprehension. In our quasi-experimental study with intact classrooms, (a) students (n = 266, 12 classrooms) who…

Concept Mapping as a Reading Strategy: Does It Scaffold Comprehension and Recall?

ERIC Educational Resources Information Center

Tajeddin, Zia; Tabatabaei, Soudabeh

2016-01-01

Concept maps reflect the linkage of concepts or facts within a text. This study was set out to investigate whether concept mapping as a learning strategy would have any scaffolding effect on the reading comprehension and recall of propositions by L2 learners. Out of 60 high school students, 30 in the experimental group were exposed to concept…

The Impact of Authentic Material Use on Development of the Reading Comprehension, Writing Skills and Motivation in Language Course

ERIC Educational Resources Information Center

Belet Boyaci, S. Dilek; Güner, Mediha

2018-01-01

The objective of the present study was to determine the impact of authentic task-based authentic material on reading comprehension, writing skills and writing motivation in the Turkish language course. The study was conducted with mixed design methodology. Quantitative data were collected with the quasi-experimental with pre-test post-test with…

The Effect of Instructing Critical Thinking through Debate on Male and Female EFL Learners' Reading Comprehension

ERIC Educational Resources Information Center

Tous, Maryam Danaye; Tahriri, Abdorreza; Haghighi, Sara

2015-01-01

The purpose of the present study was to examine the effect of instruction through debate on male and female EFL learners' reading comprehension. Also, their perception of critical thinking (CT) instruction was investigated. A quantitative research method with experimental pre-and post-tests design was conducted to collect the data. Eighty-eight…

Do Students Using Electronic Books Display Different Reading Comprehension and Motivation Levels than Students Using Traditional Print Books?

ERIC Educational Resources Information Center

Wells, Casey L.

2012-01-01

The effect of electronic books on the reading comprehension of middle and high school students was examined using an experimental posttest-only control-group design. A convenience sample of 140 randomly assigned middle and high school English students at an independent school in eastern North Carolina participated. Half of the students used…

An Initial Study of the Effects of Cooperative Learning on Reading Comprehension, Vocabulary Acquisition, and Motivation to Read

ERIC Educational Resources Information Center

Shaaban, Kassim

2006-01-01

This study investigated the effects of the Jigsaw II cooperative learning (CL) model and whole class instruction in improving learners' reading comprehension, vocabulary acquisition, and motivation to read. Forty-four grade five English as a foreign language learners participated in the study, and a posttest-only control group experimental design…

The Effects of Explicit Reading Strategy Instruction and Cooperative Learning on Reading Comprehension in Fourth Grade Students

ERIC Educational Resources Information Center

Lencioni, Gina M.

2013-01-01

The purpose of this study was to investigate the effects of explicit direct instruction and cooperative learning on reading comprehension in fourth grade students. A quasi-experimental design was used. There were six cognitive and three affective measures used to collect quantitative data. Cognitive measures included California State Test scores,…

The Effects of Teaching Informative Text through Processual Model on Reading Comprehension Skills

ERIC Educational Resources Information Center

Sulak, Süleyman Erkam; Günes, Firdevs

2017-01-01

This study was carried out in order to search the effects of teaching informative text structures through processual model on the reading comprehension skills of 4th grade students. The research was designed in accordance with experimental model with pre-test-post-test control groups. The study group of the study consisted of 62 fourth grade…

Comprehensiveness and the Challenges of Harmonization of Study and Research Programs in the CSET within ODL Context: Chemists' Perspective

ERIC Educational Resources Information Center

Mphahlele, M. J.; Tafesse, F.

2012-01-01

This article examines the comprehensiveness of the University of South Africa (UNISA) as an Open Distance Learning (ODL) institution and the challenges faced by experimental disciplines within ODL. Those challenges are brought about by the attempt to harmonize study and research programs in the College of Science, Engineering and Technology (CSET)…

The Impact of a Community-Based Comprehensive Sex Education Program on Chinese Adolescents' Sex-Related Knowledge and Attitudes

ERIC Educational Resources Information Center

Wang, Bo; Meier, Ann; Shah, Iqbal; Li, Xiaoming

2006-01-01

The purpose of this study was to evaluate a community-based comprehensive sex education program among unmarried youth in China. The impact of the intervention on sexual knowledge, attitudes, and sexual initiation were assessed, using a pre-test post-test quasi-experimental research design. The program used six methods for providing sex-related…

Amnesic H.M. Exhibits Parallel Deficits and Sparing in Language and Memory: Systems versus Binding Theory Accounts

ERIC Educational Resources Information Center

MacKay, Donald G.; James, Lori E.; Taylor, Jennifer K.; Marian, Diane E.

2007-01-01

This study examines sentence-level language abilities of amnesic H.M. to test competing theoretical conceptions of relations between language and memory. We present 11 new sources of experimental evidence indicating deficits in H.M's comprehension and production of non-cliche sentences. Contrary to recent claims that H.M.'s comprehension is…

The Effect of Video-Based Tasks in Listening Comprehension of Iranian Pre-Intermediate EFL Learners

ERIC Educational Resources Information Center

Sarani, Abdullah; Behtash, Esmail Zare; Nezhad Arani, Saieed Moslemi

2014-01-01

This study aims at finding the effect of video-based tasks in improving the listening comprehension ability of Iranian pre-intermediate EFL (English Foreign Language) learners. After determining the level of learners, an experimental and control group, each of 20 participants, were nominated to contribute to the study. From the time the pre-test…

The Comprehension Problems for Second-Language Learners with Poor Reading Comprehension Despite Adequate Decoding: A Meta-Analysis

ERIC Educational Resources Information Center

Spencer, Mercedes; Wagner, Richard K.

2017-01-01

We conducted a meta-analysis of 16 existing studies to examine the nature of the comprehension problems for children who were second-language learners with poor reading comprehension despite adequate decoding. Results indicated that these children had deficits in oral language (d = -0.80), but these deficits were not as severe as their reading…

Three-dimensional flow measurements in a tesla turbine rotor

NASA Astrophysics Data System (ADS)

Fuchs, Thomas; Schosser, Constantin; Hain, Rainer; Kaehler, Christian

2015-11-01

Tesla turbines are fluid mechanical devices converting flow energy into rotation energy by two physical effects: friction and adhesion. The advantages of the tesla turbine are its simple and robust design, as well as its scalability, which makes it suitable for custom power supply solutions, and renewable energy applications. To this day, there is a lack of experimental data to validate theoretical studies, and CFD simulations of these turbines. This work presents a comprehensive analysis of the flow through a tesla turbine rotor gap, with a gap height of only 0.5 mm, by means of three-dimensional Particle Tracking Velocimetry (3D-PTV). For laminar flows, the experimental results match the theory very well, since the measured flow profiles show the predicted second order parabolic shape in radial direction and a fourth order behavior in circumferential direction. In addition to these laminar measurements, turbulent flows at higher mass flow rates were investigated.

Calcium dynamics and signaling in vascular regulation: computational models

PubMed Central

Tsoukias, Nikolaos Michael

2013-01-01

Calcium is a universal signaling molecule with a central role in a number of vascular functions including in the regulation of tone and blood flow. Experimentation has provided insights into signaling pathways that lead to or affected by Ca2+ mobilization in the vasculature. Mathematical modeling offers a systematic approach to the analysis of these mechanisms and can serve as a tool for data interpretation and for guiding new experimental studies. Comprehensive models of calcium dynamics are well advanced for some systems such as the heart. This review summarizes the progress that has been made in modeling Ca2+ dynamics and signaling in vascular cells. Model simulations show how Ca2+ signaling emerges as a result of complex, nonlinear interactions that cannot be properly analyzed using only a reductionist's approach. A strategy of integrative modeling in the vasculature is outlined that will allow linking macroscale pathophysiological responses to the underlying cellular mechanisms. PMID:21061306

CH-47D Rotating System Fault Sensing for Condition Based Maintenance

DTIC Science & Technology

2011-03-01

replacement. This research seeks to create an analytical model in the Rotorcraft Comprehensive Analysis System which will enable the identifica- tion of...answer my many questions. Without your assistance and that of Dr. Jon Keller and Mr. Clayton Kachelle at AMRDEC, the Rotorcraft Comprehensive Analysis...20 3.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . 20 3.2 Rotorcraft Comprehensive Analysis

Numerical-experimental study of internal fixation system "Dufoo" for vertebral fractures.

PubMed

Nieto-Miranda, J Jesús; Faraón-Carbajal Romero, Manuel; Sánchez-Aguilar, Jons

2012-01-01

We describe a numerical experimental study of the stress generated by the internal fixation system "Dufoo" used in the treatment of vertebral fractures with the purpose of validating the numerical model of human lumbar vertebrae under the main physiological loads that the human body is exposed to in this area. The objective is to model and numerically simulate the elements of the musculoskeletal system to collect the stresses generated and other parameters that are difficult to measure experimentally in the thoracic lumbar vertebrae. We used an internal fixator "Dufoo" and vertebrae L2-L3-L4 specimens from pig and human. The system uses a total L3 corpectomy. The fixator acts as a mechanical bridge implant from L2 to L4. Numerical analysis was performed using the finite element method (FEM). For the experimental study, reflective photoelasticity and extensometry were used. Torsion and combined loads generate the main displacements and stresses in the study system, determining that the internal fixation carries out part of the function of the damaged organ structure when absorbing the stresses presented by applied loads. Numerical analysis allows great freedom in the management of the variables involved in the developed models using radiological images. Geometric models are obtained and are entered into FEM programs that allow testing using parameters that, under actual conditions, may not be easily carried out, allowing to comprehensively determine the biomechanical behavior of the coupled system of study.

Heat-straightening effects on the behavior of plates and rolled shapes : volume 2 : second interim report of phase 1.

DOT National Transportation Integrated Search

1987-08-01

One of the primary reasons that highway departments are hesitant to use heat-straightening techniques to repair damaged steel girders is the lack of experimental verification of the process. A comprehensive experimental program on the subject has bee...

Experimental Evaluation of the Effects of a Research-Based Preschool Mathematics Curriculum

ERIC Educational Resources Information Center

Clements, Douglas H.; Sarama, Julie

2008-01-01

A randomized-trials design was used to evaluate the effectiveness of a preschool mathematics program based on a comprehensive model of research-based curricula development. Thirty-six preschool classrooms were assigned to experimental (Building Blocks), comparison (a different preschool mathematics curriculum), or control conditions. Children were…

A twice-paired watershed experimental design to assess stacked practices through field-edge monitoring

USDA-ARS?s Scientific Manuscript database

To improve our ability to reduce nutrient losses from agricultural lands to receiving waters, comprehensive approaches that employ a variety of conservation practices placed within and below field edges will be needed. There is a need to obtain experimental data to better understand how conservation...

Effects on ESL Reading of Teaching Cultural Content Schemata.

ERIC Educational Resources Information Center

Floyd, Pamela; Carrell, Patricia

1987-01-01

Intermediate-level English as a second language students were examined for levels of reading comprehension. Half of each group (experimental and control) received more complete versions of test passages than the other half, and the experimental group was taught appropriate cultural background information between tests. Background knowledge did…

An experimental ward. Improving care and learning.

PubMed

Ronan, L; Stoeckle, J D

1992-01-01

The rapidly changing health care system is still largely organized according to old, and increasingly outdated models. The contemporary demands of patient care and residency training call for an experimental ward, which can develop and test new techniques in hospital organization and the delivery of care in a comprehensive way.

A comprehensive study of the delay vector variance method for quantification of nonlinearity in dynamical systems

PubMed Central

Mandic, D. P.; Ryan, K.; Basu, B.; Pakrashi, V.

2016-01-01

Although vibration monitoring is a popular method to monitor and assess dynamic structures, quantification of linearity or nonlinearity of the dynamic responses remains a challenging problem. We investigate the delay vector variance (DVV) method in this regard in a comprehensive manner to establish the degree to which a change in signal nonlinearity can be related to system nonlinearity and how a change in system parameters affects the nonlinearity in the dynamic response of the system. A wide range of theoretical situations are considered in this regard using a single degree of freedom (SDOF) system to obtain numerical benchmarks. A number of experiments are then carried out using a physical SDOF model in the laboratory. Finally, a composite wind turbine blade is tested for different excitations and the dynamic responses are measured at a number of points to extend the investigation to continuum structures. The dynamic responses were measured using accelerometers, strain gauges and a Laser Doppler vibrometer. This comprehensive study creates a numerical and experimental benchmark for structurally dynamical systems where output-only information is typically available, especially in the context of DVV. The study also allows for comparative analysis between different systems driven by the similar input. PMID:26909175

A mechanistic modelling approach to polymer dissolution using magnetic resonance microimaging.

PubMed

Kaunisto, Erik; Abrahmsen-Alami, Susanna; Borgquist, Per; Larsson, Anette; Nilsson, Bernt; Axelsson, Anders

2010-10-15

In this paper a computationally efficient mathematical model describing the swelling and dissolution of a polyethylene oxide tablet is presented. The model was calibrated against polymer release, front position and water concentration profile data inside the gel layer, using two different diffusion models. The water concentration profiles were obtained from magnetic resonance microimaging data which, in addition to the previously used texture analysis method, can help to validate and discriminate between the mechanisms of swelling, diffusion and erosion in relation to the dissolution process. Critical parameters were identified through a comprehensive sensitivity analysis, and the effect of hydrodynamic shearing was investigated by using two different stirring rates. Good agreement was obtained between the experimental results and the model. Copyright © 2010 Elsevier B.V. All rights reserved.

Acoustic anisotropy of acoustooptic TI(3)AsS(4) crystals.

PubMed

Martynyuk-Lototska, Iryna; Kushnirevych, Marian; Zapeka, Bohdan; Krupych, Oleh; Kokhan, Oleksandr; Pogodin, Artem; Peresh, Eugen; Mys, Oksana; Vlokh, Rostyslav

2015-02-20

We present comprehensive experimental measurements and analysis of anisotropy of the acoustic wave velocities for TI(3)AsS(4) crystals, including the obliquity and nonorthogonality of the acoustic waves, and the deviations from purely longitudinal and transverse polarization types. We have found that the crystals under analysis are characterized by rather low transverse wave velocities v(23) and v(32), which are both equal to 630 m/s. It is shown that the efficiency of acoustooptic (AO) interactions in TI(3)AsS(4) can be notably increased when providing anisotropic interaction with the slowest transverse acoustic wave. Under the previously mentioned conditions, the AO figure-of-merit can be estimated to be extremely high, i.e., approximately 3×10(-12) s(3)/kg.

Statistical analysis of trypanosomes' motility

NASA Astrophysics Data System (ADS)

Zaburdaev, Vasily; Uppaluri, Sravanti; Pfohl, Thomas; Engstler, Markus; Stark, Holger; Friedrich, Rudolf

2010-03-01

Trypanosome is a parasite causing the sleeping sickness. The way it moves in the blood stream and penetrates various obstacles is the area of active research. Our goal was to investigate a free trypanosomes' motion in the planar geometry. Our analysis of trypanosomes' trajectories reveals that there are two correlation times - one is associated with a fast motion of its body and the second one with a slower rotational diffusion of the trypanosome as a point object. We propose a system of Langevin equations to model such motion. One of its peculiarities is the presence of multiplicative noise predicting higher level of noise for higher velocity of the trypanosome. Theoretical and numerical results give a comprehensive description of the experimental data such as the mean squared displacement, velocity distribution and auto-correlation function.

An experimental paradigm for team decision processes

NASA Technical Reports Server (NTRS)

Serfaty, D.; Kleinman, D. L.

1986-01-01

The study of distributed information processing and decision making is presently hampered by two factors: (1) The inherent complexity of the mathematical formulation of decentralized problems has prevented the development of models that could be used to predict performance in a distributed environment; and (2) The lack of comprehensive scientific empirical data on human team decision making has hindered the development of significant descriptive models. As a part of a comprehensive effort to find a new framework for multihuman decision making problems, a novel experimental research paradigm was developed involving human terms in decision making tasks. Attempts to construct parts of an integrated model with ideas from queueing networks, team theory, distributed estimation and decentralized resource management are described.

Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae

PubMed Central

Reguly, Teresa; Breitkreutz, Ashton; Boucher, Lorrie; Breitkreutz, Bobby-Joe; Hon, Gary C; Myers, Chad L; Parsons, Ainslie; Friesen, Helena; Oughtred, Rose; Tong, Amy; Stark, Chris; Ho, Yuen; Botstein, David; Andrews, Brenda; Boone, Charles; Troyanskya, Olga G; Ideker, Trey; Dolinski, Kara; Batada, Nizar N; Tyers, Mike

2006-01-01

Background The study of complex biological networks and prediction of gene function has been enabled by high-throughput (HTP) methods for detection of genetic and protein interactions. Sparse coverage in HTP datasets may, however, distort network properties and confound predictions. Although a vast number of well substantiated interactions are recorded in the scientific literature, these data have not yet been distilled into networks that enable system-level inference. Results We describe here a comprehensive database of genetic and protein interactions, and associated experimental evidence, for the budding yeast Saccharomyces cerevisiae, as manually curated from over 31,793 abstracts and online publications. This literature-curated (LC) dataset contains 33,311 interactions, on the order of all extant HTP datasets combined. Surprisingly, HTP protein-interaction datasets currently achieve only around 14% coverage of the interactions in the literature. The LC network nevertheless shares attributes with HTP networks, including scale-free connectivity and correlations between interactions, abundance, localization, and expression. We find that essential genes or proteins are enriched for interactions with other essential genes or proteins, suggesting that the global network may be functionally unified. This interconnectivity is supported by a substantial overlap of protein and genetic interactions in the LC dataset. We show that the LC dataset considerably improves the predictive power of network-analysis approaches. The full LC dataset is available at the BioGRID () and SGD () databases. Conclusion Comprehensive datasets of biological interactions derived from the primary literature provide critical benchmarks for HTP methods, augment functional prediction, and reveal system-level attributes of biological networks. PMID:16762047

Similar but Different: Differences in Comprehension Diagnosis on the Neale Analysis of Reading Ability and the York Assessment of Reading for Comprehension

ERIC Educational Resources Information Center

Colenbrander, Danielle; Nickels, Lyndsey; Kohnen, Saskia

2017-01-01

Background: Identifying reading comprehension difficulties is challenging. There are many comprehension tests to choose from, and a child's diagnosis can be influenced by various factors such as a test's format and content and the choice of diagnostic criteria. We investigate these issues with reference to the Neale Analysis of Reading Ability…

Decoding and Reading Comprehension: A Meta-Analysis to Identify Which Reader and Assessment Characteristics Influence the Strength of the Relationship in English

ERIC Educational Resources Information Center

García, J. Ricardo; Cain, Kate

2014-01-01

The twofold purpose of this meta-analysis was to determine the relative importance of decoding skills to reading comprehension in reading development and to identify which reader characteristics and reading assessment characteristics contribute to differences in the decoding and reading comprehension correlation. A meta-analysis of 110 studies…

Analyse Factorielle d'une Batterie de Tests de Comprehension Orale et Ecrite (Factor Analysis of a Battery of Tests of Listening and Reading Comprehension). Melanges Pedagogiques, 1971.

ERIC Educational Resources Information Center

Lonchamp, F.

This is a presentation of the results of a factor analysis of a battery of tests intended to measure listening and reading comprehension in English as a second language. The analysis sought to answer the following questions: (1) whether the factor analysis method yields results when applied to tests which are not specifically designed for this…

A regression model for calculating the second dimension retention index in comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry.

PubMed

Wang, Bing; Shen, Hao; Fang, Aiqin; Huang, De-Shuang; Jiang, Changjun; Zhang, Jun; Chen, Peng

2016-06-17

Comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GC×GC/TOF-MS) system has become a key analytical technology in high-throughput analysis. Retention index has been approved to be helpful for compound identification in one-dimensional gas chromatography, which is also true for two-dimensional gas chromatography. In this work, a novel regression model was proposed for calculating the second dimension retention index of target components where n-alkanes were used as reference compounds. This model was developed to depict the relationship among adjusted second dimension retention time, temperature of the second dimension column and carbon number of n-alkanes by an exponential nonlinear function with only five parameters. Three different criteria were introduced to find the optimal values of parameters. The performance of this model was evaluated using experimental data of n-alkanes (C7-C31) at 24 temperatures which can cover all 0-6s adjusted retention time area. The experimental results show that the mean relative error between predicted adjusted retention time and experimental data of n-alkanes was only 2%. Furthermore, our proposed model demonstrates a good extrapolation capability for predicting adjusted retention time of target compounds which located out of the range of the reference compounds in the second dimension adjusted retention time space. Our work shows the deviation was less than 9 retention index units (iu) while the number of alkanes were added up to 5. The performance of our proposed model has also been demonstrated by analyzing a mixture of compounds in temperature programmed experiments. Copyright © 2016 Elsevier B.V. All rights reserved.

[Teaching design and practice of human blood type traits in genetics comprehensive laboratory course].

PubMed

Zhao, Jian; Hu, Dong-mei; Yu, Da-de; Dong, Ming-liang; Li, Yun; Fan, Ying-ming; Wang, Yan-wei; Zhang, Jin-feng

2016-05-01

Comprehensive laboratory courses, which enable students to aptly apply theoretic knowledge and master experiment skills, play an important role in the present educational reform of laboratory courses. We utilized human ABO blood type as the experimental subject, and designed the experiment--"Molecular Genotyping of Human ABO Blood Type and Analysis of Population Genetic Equilibrium". In the experiment, DNA in mucosal cells is extracted from students' saliva, and each student's genotype is identified using a series of molecular genetics technologies, including PCR amplification of target fragments, enzymatic digestion, and electrophoretic separation. Then, taking the whole class as an analogous Mendel population, a survey of genotype frequency of ABO blood type is conducted, followed with analyses of various population genetic parameters using Popgene. Through the open laboratory course, students can not only master molecular genetic experimental skills, but also improve their understanding of theoretic knowledge through independent design and optimization of molecular techniques. After five years of research and practice, a stable experimental system of molecular genetics has been established to identify six genotypes of ABO blood types, namely I(A)I(A), I(A)i, I(B)I(B), I(B)i, I(A)I(B) and ii. Laboratory courses of molecular and population genetics have been integrated by calculating the frequencies of the six genotypes and three multiple alleles and testing population genetic equilibrium. The goal of the open laboratory course with independent design and implementation by the students has been achieved. This laboratory course has proved effective and received good reviews from the students. It could be applied as a genetics laboratory course for the biology majors directly, and its ideas and methods could be promoted and applied to other biological laboratory courses.

Analysis of laser fluorosensor systems for remote algae detection and quantification

NASA Technical Reports Server (NTRS)

Browell, E. V.

1977-01-01

The development and performance of single- and multiple-wavelength laser fluorosensor systems for use in the remote detection and quantification of algae are discussed. The appropriate equation for the fluorescence power received by a laser fluorosensor system is derived in detail. Experimental development of a single wavelength system and a four wavelength system, which selectively excites the algae contained in the four primary algal color groups, is reviewed, and test results are presented. A comprehensive error analysis is reported which evaluates the uncertainty in the remote determination of the chlorophyll a concentration contained in algae by single- and multiple-wavelength laser fluorosensor systems. Results of the error analysis indicate that the remote quantification of chlorophyll a by a laser fluorosensor system requires optimum excitation wavelength(s), remote measurement of marine attenuation coefficients, and supplemental instrumentation to reduce uncertainties in the algal fluorescence cross sections.

TASI: A software tool for spatial-temporal quantification of tumor spheroid dynamics.

PubMed

Hou, Yue; Konen, Jessica; Brat, Daniel J; Marcus, Adam I; Cooper, Lee A D

2018-05-08

Spheroid cultures derived from explanted cancer specimens are an increasingly utilized resource for studying complex biological processes like tumor cell invasion and metastasis, representing an important bridge between the simplicity and practicality of 2-dimensional monolayer cultures and the complexity and realism of in vivo animal models. Temporal imaging of spheroids can capture the dynamics of cell behaviors and microenvironments, and when combined with quantitative image analysis methods, enables deep interrogation of biological mechanisms. This paper presents a comprehensive open-source software framework for Temporal Analysis of Spheroid Imaging (TASI) that allows investigators to objectively characterize spheroid growth and invasion dynamics. TASI performs spatiotemporal segmentation of spheroid cultures, extraction of features describing spheroid morpho-phenotypes, mathematical modeling of spheroid dynamics, and statistical comparisons of experimental conditions. We demonstrate the utility of this tool in an analysis of non-small cell lung cancer spheroids that exhibit variability in metastatic and proliferative behaviors.

BFPTool: a software tool for analysis of Biomembrane Force Probe experiments.

PubMed

Šmít, Daniel; Fouquet, Coralie; Doulazmi, Mohamed; Pincet, Frédéric; Trembleau, Alain; Zapotocky, Martin

2017-01-01

The Biomembrane Force Probe is an approachable experimental technique commonly used for single-molecule force spectroscopy and experiments on biological interfaces. The technique operates in the range of forces from 0.1 pN to 1000 pN. Experiments are typically repeated many times, conditions are often not optimal, the captured video can be unstable and lose focus; this makes efficient analysis challenging, while out-of-the-box non-proprietary solutions are not freely available. This dedicated tool was developed to integrate and simplify the image processing and analysis of videomicroscopy recordings from BFP experiments. A novel processing feature, allowing the tracking of the pipette, was incorporated to address a limitation of preceding methods. Emphasis was placed on versatility and comprehensible user interface implemented in a graphical form. An integrated analytical tool was implemented to provide a faster, simpler and more convenient way to process and analyse BFP experiments.

GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome.

PubMed

Simovski, Boris; Vodák, Daniel; Gundersen, Sveinung; Domanska, Diana; Azab, Abdulrahman; Holden, Lars; Holden, Marit; Grytten, Ivar; Rand, Knut; Drabløs, Finn; Johansen, Morten; Mora, Antonio; Lund-Andersen, Christin; Fromm, Bastian; Eskeland, Ragnhild; Gabrielsen, Odd Stokke; Ferkingstad, Egil; Nakken, Sigve; Bengtsen, Mads; Nederbragt, Alexander Johan; Thorarensen, Hildur Sif; Akse, Johannes Andreas; Glad, Ingrid; Hovig, Eivind; Sandve, Geir Kjetil

2017-07-01

Recent large-scale undertakings such as ENCODE and Roadmap Epigenomics have generated experimental data mapped to the human reference genome (as genomic tracks) representing a variety of functional elements across a large number of cell types. Despite the high potential value of these publicly available data for a broad variety of investigations, little attention has been given to the analytical methodology necessary for their widespread utilisation. We here present a first principled treatment of the analysis of collections of genomic tracks. We have developed novel computational and statistical methodology to permit comparative and confirmatory analyses across multiple and disparate data sources. We delineate a set of generic questions that are useful across a broad range of investigations and discuss the implications of choosing different statistical measures and null models. Examples include contrasting analyses across different tissues or diseases. The methodology has been implemented in a comprehensive open-source software system, the GSuite HyperBrowser. To make the functionality accessible to biologists, and to facilitate reproducible analysis, we have also developed a web-based interface providing an expertly guided and customizable way of utilizing the methodology. With this system, many novel biological questions can flexibly be posed and rapidly answered. Through a combination of streamlined data acquisition, interoperable representation of dataset collections, and customizable statistical analysis with guided setup and interpretation, the GSuite HyperBrowser represents a first comprehensive solution for integrative analysis of track collections across the genome and epigenome. The software is available at: https://hyperbrowser.uio.no. © The Author 2017. Published by Oxford University Press.

Automatic processing of pragmatic information in the human brain: a mismatch negativity study.

PubMed

Zhao, Ming; Liu, Tao; Chen, Feiyan

2018-05-23

Language comprehension involves pragmatic information processing, which allows world knowledge to influence the interpretation of a sentence. This study explored whether pragmatic information can be automatically processed during spoken sentence comprehension. The experiment adopted the mismatch negativity (MMN) paradigm to capture the neurophysiological indicators of automatic processing of spoken sentences. Pragmatically incorrect ('Foxes have wings') and correct ('Butterflies have wings') sentences were used as the experimental stimuli. In condition 1, the pragmatically correct sentence was the deviant and the pragmatically incorrect sentence was the standard stimulus, whereas the opposite case was presented in condition 2. The experimental results showed that, compared with the condition that the pragmatically correct sentence is the deviant stimulus, when the condition that the pragmatically incorrect sentence is the deviant stimulus MMN effects were induced within 60-120 and 220-260 ms. The results indicated that the human brain can monitor for incorrect pragmatic information in the inattentive state and can automatically process pragmatic information at the beginning of spoken sentence comprehension.

The Effects of Phonological Short-Term Memory and Speech Perception on Spoken Sentence Comprehension in Children: Simulating Deficits in an Experimental Design.

PubMed

Higgins, Meaghan C; Penney, Sarah B; Robertson, Erin K

2017-10-01

The roles of phonological short-term memory (pSTM) and speech perception in spoken sentence comprehension were examined in an experimental design. Deficits in pSTM and speech perception were simulated through task demands while typically-developing children (N [Formula: see text] 71) completed a sentence-picture matching task. Children performed the control, simulated pSTM deficit, simulated speech perception deficit, or simulated double deficit condition. On long sentences, the double deficit group had lower scores than the control and speech perception deficit groups, and the pSTM deficit group had lower scores than the control group and marginally lower scores than the speech perception deficit group. The pSTM and speech perception groups performed similarly to groups with real deficits in these areas, who completed the control condition. Overall, scores were lowest on noncanonical long sentences. Results show pSTM has a greater effect than speech perception on sentence comprehension, at least in the tasks employed here.

Comprehensive predictions of target proteins based on protein-chemical interaction using virtual screening and experimental verifications.

PubMed

Kobayashi, Hiroki; Harada, Hiroko; Nakamura, Masaomi; Futamura, Yushi; Ito, Akihiro; Yoshida, Minoru; Iemura, Shun-Ichiro; Shin-Ya, Kazuo; Doi, Takayuki; Takahashi, Takashi; Natsume, Tohru; Imoto, Masaya; Sakakibara, Yasubumi

2012-04-05

Identification of the target proteins of bioactive compounds is critical for elucidating the mode of action; however, target identification has been difficult in general, mostly due to the low sensitivity of detection using affinity chromatography followed by CBB staining and MS/MS analysis. We applied our protocol of predicting target proteins combining in silico screening and experimental verification for incednine, which inhibits the anti-apoptotic function of Bcl-xL by an unknown mechanism. One hundred eighty-two target protein candidates were computationally predicted to bind to incednine by the statistical prediction method, and the predictions were verified by in vitro binding of incednine to seven proteins, whose expression can be confirmed in our cell system.As a result, 40% accuracy of the computational predictions was achieved successfully, and we newly found 3 incednine-binding proteins. This study revealed that our proposed protocol of predicting target protein combining in silico screening and experimental verification is useful, and provides new insight into a strategy for identifying target proteins of small molecules.

Experimental investigation on the infrared refraction and extinction properties of rock dust in tunneling face of coal mine.

PubMed

Wang, Wenzheng; Wang, Yanming; Shi, Guoqing

2015-12-10

Comprehensive experimental research on the fundamental optical properties of dust pollution in a coal mine is presented. Rock dust generated in a tunneling roadway was sampled and the spectral complex refractive index within an infrared range of 2.5-25 μm was obtained by Fourier transform infrared spectroscopy measurement and Kramers-Kronig relation. Experimental results were validated to be consistent with equivalent optical constants simulated by effective medium theory based on component analysis of x-ray fluorescence, which illustrates that the top three mineral components are SiO2 (62.06%), Al2O3 (21.26%), and Fe2O3 (4.27%). The complex refractive index and the spatial distribution tested by a filter dust and particle size analyzer were involved in the simulation of extinction properties of rock dust along the tunneling roadway solved by the discrete ordinates method and Mie scattering model. The compared results illustrate that transmission is obviously enhanced with the increase of height from the floor but weakened with increasing horizontal distance from the air duct.

Platform construction and extraction mechanism study of magnetic mixed hemimicelles solid-phase extraction

PubMed Central

Xiao, Deli; Zhang, Chan; He, Jia; Zeng, Rong; Chen, Rong; He, Hua

2016-01-01

Simple, accurate and high-throughput pretreatment method would facilitate large-scale studies of trace analysis in complex samples. Magnetic mixed hemimicelles solid-phase extraction has the power to become a key pretreatment method in biological, environmental and clinical research. However, lacking of experimental predictability and unsharpness of extraction mechanism limit the development of this promising method. Herein, this work tries to establish theoretical-based experimental designs for extraction of trace analytes from complex samples using magnetic mixed hemimicelles solid-phase extraction. We selected three categories and six sub-types of compounds for systematic comparative study of extraction mechanism, and comprehensively illustrated the roles of different force (hydrophobic interaction, π-π stacking interactions, hydrogen-bonding interaction, electrostatic interaction) for the first time. What’s more, the application guidelines for supporting materials, surfactants and sample matrix were also summarized. The extraction mechanism and platform established in the study render its future promising for foreseeable and efficient pretreatment under theoretical based experimental design for trace analytes from environmental, biological and clinical samples. PMID:27924944

Socialisation scheme with a high staff-patient ratio.

PubMed

Hollander, D; Rao, V B; McManoman, E; Harrington, N; Weeks, A; Mann, A

1981-01-01

Six months after a comprehensive socialisation scheme began, a prospective controlled study was carried out. The patients were tested in three practical sections - Cooking; Maintenance of Home and Clothing; Other Skills (eg. form-filling); and with a Questionnaire. Forty-eight members of an experimental group received socialisation training after initial testing. They and the 20 controls who did not undergo training were re-evaluated three months later. There was no significant difference between the groups in their initial scores. On retesting, the experimental group showed a significant improvement in Cooking (p less than 0.001), Home Maintenance (p less than 0.001) and the Questionnaire (p less than 0.05). Analysis of the inter-group differences showed significant superiority of the experimental group in Cooking (p less than 0.05) and Home Maintenance (p less than 0.05). It is suggested that such a socialisation scheme be considered for inclusion alongside other rehabilitation services in psychiatric hospitals. The emphasis on a high staff-to-patient ratio and the breakdown of each task into smaller steps emerged as essential elements in the training programme.

The Comprehension Problems for Second-Language Learners with Poor Reading Comprehension despite Adequate Decoding: A Meta-Analysis

PubMed Central

Spencer, Mercedes; Wagner, Richard K.

2016-01-01

We conducted a meta-analysis of 16 existing studies to examine the nature of the comprehension problems for children who were second-language learners with poor reading comprehension despite adequate decoding. Results indicated that these children had deficits in oral language (d = −0.80), but these deficits were not as severe as their reading comprehension deficit (d = −2.47). Second-language learners also had weaker oral language skills compared to native-speaking children regardless of comprehension status (d = −0.84). We discuss theoretical and practical implications of the finding that second-language learners who are poor at reading comprehension despite adequate decoding have deficits in oral language but the deficit is not sufficient to explain their deficit in reading comprehension. PMID:28461711

The Comprehension Problems for Second-Language Learners with Poor Reading Comprehension despite Adequate Decoding: A Meta-Analysis.

PubMed

Spencer, Mercedes; Wagner, Richard K

2017-05-01

We conducted a meta-analysis of 16 existing studies to examine the nature of the comprehension problems for children who were second-language learners with poor reading comprehension despite adequate decoding. Results indicated that these children had deficits in oral language ( d = -0.80), but these deficits were not as severe as their reading comprehension deficit ( d = -2.47). Second-language learners also had weaker oral language skills compared to native-speaking children regardless of comprehension status ( d = -0.84). We discuss theoretical and practical implications of the finding that second-language learners who are poor at reading comprehension despite adequate decoding have deficits in oral language but the deficit is not sufficient to explain their deficit in reading comprehension.

Evaluating a Multidimensional Reading Comprehension Program and Reconsidering the Lowly Reputation of Tests of Near Transfer

ERIC Educational Resources Information Center

Fuchs, Douglas; Hendricks, Emma; Walsh, Meagan E.; Fuchs, Lynn S.; Gilbert, Jennifer K.; Zhang Tracy, Wen; Patton, Samuel, III.; Davis, Nicole; Kim, Wooliya; Elleman, Amy M.; Peng, Peng

2018-01-01

We conducted a 14-week experimental study of 2 versions of a relatively comprehensive RC intervention that involved 50 classroom teachers, 15 tutors, and 120 children drawn in equal proportions from grades 3 and 5 in 13 schools in a large urban school district. Students were randomly assigned in equal numbers to the 2 tutoring conditions and a…

Evaluating a Multidimensional Reading Comprehension Program and Reconsidering the Lowly Reputation of Tests of Near-Transfer

ERIC Educational Resources Information Center

Fuchs, Douglas; Hendricks, Emma; Walsh, Meagan E.; Fuchs, Lynn S.; Gilbert, Jennifer K.; Zhang Tracy, Wen; Patton, Samuel, III; Davis-Perkins, Nicole; Kim, Wooliya; Elleman, Amy M.; Peng, Peng

2018-01-01

We conducted a 14-week experimental study of 2 versions of a relatively comprehensive RC intervention that involved 50 classroom teachers, 15 tutors, and 116 children drawn in equal proportions from grades 3 and 5 in 13 schools in a large urban school district. Students were randomly assigned in equal numbers to the two tutoring conditions and a…

Comprehensive Approach to Pupil Planning: Stage III - Instructional Planning (Includes Data Sources Within the CAPP System and Teacher's Instructional Plan). Experimental Edition.

ERIC Educational Resources Information Center

Vlasak, Frances Stetson; Kaufman, Martin J.

Presented is Stage III of the Comprehensive Approach to Pupil Planning (CAPP) System, a three-stage model for planning educational interventions in the regular and special education classrooms and for guiding placement decisions. The guide focuses on the instructional planning team with sections on the following: Stage III personnel; roles and…

The Impact of Self-Regulated Learning on Reading Comprehension and Attitude towards Turkish Course and Metacognitive Thinking

ERIC Educational Resources Information Center

Oruç, Ayse; Arslan, Ali

2016-01-01

The purpose of this study was to examine the impact of self-regulated learning on students' reading comprehension and attitude towards Turkish course and metacognitive thinking skills. For this purpose, the study was carried out with the 5th graders in Zonguldak Province. In this study, one of the classes was designated as the experimental group…

The Effect of Implementing the Experiential Learning Model in Listening Comprehension for the Eleventh Graders at SMAN 1 Telaga Biru

ERIC Educational Resources Information Center

Tahir, Ismail

2017-01-01

This study is aimed to investigate the effectiveness of the experiential learning in listening comprehension with the focus on the implementation of the class story using language experience at SMAN 1 Telaga Biru. As the pre-experimental research, this study involved one class consisted of 27 students in the eleventh graders. However, most of the…

The Effects of the Comprehensive Inductive Educational Approach on the Social Behaviour of Preschool Children in Kindergarten

ERIC Educational Resources Information Center

Kroflic, Robi; Smrtnik Vitulic, Helena

2015-01-01

The aim of the present study was to ascertain the effects of the five-month implementation of the comprehensive inductive educational approach on the social behaviour of kindergarten children. The sample consisted of 52 children in the experimental group and 48 children in the control group, aged from 2.6 to 6.0 years. The kindergarten teachers…

The Effects of Homogeneous versus Heterogeneous Reading-Style Grouping on EFL Students' Non-Preferred Reading Style and Reading Comprehension

ERIC Educational Resources Information Center

El-Koumy, Abdel Salam Abdel Khalek

2009-01-01

The purpose of this study was to investigate the effects of homogeneous versus heterogeneous reading-style grouping on EFL students' non-preferred reading style and reading comprehension. The study used a pretest-posttest experimental design. The original subjects of the study (N=86) were Egyptian English major senior students during the 2005/2006…

The Effect of Reciprocal Teaching Intervention Strategy on Reading Comprehension Skills of 5th Grade Elementary School Students with Reading Disabilities

ERIC Educational Resources Information Center

Gomaa, Omema Mostafa Kamel

2015-01-01

This study investigated the effect of using reciprocal teaching intervention strategy on improving reading comprehension of reading disabled students in primary five. A total of 66 students identified with RD participated. The sample was divided into two groups; experimental (n = 33 boys) and control (n = 33 boys). ANCOVA and T test were employed…

The Effects of a Flipped English Classroom Intervention on Students' Information and Communication Technology and English Reading Comprehension

ERIC Educational Resources Information Center

Huang, Yu-Ning; Hong, Zuway-R.

2016-01-01

The purpose of this study was to explore the effects of a flipped English classroom intervention on high school students' information and communication technology (ICT) and English reading comprehension in Taiwan. Forty 10th graders were randomly selected from a representative senior high school as an experimental group (EG) to attend a 12-h…

Text-Based Vocabulary Intervention Training Study: Supporting Fourth Graders with Low Reading Comprehension and Learning Disabilities

ERIC Educational Resources Information Center

Solís, Michael; Scammacca, Nancy; Barth, Amy E.; Roberts, Garrett J.

2017-01-01

This experimental study examined the effectiveness of a text-based reading and vocabulary intervention with self-regulatory supports for 4th graders with low reading comprehension. Students with standard scores on the Gates MacGinitie Reading Test between 1.0 standard deviation (SD) and 0.5 SD below the normative sample were included (N=44) and…

The Effect of Speed Reading Strategies on Developing Reading Comprehension among the 2nd Secondary Students in English Language

ERIC Educational Resources Information Center

Abdelrahman, Mahmoud Sulaiman Hamad Bani; Bsharah, Muwafaq Saleem

2014-01-01

This study aimed to find the effect of speed reading strategies on developing reading comprehension among second secondary literary stream students in English language. The sample of the study consists of (42) students assigned into two groups who were chosen randomly from schools, a controlled group (21) students, and an experimental (21)…

Effects of a Cross-Age Peer Learning Program on the Vocabulary and Comprehension of English Learners and Non-English Learners in Elementary School

ERIC Educational Resources Information Center

Silverman, Rebecca D.; Martin-Beltran, Melinda; Peercy, Megan M.; Hartranft, Anna M.; McNeish, Daniel M.; Artzi, Lauren; Nunn, Stephanie

2017-01-01

This study evaluated the effects of a cross-age peer learning program targeting vocabulary and comprehension in kindergarten and fourth-grade classrooms with substantial proportions of English Learners (ELs). The study followed a quasi-experimental design with 12 classrooms (6 kindergarten and 6 fourth grade) in the intervention group and 12…

Social Network Supported Process Recommender System

PubMed Central

Ye, Yanming; Yin, Jianwei; Xu, Yueshen

2014-01-01

Process recommendation technologies have gained more and more attention in the field of intelligent business process modeling to assist the process modeling. However, most of the existing technologies only use the process structure analysis and do not take the social features of processes into account, while the process modeling is complex and comprehensive in most situations. This paper studies the feasibility of social network research technologies on process recommendation and builds a social network system of processes based on the features similarities. Then, three process matching degree measurements are presented and the system implementation is discussed subsequently. Finally, experimental evaluations and future works are introduced. PMID:24672309

Analysis of the Lenticular Jointed MARSIS Antenna Deployment

NASA Technical Reports Server (NTRS)

Mobrem, Mehran; Adams, Douglas S.

2006-01-01

This paper summarizes important milestones in a yearlong comprehensive effort which culminated in successful deployments of the MARSIS antenna booms in May and June of 2005. Experimentally measured straight section and hinge properties are incorporated into specialized modeling techniques that are used to simulate the boom lenticular joints. System level models are exercised to understand the boom deployment dynamics and spacecraft level implications. Discussion includes a comparison of ADAMS simulation results to measured flight data taken during the three boom deployments. Important parameters that govern lenticular joint behavior are outlined and a short summary of lessons learned and recommendations is included to better understand future applications of this technology.

Advances in high throughput DNA sequence data compression.

PubMed

Sardaraz, Muhammad; Tahir, Muhammad; Ikram, Ataul Aziz

2016-06-01

Advances in high throughput sequencing technologies and reduction in cost of sequencing have led to exponential growth in high throughput DNA sequence data. This growth has posed challenges such as storage, retrieval, and transmission of sequencing data. Data compression is used to cope with these challenges. Various methods have been developed to compress genomic and sequencing data. In this article, we present a comprehensive review of compression methods for genome and reads compression. Algorithms are categorized as referential or reference free. Experimental results and comparative analysis of various methods for data compression are presented. Finally, key challenges and research directions in DNA sequence data compression are highlighted.

An assessment on the use of stationary vehicles to support cooperative positioning systems

NASA Astrophysics Data System (ADS)

Ordóñez-Hurtado, Rodrigo H.; Crisostomi, Emanuele; Shorten, Robert N.

2018-03-01

In this paper, we evaluate the ability of stationary vehicles (e.g. parked or temporary stopped cars) as tools to enhance the capabilities of existing cooperative positioning algorithms in vehicular networks. First, some real-world facts are provided to support the feasibility of our ideas. Then, we examine the idea in greater details in terms of the technical requirements and methodological analysis, and provide a comprehensive experimental evaluation using dedicated simulations. The routing of a drone through an urban scenario is presented as a non-traditional application case, where the benefits of the proposed approach are reflected in a better utilisation of the flight time.

Development and test of different methods to improve the description and NO{sub x} emissions in staged combustion

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

Brink, A.; Kilpinen, P.; Hupa, M.

1996-01-01

Two methods to improve the modeling of NO{sub x} emissions in numerical flow simulation of combustion are investigated. The models used are a reduced mechanism for nitrogen chemistry in methane combustion and a new model based on regression analysis of perfectly stirred reactor simulations using detailed comprehensive reaction kinetics. The applicability of the methods to numerical flow simulation of practical furnaces, especially in the near burner region, is tested against experimental data from a pulverized coal fired single burner furnace. The results are also compared to those obtained using a commonly used description for the overall reaction rate of NO.

Spectroscopy of 13C above the α threshold with α +9Be reactions at low energies

NASA Astrophysics Data System (ADS)

Lombardo, I.; Dell'Aquila, D.; Spadaccini, G.; Verde, G.; Vigilante, M.

2018-03-01

In this work we reinvestigate the spectroscopy of 13C at excitation energies larger than the α emission threshold (Ex>10.648 MeV ) by means of a comprehensive R -matrix fit of experimental data concerning α +9Be collisions at low energies. Owing to the analysis of many reaction channels in a broad energy range, we improved the current knowledge on the level scheme of 13C, by contributing to remove uncertain Jπ assignments for several states. Some tentative speculations on the existence of molecular bands associated to cluster structures in this nucleus are also discussed.

HOLOMEM, optical mass memory investigations, volume 1

NASA Technical Reports Server (NTRS)

Roberts, H. N.

1977-01-01

Research and design activities in support of the development of a 10 to the 12th power-bit holographic read/write optical mass memory (HOLOMEM) with some moving parts for space applications are summarized. The report consists of four sections: (1) a general introduction, which includes a summary of key accomplishments and the principal conclusions of the study; (2) a comprehensive analysis of alternative HOLOMEM system concepts; (3) a discussion of important design and tradeoff considerations related to the fabrication, test, and evaluation of a breadboard holographic recorder/reproducer; and (4) a summary of experimental data generated to define the holographic recording performance of two quasi-commercial photoplastic recording films.

Stability and spatial arrangement of the 2,4-dichlorophenoxyacetic acid and β-cyclodextrin inclusion compound: A theoretical study

NASA Astrophysics Data System (ADS)

Pereira, Robson A.; Anconi, Cleber P. A.; Nascimento, Clebio S.; De Almeida, Wagner B.; Dos Santos, Hélio F.

2015-07-01

The present letter reports results from a comprehensive theoretical analysis of the inclusion process involving 2,4-dichlorophenoxyacetic acid (2,4-D) and β-cyclodextrin (β-CD) for which the experimental data of formation is available. Spatial arrangement and stabilization energies were evaluated in gas phase and aqueous solution through density functional theory (DFT) and through the use of SMD implicit solvation approach. The discussed methodology was applied to predict the stability and identify the most favorable form (deprotonated or neutral) as well as the most probable spatial arrangement of the studied inclusion compound.

Comprehensive School Reform and Student Achievement: A Meta-Analysis.

ERIC Educational Resources Information Center

Borman, Geoffrey D.; Hewes, Gina M.; Overman, Laura T.; Brown, Shelly

Using 232 studies, this meta analysis reviewed the research on the achievement effects of the nationally disseminated and externally developed school improvement programs known as "whole-school" or "comprehensive" reforms. In addition to reviewing the overall achievement effects of comprehensive school reform (CSR), the meta…

Student and Teacher Outcomes of The Superkids Quasi-Experimental Study

ERIC Educational Resources Information Center

Borman, Geoffrey D.; Dowling, N. Maritza

2009-01-01

In this article, we report kindergarten student and teacher outcomes from a quasi-experimental evaluation of The Superkids, a systematic, phonics-based, comprehensive K-2 reading program. We recruited 23 kindergarten teachers to implement The Superkids program from a diverse, yet predominantly ethnic minority, group of classrooms from across the…

Implementing Reading Strategies Based on Collaborative Learning Approach in an English Class

ERIC Educational Resources Information Center

Suwantharathip, Ornprapat

2015-01-01

The present study investigated the effects of reading strategies based on collaborative learning approach on students' reading comprehension and reading strategy use. The quasi-experimental research study was performed with two groups of students. While the control group was taught in the traditional way, the experimental group received reading…

Validity of Highlighting on Text Comprehension

NASA Astrophysics Data System (ADS)

So, Joey C. Y.; Chan, Alan H. S.

2009-10-01

In this study, 38 university students were tested with a Chinese reading task on an LED display under different task conditions for determining the effects of the highlighting and its validity on comprehension performance on light-emitting diodes (LED) display for Chinese reading. Four levels of validity (0%, 33%, 67% and 100%) and a control condition with no highlighting were tested. Each subject was required to perform the five experimental conditions in which different passages were read and comprehended. The results showed that the condition with 100% validity of highlighting was found to have better comprehension performance than other validity levels and conditions with no highlighting. The comprehension score of the condition without highlighting effect was comparatively lower than those highlighting conditions with distracters, though not significant.

Working Memory Training Does Not Improve Performance on Measures of Intelligence or Other Measures of “Far Transfer”

PubMed Central

Melby-Lervåg, Monica; Redick, Thomas S.; Hulme, Charles

2016-01-01

It has been claimed that working memory training programs produce diverse beneficial effects. This article presents a meta-analysis of working memory training studies (with a pretest-posttest design and a control group) that have examined transfer to other measures (nonverbal ability, verbal ability, word decoding, reading comprehension, or arithmetic; 87 publications with 145 experimental comparisons). Immediately following training there were reliable improvements on measures of intermediate transfer (verbal and visuospatial working memory). For measures of far transfer (nonverbal ability, verbal ability, word decoding, reading comprehension, arithmetic) there was no convincing evidence of any reliable improvements when working memory training was compared with a treated control condition. Furthermore, mediation analyses indicated that across studies, the degree of improvement on working memory measures was not related to the magnitude of far-transfer effects found. Finally, analysis of publication bias shows that there is no evidential value from the studies of working memory training using treated controls. The authors conclude that working memory training programs appear to produce short-term, specific training effects that do not generalize to measures of “real-world” cognitive skills. These results seriously question the practical and theoretical importance of current computerized working memory programs as methods of training working memory skills. PMID:27474138

Neural activity associated with metaphor comprehension: spatial analysis.

PubMed

Sotillo, María; Carretié, Luis; Hinojosa, José A; Tapia, Manuel; Mercado, Francisco; López-Martín, Sara; Albert, Jacobo

2005-01-03

Though neuropsychological data indicate that the right hemisphere (RH) plays a major role in metaphor processing, other studies suggest that, at least during some phases of this processing, a RH advantage may not exist. The present study explores, through a temporally agile neural signal--the event-related potentials (ERPs)--, and through source-localization algorithms applied to ERP recordings, whether the crucial phase of metaphor comprehension presents or not a RH advantage. Participants (n=24) were submitted to a S1-S2 experimental paradigm. S1 consisted of visually presented metaphoric sentences (e.g., "Green lung of the city"), followed by S2, which consisted of words that could (i.e., "Park") or could not (i.e., "Semaphore") be defined by S1. ERPs elicited by S2 were analyzed using temporal principal component analysis (tPCA) and source-localization algorithms. These analyses revealed that metaphorically related S2 words showed significantly higher N400 amplitudes than non-related S2 words. Source-localization algorithms showed differential activity between the two S2 conditions in the right middle/superior temporal areas. These results support the existence of an important RH contribution to (at least) one phase of metaphor processing and, furthermore, implicate the temporal cortex with respect to that contribution.

The humankind genome: from genetic diversity to the origin of human diseases.

PubMed

Belizário, Jose E

2013-12-01

Genome-wide association studies have failed to establish common variant risk for the majority of common human diseases. The underlying reasons for this failure are explained by recent studies of resequencing and comparison of over 1200 human genomes and 10 000 exomes, together with the delineation of DNA methylation patterns (epigenome) and full characterization of coding and noncoding RNAs (transcriptome) being transcribed. These studies have provided the most comprehensive catalogues of functional elements and genetic variants that are now available for global integrative analysis and experimental validation in prospective cohort studies. With these datasets, researchers will have unparalleled opportunities for the alignment, mining, and testing of hypotheses for the roles of specific genetic variants, including copy number variations, single nucleotide polymorphisms, and indels as the cause of specific phenotypes and diseases. Through the use of next-generation sequencing technologies for genotyping and standardized ontological annotation to systematically analyze the effects of genomic variation on humans and model organism phenotypes, we will be able to find candidate genes and new clues for disease's etiology and treatment. This article describes essential concepts in genetics and genomic technologies as well as the emerging computational framework to comprehensively search websites and platforms available for the analysis and interpretation of genomic data.

Consensus statement understanding health and malnutrition through a systems approach: the ENOUGH program for early life.

PubMed

Kaput, Jim; van Ommen, Ben; Kremer, Bas; Priami, Corrado; Monteiro, Jacqueline Pontes; Morine, Melissa; Pepping, Fre; Diaz, Zoey; Fenech, Michael; He, Yiwu; Albers, Ruud; Drevon, Christian A; Evelo, Chris T; Hancock, Robert E W; Ijsselmuiden, Carel; Lumey, L H; Minihane, Anne-Marie; Muller, Michael; Murgia, Chiara; Radonjic, Marijana; Sobral, Bruno; West, Keith P

2014-01-01

Nutrition research, like most biomedical disciplines, adopted and often uses experimental approaches based on Beadle and Tatum's one gene-one polypeptide hypothesis, thereby reducing biological processes to single reactions or pathways. Systems thinking is needed to understand the complexity of health and disease processes requiring measurements of physiological processes, as well as environmental and social factors, which may alter the expression of genetic information. Analysis of physiological processes with omics technologies to assess systems' responses has only become available over the past decade and remains costly. Studies of environmental and social conditions known to alter health are often not connected to biomedical research. While these facts are widely accepted, developing and conducting comprehensive research programs for health are often beyond financial and human resources of single research groups. We propose a new research program on essential nutrients for optimal underpinning of growth and health (ENOUGH) that will use systems approaches with more comprehensive measurements and biostatistical analysis of the many biological and environmental factors that influence undernutrition. Creating a knowledge base for nutrition and health is a necessary first step toward developing solutions targeted to different populations in diverse social and physical environments for the two billion undernourished people in developed and developing economies.

Big Data in HEP: A comprehensive use case study

NASA Astrophysics Data System (ADS)

Gutsche, Oliver; Cremonesi, Matteo; Elmer, Peter; Jayatilaka, Bo; Kowalkowski, Jim; Pivarski, Jim; Sehrish, Saba; Mantilla Surez, Cristina; Svyatkovskiy, Alexey; Tran, Nhan

2017-10-01

Experimental Particle Physics has been at the forefront of analyzing the worlds largest datasets for decades. The HEP community was the first to develop suitable software and computing tools for this task. In recent times, new toolkits and systems collectively called Big Data technologies have emerged to support the analysis of Petabyte and Exabyte datasets in industry. While the principles of data analysis in HEP have not changed (filtering and transforming experiment-specific data formats), these new technologies use different approaches and promise a fresh look at analysis of very large datasets and could potentially reduce the time-to-physics with increased interactivity. In this talk, we present an active LHC Run 2 analysis, searching for dark matter with the CMS detector, as a testbed for Big Data technologies. We directly compare the traditional NTuple-based analysis with an equivalent analysis using Apache Spark on the Hadoop ecosystem and beyond. In both cases, we start the analysis with the official experiment data formats and produce publication physics plots. We will discuss advantages and disadvantages of each approach and give an outlook on further studies needed.

GProX, a user-friendly platform for bioinformatics analysis and visualization of quantitative proteomics data.

PubMed

Rigbolt, Kristoffer T G; Vanselow, Jens T; Blagoev, Blagoy

2011-08-01

Recent technological advances have made it possible to identify and quantify thousands of proteins in a single proteomics experiment. As a result of these developments, the analysis of data has become the bottleneck of proteomics experiment. To provide the proteomics community with a user-friendly platform for comprehensive analysis, inspection and visualization of quantitative proteomics data we developed the Graphical Proteomics Data Explorer (GProX)(1). The program requires no special bioinformatics training, as all functions of GProX are accessible within its graphical user-friendly interface which will be intuitive to most users. Basic features facilitate the uncomplicated management and organization of large data sets and complex experimental setups as well as the inspection and graphical plotting of quantitative data. These are complemented by readily available high-level analysis options such as database querying, clustering based on abundance ratios, feature enrichment tests for e.g. GO terms and pathway analysis tools. A number of plotting options for visualization of quantitative proteomics data is available and most analysis functions in GProX create customizable high quality graphical displays in both vector and bitmap formats. The generic import requirements allow data originating from essentially all mass spectrometry platforms, quantitation strategies and software to be analyzed in the program. GProX represents a powerful approach to proteomics data analysis providing proteomics experimenters with a toolbox for bioinformatics analysis of quantitative proteomics data. The program is released as open-source and can be freely downloaded from the project webpage at http://gprox.sourceforge.net.

GProX, a User-Friendly Platform for Bioinformatics Analysis and Visualization of Quantitative Proteomics Data*

PubMed Central

Rigbolt, Kristoffer T. G.; Vanselow, Jens T.; Blagoev, Blagoy

2011-01-01

Recent technological advances have made it possible to identify and quantify thousands of proteins in a single proteomics experiment. As a result of these developments, the analysis of data has become the bottleneck of proteomics experiment. To provide the proteomics community with a user-friendly platform for comprehensive analysis, inspection and visualization of quantitative proteomics data we developed the Graphical Proteomics Data Explorer (GProX)1. The program requires no special bioinformatics training, as all functions of GProX are accessible within its graphical user-friendly interface which will be intuitive to most users. Basic features facilitate the uncomplicated management and organization of large data sets and complex experimental setups as well as the inspection and graphical plotting of quantitative data. These are complemented by readily available high-level analysis options such as database querying, clustering based on abundance ratios, feature enrichment tests for e.g. GO terms and pathway analysis tools. A number of plotting options for visualization of quantitative proteomics data is available and most analysis functions in GProX create customizable high quality graphical displays in both vector and bitmap formats. The generic import requirements allow data originating from essentially all mass spectrometry platforms, quantitation strategies and software to be analyzed in the program. GProX represents a powerful approach to proteomics data analysis providing proteomics experimenters with a toolbox for bioinformatics analysis of quantitative proteomics data. The program is released as open-source and can be freely downloaded from the project webpage at http://gprox.sourceforge.net. PMID:21602510

Studies on pyrolysis and gasification of automobile shredder residue in China.

PubMed

Ni, Feijian; Chen, Ming

2014-10-01

With increasing automobile ownerships in China, the number of end-of-life vehicles has also rapidly increased. However, the automobile shredder residue generated during the dismantling of end-of-life vehicles in China is not treated properly and has caused great resource waste and environmental problems. In this work, automobile shredder residue from a domestic end-of-life vehicles dismantling company was comprehensively studied through element analysis, combustion heat experiment, proximate analysis, and thermogravimetric analysis. The feasibility of using pyrolysis combined with gasification to treat and recycle automobile shredder residue was investigated. The produced gas, oil, and residue yield was measured and the correlation between their yield and the experimental temperature and ratio of air to automobile shredder residue feed was studied. It is found that when ratio of air and experimental temperature are 1.5 mol kg(-1) and 900 °C, respectively, the heat energy of the gas produced per kilogram treated automobile shredder residue reaches a maximum value of 11.28 MJ. The characteristics of pyrolysis oil and solid residue were studied. The solid residue takes up 4.65%~5.57% of the original end-of-life vehicles weight. This greatly helps to reach the target of a 95% recycling rate. © The Author(s) 2014.

Structural and vibrational spectroscopic analysis of anticancer drug mitotane using DFT method; a comparative study of its parent structure

NASA Astrophysics Data System (ADS)

Mariappan, G.; Sundaraganesan, N.

2015-04-01

A comprehensive screening of the density functional theoretical approach to structural analysis is presented in this section. DFT calculations using B3LYP/6-311++G(d,p) level of theory were found to yield results that are very comparable to experimental IR and Raman spectra. Computed geometrical parameters and harmonic vibrational wavenumbers of the fundamentals were found in satisfactory agreement with the experimental data and also its parent structure. The vibrational assignments of the normal modes were performed on the basis of the potential energy distribution (PED) calculations. It can be proven from the comparative results of mitotane and its parent structure Dichlorodiphenyldichloroethane (DDD), the intramolecular nonbonding interaction between (C1sbnd H19⋯Cl18) in the ortho position which is calculated 2.583 Å and the position of the substitution takeover the vibrational wavenumber to redshift of 47 cm-1. In addition, natural bond orbital (NBO) analysis has been performed for analyzing charge delocalization throughout the molecule. Stability of the molecule arising from hyperconjugative interactions leading to its bioactivity and charge delocalization has been analyzed. 13C and 1H nuclear magnetic resonance chemical shifts of the molecule have been calculated using the gauge independent atomic orbital (GIAO) method and compared with published results.

Two-Scale 13C Metabolic Flux Analysis for Metabolic Engineering.

PubMed

Ando, David; Garcia Martin, Hector

2018-01-01

Accelerating the Design-Build-Test-Learn (DBTL) cycle in synthetic biology is critical to achieving rapid and facile bioengineering of organisms for the production of, e.g., biofuels and other chemicals. The Learn phase involves using data obtained from the Test phase to inform the next Design phase. As part of the Learn phase, mathematical models of metabolic fluxes give a mechanistic level of comprehension to cellular metabolism, isolating the principle drivers of metabolic behavior from the peripheral ones, and directing future experimental designs and engineering methodologies. Furthermore, the measurement of intracellular metabolic fluxes is specifically noteworthy as providing a rapid and easy-to-understand picture of how carbon and energy flow throughout the cell. Here, we present a detailed guide to performing metabolic flux analysis in the Learn phase of the DBTL cycle, where we show how one can take the isotope labeling data from a 13 C labeling experiment and immediately turn it into a determination of cellular fluxes that points in the direction of genetic engineering strategies that will advance the metabolic engineering process.For our modeling purposes we use the Joint BioEnergy Institute (JBEI) Quantitative Metabolic Modeling (jQMM) library, which provides an open-source, python-based framework for modeling internal metabolic fluxes and making actionable predictions on how to modify cellular metabolism for specific bioengineering goals. It presents a complete toolbox for performing different types of flux analysis such as Flux Balance Analysis, 13 C Metabolic Flux Analysis, and it introduces the capability to use 13 C labeling experimental data to constrain comprehensive genome-scale models through a technique called two-scale 13 C Metabolic Flux Analysis (2S- 13 C MFA) [1]. In addition to several other capabilities, the jQMM is also able to predict the effects of knockouts using the MoMA and ROOM methodologies. The use of the jQMM library is illustrated through a step-by-step demonstration, which is also contained in a digital Jupyter Notebook format that enhances reproducibility and provides the capability to be adopted to the user's specific needs. As an open-source software project, users can modify and extend the code base and make improvements at will, providing a base for future modeling efforts.

Impact of comprehensive two-dimensional gas chromatography with mass spectrometry on food analysis.

PubMed

Tranchida, Peter Q; Purcaro, Giorgia; Maimone, Mariarosa; Mondello, Luigi

2016-01-01

Comprehensive two-dimensional gas chromatography with mass spectrometry has been on the separation-science scene for about 15 years. This three-dimensional method has made a great positive impact on various fields of research, and among these that related to food analysis is certainly at the forefront. The present critical review is based on the use of comprehensive two-dimensional gas chromatography with mass spectrometry in the untargeted (general qualitative profiling and fingerprinting) and targeted analysis of food volatiles; attention is focused not only on its potential in such applications, but also on how recent advances in comprehensive two-dimensional gas chromatography with mass spectrometry will potentially be important for food analysis. Additionally, emphasis is devoted to the many instances in which straightforward gas chromatography with mass spectrometry is a sufficiently-powerful analytical tool. Finally, possible future scenarios in the comprehensive two-dimensional gas chromatography with mass spectrometry food analysis field are discussed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity.

PubMed

Papaleo, Elena

2015-01-01

In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations.

Instruction of Research-Based Comprehension Strategies in Basal Reading Programs

ERIC Educational Resources Information Center

Pilonieta, Paola

2010-01-01

Research supports using research-based comprehension strategies; however, comprehension strategy instruction is not highly visible in basal reading programs or classroom instruction, resulting in many students who struggle with comprehension. A content analysis examined which research-based comprehension strategies were presented in five…

Comprehensive rotorcraft analysis methods

NASA Technical Reports Server (NTRS)

Stephens, Wendell B.; Austin, Edward E.

1988-01-01

The development and application of comprehensive rotorcraft analysis methods in the field of rotorcraft technology are described. These large scale analyses and the resulting computer programs are intended to treat the complex aeromechanical phenomena that describe the behavior of rotorcraft. They may be used to predict rotor aerodynamics, acoustic, performance, stability and control, handling qualities, loads and vibrations, structures, dynamics, and aeroelastic stability characteristics for a variety of applications including research, preliminary and detail design, and evaluation and treatment of field problems. The principal comprehensive methods developed or under development in recent years and generally available to the rotorcraft community because of US Army Aviation Research and Technology Activity (ARTA) sponsorship of all or part of the software systems are the Rotorcraft Flight Simulation (C81), Dynamic System Coupler (DYSCO), Coupled Rotor/Airframe Vibration Analysis Program (SIMVIB), Comprehensive Analytical Model of Rotorcraft Aerodynamics and Dynamics (CAMRAD), General Rotorcraft Aeromechanical Stability Program (GRASP), and Second Generation Comprehensive Helicopter Analysis System (2GCHAS).

Fixed Route Comprehensive Operational Analysis, 1994 Operating Year. Fourth Installment Route 3: Mill Ridge/Mill Plain Analysis

DOT National Transportation Integrated Search

1995-05-01

In October, of 1992, the Housatonic Area Regional Transit (HART) District published a planning study providing an in-depth analysis of its fixed route bus transit service. This comprehensive operational analysis (COA) was the first detailed analysis ...

Fixed Route Comprehensive Operational Analysis, 1994 Operating Year. First Installment, Route 1: Medical Center/Golden Hill Analysis

DOT National Transportation Integrated Search

1994-07-01

In October, of 1992, the Housatonic Area Regional Transit (HART) District published a planning study providing an in-depth analysis of its fixed route bus transit service. This comprehensive operational analysis (COA) was the first detailed analysis ...

Fixed Route Comprehensive Operational Analysis, 1994 Operating Year. Third Installment, Route 6: Lake Avenue/Danbury Fair Mall Analysis

DOT National Transportation Integrated Search

1995-02-01

In October, of 1992, the Housatonic Area Regional Transit (HART) District published a planning study providing an in-depth analysis of its fixed route bus transit service. This comprehensive operational analysis (COA) was the first detailed analysis ...

The noncavitating performance and life of a small vane-type positive displacement pump in liquid hydrogen

NASA Technical Reports Server (NTRS)

Ulbricht, T. E.; Hemminger, J. A.

1986-01-01

The low flow rate and high head rise requirements of hydrogen/oxygen auxiliary propulsion systems make the application of centrifugal pumps difficult. Positive displacement pumps are well-suited for these flow conditions, but little is known about their performance and life characteristics in liquid hydrogen. An experimental and analytical investigation was conducted to determine the performance and life characteristics of a vane-type, positive displacement pump. In the experimental part of this effort, mass flow rate and shaft torque were determined as functions of shaft speed and pump pressure rise. Since liquid hydrogen offers little lubrication in a rubbing situation, pump life is an issue. During the life test, the pump was operated intermittently for 10 hr at the steady-state point of 0.074 lbm/sec (0.03 kg/sec) flow rate, 3000 psid (2.07 MPa) pressure rise, and 8000 rpm (838 rad/sec) shaft speed. Pump performance was monitored during the life test series and the results indicated no loss in performance. Material loss from the vanes was recorded and wear of the other components was documented. In the analytical part of this effort, a comprehensive pump performance analysis computer code, developed in-house, was used to predict pump performance. The results of the experimental investigation are presented and compared with the results of the analysis. Results of the life test are also presented.

A novel approach to the analysis of squeezed-film air damping in microelectromechanical systems

NASA Astrophysics Data System (ADS)

Yang, Weilin; Li, Hongxia; Chatterjee, Aveek N.; Elfadel, Ibrahim (Abe M.; Ender Ocak, Ilker; Zhang, TieJun

2017-01-01

Squeezed-film damping (SFD) is a phenomenon that significantly affects the performance of micro-electro-mechanical systems (MEMS). The total damping force in MEMS mainly include the viscous damping force and elastic damping force. Quality factor (Q factor) is usually used to evaluate the damping in MEMS. In this work, we measure the Q factor of a resonator through experiments in a wide range of pressure levels. In fact, experimental characterizations of MEMS have some limitations because it is difficult to conduct experiments at very high vacuum and also hard to differentiate the damping mechanisms from the overall Q factor measurements. On the other hand, classical theoretical analysis of SFD is restricted to strong assumptions and simple geometries. In this paper, a novel numerical approach, which is based on lattice Boltzmann simulations, is proposed to investigate SFD in MEMS. Our method considers the dynamics of squeezed air flow as well as fluid-solid interactions in MEMS. It is demonstrated that Q factor can be directly predicted by numerical simulation, and our simulation results agree well with experimental data. Factors that influence SFD, such as pressure, oscillating amplitude, and driving frequency, are investigated separately. Furthermore, viscous damping and elastic damping forces are quantitatively compared based on comprehensive simulation. The proposed numerical approach as well as experimental characterization enables us to reveal the insightful physics of squeezed-film air damping in MEMS.

Study/Experimental/Research Design: Much More Than Statistics

PubMed Central

Knight, Kenneth L.

2010-01-01

Abstract Context: The purpose of study, experimental, or research design in scientific manuscripts has changed significantly over the years. It has evolved from an explanation of the design of the experiment (ie, data gathering or acquisition) to an explanation of the statistical analysis. This practice makes “Methods” sections hard to read and understand. Objective: To clarify the difference between study design and statistical analysis, to show the advantages of a properly written study design on article comprehension, and to encourage authors to correctly describe study designs. Description: The role of study design is explored from the introduction of the concept by Fisher through modern-day scientists and the AMA Manual of Style. At one time, when experiments were simpler, the study design and statistical design were identical or very similar. With the complex research that is common today, which often includes manipulating variables to create new variables and the multiple (and different) analyses of a single data set, data collection is very different than statistical design. Thus, both a study design and a statistical design are necessary. Advantages: Scientific manuscripts will be much easier to read and comprehend. A proper experimental design serves as a road map to the study methods, helping readers to understand more clearly how the data were obtained and, therefore, assisting them in properly analyzing the results. PMID:20064054

LOX/LH2 vane pump for auxiliary propulsion systems

NASA Technical Reports Server (NTRS)

Hemminger, J. A.; Ulbricht, T. E.

1985-01-01

Positive displacement pumps offer potential efficiency advantages over centrifugal pumps for future low thrust space missions. Low flow rate applications, such as space station auxiliary propulsion or dedicated low thrust orbiter transfer vehicles, are typical of missions where low flow and high head rise challenge centrifugal pumps. The positive displacement vane pump for pumping of LOX and LH2 is investigated. This effort has included: (1) a testing program in which pump performance was investigated for differing pump clearances and for differing pump materials while pumping LN2, LOX, and LH2; and (2) an analysis effort, in which a comprehensive pump performance analysis computer code was developed and exercised. An overview of the theoretical framework of the performance analysis computer code is presented, along with a summary of analysis results. Experimental results are presented for pump operating in liquid nitrogen. Included are data on the effects on pump performance of pump clearance, speed, and pressure rise. Pump suction performance is also presented.

Quantitative Analysis of the Efficiency of OLEDs.

PubMed

Sim, Bomi; Moon, Chang-Ki; Kim, Kwon-Hyeon; Kim, Jang-Joo

2016-12-07

We present a comprehensive model for the quantitative analysis of factors influencing the efficiency of organic light-emitting diodes (OLEDs) as a function of the current density. The model takes into account the contribution made by the charge carrier imbalance, quenching processes, and optical design loss of the device arising from various optical effects including the cavity structure, location and profile of the excitons, effective radiative quantum efficiency, and out-coupling efficiency. Quantitative analysis of the efficiency can be performed with an optical simulation using material parameters and experimental measurements of the exciton profile in the emission layer and the lifetime of the exciton as a function of the current density. This method was applied to three phosphorescent OLEDs based on a single host, mixed host, and exciplex-forming cohost. The three factors (charge carrier imbalance, quenching processes, and optical design loss) were influential in different ways, depending on the device. The proposed model can potentially be used to optimize OLED configurations on the basis of an analysis of the underlying physical processes.

Comprehensive machine learning analysis of Hydra behavior reveals a stable basal behavioral repertoire.

PubMed

Han, Shuting; Taralova, Ekaterina; Dupre, Christophe; Yuste, Rafael

2018-03-28

Animal behavior has been studied for centuries, but few efficient methods are available to automatically identify and classify it. Quantitative behavioral studies have been hindered by the subjective and imprecise nature of human observation, and the slow speed of annotating behavioral data. Here, we developed an automatic behavior analysis pipeline for the cnidarian Hydra vulgaris using machine learning. We imaged freely behaving Hydra , extracted motion and shape features from the videos, and constructed a dictionary of visual features to classify pre-defined behaviors. We also identified unannotated behaviors with unsupervised methods. Using this analysis pipeline, we quantified 6 basic behaviors and found surprisingly similar behavior statistics across animals within the same species, regardless of experimental conditions. Our analysis indicates that the fundamental behavioral repertoire of Hydra is stable. This robustness could reflect a homeostatic neural control of "housekeeping" behaviors which could have been already present in the earliest nervous systems. © 2018, Han et al.

Opto-electronic characterization of third-generation solar cells.

PubMed

Neukom, Martin; Züfle, Simon; Jenatsch, Sandra; Ruhstaller, Beat

2018-01-01

We present an overview of opto-electronic characterization techniques for solar cells including light-induced charge extraction by linearly increasing voltage, impedance spectroscopy, transient photovoltage, charge extraction and more. Guidelines for the interpretation of experimental results are derived based on charge drift-diffusion simulations of solar cells with common performance limitations. It is investigated how nonidealities like charge injection barriers, traps and low mobilities among others manifest themselves in each of the studied cell characterization techniques. Moreover, comprehensive parameter extraction for an organic bulk-heterojunction solar cell comprising PCDTBT:PC 70 BM is demonstrated. The simulations reproduce measured results of 9 different experimental techniques. Parameter correlation is minimized due to the combination of various techniques. Thereby a route to comprehensive and accurate parameter extraction is identified.

[Improving the teaching quality by multiple tools and technology in oral histopathology experimental course].

PubMed

Tian, Zhen; Wang, Li-Zhen; Hu, Yu-Hua; Zhang, Chun-Ye; Li, Jiang

2017-04-01

Oral histopathology is a course which needs to be combined with theory and practice closely. Experimental course plays an important role in teaching oral histopathology. Here, we aim to explore a series of effective measures to improve the teaching quality of experimental course and tried to train observation, thinking, analysis and problem solving skills of dental students. We re-edited and updated the experimental textbook "guidelines of experimental course of oral histopathology", and published the reference book for experimental course--"color pocket atlas of oral histopathology: experiment and diadactic teaching". The number of clinicopathological cases for presentation and class discussion was increased, and high-quality teaching slides were added and replaced the poor-quality or worn out slides. We established a variety of teaching methods based on the internet, which provided an environment of self-directed learning for dental students. Instead of simple slice-reading examination, a new evaluation system based on computer was established. The questionnaire survey showed that the students spoke positively on the teaching reform for experimental course. They thought that the reform played a significant role in enriching the teaching content, motivating learning interest and promoting self-study. Compared with traditional examination, computer-based examination showed a great advantage on mastering professional knowledge systematically and comprehensively. The measures adopted in our teaching reform not only effectively improve the teaching quality of experimental course of oral histopathology, but also help the students to have a clear, logical thinking when facing complicated diseases and have the ability to apply theoretical knowledge into clinical practice.

Curriculum system for experimental teaching in optoelectronic information

NASA Astrophysics Data System (ADS)

Di, Hongwei; Chen, Zhenqiang; Zhang, Jun; Luo, Yunhan

2017-08-01

The experimental curriculum system is directly related to talent training quality. Based on the careful investigation of the developing request of the optoelectronic information talents in the new century, the experimental teaching goal and the content, the teaching goal was set to cultivate students' innovative consciousness, innovative thinking, creativity and problem solving ability. Through straightening out the correlation among the experimental teaching in the main courses, the whole structure design was phased out, as well as the hierarchical curriculum connotation. According to the ideas of "basic, comprehensive, applied and innovative", the construction of experimental teaching system called "triple-three" was put forward for the optoelectronic information experimental teaching practice.

Joint Sparse Representation for Robust Multimodal Biometrics Recognition

DTIC Science & Technology

2012-01-01

described in III. Experimental evaluations on a comprehensive multimodal dataset and a face database have been described in section V. Finally, in...WVU Multimodal Dataset The WVU multimodal dataset is a comprehensive collection of different biometric modalities such as fingerprint, iris, palmprint ...Martnez and R. Benavente, “The AR face database ,” CVC Technical Report, June 1998. [29] U. Park and A. Jain, “Face matching and retrieval using soft

Influence of Prior Knowledge and Interest on Fourth- and Fifth-Grade Passage Comprehension on the Qualitative Reading Inventory-4

ERIC Educational Resources Information Center

Clark, Mary Kristen; Kamhi, Alan G.

2014-01-01

Purpose: In 2 experiments, we examined the influence of prior knowledge and interest on 4th- and 5th-grade students' passage comprehension scores on the Qualitative Reading Inventory-4 (QRI-4) and 2 experimenter constructed passages. Method: In Experiment 1, 4th- and 5th-grade students were administered 4 Level 4 passages or 4 Level 5…

Comprehension of Elided Phrases in Korean and English: VP-Ellipsis, Null Object Constructions, and One-Substitution

ERIC Educational Resources Information Center

Kim, Jinsook

2012-01-01

The purpose of this study is to experimentally investigate the comprehension of elided phrases in Korean and English, focusing on the patterns exemplified below. (1) Korean a. VP-ellipsis: Sungki-ka phalan kabang-ul sa-ss-e-yo. Sunhuy-to-yey-yo Sungki-NOM blue bag-ACC buy-PST-DECL-POL Sunhuy-also-be-POL "Sungki bought a blue bag. Sunhuy did…

Reading Pictures for Story Comprehension Requires Mental Imagery Skills

PubMed Central

Boerma, Inouk E.; Mol, Suzanne E.; Jolles, Jelle

2016-01-01

We examined the role of mental imagery skills on story comprehension in 150 fifth graders (10- to 12-year-olds), when reading a narrative book chapter with alternating words and pictures (i.e., text blocks were alternated by one- or two-page picture spreads). A parallel group design was used, in which we compared our experimental book version, in which pictures were used to replace parts of the corresponding text, to two control versions, i.e., a text-only version and a version with the full story text and all pictures. Analyses showed an interaction between mental imagery and book version: children with higher mental imagery skills outperformed children with lower mental imagery skills on story comprehension after reading the experimental narrative. This was not the case for both control conditions. This suggests that children’s mental imagery skills significantly contributed to the mental representation of the story that they created, by successfully integrating information from both words and pictures. The results emphasize the importance of mental imagery skills for explaining individual variability in reading development. Implications for educational practice are that we should find effective ways to instruct children how to “read” pictures and how to develop and use their mental imagery skills. This will probably contribute to their mental models and therefore their story comprehension. PMID:27822194

A Comprehensive Mixture of Tobacco Smoke Components Retards Orthodontic Tooth Movement via the Inhibition of Osteoclastogenesis in a Rat Model

PubMed Central

Nagaie, Maya; Nishiura, Aki; Honda, Yoshitomo; Fujiwara, Shin-Ichi; Matsumoto, Naoyuki

2014-01-01

Tobacco smoke is a complex mixture of numerous components. Nevertheless, most experiments have examined the effects of individual chemicals in tobacco smoke. The comprehensive effects of components on tooth movement and bone resorption remain unexplored. Here, we have shown that a comprehensive mixture of tobacco smoke components (TSCs) attenuated bone resorption through osteoclastogenesis inhibition, thereby retarding experimental tooth movement in a rat model. An elastic power chain (PC) inserted between the first and second maxillary molars robustly yielded experimental tooth movement within 10 days. TSC administration effectively retarded tooth movement since day 4. Histological evaluation disclosed that tooth movement induced bone resorption at two sites: in the bone marrow and the peripheral bone near the root. TSC administration significantly reduced the number of tartrate-resistant acid phosphatase (TRAP)-positive osteoclastic cells in the bone marrow cavity of the PC-treated dentition. An in vitro study indicated that the inhibitory effects of TSCs on osteoclastogenesis seemed directed more toward preosteoclasts than osteoblasts. These results indicate that the comprehensive mixture of TSCs might be a useful tool for detailed verification of the adverse effects of tobacco smoke, possibly contributing to the development of reliable treatments in various fields associated with bone resorption. PMID:25322153

Influence of text type, topic familiarity, and stuttering frequency on listener recall, comprehension, and mental effort.

PubMed

Panico, James; Healey, E Charles

2009-04-01

To determine how text type, topic familiarity, and stuttering frequency influence listener recall, comprehension, and perceived mental effort. Sixty adults listened to familiar and unfamiliar narrative and expository texts produced with 0%, 5%, 10%, and 15% stuttering. Participants listened to 4 experimental text samples at only 1 stuttering frequency. After hearing the text samples, each listener performed a free recall task, answered cued recall questions, answered story comprehension questions, and rated their perceived mental effort. Free and cued recall as well as story comprehension scores were higher for narrative than for expository texts. Free and cued recall scores were better for familiar than for unfamiliar stories, although topic familiarity did not affect story comprehension scores. Samples with all levels of stuttering resulted in higher mental effort ratings for both text types and topic familiarities. Stuttering has a greater influence on listener recall and comprehension for narrative than for expository texts. Topic familiarity affects free and cued recall but has no influence on story comprehension. Regardless of the amount of stuttering, mental effort was high for both text types and levels of familiarity.

Why does working memory capacity predict variation in reading comprehension? On the influence of mind wandering and executive attention.

PubMed

McVay, Jennifer C; Kane, Michael J

2012-05-01

Some people are better readers than others, and this variation in comprehension ability is predicted by measures of working memory capacity (WMC). The primary goal of this study was to investigate the mediating role of mind-wandering experiences in the association between WMC and normal individual differences in reading comprehension, as predicted by the executive-attention theory of WMC (e.g., Engle & Kane, 2004). We used a latent-variable, structural-equation-model approach, testing skilled adult readers on 3 WMC span tasks, 7 varied reading-comprehension tasks, and 3 attention-control tasks. Mind wandering was assessed using experimenter-scheduled thought probes during 4 different tasks (2 reading, 2 attention-control). The results support the executive-attention theory of WMC. Mind wandering across the 4 tasks loaded onto a single latent factor, reflecting a stable individual difference. Most important, mind wandering was a significant mediator in the relationship between WMC and reading comprehension, suggesting that the WMC-comprehension correlation is driven, in part, by attention control over intruding thoughts. We discuss implications for theories of WMC, attention control, and reading comprehension.

Revealing and Quantifying the Impaired Phonological Analysis Underpinning Impaired Comprehension in Wernicke's Aphasia

ERIC Educational Resources Information Center

Robson, Holly; Keidel, James L.; Lambon Ralph, Matthew A.; Sage, Karen

2012-01-01

Wernicke's aphasia is a condition which results in severely disrupted language comprehension following a lesion to the left temporo-parietal region. A phonological analysis deficit has traditionally been held to be at the root of the comprehension impairment in Wernicke's aphasia, a view consistent with current functional neuroimaging which finds…

PHENOPSIS DB: an Information System for Arabidopsis thaliana phenotypic data in an environmental context

PubMed Central

2011-01-01

Background Renewed interest in plant × environment interactions has risen in the post-genomic era. In this context, high-throughput phenotyping platforms have been developed to create reproducible environmental scenarios in which the phenotypic responses of multiple genotypes can be analysed in a reproducible way. These platforms benefit hugely from the development of suitable databases for storage, sharing and analysis of the large amount of data collected. In the model plant Arabidopsis thaliana, most databases available to the scientific community contain data related to genetic and molecular biology and are characterised by an inadequacy in the description of plant developmental stages and experimental metadata such as environmental conditions. Our goal was to develop a comprehensive information system for sharing of the data collected in PHENOPSIS, an automated platform for Arabidopsis thaliana phenotyping, with the scientific community. Description PHENOPSIS DB is a publicly available (URL: http://bioweb.supagro.inra.fr/phenopsis/) information system developed for storage, browsing and sharing of online data generated by the PHENOPSIS platform and offline data collected by experimenters and experimental metadata. It provides modules coupled to a Web interface for (i) the visualisation of environmental data of an experiment, (ii) the visualisation and statistical analysis of phenotypic data, and (iii) the analysis of Arabidopsis thaliana plant images. Conclusions Firstly, data stored in the PHENOPSIS DB are of interest to the Arabidopsis thaliana community, particularly in allowing phenotypic meta-analyses directly linked to environmental conditions on which publications are still scarce. Secondly, data or image analysis modules can be downloaded from the Web interface for direct usage or as the basis for modifications according to new requirements. Finally, the structure of PHENOPSIS DB provides a useful template for the development of other similar databases related to genotype × environment interactions. PMID:21554668

Analysis of l-glutamic acid fermentation by using a dynamic metabolic simulation model of Escherichia coli

PubMed Central

2013-01-01

Background Understanding the process of amino acid fermentation as a comprehensive system is a challenging task. Previously, we developed a literature-based dynamic simulation model, which included transcriptional regulation, transcription, translation, and enzymatic reactions related to glycolysis, the pentose phosphate pathway, the tricarboxylic acid (TCA) cycle, and the anaplerotic pathway of Escherichia coli. During simulation, cell growth was defined such as to reproduce the experimental cell growth profile of fed-batch cultivation in jar fermenters. However, to confirm the biological appropriateness of our model, sensitivity analysis and experimental validation were required. Results We constructed an l-glutamic acid fermentation simulation model by removing sucAB, a gene encoding α-ketoglutarate dehydrogenase. We then performed systematic sensitivity analysis for l-glutamic acid production; the results of this process corresponded with previous experimental data regarding l-glutamic acid fermentation. Furthermore, it allowed us to predicted the possibility that accumulation of 3-phosphoglycerate in the cell would regulate the carbon flux into the TCA cycle and lead to an increase in the yield of l-glutamic acid via fermentation. We validated this hypothesis through a fermentation experiment involving a model l-glutamic acid-production strain, E. coli MG1655 ΔsucA in which the phosphoglycerate kinase gene had been amplified to cause accumulation of 3-phosphoglycerate. The observed increase in l-glutamic acid production verified the biologically meaningful predictive power of our dynamic metabolic simulation model. Conclusions In this study, dynamic simulation using a literature-based model was shown to be useful for elucidating the precise mechanisms involved in fermentation processes inside the cell. Further exhaustive sensitivity analysis will facilitate identification of novel factors involved in the metabolic regulation of amino acid fermentation. PMID:24053676

Analysis of L-glutamic acid fermentation by using a dynamic metabolic simulation model of Escherichia coli.

PubMed

Nishio, Yousuke; Ogishima, Soichi; Ichikawa, Masao; Yamada, Yohei; Usuda, Yoshihiro; Masuda, Tadashi; Tanaka, Hiroshi

2013-09-22

Understanding the process of amino acid fermentation as a comprehensive system is a challenging task. Previously, we developed a literature-based dynamic simulation model, which included transcriptional regulation, transcription, translation, and enzymatic reactions related to glycolysis, the pentose phosphate pathway, the tricarboxylic acid (TCA) cycle, and the anaplerotic pathway of Escherichia coli. During simulation, cell growth was defined such as to reproduce the experimental cell growth profile of fed-batch cultivation in jar fermenters. However, to confirm the biological appropriateness of our model, sensitivity analysis and experimental validation were required. We constructed an L-glutamic acid fermentation simulation model by removing sucAB, a gene encoding α-ketoglutarate dehydrogenase. We then performed systematic sensitivity analysis for L-glutamic acid production; the results of this process corresponded with previous experimental data regarding L-glutamic acid fermentation. Furthermore, it allowed us to predicted the possibility that accumulation of 3-phosphoglycerate in the cell would regulate the carbon flux into the TCA cycle and lead to an increase in the yield of L-glutamic acid via fermentation. We validated this hypothesis through a fermentation experiment involving a model L-glutamic acid-production strain, E. coli MG1655 ΔsucA in which the phosphoglycerate kinase gene had been amplified to cause accumulation of 3-phosphoglycerate. The observed increase in L-glutamic acid production verified the biologically meaningful predictive power of our dynamic metabolic simulation model. In this study, dynamic simulation using a literature-based model was shown to be useful for elucidating the precise mechanisms involved in fermentation processes inside the cell. Further exhaustive sensitivity analysis will facilitate identification of novel factors involved in the metabolic regulation of amino acid fermentation.

Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights

PubMed Central

2011-01-01

Background Transcription factors (TFs) play a central role in regulating gene expression by interacting with cis-regulatory DNA elements associated with their target genes. Recent surveys have examined the DNA binding specificities of most Saccharomyces cerevisiae TFs, but a comprehensive evaluation of their data has been lacking. Results We analyzed in vitro and in vivo TF-DNA binding data reported in previous large-scale studies to generate a comprehensive, curated resource of DNA binding specificity data for all characterized S. cerevisiae TFs. Our collection comprises DNA binding site motifs and comprehensive in vitro DNA binding specificity data for all possible 8-bp sequences. Investigation of the DNA binding specificities within the basic leucine zipper (bZIP) and VHT1 regulator (VHR) TF families revealed unexpected plasticity in TF-DNA recognition: intriguingly, the VHR TFs, newly characterized by protein binding microarrays in this study, recognize bZIP-like DNA motifs, while the bZIP TF Hac1 recognizes a motif highly similar to the canonical E-box motif of basic helix-loop-helix (bHLH) TFs. We identified several TFs with distinct primary and secondary motifs, which might be associated with different regulatory functions. Finally, integrated analysis of in vivo TF binding data with protein binding microarray data lends further support for indirect DNA binding in vivo by sequence-specific TFs. Conclusions The comprehensive data in this curated collection allow for more accurate analyses of regulatory TF-DNA interactions, in-depth structural studies of TF-DNA specificity determinants, and future experimental investigations of the TFs' predicted target genes and regulatory roles. PMID:22189060

Revealing and quantifying the impaired phonological analysis underpinning impaired comprehension in Wernicke's aphasia.

PubMed

Robson, Holly; Keidel, James L; Ralph, Matthew A Lambon; Sage, Karen

2012-01-01

Wernicke's aphasia is a condition which results in severely disrupted language comprehension following a lesion to the left temporo-parietal region. A phonological analysis deficit has traditionally been held to be at the root of the comprehension impairment in Wernicke's aphasia, a view consistent with current functional neuroimaging which finds areas in the superior temporal cortex responsive to phonological stimuli. However behavioural evidence to support the link between a phonological analysis deficit and auditory comprehension has not been yet shown. This study extends seminal work by Blumstein, Baker, and Goodglass (1977) to investigate the relationship between acoustic-phonological perception, measured through phonological discrimination, and auditory comprehension in a case series of Wernicke's aphasia participants. A novel adaptive phonological discrimination task was used to obtain reliable thresholds of the phonological perceptual distance required between nonwords before they could be discriminated. Wernicke's aphasia participants showed significantly elevated thresholds compared to age and hearing matched control participants. Acoustic-phonological thresholds correlated strongly with auditory comprehension abilities in Wernicke's aphasia. In contrast, nonverbal semantic skills showed no relationship with auditory comprehension. The results are evaluated in the context of recent neurobiological models of language and suggest that impaired acoustic-phonological perception underlies the comprehension impairment in Wernicke's aphasia and favour models of language which propose a leftward asymmetry in phonological analysis. Copyright © 2011 Elsevier Ltd. All rights reserved.

Microarray R-based analysis of complex lysate experiments with MIRACLE

PubMed Central

List, Markus; Block, Ines; Pedersen, Marlene Lemvig; Christiansen, Helle; Schmidt, Steffen; Thomassen, Mads; Tan, Qihua; Baumbach, Jan; Mollenhauer, Jan

2014-01-01

Motivation: Reverse-phase protein arrays (RPPAs) allow sensitive quantification of relative protein abundance in thousands of samples in parallel. Typical challenges involved in this technology are antibody selection, sample preparation and optimization of staining conditions. The issue of combining effective sample management and data analysis, however, has been widely neglected. Results: This motivated us to develop MIRACLE, a comprehensive and user-friendly web application bridging the gap between spotting and array analysis by conveniently keeping track of sample information. Data processing includes correction of staining bias, estimation of protein concentration from response curves, normalization for total protein amount per sample and statistical evaluation. Established analysis methods have been integrated with MIRACLE, offering experimental scientists an end-to-end solution for sample management and for carrying out data analysis. In addition, experienced users have the possibility to export data to R for more complex analyses. MIRACLE thus has the potential to further spread utilization of RPPAs as an emerging technology for high-throughput protein analysis. Availability: Project URL: http://www.nanocan.org/miracle/ Contact: mlist@health.sdu.dk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25161257

Microarray R-based analysis of complex lysate experiments with MIRACLE.

PubMed

List, Markus; Block, Ines; Pedersen, Marlene Lemvig; Christiansen, Helle; Schmidt, Steffen; Thomassen, Mads; Tan, Qihua; Baumbach, Jan; Mollenhauer, Jan

2014-09-01

Reverse-phase protein arrays (RPPAs) allow sensitive quantification of relative protein abundance in thousands of samples in parallel. Typical challenges involved in this technology are antibody selection, sample preparation and optimization of staining conditions. The issue of combining effective sample management and data analysis, however, has been widely neglected. This motivated us to develop MIRACLE, a comprehensive and user-friendly web application bridging the gap between spotting and array analysis by conveniently keeping track of sample information. Data processing includes correction of staining bias, estimation of protein concentration from response curves, normalization for total protein amount per sample and statistical evaluation. Established analysis methods have been integrated with MIRACLE, offering experimental scientists an end-to-end solution for sample management and for carrying out data analysis. In addition, experienced users have the possibility to export data to R for more complex analyses. MIRACLE thus has the potential to further spread utilization of RPPAs as an emerging technology for high-throughput protein analysis. Project URL: http://www.nanocan.org/miracle/. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Advanced Stoichiometric Analysis of Metabolic Networks of Mammalian Systems

PubMed Central

Orman, Mehmet A.; Berthiaume, Francois; Androulakis, Ioannis P.; Ierapetritou, Marianthi G.

2013-01-01

Metabolic engineering tools have been widely applied to living organisms to gain a comprehensive understanding about cellular networks and to improve cellular properties. Metabolic flux analysis (MFA), flux balance analysis (FBA), and metabolic pathway analysis (MPA) are among the most popular tools in stoichiometric network analysis. Although application of these tools into well-known microbial systems is extensive in the literature, various barriers prevent them from being utilized in mammalian cells. Limited experimental data, complex regulatory mechanisms, and the requirement of more complex nutrient media are some major obstacles in mammalian cell systems. However, mammalian cells have been used to produce therapeutic proteins, to characterize disease states or related abnormal metabolic conditions, and to analyze the toxicological effects of some medicinally important drugs. Therefore, there is a growing need for extending metabolic engineering principles to mammalian cells in order to understand their underlying metabolic functions. In this review article, advanced metabolic engineering tools developed for stoichiometric analysis including MFA, FBA, and MPA are described. Applications of these tools in mammalian cells are discussed in detail, and the challenges and opportunities are highlighted. PMID:22196224

Instructional Strategies for Enhancing Learning Disabled Students' Reading Comprehension and Comprehension Test Performance.

ERIC Educational Resources Information Center

Wong, Bernice Y. L.

1986-01-01

Successful instructional strategies for enhancing the reading comprehension and comprehension test performance of learning disabled students are described. Students are taught to self-monitor their comprehension of expository materials and stories through recognition and analysis of recurrent elements and problem passages, content summarization,…

High-throughput protein analysis integrating bioinformatics and experimental assays

PubMed Central

del Val, Coral; Mehrle, Alexander; Falkenhahn, Mechthild; Seiler, Markus; Glatting, Karl-Heinz; Poustka, Annemarie; Suhai, Sandor; Wiemann, Stefan

2004-01-01

The wealth of transcript information that has been made publicly available in recent years requires the development of high-throughput functional genomics and proteomics approaches for its analysis. Such approaches need suitable data integration procedures and a high level of automation in order to gain maximum benefit from the results generated. We have designed an automatic pipeline to analyse annotated open reading frames (ORFs) stemming from full-length cDNAs produced mainly by the German cDNA Consortium. The ORFs are cloned into expression vectors for use in large-scale assays such as the determination of subcellular protein localization or kinase reaction specificity. Additionally, all identified ORFs undergo exhaustive bioinformatic analysis such as similarity searches, protein domain architecture determination and prediction of physicochemical characteristics and secondary structure, using a wide variety of bioinformatic methods in combination with the most up-to-date public databases (e.g. PRINTS, BLOCKS, INTERPRO, PROSITE SWISSPROT). Data from experimental results and from the bioinformatic analysis are integrated and stored in a relational database (MS SQL-Server), which makes it possible for researchers to find answers to biological questions easily, thereby speeding up the selection of targets for further analysis. The designed pipeline constitutes a new automatic approach to obtaining and administrating relevant biological data from high-throughput investigations of cDNAs in order to systematically identify and characterize novel genes, as well as to comprehensively describe the function of the encoded proteins. PMID:14762202

Experimental Evaluation of the Value Added by Raising a Reader and Supplemental Parent Training in Shared Reading

ERIC Educational Resources Information Center

Anthony, Jason L.; Williams, Jeffrey M.; Zhang, Zhoe; Landry, Susan H.; Dunkelberger, Martha J.

2014-01-01

Research Findings: In an effort toward developing a comprehensive, effective, scalable, and sustainable early childhood education program for at-risk populations, we conducted an experimental evaluation of the value added by 2 family involvement programs to the Texas Early Education Model (TEEM). A total of 91 preschool classrooms that served…

Enhancing Foreign Language Learning through Listening Strategies Delivered in L1: An Experimental Study

ERIC Educational Resources Information Center

Bozorgian, Hossein; Pillay, Hitendra

2013-01-01

Listening used in language teaching refers to a complex process that allows us to understand spoken language. The current study, conducted in Iran with an experimental design, investigated the effectiveness of teaching listening strategies delivered in L1 (Persian) and its effect on listening comprehension in L2. Five listening strategies:…

Reading Interventions for the Improvements of the Reading Performances of Bilingual and Bi-Dialectal Children

ERIC Educational Resources Information Center

Johnson, Afra Kaletta

2012-01-01

The purpose of this quasi-experimental study examines the effects of reading interventions for bi-lingual and bi-dialectal Broward County School District middle school children using research-based strategies combined with metacognitive and meta-comprehension frameworks. The experimental study reports findings on the effects of an 8-week…

Vascular flora and macroscopic fauna on the Fernow Experimental Forest

Treesearch

Darlene M. Madarish; Jane L. Rodrigue; Mary Beth Adams

2002-01-01

This report is the first comprehensive inventory of the vascular flora and macroscopic fauna known to occur within the Fernow Experimental Forest in north-central West Virignia. The compendium is based on information obtained from previous surveys, current research, and the personal observations of USDA Forest Service personnel and independent scientists. More than 750...

One-Tube-Only Standardized Site-Directed Mutagenesis: An Alternative Approach to Generate Amino Acid Substitution Collections

PubMed Central

Mingo, Janire; Erramuzpe, Asier; Luna, Sandra; Aurtenetxe, Olaia; Amo, Laura; Diez, Ibai; Schepens, Jan T. G.; Hendriks, Wiljan J. A. J.; Cortés, Jesús M.; Pulido, Rafael

2016-01-01

Site-directed mutagenesis (SDM) is a powerful tool to create defined collections of protein variants for experimental and clinical purposes, but effectiveness is compromised when a large number of mutations is required. We present here a one-tube-only standardized SDM approach that generates comprehensive collections of amino acid substitution variants, including scanning- and single site-multiple mutations. The approach combines unified mutagenic primer design with the mixing of multiple distinct primer pairs and/or plasmid templates to increase the yield of a single inverse-PCR mutagenesis reaction. Also, a user-friendly program for automatic design of standardized primers for Ala-scanning mutagenesis is made available. Experimental results were compared with a modeling approach together with stochastic simulation data. For single site-multiple mutagenesis purposes and for simultaneous mutagenesis in different plasmid backgrounds, combination of primer sets and/or plasmid templates in a single reaction tube yielded the distinct mutations in a stochastic fashion. For scanning mutagenesis, we found that a combination of overlapping primer sets in a single PCR reaction allowed the yield of different individual mutations, although this yield did not necessarily follow a stochastic trend. Double mutants were generated when the overlap of primer pairs was below 60%. Our results illustrate that one-tube-only SDM effectively reduces the number of reactions required in large-scale mutagenesis strategies, facilitating the generation of comprehensive collections of protein variants suitable for functional analysis. PMID:27548698

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

PubMed

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

2011-03-01

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

Numerical analysis of stress effects on Frank loop evolution during irradiation in austenitic Fe&z.sbnd;Cr&z.sbnd;Ni alloy

NASA Astrophysics Data System (ADS)

Tanigawa, Hiroyasu; Katoh, Yutai; Kohyama, Akira

1995-08-01

Effects of applied stress on early stages of interstitial type Frank loop evolution were investigated by both numerical calculation and irradiation experiments. The final objective of this research is to propose a comprehensive model of complex stress effects on microstructural evolution under various conditions. In the experimental part of this work, the microstructural analysis revealed that the differences in resolved normal stress caused those in the nucleation rates of Frank loops on {111} crystallographic family planes, and that with increasing external applied stress the total nucleation rate of Frank loops was increased. A numerical calculation was carried out primarily to evaluate the validity of models of stress effects on nucleation processes of Frank loop evolution. The calculation stands on rate equuations which describe evolution of point defects, small points defect clusters and Frank loops. The rate equations of Frank loop evolution were formulated for {111} planes, considering effects of resolved normal stress to clustering processes of small point defects and growth processes of Frank loops, separately. The experimental results and the predictions from the numerical calculation qualitatively coincided well with each other.

Uniform Sampling Table Method and its Applications II--Evaluating the Uniform Sampling by Experiment.

PubMed

Chen, Yibin; Chen, Jiaxi; Chen, Xuan; Wang, Min; Wang, Wei

2015-01-01

A new method of uniform sampling is evaluated in this paper. The items and indexes were adopted to evaluate the rationality of the uniform sampling. The evaluation items included convenience of operation, uniformity of sampling site distribution, and accuracy and precision of measured results. The evaluation indexes included operational complexity, occupation rate of sampling site in a row and column, relative accuracy of pill weight, and relative deviation of pill weight. They were obtained from three kinds of drugs with different shape and size by four kinds of sampling methods. Gray correlation analysis was adopted to make the comprehensive evaluation by comparing it with the standard method. The experimental results showed that the convenience of uniform sampling method was 1 (100%), odds ratio of occupation rate in a row and column was infinity, relative accuracy was 99.50-99.89%, reproducibility RSD was 0.45-0.89%, and weighted incidence degree exceeded the standard method. Hence, the uniform sampling method was easy to operate, and the selected samples were distributed uniformly. The experimental results demonstrated that the uniform sampling method has good accuracy and reproducibility, which can be put into use in drugs analysis.

A Comprehensive Subcellular Proteomic Survey of Salmonella Grown under Phagosome-Mimicking versus Standard Laboratory Conditions

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

Brown, Roslyn N.; Sanford, James A.; Park, Jea H.

Towards developing a systems-level pathobiological understanding of Salmonella enterica, we performed a subcellular proteomic analysis of this pathogen grown under standard laboratory and infection-mimicking conditions in vitro. Analysis of proteins from cytoplasmic, inner membrane, periplasmic, and outer membrane fractions yielded coverage of over 30% of the theoretical proteome. Confident subcellular location could be assigned to over 1000 proteins, with good agreement between experimentally observed location and predicted/known protein properties. Comparison of protein location under the different environmental conditions provided insight into dynamic protein localization and possible moonlighting (multiple function) activities. Notable examples of dynamic localization were the response regulators ofmore » two-component regulatory systems (e.g., ArcB, PhoQ). The DNA-binding protein Dps that is generally regarded as cytoplasmic was significantly enriched in the outer membrane for all growth conditions examined, suggestive of moonlighting activities. These observations imply the existence of unknown transport mechanisms and novel functions for a subset of Salmonella proteins. Overall, this work provides a catalog of experimentally verified subcellular protein location for Salmonella and a framework for further investigations using computational modeling.« less

Aeroelastic loads and stability investigation of a full-scale hingeless rotor

NASA Technical Reports Server (NTRS)

Peterson, Randall L.; Johnson, Wayne

1991-01-01

An analytical investigation was conducted to study the influence of various parameters on predicting the aeroelastic loads and stability of a full-scale hingeless rotor in hover and forward flight. The CAMRAD/JA (Comprehensive Analytical Model of Rotorcraft Aerodynamics and Dynamics, Johnson Aeronautics) analysis code is used to obtain the analytical predictions. Data are presented for rotor blade bending and torsional moments as well as inplane damping data obtained for rotor operation in hover at a constant rotor rotational speed of 425 rpm and thrust coefficients between 0.0 and 0.12. Experimental data are presented from a test in the wind tunnel. Validation of the rotor system structural model with experimental rotor blade loads data shows excellent correlation with analytical results. Using this analysis, the influence of different aerodynamic inflow models, the number of generalized blade and body degrees of freedom, and the control-system stiffness at predicted stability levels are shown. Forward flight predictions of the BO-105 rotor system for 1-G thrust conditions at advance ratios of 0.0 to 0.35 are presented. The influence of different aerodynamic inflow models, dynamic inflow models and shaft angle variations on predicted stability levels are shown as a function of advance ratio.

Exploration of gated ligand binding recognizes an allosteric site for blocking FABP4-protein interaction.

PubMed

Li, Yan; Li, Xiang; Dong, Zigang

2015-12-28

Fatty acid binding protein 4 (FABP4), reversibly binding to fatty acids and other lipids with high affinities, is a potential target for treatment of cancers. The binding site of FABP4 is buried in an interior cavity and thereby ligand binding/unbinding is coupled with opening/closing of FABP4. It is a difficult task both experimentally and computationally to illuminate the entry or exit pathway, especially with the conformational gating. In this report we combine extensive computer simulations, clustering analysis, and the Markov state model to investigate the binding mechanism of FABP4 and troglitazone. Our simulations capture spontaneous binding and unbinding events as well as the conformational transition of FABP4 between the open and closed states. An allosteric binding site on the protein surface is recognized for the development of novel FABP4 inhibitors. The binding affinity is calculated and compared with the experimental value. The kinetic analysis suggests that ligand residence on the protein surface may delay the binding process. Overall, our results provide a comprehensive picture of ligand diffusion on the protein surface, ligand migration into the buried cavity, and the conformational change of FABP4 at an atomic level.

Deformation behavior of coherently strained InAs/GaAs(111)A heteroepitaxial systems: Theoretical calculations and experimental measurements

NASA Astrophysics Data System (ADS)

Zepeda-Ruiz, Luis A.; Pelzel, Rodney I.; Nosho, Brett Z.; Weinberg, W. Henry; Maroudas, Dimitrios

2001-09-01

A comprehensive, quantitative analysis is presented of the deformation behavior of coherently strained InAs/GaAs(111)A heteroepitaxial systems. The analysis combines a hierarchical theoretical approach with experimental measurements. Continuum linear elasticity theory is linked with atomic-scale calculations of structural relaxation for detailed theoretical studies of deformation in systems consisting of InAs thin films on thin GaAs(111)A substrates that are mechanically unconstrained at their bases. Molecular-beam epitaxy is used to grow very thin InAs films on both thick and thin GaAs buffer layers on epi-ready GaAs(111)A substrates. The deformation state of these samples is characterized by x-ray diffraction (XRD). The interplanar distances of thin GaAs buffer layers along the [220] and [111] crystallographic directions obtained from the corresponding XRD spectra indicate clearly that thin buffer layers deform parallel to the InAs/GaAs(111)A interfacial plane, thus aiding in the accommodation of the strain induced by lattice mismatch. The experimental measurements are in excellent agreement with the calculated lattice interplanar distances and the corresponding strain fields in the thin mechanically unconstrained substrates considered in the theoretical analysis. Therefore, this work contributes direct evidence in support of our earlier proposal that thin buffer layers in layer-by-layer semiconductor heteroepitaxy exhibit mechanical behavior similar to that of compliant substrates [see, e.g., B. Z. Nosho, L. A. Zepeda-Ruiz, R. I. Pelzel, W. H. Weinberg, and D. Maroudas, Appl. Phys. Lett. 75, 829 (1999)].

Comprehensive benefit analysis of regional water resources based on multi-objective evaluation

NASA Astrophysics Data System (ADS)

Chi, Yixia; Xue, Lianqing; Zhang, Hui

2018-01-01

The purpose of the water resources comprehensive benefits analysis is to maximize the comprehensive benefits on the aspects of social, economic and ecological environment. Aiming at the defects of the traditional analytic hierarchy process in the evaluation of water resources, it proposed a comprehensive benefit evaluation of social, economic and environmental benefits index from the perspective of water resources comprehensive benefit in the social system, economic system and environmental system; determined the index weight by the improved fuzzy analytic hierarchy process (AHP), calculated the relative index of water resources comprehensive benefit and analyzed the comprehensive benefit of water resources in Xiangshui County by the multi-objective evaluation model. Based on the water resources data in Xiangshui County, 20 main comprehensive benefit assessment factors of 5 districts belonged to Xiangshui County were evaluated. The results showed that the comprehensive benefit of Xiangshui County was 0.7317, meanwhile the social economy has a further development space in the current situation of water resources.

Beyond the Flipped Classroom: A Highly Interactive Cloud-Classroom (HIC) Embedded into Basic Materials Science Courses

NASA Astrophysics Data System (ADS)

Liou, Wei-Kai; Bhagat, Kaushal Kumar; Chang, Chun-Yen

2016-06-01

The present study compares the highly interactive cloud-classroom (HIC) system with traditional methods of teaching materials science that utilize crystal structure picture or real crystal structure model, in order to examine its learning effectiveness across three dimensions: knowledge, comprehension and application. The aim of this study was to evaluate the (HIC) system, which incorporates augmented reality, virtual reality and cloud-classroom to teach basic materials science courses. The study followed a pretest-posttest quasi-experimental research design. A total of 92 students (aged 19-20 years), in a second-year undergraduate program, participated in this 18-week-long experiment. The students were divided into an experimental group and a control group. The experimental group (36 males and 10 females) was instructed utilizing the HIC system, while the control group (34 males and 12 females) was led through traditional teaching methods. Pretest, posttest, and delayed posttest scores were evaluated by multivariate analysis of covariance. The results indicated that participants in the experimental group who used the HIC system outperformed the control group, in the both posttest and delayed posttest, across three learning dimensions. Based on these results, the HIC system is recommended to be incorporated in formal materials science learning settings.

The class inclusion question: a case study in applying pragmatics to the experimental study of cognition.

PubMed

Politzer, Guy

2016-01-01

For more than 70 years, Piaget's class-inclusion task (given, e.g., five asters and three tulips, the child is asked whether "there are more asters or more flowers") has been the object of experimental investigation. Inclusion is of considerable importance for cognitive science as it is a key concept for logical operations and knowledge representation. It is shown that the question can be characterised by a kind of privative ambiguity which is at the source of the younger children's answer, "more asters". A relevance-theoretic explanation of children's interpretation of the question and of the subsequent responses is expounded. This account can explain the effect of all the factors that are known to influence performance (e.g., role of collections, counting, typicality, qualification, syntax, etc.), a review of which is presented. It is further tested experimentally. The development of performance is explained on the basis of the way children disambiguate the question. This study exemplifies the two ways in which pragmatic analysis is pertinent to the study of children's (as well as adults') reasoning and judgement, namely in explaining and predicting participants' comprehension of the statements and questions, and in taking into account attribution processes that occur in the experimental setting.

eSBMTools 1.0: enhanced native structure-based modeling tools.

PubMed

Lutz, Benjamin; Sinner, Claude; Heuermann, Geertje; Verma, Abhinav; Schug, Alexander

2013-11-01

Molecular dynamics simulations provide detailed insights into the structure and function of biomolecular systems. Thus, they complement experimental measurements by giving access to experimentally inaccessible regimes. Among the different molecular dynamics techniques, native structure-based models (SBMs) are based on energy landscape theory and the principle of minimal frustration. Typically used in protein and RNA folding simulations, they coarse-grain the biomolecular system and/or simplify the Hamiltonian resulting in modest computational requirements while achieving high agreement with experimental data. eSBMTools streamlines running and evaluating SBM in a comprehensive package and offers high flexibility in adding experimental- or bioinformatics-derived restraints. We present a software package that allows setting up, modifying and evaluating SBM for both RNA and proteins. The implemented workflows include predicting protein complexes based on bioinformatics-derived inter-protein contact information, a standardized setup of protein folding simulations based on the common PDB format, calculating reaction coordinates and evaluating the simulation by free-energy calculations with weighted histogram analysis method or by phi-values. The modules interface with the molecular dynamics simulation program GROMACS. The package is open source and written in architecture-independent Python2. http://sourceforge.net/projects/esbmtools/. alexander.schug@kit.edu. Supplementary data are available at Bioinformatics online.

Mass Spectrometric Analysis of the Cell Surface N-Glycoproteome by Combining Metabolic Labeling and Click Chemistry

NASA Astrophysics Data System (ADS)

Smeekens, Johanna M.; Chen, Weixuan; Wu, Ronghu

2015-04-01

Cell surface N-glycoproteins play extraordinarily important roles in cell-cell communication, cell-matrix interactions, and cellular response to environmental cues. Global analysis is exceptionally challenging because many N-glycoproteins are present at low abundances and effective separation is difficult to achieve. Here, we have developed a novel strategy integrating metabolic labeling, copper-free click chemistry, and mass spectrometry (MS)-based proteomics methods to analyze cell surface N-glycoproteins comprehensively and site-specifically. A sugar analog containing an azido group, N-azidoacetylgalactosamine, was fed to cells to label glycoproteins. Glycoproteins with the functional group on the cell surface were then bound to dibenzocyclooctyne-sulfo-biotin via copper-free click chemistry under physiological conditions. After protein extraction and digestion, glycopeptides with the biotin tag were enriched by NeutrAvidin conjugated beads. Enriched glycopeptides were deglycosylated with peptide- N-glycosidase F in heavy-oxygen water, and in the process of glycan removal, asparagine was converted to aspartic acid and tagged with 18O for MS analysis. With this strategy, 144 unique N-glycopeptides containing 152 N-glycosylation sites were identified in 110 proteins in HEK293T cells. As expected, 95% of identified glycoproteins were membrane proteins, which were highly enriched. Many sites were located on important receptors, transporters, and cluster of differentiation proteins. The experimental results demonstrated that the current method is very effective for the comprehensive and site-specific identification of the cell surface N-glycoproteome and can be extensively applied to other cell surface protein studies.

Practical limits for reverse engineering of dynamical systems: a statistical analysis of sensitivity and parameter inferability in systems biology models.

PubMed

Erguler, Kamil; Stumpf, Michael P H

2011-05-01

The size and complexity of cellular systems make building predictive models an extremely difficult task. In principle dynamical time-course data can be used to elucidate the structure of the underlying molecular mechanisms, but a central and recurring problem is that many and very different models can be fitted to experimental data, especially when the latter are limited and subject to noise. Even given a model, estimating its parameters remains challenging in real-world systems. Here we present a comprehensive analysis of 180 systems biology models, which allows us to classify the parameters with respect to their contribution to the overall dynamical behaviour of the different systems. Our results reveal candidate elements of control in biochemical pathways that differentially contribute to dynamics. We introduce sensitivity profiles that concisely characterize parameter sensitivity and demonstrate how this can be connected to variability in data. Systematically linking data and model sloppiness allows us to extract features of dynamical systems that determine how well parameters can be estimated from time-course measurements, and associates the extent of data required for parameter inference with the model structure, and also with the global dynamical state of the system. The comprehensive analysis of so many systems biology models reaffirms the inability to estimate precisely most model or kinetic parameters as a generic feature of dynamical systems, and provides safe guidelines for performing better inferences and model predictions in the context of reverse engineering of mathematical models for biological systems.

Development of Prescription Drug Information Leaflets: Impact of Cognitive Effort and Patient Involvement on Prescription Medication Information Processing.

PubMed

Patel, Harshali K; Bapat, Shweta S; Bhansali, Archita H; Sansgiry, Sujit S

2018-01-01

The objective of this study was to develop a one-page (1-page) prescription drug information leaflet (PILs) and assess their impact on the information processing variables, across 2 levels of patient involvement. One-page PILs were developed using cognitive principles to lower mental effort and improve comprehension. An experimental, 3 × 2 repeated measures study was conducted to determine the impact of cognitive effort, manipulated using leaflet type on comprehension across 2 levels (high/low) of patient involvement. Adults (≥18 years) in a university setting in Houston were recruited for the study. Each participant was exposed to 3 different types of prescription drug information leaflet (the current practice, preexisting 1-page text-only, and 1-page PILs) for the 3 drugs (Celebrex, Ventolin HFA, Prezista) for a given involvement scenario. A prevalidated survey instrument was used to measure product knowledge, attitude toward leaflet, and intention to read. Multivariate analysis of variance indicated significant positive effect of cognitive effort, involvement, and their interaction effect across all measured variables. Mean scores for product knowledge, attitude toward leaflet, and intention to read were highest for PILs ( P < .001), indicating that PILs exerted lowest cognitive effort. Univariate and post hoc analysis indicate that product knowledge significantly increases with high involvement. Patients reading PILs have higher comprehension compared with the current practice and text-only prototype leaflets evaluated. Higher levels of involvement further improve participant knowledge about the drug, increase their intention to read the leaflet, and change their attitude toward the leaflet. Implementation of PILs would improve information processing for consumers by reducing their cognitive effort.

A Set of Functional Brain Networks for the Comprehensive Evaluation of Human Characteristics.

PubMed

Sung, Yul-Wan; Kawachi, Yousuke; Choi, Uk-Su; Kang, Daehun; Abe, Chihiro; Otomo, Yuki; Ogawa, Seiji

2018-01-01

Many human characteristics must be evaluated to comprehensively understand an individual, and measurements of the corresponding cognition/behavior are required. Brain imaging by functional MRI (fMRI) has been widely used to examine brain function related to human cognition/behavior. However, few aspects of cognition/behavior of individuals or experimental groups can be examined through task-based fMRI. Recently, resting state fMRI (rs-fMRI) signals have been shown to represent functional infrastructure in the brain that is highly involved in processing information related to cognition/behavior. Using rs-fMRI may allow diverse information about the brain through a single MRI scan to be obtained, as rs-fMRI does not require stimulus tasks. In this study, we attempted to identify a set of functional networks representing cognition/behavior that are related to a wide variety of human characteristics and to evaluate these characteristics using rs-fMRI data. If possible, these findings would support the potential of rs-fMRI to provide diverse information about the brain. We used resting-state fMRI and a set of 130 psychometric parameters that cover most human characteristics, including those related to intelligence and emotional quotients and social ability/skill. We identified 163 brain regions by VBM analysis using regression analysis with 130 psychometric parameters. Next, using a 163 × 163 correlation matrix, we identified functional networks related to 111 of the 130 psychometric parameters. Finally, we made an 8-class support vector machine classifiers corresponding to these 111 functional networks. Our results demonstrate that rs-fMRI signals contain intrinsic information about brain function related to cognition/behaviors and that this set of 111 networks/classifiers can be used to comprehensively evaluate human characteristics.

Systems biology of embryonic development: Prospects for a complete understanding of the Caenorhabditis elegans embryo.

PubMed

Murray, John Isaac

2018-05-01

The convergence of developmental biology and modern genomics tools brings the potential for a comprehensive understanding of developmental systems. This is especially true for the Caenorhabditis elegans embryo because its small size, invariant developmental lineage, and powerful genetic and genomic tools provide the prospect of a cellular resolution understanding of messenger RNA (mRNA) expression and regulation across the organism. We describe here how a systems biology framework might allow large-scale determination of the embryonic regulatory relationships encoded in the C. elegans genome. This framework consists of two broad steps: (a) defining the "parts list"-all genes expressed in all cells at each time during development and (b) iterative steps of computational modeling and refinement of these models by experimental perturbation. Substantial progress has been made towards defining the parts list through imaging methods such as large-scale green fluorescent protein (GFP) reporter analysis. Imaging results are now being augmented by high-resolution transcriptome methods such as single-cell RNA sequencing, and it is likely the complete expression patterns of all genes across the embryo will be known within the next few years. In contrast, the modeling and perturbation experiments performed so far have focused largely on individual cell types or genes, and improved methods will be needed to expand them to the full genome and organism. This emerging comprehensive map of embryonic expression and regulatory function will provide a powerful resource for developmental biologists, and would also allow scientists to ask questions not accessible without a comprehensive picture. This article is categorized under: Invertebrate Organogenesis > Worms Technologies > Analysis of the Transcriptome Gene Expression and Transcriptional Hierarchies > Gene Networks and Genomics. © 2018 Wiley Periodicals, Inc.

Comprehension of human pointing gestures in horses (Equus caballus).

PubMed

Maros, Katalin; Gácsi, Márta; Miklósi, Adám

2008-07-01

Twenty domestic horses (Equus caballus) were tested for their ability to rely on different human gesticular cues in a two-way object choice task. An experimenter hid food under one of two bowls and after baiting, indicated the location of the food to the subjects by using one of four different cues. Horses could locate the hidden reward on the basis of the distal dynamic-sustained, proximal momentary and proximal dynamic-sustained pointing gestures but failed to perform above chance level when the experimenter performed a distal momentary pointing gesture. The results revealed that horses could rely spontaneously on those cues that could have a stimulus or local enhancement effect, but the possible comprehension of the distal momentary pointing remained unclear. The results are discussed with reference to the involvement of various factors such as predisposition to read human visual cues, the effect of domestication and extensive social experience and the nature of the gesture used by the experimenter in comparative investigations.

Sex-specific effect of CPB2 Ala147Thr but not Thr325Ile variants on the risk of venous thrombosis: A comprehensive meta-analysis

PubMed Central

Zwingerman, Nora; Medina-Rivera, Alejandra; Kassam, Irfahan; Wilson, Michael D.; Morange, Pierre-Emmanuel; Trégouët, David-Alexandre; Gagnon, France

2017-01-01

Background Thrombin activatable fibrinolysis inhibitor (TAFI), encoded by the Carboxypeptidase B2 gene (CPB2), is an inhibitor of fibrinolysis and plays a role in the pathogenesis of venous thrombosis. Experimental findings support a functional role of genetic variants in CPB2, while epidemiological studies have been unable to confirm associations with risk of venous thrombosis. Sex-specific effects could underlie the observed inconsistent associations between CPB2 genetic variants and venous thrombosis. Methods A comprehensive literature search was conducted for associations between Ala147Thr and Thr325Ile variants with venous thrombosis. Authors were contacted to provide sex-specific genotype counts from their studies. Combined and sex-specific random effects meta-analyses were used to estimate a pooled effect estimate for primary and secondary genetic models. Results A total of 17 studies met the inclusion criteria. A sex-specific meta-analysis applying a dominant model supported a protective effect of Ala147Thr on venous thrombosis in females (OR = 0.81, 95%CI: 0.68,0.97; p = 0.018), but not in males (OR = 1.06, 95%CI:0.96–1.16; p = 0.263). The Thr325Ile did not show a sex-specific effect but showed variation in allele frequencies by geographic region. A subgroup analysis of studies in European countries showed decreased risk, with a recessive model (OR = 0.83, 95%CI:0.71–0.97, p = 0.021) for venous thrombosis. Conclusions A comprehensive literature review, including unpublished data, provided greater statistical power for the analyses and decreased the likelihood of publication bias influencing the results. Sex-specific analyses explained apparent discrepancies across genetic studies of Ala147Thr and venous thrombosis. While, careful selection of genetic models based on population genetics, evolutionary and biological knowledge can increase power by decreasing the need to adjust for testing multiple models. PMID:28552956

Sex-specific effect of CPB2 Ala147Thr but not Thr325Ile variants on the risk of venous thrombosis: A comprehensive meta-analysis.

PubMed

Zwingerman, Nora; Medina-Rivera, Alejandra; Kassam, Irfahan; Wilson, Michael D; Morange, Pierre-Emmanuel; Trégouët, David-Alexandre; Gagnon, France

2017-01-01

Thrombin activatable fibrinolysis inhibitor (TAFI), encoded by the Carboxypeptidase B2 gene (CPB2), is an inhibitor of fibrinolysis and plays a role in the pathogenesis of venous thrombosis. Experimental findings support a functional role of genetic variants in CPB2, while epidemiological studies have been unable to confirm associations with risk of venous thrombosis. Sex-specific effects could underlie the observed inconsistent associations between CPB2 genetic variants and venous thrombosis. A comprehensive literature search was conducted for associations between Ala147Thr and Thr325Ile variants with venous thrombosis. Authors were contacted to provide sex-specific genotype counts from their studies. Combined and sex-specific random effects meta-analyses were used to estimate a pooled effect estimate for primary and secondary genetic models. A total of 17 studies met the inclusion criteria. A sex-specific meta-analysis applying a dominant model supported a protective effect of Ala147Thr on venous thrombosis in females (OR = 0.81, 95%CI: 0.68,0.97; p = 0.018), but not in males (OR = 1.06, 95%CI:0.96-1.16; p = 0.263). The Thr325Ile did not show a sex-specific effect but showed variation in allele frequencies by geographic region. A subgroup analysis of studies in European countries showed decreased risk, with a recessive model (OR = 0.83, 95%CI:0.71-0.97, p = 0.021) for venous thrombosis. A comprehensive literature review, including unpublished data, provided greater statistical power for the analyses and decreased the likelihood of publication bias influencing the results. Sex-specific analyses explained apparent discrepancies across genetic studies of Ala147Thr and venous thrombosis. While, careful selection of genetic models based on population genetics, evolutionary and biological knowledge can increase power by decreasing the need to adjust for testing multiple models.

Improving Reading Comprehension Using Digital Text: A Meta-Analysis of Interventions

ERIC Educational Resources Information Center

Berkeley, Sheri; Kurz, Leigh Ann; Boykin, Andrea; Evmenova, Anya S.

2015-01-01

Much is known about how to improve students' comprehension when reading printed text; less is known about outcomes when reading digital text. The purpose of this meta-analysis was to analyze research on the impact of digital text interventions. A comprehensive literature search resulted in 27 group intervention studies with 16,513 participants.…