Model updating in flexible-link multibody systems

NASA Astrophysics Data System (ADS)

Belotti, R.; Caneva, G.; Palomba, I.; Richiedei, D.; Trevisani, A.

2016-09-01

The dynamic response of flexible-link multibody systems (FLMSs) can be predicted through nonlinear models based on finite elements, to describe the coupling between rigid- body and elastic behaviour. Their accuracy should be as high as possible to synthesize controllers and observers. Model updating based on experimental measurements is hence necessary. By taking advantage of the experimental modal analysis, this work proposes a model updating procedure for FLMSs and applies it experimentally to a planar robot. Indeed, several peculiarities of the model of FLMS should be carefully tackled. On the one hand, nonlinear models of a FLMS should be linearized about static equilibrium configurations. On the other, the experimental mode shapes should be corrected to be consistent with the elastic displacements represented in the model, which are defined with respect to a fictitious moving reference (the equivalent rigid link system). Then, since rotational degrees of freedom are also represented in the model, interpolation of the experimental data should be performed to match the model displacement vector. Model updating has been finally cast as an optimization problem in the presence of bounds on the feasible values, by also adopting methods to improve the numerical conditioning and to compute meaningful updated inertial and elastic parameters.

Sources of variation in an enzyme-linked immunoassay of bluetongue virus in Culicoides variipennis (Diptera: Ceratopogonidae).

PubMed

Tabachnick, W J; Mecham, J O

1991-03-01

An enzyme-linked immunoassay for detecting bluetongue virus in infected Culicoides variipennis was evaluated using a nested analysis of variance to determine sources of experimental error in the procedure. The major source of variation was differences among individual insects (84% of the total variance). Storing insects at -70 degrees C for two months contributed to experimental variation in the ELISA reading (14% of the total variance) and should be avoided. Replicate assays of individual insects were shown to be unnecessary, since variation among replicate wells and plates was minor (2% of the total variance).

Probabilistic cross-link analysis and experiment planning for high-throughput elucidation of protein structure.

PubMed

Ye, Xiaoduan; O'Neil, Patrick K; Foster, Adrienne N; Gajda, Michal J; Kosinski, Jan; Kurowski, Michal A; Bujnicki, Janusz M; Friedman, Alan M; Bailey-Kellogg, Chris

2004-12-01

Emerging high-throughput techniques for the characterization of protein and protein-complex structures yield noisy data with sparse information content, placing a significant burden on computation to properly interpret the experimental data. One such technique uses cross-linking (chemical or by cysteine oxidation) to confirm or select among proposed structural models (e.g., from fold recognition, ab initio prediction, or docking) by testing the consistency between cross-linking data and model geometry. This paper develops a probabilistic framework for analyzing the information content in cross-linking experiments, accounting for anticipated experimental error. This framework supports a mechanism for planning experiments to optimize the information gained. We evaluate potential experiment plans using explicit trade-offs among key properties of practical importance: discriminability, coverage, balance, ambiguity, and cost. We devise a greedy algorithm that considers those properties and, from a large number of combinatorial possibilities, rapidly selects sets of experiments expected to discriminate pairs of models efficiently. In an application to residue-specific chemical cross-linking, we demonstrate the ability of our approach to plan experiments effectively involving combinations of cross-linkers and introduced mutations. We also describe an experiment plan for the bacteriophage lambda Tfa chaperone protein in which we plan dicysteine mutants for discriminating threading models by disulfide formation. Preliminary results from a subset of the planned experiments are consistent and demonstrate the practicality of planning. Our methods provide the experimenter with a valuable tool (available from the authors) for understanding and optimizing cross-linking experiments.

Experimental design and quantitative analysis of microbial community multiomics.

PubMed

Mallick, Himel; Ma, Siyuan; Franzosa, Eric A; Vatanen, Tommi; Morgan, Xochitl C; Huttenhower, Curtis

2017-11-30

Studies of the microbiome have become increasingly sophisticated, and multiple sequence-based, molecular methods as well as culture-based methods exist for population-scale microbiome profiles. To link the resulting host and microbial data types to human health, several experimental design considerations, data analysis challenges, and statistical epidemiological approaches must be addressed. Here, we survey current best practices for experimental design in microbiome molecular epidemiology, including technologies for generating, analyzing, and integrating microbiome multiomics data. We highlight studies that have identified molecular bioactives that influence human health, and we suggest steps for scaling translational microbiome research to high-throughput target discovery across large populations.

Exploiting Information Diffusion Feature for Link Prediction in Sina Weibo

NASA Astrophysics Data System (ADS)

Li, Dong; Zhang, Yongchao; Xu, Zhiming; Chu, Dianhui; Li, Sheng

2016-01-01

The rapid development of online social networks (e.g., Twitter and Facebook) has promoted research related to social networks in which link prediction is a key problem. Although numerous attempts have been made for link prediction based on network structure, node attribute and so on, few of the current studies have considered the impact of information diffusion on link creation and prediction. This paper mainly addresses Sina Weibo, which is the largest microblog platform with Chinese characteristics, and proposes the hypothesis that information diffusion influences link creation and verifies the hypothesis based on real data analysis. We also detect an important feature from the information diffusion process, which is used to promote link prediction performance. Finally, the experimental results on Sina Weibo dataset have demonstrated the effectiveness of our methods.

Exploiting Information Diffusion Feature for Link Prediction in Sina Weibo.

PubMed

Li, Dong; Zhang, Yongchao; Xu, Zhiming; Chu, Dianhui; Li, Sheng

2016-01-28

The rapid development of online social networks (e.g., Twitter and Facebook) has promoted research related to social networks in which link prediction is a key problem. Although numerous attempts have been made for link prediction based on network structure, node attribute and so on, few of the current studies have considered the impact of information diffusion on link creation and prediction. This paper mainly addresses Sina Weibo, which is the largest microblog platform with Chinese characteristics, and proposes the hypothesis that information diffusion influences link creation and verifies the hypothesis based on real data analysis. We also detect an important feature from the information diffusion process, which is used to promote link prediction performance. Finally, the experimental results on Sina Weibo dataset have demonstrated the effectiveness of our methods.

Dynamic Analysis and Control of Lightweight Manipulators with Flexible Parallel Link Mechanisms. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Lee, Jeh Won

1990-01-01

The objective is the theoretical analysis and the experimental verification of dynamics and control of a two link flexible manipulator with a flexible parallel link mechanism. Nonlinear equations of motion of the lightweight manipulator are derived by the Lagrangian method in symbolic form to better understand the structure of the dynamic model. The resulting equation of motion have a structure which is useful to reduce the number of terms calculated, to check correctness, or to extend the model to higher order. A manipulator with a flexible parallel link mechanism is a constrained dynamic system whose equations are sensitive to numerical integration error. This constrained system is solved using singular value decomposition of the constraint Jacobian matrix. Elastic motion is expressed by the assumed mode method. Mode shape functions of each link are chosen using the load interfaced component mode synthesis. The discrepancies between the analytical model and the experiment are explained using a simplified and a detailed finite element model.

Progression of Inflammatory Bowel Disease to Cancer: Is the Patient Better Off without Lymphatic Vessels or Nodes (or Angiopoietin 2)?

DTIC Science & Technology

2013-12-01

carcinoma (CRC) in IBD patients and experimental models. Nonetheless, the pathogenic link, interrelationship, and practical clinical application of these...and are continuing final data analysis and latest imaging studies. This project has potentially high impact because of the substantial incidence of...pathogenic link, interrelationship, and practical clinical application of these various theories of progression have remained elusive. We proposed that

PHYSIOLOCIGALLY BASED PHARMACOKINETIC (PBPK) MODELING AND MODE OF ACTION IN DOSE-RESPONSE ASSESSMENT

EPA Science Inventory

PHYSIOLOGICALLY BASED PHARMACOKINETIC (PBPK) MODELING AND MODE OF ACTION IN DOSE-RESPONSE ASSESSMENT. Barton HA. Experimental Toxicology Division, National Health and Environmental Effects Laboratory, ORD, U.S. EPA
Dose-response analysis requires quantitatively linking infor...

Preliminary analyses of WL experiment No. 701, space environment effects on operating fiber optic systems

NASA Technical Reports Server (NTRS)

Taylor, E. W.; Berry, J. N.; Sanchez, A. D.; Padden, R. J.; Chapman, S. P.

1992-01-01

A brief overview of the analyses performed to date on WL Experiment-701 is presented. Four active digital fiber optic links were directly exposed to the space environment for a period of 2114 days. The links were situated aboard the Long Duration Exposure Facility (LDEF) with the cabled, single fiber windings atop an experimental tray containing instrumentation for exercising the experiment in orbit. Despite the unplanned and prolonged exposure to trapped and galactic radiation, wide temperature extremes, atomic oxygen interactions, and micro-meteorite and debris impacts, in most instances the optical data links performed well within the experimental limits. Analysis of the recorded orbital data clearly indicates that fiber optic applications in space will meet with success. Ongoing tests and analysis of the experiment at the Phillips Laboratory's Optoelectronics Laboratory will expand this premise, and establish the first known and extensive database of active fiber optic link performance during prolonged space exposure. WL Exp-701 was designed as a feasibility demonstration for fiber optic technology in space applications, and to study the performance of operating fiber systems exposed to space environmental factors such as galactic radiation, and wide temperature cycling. WL Exp-701 is widely acknowledged as a benchmark accomplishment that clearly demonstrates, for the first time, that fiber optic technology can be successfully used in a variety of space applications.

A class-based link prediction using Distance Dependent Chinese Restaurant Process

NASA Astrophysics Data System (ADS)

Andalib, Azam; Babamir, Seyed Morteza

2016-08-01

One of the important tasks in relational data analysis is link prediction which has been successfully applied on many applications such as bioinformatics, information retrieval, etc. The link prediction is defined as predicting the existence or absence of edges between nodes of a network. In this paper, we propose a novel method for link prediction based on Distance Dependent Chinese Restaurant Process (DDCRP) model which enables us to utilize the information of the topological structure of the network such as shortest path and connectivity of the nodes. We also propose a new Gibbs sampling algorithm for computing the posterior distribution of the hidden variables based on the training data. Experimental results on three real-world datasets show the superiority of the proposed method over other probabilistic models for link prediction problem.

National Centers for Environmental Prediction

Science.gov Websites

---------------------------------------------------------------------------------------------------------------------------------------------------- IITM CFS v2 Forecast for 2017 monsoon : link Experimental short-range GEFS ensemble forecast : link Experimental short-range GFS-T1534(upto 8days) forecast : link

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

A two cable, six link boom crane for lunar construction

NASA Technical Reports Server (NTRS)

Taylor, Robert M.; Mikulas, Martin M., Jr.; Hedgepeth, John M.

1993-01-01

This paper presents the conceptual design and analysis of a modified crane boom and cable suspension which provide contro1 over all six degrees of freedom of a payload. Two cables pass around pulleys to form six links between the payload and boom. A linearization of the pulley mechanics was derived to create finite element models of the system. The models were experimentally verified and used to explore variations of the suspension geometry. Several crane concepts which use the suspension are discussed and illustrated.

Alcohol Use Predicts Sexual Decision-Making: A Systematic Review and Meta-Analysis of the Experimental Literature

PubMed Central

Scott-Sheldon, Lori A. J.; Carey, Kate B.; Cunningham, Karlene; Johnson, Blair T.; Carey, Michael P.

2015-01-01

Alcohol is associated with HIV and other sexually transmitted infections through increased sexual risk-taking behavior. Establishing a causal link between alcohol and sexual behavior has been challenging due to methodological limitations (e.g., reliance on cross-sectional designs). Experimental methods can be used to establish causality. The purpose of this meta-analysis was to evaluate the effects of alcohol consumption on unprotected sex intentions. We searched electronic bibliographic databases for records with relevant keywords; 26 manuscripts (k = 30 studies) met inclusion criteria. Results indicate that alcohol consumption is associated with greater intentions to engage in unprotected sex (d+s = 0.24, 0.35). The effect of alcohol on unprotected sex intentions was greater when sexual arousal was heightened. Alcohol consumption is causally linked to theoretical antecedents of sexual risk behavior, consistent with the alcohol myopia model. Addressing alcohol consumption as a determinant of unprotected sex intentions may lead to more effective HIV interventions. PMID:26080689

An inverse method for determining the spatially resolved properties of viscoelastic–viscoplastic three-dimensional printed materials

PubMed Central

Chen, X.; Ashcroft, I. A.; Wildman, R. D.; Tuck, C. J.

2015-01-01

A method using experimental nanoindentation and inverse finite-element analysis (FEA) has been developed that enables the spatial variation of material constitutive properties to be accurately determined. The method was used to measure property variation in a three-dimensional printed (3DP) polymeric material. The accuracy of the method is dependent on the applicability of the constitutive model used in the inverse FEA, hence four potential material models: viscoelastic, viscoelastic–viscoplastic, nonlinear viscoelastic and nonlinear viscoelastic–viscoplastic were evaluated, with the latter enabling the best fit to experimental data. Significant changes in material properties were seen in the depth direction of the 3DP sample, which could be linked to the degree of cross-linking within the material, a feature inherent in a UV-cured layer-by-layer construction method. It is proposed that the method is a powerful tool in the analysis of manufacturing processes with potential spatial property variation that will also enable the accurate prediction of final manufactured part performance. PMID:26730216

An inverse method for determining the spatially resolved properties of viscoelastic-viscoplastic three-dimensional printed materials.

PubMed

Chen, X; Ashcroft, I A; Wildman, R D; Tuck, C J

2015-11-08

A method using experimental nanoindentation and inverse finite-element analysis (FEA) has been developed that enables the spatial variation of material constitutive properties to be accurately determined. The method was used to measure property variation in a three-dimensional printed (3DP) polymeric material. The accuracy of the method is dependent on the applicability of the constitutive model used in the inverse FEA, hence four potential material models: viscoelastic, viscoelastic-viscoplastic, nonlinear viscoelastic and nonlinear viscoelastic-viscoplastic were evaluated, with the latter enabling the best fit to experimental data. Significant changes in material properties were seen in the depth direction of the 3DP sample, which could be linked to the degree of cross-linking within the material, a feature inherent in a UV-cured layer-by-layer construction method. It is proposed that the method is a powerful tool in the analysis of manufacturing processes with potential spatial property variation that will also enable the accurate prediction of final manufactured part performance.

Evaluation of selective control information detection scheme in orthogonal frequency division multiplexing-based radio-over-fiber and visible light communication links

NASA Astrophysics Data System (ADS)

Dalarmelina, Carlos A.; Adegbite, Saheed A.; Pereira, Esequiel da V.; Nunes, Reginaldo B.; Rocha, Helder R. O.; Segatto, Marcelo E. V.; Silva, Jair A. L.

2017-05-01

Block-level detection is required to decode what may be classified as selective control information (SCI) such as control format indicator in 4G-long-term evolution systems. Using optical orthogonal frequency division multiplexing over radio-over-fiber (RoF) links, we report the experimental evaluation of an SCI detection scheme based on a time-domain correlation (TDC) technique in comparison with the conventional maximum likelihood (ML) approach. When compared with the ML method, it is shown that the TDC method improves detection performance over both 20 and 40 km of standard single mode fiber (SSMF) links. We also report a performance analysis of the TDC scheme in noisy visible light communication channel models after propagation through 40 km of SSMF. Experimental and simulation results confirm that the TDC method is attractive for practical orthogonal frequency division multiplexing-based RoF and fiber-wireless systems. Unlike the ML method, another key benefit of the TDC is that it requires no channel estimation.

Revealing how network structure affects accuracy of link prediction

NASA Astrophysics Data System (ADS)

Yang, Jin-Xuan; Zhang, Xiao-Dong

2017-08-01

Link prediction plays an important role in network reconstruction and network evolution. The network structure affects the accuracy of link prediction, which is an interesting problem. In this paper we use common neighbors and the Gini coefficient to reveal the relation between them, which can provide a good reference for the choice of a suitable link prediction algorithm according to the network structure. Moreover, the statistical analysis reveals correlation between the common neighbors index, Gini coefficient index and other indices to describe the network structure, such as Laplacian eigenvalues, clustering coefficient, degree heterogeneity, and assortativity of network. Furthermore, a new method to predict missing links is proposed. The experimental results show that the proposed algorithm yields better prediction accuracy and robustness to the network structure than existing currently used methods for a variety of real-world networks.

An Integrated Approach Linking Process to Structural Modeling With Microstructural Characterization for Injections-Molded Long-Fiber Thermoplastics

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

Nguyen, Ba Nghiep; Bapanapalli, Satish K.; Smith, Mark T.

2008-09-01

The objective of our work is to enable the optimum design of lightweight automotive structural components using injection-molded long fiber thermoplastics (LFTs). To this end, an integrated approach that links process modeling to structural analysis with experimental microstructural characterization and validation is developed. First, process models for LFTs are developed and implemented into processing codes (e.g. ORIENT, Moldflow) to predict the microstructure of the as-formed composite (i.e. fiber length and orientation distributions). In parallel, characterization and testing methods are developed to obtain necessary microstructural data to validate process modeling predictions. Second, the predicted LFT composite microstructure is imported into amore » structural finite element analysis by ABAQUS to determine the response of the as-formed composite to given boundary conditions. At this stage, constitutive models accounting for the composite microstructure are developed to predict various types of behaviors (i.e. thermoelastic, viscoelastic, elastic-plastic, damage, fatigue, and impact) of LFTs. Experimental methods are also developed to determine material parameters and to validate constitutive models. Such a process-linked-structural modeling approach allows an LFT composite structure to be designed with confidence through numerical simulations. Some recent results of our collaborative research will be illustrated to show the usefulness and applications of this integrated approach.« less

Complexity and dynamics of switched human balance control during quiet standing.

PubMed

Nema, Salam; Kowalczyk, Piotr; Loram, Ian

2015-10-01

In this paper, we use a combination of numerical simulations, time series analysis, and complexity measures to investigate the dynamics of switched systems with noise, which are often used as models of human balance control during quiet standing. We link the results with complexity measures found in experimental data of human sway motion during quiet standing. The control model ensuring balance, which we use, is based on an act-and-wait control concept, that is, a human controller is switched on when a certain sway angle is reached. Otherwise, there is no active control present. Given a time series data, we determine how does it look a typical pattern of control strategy in our model system. We detect the switched nonlinearity in the system using a frequency analysis method in the absence of noise. We also analyse the effect of time delay on the existence of limit cycles in the system in the absence of noise. We perform the entropy and detrended fluctuation analyses in view of linking the switchings (and the dead zone) with the occurrences of complexity in the model system in the presence of noise. Finally, we perform the entropy and detrended fluctuation analyses on experimental data and link the results with numerical findings in our model example.

Correlations between Community Structure and Link Formation in Complex Networks

PubMed Central

Liu, Zhen; He, Jia-Lin; Kapoor, Komal; Srivastava, Jaideep

2013-01-01

Background Links in complex networks commonly represent specific ties between pairs of nodes, such as protein-protein interactions in biological networks or friendships in social networks. However, understanding the mechanism of link formation in complex networks is a long standing challenge for network analysis and data mining. Methodology/Principal Findings Links in complex networks have a tendency to cluster locally and form so-called communities. This widely existed phenomenon reflects some underlying mechanism of link formation. To study the correlations between community structure and link formation, we present a general computational framework including a theory for network partitioning and link probability estimation. Our approach enables us to accurately identify missing links in partially observed networks in an efficient way. The links having high connection likelihoods in the communities reveal that links are formed preferentially to create cliques and accordingly promote the clustering level of the communities. The experimental results verify that such a mechanism can be well captured by our approach. Conclusions/Significance Our findings provide a new insight into understanding how links are created in the communities. The computational framework opens a wide range of possibilities to develop new approaches and applications, such as community detection and missing link prediction. PMID:24039818

Agreement and Movement: A Syntactic Analysis of Attraction

ERIC Educational Resources Information Center

Franck, Julie; Lassi, Glenda; Frauenfelder, Ulrich H.; Rizzi, Luigi

2006-01-01

This paper links experimental psycholinguistics and theoretical syntax in the study of subject--verb agreement. Three experiments of elicited spoken production making use of specific characteristics of Italian and French are presented. They manipulate and examine its impact on the occurrence of "attraction" errors (i.e. incorrect agreement with a…

Software for an Experimental Air-Ground Data Link : Volume 2. System Operation Manual

DOT National Transportation Integrated Search

1975-10-01

This report documents the complete software system developed for the Experimental Data Link System which was implemented for flight test during the Air-Ground Data Link Development Program (FAA-TSC- Project Number FA-13). The software development is ...

Software for Experimental Air-Ground Data Link Volume I : Functional Description and Flowcharts.

DOT National Transportation Integrated Search

1975-10-01

Experimental Data Link System which was implemented for flight test during the Air-Ground Data Link Development Program (FAA-TSC Project Number FA-13). : The software development is presented in three volumes as follows: : Volume I: -- Functional Des...

A Data Analysis Center for Electromagnetic and Hadronic Interaction

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

Briscoe, William John; Strakovsky, Igor I.; Workman, Ronald L.

2015-05-31

The GW Data Analysis Center (DAC) has made significant progress in its program to enhance and expand the partial-wave and multipole analyses of fundamental reactions, while maintaining and expanding each associated database. These efforts provide guidance to national and international experimental and theoretical efforts, and are an important link between theory and experiment. Our principal goals are focused on baryon and meson physics programs and related topics.

The Behavior of TCP and Its Extensions in Space

NASA Technical Reports Server (NTRS)

Wang, Ruhai; Horan, Stephen

2001-01-01

The performance of Transmission Control Protocol (TCP) in space has been examined from the observations of simulation and experimental tests for several years at National Aeronautics and Space Administration (NASA), Department of Defense (DoD) and universities. At New Mexico State University (NMSU), we have been concentrating on studying the performance of two protocol suites: the file transfer protocol (ftp) running over Transmission Control Protocol/Internet Protocol (TCP/IP) stack and the file protocol (fp) running over the Space Communications Protocol Standards (SCPS)-Transport Protocol (TP) developed under the Consultative Committee for Space Data Systems (CCSDS) standards process. SCPS-TP is considered to be TCP's extensions for space communications. This dissertation experimentally studies the behavior of TCP and SCPS-TP by running the protocol suites over both the Space-to-Ground Link Simulator (SGLS) test-bed and realistic satellite link. The study concentrates on comparing protocol behavior by plotting the averaged file transfer times for different experimental configurations and analyzing them using Statistical Analysis System (SAS) based procedures. The effects of different link delays and various Bit-Error-Rates (BERS) on each protocol performance are also studied and linear regression models are built for experiments over SGLS test-bed to reflect the relationships between the file transfer time and various transmission conditions.

Link-state-estimation-based transmission power control in wireless body area networks.

PubMed

Kim, Seungku; Eom, Doo-Seop

2014-07-01

This paper presents a novel transmission power control protocol to extend the lifetime of sensor nodes and to increase the link reliability in wireless body area networks (WBANs). We first experimentally investigate the properties of the link states using the received signal strength indicator (RSSI). We then propose a practical transmission power control protocol based on both short- and long-term link-state estimations. Both the short- and long-term link-state estimations enable the transceiver to adapt the transmission power level and target the RSSI threshold range, respectively, to simultaneously satisfy the requirements of energy efficiency and link reliability. Finally, the performance of the proposed protocol is experimentally evaluated in two experimental scenarios-body posture change and dynamic body motion-and compared with the typical WBAN transmission power control protocols, a real-time reactive scheme, and a dynamic postural position inference mechanism. From the experimental results, it is found that the proposed protocol increases the lifetime of the sensor nodes by a maximum of 9.86% and enhances the link reliability by reducing the packet loss by a maximum of 3.02%.

Software for an experimental air-ground data link : volume 1. functional description and flowcharts.

DOT National Transportation Integrated Search

1975-10-01

This report documents the complete software system developed for the Experimental Data Link System which was implementd for flight test during the Air-Ground Data Link Development Program. The software development is presented in three volumes as fol...

Pervaporation separation of thiophene-heptane mixtures with polydimethylsiloxane (PDMS) membrane for desulfurization.

PubMed

Chen, Jian; Li, Jiding; Qi, Rongbin; Ye, Hong; Chen, Cuixian

2010-01-01

Cross-linked polydimethylsiloxane (PDMS)-polyetherimide (PEI) composite membranes were prepared, in which asymmetric microporous PEI membrane prepared with phase inversion method was acted as the microporous supporting layer in the flat-plate composite membrane. Membrane characterization was conducted by Fourier transform infrared and scanning electronic microscopy analysis. The composite membranes were employed in pervaporation separation of n-heptane-thiophene mixtures. Effect of amount of PDMS, cross-linking temperature, amount of cross-linking agent, and cross-linking time on the separation efficiency of n-heptane-thiophene mixtures was investigated experimentally. Experiment results demonstrated that 80-100 degrees degrees C of cross-linking temperature was more preferable for practical application, as the amount of cross-linking agent was up to 20 wt.%, and 25 wt.% of PDMS amount was more optimal as far as flux and sulfur enrichment factor were concerned. In addition, the swelling degree of and stableness of composite membrane during long-time operation were studied, which should be significant for practical application.

Improving local clustering based top-L link prediction methods via asymmetric link clustering information

NASA Astrophysics Data System (ADS)

Wu, Zhihao; Lin, Youfang; Zhao, Yiji; Yan, Hongyan

2018-02-01

Networks can represent a wide range of complex systems, such as social, biological and technological systems. Link prediction is one of the most important problems in network analysis, and has attracted much research interest recently. Many link prediction methods have been proposed to solve this problem with various techniques. We can note that clustering information plays an important role in solving the link prediction problem. In previous literatures, we find node clustering coefficient appears frequently in many link prediction methods. However, node clustering coefficient is limited to describe the role of a common-neighbor in different local networks, because it cannot distinguish different clustering abilities of a node to different node pairs. In this paper, we shift our focus from nodes to links, and propose the concept of asymmetric link clustering (ALC) coefficient. Further, we improve three node clustering based link prediction methods via the concept of ALC. The experimental results demonstrate that ALC-based methods outperform node clustering based methods, especially achieving remarkable improvements on food web, hamster friendship and Internet networks. Besides, comparing with other methods, the performance of ALC-based methods are very stable in both globalized and personalized top-L link prediction tasks.

On heart rate variability and autonomic activity in homeostasis and in systemic inflammation.

PubMed

Scheff, Jeremy D; Griffel, Benjamin; Corbett, Siobhan A; Calvano, Steve E; Androulakis, Ioannis P

2014-06-01

Analysis of heart rate variability (HRV) is a promising diagnostic technique due to the noninvasive nature of the measurements involved and established correlations with disease severity, particularly in inflammation-linked disorders. However, the complexities underlying the interpretation of HRV complicate understanding the mechanisms that cause variability. Despite this, such interpretations are often found in literature. In this paper we explored mathematical modeling of the relationship between the autonomic nervous system and the heart, incorporating basic mechanisms such as perturbing mean values of oscillating autonomic activities and saturating signal transduction pathways to explore their impacts on HRV. We focused our analysis on human endotoxemia, a well-established, controlled experimental model of systemic inflammation that provokes changes in HRV representative of acute stress. By contrasting modeling results with published experimental data and analyses, we found that even a simple model linking the autonomic nervous system and the heart confound the interpretation of HRV changes in human endotoxemia. Multiple plausible alternative hypotheses, encoded in a model-based framework, equally reconciled experimental results. In total, our work illustrates how conventional assumptions about the relationships between autonomic activity and frequency-domain HRV metrics break down, even in a simple model. This underscores the need for further experimental work towards unraveling the underlying mechanisms of autonomic dysfunction and HRV changes in systemic inflammation. Understanding the extent of information encoded in HRV signals is critical in appropriately analyzing prior and future studies. Copyright © 2014 Elsevier Inc. All rights reserved.

On heart rate variability and autonomic activity in homeostasis and in systemic inflammation

PubMed Central

Scheff, Jeremy D.; Griffel, Benjamin; Corbett, Siobhan A.; Calvano, Steve E.; Androulakis, Ioannis P.

2014-01-01

Analysis of heart rate variability (HRV) is a promising diagnostic technique due to the noninvasive nature of the measurements involved and established correlations with disease severity, particularly in inflammation-linked disorders. However, the complexities underlying the interpretation of HRV complicate understanding the mechanisms that cause variability. Despite this, such interpretations are often found in literature. In this paper we explored mathematical modeling of the relationship between the autonomic nervous system and the heart, incorporating basic mechanisms such as perturbing mean values of oscillating autonomic activities and saturating signal transduction pathways to explore their impacts on HRV. We focused our analysis on human endotoxemia, a well-established, controlled experimental model of systemic inflammation that provokes changes in HRV representative of acute stress. By contrasting modeling results with published experimental data and analyses, we found that even a simple model linking the autonomic nervous system and the heart confound the interpretation of HRV changes in human endotoxemia. Multiple plausible alternative hypotheses, encoded in a model-based framework, equally reconciled experimental results. In total, our work illustrates how conventional assumptions about the relationships between autonomic activity and frequency-domain HRV metrics break down, even in a simple model. This underscores the need for further experimental work towards unraveling the underlying mechanisms of autonomic dysfunction and HRV changes in systemic inflammation. Understanding the extent of information encoded in HRV signals is critical in appropriately analyzing prior and future studies. PMID:24680646

A Quasi-Experimental Analysis of Second Graders with Dyslexia Using the Motor Markers in the Cerebellar Deficit Hypothesis

ERIC Educational Resources Information Center

Stark, Sandra Kathleen

2013-01-01

Developmental dyslexia is a specific impairment of reading ability in the presence of normal intelligence and adequate reading instruction. Current research has linked dyslexia to genetic underpinnings, which are identifiable. Furthermore, there are cognitive processes that are influenced by unique genetically programmed neural networks that…

Characterization and Uncertainty Analysis of a Reference Pressure Measurement System for Wind Tunnels

NASA Technical Reports Server (NTRS)

Amer, Tahani; Tripp, John; Tcheng, Ping; Burkett, Cecil; Sealey, Bradley

2004-01-01

This paper presents the calibration results and uncertainty analysis of a high-precision reference pressure measurement system currently used in wind tunnels at the NASA Langley Research Center (LaRC). Sensors, calibration standards, and measurement instruments are subject to errors due to aging, drift with time, environment effects, transportation, the mathematical model, the calibration experimental design, and other factors. Errors occur at every link in the chain of measurements and data reduction from the sensor to the final computed results. At each link of the chain, bias and precision uncertainties must be separately estimated for facility use, and are combined to produce overall calibration and prediction confidence intervals for the instrument, typically at a 95% confidence level. The uncertainty analysis and calibration experimental designs used herein, based on techniques developed at LaRC, employ replicated experimental designs for efficiency, separate estimation of bias and precision uncertainties, and detection of significant parameter drift with time. Final results, including calibration confidence intervals and prediction intervals given as functions of the applied inputs, not as a fixed percentage of the full-scale value are presented. System uncertainties are propagated beginning with the initial reference pressure standard, to the calibrated instrument as a working standard in the facility. Among the several parameters that can affect the overall results are operating temperature, atmospheric pressure, humidity, and facility vibration. Effects of factors such as initial zeroing and temperature are investigated. The effects of the identified parameters on system performance and accuracy are discussed.

Increased Bisecting N-Acetylglucosamine and Decreased Branched Chain Glycans of N-linked Glycoproteins in Expressed Prostatic Secretions Associated with Prostate Cancer Progression

PubMed Central

Nyalwidhe, Julius O.; Betesh, Lucy R.; Powers, Thomas W.; Jones, E. Ellen; White, Krista Y.; Burch, Tanya C.; Brooks, Jasmin; Watson, Megan T.; Lance, Raymond S.; Troyer, Dean A.; Semmes, O. John; Mehta, Anand; Drake, Richard R.

2013-01-01

Purpose Using prostatic fluids rich in glycoproteins like prostate specific antigen (PSA) and prostatic acid phosphatase (PAP) , the goal of this study was to identify the structural types and relative abundance of glycans associated with prostate cancer status for subsequent use in emerging mass spectrometry-based glycopeptide analysis platforms. Experimental Design A series of pooled samples of expressed prostatic secretions (EPS) and exosomes reflecting different stages of prostate cancer disease were used for N-linked glycan profiling by three complementary methods, MALDI-TOF profiling, normal-phase HPLC separation, and triple quadropole MS analysis of PAP glycopeptides. Results Glycan profiling of N-linked glycans from different EPS fluids indicated a global decrease in larger branched tri- and tetra-antennary glycans. Differential exoglycosidase treatments indicated a substantial increase in bisecting N-acetylglucosamines correlated with disease severity. A triple quadrupole MS analysis of the N-linked glycopeptides sites from PAP in aggressive prostate cancer pools was done to cross-reference with the glycan profiling data. Conclusion and clinical relevance Changes in glycosylation as detected in EPS fluids reflect the clinical status of prostate cancer. Defining these molecular signatures at the glycopeptide level in individual samples could improve current approaches of diagnosis and prognosis. PMID:23775902

A new method of radio frequency links by coplanar coils for implantable medical devices.

PubMed

Xue, L; Hao, H W; Li, L; Ma, B Z

2005-01-01

A new method based on coplanar coils for the design of radio frequency links has been developed, to realize the communication between the programming wand and the implantable medical devices with shielding container simply and reliably. With the analysis of electronic and magnetic field theory, the communication model has been established and simulated, and the circuit has been designed and tested. The experimental results are consistent with the simulation fairly well. The voltage transfer ratio of the typical circuit with present parameters can reach as high as 0.02, which can fulfill the requirements of communication.

A Quasi-Experimental Analysis of Fraternity or Sorority Membership and College Student Success

ERIC Educational Resources Information Center

Bowman, Nicholas A.; Holmes, Joshua M.

2017-01-01

Despite considerable debate about the effects of fraternities and sororities on college campuses, the extent to which these organizations promote or detract from student success is unclear. Therefore, we used propensity score analyses to examine the link between membership in a social fraternity or sorority and several student success outcomes.…

On Money and Motivation: A Quasi-Experimental Analysis of Financial Incentives for College Achievement

ERIC Educational Resources Information Center

Scott-Clayton, Judith

2011-01-01

Programs linking college aid to academic achievement could work either by lowering the cost of college or by inducing additional student effort. I examine the PROMISE program in West Virginia, which offers free tuition to students who maintain a minimum GPA and course load. Using administrative data, I exploit discontinuities in the eligibility…

Text Talk, Body Talk, Table Talk: A Design of Ratio and Proportion as Classroom Parallel Events

ERIC Educational Resources Information Center

Abrahamson, Dor

2003-01-01

The paper describes the rationale and 10-day implementation in a 5th-grade classroom (n=19) of an experimental ratio-and-proportion instructional design. In this constructivist-phenomenological design, coming from our theoretical perspective, design research, and domain analysis, students: (1) link "real-world" and "mathematical" objects…

Sex Reversal and Comparative Data Undermine the W Chromosome and Support Z-linked DMRT1 as the Regulator of Gonadal Sex Differentiation in Birds.

PubMed

Hirst, Claire E; Major, Andrew T; Ayers, Katie L; Brown, Rosie J; Mariette, Mylene; Sackton, Timothy B; Smith, Craig A

2017-09-01

The exact genetic mechanism regulating avian gonadal sex differentiation has not been completely resolved. The most likely scenario involves a dosage mechanism, whereby the Z-linked DMRT1 gene triggers testis development. However, the possibility still exists that the female-specific W chromosome may harbor an ovarian determining factor. In this study, we provide evidence that the universal gene regulating gonadal sex differentiation in birds is Z-linked DMRT1 and not a W-linked (ovarian) factor. Three candidate W-linked ovarian determinants are HINTW, female-expressed transcript 1 (FET1), and female-associated factor (FAF). To test the association of these genes with ovarian differentiation in the chicken, we examined their expression following experimentally induced female-to-male sex reversal using the aromatase inhibitor fadrozole (FAD). Administration of FAD on day 3 of embryogenesis induced a significant loss of aromatase enzyme activity in female gonads and masculinization. However, expression levels of HINTW, FAF, and FET1 were unaltered after experimental masculinization. Furthermore, comparative analysis showed that FAF and FET1 expression could not be detected in zebra finch gonads. Additionally, an antibody raised against the predicted HINTW protein failed to detect it endogenously. These data do not support a universal role for these genes or for the W sex chromosome in ovarian development in birds. We found that DMRT1 (but not the recently identified Z-linked HEMGN gene) is male upregulated in embryonic zebra finch and emu gonads, as in the chicken. As chicken, zebra finch, and emu exemplify the major evolutionary clades of birds, we propose that Z-linked DMRT1, and not the W sex chromosome, regulates gonadal sex differentiation in birds. Copyright © 2017 Endocrine Society.

Experimental validation of predicted cancer genes using FRET

NASA Astrophysics Data System (ADS)

Guala, Dimitri; Bernhem, Kristoffer; Ait Blal, Hammou; Jans, Daniel; Lundberg, Emma; Brismar, Hjalmar; Sonnhammer, Erik L. L.

2018-07-01

Huge amounts of data are generated in genome wide experiments, designed to investigate diseases with complex genetic causes. Follow up of all potential leads produced by such experiments is currently cost prohibitive and time consuming. Gene prioritization tools alleviate these constraints by directing further experimental efforts towards the most promising candidate targets. Recently a gene prioritization tool called MaxLink was shown to outperform other widely used state-of-the-art prioritization tools in a large scale in silico benchmark. An experimental validation of predictions made by MaxLink has however been lacking. In this study we used Fluorescence Resonance Energy Transfer, an established experimental technique for detection of protein-protein interactions, to validate potential cancer genes predicted by MaxLink. Our results provide confidence in the use of MaxLink for selection of new targets in the battle with polygenic diseases.

Cross-Linking and Mass Spectrometry Methodologies to Facilitate Structural Biology: Finding a Path through the Maze

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

Merkley, Eric D.; Cort, John R.; Adkins, Joshua N.

2013-09-01

Multiprotein complexes, rather than individual proteins, make up a large part of the biological macromolecular machinery of a cell. Understanding the structure and organization of these complexes is critical to understanding cellular function. Chemical cross-linking coupled with mass spectrometry is emerging as a complementary technique to traditional structural biology methods and can provide low-resolution structural information for a multitude of purposes, such as distance constraints in computational modeling of protein complexes. In this review, we discuss the experimental considerations for successful application of chemical cross-linking-mass spectrometry in biological studies and highlight three examples of such studies from the recent literature.more » These examples (as well as many others) illustrate the utility of a chemical cross-linking-mass spectrometry approach in facilitating structural analysis of large and challenging complexes.« less

Network exploitation using WAMI tracks

NASA Astrophysics Data System (ADS)

Rimey, Ray; Record, Jim; Keefe, Dan; Kennedy, Levi; Cramer, Chris

2011-06-01

Creating and exploiting network models from wide area motion imagery (WAMI) is an important task for intelligence analysis. Tracks of entities observed moving in the WAMI sensor data are extracted, then large numbers of tracks are studied over long time intervals to determine specific locations that are visited (e.g., buildings in an urban environment), what locations are related to other locations, and the function of each location. This paper describes several parts of the network detection/exploitation problem, and summarizes a solution technique for each: (a) Detecting nodes; (b) Detecting links between known nodes; (c) Node attributes to characterize a node; (d) Link attributes to characterize each link; (e) Link structure inferred from node attributes and vice versa; and (f) Decomposing a detected network into smaller networks. Experimental results are presented for each solution technique, and those are used to discuss issues for each problem part and its solution technique.

Experimental Test Rig for Optimal Control of Flexible Space Robotic Arms

DTIC Science & Technology

2016-12-01

was used to refine the test bed design and the experimental workflow. Three concepts incorporated various strategies to design a robust flexible link...used to refine the test bed design and the experimental workflow. Three concepts incorporated various strategies to design a robust flexible link... designed to perform the experimentation . The first and second concepts use traditional elastic springs in varying configurations while a third uses a

Measurement of optical intensity fluctuation over an 11.8 km turbulent path.

PubMed

Jiang, Yijun; Ma, Jing; Tan, Liying; Yu, Siyuan; Du, Wenhe

2008-05-12

An 11.8km optical link is established to examine the intensity fluctuation of the laser beam transmission through atmosphere turbulence. Probability density function, fade statistic, and high-frequency spectrum are researched based on the analysis of the experimental data collected in each season of a year, including both weak and strong fluctuation cases. Finally, the daily variation curve of scintillation index is given, compared with the variation of refractive-index structure parameter C(n) (2), which is calculated from the experimental data of angle of arrival. This work provides the experimental results that are helpful to the atmospheric propagation research and the free-space optical communication system design.

TargetLink, a new method for identifying the endogenous target set of a specific microRNA in intact living cells.

PubMed

Xu, Yan; Chen, Yan; Li, Daliang; Liu, Qing; Xuan, Zhenyu; Li, Wen-Hong

2017-02-01

MicroRNAs are small non-coding RNAs acting as posttranscriptional repressors of gene expression. Identifying mRNA targets of a given miRNA remains an outstanding challenge in the field. We have developed a new experimental approach, TargetLink, that applied locked nucleic acid (LNA) as the affinity probe to enrich target genes of a specific microRNA in intact cells. TargetLink also consists a rigorous and systematic data analysis pipeline to identify target genes by comparing LNA-enriched sequences between experimental and control samples. Using miR-21 as a test microRNA, we identified 12 target genes of miR-21 in a human colorectal cancer cell by this approach. The majority of the identified targets interacted with miR-21 via imperfect seed pairing. Target validation confirmed that miR-21 repressed the expression of the identified targets. The cellular abundance of the identified miR-21 target transcripts varied over a wide range, with some targets expressed at a rather low level, confirming that both abundant and rare transcripts are susceptible to regulation by microRNAs, and that TargetLink is an efficient approach for identifying the target set of a specific microRNA in intact cells. C20orf111, one of the novel targets identified by TargetLink, was found to reside in the nuclear speckle and to be reliably repressed by miR-21 through the interaction at its coding sequence.

Theoretical and experimental research in aeroelastic stability of an advanced bearingless rotor for future helicopters

NASA Technical Reports Server (NTRS)

Wang, James M.

1991-01-01

The aeroelastic stability of a shaft-fixed bearingless rotor is analyzed in wind-tunnel tests for a wide range of operating conditions in order to determine whether such a system could be made aeroelastically stable without incorporating auxiliary dampers. The model rotor and blade properties are determined and used as an input to a bearingless-rotor analysis. Theoretical predictions are compared with experimental results in hover and forward flights. The analysis predicts the lag mode damping satisfactorily for collective pitch between 5 deg and 10 deg; however, the quasi-steady linear aerodynamic modeling overpredicts the damping values for higher collective pitch settings. It is noted that soft blade pitch links improve aeroelastic stability in hover and at low advance ratio.

XLinkDB 2.0: integrated, large-scale structural analysis of protein crosslinking data

PubMed Central

Schweppe, Devin K.; Zheng, Chunxiang; Chavez, Juan D.; Navare, Arti T.; Wu, Xia; Eng, Jimmy K.; Bruce, James E.

2016-01-01

Motivation: Large-scale chemical cross-linking with mass spectrometry (XL-MS) analyses are quickly becoming a powerful means for high-throughput determination of protein structural information and protein–protein interactions. Recent studies have garnered thousands of cross-linked interactions, yet the field lacks an effective tool to compile experimental data or access the network and structural knowledge for these large scale analyses. We present XLinkDB 2.0 which integrates tools for network analysis, Protein Databank queries, modeling of predicted protein structures and modeling of docked protein structures. The novel, integrated approach of XLinkDB 2.0 enables the holistic analysis of XL-MS protein interaction data without limitation to the cross-linker or analytical system used for the analysis. Availability and Implementation: XLinkDB 2.0 can be found here, including documentation and help: http://xlinkdb.gs.washington.edu/. Contact: jimbruce@uw.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153666

Cross-study projections of genomic biomarkers: an evaluation in cancer genomics.

PubMed

Lucas, Joseph E; Carvalho, Carlos M; Chen, Julia Ling-Yu; Chi, Jen-Tsan; West, Mike

2009-01-01

Human disease studies using DNA microarrays in both clinical/observational and experimental/controlled studies are having increasing impact on our understanding of the complexity of human diseases. A fundamental concept is the use of gene expression as a "common currency" that links the results of in vitro controlled experiments to in vivo observational human studies. Many studies--in cancer and other diseases--have shown promise in using in vitro cell manipulations to improve understanding of in vivo biology, but experiments often simply fail to reflect the enormous phenotypic variation seen in human diseases. We address this with a framework and methods to dissect, enhance and extend the in vivo utility of in vitro derived gene expression signatures. From an experimentally defined gene expression signature we use statistical factor analysis to generate multiple quantitative factors in human cancer gene expression data. These factors retain their relationship to the original, one-dimensional in vitro signature but better describe the diversity of in vivo biology. In a breast cancer analysis, we show that factors can reflect fundamentally different biological processes linked to molecular and clinical features of human cancers, and that in combination they can improve prediction of clinical outcomes.

Cross-Link Guided Molecular Modeling with ROSETTA

PubMed Central

Leitner, Alexander; Rosenberger, George; Aebersold, Ruedi; Malmström, Lars

2013-01-01

Chemical cross-links identified by mass spectrometry generate distance restraints that reveal low-resolution structural information on proteins and protein complexes. The technology to reliably generate such data has become mature and robust enough to shift the focus to the question of how these distance restraints can be best integrated into molecular modeling calculations. Here, we introduce three workflows for incorporating distance restraints generated by chemical cross-linking and mass spectrometry into ROSETTA protocols for comparative and de novo modeling and protein-protein docking. We demonstrate that the cross-link validation and visualization software Xwalk facilitates successful cross-link data integration. Besides the protocols we introduce XLdb, a database of chemical cross-links from 14 different publications with 506 intra-protein and 62 inter-protein cross-links, where each cross-link can be mapped on an experimental structure from the Protein Data Bank. Finally, we demonstrate on a protein-protein docking reference data set the impact of virtual cross-links on protein docking calculations and show that an inter-protein cross-link can reduce on average the RMSD of a docking prediction by 5.0 Å. The methods and results presented here provide guidelines for the effective integration of chemical cross-link data in molecular modeling calculations and should advance the structural analysis of particularly large and transient protein complexes via hybrid structural biology methods. PMID:24069194

Simulation of Delamination Under High Cycle Fatigue in Composite Materials Using Cohesive Models

NASA Technical Reports Server (NTRS)

Camanho, Pedro P.; Turon, Albert; Costa, Josep; Davila, Carlos G.

2006-01-01

A new thermodynamically consistent damage model is proposed for the simulation of high-cycle fatigue crack growth. The basis for the formulation is an interfacial degradation law that links Fracture Mechanics and Damage Mechanics to relate the evolution of the damage variable, d, with the crack growth rate da/dN. The damage state is a function of the loading conditions (R and (Delta)G) as well as the experimentally-determined crack growth rates for the material. The formulation ensures that the experimental results can be reproduced by the analysis without the need of additional adjustment parameters.

Topology association analysis in weighted protein interaction network for gene prioritization

NASA Astrophysics Data System (ADS)

Wu, Shunyao; Shao, Fengjing; Zhang, Qi; Ji, Jun; Xu, Shaojie; Sun, Rencheng; Sun, Gengxin; Du, Xiangjun; Sui, Yi

2016-11-01

Although lots of algorithms for disease gene prediction have been proposed, the weights of edges are rarely taken into account. In this paper, the strengths of topology associations between disease and essential genes are analyzed in weighted protein interaction network. Empirical analysis demonstrates that compared to other genes, disease genes are weakly connected with essential genes in protein interaction network. Based on this finding, a novel global distance measurement for gene prioritization with weighted protein interaction network is proposed in this paper. Positive and negative flow is allocated to disease and essential genes, respectively. Additionally network propagation model is extended for weighted network. Experimental results on 110 diseases verify the effectiveness and potential of the proposed measurement. Moreover, weak links play more important role than strong links for gene prioritization, which is meaningful to deeply understand protein interaction network.

Telescience testbed: operational support functions for biomedical experiments.

PubMed

Yamashita, M; Watanabe, S; Shoji, T; Clarke, A H; Suzuki, H; Yanagihara, D

1992-07-01

A telescience testbed was conducted to study the methodology of space biomedicine with simulated constraints imposed on space experiments. An experimental subject selected for this testbedding was an elaborate surgery of animals and electrophysiological measurements conducted by an operator onboard. The standing potential in the ampulla of the pigeon's semicircular canal was measured during gravitational and caloric stimulation. A principal investigator, isolated from the operation site, participated in the experiment interactively by telecommunication links. Reliability analysis was applied to the whole layers of experimentation, including design of experimental objectives and operational procedures. Engineering and technological aspects of telescience are discussed in terms of reliability to assure quality of science. Feasibility of robotics was examined for supportive functions to reduce the workload of the onboard operator.

Linking water age and solute dynamics in streamflow at the Hubbard Brook Experimental Forest, NH, USA

Treesearch

Paolo Benettin; Scott W. Bailey; John L. Campbell; Mark B. Green; Andrea Rinaldo; Gene E. Likens; Kevin J. McGuire; Gianluca Botter

2015-01-01

We combine experimental and modeling results from a headwater catchment at the Hubbard Brook Experimental Forest (HBEF), New Hampshire, USA, to explore the link between stream solute dynamics and water age. A theoretical framework based on water age dynamics, which represents a general basis for characterizing solute transport at the catchment scale, is here applied to...

Integration, warehousing, and analysis strategies of Omics data.

PubMed

Gedela, Srinubabu

2011-01-01

"-Omics" is a current suffix for numerous types of large-scale biological data generation procedures, which naturally demand the development of novel algorithms for data storage and analysis. With next generation genome sequencing burgeoning, it is pivotal to decipher a coding site on the genome, a gene's function, and information on transcripts next to the pure availability of sequence information. To explore a genome and downstream molecular processes, we need umpteen results at the various levels of cellular organization by utilizing different experimental designs, data analysis strategies and methodologies. Here comes the need for controlled vocabularies and data integration to annotate, store, and update the flow of experimental data. This chapter explores key methodologies to merge Omics data by semantic data carriers, discusses controlled vocabularies as eXtensible Markup Languages (XML), and provides practical guidance, databases, and software links supporting the integration of Omics data.

Music and suicidality: a quantitative review and extension.

PubMed

Stack, Steven; Lester, David; Rosenberg, Jonathan S

2012-12-01

This article provides the first quantitative review of the literature on music and suicidality. Multivariate logistic regression techniques are applied to 90 findings from 21 studies. Investigations employing ecological data on suicide completions are 19.2 times more apt than other studies to report a link between music and suicide. More recent and studies with large samples are also more apt than their counterparts to report significant results. Further, none of the studies based on experimental research designs found a link between music and suicide ideation, prompting us to do a brief content analysis of 24 suicide songs versus 24 nonsuicide songs from the same album. Using Linguistic Inquiry and Word Count software, we found no difference in the content of the suicide songs and controls, including the percentage of sad words, negative affect, and mentions of death, thus providing an explanation for nonfindings from experimental research. In summary, ecologically based (which capture at-risk persons not in typical school-based samples) and more recent investigations (which have used superior or new methodologies) tend to demonstrate a linkage between music and suicidality. Experimental research is needed with a control group of songs from an alternative genre with low suicidogenic content. © 2012 The American Association of Suicidology.

Analysis of a SNP Linked to Lactase Persistence: An Exercise for Teaching Molecular Biology Techniques to Undergraduates

ERIC Educational Resources Information Center

Schultheis, Patrick J.; Bowling, Bethany V.

2011-01-01

Recent experimental evidence indicates that the ability of adults to tolerate milk, cheese, and other lactose-containing dairy products is an autosomal dominant trait that co-evolved with dairy farming in Central Europe about 7,500 years ago. Among persons of European descent, this trait is strongly associated with a C to T substitution at a…

Effect of low molecular weight heparin rectal suppository on experimental ulcerative colitis in mice.

PubMed

Luo, Junyong; Cao, Jichao; Jiang, Xueliang; Cui, Huifei

2010-09-01

The objective of this study was to investigate the effect and possible mechanism of rectally administered low molecular weight heparin (LMWH) on experimental ulcerative colitis. LMWH rectal suppository was prepared and its efficacy was studied by macroscopical and histological scoring systems as well as myeloperoxidase activity. Serum levels, including tumor necrosis factor-α (TNFα), interleukin-6 (IL-6) and a link factor of blood coagulation and inflammation factor Xa (FXa) were assayed by enzyme-linked immunosorbent assay. The expression of Musashi-1 (as an intestinal stem cell marker) in the colons was assessed by immunohistochemical analysis. The results showed that LMWH rectal suppository significantly decreased serum levels of TNF-α, IL-6 as well as FXa, while increased the expression of Musashi-1 in colon compared with acetic acid induced ulcerative colitis model group. All these preliminary results indicate LMWH rectal suppository is promising for treatment of ulcerative colitis. 2010 Elsevier Masson SAS. All rights reserved.

A propagation effects handbook for satellite systems design. A summary of propagation impairments on 10-100 GHz satellite links, with techniques for system design. [tropospheric scattering

NASA Technical Reports Server (NTRS)

Kaul, R.; Wallace, R.; Kinal, G.

1980-01-01

This handbook provides satellite system engineers with a concise summary of the major propagation effects experienced on Earth-space paths in the 10 to 100 GHz frequency range. The dominant effect, attenuation due to rain, is dealt with in terms of both experimental data from measurements made in the U.S. and Canada, and the mathematical and conceptual models devised to explain the data. Rain systems, rain and attenuation models, depolarization and experimental data are described. The design techniques recommended for predicting propagation effects in Earth-space communications systems are presented. The questions of where in the system design process the effects of propagation should be considered, and what precautions should be taken when applying the propagation results are addressed in order to bridge the gap between the propagation research data and the classical link budget analysis of Earth-space communications system.

Differential expression of the Nrf2-linked genes in pediatric septic shock.

PubMed

Grunwell, Jocelyn R; Weiss, Scott L; Cvijanovich, Natalie Z; Allen, Geoffrey L; Thomas, Neal J; Freishtat, Robert J; Anas, Nick; Meyer, Keith; Checchia, Paul A; Shanley, Thomas P; Bigham, Michael T; Fitzgerald, Julie; Howard, Kelli; Frank, Erin; Harmon, Kelli; Wong, Hector R

2015-09-17

Experimental data from animal models of sepsis support a role for a transcription factor, nuclear erythroid-related factor 2 p45-related factor 2 (Nrf2), as a master regulator of antioxidant and detoxifying genes and intermediary metabolism during stress. Prior analysis of a pediatric septic shock transcriptomic database showed that the Nrf2 response is a top 5 upregulated signaling pathway in early pediatric septic shock. We conducted a focused analysis of 267 Nrf2-linked genes using a multicenter, genome-wide expression database of 180 children with septic shock 10 years of age or younger and 53 healthy controls. The analysis involved RNA isolated from whole blood within 24 h of pediatric intensive care unit admission for septic shock and a false discovery rate of 5 %. We compared differentially expressed genes from (1) patients with septic shock and healthy controls and (2) across validated gene expression-based subclasses of pediatric septic shock (endotypes A and B) using several bioinformatic methods. We found upregulation of 123 Nrf2-linked genes in children with septic shock. The top gene network represented by these genes contained primarily enzymes with oxidoreductase activity involved in cellular lipid metabolism that were highly connected to the peroxisome proliferator activated receptor and the retinoic acid receptor families. Endotype A, which had higher organ failure burden and mortality, exhibited a greater downregulation of Nrf2-linked genes than endotype B, with 92 genes differentially regulated between endotypes. Our findings indicate that Nrf2-linked genes may contribute to alterations in oxidative signaling and intermediary metabolism in pediatric septic shock.

Anatomy of an experimental two-link flexible manipulator under end-point control

NASA Technical Reports Server (NTRS)

Oakley, Celia M.; Cannon, Robert H., Jr.

1990-01-01

The design and experimental implementation of an end-point controller for two-link flexible manipulators are presented. The end-point controller is based on linear quadratic Gaussian (LQG) theory and is shown to exhibit significant improvements in trajectory tracking over a conventional controller design. To understand the behavior of the manipulator structure under end-point control, a strobe sequence illustrating the link deflections during a typical slew maneuver is included.

Phenotypic and functional characterization of earthworm coelomocyte subsets: Linking light scatter-based cell typing and imaging of the sorted populations.

PubMed

Engelmann, Péter; Hayashi, Yuya; Bodó, Kornélia; Ernszt, Dávid; Somogyi, Ildikó; Steib, Anita; Orbán, József; Pollák, Edit; Nyitrai, Miklós; Németh, Péter; Molnár, László

2016-12-01

Flow cytometry is a common approach to study invertebrate immune cells including earthworm coelomocytes. However, the link between light-scatter- and microscopy-based phenotyping remains obscured. Here we show, by means of light scatter-based cell sorting, both subpopulations (amoebocytes and eleocytes) can be physically isolated with good sort efficiency and purity confirmed by downstream morphological and cytochemical applications. Immunocytochemical analysis using anti-EFCC monoclonal antibodies combined with phalloidin staining has revealed antigenically distinct, sorted subsets. Screening of lectin binding capacity indicated wheat germ agglutinin (WGA) as the strongest reactor to amoebocytes. This is further evidenced by WGA inhibition assays that suggest high abundance of N-acetyl-d-glucosamine in amoebocytes. Post-sort phagocytosis assays confirmed the functional differences between amoebocytes and eleocytes, with the former being in favor of bacterial engulfment. This study has proved successful in linking flow cytometry and microscopy analysis and provides further experimental evidence of phenotypic and functional heterogeneity in earthworm coelomocyte subsets. Copyright © 2016 Elsevier Ltd. All rights reserved.

N-Glycan Structure Annotation of Glycopeptides Using a Linearized Glycan Structure Database (GlyDB)

PubMed Central

Ren, Jian Min; Rejtar, Tomas; Li, Lingyun; Karger, Barry L.

2008-01-01

While glycoproteins are abundant in nature, and changes in glycosylation occur in cancer and other diseases, glycoprotein characterization remains a challenge due to the structural complexity of the biopolymers. This paper presents a general strategy, termed GlyDB, for glycan structure annotation of N-linked glycopeptides from tandem mass spectra in the LC-MS analysis of proteolytic digests of glycoproteins. The GlyDB approach takes advantage of low-energy collision induced dissociation of N-linked glycopeptides that preferentially cleaves the glycosidic bonds while the peptide backbone remains intact. A theoretical glycan structure database derived from biosynthetic rules for N-linked glycans was constructed employing a novel representation of branched glycan structures consisting of multiple linear sequences. The commonly used peptide identification program, Sequest, could then be utilized to assign experimental tandem mass spectra to individual glycoforms. Analysis of synthetic glycopeptides and well-characterized glycoproteins demonstrate that the GlyDB approach can be a useful tool for annotation of glycan structures and for selection of a limited number of potential glycan structure candidates for targeted validation. PMID:17625816

An Experimental Comparison of CLOS and C++ Implementations of An Object- Oriented Graphical Simulation of Walking Robot Kinematics

DTIC Science & Technology

1993-03-25

attachment-angle :accessor leg-attachment-angle) (linkO :initform (make-instance ’linkO) :accessor linkO) ( linki :initform (make-instance ’ linki ...accessor linki ) (link2 :initform (make-instance ’link2) :accessor link2) (link3 :initform (make-instance ’link3) :accessor link3) (motion-complete-flag...inboard-link ( linki leg)) (linkO leg)) (setf (inboard-link (link2 leg)) ( linki leg)) (setf (inboard-link (link3 leg)) (link2 leg)) (rotate-link (linkO

Anomalous waves propagating at very high frequency in the atmosphere and their disturbances due to changes in refractivity profiles

NASA Astrophysics Data System (ADS)

Alam, Imtiaz; Waqar, Asad; Aamir, Muhammad; Hassan, Shahzad; Shah, Syed Asim Ali

2018-03-01

Anomalous waves propagation is severely affected due to almost always present variations in refractivity under various environmental conditions at different time, location and frequency. These conditions, representing different state of the atmosphere including e.g. foggy, rainy and cloudy etc., not only degrade the quality of the signal but sometimes completely eradicate the communication link. Such severe impact on propagation cannot be ignored by the designers of communication systems. The aim of this research is to present correlation between experimental and modelled link losses for variations in refractivity values recommended by International Telecommunication Union-Recommendations (ITU-R) as well as that of standard profiles. To do so, a communication setup of 50 km over the Sea operating experimentally over a period of a year at 240 MHz is analyzed for different refractivity profiles and their impact on propagation. A median value is taken for every set of 6000 values taken from the recorded data set of more than 48 million experimental link losses. This reduces the huge data set of the experimental link losses to 8000 values only. This reduced data set of experimental and modelled link losses were correlated and investigated for different evaporation duct heights throughout the year. For the considered link, the ITU-R refractivity profile was found to perform better than the standard refractivity profile. However, the new findings as observed in this research, which may be helpful for the recommendations authorities, is the existing of evaporation duct up to 10 m height.

Experimental verification of a model of a two-link flexible, lightweight manipulator. M.S. Thesis

NASA Technical Reports Server (NTRS)

Huggins, James David

1988-01-01

Experimental verification is presented for an assumed modes model of a large, two link, flexible manipulator design and constructed in the School of Mechanical Engineering at Georgia Institute of Technology. The structure was designed to have typical characteristics of a lightweight manipulator.

End-point controller design for an experimental two-link flexible manipulator using convex optimization

NASA Technical Reports Server (NTRS)

Oakley, Celia M.; Barratt, Craig H.

1990-01-01

Recent results in linear controller design are used to design an end-point controller for an experimental two-link flexible manipulator. A nominal 14-state linear-quadratic-Gaussian (LQG) controller was augmented with a 528-tap finite-impulse-response (FIR) filter designed using convex optimization techniques. The resulting 278-state controller produced improved end-point trajectory tracking and disturbance rejection in simulation and experimentally in real time.

Analytical performance study of solar blind non-line-of-sight ultraviolet short-range communication links.

PubMed

Xu, Zhengyuan; Ding, Haipeng; Sadler, Brian M; Chen, Gang

2008-08-15

Motivated by recent advances in solid-state incoherent ultraviolet sources and solar blind detectors, we study communication link performance over a range of less than 1 km with a bit error rate (BER) below 10(-3) in solar blind non-line-of-sight situation. The widely adopted yet complex single scattering channel model is significantly simplified by means of a closed-form expression for tractable analysis. Path loss is given as a function of transceiver geometry as well as atmospheric scattering and attenuation and is compared with experimental data for model validation. The BER performance of a shot-noise-limited receiver under this channel model is demonstrated.

Influence of galactose cataract on erythrocytic and lenticular glutathione metabolism in albino rats.

PubMed

Jyothi, M; Sanil, R; Shashidhar, S

2011-01-01

Glutathione depletion has been postulated to be the prime reason for galactose cataract. The current research seeks the prospect of targeting erythrocytes to pursue the lens metabolism by studying the glutathione system. To study the activity of the glutathione-linked scavenger enzyme system in the erythrocyte and lens of rats with cataract. Experiments were conducted in 36 male albino rats weighing 80 ± 20 g of 28 days of age. The rats were divided into two major groups, viz. experimental and control. Six rats in each group were sacrificed every 10 days, for 30 days. Cataract was induced in the experimental group by feeding the rats 30% galactose (w/w). The involvement of reduced glutathione (GSH) and the linked enzymes was studied in the erythrocytes and lens of cataractous as well as control rats. Parametric tests like one-way ANOVA and Student's 't' test were used for comparison. Correlation linear plot was used to compare the erythrocyte and lens metabolism. The concentration of GSH and the activity of linked enzymes were found decreased with the progression of cataract, and also in comparison to the control. The same linear fashion was also observed in the erythrocytes. Depletion of GSH was the prime factor for initiating galactose cataract in the rat model. This depletion may in turn result in enzyme inactivation leading to cross-linking of protein and glycation. The correlation analysis specifies that the biochemical mechanism in the erythrocytes and lens is similar in the rat model.

Evolution of apomixis loci in Pilosella and Hieracium (Asteraceae) inferred from the conservation of apomixis-linked markers in natural and experimental populations

PubMed Central

Hand, M L; Vít, P; Krahulcová, A; Johnson, S D; Oelkers, K; Siddons, H; Chrtek, J; Fehrer, J; Koltunow, A M G

2015-01-01

The Hieracium and Pilosella (Lactuceae, Asteraceae) genera of closely related hawkweeds contain species with two different modes of gametophytic apomixis (asexual seed formation). Both genera contain polyploid species, and in wild populations, sexual and apomictic species co-exist. Apomixis is known to co-exist with sexuality in apomictic Pilosella individuals, however, apomictic Hieracium have been regarded as obligate apomicts. Here, a developmental analysis of apomixis within 16 Hieracium species revealed meiosis and megaspore tetrad formation in 1 to 7% of ovules, for the first time indicating residual sexuality in this genus. Molecular markers linked to the two independent, dominant loci LOSS OF APOMEIOSIS (LOA) and LOSS OF PARTHENOGENESIS (LOP) controlling apomixis in Pilosella piloselloides subsp. praealta were screened across 20 phenotyped Hieracium individuals from natural populations, and 65 phenotyped Pilosella individuals from natural and experimental cross populations, to examine their conservation, inheritance and association with reproductive modes. All of the tested LOA and LOP-linked markers were absent in the 20 Hieracium samples irrespective of their reproductive mode. Within Pilosella, LOA and LOP-linked markers were essentially absent within the sexual plants, although they were not conserved in all apomictic individuals. Both loci appeared to be inherited independently, and evidence for additional genetic factors influencing quantitative expression of LOA and LOP was obtained. Collectively, these data suggest independent evolution of apomixis in Hieracium and Pilosella and are discussed with respect to current knowledge of the evolution of apomixis. PMID:25026970

Complex interaction of dendritic connectivity and hierarchical patch size on biodiversity in river-like landscapes.

PubMed

Carrara, Francesco; Rinaldo, Andrea; Giometto, Andrea; Altermatt, Florian

2014-01-01

Habitat fragmentation and land use changes are causing major biodiversity losses. Connectivity of the landscape or environmental conditions alone can shape biodiversity patterns. In nature, however, local habitat characteristics are often intrinsically linked to a specific connectivity. Such a link is evident in riverine ecosystems, where hierarchical dendritic structures command related scaling on habitat capacity. We experimentally disentangled the effect of local habitat capacity (i.e., the patch size) and dendritic connectivity on biodiversity in aquatic microcosm metacommunities by suitably arranging patch sizes within river-like networks. Overall, more connected communities that occupy a central position in the network exhibited higher species richness, irrespective of patch size arrangement. High regional evenness in community composition was found only in landscapes preserving geomorphological scaling properties of patch sizes. In these landscapes, some of the rarer species sustained regionally more abundant populations better tracking their own niche requirements compared to landscapes with homogeneous patch size or landscapes with spatially uncorrelated patch size. Our analysis suggests that altering the natural link between dendritic connectivity and patch size strongly affects community composition and population persistence at multiple scales. The experimental results are demonstrating a principle that can be tested in theoretical metacommunity models and eventually be projected to real riverine ecosystems.

In-orbit verification of small optical transponder (SOTA): evaluation of satellite-to-ground laser communication links

NASA Astrophysics Data System (ADS)

Takenaka, Hideki; Koyama, Yoshisada; Akioka, Maki; Kolev, Dimitar; Iwakiri, Naohiko; Kunimori, Hiroo; Carrasco-Casado, Alberto; Munemasa, Yasushi; Okamoto, Eiji; Toyoshima, Morio

2016-03-01

Research and development of space optical communications is conducted in the National Institute of Information and Communications Technology (NICT). The NICT developed the Small Optical TrAnsponder (SOTA), which was embarked on a 50kg-class satellite and launched into a low earth orbit (LEO). The space-to-ground laser communication experiments have been conducted with the SOTA. Atmospheric turbulence causes signal fadings and becomes an issue to be solved in satellite-to-ground laser communication links. Therefore, as error-correcting functions, a Reed-Solomon (RS) code and a Low-Density Generator Matrix (LDGM) code are implemented in the communication system onboard the SOTA. In this paper, we present the in-orbit verification results of SOTA including the characteristic of the functions, the communication performance with the LDGM code via satellite-to-ground atmospheric paths, and the link budget analysis and the comparison between theoretical and experimental results.

Adsorption of hexavalent chromium on modified corn stalk using different cross-linking agents

NASA Astrophysics Data System (ADS)

Chen, Suhong; Zhu, Yi; Han, Zhijun; Feng, Gao; Jia, Yuling; Fu, Kaifang; Yue, Qinyan

2017-12-01

In this study, four different types of adsorbents modified from corn stalk were synthesized after the reaction with epichlorohydrin, N,N-dimethylformamide, triethylamine and different cross-linking agents. The surface functional groups and thermal stability of modified corn stalk (MCSs) were characterized using FTIR and TG analysis, respectively. The feasibility of using MCSs to remove Cr(VI) were evaluated. Adsorption isotherms were determined and modeled with Langmuir, Freundlich and Temkin equations. The experimental results showed that MCS modified using diethylenetriamine (DETA) had the best modification effect, and the adsorption capacity of Cr(VI) reached as high as 227.27 mg/g at 323 K. Thermodynamic study showed that the Cr(VI) adsorption onto MCSs was endothermic processes. As a result, MCS by using DETA as cross-linking agent has good potential for the removal of Cr(VI) from aqueous solutions.

Experimental FSO network availability estimation using interactive fog condition monitoring

NASA Astrophysics Data System (ADS)

Turán, Ján.; Ovseník, Łuboš

2016-12-01

Free Space Optics (FSO) is a license free Line of Sight (LOS) telecommunication technology which offers full duplex connectivity. FSO uses infrared beams of light to provide optical broadband connection and it can be installed literally in a few hours. Data rates go through from several hundreds of Mb/s to several Gb/s and range is from several 100 m up to several km. FSO link advantages: Easy connection establishment, License free communication, No excavation are needed, Highly secure and safe, Allows through window connectivity and single customer service and Compliments fiber by accelerating the first and last mile. FSO link disadvantages: Transmission media is air, Weather and climate dependence, Attenuation due to rain, snow and fog, Scattering of laser beam, Absorption of laser beam, Building motion and Air pollution. In this paper FSO availability evaluation is based on long term measured data from Fog sensor developed and installed at TUKE experimental FSO network in TUKE campus, Košice, Slovakia. Our FSO experimental network has three links with different physical distances between each FSO heads. Weather conditions have a tremendous impact on FSO operation in terms of FSO availability. FSO link availability is the percentage of time over a year that the FSO link will be operational. It is necessary to evaluate the climate and weather at the actual geographical location where FSO link is going to be mounted. It is important to determine the impact of a light scattering, absorption, turbulence and receiving optical power at the particular FSO link. Visibility has one of the most critical influences on the quality of an FSO optical transmission channel. FSO link availability is usually estimated using visibility information collected from nearby airport weather stations. Raw data from fog sensor (Fog Density, Relative Humidity, Temperature measured at each ms) are collected and processed by FSO Simulator software package developed at our Department. Based on FSO link data the FSO link and experimental FSO network availability was estimated for years from 2007 up to 2015. The average FSO network availability up to 98,3378 % was measured (for the BER 10-9). From the experimental data also Hybrid RF/FSO link availability was evaluated. As the weather conditions for FSO and RF link are complementary (FSO works well in rain and RF works well in fog) Hybrid FSO/RF system long time average availability was much better up to 99,9986 %.

Microstructure and rheology of thermoreversible nanoparticle gels.

PubMed

Ramakrishnan, S; Zukoski, C F

2006-08-29

Naïve mode coupling theory is applied to particles interacting with short-range Yukawa attractions. Model results for the location of the gel line and the modulus of the resulting gels are reduced to algebraic equations capturing the effects of the range and strength of attraction. This model is then applied to thermo reversible gels composed of octadecyl silica particles suspended in decalin. The application of the model to the experimental system requires linking the experimental variable controlling strength of attraction, temperature, to the model strength of attraction. With this link, the model predicts temperature and volume fraction dependencies of gelation and modulus with five parameters: particle size, particle volume fraction, overlap volume of surface hairs, and theta temperature. In comparing model predictions with experimental results, we first observe that in these thermal gels there is no evidence of clustering as has been reported in depletion gels. One consequence of this observation is that there are no additional adjustable parameters required to make quantitative comparisons between experimental results and model predictions. Our results indicate that the naïve mode coupling approach taken here in conjunction with a model linking temperature to strength of attraction provides a robust approach for making quantitative predictions of gel mechanical properties. Extension of model predictions to additional experimental systems requires linking experimental variables to the Yukawa strength and range of attraction.

How and Why Affective and Reactive Virtual Agents Will Bring New Insights on Social Cognitive Disorders in Schizophrenia? An Illustration with a Virtual Card Game Paradigm

PubMed Central

Oker, Ali; Prigent, Elise; Courgeon, Matthieu; Eyharabide, Victoria; Urbach, Mathieu; Bazin, Nadine; Amorim, Michel-Ange; Passerieux, Christine; Martin, Jean-Claude; Brunet-Gouet, Eric

2015-01-01

In recent decades, many studies have shown that schizophrenia is associated with severe social cognitive impairments affecting key components, such as the recognition of emotions, theory of mind, attributional style, and metacognition. Most studies investigated each construct separately, precluding analysis of the interactive and immersive nature of real-life situation. Specialized batteries of tests are under investigation to assess social cognition, which is thought now as a link between neurocognitive disorders and impaired functioning. However, this link accounts for a limited part of the variance of real-life functioning. To fill this gap, advances in virtual reality and affective computing have made it possible to carry out experimental investigations of naturalistic social cognition, in controlled conditions, with good reproducibility. This approach is illustrated with the description of a new paradigm based on an original virtual card game in which subjects interpret emotional displays from a female virtual agent, and decipher her helping intentions. Independent variables concerning emotional expression in terms of valence and intensity were manipulated. We show how several useful dependant variables, ranging from classic experimental psychology data to metacognition or subjective experiences records, may be extracted from a single experiment. Methodological issues about the immersion into a simulated intersubjective situation are considered. The example of this new flexible experimental setting, with regards to the many constructs recognized in social neurosciences, constitutes a rationale for focusing on this potential intermediate link between standardized tests and real-life functioning, and also for using it as an innovative media for cognitive remediation. PMID:25870549

How and why affective and reactive virtual agents will bring new insights on social cognitive disorders in schizophrenia? An illustration with a virtual card game paradigm.

PubMed

Oker, Ali; Prigent, Elise; Courgeon, Matthieu; Eyharabide, Victoria; Urbach, Mathieu; Bazin, Nadine; Amorim, Michel-Ange; Passerieux, Christine; Martin, Jean-Claude; Brunet-Gouet, Eric

2015-01-01

In recent decades, many studies have shown that schizophrenia is associated with severe social cognitive impairments affecting key components, such as the recognition of emotions, theory of mind, attributional style, and metacognition. Most studies investigated each construct separately, precluding analysis of the interactive and immersive nature of real-life situation. Specialized batteries of tests are under investigation to assess social cognition, which is thought now as a link between neurocognitive disorders and impaired functioning. However, this link accounts for a limited part of the variance of real-life functioning. To fill this gap, advances in virtual reality and affective computing have made it possible to carry out experimental investigations of naturalistic social cognition, in controlled conditions, with good reproducibility. This approach is illustrated with the description of a new paradigm based on an original virtual card game in which subjects interpret emotional displays from a female virtual agent, and decipher her helping intentions. Independent variables concerning emotional expression in terms of valence and intensity were manipulated. We show how several useful dependant variables, ranging from classic experimental psychology data to metacognition or subjective experiences records, may be extracted from a single experiment. Methodological issues about the immersion into a simulated intersubjective situation are considered. The example of this new flexible experimental setting, with regards to the many constructs recognized in social neurosciences, constitutes a rationale for focusing on this potential intermediate link between standardized tests and real-life functioning, and also for using it as an innovative media for cognitive remediation.

Intuitive web-based experimental design for high-throughput biomedical data.

PubMed

Friedrich, Andreas; Kenar, Erhan; Kohlbacher, Oliver; Nahnsen, Sven

2015-01-01

Big data bioinformatics aims at drawing biological conclusions from huge and complex biological datasets. Added value from the analysis of big data, however, is only possible if the data is accompanied by accurate metadata annotation. Particularly in high-throughput experiments intelligent approaches are needed to keep track of the experimental design, including the conditions that are studied as well as information that might be interesting for failure analysis or further experiments in the future. In addition to the management of this information, means for an integrated design and interfaces for structured data annotation are urgently needed by researchers. Here, we propose a factor-based experimental design approach that enables scientists to easily create large-scale experiments with the help of a web-based system. We present a novel implementation of a web-based interface allowing the collection of arbitrary metadata. To exchange and edit information we provide a spreadsheet-based, humanly readable format. Subsequently, sample sheets with identifiers and metainformation for data generation facilities can be created. Data files created after measurement of the samples can be uploaded to a datastore, where they are automatically linked to the previously created experimental design model.

Bridging the Gap: Linking Simulation and Testing

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

Krajewski, Paul E.; Carsley, John; Stoudt, Mark R.

2012-09-01

The Materials Genome Initiative (MGI) which is a key enabler for the Advanced Manufacturing Partnership, announced in 2011 by U.S. President Barack Obama, was established to accelerate the development and deployment of advanced materials. The MGI is driven by the need to "bridge the gap" between (I) experimental results and computational analysis to enable the rapid development and validation of new mateirals, and (II) the processes required to convert these materials into useable goods.

An experimental analysis of granivory in desert ecosystems

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

Davidson, D.W.

1988-01-01

In our studies of desert granivore ecology, we have outlined the network of interaction pathways linking granivore and resource species in a Chihuahuan Desert Ecosystem. Here, a major fraction of the primary productivity takes the form of the seeds of annual plants. These seeds support two major resident taxa of desert granivores, ants and rodents. Population responses to removal of various taxa of granivores or seasonal classes of resource species are described.

Linking Proteomic and Transcriptional Data through the Interactome and Epigenome Reveals a Map of Oncogene-induced Signaling

PubMed Central

Huang, Shao-shan Carol; Clarke, David C.; Gosline, Sara J. C.; Labadorf, Adam; Chouinard, Candace R.; Gordon, William; Lauffenburger, Douglas A.; Fraenkel, Ernest

2013-01-01

Cellular signal transduction generally involves cascades of post-translational protein modifications that rapidly catalyze changes in protein-DNA interactions and gene expression. High-throughput measurements are improving our ability to study each of these stages individually, but do not capture the connections between them. Here we present an approach for building a network of physical links among these data that can be used to prioritize targets for pharmacological intervention. Our method recovers the critical missing links between proteomic and transcriptional data by relating changes in chromatin accessibility to changes in expression and then uses these links to connect proteomic and transcriptome data. We applied our approach to integrate epigenomic, phosphoproteomic and transcriptome changes induced by the variant III mutation of the epidermal growth factor receptor (EGFRvIII) in a cell line model of glioblastoma multiforme (GBM). To test the relevance of the network, we used small molecules to target highly connected nodes implicated by the network model that were not detected by the experimental data in isolation and we found that a large fraction of these agents alter cell viability. Among these are two compounds, ICG-001, targeting CREB binding protein (CREBBP), and PKF118–310, targeting β-catenin (CTNNB1), which have not been tested previously for effectiveness against GBM. At the level of transcriptional regulation, we used chromatin immunoprecipitation sequencing (ChIP-Seq) to experimentally determine the genome-wide binding locations of p300, a transcriptional co-regulator highly connected in the network. Analysis of p300 target genes suggested its role in tumorigenesis. We propose that this general method, in which experimental measurements are used as constraints for building regulatory networks from the interactome while taking into account noise and missing data, should be applicable to a wide range of high-throughput datasets. PMID:23408876

Analysis of an experiment aimed at improving the reliability of transmission centre shafts.

PubMed

Davis, T P

1995-01-01

Smith (1991) presents a paper proposing the use of Weibull regression models to establish dependence of failure data (usually times) on covariates related to the design of the test specimens and test procedures. In his article Smith made the point that good experimental design was as important in reliability applications as elsewhere, and in view of the current interest in design inspired by Taguchi and others, we pay some attention in this article to that topic. A real case study from the Ford Motor Company is presented. Our main approach is to utilize suggestions in the literature for applying standard least squares techniques of experimental analysis even when there is likely to be nonnormal error, and censoring. This approach lacks theoretical justification, but its appeal is its simplicity and flexibility. For completeness we also include some analysis based on the proportional hazards model, and in an attempt to link back to Smith (1991), look at a Weibull regression model.

Experimental demonstration of optical data links using a hybrid CAP/QAM modulation scheme.

PubMed

Wei, J L; Ingham, J D; Cheng, Q; Cunningham, D G; Penty, R V; White, I H

2014-03-15

The first known experimental demonstrations of a 10  Gb/s hybrid CAP-2/QAM-2 and a 20  Gb/s hybrid CAP-4/QAM-4 transmitter/receiver-based optical data link are performed. Successful transmission over 4.3 km of standard single-mode fiber (SMF) is achieved, with a link power penalty ∼0.4  dBo for CAP-2/QAM-2 and ∼1.5  dBo for CAP-4/QAM-4 at BER=10(-9).

A quantitative link between microplastic instability and macroscopic deformation behaviors in metallic glasses

NASA Astrophysics Data System (ADS)

Wu, Y.; Chen, G. L.; Hui, X. D.; Liu, C. T.; Lin, Y.; Shang, X. C.; Lu, Z. P.

2009-10-01

Based on mechanical instability of individual shear transformation zones (STZs), a quantitative link between the microplastic instability and macroscopic deformation behavior of metallic glasses was proposed. Our analysis confirms that macroscopic metallic glasses comprise a statistical distribution of STZ embryos with distributed values of activation energy, and the microplastic instability of all the individual STZs dictates the macroscopic deformation behavior of amorphous solids. The statistical model presented in this paper can successfully reproduce the macroscopic stress-strain curves determined experimentally and readily be used to predict strain-rate effects on the macroscopic responses with the availability of the material parameters at a certain strain rate, which offer new insights into understanding the actual deformation mechanism in amorphous solids.

Conjunctive Conceptual Clustering: A Methodology and Experimentation.

DTIC Science & Technology

1987-09-01

observing a typical restaurant table on vhich there are such objects as food on a plate, a salad, utensils, salt and pepper, napkins , a ase with flowers, a...colored graph has nodes and inks that match only if they have corre-ponding link-olor and node-color labelg 4w 80 [SEtexture sa lif ba p S M i e d If...LINK LINK LINK LINK LINK 9 0 1 OPENdRECT RECTLOD 1 2 CL 10 0 0 LINK LINK INK LINK LINK ,~ . 0.5. Input file for attribute-based clustering The

Electron tomography provides a direct link between the Payne effect and the inter-particle spacing of rubber composites

PubMed Central

Staniewicz, Lech; Vaudey, Thomas; Degrandcourt, Christophe; Couty, Marc; Gaboriaud, Fabien; Midgley, Paul

2014-01-01

Rubber-filler composites are a key component in the manufacture of tyres. The filler provides mechanical reinforcement and additional wear resistance to the rubber, but it in turn introduces non-linear mechanical behaviour to the material which most likely arises from interactions between the filler particles, mediated by the rubber matrix. While various studies have been made on the bulk mechanical properties and of the filler network structure (both imaging and by simulations), there presently does not exist any work directly linking filler particle spacing and mechanical properties. Here we show that using STEM tomography, aided by a machine learning image analysis procedure, to measure silica particle spacings provides a direct link between the inter-particle spacing and the reduction in shear modulus as a function of strain (the Payne effect), measured using dynamic mechanical analysis. Simulations of filler network formation using attractive, repulsive and non-interacting potentials were processed using the same method and compared with the experimental data, with the net result being that an attractive inter-particle potential is the most accurate way of modelling styrene-butadiene rubber-silica composite formation. PMID:25487130

Preliminary Analysis of Fluctuations in the Received Uplink-Beacon-Power Data Obtained From the GOLD Experiments

NASA Technical Reports Server (NTRS)

Jeganathan, M.; Wilson, K. E.; Lesh, J. R.

1996-01-01

Uplink data from recent free-space optical communication experiments carried out between the Table Mountain Facility and the Japanese Engineering Test Satellite are used to study fluctuations caused by beam propagation through the atmosphere. The influence of atmospheric scintillation, beam wander and jitter, and multiple uplink beams on the statistics of power received by the satellite is analyzed and compared to experimental data. Preliminary analysis indicates the received signal obeys an approximate lognormal distribution, as predicted by the weak-turbulence model, but further characterization of other sources of fluctuations is necessary for accurate link predictions.

Preliminary analysis of fluctuations in the received uplink-beacon-power data obtained from the GOLD experiments

NASA Technical Reports Server (NTRS)

Jeganathan, M.; Wilson, K. E.; Lesh, J. R.

1996-01-01

Uplink data from recent free-space optical communication experiments carried out between the Table Mountain Facility and the Japanese Engineering Test Satellite are used to study fluctuations caused by beam propagation through the atmosphere. The influence of atmospheric scintillation, beam wander and jitter, and multiple uplink beams on the statistics of power received by the satellite is analyzed and compared to experimental data. Preliminary analysis indicates the received signal obeys an approximate lognormal distribution, as predicted by the weak-turbulence model, but further characterization of other sources of fluctuations is necessary for accurate link predictions.

Reconfiguring practice: the interdependence of experimental procedure and computing infrastructure in distributed earthquake engineering.

PubMed

De La Flor, Grace; Ojaghi, Mobin; Martínez, Ignacio Lamata; Jirotka, Marina; Williams, Martin S; Blakeborough, Anthony

2010-09-13

When transitioning local laboratory practices into distributed environments, the interdependent relationship between experimental procedure and the technologies used to execute experiments becomes highly visible and a focal point for system requirements. We present an analysis of ways in which this reciprocal relationship is reconfiguring laboratory practices in earthquake engineering as a new computing infrastructure is embedded within three laboratories in order to facilitate the execution of shared experiments across geographically distributed sites. The system has been developed as part of the UK Network for Earthquake Engineering Simulation e-Research project, which links together three earthquake engineering laboratories at the universities of Bristol, Cambridge and Oxford. We consider the ways in which researchers have successfully adapted their local laboratory practices through the modification of experimental procedure so that they may meet the challenges of coordinating distributed earthquake experiments.

Experimental validation of a distribution theory based analysis of the effect of manufacturing tolerances on permanent magnet synchronous machines

NASA Astrophysics Data System (ADS)

Boscaino, V.; Cipriani, G.; Di Dio, V.; Corpora, M.; Curto, D.; Franzitta, V.; Trapanese, M.

2017-05-01

An experimental study on the effect of permanent magnet tolerances on the performances of a Tubular Linear Ferrite Motor is presented in this paper. The performances that have been investigated are: cogging force, end effect cogging force and generated thrust. It is demonstrated that: 1) the statistical variability of the magnets introduces harmonics in the spectrum of the cogging force; 2) the value of the end effect cogging force is directly linked to the values of then remanence field of the external magnets placed on the slider; 3) the generated thrust and its statistical distribution depend on the remanence field of the magnets placed on the translator.

Simulation of Delamination Propagation in Composites Under High-Cycle Fatigue by Means of Cohesive-Zone Models

NASA Technical Reports Server (NTRS)

Turon, Albert; Costa, Josep; Camanho, Pedro P.; Davila, Carlos G.

2006-01-01

A damage model for the simulation of delamination propagation under high-cycle fatigue loading is proposed. The basis for the formulation is a cohesive law that links fracture and damage mechanics to establish the evolution of the damage variable in terms of the crack growth rate dA/dN. The damage state is obtained as a function of the loading conditions as well as the experimentally-determined coefficients of the Paris Law crack propagation rates for the material. It is shown that by using the constitutive fatigue damage model in a structural analysis, experimental results can be reproduced without the need of additional model-specific curve-fitting parameters.

The shallow water equations as a hybrid flow model for the numerical and experimental analysis of hydro power stations

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

Ostermann, Lars; Seidel, Christian

2015-03-10

The numerical analysis of hydro power stations is an important method of the hydraulic design and is used for the development and optimisation of hydro power stations in addition to the experiments with the physical submodel of a full model in the hydraulic laboratory. For the numerical analysis, 2D and 3D models are appropriate and commonly used.The 2D models refer mainly to the shallow water equations (SWE), since for this flow model a large experience on a wide field of applications for the flow analysis of numerous problems in hydraulic engineering already exists. Often, the flow model is verified bymore » in situ measurements. In order to consider 3D flow phenomena close to singularities like weirs, hydro power stations etc. the development of a hybrid fluid model is advantageous to improve the quality and significance of the global model. Here, an extended hybrid flow model based on the principle of the SWE is presented. The hybrid flow model directly links the numerical model with the experimental data, which may originate from physical full models, physical submodels and in-situ measurements. Hence a wide field of application of the hybrid model emerges including the improvement of numerical models and the strong coupling of numerical and experimental analysis.« less

Glycosylation patterns of kidney proteins differ in rat diabetic nephropathy.

PubMed

Ravidà, Alessandra; Musante, Luca; Kreivi, Marjut; Miinalainen, Ilkka; Byrne, Barry; Saraswat, Mayank; Henry, Michael; Meleady, Paula; Clynes, Martin; Holthofer, Harry

2015-05-01

Diabetic nephropathy often progresses to end-stage kidney disease and, ultimately, to renal replacement therapy. Hyperglycemia per se is expected to have a direct impact on the biosynthesis of N- and O-linked glycoproteins. This study aims to establish the link between protein glycosylation and progression of experimental diabetic kidney disease using orthogonal methods. Kidneys of streptozotocin-diabetic and control rats were harvested at three different time points post streptozotocin injection. A panel of 12 plant lectins was used in the screening of lectin blots. The lectins UEAI, PHA-E, GSI, PNA, and RCA identified remarkable disease-associated differences in glycoprotein expression. Lectin affinity chromatography followed by mass spectrometric analyses led to the identification of several glycoproteins involved in salt-handling, angiogenesis, and extracellular matrix degradation. Our data confirm a substantial link between glycosylation signature and diabetes progression. Furthermore, as suggested by our findings on dipeptidyl peptidase-IV, altered protein glycosylation may reflect changes in biochemical properties such as enzymatic activity. Thus, our study demonstrates the unexplored potential of protein glycosylation analysis in the discovery of molecules linked to diabetic kidney disease.

Towards understanding addiction factors of mobile devices: An eye tracking study on effect of screen size.

PubMed

Wibirama, Sunu; Nugroho, Hanung A

2017-07-01

Mobile devices addiction has been an important research topic in cognitive science, mental health, and human-machine interaction. Previous works observed mobile device addiction by logging mobile devices activity. Although immersion has been linked as a significant predictor of video game addiction, investigation on addiction factors of mobile device with behavioral measurement has never been done before. In this research, we demonstrated the usage of eye tracking to observe effect of screen size on experience of immersion. We compared subjective judgment with eye movements analysis. Non-parametric analysis on immersion score shows that screen size affects experience of immersion (p<;0.05). Furthermore, our experimental results suggest that fixational eye movements may be used as an indicator for future investigation of mobile devices addiction. Our experimental results are also useful to develop a guideline as well as intervention strategy to deal with smartphone addiction.

Data integration in biological research: an overview.

PubMed

Lapatas, Vasileios; Stefanidakis, Michalis; Jimenez, Rafael C; Via, Allegra; Schneider, Maria Victoria

2015-12-01

Data sharing, integration and annotation are essential to ensure the reproducibility of the analysis and interpretation of the experimental findings. Often these activities are perceived as a role that bioinformaticians and computer scientists have to take with no or little input from the experimental biologist. On the contrary, biological researchers, being the producers and often the end users of such data, have a big role in enabling biological data integration. The quality and usefulness of data integration depend on the existence and adoption of standards, shared formats, and mechanisms that are suitable for biological researchers to submit and annotate the data, so it can be easily searchable, conveniently linked and consequently used for further biological analysis and discovery. Here, we provide background on what is data integration from a computational science point of view, how it has been applied to biological research, which key aspects contributed to its success and future directions.

ATS-5 millimeter wave propagation measurements

NASA Technical Reports Server (NTRS)

Ippolito, L. J.

1973-01-01

Long term experimental measurements to determine the propagation characteristics of 15 and 32 GHz earth-space links and to evaluate performance characteristics of operational millimeter wave systems are reported. The ATS 5 millimeter wave experimental link experienced attenuation and fading characteristics as a function of rainfall rate and other meteorological parameters. A method of site selection for the lowest attenuation rainfall rate improved reception tremendously.

System and Propagation Availability Analysis for NASA's Advanced Air Transportation Technologies

NASA Technical Reports Server (NTRS)

Ugweje, Okechukwu C.

2000-01-01

This report summarizes the research on the System and Propagation Availability Analysis for NASA's project on Advanced Air Transportation Technologies (AATT). The objectives of the project were to determine the communication systems requirements and architecture, and to investigate the effect of propagation on the transmission of space information. In this report, results from the first year investigation are presented and limitations are highlighted. To study the propagation links, an understanding of the total system architecture is necessary since the links form the major component of the overall architecture. This study was conducted by way of analysis, modeling and simulation on the system communication links. The overall goals was to develop an understanding of the space communication requirements relevant to the AATT project, and then analyze the links taking into consideration system availability under adverse atmospheric weather conditions. This project began with a preliminary study of the end-to-end system architecture by modeling a representative communication system in MATLAB SIMULINK. Based on the defining concepts, the possibility of computer modeling was determined. The investigations continue with the parametric studies of the communication system architecture. These studies were also carried out with SIMULINK modeling and simulation. After a series of modifications, two end-to-end communication links were identified as the most probable models for the communication architecture. Link budget calculations were then performed in MATHCAD and MATLAB for the identified communication scenarios. A remarkable outcome of this project is the development of a graphic user interface (GUI) program for the computation of the link budget parameters in real time. Using this program, one can interactively compute the link budget requirements after supplying a few necessary parameters. It provides a framework for the eventual automation of several computations required in many experimental NASA missions. For the first year of this project, most of the stated objectives were accomplished. We were able to identify probable communication systems architectures, model and analyze several communication links, perform numerous simulation on different system models, and then develop a program for the link budget analysis. However, most of the work is still unfinished. The effect of propagation on the transmission of information in the identified communication channels has not been performed. Propagation effects cannot be studied until the system under consideration is identified and characterized. To study the propagation links, an understanding of the total communications architecture is necessary. It is important to mention that the original project was intended for two years and the results presented here are only for the first year of research. It is prudent therefore that these efforts be continued in order to obtain a complete picture of the system and propagation availability requirements.

Poverty, inequality, and increased consumption of high calorie food: Experimental evidence for a causal link.

PubMed

Bratanova, Boyka; Loughnan, Steve; Klein, Olivier; Claassen, Almudena; Wood, Robert

2016-05-01

Rising obesity represents a serious, global problem. It is now well established that obesity is associated with poverty and wealth inequality, suggesting that these factors may promote caloric intake. Whereas previous work has examined these links from an epidemiological perspective, the current paper examined them experimentally. In Study 1 we found that people experimentally induced to view themselves as poor (v. wealthy) exhibited increased calorie intake. In Study 2, participants who believed that they were poorer or wealthier than their interaction partners exhibited higher levels of anxiety compared to those in an equal partners condition; this anxiety in turn led to increased calorie consumption for people who had a strong need to belong. The findings provide causal evidence for the poverty-intake and inequality-intake links. Further, we identify social anxiety and a strong need to belong as important social psychological factors linking inequality to increased calorie intake. Copyright © 2016. Published by Elsevier Ltd.

Domain fusion analysis by applying relational algebra to protein sequence and domain databases

PubMed Central

Truong, Kevin; Ikura, Mitsuhiko

2003-01-01

Background Domain fusion analysis is a useful method to predict functionally linked proteins that may be involved in direct protein-protein interactions or in the same metabolic or signaling pathway. As separate domain databases like BLOCKS, PROSITE, Pfam, SMART, PRINTS-S, ProDom, TIGRFAMs, and amalgamated domain databases like InterPro continue to grow in size and quality, a computational method to perform domain fusion analysis that leverages on these efforts will become increasingly powerful. Results This paper proposes a computational method employing relational algebra to find domain fusions in protein sequence databases. The feasibility of this method was illustrated on the SWISS-PROT+TrEMBL sequence database using domain predictions from the Pfam HMM (hidden Markov model) database. We identified 235 and 189 putative functionally linked protein partners in H. sapiens and S. cerevisiae, respectively. From scientific literature, we were able to confirm many of these functional linkages, while the remainder offer testable experimental hypothesis. Results can be viewed at . Conclusion As the analysis can be computed quickly on any relational database that supports standard SQL (structured query language), it can be dynamically updated along with the sequence and domain databases, thereby improving the quality of predictions over time. PMID:12734020

NovelFam3000 – Uncharacterized human protein domains conserved across model organisms

PubMed Central

Kemmer, Danielle; Podowski, Raf M; Arenillas, David; Lim, Jonathan; Hodges, Emily; Roth, Peggy; Sonnhammer, Erik LL; Höög, Christer; Wasserman, Wyeth W

2006-01-01

Background Despite significant efforts from the research community, an extensive portion of the proteins encoded by human genes lack an assigned cellular function. Most metazoan proteins are composed of structural and/or functional domains, of which many appear in multiple proteins. Once a domain is characterized in one protein, the presence of a similar sequence in an uncharacterized protein serves as a basis for inference of function. Thus knowledge of a domain's function, or the protein within which it arises, can facilitate the analysis of an entire set of proteins. Description From the Pfam domain database, we extracted uncharacterized protein domains represented in proteins from humans, worms, and flies. A data centre was created to facilitate the analysis of the uncharacterized domain-containing proteins. The centre both provides researchers with links to dispersed internet resources containing gene-specific experimental data and enables them to post relevant experimental results or comments. For each human gene in the system, a characterization score is posted, allowing users to track the progress of characterization over time or to identify for study uncharacterized domains in well-characterized genes. As a test of the system, a subset of 39 domains was selected for analysis and the experimental results posted to the NovelFam3000 system. For 25 human protein members of these 39 domain families, detailed sub-cellular localizations were determined. Specific observations are presented based on the analysis of the integrated information provided through the online NovelFam3000 system. Conclusion Consistent experimental results between multiple members of a domain family allow for inferences of the domain's functional role. We unite bioinformatics resources and experimental data in order to accelerate the functional characterization of scarcely annotated domain families. PMID:16533400

Data-assisted protein structure modeling by global optimization in CASP12.

PubMed

Joo, Keehyoung; Heo, Seungryong; Joung, InSuk; Hong, Seung Hwan; Lee, Sung Jong; Lee, Jooyoung

2018-03-01

In CASP12, 2 types of data-assisted protein structure modeling were experimented. Either SAXS experimental data or cross-linking experimental data was provided for a selected number of CASP12 targets that the CASP12 predictor could utilize for better protein structure modeling. We devised 2 separate energy terms for SAXS data and cross-linking data to drive the model structures into more native-like structures that satisfied the given experimental data as much as possible. In CASP11, we successfully performed protein structure modeling using simulated sparse and ambiguously assigned NOE data and/or correct residue-residue contact information, where the only energy term that folded the protein into its native structure was the term which was originated from the given experimental data. However, the 2 types of experimental data provided in CASP12 were far from being sufficient enough to fold the target protein into its native structure because SAXS data provides only the overall shape of the molecule and the cross-linking contact information provides only very low-resolution distance information. For this reason, we combined the SAXS or cross-linking energy term with our regular modeling energy function that includes both the template energy term and the de novo energy terms. By optimizing the newly formulated energy function, we obtained protein models that fit better with provided SAXS data than the X-ray structure of the target. However, the improvement of the model relative to the 1 modeled without the SAXS data, was not significant. Consistent structural improvement was achieved by incorporating cross-linking data into the protein structure modeling. © 2018 Wiley Periodicals, Inc.

Decentralising Curriculum Reform: The Link Teacher Model of In-Service Training.

ERIC Educational Resources Information Center

Wildy, Helen; And Others

1996-01-01

Presents a (Western Australian) case study of the link teacher model, a decentralized, "train the trainer" approach to inservice education. Discusses the model's perceived effectiveness, the link teachers' role, central authority support, and new experimentation opportunities. Combining centralized syllabus change with decentralized…

Frequent statistics of link-layer bit stream data based on AC-IM algorithm

NASA Astrophysics Data System (ADS)

Cao, Chenghong; Lei, Yingke; Xu, Yiming

2017-08-01

At present, there are many relevant researches on data processing using classical pattern matching and its improved algorithm, but few researches on statistical data of link-layer bit stream. This paper adopts a frequent statistical method of link-layer bit stream data based on AC-IM algorithm for classical multi-pattern matching algorithms such as AC algorithm has high computational complexity, low efficiency and it cannot be applied to binary bit stream data. The method's maximum jump distance of the mode tree is length of the shortest mode string plus 3 in case of no missing? In this paper, theoretical analysis is made on the principle of algorithm construction firstly, and then the experimental results show that the algorithm can adapt to the binary bit stream data environment and extract the frequent sequence more accurately, the effect is obvious. Meanwhile, comparing with the classical AC algorithm and other improved algorithms, AC-IM algorithm has a greater maximum jump distance and less time-consuming.

Lightweight Biometric Sensing for Walker Classification Using Narrowband RF Links

PubMed Central

Liang, Zhuo-qian

2017-01-01

This article proposes a lightweight biometric sensing system using ubiquitous narrowband radio frequency (RF) links for path-dependent walker classification. The fluctuated received signal strength (RSS) sequence generated by human motion is used for feature representation. To capture the most discriminative characteristics of individuals, a three-layer RF sensing network is organized for building multiple sampling links at the most common heights of upper limbs, thighs, and lower legs. The optimal parameters of sensing configuration, such as the height of link location and number of fused links, are investigated to improve sensory data distinctions among subjects, and the experimental results suggest that the synergistic sensing by using multiple links can contribute a better performance. This is the new consideration of using RF links in building a biometric sensing system. In addition, two types of classification methods involving vector quantization (VQ) and hidden Markov models (HMMs) are developed and compared for closed-set walker recognition and verification. Experimental studies in indoor line-of-sight (LOS) and non-line-of-sight (NLOS) scenarios are conducted to validate the proposed method. PMID:29206188

Lightweight Biometric Sensing for Walker Classification Using Narrowband RF Links.

PubMed

Liu, Tong; Liang, Zhuo-Qian

2017-12-05

This article proposes a lightweight biometric sensing system using ubiquitous narrowband radio frequency (RF) links for path-dependent walker classification. The fluctuated received signal strength (RSS) sequence generated by human motion is used for feature representation. To capture the most discriminative characteristics of individuals, a three-layer RF sensing network is organized for building multiple sampling links at the most common heights of upper limbs, thighs, and lower legs. The optimal parameters of sensing configuration, such as the height of link location and number of fused links, are investigated to improve sensory data distinctions among subjects, and the experimental results suggest that the synergistic sensing by using multiple links can contribute a better performance. This is the new consideration of using RF links in building a biometric sensing system. In addition, two types of classification methods involving vector quantization (VQ) and hidden Markov models (HMMs) are developed and compared for closed-set walker recognition and verification. Experimental studies in indoor line-of-sight (LOS) and non-line-of-sight (NLOS) scenarios are conducted to validate the proposed method.

Immunological tools: engaging students in the use and analysis of flow cytometry and enzyme-linked immunosorbent assay (ELISA).

PubMed

Ott, Laura E; Carson, Susan

2014-01-01

Flow cytometry and enzyme-linked immunosorbent assay (ELISA) are commonly used techniques associated with clinical and research applications within the immunology and medical fields. The use of these techniques is becoming increasingly valuable in many life science and engineering disciplines as well. Herein, we report the development and evaluation of a novel half-semester course that focused on introducing undergraduate and graduate students to advance conceptual and technical skills associated with flow cytometry and ELISA, with emphasis on applications, experimental design, and data analysis. This course was offered in the North Carolina State University Biotechnology Program over three semesters and consisted of weekly lectures and laboratories. Students performed and/or analyzed flow cytometry and ELISA in three separate laboratory exercises: (1) identification of transgenic zebrafish hematopoietic cells, (2) analysis of transfection efficiency, and (3) analysis of cytokine production upon lipopolysaccharide stimulation. Student learning outcomes were achieved as demonstrated by multiple means of assessment, including three laboratory reports, a data analysis laboratory practicum, and a cumulative final exam. Further, anonymous student self-assessment revealed increased student confidence in the knowledge and skill sets defined in the learning outcomes. Copyright © 2014 The International Union of Biochemistry and Molecular Biology.

The TEF modeling and analysis approach to advance thermionic space power technology

NASA Astrophysics Data System (ADS)

Marshall, Albert C.

1997-01-01

Thermionics space power systems have been proposed as advanced power sources for future space missions that require electrical power levels significantly above the capabilities of current space power systems. The Defense Special Weapons Agency's (DSWA) Thermionic Evaluation Facility (TEF) is carrying out both experimental and analytical research to advance thermionic space power technology to meet this expected need. A Modeling and Analysis (M&A) project has been created at the TEF to develop analysis tools, evaluate concepts, and guide research. M&A activities are closely linked to the TEF experimental program, providing experiment support and using experimental data to validate models. A planning exercise has been completed for the M&A project, and a strategy for implementation was developed. All M&A activities will build on a framework provided by a system performance model for a baseline Thermionic Fuel Element (TFE) concept. The system model is composed of sub-models for each of the system components and sub-systems. Additional thermionic component options and model improvements will continue to be incorporated in the basic system model during the course of the program. All tasks are organized into four focus areas: 1) system models, 2) thermionic research, 3) alternative concepts, and 4) documentation and integration. The M&A project will provide a solid framework for future thermionic system development.

Immunoinformatics Features Linked to Leishmania Vaccine Development: Data Integration of Experimental and In Silico Studies

PubMed Central

Brito, Rory C. F.; Guimarães, Frederico G.; Velloso, João P. L.; Corrêa-Oliveira, Rodrigo; Ruiz, Jeronimo C.; Reis, Alexandre B.; Resende, Daniela M.

2017-01-01

Leishmaniasis is a wide-spectrum disease caused by parasites from Leishmania genus. There is no human vaccine available and it is considered by many studies as apotential effective tool for disease control. To discover novel antigens, computational programs have been used in reverse vaccinology strategies. In this work, we developed a validation antigen approach that integrates prediction of B and T cell epitopes, analysis of Protein-Protein Interaction (PPI) networks and metabolic pathways. We selected twenty candidate proteins from Leishmania tested in murine model, with experimental outcome published in the literature. The predictions for CD4+ and CD8+ T cell epitopes were correlated with protection in experimental outcomes. We also mapped immunogenic proteins on PPI networks in order to find Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways associated with them. Our results suggest that non-protective antigens have lowest frequency of predicted T CD4+ and T CD8+ epitopes, compared with protective ones. T CD4+ and T CD8+ cells are more related to leishmaniasis protection in experimental outcomes than B cell predicted epitopes. Considering KEGG analysis, the proteins considered protective are connected to nodes with few pathways, including those associated with ribosome biosynthesis and purine metabolism. PMID:28208616

Immunoinformatics Features Linked to Leishmania Vaccine Development: Data Integration of Experimental and In Silico Studies.

PubMed

Brito, Rory C F; Guimarães, Frederico G; Velloso, João P L; Corrêa-Oliveira, Rodrigo; Ruiz, Jeronimo C; Reis, Alexandre B; Resende, Daniela M

2017-02-10

Leishmaniasis is a wide-spectrum disease caused by parasites from Leishmania genus. There is no human vaccine available and it is considered by many studies as apotential effective tool for disease control. To discover novel antigens, computational programs have been used in reverse vaccinology strategies. In this work, we developed a validation antigen approach that integrates prediction of B and T cell epitopes, analysis of Protein-Protein Interaction (PPI) networks and metabolic pathways. We selected twenty candidate proteins from Leishmania tested in murine model, with experimental outcome published in the literature. The predictions for CD4⁺ and CD8⁺ T cell epitopes were correlated with protection in experimental outcomes. We also mapped immunogenic proteins on PPI networks in order to find Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways associated with them. Our results suggest that non-protective antigens have lowest frequency of predicted T CD4⁺ and T CD8⁺ epitopes, compared with protective ones. T CD4⁺ and T CD8⁺ cells are more related to leishmaniasis protection in experimental outcomes than B cell predicted epitopes. Considering KEGG analysis, the proteins considered protective are connected to nodes with few pathways, including those associated with ribosome biosynthesis and purine metabolism.

An experimental and theoretical analysis of a foil-air bearing rotor system

NASA Astrophysics Data System (ADS)

Bonello, P.; Hassan, M. F. Bin

2018-01-01

Although there is considerable research on the experimental testing of foil-air bearing (FAB) rotor systems, only a small fraction has been correlated with simulations from a full nonlinear model that links the rotor, air film and foil domains, due to modelling complexity and computational burden. An approach for the simultaneous solution of the three domains as a coupled dynamical system, introduced by the first author and adopted by independent researchers, has recently demonstrated its capability to address this problem. This paper uses this approach, with further developments, in an experimental and theoretical study of a FAB-rotor test rig. The test rig is described in detail, including issues with its commissioning. The theoretical analysis uses a recently introduced modal-based bump foil model that accounts for interaction between the bumps and their inertia. The imposition of pressure constraints on the air film is found to delay the predicted onset of instability speed. The results lend experimental validation to a recent theoretically-based claim that the Gümbel condition may not be appropriate for a practical single-pad FAB. The satisfactory prediction of the salient features of the measured nonlinear behavior shows that the air film is indeed highly influential on the response, in contrast to an earlier finding.

A Biomechanical Analysis Of Craniofacial Form And Function

NASA Astrophysics Data System (ADS)

Oyen, Ordean J.

1989-04-01

In vivo measures of bite force and bone strain obtained in growing African green monkeys (Cercopeithecus aethiops) are being used to study skull biology and geometry. Strain values and distributional patterns seen in association with forceful jaw elevation are inconsistent with conventional explanations linking upper facial morphology with masticatory function and/or using beam models of craniofacial architecture. These results mandate careful use of notions about skeletal geometry based on static analyses that have not been experimentally verified using in vivo procedures.

Ecogenomics: Ensemble Analysis of Gene Expression in Microbial Communities

NASA Technical Reports Server (NTRS)

Sogin, Mitchell; DesMarais, David J.; Stahl, D. A.; Pace, Norman R.

2001-01-01

The hierarchical organization of microbial ecosystems determines process rates that shape Earth's environment, create the biomarker sedimentary and atmospheric signatures of life, and define the stage upon which major evolutionary events occurred. In order to understand how microorganisms have shaped the global environment of Earth and, potentially, other worlds, we must develop an experimental paradigm that links biogeochemical processes with ever-changing temporal and spatial distributions of microbial populations and their metabolic properties. Additional information is contained in the original extended abstract.

2015 Summer Series - Lee Stone - Brain Function Through the Eyes of the Beholder

NASA Image and Video Library

2015-06-09

The Visuomotor Control Laboratory (VCL) at NASA Ames conducts neuroscience research on the link between eye movements and brain function to provide an efficient and quantitative means of monitoring human perceptual performance. The VCL aims to make dramatic improvements in mission success through analysis, experimentation, and modeling of human performance and human-automation interaction. Dr. Lee Stone elaborates on how this research is conducted and how it contributes to NASA's mission and advances human-centered design and operations of complex aerospace systems.

Combined node and link partitions method for finding overlapping communities in complex networks

PubMed Central

Jin, Di; Gabrys, Bogdan; Dang, Jianwu

2015-01-01

Community detection in complex networks is a fundamental data analysis task in various domains, and how to effectively find overlapping communities in real applications is still a challenge. In this work, we propose a new unified model and method for finding the best overlapping communities on the basis of the associated node and link partitions derived from the same framework. Specifically, we first describe a unified model that accommodates node and link communities (partitions) together, and then present a nonnegative matrix factorization method to learn the parameters of the model. Thereafter, we infer the overlapping communities based on the derived node and link communities, i.e., determine each overlapped community between the corresponding node and link community with a greedy optimization of a local community function conductance. Finally, we introduce a model selection method based on consensus clustering to determine the number of communities. We have evaluated our method on both synthetic and real-world networks with ground-truths, and compared it with seven state-of-the-art methods. The experimental results demonstrate the superior performance of our method over the competing ones in detecting overlapping communities for all analysed data sets. Improved performance is particularly pronounced in cases of more complicated networked community structures. PMID:25715829

2DB: a Proteomics database for storage, analysis, presentation, and retrieval of information from mass spectrometric experiments.

PubMed

Allmer, Jens; Kuhlgert, Sebastian; Hippler, Michael

2008-07-07

The amount of information stemming from proteomics experiments involving (multi dimensional) separation techniques, mass spectrometric analysis, and computational analysis is ever-increasing. Data from such an experimental workflow needs to be captured, related and analyzed. Biological experiments within this scope produce heterogenic data ranging from pictures of one or two-dimensional protein maps and spectra recorded by tandem mass spectrometry to text-based identifications made by algorithms which analyze these spectra. Additionally, peptide and corresponding protein information needs to be displayed. In order to handle the large amount of data from computational processing of mass spectrometric experiments, automatic import scripts are available and the necessity for manual input to the database has been minimized. Information is in a generic format which abstracts from specific software tools typically used in such an experimental workflow. The software is therefore capable of storing and cross analysing results from many algorithms. A novel feature and a focus of this database is to facilitate protein identification by using peptides identified from mass spectrometry and link this information directly to respective protein maps. Additionally, our application employs spectral counting for quantitative presentation of the data. All information can be linked to hot spots on images to place the results into an experimental context. A summary of identified proteins, containing all relevant information per hot spot, is automatically generated, usually upon either a change in the underlying protein models or due to newly imported identifications. The supporting information for this report can be accessed in multiple ways using the user interface provided by the application. We present a proteomics database which aims to greatly reduce evaluation time of results from mass spectrometric experiments and enhance result quality by allowing consistent data handling. Import functionality, automatic protein detection, and summary creation act together to facilitate data analysis. In addition, supporting information for these findings is readily accessible via the graphical user interface provided. The database schema and the implementation, which can easily be installed on virtually any server, can be downloaded in the form of a compressed file from our project webpage.

Biodegradation pattern and tissue integration of native and cross-linked porcine collagen soft tissue augmentation matrices – an experimental study in the rat

PubMed Central

2014-01-01

Introduction Within the last decades, collagen types I and III have been established as a sufficient biomaterial for GBR and GTR procedures. They might also be an adequate matrix for soft tissue augmentations. However, collagen materials differ significantly regarding resorption time, biodegradation pattern and the invasion of inflammatory cells. The aim of the present study was to compare the biodegradation and tissue integration of native, differently processed and cross-linked collagen scaffolds in rats. Methods Four experimental porcine collagen matrices of 1.0 mm thickness, developed for soft tissue augmentation procedures, were tested. Based on the same native dermal Type I and III collagen, native (ND, Mucoderm® prototype), specifically defatted (DD), ethylene dioxide cross-linked (ECL) and dehydrothermally cross-linked (DCL) dermis collagen (AAP/Botiss Biomaterials, Berlin, Germany) were evaluated. Two specimens of 1 × 1 cm were fixed around a non-absorbable spacer using non-absorbable sutures. After rehydration, specimens (N = 8) were randomly allocated in unconnected subcutaneous pouches on the back of 40 Wistar rats. Rats were divided into five groups (1, 2, 4, 8 and 12 weeks), including eight animals each. After each period, eight rats were sacrificed and explanted specimens were prepared for histological analysis. The following parameters were evaluated: membrane thickness as a sign of biodegradation and volume stability, cell ingrowth, vascularization, tissue integration and foreign body reaction. Results Biodegradation pattern of the non cross-linked collagen scaffolds differed only slightly in terms of presence of inflammatory cells and cell invasion into the matrix. In terms of biodegradation, ECL displayed a considerable slower resorption than ND, DCL and DD. Chemical cross-linking using ethylene dioxide showed a significant higher invasion of inflammatory cells. Conclusion Within the limits of the present study it was concluded that the processing techniques influenced the collagen properties in a different intensity. Dehydrothermal cross-linking and special defatting did not notably change the biodegradation pattern, whereas cross-linking using ethylene dioxide led to significant higher volume stability of the matrix. However, ECL showed an increased inflammatory response and compromised tissue integration. Therefore, ethylene dioxide seems to be not suitable for stabilization of collagen matrices for soft tissue augmentation procedures. PMID:24670219

Atmospheric turbulence effects on the performance of a free space optical link employing orbital angular momentum multiplexing.

PubMed

Ren, Yongxiong; Huang, Hao; Xie, Guodong; Ahmed, Nisar; Yan, Yan; Erkmen, Baris I; Chandrasekaran, Nivedita; Lavery, Martin P J; Steinhoff, Nicholas K; Tur, Moshe; Dolinar, Samuel; Neifeld, Mark; Padgett, Miles J; Boyd, Robert W; Shapiro, Jeffrey H; Willner, Alan E

2013-10-15

We experimentally investigate the performance of an orbital angular momentum (OAM) multiplexed free space optical (FSO) communication link through emulated atmospheric turbulence. The turbulence effects on the crosstalk and system power penalty of the FSO link are characterized. The experimental results show that the power of the transmitted OAM mode will tend to spread uniformly onto the neighboring mode in medium-to-strong turbulence, resulting in severe crosstalk at the receiver. The power penalty is found to exceed 10 dB in a weak-to-medium turbulence condition due to the turbulence-induced crosstalk and power fluctuation of the received signal.

A three-way parallel ICA approach to analyze links among genetics, brain structure and brain function.

PubMed

Vergara, Victor M; Ulloa, Alvaro; Calhoun, Vince D; Boutte, David; Chen, Jiayu; Liu, Jingyu

2014-09-01

Multi-modal data analysis techniques, such as the Parallel Independent Component Analysis (pICA), are essential in neuroscience, medical imaging and genetic studies. The pICA algorithm allows the simultaneous decomposition of up to two data modalities achieving better performance than separate ICA decompositions and enabling the discovery of links between modalities. However, advances in data acquisition techniques facilitate the collection of more than two data modalities from each subject. Examples of commonly measured modalities include genetic information, structural magnetic resonance imaging (MRI) and functional MRI. In order to take full advantage of the available data, this work extends the pICA approach to incorporate three modalities in one comprehensive analysis. Simulations demonstrate the three-way pICA performance in identifying pairwise links between modalities and estimating independent components which more closely resemble the true sources than components found by pICA or separate ICA analyses. In addition, the three-way pICA algorithm is applied to real experimental data obtained from a study that investigate genetic effects on alcohol dependence. Considered data modalities include functional MRI (contrast images during alcohol exposure paradigm), gray matter concentration images from structural MRI and genetic single nucleotide polymorphism (SNP). The three-way pICA approach identified links between a SNP component (pointing to brain function and mental disorder associated genes, including BDNF, GRIN2B and NRG1), a functional component related to increased activation in the precuneus area, and a gray matter component comprising part of the default mode network and the caudate. Although such findings need further verification, the simulation and in-vivo results validate the three-way pICA algorithm presented here as a useful tool in biomedical data fusion applications. Copyright © 2014 Elsevier Inc. All rights reserved.

50 CFR 648.12 - Experimental fishing.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 50 Wildlife and Fisheries 10 2011-10-01 2011-10-01 false Experimental fishing. 648.12 Section 648... Experimental fishing. Link to an amendment published at 76 FR 60649, Sept. 29, 2011. The Regional Administrator... part for the conduct of experimental fishing beneficial to the management of the resources or fishery...

Experimental evaluation of LED-based solar blind NLOS communication links.

PubMed

Chen, Gang; Abou-Galala, Feras; Xu, Zhengyuan; Sadler, Brian M

2008-09-15

Experimental results are reported demonstrating non-line of sight short-range ultraviolet communication link losses, and performance of photon counting detectors, operating in the solar blind spectrum regime. We employ light emitting diodes with divergent beams, a solar blind filter, and a wide field-of-view detector. Signal and noise statistics are characterized, and receiver performance is demonstrated. The effects of transmitter and receiver elevation angles, separation distance, and path loss are included.

A neural link between generosity and happiness

PubMed Central

Park, Soyoung Q.; Kahnt, Thorsten; Dogan, Azade; Strang, Sabrina; Fehr, Ernst; Tobler, Philippe N.

2017-01-01

Generous behaviour is known to increase happiness, which could thereby motivate generosity. In this study, we use functional magnetic resonance imaging and a public pledge for future generosity to investigate the brain mechanisms that link generous behaviour with increases in happiness. Participants promised to spend money over the next 4 weeks either on others (experimental group) or on themselves (control group). Here, we report that, compared to controls, participants in the experimental group make more generous choices in an independent decision-making task and show stronger increases in self-reported happiness. Generous decisions engage the temporo-parietal junction (TPJ) in the experimental more than in the control group and differentially modulate the connectivity between TPJ and ventral striatum. Importantly, striatal activity during generous decisions is directly related to changes in happiness. These results demonstrate that top–down control of striatal activity plays a fundamental role in linking commitment-induced generosity with happiness. PMID:28696410

R Dump Converter without DC Link Capacitor for an 8/6 SRM: Experimental Investigation

PubMed Central

Kavitha, Pasumalaithevan; Umamaheswari, Bhaskaran

2015-01-01

The objective of this paper is to investigate the performance of 8/6 switched reluctance motor (SRM) when excited with sinusoidal voltage. The conventional R dump converter provides DC excitation with the help of capacitor. In this paper the converter used is the modified R dump converter without DC link capacitor providing AC or sinusoidal excitation. Torque ripple and speed ripple are investigated based on hysteresis current control. Constant and sinusoidal current references are considered for comparison in both DC and AC excitation. Extensive theoretical and experimental investigations are made to bring out the merits and demerits of AC versus DC excitation. It is shown that the constructionally simple SRM can be favorably controlled with simple R dump converter with direct AC excitation without need for DC link capacitor. A 4-phase 8/6 0.5 kW SRM is used for experimentation. PMID:25642452

R dump converter without DC link capacitor for an 8/6 SRM: experimental investigation.

PubMed

Kavitha, Pasumalaithevan; Umamaheswari, Bhaskaran

2015-01-01

The objective of this paper is to investigate the performance of 8/6 switched reluctance motor (SRM) when excited with sinusoidal voltage. The conventional R dump converter provides DC excitation with the help of capacitor. In this paper the converter used is the modified R dump converter without DC link capacitor providing AC or sinusoidal excitation. Torque ripple and speed ripple are investigated based on hysteresis current control. Constant and sinusoidal current references are considered for comparison in both DC and AC excitation. Extensive theoretical and experimental investigations are made to bring out the merits and demerits of AC versus DC excitation. It is shown that the constructionally simple SRM can be favorably controlled with simple R dump converter with direct AC excitation without need for DC link capacitor. A 4-phase 8/6 0.5 kW SRM is used for experimentation.

Mining high-throughput experimental data to link gene and function

PubMed Central

Blaby-Haas, Crysten E.; de Crécy-Lagard, Valérie

2011-01-01

Nearly 2200 genomes encoding some 6 million proteins have now been sequenced. Around 40% of these proteins are of unknown function even when function is loosely and minimally defined as “belonging to a superfamily”. In addition to in silico methods, the swelling stream of high-throughput experimental data can give valuable clues for linking these “unknowns” with precise biological roles. The goal is to develop integrative data-mining platforms that allow the scientific community at large to access and utilize this rich source of experimental knowledge. To this end, we review recent advances in generating whole-genome experimental datasets, where this data can be accessed, and how it can be used to drive prediction of gene function. PMID:21310501

Social capital calculations in economic systems: Experimental study

NASA Astrophysics Data System (ADS)

Chepurov, E. G.; Berg, D. B.; Zvereva, O. M.; Nazarova, Yu. Yu.; Chekmarev, I. V.

2017-11-01

The paper describes the social capital study for a system where actors are engaged in an economic activity. The focus is on the analysis of communications structural parameters (transactions) between the actors. Comparison between transaction network graph structure and the structure of a random Bernoulli graph of the same dimension and density allows revealing specific structural features of the economic system under study. Structural analysis is based on SNA-methodology (SNA - Social Network Analysis). It is shown that structural parameter values of the graph formed by agent relationship links may well characterize different aspects of the social capital structure. The research advocates that it is useful to distinguish the difference between each agent social capital and the whole system social capital.

Metadata management for high content screening in OMERO

PubMed Central

Li, Simon; Besson, Sébastien; Blackburn, Colin; Carroll, Mark; Ferguson, Richard K.; Flynn, Helen; Gillen, Kenneth; Leigh, Roger; Lindner, Dominik; Linkert, Melissa; Moore, William J.; Ramalingam, Balaji; Rozbicki, Emil; Rustici, Gabriella; Tarkowska, Aleksandra; Walczysko, Petr; Williams, Eleanor; Allan, Chris; Burel, Jean-Marie; Moore, Josh; Swedlow, Jason R.

2016-01-01

High content screening (HCS) experiments create a classic data management challenge—multiple, large sets of heterogeneous structured and unstructured data, that must be integrated and linked to produce a set of “final” results. These different data include images, reagents, protocols, analytic output, and phenotypes, all of which must be stored, linked and made accessible for users, scientists, collaborators and where appropriate the wider community. The OME Consortium has built several open source tools for managing, linking and sharing these different types of data. The OME Data Model is a metadata specification that supports the image data and metadata recorded in HCS experiments. Bio-Formats is a Java library that reads recorded image data and metadata and includes support for several HCS screening systems. OMERO is an enterprise data management application that integrates image data, experimental and analytic metadata and makes them accessible for visualization, mining, sharing and downstream analysis. We discuss how Bio-Formats and OMERO handle these different data types, and how they can be used to integrate, link and share HCS experiments in facilities and public data repositories. OME specifications and software are open source and are available at https://www.openmicroscopy.org. PMID:26476368

Metadata management for high content screening in OMERO.

PubMed

Li, Simon; Besson, Sébastien; Blackburn, Colin; Carroll, Mark; Ferguson, Richard K; Flynn, Helen; Gillen, Kenneth; Leigh, Roger; Lindner, Dominik; Linkert, Melissa; Moore, William J; Ramalingam, Balaji; Rozbicki, Emil; Rustici, Gabriella; Tarkowska, Aleksandra; Walczysko, Petr; Williams, Eleanor; Allan, Chris; Burel, Jean-Marie; Moore, Josh; Swedlow, Jason R

2016-03-01

High content screening (HCS) experiments create a classic data management challenge-multiple, large sets of heterogeneous structured and unstructured data, that must be integrated and linked to produce a set of "final" results. These different data include images, reagents, protocols, analytic output, and phenotypes, all of which must be stored, linked and made accessible for users, scientists, collaborators and where appropriate the wider community. The OME Consortium has built several open source tools for managing, linking and sharing these different types of data. The OME Data Model is a metadata specification that supports the image data and metadata recorded in HCS experiments. Bio-Formats is a Java library that reads recorded image data and metadata and includes support for several HCS screening systems. OMERO is an enterprise data management application that integrates image data, experimental and analytic metadata and makes them accessible for visualization, mining, sharing and downstream analysis. We discuss how Bio-Formats and OMERO handle these different data types, and how they can be used to integrate, link and share HCS experiments in facilities and public data repositories. OME specifications and software are open source and are available at https://www.openmicroscopy.org. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

A Hierarchical Mechanism of RIG-I Ubiquitination Provides Sensitivity, Robustness and Synergy in Antiviral Immune Responses.

PubMed

Sun, Xiaoqiang; Xian, Huifang; Tian, Shuo; Sun, Tingzhe; Qin, Yunfei; Zhang, Shoutao; Cui, Jun

2016-07-08

RIG-I is an essential receptor in the initiation of the type I interferon (IFN) signaling pathway upon viral infection. Although K63-linked ubiquitination plays an important role in RIG-I activation, the optimal modulation of conjugated and unanchored ubiquitination of RIG-I as well as its functional implications remains unclear. In this study, we determined that, in contrast to the RIG-I CARD domain, full-length RIG-I must undergo K63-linked ubiquitination at multiple sites to reach full activity. A systems biology approach was designed based on experiments using full-length RIG-I. Model selection for 7 candidate mechanisms of RIG-I ubiquitination inferred a hierarchical architecture of the RIG-I ubiquitination mode, which was then experimentally validated. Compared with other mechanisms, the selected hierarchical mechanism exhibited superior sensitivity and robustness in RIG-I-induced type I IFN activation. Furthermore, our model analysis and experimental data revealed that TRIM4 and TRIM25 exhibited dose-dependent synergism. These results demonstrated that the hierarchical mechanism of multi-site/type ubiquitination of RIG-I provides an efficient, robust and optimal synergistic regulatory module in antiviral immune responses.

A Hierarchical Mechanism of RIG-I Ubiquitination Provides Sensitivity, Robustness and Synergy in Antiviral Immune Responses

PubMed Central

Sun, Xiaoqiang; Xian, Huifang; Tian, Shuo; Sun, Tingzhe; Qin, Yunfei; Zhang, Shoutao; Cui, Jun

2016-01-01

RIG-I is an essential receptor in the initiation of the type I interferon (IFN) signaling pathway upon viral infection. Although K63-linked ubiquitination plays an important role in RIG-I activation, the optimal modulation of conjugated and unanchored ubiquitination of RIG-I as well as its functional implications remains unclear. In this study, we determined that, in contrast to the RIG-I CARD domain, full-length RIG-I must undergo K63-linked ubiquitination at multiple sites to reach full activity. A systems biology approach was designed based on experiments using full-length RIG-I. Model selection for 7 candidate mechanisms of RIG-I ubiquitination inferred a hierarchical architecture of the RIG-I ubiquitination mode, which was then experimentally validated. Compared with other mechanisms, the selected hierarchical mechanism exhibited superior sensitivity and robustness in RIG-I-induced type I IFN activation. Furthermore, our model analysis and experimental data revealed that TRIM4 and TRIM25 exhibited dose-dependent synergism. These results demonstrated that the hierarchical mechanism of multi-site/type ubiquitination of RIG-I provides an efficient, robust and optimal synergistic regulatory module in antiviral immune responses. PMID:27387525

A Hierarchical Mechanism of RIG-I Ubiquitination Provides Sensitivity, Robustness and Synergy in Antiviral Immune Responses

NASA Astrophysics Data System (ADS)

Sun, Xiaoqiang; Xian, Huifang; Tian, Shuo; Sun, Tingzhe; Qin, Yunfei; Zhang, Shoutao; Cui, Jun

2016-07-01

RIG-I is an essential receptor in the initiation of the type I interferon (IFN) signaling pathway upon viral infection. Although K63-linked ubiquitination plays an important role in RIG-I activation, the optimal modulation of conjugated and unanchored ubiquitination of RIG-I as well as its functional implications remains unclear. In this study, we determined that, in contrast to the RIG-I CARD domain, full-length RIG-I must undergo K63-linked ubiquitination at multiple sites to reach full activity. A systems biology approach was designed based on experiments using full-length RIG-I. Model selection for 7 candidate mechanisms of RIG-I ubiquitination inferred a hierarchical architecture of the RIG-I ubiquitination mode, which was then experimentally validated. Compared with other mechanisms, the selected hierarchical mechanism exhibited superior sensitivity and robustness in RIG-I-induced type I IFN activation. Furthermore, our model analysis and experimental data revealed that TRIM4 and TRIM25 exhibited dose-dependent synergism. These results demonstrated that the hierarchical mechanism of multi-site/type ubiquitination of RIG-I provides an efficient, robust and optimal synergistic regulatory module in antiviral immune responses.

Carbonate hosted fault rocks: A review of structural and microstructural characteristic with implications for seismicity in the upper crust

NASA Astrophysics Data System (ADS)

Delle Piane, Claudio; Clennell, M. Ben; Keller, Joao V. A.; Giwelli, Ausama; Luzin, Vladimir

2017-10-01

The structure, frictional properties and permeability of faults within carbonate rocks exhibit a dynamic interplay that controls both seismicity and the exchange of fluid between different crustal levels. Here we review field and experimental studies focused on the characterization of fault zones in carbonate rocks with the aim of identifying the microstructural indicators of rupture nucleation and seismic slip. We highlight results from experimental research linked to observations on exhumed fault zones in carbonate rocks. From the analysis of these accumulated results we identify the meso and microstructural deformation styles in carbonates rocks and link them to the lithology of the protolith and their potential as seismic indicators. Although there has been significant success in the laboratory reproduction of deformation structures observed in the field, the range of slip rates and dynamic friction under which most of the potential seismic indicators is formed in the laboratory urges caution when using them as a diagnostic for seismic slip. We finally outline what we think are key topics for future research that would lead to a more in-depth understanding of the record of seismic slip in carbonate rocks.

Establishing Corneal Cross-Linking With Riboflavin and UV-A in the Mouse Cornea In Vivo: Biomechanical Analysis.

PubMed

Hammer, Arthur; Kling, Sabine; Boldi, Marc-Olivier; Richoz, Olivier; Tabibian, David; Randleman, J Bradley; Hafezi, Farhad

2015-10-01

To establish corneal cross-linking (CXL) with riboflavin and UV-A in in the mouse cornea in vivo and to develop tools to measure the biomechanical changes observed. A total of 55 male C57BL/6 wild-type mice (aged 5 weeks) were divided into 14 groups. Standard CXL parameters were adapted to the anatomy of the mouse cornea, and riboflavin concentration (0.1%-0.5%) and fluence series (0.09-5.4 J/cm²) were performed on the assumption of the endothelial damage thresholds. Untreated and riboflavin only corneas were used as controls. Animals were killed at 30 minutes and at 1 month after CXL. Corneas were harvested. Two-dimensional (2D) biomechanical testing was performed using a customized corneal holder in a commercially available stress-strain extensometer/indenter. Both elastic and viscoelastic analyses were performed. Statistical inference was performed using t-tests and specific mathematical models fitted to the experimental stress-strain and stress-relaxation data. Adjusted P values by the method of Benjamini and Hochberg are reported. For all CXL treatment groups, stress-relaxation showed significant differences (P < 0.0001) after 120 seconds of constant strain application, with cross-linked corneas maintaining a higher stress (441 ± 40 kPa) when compared with controls (337 ± 39 kPa). Stress-strain analysis confirmed these findings but was less sensitive to CXL-induced changes: at 0.5% of strain, cross-linked corneas remained at higher stress (778 ± 111 kPa) when compared with controls (659 ± 121 kPa). Cross-linking was induced in the mouse cornea in vivo, and its biomechanical effect successfully measured. This could create opportunities to study molecular pathways of CXL in transgenic mice.

In pursuit of a science of agriculture: the role of statistics in field experiments.

PubMed

Parolini, Giuditta

2015-09-01

Since the beginning of the twentieth century statistics has reshaped the experimental cultures of agricultural research taking part in the subtle dialectic between the epistemic and the material that is proper to experimental systems. This transformation has become especially relevant in field trials and the paper will examine the British agricultural institution, Rothamsted Experimental Station, where statistical methods nowadays popular in the planning and analysis of field experiments were developed in the 1920s. At Rothamsted statistics promoted randomisation over systematic arrangements, factorisation over one-question trials, and emphasised the importance of the experimental error in assessing field trials. These changes in methodology transformed also the material culture of agricultural science, and a new body, the Field Plots Committee, was created to manage the field research of the agricultural institution. Although successful, the vision of field experimentation proposed by the Rothamsted statisticians was not unproblematic. Experimental scientists closely linked to the farming community questioned it in favour of a field research that could be more easily understood by farmers. The clash between the two agendas reveals how the role attributed to statistics in field experimentation defined different pursuits of agricultural research, alternately conceived of as a scientists' science or as a farmers' science.

The influence of essential oils on human attention. I: alertness.

PubMed

Ilmberger, J; Heuberger, E; Mahrhofer, C; Dessovic, H; Kowarik, D; Buchbauer, G

2001-03-01

Scientific research on the effects of essential oils on human behavior lags behind the promises made by popular aromatherapy. Nearly all aspects of human behavior are closely linked to processes of attention, the basic level being that of alertness, which ranges from sleep to wakefulness. In our study we measured the influence of essential oils and components of essential oils [peppermint, jasmine, ylang-ylang, 1,8-cineole (in two different dosages) and menthol] on this core attentional function, which can be experimentally defined as speed of information processing. Substances were administered by inhalation; levels of alertness were assessed by measuring motor and reaction times in a reaction time paradigm. The performances of the six experimental groups receiving substances (n = 20 in four groups, n = 30 in two groups) were compared with those of corresponding control groups receiving water. Between-group analysis, i.e. comparisons between experimental groups and their respective control groups, mainly did not reach statistical significance. However, within-group analysis showed complex correlations between subjective evaluations of substances and objective performance, indicating that effects of essentials oils or their components on basic forms of attentional behavior are mainly psychological.

Earth-space links and fade-duration statistics

NASA Technical Reports Server (NTRS)

Davarian, Faramaz

1995-01-01

In recent years, fade-duration statistics have been the subject of several experimental investigations. A good knowledge of the fade-duration distribution is important for the assessment of a satellite communication system's channel dynamics: What is a typical link outage duration? How often do link outages exceeding a given duration occur? Unfortunately there is yet no model that can universally answer the above questions. The available field measurements mainly come from temperate climatic zones and only from a few sites. Furthermore, the available statistics are also limited in the choice of frequency and path elevation angle. Yet, much can be learned from the available information. For example, we now know that the fade-duration distribution is approximately lognormal. Under certain conditions, we can even determine the median and other percentiles of the distribution. This paper reviews the available data obtained by several experimenters in different parts of the world. Areas of emphasis are mobile and fixed satellite links. Fades in mobile links are due to roadside-tree shadowing, whereas fades in fixed links are due to rain attenuation.

Earth-Space Links and Fade-Duration Statistics

NASA Technical Reports Server (NTRS)

Davarian, Faramaz

1996-01-01

In recent years, fade-duration statistics have been the subject of several experimental investigations. A good knowledge of the fade-duration distribution is important for the assessment of a satellite communication system's channel dynamics: What is a typical link outage duration? How often do link outages exceeding a given duration occur? Unfortunately there is yet no model that can universally answer the above questions. The available field measurements mainly come from temperate climatic zones and only from a few sites. Furthermore, the available statistics are also limited in the choice of frequency and path elevation angle. Yet, much can be learned from the available information. For example, we now know that the fade-duration distribution is approximately lognormal. Under certain conditions, we can even determine the median and other percentiles of the distribution. This paper reviews the available data obtained by several experimenters in different parts of the world. Areas of emphasis are mobile and fixed satellite links. Fades in mobile links are due to roadside-tree shadowing, whereas fades in fixed links are due to rain attenuation.

Experimental scleral cross-linking increases glaucoma damage in a mouse model

PubMed Central

Kimball, Elizabeth C.; Nguyen, Cathy; Steinhart, Matthew R.; Nguyen, Thao D.; Pease, Mary E.; Oglesby, Ericka N.; Oveson, Brian C.; Quigley, Harry A.

2014-01-01

The purpose of this study was to assess the effect of a scleral cross-linking agent on susceptibility to glaucoma damage in a mouse model. CD1 mice underwent 3 subconjunctival injections of 0.5 M glyceraldehyde (GA) in 1 week, then had elevated intraocular pressure (IOP) induced by bead injection. Degree of cross-linking was measured by enzyme-linked immunosorbent assay (ELISA), scleral permeability was measured by fluorescence recovery after photobleaching (FRAP), and the mechanical effects of GA exposure were measured by inflation testing. Control mice had buffer injection or no injection in 2 separate glaucoma experiments. IOP was monitored by Tonolab and retinal ganglion cell (RGC) loss was measured by histological axon counting. To rule out undesirable effects of GA, we performed electroretinography and detailed histology of the retina. GA exposure had no detectable effects on RGC number, retinal structure or function either histologically or electrophysiologically. GA increased cross-linking of sclera by 37% in an ELISA assay, decreased scleral permeability (FRAP, p = 0.001), and produced a steeper pressure—strain behavior by in vitro inflation testing. In two experimental glaucoma experiments, GA-treated eyes had greater RGC axon loss from elevated IOP than either buffer-injected or control eyes, controlling for level of IOP exposure over time (p = 0.01, and 0.049, multivariable regression analyses). This is the first report that experimental alteration of the sclera, by cross-linking, increases susceptibility to RGC damage in mice. PMID:25285424

Gambling, games of skill and human ecology: a pilot study by a multidimensional analysis approach.

PubMed

Valera, Luca; Giuliani, Alessandro; Gizzi, Alessio; Tartaglia, Francesco; Tambone, Vittoradolfo

2015-01-01

The present pilot study aims at analyzing the human activity of playing in the light of an indicator of human ecology (HE). We highlighted the four essential anthropological dimensions (FEAD), starting from the analysis of questionnaires administered to actual gamers. The coherence between theoretical construct and observational data is a remarkable proof-of-concept of the possibility of establishing an experimentally motivated link between a philosophical construct (coming from Huizinga's Homo ludens definition) and actual gamers' motivation pattern. The starting hypothesis is that the activity of playing becomes ecological (and thus not harmful) when it achieves the harmony between the FEAD, thus realizing HE; conversely, it becomes at risk of creating some form of addiction, when destroying FEAD balance. We analyzed the data by means of variable clustering (oblique principal components) so to experimentally verify the existence of the hypothesized dimensions. The subsequent projection of statistical units (gamers) on the orthogonal space spanned by principal components allowed us to generate a meaningful, albeit preliminary, clusterization of gamer profiles.

Rainfall estimation using microwave links. Results from an experimental setup in Luxembourg

NASA Astrophysics Data System (ADS)

Fenicia, Fabrizio; Matgen, Patrick; Pfister, Laurent

2010-05-01

Microwave links represent a valid alternative to traditional rainfall estimation methods. They are commonly used in mobile phone communication, and they constitute built-in widely distributed networks. Due to their ability of providing high temporal and spatial resolution measurements, their use is particularly suitable in urban settings. We here show results from an experimental setup in Luxembourg City, where two dual frequency links have been installed. The links cover a distance of about 4km, and measure power attenuation at 1 min. timestep. The links have been equipped with several recording raingauges, which measure rainfall in real-time communicating through a wireless connection. This set-up has been used to analyze in detail the mapping between attenuation and rainfall intensity, and gain insights into the potential accuracy of these instruments. In addition, we investigated the relation between rainfall and discharge response of the urban area of Luxembourg, which shows the potential utility of high frequency rainfall measurements for urban environments.

Experiment definition phase shuttle laboratory LDRL-10.6 experiment

NASA Technical Reports Server (NTRS)

1975-01-01

This report for the Experiment Definition Phase of the Shuttle Laboratory LDRL 10.6 Micrometer Experiment covers period 27 June through 26 September 1975. Activities during the fifth quarter included: (1) reevaluation of system obscuration ratio with a subsequent reduction of this ratio from 0.417 to 0.362, (2) completion of detail drawings for the 6X pre-expander, (3) completion of detail drawings for the nine mirrors that comprise pointing and tracking optomechanical subsystem, (4) continuation of detailing of mechanical portions of CMSS and modifications to accommodate new obscuration ratio, (5) qualitative operation of the optomechanical subsystem of the 10.6 um receiver achieved under experiment measurement task; receiver fully integrated and operation demonstrated over a 10 km experimental link, and (6) data collection task initiated to begin preparation of link analysis volumes.

Domain fusion analysis by applying relational algebra to protein sequence and domain databases.

PubMed

Truong, Kevin; Ikura, Mitsuhiko

2003-05-06

Domain fusion analysis is a useful method to predict functionally linked proteins that may be involved in direct protein-protein interactions or in the same metabolic or signaling pathway. As separate domain databases like BLOCKS, PROSITE, Pfam, SMART, PRINTS-S, ProDom, TIGRFAMs, and amalgamated domain databases like InterPro continue to grow in size and quality, a computational method to perform domain fusion analysis that leverages on these efforts will become increasingly powerful. This paper proposes a computational method employing relational algebra to find domain fusions in protein sequence databases. The feasibility of this method was illustrated on the SWISS-PROT+TrEMBL sequence database using domain predictions from the Pfam HMM (hidden Markov model) database. We identified 235 and 189 putative functionally linked protein partners in H. sapiens and S. cerevisiae, respectively. From scientific literature, we were able to confirm many of these functional linkages, while the remainder offer testable experimental hypothesis. Results can be viewed at http://calcium.uhnres.utoronto.ca/pi. As the analysis can be computed quickly on any relational database that supports standard SQL (structured query language), it can be dynamically updated along with the sequence and domain databases, thereby improving the quality of predictions over time.

Application of two-dimensional NMR spectroscopy and molecular dynamics simulations to the conformational analysis of oligosaccharides corresponding to the cell-wall polysaccharide of Streptococcus group A.

PubMed

Kreis, U C; Varma, V; Pinto, B M

1995-06-01

This paper describes the use of a protocol for conformational analysis of oligosaccharide structures related to the cell-wall polysaccharide of Streptococcus group A. The polysaccharide features a branched structure with an L-rhamnopyranose (Rhap) backbone consisting of alternating alpha-(1-->2) and alpha-(1-->3) links and D-N-acetylglucosamine (GlcpNAc) residues beta-(1-->3)-connected to alternating rhamnose rings: [formula: see text] Oligomers consisting of three to six residues have been synthesized and nuclear magnetic resonance (NMR) assignments have been made. The protocol for conformational analysis of the solution structure of these oligosaccharides involves experimental and theoretical methods. Two-dimensional NMR spectroscopy methods (TOCSY, ROESY and NOESY) are utilized to obtain chemical shift data and proton-proton distances. These distances are used as constraints in 100 ps molecular dynamics simulations in water using QUANTA and CHARMm. In addition, the dynamics simulations are performed without constraints. ROE build-up curves are computed from the averaged structures of the molecular dynamics simulations using the CROSREL program and compared with the experimental curves. Thus, a refinement of the initial structure may be obtained. The alpha-(1-->2) and the beta-(1-->3) links are unambiguously defined by the observed ROE cross peaks between the A-B',A'-B and C-B,C'-B' residues, respectively. The branch-point of the trisaccharide CBA' is conformationally well-defined. Assignment of the conformation of the B-A linkage (alpha-(1-->3)) was problematic due to TOCSY relay, but could be solved by NOESY and T-ROESY techniques. A conformational model for the polysaccharide is proposed.

Mach-Zehnder Fiber-Optic Links for ICF Diagnostics

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

Miller, E. K., Hermann, H. W.

2012-11-01

This article describes the operation and evolution of Mach-Zehnder links for single-point detectors in inertial confinement fusion experimental facilities, based on the Gamma Reaction History (GRH) diagnostic at the National Ignition Facility.

Functional Utilization of DABS Data Link Discrete Address Beacon System

DOT National Transportation Integrated Search

1978-10-01

The report describes the output of a Task Force established by FAA Headquarters, SRDS, Robert Wedan, in June 1977 to study and recommend potential applications for Data Link to the DABS Experimentation Program

Chapter 15: Disease Gene Prioritization

PubMed Central

Bromberg, Yana

2013-01-01

Disease-causing aberrations in the normal function of a gene define that gene as a disease gene. Proving a causal link between a gene and a disease experimentally is expensive and time-consuming. Comprehensive prioritization of candidate genes prior to experimental testing drastically reduces the associated costs. Computational gene prioritization is based on various pieces of correlative evidence that associate each gene with the given disease and suggest possible causal links. A fair amount of this evidence comes from high-throughput experimentation. Thus, well-developed methods are necessary to reliably deal with the quantity of information at hand. Existing gene prioritization techniques already significantly improve the outcomes of targeted experimental studies. Faster and more reliable techniques that account for novel data types are necessary for the development of new diagnostics, treatments, and cure for many diseases. PMID:23633938

Mining high-throughput experimental data to link gene and function.

PubMed

Blaby-Haas, Crysten E; de Crécy-Lagard, Valérie

2011-04-01

Nearly 2200 genomes that encode around 6 million proteins have now been sequenced. Around 40% of these proteins are of unknown function, even when function is loosely and minimally defined as 'belonging to a superfamily'. In addition to in silico methods, the swelling stream of high-throughput experimental data can give valuable clues for linking these unknowns with precise biological roles. The goal is to develop integrative data-mining platforms that allow the scientific community at large to access and utilize this rich source of experimental knowledge. To this end, we review recent advances in generating whole-genome experimental datasets, where this data can be accessed, and how it can be used to drive prediction of gene function. Copyright © 2011 Elsevier Ltd. All rights reserved.

Experimental study on behaviors of dielectric elastomer based on acrylonitrile butadiene rubber

NASA Astrophysics Data System (ADS)

An, Kuangjun; Chuc, Nguyen Huu; Kwon, Hyeok Yong; Phuc, Vuong Hong; Koo, Jachoon; Lee, Youngkwan; Nam, Jaedo; Choi, Hyouk Ryeol

2010-04-01

Previously, the dielectric elastomer based on Acrylonitrile Butadiene Rubber (NBR), called synthetic elastomer has been reported by our group. It has the advantages that its characteristics can be modified according to the requirements of performances, and thus, it is applicable to a wide variety of applications. In this paper, we address the effects of additives and vulcanization conditions on the overall performance of synthetic elastomer. In the present work, factors to have effects on the performances are extracted, e.g additives such as dioctyl phthalate (DOP), barium titanium dioxide (BaTiO3) and vulcanization conditions such as dicumyl peroxide (DCP), cross-linking times. Also, it is described how the performances can be optimized by using DOE (Design of Experiments) technique and experimental results are analyzed by ANOVA (Analysis of variance).

Free volumes and gas transport in polymers: amine-modified epoxy resins as a case study.

PubMed

Patil, Pushkar N; Roilo, David; Brusa, Roberto S; Miotello, Antonio; Aghion, Stefano; Ferragut, Rafael; Checchetto, Riccardo

2016-02-07

The CO2 transport process was studied in a series of amine-modified epoxy resins having different cross-linking densities but the same chemical environment for the penetrant molecules. Positron Annihilation Lifetime Spectroscopy (PALS) was used to monitor the free volume structure of the samples and experimentally evaluate their fractional free volume fh(T) and its temperature evolution. The analysis of the free volume hole size distribution showed that all the holes have a size large enough to accommodate the penetrant molecules at temperatures T above the glass transition temperature Tg. The measured gas diffusion constants at T > Tg have been reproduced in the framework of the free volume theory of diffusion using a novel procedure based on the use of fh(T) as an input experimental parameter.

Flexible manipulator control experiments and analysis

NASA Technical Reports Server (NTRS)

Yurkovich, S.; Ozguner, U.; Tzes, A.; Kotnik, P. T.

1987-01-01

Modeling and control design for flexible manipulators, both from an experimental and analytical viewpoint, are described. From the application perspective, an ongoing effort within the laboratory environment at the Ohio State University, where experimentation on a single link flexible arm is underway is described. Several unique features of this study are described here. First, the manipulator arm is slewed by a direct drive dc motor and has a rigid counterbalance appendage. Current experimentation is from two viewpoints: (1) rigid body slewing and vibration control via actuation with the hub motor, and (2) vibration suppression through the use of structure-mounted proof-mass actuation at the tip. Such an application to manipulator control is of interest particularly in design of space-based telerobotic control systems, but has received little attention to date. From an analytical viewpoint, parameter estimation techniques within the closed-loop for self-tuning adaptive control approaches are discussed. Also introduced is a control approach based on output feedback and frequency weighting to counteract effects of spillover in reduced-order model design. A model of the flexible manipulator based on experimental measurements is evaluated for such estimation and control approaches.

RFI simulation definition study, exhibit D

NASA Technical Reports Server (NTRS)

Braun, W. R.

1981-01-01

Comparative analyses of experimental and predicted effects of the radio frequency interference (RFI) environment on the Shuttle/TDRSS S-band links were performed. Specifications are defined ad ESTL test requirements are presented. Procedures for using the RFI test generator in the ESTL S-band link tests are presented and performance predictions for these links in the RFI environment are provided.

Statistical modelling of networked human-automation performance using working memory capacity.

PubMed

Ahmed, Nisar; de Visser, Ewart; Shaw, Tyler; Mohamed-Ameen, Amira; Campbell, Mark; Parasuraman, Raja

2014-01-01

This study examines the challenging problem of modelling the interaction between individual attentional limitations and decision-making performance in networked human-automation system tasks. Analysis of real experimental data from a task involving networked supervision of multiple unmanned aerial vehicles by human participants shows that both task load and network message quality affect performance, but that these effects are modulated by individual differences in working memory (WM) capacity. These insights were used to assess three statistical approaches for modelling and making predictions with real experimental networked supervisory performance data: classical linear regression, non-parametric Gaussian processes and probabilistic Bayesian networks. It is shown that each of these approaches can help designers of networked human-automated systems cope with various uncertainties in order to accommodate future users by linking expected operating conditions and performance from real experimental data to observable cognitive traits like WM capacity. Practitioner Summary: Working memory (WM) capacity helps account for inter-individual variability in operator performance in networked unmanned aerial vehicle supervisory tasks. This is useful for reliable performance prediction near experimental conditions via linear models; robust statistical prediction beyond experimental conditions via Gaussian process models and probabilistic inference about unknown task conditions/WM capacities via Bayesian network models.

Modeling and tachometer feedback in the control of an experimental single link flexible structure

NASA Technical Reports Server (NTRS)

Garcia, Ephrahim; Inman, Daniel J.

1990-01-01

In this work a formulation for the modeling of a single link flexible structure will be introduced that includes the effects of dynamic interaction between the actuator and structure. These effects are the rotational modal participation factors for the structure's vibratory motion that occurs at the slewing axis. It will be shown, both theoretically and experimentally, that this dynamic interaction can be advantageous for vibration suppression of the flexible modes of the system during slewing positioning maneuvers.

Vibro-acoustic modelling of aircraft double-walls with structural links using Statistical Energy Analysis

NASA Astrophysics Data System (ADS)

Campolina, Bruno L.

The prediction of aircraft interior noise involves the vibroacoustic modelling of the fuselage with noise control treatments. This structure is composed of a stiffened metallic or composite panel, lined with a thermal and acoustic insulation layer (glass wool), and structurally connected via vibration isolators to a commercial lining panel (trim). The goal of this work aims at tailoring the noise control treatments taking design constraints such as weight and space optimization into account. For this purpose, a representative aircraft double-wall is modelled using the Statistical Energy Analysis (SEA) method. Laboratory excitations such as diffuse acoustic field and point force are addressed and trends are derived for applications under in-flight conditions, considering turbulent boundary layer excitation. The effect of the porous layer compression is firstly addressed. In aeronautical applications, compression can result from the installation of equipment and cables. It is studied analytically and experimentally, using a single panel and a fibrous uniformly compressed over 100% of its surface. When compression increases, a degradation of the transmission loss up to 5 dB for a 50% compression of the porous thickness is observed mainly in the mid-frequency range (around 800 Hz). However, for realistic cases, the effect should be reduced since the compression rate is lower and compression occurs locally. Then the transmission through structural connections between panels is addressed using a four-pole approach that links the force-velocity pair at each side of the connection. The modelling integrates experimental dynamic stiffness of isolators, derived using an adapted test rig. The structural transmission is then experimentally validated and included in the double-wall SEA model as an equivalent coupling loss factor (CLF) between panels. The tested structures being flat, only axial transmission is addressed. Finally, the dominant sound transmission paths are identified in the 100 Hz to 10 kHz frequency range for double-walls under diffuse acoustic field and under point-force excitations. Non-resonant transmission is higher at low frequencies (frequencies lower than 1 kHz) while the structure-borne and the airborne paths dominate at mid- and high-frequencies, around 1 kHz and higher, respectively. An experimental validation on double-walls shows that the model is able to predict changes in the overall transmission caused by different structural couplings (rigid coupling, coupling via isolators and structurally uncoupled). Noise reduction means adapted to each transmission path, such as absorption, dissipation and structural decoupling, may be then derived. Keywords: Statistical energy analysis, Vibration isolator, Double-wall, Transfer path analysis, Transmission Loss.

Oxygenation-linked subunit interactions in human hemoglobin: analysis of linkage functions for constituent energy terms.

PubMed

Johnson, M L; Halvorson, H R; Ackers, G K

1976-11-30

Resolution of the linkage functions between oxygenation and subunit association-dissociation equilibria in human hemoglobin into the constituent microscopic terms has been explored by numerical simulation and least-squares analysis. The correlation properties between parameters has been studied using several choices of parameter sets in order to optimize resolution. It is found that, with currently available levels of experimental precision and ranges of variables, neither linkage function can provide sufficient resolution of all the desired energy terms. The most difficult quantities to resolve always include the dimer-tetramer association constant for unliganded hemoglobin and the oxygen binding constants to alphabeta dimers. A feasible experimental strategy for overcoming these difficulties lies in independent determination of the dimer-tetramer association constants for unliganded and fully oxygenated hemoglobin. These constants, in combination with the median lignad concentration, provide an estimate of the energy for total oxygenation of tetramers which is essentially independent of the other constituent energies. It is shown that if these separately determinable parameters are fixed, the remaining terms may be estimated to good accuracy using data which represents either linkage function. In general it is desirable to combine information from both types of experimental quantities. A previous paper (Mills, F.C., Johnson, M.L., and Ackers, G.K. (1976), Biochemestry, 15, the preceding paper in this issue) describes the experimental implementation of this strategy.

Modeling the atomistic growth behavior of gold nanoparticles in solution

NASA Astrophysics Data System (ADS)

Turner, C. Heath; Lei, Yu; Bao, Yuping

2016-04-01

The properties of gold nanoparticles strongly depend on their three-dimensional atomic structure, leading to an increased emphasis on controlling and predicting nanoparticle structural evolution during the synthesis process. In order to provide this atomistic-level insight and establish a link to the experimentally-observed growth behavior, a kinetic Monte Carlo simulation (KMC) approach is developed for capturing Au nanoparticle growth characteristics. The advantage of this approach is that, compared to traditional molecular dynamics simulations, the atomistic nanoparticle structural evolution can be tracked on time scales that approach the actual experiments. This has enabled several different comparisons against experimental benchmarks, and it has helped transition the KMC simulations from a hypothetical toy model into a more experimentally-relevant test-bed. The model is initially parameterized by performing a series of automated comparisons of Au nanoparticle growth curves versus the experimental observations, and then the refined model allows for detailed structural analysis of the nanoparticle growth behavior. Although the Au nanoparticles are roughly spherical, the maximum/minimum dimensions deviate from the average by approximately 12.5%, which is consistent with the corresponding experiments. Also, a surface texture analysis highlights the changes in the surface structure as a function of time. While the nanoparticles show similar surface structures throughout the growth process, there can be some significant differences during the initial growth at different synthesis conditions.

Methods for processing high-throughput RNA sequencing data.

PubMed

Ares, Manuel

2014-11-03

High-throughput sequencing (HTS) methods for analyzing RNA populations (RNA-Seq) are gaining rapid application to many experimental situations. The steps in an RNA-Seq experiment require thought and planning, especially because the expense in time and materials is currently higher and the protocols are far less routine than those used for other high-throughput methods, such as microarrays. As always, good experimental design will make analysis and interpretation easier. Having a clear biological question, an idea about the best way to do the experiment, and an understanding of the number of replicates needed will make the entire process more satisfying. Whether the goal is capturing transcriptome complexity from a tissue or identifying small fragments of RNA cross-linked to a protein of interest, conversion of the RNA to cDNA followed by direct sequencing using the latest methods is a developing practice, with new technical modifications and applications appearing every day. Even more rapid are the development and improvement of methods for analysis of the very large amounts of data that arrive at the end of an RNA-Seq experiment, making considerations regarding reproducibility, validation, visualization, and interpretation increasingly important. This introduction is designed to review and emphasize a pathway of analysis from experimental design through data presentation that is likely to be successful, with the recognition that better methods are right around the corner. © 2014 Cold Spring Harbor Laboratory Press.

Theoretical and experimental studies on alpha/epsilon-hybrid peptides: design of a 14/12-helix from peptides with alternating (S)-C-linked carbo-epsilon-amino acid [(S)-epsilon-Caa((x))] and L-ala.

PubMed

Sharma, Gangavaram V M; Babu, Bommagani Shoban; Chatterjee, Deepak; Ramakrishna, Kallaganti V S; Kunwar, Ajit C; Schramm, Peter; Hofmann, Hans-Jörg

2009-09-04

An (S)-C-linked carbo-epsilon-amino acid [(S)-epsilon-Caa((x))] was prepared from the known (S)-delta-Caa. This monomer was utilized together with l-Ala to give novel alpha/epsilon-hybrid peptides in 1:1 alternation. Conformational analysis on penta- and hexapeptides by NMR (in CDCl(3)), CD, and MD studies led to the identification of robust 14/12-mixed helices. This is in agreement with the data from a theoretical conformational analysis on the basis of ab initio MO theory providing a complete overview on all formally possible hydrogen-bonded helix patterns of alpha/epsilon-hybrid peptides with 1:1 backbone alternation. The "new motif" of a mixed 14/12-helix was predicted as most stable in vacuum. Obviously, the formation of ordered secondary structures is also possible in peptide foldamers with amino acid constituents of considerable backbone lengths. Thus, alpha/epsilon-hybrid peptides expand the domain of foldamers and allow the introduction of desired functionalities via the alpha-amino acid constituents.

Control of a small working robot on a large flexible manipulator for suppressing vibrations: Development of a robust control law for flexible robot and it's stability analysis

NASA Technical Reports Server (NTRS)

Soo, Han Lee

1991-01-01

Researchers developed a robust control law for slow motions for the accurate trajectory control of a flexible robot. The control law does not need larger velocity gains than position gains, which some researchers need to ensure the stability of a rigid robot. Initial experimentation for the Small Articulated Manipulator (SAM) shows that control laws that use smaller velocity gains are more robust to signal noise than the control laws that use larger velocity gains. Researchers analyzed the stability of the composite control law, the robust control for the slow motion, and the strain rate feedback for the fast control. The stability analysis was done by using a quadratic Liapunov function. Researchers found that the flexible motion of links could be controlled by relating the input force to the flexible signals which are sensed at the near tip of each link. The signals are contaminated by the time delayed input force. However, the effect of the time delayed input force can be reduced by giving a certain configuration to the SAM.

Multi-locus analysis of genomic time series data from experimental evolution.

PubMed

Terhorst, Jonathan; Schlötterer, Christian; Song, Yun S

2015-04-01

Genomic time series data generated by evolve-and-resequence (E&R) experiments offer a powerful window into the mechanisms that drive evolution. However, standard population genetic inference procedures do not account for sampling serially over time, and new methods are needed to make full use of modern experimental evolution data. To address this problem, we develop a Gaussian process approximation to the multi-locus Wright-Fisher process with selection over a time course of tens of generations. The mean and covariance structure of the Gaussian process are obtained by computing the corresponding moments in discrete-time Wright-Fisher models conditioned on the presence of a linked selected site. This enables our method to account for the effects of linkage and selection, both along the genome and across sampled time points, in an approximate but principled manner. We first use simulated data to demonstrate the power of our method to correctly detect, locate and estimate the fitness of a selected allele from among several linked sites. We study how this power changes for different values of selection strength, initial haplotypic diversity, population size, sampling frequency, experimental duration, number of replicates, and sequencing coverage depth. In addition to providing quantitative estimates of selection parameters from experimental evolution data, our model can be used by practitioners to design E&R experiments with requisite power. We also explore how our likelihood-based approach can be used to infer other model parameters, including effective population size and recombination rate. Then, we apply our method to analyze genome-wide data from a real E&R experiment designed to study the adaptation of D. melanogaster to a new laboratory environment with alternating cold and hot temperatures.

[Effects of prevention education on Human Papillomavirus linked to cervix cancer for unmarried female university students].

PubMed

Kim, Hae Won

2009-08-01

This study was done to identify the effects of a Human Papillomavirus (HPV) linked to cervix cancer prevention education program for unmarried university female students. A new model in the cervix cancer prevention is provided. The research design was a nonequivalent control group pretest-posttest design. Participants were 63 female students in one of two university in an experimental group (29 students) and control group (34 students). After 4 weeks education, the differences between the two groups in the measurement variables were compared. Twelve weeks later, a follow-up test was done for experimental group only. After the education, experimental group showed significantly higher scores in all variables, the intention for Pap test (Z=-3.73, p<.001), intention for HPV vaccination (Z=-3.14, p=.002), general cancer prevention behavior (Z=-2.20, p=.028), attitudes to Pap (Z=-3.23, p=.001), benefits of cancer prevention behavior (Z=-3.97, p<.001), and HPV linked to cervix cancer knowledge (Z=-5.40, p<.001). In the follow-up study, the experimental group showed intermediate effects in intention for Pap test, intention of HPV vaccination and HPV linked to cervix cancer knowledge as well as short term effects in general cancer prevention behavior, attitudes to Pap and benefits of cancer prevention behavior. The program developed for this study on prevention education of HPV linked to cervix cancer was effective for unmarried university students in the short term and intermediate duration. Other educational approaches should be developed and short term effects and longitudinal changes of the education should be assessed. This education program should also be replicated for other female groups including unmarried working women or female adolescents.

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.

Shuttle/GPSPAC experimentation study

NASA Technical Reports Server (NTRS)

Moses, J.; Flack, J. F.

1977-01-01

The utilization is discussed of the GPSPAC, which is presently being developed to be used on the low altitude host vehicle (LAHV), for possible use in the shuttle avionics system to evaluate shuttle/GPS navigation performance. Analysis and tradeoffs of the shuttle/GPS link, shuttle signal interface requirements, oscillator tradeoffs and GPSPAC mechanical modifications for shuttle are included. Only the on-orbit utilization of GPSPAC for the shuttle is discussed. Other phases are briefly touched upon. Recommendations are provided for using the present GPSPAC and the changes required to perform shuttle on-orbit navigation.

Simulink models for performance analysis of high speed DQPSK modulated optical link

NASA Astrophysics Data System (ADS)

Sharan, Lucky; Rupanshi, Chaubey, V. K.

2016-03-01

This paper attempts to present the design approach for development of simulation models to study and analyze the transmission of 10 Gbps DQPSK signal over a single channel Peer to Peer link using Matlab Simulink. The simulation model considers the different optical components used in link design with their behavior represented initially by theoretical interpretation, including the transmitter topology, Mach Zehnder Modulator(MZM) module and, the propagation model for optical fibers etc. thus allowing scope for direct realization in experimental configurations. It provides the flexibility to incorporate the various photonic components as either user-defined or fixed and, can also be enhanced or removed from the model as per the design requirements. We describe the detailed operation and need of every component model and its representation in Simulink blocksets. Moreover the developed model can be extended in future to support Dense Wavelength Division Multiplexing (DWDM) system, thereby allowing high speed transmission with N × 40 Gbps systems. The various compensation techniques and their influence on system performance can be easily investigated by using such models.

Simulink models for performance analysis of high speed DQPSK modulated optical link

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

Sharan, Lucky, E-mail: luckysharan@pilani.bits-pilani.ac.in; Rupanshi,, E-mail: f2011222@pilani.bits-pilani.ac.in; Chaubey, V. K., E-mail: vkc@pilani.bits-pilani.ac.in

2016-03-09

This paper attempts to present the design approach for development of simulation models to study and analyze the transmission of 10 Gbps DQPSK signal over a single channel Peer to Peer link using Matlab Simulink. The simulation model considers the different optical components used in link design with their behavior represented initially by theoretical interpretation, including the transmitter topology, Mach Zehnder Modulator(MZM) module and, the propagation model for optical fibers etc. thus allowing scope for direct realization in experimental configurations. It provides the flexibility to incorporate the various photonic components as either user-defined or fixed and, can also be enhancedmore » or removed from the model as per the design requirements. We describe the detailed operation and need of every component model and its representation in Simulink blocksets. Moreover the developed model can be extended in future to support Dense Wavelength Division Multiplexing (DWDM) system, thereby allowing high speed transmission with N × 40 Gbps systems. The various compensation techniques and their influence on system performance can be easily investigated by using such models.« less

Experimental characterization of a 400 Gbit/s orbital angular momentum multiplexed free-space optical link over 120 m.

PubMed

Ren, Yongxiong; Wang, Zhe; Liao, Peicheng; Li, Long; Xie, Guodong; Huang, Hao; Zhao, Zhe; Yan, Yan; Ahmed, Nisar; Willner, Asher; Lavery, Martin P J; Ashrafi, Nima; Ashrafi, Solyman; Bock, Robert; Tur, Moshe; Djordjevic, Ivan B; Neifeld, Mark A; Willner, Alan E

2016-02-01

We experimentally demonstrate and characterize the performance of a 400-Gbit/s orbital angular momentum (OAM) multiplexed free-space optical link over 120 m on the roof of a building. Four OAM beams, each carrying a 100-Gbit/s quadrature-phase-shift-keyed channel are multiplexed and transmitted. We investigate the influence of channel impairments on the received power, intermodal crosstalk among channels, and system power penalties. Without laser tracking and compensation systems, the measured received power and crosstalk among OAM channels fluctuate by 4.5 dB and 5 dB, respectively, over 180 s. For a beam displacement of 2 mm that corresponds to a pointing error less than 16.7 μrad, the link bit error rates are below the forward error correction threshold of 3.8×10(-3) for all channels. Both experimental and simulation results show that power penalties increase rapidly when the displacement increases.

An experimental analysis on OSPF-TE convergence time

NASA Astrophysics Data System (ADS)

Huang, S.; Kitayama, K.; Cugini, F.; Paolucci, F.; Giorgetti, A.; Valcarenghi, L.; Castoldi, P.

2008-11-01

Open shortest path first (OSPF) protocol is commonly used as an interior gateway protocol (IGP) in MPLS and generalized MPLS (GMPLS) networks to determine the topology over which label-switched paths (LSPs) can be established. Traffic-engineering extensions (network states such as link bandwidth information, available wavelengths, signal quality, etc) have been recently enabled in OSPF (henceforth, called OSPF-TE) to support shortest path first (SPF) tree calculation upon different purposes, thus possibly achieving optimal path computation and helping improve resource utilization efficiency. Adding these features into routing phase can exploit the OSPF robustness, and no additional network component is required to manage the traffic-engineering information. However, this traffic-engineering enhancement also complicates OSPF behavior. Since network states change frequently upon the dynamic trafficengineered LSP setup and release, the network is easily driven from a stable state to unstable operating regimes. In this paper, we focus on studying the OSPF-TE stability in terms of convergence time. Convergence time is referred to the time spent by the network to go back to steady states upon any network state change. An external observation method (based on black-box method) is employed to estimate the convergence time. Several experimental test-beds are developed to emulate dynamic LSP setup/release, re-routing upon single-link failure. The experimental results show that with OSPF-TE the network requires more time to converge compared to the conventional OSPF protocol without TE extension. Especially, in case of wavelength-routed optical network (WRON), introducing per wavelength availability and wavelength continuity constraint to OSPF-TE suffers severe convergence time and a large number of advertised link state advertisements (LSAs). Our study implies that long convergence time and large number of LSAs flooded in the network might cause scalability problems in OSPF-TE and impose limitations on OSPF-TE applications. New solutions to mitigate the s convergence time and to reduce the amount of state information are desired in the future.

PGCA: An algorithm to link protein groups created from MS/MS data

PubMed Central

Sasaki, Mayu; Hollander, Zsuzsanna; Smith, Derek; McManus, Bruce; McMaster, W. Robert; Ng, Raymond T.; Cohen Freue, Gabriela V.

2017-01-01

The quantitation of proteins using shotgun proteomics has gained popularity in the last decades, simplifying sample handling procedures, removing extensive protein separation steps and achieving a relatively high throughput readout. The process starts with the digestion of the protein mixture into peptides, which are then separated by liquid chromatography and sequenced by tandem mass spectrometry (MS/MS). At the end of the workflow, recovering the identity of the proteins originally present in the sample is often a difficult and ambiguous process, because more than one protein identifier may match a set of peptides identified from the MS/MS spectra. To address this identification problem, many MS/MS data processing software tools combine all plausible protein identifiers matching a common set of peptides into a protein group. However, this solution introduces new challenges in studies with multiple experimental runs, which can be characterized by three main factors: i) protein groups’ identifiers are local, i.e., they vary run to run, ii) the composition of each group may change across runs, and iii) the supporting evidence of proteins within each group may also change across runs. Since in general there is no conclusive evidence about the absence of proteins in the groups, protein groups need to be linked across different runs in subsequent statistical analyses. We propose an algorithm, called Protein Group Code Algorithm (PGCA), to link groups from multiple experimental runs by forming global protein groups from connected local groups. The algorithm is computationally inexpensive and enables the connection and analysis of lists of protein groups across runs needed in biomarkers studies. We illustrate the identification problem and the stability of the PGCA mapping using 65 iTRAQ experimental runs. Further, we use two biomarker studies to show how PGCA enables the discovery of relevant candidate protein group markers with similar but non-identical compositions in different runs. PMID:28562641

Virtual experiments in electronics: beyond logistics, budgets, and the art of the possible

NASA Astrophysics Data System (ADS)

Chapman, Brian

1999-09-01

It is common and correct to suppose that computers support flexible delivery of educational resources by offering virtual experiments that replicate and substitute for experiments traditionally offered in conventional teaching laboratories. However, traditional methods are limited by logistics, costs, and what is physically possible to accomplish on a laboratory bench. Virtual experiments allow experimental approaches to teaching and learning to transcend these limits. This paper analyses recent and current developments in educational software for 1st- year physics, 2nd-year electronics engineering and 3rd-year communication engineering, based on three criteria: (1)Is the virtual experiment possible in a real laboratory? (2)How direct is the link between the experimental manipulation and the reinforcement of theoretical learning? (3) What impact might the virtual experiment have on the learner's acquisition of practical measurement skills? Virtual experiments allow more flexibility in the directness of the link between experimental manipulation and the theoretical message. However, increasing the directness of this link may reduce or even abolish the measurement processes associated with traditional experiments. Virtual experiments thus pose educational challenges: (a) expanding the design of experimentally based curricula beyond traditional boundaries and (b) ensuring that the learner acquires sufficient experience in making practical measurements.

An ontology of scientific experiments

PubMed Central

Soldatova, Larisa N; King, Ross D

2006-01-01

The formal description of experiments for efficient analysis, annotation and sharing of results is a fundamental part of the practice of science. Ontologies are required to achieve this objective. A few subject-specific ontologies of experiments currently exist. However, despite the unity of scientific experimentation, no general ontology of experiments exists. We propose the ontology EXPO to meet this need. EXPO links the SUMO (the Suggested Upper Merged Ontology) with subject-specific ontologies of experiments by formalizing the generic concepts of experimental design, methodology and results representation. EXPO is expressed in the W3C standard ontology language OWL-DL. We demonstrate the utility of EXPO and its ability to describe different experimental domains, by applying it to two experiments: one in high-energy physics and the other in phylogenetics. The use of EXPO made the goals and structure of these experiments more explicit, revealed ambiguities, and highlighted an unexpected similarity. We conclude that, EXPO is of general value in describing experiments and a step towards the formalization of science. PMID:17015305

Design and Experimental Implementation of Optimal Spacecraft Antenna Slews

DTIC Science & Technology

2013-12-01

LINK PENDULUM MODEL ............................................................58  C.  AZIMUTH-ELEVATION SYSTEM...BOUNDARY VALUE PROBLEM ......................77  B.  DOUBLE PENDULUM EXAMPLE............................................................82  C.  SOLVING THE...Figure 15.  Two-link Pendulum .........................................................................................58  Figure 16.  Double

Long microwave delay fiber-optic link for radar testing

NASA Astrophysics Data System (ADS)

Newberg, I. L.; Gee, C. M.; Thurmond, G. D.; Yen, H. W.

1990-05-01

A long fiberoptic delay line is used as a radar repeater to improve radar testing capabilities. The first known generation of 152 microsec delayed ideal target at X-band (10 GHz) frequencies having the phase stability and signal-to-noise ratio (SNR) needed for testing modern high-resolution Doppler radars is demonstrated with a 31.6-km experimental externally modulated fiberoptic link with a distributed-feedback (DFB) laser. The test application, link configuration, and link testing are discussed.

Ka-Band Link Study and Analysis for a Mars Hybrid RF/Optical Software Defined Radio

NASA Technical Reports Server (NTRS)

Zeleznikar, Daniel J.; Nappier, Jennifer M.; Downey, Joseph A.

2014-01-01

The integrated radio and optical communications (iROC) project at the NASA Glenn Research Center (GRC) is investigating the feasibility of a hybrid RF and optical communication subsystem for future deep space missions. The hybrid communications subsystem enables the advancement of optical communications while simultaneously mitigating the risk of infusion by combining an experimental optical transmitter and telescope with a reliable Ka-band RF transmitter and antenna. The iROC communications subsystem seeks to maximize the total data return over the course of a potential 2-year mission in Mars orbit beginning in 2021. Although optical communication by itself offers potential for greater data return over RF, the reliable Ka-band link is also being designed for high data return capability in this hybrid system. A daily analysis of the RF link budget over the 2-year span is performed to optimize and provide detailed estimates of the RF data return. In particular, the bandwidth dependence of these data return estimates is analyzed for candidate waveforms. In this effort, a data return modeling tool was created to analyze candidate RF modulation and coding schemes with respect to their spectral efficiency, amplifier output power back-off, required digital to analog conversion (DAC) sampling rates, and support by ground receivers. A set of RF waveforms is recommended for use on the iROC platform.

Formation and cleaning function of physically cross-linked dual strengthened water-soluble chitosan-based core-shell particles.

PubMed

Dong, Yanrui; Xiao, Congming

2017-09-01

Facile and mild ionic cross-linking and freezing/thawing technologies were applied to prepare double strengthened core-shell particles by using water-soluble chitosan (WSC), sodium alginate (SA) and poly(vinyl alcohol) (PVA) as starting materials. The aqueous solution contained WSC and PVA was dropped in ethanol to form beads. The beads were converted into WSC/PVA hydrogel particles by being subjected to three freeze/thaw cycles. Subsequently, ionic cross-linked hydrogel layer was formed around each WSC/PVA particle to generate core-shell particulates. Fourier transform infrared spectra confirmed the combination among various components. Dynamic mechanical thermal analysis indicated that the storage modulus of the core-shell hydrogel was improved obviously. Thermogravimetric analysis exhibited the thermal stability of the particles was also enhanced by incorporation of PVA. It was found that the particles were able to adsorb carbon dioxide, lead ion and copper ion. The adsorption capacities of dry particles toward carbon dioxide, Pb(II) and Cu(II) could reach 199.62, 39.28 and 26.03mg/g, respectively. The rates of the particles for binding Pb(II) and Cu(II) at initial stage were 26.57 and 4.30%/min, respectively. These experimental results suggested that the particles were an efficient sorbent for removing hazardous substances such as carbon dioxide and heavy-metal ions. Copyright © 2017 Elsevier B.V. All rights reserved.

The alliance relationship analysis of international terrorist organizations with link prediction

NASA Astrophysics Data System (ADS)

Fang, Ling; Fang, Haiyang; Tian, Yanfang; Yang, Tinghong; Zhao, Jing

2017-09-01

Terrorism is a huge public hazard of the international community. Alliances of terrorist organizations may cause more serious threat to national security and world peace. Understanding alliances between global terrorist organizations will facilitate more effective anti-terrorism collaboration between governments. Based on publicly available data, this study constructed a alliance network between terrorist organizations and analyzed the alliance relationships with link prediction. We proposed a novel index based on optimal weighted fusion of six similarity indices, in which the optimal weight is calculated by genetic algorithm. Our experimental results showed that this algorithm could achieve better results on the networks than other algorithms. Using this method, we successfully digged out 21 real terrorist organizations alliance from current data. Our experiment shows that this approach used for terrorist organizations alliance mining is effective and this study is expected to benefit the form of a more powerful anti-terrorism strategy.

Krebs cycle metabolon: structural evidence of substrate channeling revealed by cross-linking and mass spectrometry.

PubMed

Wu, Fei; Minteer, Shelley

2015-02-02

It has been hypothesized that the high metabolic flux in the mitochondria is due to the self-assembly of enzyme supercomplexes (called metabolons) that channel substrates from one enzyme to another, but there has been no experimental confirmation of this structure or the channeling. A structural investigation of enzyme organization within the Krebs cycle metabolon was accomplished by in vivo cross-linking and mass spectrometry. Eight Krebs cycle enzyme components were isolated upon chemical fixation, and interfacial residues between mitochondrial malate dehydrogenase, citrate synthase, and aconitase were identified. Using constraint protein docking, a low-resolution structure for the three-enzyme complex was achieved, as well as the two-fold symmetric octamer. Surface analysis showed formation of electrostatic channeling upon protein-protein association, which is the first structural evidence of substrate channeling in the Krebs cycle metabolon. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Simulation Study of Threats to Validity in Quasi-Experimental Designs: Interrelationship between Design, Measurement, and Analysis.

PubMed

Holgado-Tello, Fco P; Chacón-Moscoso, Salvador; Sanduvete-Chaves, Susana; Pérez-Gil, José A

2016-01-01

The Campbellian tradition provides a conceptual framework to assess threats to validity. On the other hand, different models of causal analysis have been developed to control estimation biases in different research designs. However, the link between design features, measurement issues, and concrete impact estimation analyses is weak. In order to provide an empirical solution to this problem, we use Structural Equation Modeling (SEM) as a first approximation to operationalize the analytical implications of threats to validity in quasi-experimental designs. Based on the analogies established between the Classical Test Theory (CTT) and causal analysis, we describe an empirical study based on SEM in which range restriction and statistical power have been simulated in two different models: (1) A multistate model in the control condition (pre-test); and (2) A single-trait-multistate model in the control condition (post-test), adding a new mediator latent exogenous (independent) variable that represents a threat to validity. Results show, empirically, how the differences between both the models could be partially or totally attributed to these threats. Therefore, SEM provides a useful tool to analyze the influence of potential threats to validity.

A Simulation Study of Threats to Validity in Quasi-Experimental Designs: Interrelationship between Design, Measurement, and Analysis

PubMed Central

Holgado-Tello, Fco. P.; Chacón-Moscoso, Salvador; Sanduvete-Chaves, Susana; Pérez-Gil, José A.

2016-01-01

The Campbellian tradition provides a conceptual framework to assess threats to validity. On the other hand, different models of causal analysis have been developed to control estimation biases in different research designs. However, the link between design features, measurement issues, and concrete impact estimation analyses is weak. In order to provide an empirical solution to this problem, we use Structural Equation Modeling (SEM) as a first approximation to operationalize the analytical implications of threats to validity in quasi-experimental designs. Based on the analogies established between the Classical Test Theory (CTT) and causal analysis, we describe an empirical study based on SEM in which range restriction and statistical power have been simulated in two different models: (1) A multistate model in the control condition (pre-test); and (2) A single-trait-multistate model in the control condition (post-test), adding a new mediator latent exogenous (independent) variable that represents a threat to validity. Results show, empirically, how the differences between both the models could be partially or totally attributed to these threats. Therefore, SEM provides a useful tool to analyze the influence of potential threats to validity. PMID:27378991

Interpreting lateral dynamic weight shifts using a simple inverted pendulum model.

PubMed

Kennedy, Michael W; Bretl, Timothy; Schmiedeler, James P

2014-01-01

Seventy-five young, healthy adults completed a lateral weight-shifting activity in which each shifted his/her center of pressure (CoP) to visually displayed target locations with the aid of visual CoP feedback. Each subject's CoP data were modeled using a single-link inverted pendulum system with a spring-damper at the joint. This extends the simple inverted pendulum model of static balance in the sagittal plane to lateral weight-shifting balance. The model controlled pendulum angle using PD control and a ramp setpoint trajectory, and weight-shifting was characterized by both shift speed and a non-minimum phase (NMP) behavior metric. This NMP behavior metric examines the force magnitude at shift initiation and provides weight-shifting balance performance information that parallels the examination of peak ground reaction forces in gait analysis. Control parameters were optimized on a subject-by-subject basis to match balance metrics for modeled results to metric values calculated from experimental data. Overall, the model matches experimental data well (average percent error of 0.35% for shifting speed and 0.05% for NMP behavior). These results suggest that the single-link inverted pendulum model can be used effectively to capture lateral weight-shifting balance, as it has been shown to model static balance. Copyright © 2014 Elsevier B.V. All rights reserved.

Integration of cell-free protein coexpression with an enzyme-linked immunosorbent assay enables rapid analysis of protein–protein interactions directly from DNA

PubMed Central

Layton, Curtis J; Hellinga, Homme W

2011-01-01

Assays that integrate detection of binding with cell-free protein expression directly from DNA can dramatically increase the pace at which protein–protein interactions (PPIs) can be analyzed by mutagenesis. In this study, we present a method that combines in vitro protein production with an enzyme-linked immunosorbent assay (ELISA) to measure PPIs. This method uses readily available commodity instrumentation and generic antibody–affinity tag interactions. It is straightforward and rapid to execute, enabling many interactions to be assessed in parallel. In traditional ELISAs, reporter complexes are assembled stepwise with one layer at a time. In the method presented here, all the members of the reporter complex are present and assembled together. The signal strength is dependent on all the intercomponent interaction affinities and concentrations. Although this assay is straightforward to execute, establishing proper conditions and analysis of the results require a thorough understanding of the processes that determine the signal strength. The formation of the fully assembled reporter sandwich can be modeled as a competition between Langmuir adsorption isotherms for the immobilized components and binding equilibria of the solution components. We have shown that modeling this process provides semiquantitative understanding of the effects of affinity and concentration and can guide strategies for the development of experimental protocols. We tested the method experimentally using the interaction between a synthetic ankyrin repeat protein (Off7) and maltose-binding protein. Measurements obtained for a collection of alanine mutations in the interface between these two proteins demonstrate that a range of affinities can be analyzed. PMID:21674663

Direct mechanical stimulation of tip links in hair cells through DNA tethers

PubMed Central

Basu, Aakash; Lagier, Samuel; Vologodskaia, Maria; Fabella, Brian A; Hudspeth, AJ

2016-01-01

Mechanoelectrical transduction by hair cells commences with hair-bundle deflection, which is postulated to tense filamentous tip links connected to transduction channels. Because direct mechanical stimulation of tip links has not been experimentally possible, this hypothesis has not been tested. We have engineered DNA tethers that link superparamagnetic beads to tip links and exert mechanical forces on the links when exposed to a magnetic-field gradient. By pulling directly on tip links of the bullfrog's sacculus we have evoked transduction currents from hair cells, confirming the hypothesis that tension in the tip links opens transduction channels. This demonstration of direct mechanical access to tip links additionally lays a foundation for experiments probing the mechanics of individual channels. DOI: http://dx.doi.org/10.7554/eLife.16041.001 PMID:27331611

A genome-wide longitudinal transcriptome analysis of the aging model Podospora anserina.

PubMed

Philipp, Oliver; Hamann, Andrea; Servos, Jörg; Werner, Alexandra; Koch, Ina; Osiewacz, Heinz D

2013-01-01

Aging of biological systems is controlled by various processes which have a potential impact on gene expression. Here we report a genome-wide transcriptome analysis of the fungal aging model Podospora anserina. Total RNA of three individuals of defined age were pooled and analyzed by SuperSAGE (serial analysis of gene expression). A bioinformatics analysis identified different molecular pathways to be affected during aging. While the abundance of transcripts linked to ribosomes and to the proteasome quality control system were found to decrease during aging, those associated with autophagy increase, suggesting that autophagy may act as a compensatory quality control pathway. Transcript profiles associated with the energy metabolism including mitochondrial functions were identified to fluctuate during aging. Comparison of wild-type transcripts, which are continuously down-regulated during aging, with those down-regulated in the long-lived, copper-uptake mutant grisea, validated the relevance of age-related changes in cellular copper metabolism. Overall, we (i) present a unique age-related data set of a longitudinal study of the experimental aging model P. anserina which represents a reference resource for future investigations in a variety of organisms, (ii) suggest autophagy to be a key quality control pathway that becomes active once other pathways fail, and (iii) present testable predictions for subsequent experimental investigations.

Realization of the Najafi-Golestanian microswimmer

NASA Astrophysics Data System (ADS)

Grosjean, Galien; Hubert, Maxime; Lagubeau, Guillaume; Vandewalle, Nicolas

2016-08-01

A paradigmatic microswimmer is the three-linked-spheres model, which follows a minimalist approach for propulsion by shape shifting. As such, it has been the subject of numerous analytical and numerical studies. In this Rapid Communication, an experimental three-linked-spheres swimmer is created by self-assembling ferromagnetic particles at an air-water interface. It is powered by a uniform oscillating magnetic field. A model, using two harmonic oscillators, reproduces the experimental findings. Because the model remains general, the same approach could be used to design a variety of efficient microswimmers.

National Centers for Environmental Prediction

Science.gov Websites

available at IMD Click here to go to the Special Report page Aug 2016 - IITM started experimental real-time Experimental version of GFS 10.0.0 ported to IITM & NCMRWF - February 2012 EnKF Hybrid GSI update - Spring diagnostics *Experimental* Climate Prediction Center (CPC) links... African Desk: SWFDP GFS forecasts South

The design and realisation of the IXV Mission Analysis and Flight Mechanics

NASA Astrophysics Data System (ADS)

Haya-Ramos, Rodrigo; Blanco, Gonzalo; Pontijas, Irene; Bonetti, Davide; Freixa, Jordi; Parigini, Cristina; Bassano, Edmondo; Carducci, Riccardo; Sudars, Martins; Denaro, Angelo; Angelini, Roberto; Mancuso, Salvatore

2016-07-01

The Intermediate eXperimental Vehicle (IXV) is a suborbital re-entry demonstrator successfully launched in February 2015 focusing on the in-flight demonstration of a lifting body system with active aerodynamic control surfaces. This paper presents an overview of the Mission Analysis and Flight Mechanics of the IXV vehicle, which comprises computation of the End-to-End (launch to splashdown) design trajectories, characterisation of the Entry Corridor, assessment of the Mission Performances through Monte Carlo campaigns, contribution to the aerodynamic database, analysis of the Visibility and link budget from Ground Stations and GPS, support to safety analyses (off nominal footprints), specification of the Centre of Gravity box, selection of the Angle of Attack trim line to be flown and characterisation of the Flying Qualities performances. An initial analysis and comparison with the raw flight data obtained during the flight will be discussed and first lessons learned derived.

Evaluation of performance and maximum length of continuous decks in bridges : part 2.

DOT National Transportation Integrated Search

2012-08-01

Field experimental measurements and analytical studies showed that the link-slab reinforcement : experiences almost no axial load due to thermal and gravity loading. One of the fundamental : reasons for the low loads in the link-slab reinforcement is...

"Hearing" Electromagnetic Waves

ERIC Educational Resources Information Center

Rojo, Marta; Munoz, Juan

2014-01-01

In this work, an educational experience is described in which a microwave communication link is used to make students aware that all electromagnetic waves have the same physical nature and properties. Experimental demonstrations are linked to theoretical concepts to increase comprehension of the physical principles underlying electromagnetic…

A genetic method for sex determination in Ovis spp. by interruption of the zinc finger protein, Y-linked (ZFY) gene on the Y chromosome.

PubMed

Zhang, Yong Sheng; Du, Ying Chun; Sun, Li Rong; Wang, Xu Hai; Liu, Shuai Bing; Xi, Ji Feng; Li, Chao Cheng; Ying, Rui Wen; Jiang, Song; Wang, Xiang Zu; Shen, Hong; Jia, Bin

2018-03-06

The mammalian Y chromosome plays a critical role in spermatogenesis. However, the exact functions of each gene on the Y chromosome have not been completely elucidated, due, in part, to difficulties in gene targeting analysis of the Y chromosome. The zinc finger protein, Y-linked (ZFY) gene was first proposed to be a sex determination factor, although its function in spermatogenesis has recently been elucidated. Nevertheless, ZFY gene targeting analysis has not been performed to date. In the present study, RNA interference (RNAi) was used to generate ZFY-interrupted Hu sheep by injecting short hairpin RNA (shRNA) into round spermatids. The resulting spermatozoa exhibited abnormal sperm morphology, including spermatozoa without tails and others with head and tail abnormalities. Quantitative real-time polymerase chain reaction analysis showed that ZFY mRNA expression was decreased significantly in Hu sheep with interrupted ZFY compared with wild-type Hu sheep. The sex ratio of lambs also exhibited a bias towards females. Together, the experimental strategy and findings of the present study reveal that ZFY also functions in spermatogenesis in Hu sheep and facilitate the use of RNAi in the control of sex in Hu sheep.

An efficient sensitivity analysis method for modified geometry of Macpherson suspension based on Pearson correlation coefficient

NASA Astrophysics Data System (ADS)

Shojaeefard, Mohammad Hasan; Khalkhali, Abolfazl; Yarmohammadisatri, Sadegh

2017-06-01

The main purpose of this paper is to propose a new method for designing Macpherson suspension, based on the Sobol indices in terms of Pearson correlation which determines the importance of each member on the behaviour of vehicle suspension. The formulation of dynamic analysis of Macpherson suspension system is developed using the suspension members as the modified links in order to achieve the desired kinematic behaviour. The mechanical system is replaced with an equivalent constrained links and then kinematic laws are utilised to obtain a new modified geometry of Macpherson suspension. The equivalent mechanism of Macpherson suspension increased the speed of analysis and reduced its complexity. The ADAMS/CAR software is utilised to simulate a full vehicle, Renault Logan car, in order to analyse the accuracy of modified geometry model. An experimental 4-poster test rig is considered for validating both ADAMS/CAR simulation and analytical geometry model. Pearson correlation coefficient is applied to analyse the sensitivity of each suspension member according to vehicle objective functions such as sprung mass acceleration, etc. Besides this matter, the estimation of Pearson correlation coefficient between variables is analysed in this method. It is understood that the Pearson correlation coefficient is an efficient method for analysing the vehicle suspension which leads to a better design of Macpherson suspension system.

HERALD (health economics using routine anonymised linked data).

PubMed

Husain, Muhammad J; Brophy, Sinead; Macey, Steven; Pinder, Leila M; Atkinson, Mark D; Cooksey, Roxanne; Phillips, Ceri J; Siebert, Stefan

2012-03-29

Health economic analysis traditionally relies on patient derived questionnaire data, routine datasets, and outcomes data from experimental randomised control trials and other clinical studies, which are generally used as stand-alone datasets. Herein, we outline the potential implications of linking these datasets to give one single joined up data-resource for health economic analysis. The linkage of individual level data from questionnaires with routinely-captured health care data allows the entire patient journey to be mapped both retrospectively and prospectively. We illustrate this with examples from an Ankylosing Spondylitis (AS) cohort by linking patient reported study dataset with the routinely collected general practitioner (GP) data, inpatient (IP) and outpatient (OP) datasets, and Accident and Emergency department data in Wales. The linked data system allows: (1) retrospective and prospective tracking of patient pathways through multiple healthcare facilities; (2) validation and clarification of patient-reported recall data, complementing the questionnaire/routine data information; (3) obtaining objective measure of the costs of chronic conditions for a longer time horizon, and during the pre-diagnosis period; (4) assessment of health service usage, referral histories, prescribed drugs and co-morbidities; and (5) profiling and stratification of patients relating to disease manifestation, lifestyles, co-morbidities, and associated costs. Using the GP data system we tracked about 183 AS patients retrospectively and prospectively from the date of questionnaire completion to gather the following information: (a) number of GP events; (b) presence of a GP 'drug' read codes; and (c) the presence of a GP 'diagnostic' read codes. We tracked 236 and 296 AS patients through the OP and IP data systems respectively to count the number of OP visits; and IP admissions and duration. The results are presented under several patient stratification schemes based on disease severity, functions, age, sex, and the onset of disease symptoms. The linked data system offers unique opportunities for enhanced longitudinal health economic analysis not possible through the use of traditional isolated datasets. Additionally, this data linkage provides important information to improve diagnostic and referral pathways, and thus helps maximise clinical efficiency and efficiency in the use of resources.

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 Application of an Emerging Technique for Protein–Protein Interaction Interface Mapping: The Combination of Photo-Initiated Cross-Linking Protein Nanoprobes with Mass Spectrometry

PubMed Central

Ptáčková, Renata; Ječmen, Tomáš; Novák, Petr; Hudeček, Jiří; Stiborová, Marie; Šulc, Miroslav

2014-01-01

Protein–protein interaction was investigated using a protein nanoprobe capable of photo-initiated cross-linking in combination with high-resolution and tandem mass spectrometry. This emerging experimental approach introduces photo-analogs of amino acids within a protein sequence during its recombinant expression, preserves native protein structure and is suitable for mapping the contact between two proteins. The contact surface regions involved in the well-characterized interaction between two molecules of human 14-3-3ζ regulatory protein were used as a model. The employed photo-initiated cross-linking techniques extend the number of residues shown to be within interaction distance in the contact surface of the 14-3-3ζ dimer (Gln8–Met78). The results of this study are in agreement with our previously published data from molecular dynamic calculations based on high-resolution chemical cross-linking data and Hydrogen/Deuterium exchange mass spectrometry. The observed contact is also in accord with the 14-3-3ζ X-ray crystal structure (PDB 3dhr). The results of the present work are relevant to the structural biology of transient interaction in the 14-3-3ζ protein, and demonstrate the ability of the chosen methodology (the combination of photo-initiated cross-linking protein nanoprobes and mass spectrometry analysis) to map the protein-protein interface or regions with a flexible structure. PMID:24865487

Parallel computational and experimental studies of the morphological modification of calcium carbonate by cobalt

NASA Astrophysics Data System (ADS)

Braybrook, A. L.; Heywood, B. R.; Jackson, R. A.; Pitt, K.

2002-08-01

Crystal growth can be controlled by the incorporation of dopant ions into the lattice and yet the question of how such substituents affect the morphology has not been addressed. This paper describes the forms of calcite (CaCO 3) which arise when the growth assay is doped with cobalt. Distinct and specific morphological changes are observed; the calcite crystals adopt a morphology which is dominated by the {01.1} family of faces. These experimental studies paralleled the development of computational methods for the analysis of crystal habit as a function of dopant concentration. In this case, the predicted defect morphology also argued for the dominance of the (01.1) face in the growth form. The appearance of this face was related to the preferential segregation of the dopant ions to the crystal surface. This study confirms the evolution of a robust computational model for the analysis of calcite growth forms under a range of environmental conditions and presages the use of such tools for the predictive development of crystal morphologies in those applications where chemico-physical functionality is linked closely to a specific crystallographic form.

A new online database of nuclear electromagnetic moments

NASA Astrophysics Data System (ADS)

Mertzimekis, Theo J.

2017-09-01

Nuclear electromagnetic (EM) moments, i.e., the magnetic dipole and the electric quadrupole moments, provide important information of nuclear structure. As in other types of experimental data available to the community, measurements of nuclear EM moments have been organized systematically in compilations since the dawn of nuclear science. However, the wealth of recent moments measurements with radioactive beams, as well as earlier existing measurements, lack an online, easy-to-access, systematically organized presence to disseminate information to researchers. In addition, available printed compilations suffer a rather long life cycle, being left behind experimental measurements published in journals or elsewhere. A new, online database (http://magneticmoments.info) focusing on nuclear EM moments has been recently developed to disseminate experimental data to the community. The database includes non-evaluated experimental data of nuclear EM moments, giving strong emphasis on frequent updates (life cycle is 3 months) and direct connection to the sources via DOI and NSR hyperlinks. It has been recently integrated in IAEA LiveChart [1], but can also be found as a standalone webapp [2]. A detailed review of the database features, as well as plans for further development and expansion in the near future is discussed.

Defensive response of European sea bass (Dicentrarchus labrax) against Listonella anguillarum or Photobacterium damselae subsp. piscicida experimental infection.

PubMed

Mosca, Francesco; Ciulli, Sara; Volpatti, Donatella; Romano, Nicla; Volpe, Enrico; Bulfon, Chiara; Massimini, Marcella; Caccia, Elisabetta; Galeotti, Marco; Tiscar, Pietro G

2014-12-15

Sea bass were experimentally infected with Listonella anguillarum or Photobacterium damselae subsp. piscicida (Phdp). At 24 and 72h post-infection, the expression analysis of immune-relevant genes (IL-1β, IL-6, IL-8, Hepcidin), the transcriptional level and detection of HSP70, and the quantification of serum iron were investigated in association with the histological analysis and the bacterial recognition in tissues by immunohistochemistry. At 15 days post-infection, the specific antibody response was detected in surviving fish, as well as the transcriptional levels of TcR and BcR sequences. Both experimental infections were characterized by a similar acute response, whereas different histological and immunohistochemistry evidences were observed. In particular, the early reaction appeared suitable for the clearance of L. anguillarum, thus limiting the histological lesions, the bacterial dissemination and the further development of acquired immunity in surviving fish. On the contrary, the innate response appeared not enough to resolve the Phdp infection, which was characterized by tissue damage, bacterial widespread and substantial detection of specific humoral immunity in surviving fish, also associated to lymphocytes clonal expansion. Besides the opportunistic conditions involved in fish vibriosis and pasteurellosis, the comparison between these experimental infection models seems to suggest that the rate of development of the acquired immunity is strictly linked to the activation of the host innate response combined to the degree of bacterial virulence. Copyright © 2014 Elsevier B.V. All rights reserved.

Suppression of Even-Order Photodiode Nonlinearities in Multioctave Photonic Links

NASA Astrophysics Data System (ADS)

Hastings, Alexander S.; Urick, Vincent J.; Sunderman, Christopher; Diehl, John F.; McKinney, Jason D.; Tulchinsky, David A.; Devgan, Preetpaul S.; Williams, Keith J.

2008-08-01

A balanced photonic receiver is demonstrated to suppress photodiode-generated even-order nonlinearities in a photonic link. This result is especially important for multioctave analog applications. Experimental results are presented for a high-frequency (2-30 MHz) link exhibiting 33-dB suppression of the second harmonic, resulting in an output intercept point of 99 dBm due to second-order intermodulation distortion at 26-mA average photocurrent.

Comparison of three microarray probe annotation pipelines: differences in strategies and their effect on downstream analysis

PubMed Central

Neerincx, Pieter BT; Casel, Pierrot; Prickett, Dennis; Nie, Haisheng; Watson, Michael; Leunissen, Jack AM; Groenen, Martien AM; Klopp, Christophe

2009-01-01

Background Reliable annotation linking oligonucleotide probes to target genes is essential for functional biological analysis of microarray experiments. We used the IMAD, OligoRAP and sigReannot pipelines to update the annotation for the ARK-Genomics Chicken 20 K array as part of a joined EADGENE/SABRE workshop. In this manuscript we compare their annotation strategies and results. Furthermore, we analyse the effect of differences in updated annotation on functional analysis for an experiment involving Eimeria infected chickens and finally we propose guidelines for optimal annotation strategies. Results IMAD, OligoRAP and sigReannot update both annotation and estimated target specificity. The 3 pipelines can assign oligos to target specificity categories although with varying degrees of resolution. Target specificity is judged based on the amount and type of oligo versus target-gene alignments (hits), which are determined by filter thresholds that users can adjust based on their experimental conditions. Linking oligos to annotation on the other hand is based on rigid rules, which differ between pipelines. For 52.7% of the oligos from a subset selected for in depth comparison all pipelines linked to one or more Ensembl genes with consensus on 44.0%. In 31.0% of the cases none of the pipelines could assign an Ensembl gene to an oligo and for the remaining 16.3% the coverage differed between pipelines. Differences in updated annotation were mainly due to different thresholds for hybridisation potential filtering of oligo versus target-gene alignments and different policies for expanding annotation using indirect links. The differences in updated annotation packages had a significant effect on GO term enrichment analysis with consensus on only 67.2% of the enriched terms. Conclusion In addition to flexible thresholds to determine target specificity, annotation tools should provide metadata describing the relationships between oligos and the annotation assigned to them. These relationships can then be used to judge the varying degrees of reliability allowing users to fine-tune the balance between reliability and coverage. This is important as it can have a significant effect on functional microarray analysis as exemplified by the lack of consensus on almost one third of the terms found with GO term enrichment analysis based on updated IMAD, OligoRAP or sigReannot annotation. PMID:19615109

Comparison of three microarray probe annotation pipelines: differences in strategies and their effect on downstream analysis.

PubMed

Neerincx, Pieter Bt; Casel, Pierrot; Prickett, Dennis; Nie, Haisheng; Watson, Michael; Leunissen, Jack Am; Groenen, Martien Am; Klopp, Christophe

2009-07-16

Reliable annotation linking oligonucleotide probes to target genes is essential for functional biological analysis of microarray experiments. We used the IMAD, OligoRAP and sigReannot pipelines to update the annotation for the ARK-Genomics Chicken 20 K array as part of a joined EADGENE/SABRE workshop. In this manuscript we compare their annotation strategies and results. Furthermore, we analyse the effect of differences in updated annotation on functional analysis for an experiment involving Eimeria infected chickens and finally we propose guidelines for optimal annotation strategies. IMAD, OligoRAP and sigReannot update both annotation and estimated target specificity. The 3 pipelines can assign oligos to target specificity categories although with varying degrees of resolution. Target specificity is judged based on the amount and type of oligo versus target-gene alignments (hits), which are determined by filter thresholds that users can adjust based on their experimental conditions. Linking oligos to annotation on the other hand is based on rigid rules, which differ between pipelines.For 52.7% of the oligos from a subset selected for in depth comparison all pipelines linked to one or more Ensembl genes with consensus on 44.0%. In 31.0% of the cases none of the pipelines could assign an Ensembl gene to an oligo and for the remaining 16.3% the coverage differed between pipelines. Differences in updated annotation were mainly due to different thresholds for hybridisation potential filtering of oligo versus target-gene alignments and different policies for expanding annotation using indirect links. The differences in updated annotation packages had a significant effect on GO term enrichment analysis with consensus on only 67.2% of the enriched terms. In addition to flexible thresholds to determine target specificity, annotation tools should provide metadata describing the relationships between oligos and the annotation assigned to them. These relationships can then be used to judge the varying degrees of reliability allowing users to fine-tune the balance between reliability and coverage. This is important as it can have a significant effect on functional microarray analysis as exemplified by the lack of consensus on almost one third of the terms found with GO term enrichment analysis based on updated IMAD, OligoRAP or sigReannot annotation.

To Cross-Link or Not to Cross-Link? Cross-Linking Associated Foreign Body Response of Collagen-Based Devices

PubMed Central

Delgado, Luis M.; Bayon, Yves; Pandit, Abhay

2015-01-01

Collagen-based devices, in various physical conformations, are extensively used for tissue engineering and regenerative medicine applications. Given that the natural cross-linking pathway of collagen does not occur in vitro, chemical, physical, and biological cross-linking methods have been assessed over the years to control mechanical stability, degradation rate, and immunogenicity of the device upon implantation. Although in vitro data demonstrate that mechanical properties and degradation rate can be accurately controlled as a function of the cross-linking method utilized, preclinical and clinical data indicate that cross-linking methods employed may have adverse effects on host response, especially when potent cross-linking methods are employed. Experimental data suggest that more suitable cross-linking methods should be developed to achieve a balance between stability and functional remodeling. PMID:25517923

Improving Our Ability to Assess Land Management and Disturbance by Linking Traditional Ecosystem Measurements with UAV Spectral Analysis

NASA Astrophysics Data System (ADS)

Sutter, L., Jr.; Barron-Gafford, G.; Smith, W. K.; Minor, R. L.; Raub, H.; Jimenez, J. R.; Wolsiffer, S. K.; Escobedo, E. B.; Smith, J.

2017-12-01

Drylands are dynamic landscapes of mixed plant functional types that vary in their response to abiotic and biotic drivers of change. Within these regions, woody plant-herbaceous relationships have generally been viewed as negative: woody plants within these ecosystems have been shown to negatively impact herbaceous growth by taking advantage of both deeper stored water and intercepting near surface moisture after precipitation events. There has been a long-invested effort to eliminate woody plants in many areas of the world, and analyzing and assessing land management decisions has historically required high monetary and time inputs. Unfortunately, both management practices and disturbances from fire can leave a very heterogeneous landscape, making assessment of their impacts difficult to assess. This study has attempted to address the effectiveness of two commonly used treatments within woody plant invaded areas, fire and herbicide application, by linking plant physiological measurements with the emerging technology of unmanned aerial vehicle (UAV) spectral analysis. Taking advantage of a USDA-ARS sponsored herbicide treatment in 2016 and the accidental Sawmill Fire of 2017, both within the Santa Rita Experimental Range (SRER) of Southern Arizona, USA, we linked spectral data collected via UAV with ground-based photosynthetic measurements. Given the high repeatability, and both spatial and spectral resolution of low-flying UAV measurements, we found that there are a variety of spectral indices that can be derived and accurately linked with traditional ecological measurements. Results and techniques from this study can be immediately applied to land management plans as well as be improved for other ecological parameters, such as those obtained from long-term study sites containing eddy covariance towers.

MARVEL analysis of the measured high-resolution rovibrational spectra of C2H2

NASA Astrophysics Data System (ADS)

Chubb, Katy L.; Joseph, Megan; Franklin, Jack; Choudhury, Naail; Furtenbacher, Tibor; Császár, Attila G.; Gaspard, Glenda; Oguoko, Patari; Kelly, Adam; Yurchenko, Sergei N.; Tennyson, Jonathan; Sousa-Silva, Clara

2018-01-01

Rotation-vibration energy levels are determined for the electronic ground state of the acetylene molecule, 12C2H2, using the Measured Active Rotational-Vibrational Energy Levels (MARVEL) technique. 37,813 measured transitions from 61 publications are considered. The distinct components of the spectroscopic network linking ortho and para states of the molecule are considered separately. The 20,717 ortho and 17,096 para transitions measured experimentally are used to determine 6013 ortho and 5200 para energy levels. The MARVEL results are compared with alternative compilations based on the use of effective Hamiltonians.

Health values and prospect theory.

PubMed

Treadwell, J R; Lenert, L A

1999-01-01

Health values are important components of medical decisions. Experimental data suggest that people value health in complex and dynamic ways. Prospect theory is a descriptive theory of choice that may accurately characterize how people assign values to health states. The authors first provide background on prospect theory and how it can be applied to health values. Next, they review the relevant health research and find mixed support for prospect theory. Last, they discuss implications of prospect theory for cost-effectiveness analysis. The application of prospect theory to health deserves further research because it may help clarify the link between health and values.

Research of energy characteristics of frequency-regulated electric drive

NASA Astrophysics Data System (ADS)

Arsentiev, O. V.; Arsentiev, G. O.; Dunaev, M. P.

2018-03-01

The paper considers the urgency of the research problems of the inverter as a part of the frequency converter. Experimental studies on the influence of the nature of the load on the structure of the distribution of power consumption are used. The authors described virtual models, allowing for analysis of changes in the cardinality of the inverter-factor when using it on an active-inductive load. According to the results, there are research conclusions to determine the relationship between the current form in the DC- link constant voltage and the mode of operation of the induction motor.

Localized temperature and chemical reaction control in nanoscale space by nanowire array.

PubMed

Jin, C Yan; Li, Zhiyong; Williams, R Stanley; Lee, K-Cheol; Park, Inkyu

2011-11-09

We introduce a novel method for chemical reaction control with nanoscale spatial resolution based on localized heating by using a well-aligned nanowire array. Numerical and experimental analysis shows that each individual nanowire could be selectively and rapidly Joule heated for local and ultrafast temperature modulation in nanoscale space (e.g., maximum temperature gradient 2.2 K/nm at the nanowire edge; heating/cooling time < 2 μs). By taking advantage of this capability, several nanoscale chemical reactions such as polymer decomposition/cross-linking and direct and localized hydrothermal synthesis of metal oxide nanowires were demonstrated.

Scintillation statistics measured in an earth-space-earth retroreflector link

NASA Technical Reports Server (NTRS)

Bufton, J. L.

1977-01-01

Scintillation was measured in a vertical path from a ground-based laser transmitter to the Geos 3 satellite and back to a ground-based receiver telescope and, the experimental results were compared with analytical results presented in a companion paper (Bufton, 1977). The normalized variance, the probability density function and the power spectral density of scintillation were all measured. Moments of the satellite scintillation data in terms of normalized variance were lower than expected. The power spectrum analysis suggests that there were scintillation components at frequencies higher than the 250 Hz bandwidth available in the experiment.

Fabrication and evaluation of magnetic phosphodiesterase-5 linked nanoparticles as adsorbent for magnetic dispersive solid-phase extraction of inhibitors from Chinese herbal medicine prior to ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry analysis.

PubMed

Tao, Yi; Gu, Xianghui; Li, Weidong; Cai, Baochang

2018-01-12

In the present study, the preparation of the magnetic phosphodiesterase-5 linked Fe 3 O 4 @ SiO 2 nanoparticles was successfully achieved by amide reaction and the magnetic phosphodiesterase-5 linked Fe 3 O 4 @SiO 2 nanoparticles were evaluated as a new adsorbent for magnetic dispersive solid-phase extraction of ligands from medicinal plant samples before the analysis by UHPLC-Q-TOF/MS. The prepared phosphodiesterase-5 linked Fe 3 O 4 @SiO 2 nanoparticles were characterized by X-ray diffraction, Fourier transform infrared spectroscopy, transmission electron microscopy, vibration sample magnetometer and potential laser particle size analyzer. The effects of EDC concentration, incubation time and bead-protein ratio on the amount of immobilized protein were studied. The main experimental parameters affect extraction efficiency of ligands, such as wash times, wash solvents, incubation pH, ion strength and incubation temperature, were investigated and optimized by using echinacoside as a model compound. The absolute recovery of echinacoside was ranged from 98.36%-102.16% in Cistanche tubulosa sample under the optimal extraction conditions. Good linearity was observed in the investigated concentration range of 0.006 mgmL -1 -0.97 mgmL -1 (R 2  = 0.9999). The limit of detection was 0.002 mgmL -1 . The RSDs of within-day and between-day precision were less than 2.3%. Due to the excellent magnetic behavior of Fe 3 O 4 @SiO 2 nanoparticles, the proposed method was shown to be simple and rapid. Remarkably, the magnetic phosphodiesterase-5 linked Fe 3 O 4 @SiO 2 nanoparticles could be recycled for ten times with loss of 10% activity. Copyright © 2017 Elsevier B.V. All rights reserved.

Temperature dependence of creep compliance of highly cross-linked epoxy: A molecular simulation study

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

Khabaz, Fardin, E-mail: rajesh.khare@ttu.edu; Khare, Ketan S., E-mail: rajesh.khare@ttu.edu; Khare, Rajesh, E-mail: rajesh.khare@ttu.edu

2014-05-15

We have used molecular dynamics (MD) simulations to study the effect of temperature on the creep compliance of neat cross-linked epoxy. Experimental studies of mechanical behavior of cross-linked epoxy in literature commonly report creep compliance values, whereas molecular simulations of these systems have primarily focused on the Young’s modulus. In this work, in order to obtain a more direct comparison between experiments and simulations, atomistically detailed models of the cross-linked epoxy are used to study their creep compliance as a function of temperature using MD simulations. The creep tests are performed by applying a constant tensile stress and monitoring themore » resulting strain in the system. Our results show that simulated values of creep compliance increase with an increase in both time and temperature. We believe that such calculations of the creep compliance, along with the use of time temperature superposition, hold great promise in connecting the molecular insight obtained from molecular simulation at small length- and time-scales with the experimental behavior of such materials. To the best of our knowledge, this work is the first reported effort that investigates the creep compliance behavior of cross-linked epoxy using MD simulations.« less

Vocal acoustic analysis as a biometric indicator of information processing: implications for neurological and psychiatric disorders.

PubMed

Cohen, Alex S; Dinzeo, Thomas J; Donovan, Neila J; Brown, Caitlin E; Morrison, Sean C

2015-03-30

Vocal expression reflects an integral component of communication that varies considerably within individuals across contexts and is disrupted in a range of neurological and psychiatric disorders. There is reason to suspect that variability in vocal expression reflects, in part, the availability of "on-line" resources (e.g., working memory, attention). Thus, understanding vocal expression is a potentially important biometric index of information processing, not only across but within individuals over time. A first step in this line of research involves establishing a link between vocal expression and information processing systems in healthy adults. The present study employed a dual attention experimental task where participants provided natural speech while simultaneously engaged in a baseline, medium or high nonverbal processing-load task. Objective, automated, and computerized analysis was employed to measure vocal expression in 226 adults. Increased processing load resulted in longer pauses, fewer utterances, greater silence overall and less variability in frequency and intensity levels. These results provide compelling evidence of a link between information processing resources and vocal expression, and provide important information for the development of an automated, inexpensive and uninvasive biometric measure of information processing. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

PRGdb: a bioinformatics platform for plant resistance gene analysis

PubMed Central

Sanseverino, Walter; Roma, Guglielmo; De Simone, Marco; Faino, Luigi; Melito, Sara; Stupka, Elia; Frusciante, Luigi; Ercolano, Maria Raffaella

2010-01-01

PRGdb is a web accessible open-source (http://www.prgdb.org) database that represents the first bioinformatic resource providing a comprehensive overview of resistance genes (R-genes) in plants. PRGdb holds more than 16 000 known and putative R-genes belonging to 192 plant species challenged by 115 different pathogens and linked with useful biological information. The complete database includes a set of 73 manually curated reference R-genes, 6308 putative R-genes collected from NCBI and 10463 computationally predicted putative R-genes. Thanks to a user-friendly interface, data can be examined using different query tools. A home-made prediction pipeline called Disease Resistance Analysis and Gene Orthology (DRAGO), based on reference R-gene sequence data, was developed to search for plant resistance genes in public datasets such as Unigene and Genbank. New putative R-gene classes containing unknown domain combinations were discovered and characterized. The development of the PRG platform represents an important starting point to conduct various experimental tasks. The inferred cross-link between genomic and phenotypic information allows access to a large body of information to find answers to several biological questions. The database structure also permits easy integration with other data types and opens up prospects for future implementations. PMID:19906694

CellLineNavigator: a workbench for cancer cell line analysis

PubMed Central

Krupp, Markus; Itzel, Timo; Maass, Thorsten; Hildebrandt, Andreas; Galle, Peter R.; Teufel, Andreas

2013-01-01

The CellLineNavigator database, freely available at http://www.medicalgenomics.org/celllinenavigator, is a web-based workbench for large scale comparisons of a large collection of diverse cell lines. It aims to support experimental design in the fields of genomics, systems biology and translational biomedical research. Currently, this compendium holds genome wide expression profiles of 317 different cancer cell lines, categorized into 57 different pathological states and 28 individual tissues. To enlarge the scope of CellLineNavigator, the database was furthermore closely linked to commonly used bioinformatics databases and knowledge repositories. To ensure easy data access and search ability, a simple data and an intuitive querying interface were implemented. It allows the user to explore and filter gene expression, focusing on pathological or physiological conditions. For a more complex search, the advanced query interface may be used to query for (i) differentially expressed genes; (ii) pathological or physiological conditions; or (iii) gene names or functional attributes, such as Kyoto Encyclopaedia of Genes and Genomes pathway maps. These queries may also be combined. Finally, CellLineNavigator allows additional advanced analysis of differentially regulated genes by a direct link to the Database for Annotation, Visualization and Integrated Discovery (DAVID) Bioinformatics Resources. PMID:23118487

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.

Bit-error-rate testing of fiber optic data links for MMIC-based phased array antennas

NASA Technical Reports Server (NTRS)

Shalkhauser, K. A.; Kunath, R. R.; Daryoush, A. S.

1990-01-01

The measured bit-error-rate (BER) performance of a fiber optic data link to be used in satellite communications systems is presented and discussed. In the testing, the link was measured for its ability to carry high burst rate, serial-minimum shift keyed (SMSK) digital data similar to those used in actual space communications systems. The fiber optic data link, as part of a dual-segment injection-locked RF fiber optic link system, offers a means to distribute these signals to the many radiating elements of a phased array antenna. Test procedures, experimental arrangements, and test results are presented.

Linking School and Work. Promising Practices from a National Demonstration.

ERIC Educational Resources Information Center

Pressman, Harvey

This book describes experimental demonstration programs in the United States on different ways to link school and work more meaningfully for disadvantaged teenagers. The programs are sponsored by Youthwork, Incorporated, a public-private partnership concerned with youth unemployment and the transition from school to work. The book provides…

Design and development aspects of flexure mechanism for high precision application

NASA Astrophysics Data System (ADS)

Sollapur, Shrishail B.; Patil, M. S.; Deshmukh, S. P.

2018-04-01

Planer XY Flexurel Mechanisms has various applications in precision motion mechanisms. A flexural mechanism generates relative motion between fixed support and motion stage using flexibility of material. This mechanism offers zero backlash, frictionless motion and high order repeatability. It is relatively compact in design as compared to rigid link mechanism. The merits of using flexure is complete mechanism can be from single monolith. Modelling of flexural mechanism to provide accurate scanning of comparatively larger range at a higher speed. Static Analysis of mechanism is carried out on FEA tool to determine static deflection of motion stage. Further Mechanism is actuated with the help of weight pan and weights. The resultant displacement is measured on Dial Gauge Indicator. Experimental set-up consists of Flexural mechanism, Dial Gauge, Weight Pan and Weights, Pulley, String, Small metal strip, Optical Bread Board etc. Further experimental Results and Analytical Results are compared and minimum deviation is found.

Hydrologic drivers and controls of stream biofilm-grazer interactions

NASA Astrophysics Data System (ADS)

Ceola, S.; Bertuzzo, E.; Mari, L.; Botter, G.; Hödl, I.; Battin, T.; Rinaldo, A.

2012-04-01

Understanding the dynamics of fluvial ecosystems linked to hydrology is one of the most important challenges of ecohydrology. In fact, streamflow, which chiefly relies on rainfall, climate, land use and geomorphologic properties, plays a fundamental role in sustaining and regulating fluvial ecosystem integrity. To analyze possible implications of hydrological fluctuations on the biofilm-grazer interaction, an experimental campaign has been conducted between June and September 2011 at the Wasser Cluster Lunz, in Lunz am See (AU). 36 flumes have been used to perform biofilm growth and grazing activity under two distinct discharge conditions (i.e., constant and stochastic discharge regimes) and four different light regimes (from natural light conditions to nearly 70% attenuation). Experimental results concerning (i) dynamics of biofilm growth, (ii) grazing effect, and (iii) grazing rate will be presented. Results of performed statistical analysis for testing the effects of discharge treatment and light regime on the grazing rate will be also discussed.

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

Recent advances in the evolutionary engineering of industrial biocatalysts.

PubMed

Winkler, James D; Kao, Katy C

2014-12-01

Evolutionary engineering has been used to improve key industrial strain traits, such as carbon source utilization, tolerance to adverse environmental conditions, and resistance to chemical inhibitors, for many decades due to its technical simplicity and effectiveness. The lack of need for prior genetic knowledge underlying the phenotypes of interest makes this a powerful approach for strain development for even species with minimal genotypic information. While the basic experimental procedure for laboratory adaptive evolution has remained broadly similar for many years, a range of recent advances show promise for improving the experimental workflows for evolutionary engineering by accelerating the pace of evolution, simplifying the analysis of evolved mutants, and providing new ways of linking desirable phenotypes to selectable characteristics. This review aims to highlight some of these recent advances and discuss how they may be used to improve industrially relevant microbial phenotypes. Copyright © 2014 Elsevier Inc. All rights reserved.

Customized Corneal Cross-Linking-A Mathematical Model.

PubMed

Caruso, Ciro; Epstein, Robert L; Ostacolo, Carmine; Pacente, Luigi; Troisi, Salvatore; Barbaro, Gaetano

2017-05-01

To improve the safety, reproducibility, and depth of effect of corneal cross-linking with the ultraviolet A (UV-A) exposure time and fluence customized according to the corneal thickness. Twelve human corneas were used for the experimental protocol. They were soaked using a transepithelial (EPI-ON) technique using riboflavin with the permeation enhancer vitamin E-tocopheryl polyethylene glycol succinate. The corneas were then placed on microscope slides and irradiated at 3 mW/cm for 30 minutes. The UV-A output parameters were measured to build a new equation describing the time-dependent loss of endothelial protection induced by riboflavin during cross-linking, as well as a pachymetry-dependent and exposure time-dependent prescription for input UV-A fluence. The proposed equation was used to establish graphs prescribing the maximum UV-A fluence input versus exposure time that always maintains corneal endothelium exposure below toxicity limits. Analysis modifying the Lambert-Beer law for riboflavin oxidation leads to graphs of the maximum safe level of UV-A radiation fluence versus the time applied and thickness of the treated cornea. These graphs prescribe UV-A fluence levels below 1.8 mW/cm for corneas of thickness 540 μm down to 1.2 mW/cm for corneas of thickness 350 μm. Irradiation times are typically below 15 minutes. The experimental and mathematical analyses establish the basis for graphs that prescribe maximum safe fluence and UV-A exposure time for corneas of different thicknesses. Because this clinically tested protocol specifies a corneal surface clear of shielding riboflavin on the corneal surface during UV-A irradiation, it allows for shorter UV-A irradiation time and lower fluence than in the Dresden protocol.

Long-term treatment with green tea polyphenols modifies the gut microbiome of female sprague-dawley rats.

PubMed

Wang, Jincheng; Tang, Lili; Zhou, Hongyuan; Zhou, Jun; Glenn, Travis C; Shen, Chwan-Li; Wang, Jia-Sheng

2018-06-01

Green tea polyphenols (GTP) have been shown to exert a spectrum of health benefits to animals and humans. It is plausible that the beneficial effects of GTP are a result of its interaction with the gut microbiota. This study evaluated the effect of long-term treatment with GTP on the gut microbiota of experimental rats and the potential linkage between changes of the gut microbiota with the beneficial effects of GTP. Six-month-old Sprague-Dawley rats were randomly allocated into three dosing regimens (0, 0.5%, and 1.5% of GTP) and followed for 6 months. At the end of month 3 or month 6, half of the animals from each group were sacrificed and their colon contents were collected for microbiome analysis using 16S ribosomal RNA and shotgun metagenomic community sequencing. GTP treatment significantly decreased the biodiversity and modified the microbial community in a dose-dependent manner; similar patterns were observed at both sampling times. Multiple operational taxonomic units and phylotypes were modified: the phylotypes Bacteroidetes and Oscillospira, previously linked to the lean phenotype in human and animal studies, were enriched; and Peptostreptococcaceae previously linked to colorectal cancer phenotype was depleted in GTP treated groups in a dose-dependent manner. Several microbial gene orthologs were modified, among which genes related to energy production and conversion were consistently enriched in samples from month 6 in a dose-dependent manner. This study showed that long-term treatment with GTP induced a dose-dependent modification of the gut microbiome in experimental rats, which might be linked to beneficial effects of GTP. Copyright © 2018 Elsevier Inc. All rights reserved.

From theory to experimental design-Quantifying a trait-based theory of predator-prey dynamics.

PubMed

Laubmeier, A N; Wootton, Kate; Banks, J E; Bommarco, Riccardo; Curtsdotter, Alva; Jonsson, Tomas; Roslin, Tomas; Banks, H T

2018-01-01

Successfully applying theoretical models to natural communities and predicting ecosystem behavior under changing conditions is the backbone of predictive ecology. However, the experiments required to test these models are dictated by practical constraints, and models are often opportunistically validated against data for which they were never intended. Alternatively, we can inform and improve experimental design by an in-depth pre-experimental analysis of the model, generating experiments better targeted at testing the validity of a theory. Here, we describe this process for a specific experiment. Starting from food web ecological theory, we formulate a model and design an experiment to optimally test the validity of the theory, supplementing traditional design considerations with model analysis. The experiment itself will be run and described in a separate paper. The theory we test is that trophic population dynamics are dictated by species traits, and we study this in a community of terrestrial arthropods. We depart from the Allometric Trophic Network (ATN) model and hypothesize that including habitat use, in addition to body mass, is necessary to better model trophic interactions. We therefore formulate new terms which account for micro-habitat use as well as intra- and interspecific interference in the ATN model. We design an experiment and an effective sampling regime to test this model and the underlying assumptions about the traits dominating trophic interactions. We arrive at a detailed sampling protocol to maximize information content in the empirical data obtained from the experiment and, relying on theoretical analysis of the proposed model, explore potential shortcomings of our design. Consequently, since this is a "pre-experimental" exercise aimed at improving the links between hypothesis formulation, model construction, experimental design and data collection, we hasten to publish our findings before analyzing data from the actual experiment, thus setting the stage for strong inference.

Network analysis of mesoscale optical recordings to assess regional, functional connectivity.

PubMed

Lim, Diana H; LeDue, Jeffrey M; Murphy, Timothy H

2015-10-01

With modern optical imaging methods, it is possible to map structural and functional connectivity. Optical imaging studies that aim to describe large-scale neural connectivity often need to handle large and complex datasets. In order to interpret these datasets, new methods for analyzing structural and functional connectivity are being developed. Recently, network analysis, based on graph theory, has been used to describe and quantify brain connectivity in both experimental and clinical studies. We outline how to apply regional, functional network analysis to mesoscale optical imaging using voltage-sensitive-dye imaging and channelrhodopsin-2 stimulation in a mouse model. We include links to sample datasets and an analysis script. The analyses we employ can be applied to other types of fluorescence wide-field imaging, including genetically encoded calcium indicators, to assess network properties. We discuss the benefits and limitations of using network analysis for interpreting optical imaging data and define network properties that may be used to compare across preparations or other manipulations such as animal models of disease.

Minimally complex ion traps as modules for quantum communication and computing

NASA Astrophysics Data System (ADS)

Nigmatullin, Ramil; Ballance, Christopher J.; de Beaudrap, Niel; Benjamin, Simon C.

2016-10-01

Optically linked ion traps are promising as components of network-based quantum technologies, including communication systems and modular computers. Experimental results achieved to date indicate that the fidelity of operations within each ion trap module will be far higher than the fidelity of operations involving the links; fortunately internal storage and processing can effectively upgrade the links through the process of purification. Here we perform the most detailed analysis to date on this purification task, using a protocol which is balanced to maximise fidelity while minimising the device complexity and the time cost of the process. Moreover we ‘compile down’ the quantum circuit to device-level operations including cooling and shuttling events. We find that a linear trap with only five ions (two of one species, three of another) can support our protocol while incorporating desirable features such as global control, i.e. laser control pulses need only target an entire zone rather than differentiating one ion from its neighbour. To evaluate the capabilities of such a module we consider its use both as a universal communications node for quantum key distribution, and as the basic repeating unit of a quantum computer. For the latter case we evaluate the threshold for fault tolerant quantum computing using the surface code, finding acceptable fidelities for the ‘raw’ entangling link as low as 83% (or under 75% if an additional ion is available).

Optimizing performance of hybrid FSO/RF networks in realistic dynamic scenarios

NASA Astrophysics Data System (ADS)

Llorca, Jaime; Desai, Aniket; Baskaran, Eswaran; Milner, Stuart; Davis, Christopher

2005-08-01

Hybrid Free Space Optical (FSO) and Radio Frequency (RF) networks promise highly available wireless broadband connectivity and quality of service (QoS), particularly suitable for emerging network applications involving extremely high data rate transmissions such as high quality video-on-demand and real-time surveillance. FSO links are prone to atmospheric obscuration (fog, clouds, snow, etc) and are difficult to align over long distances due the use of narrow laser beams and the effect of atmospheric turbulence. These problems can be mitigated by using adjunct directional RF links, which provide backup connectivity. In this paper, methodologies for modeling and simulation of hybrid FSO/RF networks are described. Individual link propagation models are derived using scattering theory, as well as experimental measurements. MATLAB is used to generate realistic atmospheric obscuration scenarios, including moving cloud layers at different altitudes. These scenarios are then imported into a network simulator (OPNET) to emulate mobile hybrid FSO/RF networks. This framework allows accurate analysis of the effects of node mobility, atmospheric obscuration and traffic demands on network performance, and precise evaluation of topology reconfiguration algorithms as they react to dynamic changes in the network. Results show how topology reconfiguration algorithms, together with enhancements to TCP/IP protocols which reduce the network response time, enable the network to rapidly detect and act upon link state changes in highly dynamic environments, ensuring optimized network performance and availability.

Formation and rupture of Ca(2+) induced pectin biopolymer gels.

PubMed

Basak, Rajib; Bandyopadhyay, Ranjini

2014-10-07

When calcium salts are added to an aqueous solution of polysaccharide pectin, ionic cross-links form between pectin chains, giving rise to a gel network in dilute solution. In this work, dynamic light scattering (DLS) is employed to study the microscopic dynamics of the fractal aggregates (flocs) that constitute the gels, while rheological measurements are carried out to study the process of gel rupture. As the calcium salt concentration is increased, DLS experiments reveal that the polydispersity of the flocs increase simultaneously with the characteristic relaxation times of the gel network. Above a critical salt concentration, the flocs become interlinked to form a reaction-limited fractal gel network. Rheological studies demonstrate that the limits of the linear rheological response and the critical stresses required to rupture these networks both decrease with the increase in salt concentration. These features indicate that the ion-mediated pectin gels studied here lie in a 'strong link' regime that is characterised by inter-floc links that are stronger than intra-floc links. A scaling analysis of the experimental data presented here demonstrates that the elasticities of the individual fractal flocs exhibit power-law dependences on the added salt concentration. We conclude that when both pectin and salt concentrations are increased, the number of fractal flocs of pectin increases simultaneously with the density of crosslinks, giving rise to very large values of the bulk elastic modulus.

The mare reproductive loss syndrome and the eastern tent caterpillar: a toxicokinetic/statistical analysis with clinical, epidemiologic, and mechanistic implications.

PubMed

Sebastian, Manu; Gantz, Marie G; Tobin, Thomas; Harkins, J Daniel; Bosken, Jeffrey M; Hughes, Charlie; Harrison, Lenn R; Bernard, William V; Richter, Dana L; Fitzgerald, Terrence D

2003-01-01

During 2001, central Kentucky experienced acute transient epidemics of early and late fetal losses, pericarditis, and unilateral endophthalmitis, collectively referred to as mare reproductive loss syndrome (MRLS). A toxicokinetic/statistical analysis of experimental and field MRLS data was conducted using accelerated failure time (AFT) analysis of abortions following administration of Eastern tent caterpillars (ETCs; 100 or 50 g/day or 100 g of irradiated caterpillars/day) to late-term pregnant mares. In addition, 2001 late-term fetal loss field data were used in the analysis. Experimental data were fitted by AFT analysis at a high (P <.0001) significance. Times to first abortion ("lag time") and abortion rates were dose dependent. Lag times decreased and abortion rates increased exponentially with dose. Calculated dose x response data curves allow interpretation of abortion data in terms of "intubated ETC equivalents." Analysis suggested that field exposure to ETCs in 2001 in central Kentucky commenced on approximately April 27, was initially equivalent to approximately 5 g of intubated ETCs/day, and increased to approximately 30 g/day at the outbreak peak. This analysis accounts for many aspects of the epidemiology, clinical presentations, and manifestations of MRLS. It allows quantitative interpretation of experimental and field MRLS data and has implications for the basic mechanisms underlying MRLS. The results support suggestions that MRLS is caused by exposure to or ingestion of ETCs. The results also show that high levels of ETC exposure produce intense, focused outbreaks of MRLS, closely linked in time and place to dispersing ETCs, as occurred in central Kentucky in 2001. With less intense exposure, lag time is longer and abortions tend to spread out over time and may occur out of phase with ETC exposure, obscuring both diagnosis of this syndrome and the role of the caterpillars.

Near-Field Based Communication and Electrical Systems

NASA Astrophysics Data System (ADS)

Azad, Umar

A near-field power transfer equation for an inductively coupled near-field system is derived based on the equivalent circuit model of the coupled resonant loops. Experimental results show that the proposed near-field coupling equation is trustworthy as it correctly predicts the transferred power versus distance relationship for different values of loaded quality factors at the transmitter and the receiver. Capacity performance of near-field communication (NFC) links is analyzed for noise limited and interference limited scenarios based on information theory. The analytical results provide guidelines for design of inductively coupled antenna systems as the power and capacity budget of the link is carried out. Examples of inductively coupled VLF NFC links are evaluated for different operating scenarios, demonstrating the efficacy and importance of the proposed near-field link budget. However, in a conventional setup of inductively coupled NFC link, the power coupled through and the bandwidth must be traded off. Direct Antenna Modulation (DAM) is a feasible scheme to break this dilemma. With DAM utilized in NFC link, the power and bandwidth product limit in a high Q system can be circumvented because the non-linear/time-varying nature of the operation allows high speed modulations decoupled from the charging and discharging process of the high-Q resonator. In this work, the theory of NFC link with DAM on the transmitter is presented and validated with an experimental setup. Improvement in reception of the high-speed modulation information is observed in the experiment, implying that a superior capacity performance of a NFC link is achieved through DAM versus the traditional scheme. The resonant coupling efficiency is limited by the product of the quality factors Q, of the transmitter and receiver and the coupling coefficient k. We observe that in order to achieve maximum efficiency, the ratio of the load-to-loss impedances at both the source and load should be equal to a prescribed value. This is the same condition that yields simultaneous impedance matching at source and load. The efficiency limit is then calculated for single transmitter and two uncoupled receivers. In that case, optimal efficiency is obtained when the load-to-loss impedance ratio is equal to the same prescribed value for all devices simultaneously. However, this condition does not provide for simultaneous matching at the source and loads, which turns out to be impossible. The analysis is then generalized for a single transmitter and N uncoupled receivers and we find that as the number of receivers increases, the total efficiency limit also increases. Finally, we present the efficiency limits and optimal conditions for a system consisting of single and multiple repeaters between transmitter and receiver, which have been shown previously to relay power to larger distances.

Nanostructured diamine-fullerene derivatives: computational density functional theory study and experimental evidence for their formation via gas-phase functionalization.

PubMed

Contreras-Torres, Flavio F; Basiuk, Elena V; Basiuk, Vladimir A; Meza-Laguna, Víctor; Gromovoy, Taras Yu

2012-02-16

Nanostructure derivatives of fullerene C(60) are used in emerging applications of composite matrices, including protective and decorative coating, superadsorbent material, thin films, and lightweight high-strength fiber-reinforced materials, etc. In this study, quantum chemical calculations and experimental studies were performed to analyze the derivatives of diamine-fullerene prepared by the gas-phase solvent-free functionalization technique. In particular, the aliphatic 1,8-diamino-octane and the aromatic 1,5-diaminonaphthalene, which are diamines volatile in vacuum, were studied. We addressed two alternative mechanisms of the amination reaction via polyaddition and cross-linking of C(60) with diamines, using the pure GGA BLYP, PW91, and PBE functionals; further validation calculations were performed using the semiempirical dispersion GGA B97-D functional which contains parameters that have been specially adjusted by a more realistic view on dispersion contributions. In addition, we looked for experimental evidence for the covalent functionalization by using laser desorption/ionization time-of-flight mass spectrometry, thermogravimetric analysis, and atomic force microscopy.

Acute effects of whole-body cryotherapy on sit-and-reach amplitude in women and men.

PubMed

De Nardi, Massimo; La Torre, Antonio; Benis, Roberto; Sarabon, Nejc; Fonda, Borut

2015-12-01

Flexibility is an intrinsic property of body tissues, which among other factors determines the range of motion (ROM). A decrease in neural activation of the muscle has been linked with greater ROM. Cryotherapy is an effective technique to reduces neural activation. Hence, the aim of the present study was to evaluate if a single session of whole-body cryotherapy (WBC) affects ROM. 60 women and 60 men were divided into two groups (control and experimental). After the initial sit-and-reach test, experimental group performed a 150 s session of WBC, whereas the control group stayed in thermo-neutral environment. Immediately after, both groups performed another sit-and-reach test. A 3-way analysis of variance revealed statistically significant time×group and time × gender interaction. Experimental groups improved sit-and-reach amplitude to a greater extend than the control group. Our results support the hypothesis that ROM is increased immediately after a single session of WBC. Copyright © 2015 Elsevier Inc. All rights reserved.

Prediction of Multi-Target Networks of Neuroprotective Compounds with Entropy Indices and Synthesis, Assay, and Theoretical Study of New Asymmetric 1,2-Rasagiline Carbamates

PubMed Central

Romero Durán, Francisco J.; Alonso, Nerea; Caamaño, Olga; García-Mera, Xerardo; Yañez, Matilde; Prado-Prado, Francisco J.; González-Díaz, Humberto

2014-01-01

In a multi-target complex network, the links (Lij) represent the interactions between the drug (di) and the target (tj), characterized by different experimental measures (Ki, Km, IC50, etc.) obtained in pharmacological assays under diverse boundary conditions (cj). In this work, we handle Shannon entropy measures for developing a model encompassing a multi-target network of neuroprotective/neurotoxic compounds reported in the CHEMBL database. The model predicts correctly >8300 experimental outcomes with Accuracy, Specificity, and Sensitivity above 80%–90% on training and external validation series. Indeed, the model can calculate different outcomes for >30 experimental measures in >400 different experimental protocolsin relation with >150 molecular and cellular targets on 11 different organisms (including human). Hereafter, we reported by the first time the synthesis, characterization, and experimental assays of a new series of chiral 1,2-rasagiline carbamate derivatives not reported in previous works. The experimental tests included: (1) assay in absence of neurotoxic agents; (2) in the presence of glutamate; and (3) in the presence of H2O2. Lastly, we used the new Assessing Links with Moving Averages (ALMA)-entropy model to predict possible outcomes for the new compounds in a high number of pharmacological tests not carried out experimentally. PMID:25255029

Statistical analysis of early failures in electromigration

NASA Astrophysics Data System (ADS)

Gall, M.; Capasso, C.; Jawarani, D.; Hernandez, R.; Kawasaki, H.; Ho, P. S.

2001-07-01

The detection of early failures in electromigration (EM) and the complicated statistical nature of this important reliability phenomenon have been difficult issues to treat in the past. A satisfactory experimental approach for the detection and the statistical analysis of early failures has not yet been established. This is mainly due to the rare occurrence of early failures and difficulties in testing of large sample populations. Furthermore, experimental data on the EM behavior as a function of varying number of failure links are scarce. In this study, a technique utilizing large interconnect arrays in conjunction with the well-known Wheatstone Bridge is presented. Three types of structures with a varying number of Ti/TiN/Al(Cu)/TiN-based interconnects were used, starting from a small unit of five lines in parallel. A serial arrangement of this unit enabled testing of interconnect arrays encompassing 480 possible failure links. In addition, a Wheatstone Bridge-type wiring using four large arrays in each device enabled simultaneous testing of 1920 interconnects. In conjunction with a statistical deconvolution to the single interconnect level, the results indicate that the electromigration failure mechanism studied here follows perfect lognormal behavior down to the four sigma level. The statistical deconvolution procedure is described in detail. Over a temperature range from 155 to 200 °C, a total of more than 75 000 interconnects were tested. None of the samples have shown an indication of early, or alternate, failure mechanisms. The activation energy of the EM mechanism studied here, namely the Cu incubation time, was determined to be Q=1.08±0.05 eV. We surmise that interface diffusion of Cu along the Al(Cu) sidewalls and along the top and bottom refractory layers, coupled with grain boundary diffusion within the interconnects, constitutes the Cu incubation mechanism.

An Information NEXUS: The NASA Global Hawk Link Module

NASA Technical Reports Server (NTRS)

Sullivan, D. V.

2012-01-01

The Link Module described in this paper was first developed for the NASA Global Hawk Pacific Mission (GloPAC), four flights of 30 hour duration, supporting the Aura Validation Experiment (AVE). Its second use was during the Genesis and Rapid Intensification Processes (GRIP) experiment, a NASA Earth Science field experiment to better understand how tropical storms form and develop into major hurricanes. In these missions, the Link module negotiated all communication over the high bandwidth Ku satellite link, archived al the science data from onboard experiments in a spatially enable database, routed command and control of the instruments from the Global Hawk Operations Center, and retransmitted select data sets directly to experimenters control and analysis systems. The availability of aggregated information from collections of sensors, and remote control capabilities, in real-time, is revolutionizing the way Airborne Science is being conducted. Also described is the next generation Link Module now being designed and tested to support the NASA Earth Venture missions, the Hurricane and Severe Storm Sentinel (HS3) mission, and Airborne Tropical Tropopause Experiment (ATTREX) mission. Advanced data fusion technologies being developed will further advance the Scientific productivity, flexibility and robustness of these systems. Historically, the Link module evolved from the instrument and communication interface controller used by NASA's Pathfinder and Pathfinder plus solar powered UAS's in the late 1990's. It later was expanded for use in the AIRDAS four channel scanner flown on the NASA Altus UAS, and then again to a module in the AMS twelve channel multispectral scanner flying on the NASA (Predator-b) Ikhana UAS. The current system is the next step in the evolution, a multi board system packaged in a Curtiss Wright MIL-spec, flight qualified enclosure.

Wageningen Urban Rainfall Experiment 2014 (WURex14): Experimental Setup and First Results

NASA Astrophysics Data System (ADS)

Uijlenhoet, R.; Overeem, A.; Leijnse, H.; Hazenberg, P.

2014-12-01

Microwave links from cellular communication networks have been shown to be able to provide valuable information concerning the space-time variability of rainfall. In particular over urban areas, where network densities are generally high, they have the potential to complement existing dedicated infrastructure to measure rainfall (gauges, radars). In addition, microwave links provide a great opportunity for ground-based rainfall measurement for those land surface areas of the world where gauges and radars are generally lacking, e.g. Africa, Latin America, and large parts of Asia. Such information is not only crucial for water management and agriculture, but also for instance for ground validation of space-borne rainfall estimates such as those provided by the recently launched core satellite of the GPM (Global Precipitation Measurement) mission. WURex14 is dedicated to address several errors and uncertainties associated with such quantitative precipitation estimates in detail. The core of the experiment is provided by two co-located microwave links installed between two major buildings on the Wageningen University campus, approximately 2 km apart: a 38 GHz commercial microwave link, kindly provided to us by T-Mobile NL, and a 38 GHz dual-polarization research microwave link from RAL. Transmitting and receiving antennas have been attached to masts installed on the roofs of the two buildings, about 30 m above the ground. This setup has been complemented with a Scintec infrared Large-Aperture Scintillometer, installed over the same path, as well as a Parsivel optical disdrometer, located close to the mast on the receiving end of the links. During the course of the experiment, a 26 GHz RAL research microwave link was added to the experimental setup. Temporal sampling of the received signals was performed at a rate of 20 Hz. In addition, two time-lapse cameras have been installed on either side of the path to monitor the wetness of the antennas as well as the state of the atmosphere. Approximately halfway along the link path a rain gauge from the KNMI operational network is located. Finally, data is available from several commercial microwave links in the vicinity of the experimental setup, as well as from the KNMI weather radars. We report on the first results from this experiment, collected during the Summer and Fall of 2014.

Wageningen Urban Rainfall Experiment 2014 (WURex14): Experimental Setup and First Results

NASA Astrophysics Data System (ADS)

van Leth, Thomas; Uijlenhoet, Remko; Overeem, Aart; Leijnse, Hidde; Hazenberg, Pieter

2015-04-01

Microwave links from cellular communication networks have been shown to be able to provide valuable information concerning the space-time variability of rainfall. In particular over urban areas, where network densities are generally high, they have the potential to complement existing dedicated infrastructure to measure rainfall (gauges, radars). In addition, microwave links provide a great opportunity for ground-based rainfall measurement for those land surface areas of the world where gauges and radars are generally lacking, e.g. Africa, Latin America, and large parts of Asia. Such information is not only crucial for water management and agriculture, but also for instance for ground validation of space-borne rainfall estimates such as those provided by the recently launched core satellite of the GPM (Global Precipitation Measurement) mission. WURex14 is dedicated to address several errors and uncertainties associated with such quantitative precipitation estimates in detail. The core of the experiment is provided by two co-located microwave links installed between two major buildings on the Wageningen University campus, approximately 2 km apart: a 38 GHz commercial microwave link, kindly provided to us by T-Mobile NL, and a 38 GHz dual-polarization research microwave link from RAL. Transmitting and receiving antennas have been attached to masts installed on the roofs of the two buildings, about 30 m above the ground. This setup has been complemented with a Scintec infrared Large-Aperture Scintillometer, installed over the same path, as well as a Parsivel optical disdrometer, located close to the mast on the receiving end of the links. During the course of the experiment, a 26 GHz RAL research microwave link was added to the experimental setup. Temporal sampling of the received signals was performed at a rate of 20 Hz. In addition, two time-lapse cameras have been installed on either side of the path to monitor the wetness of the antennas as well as the state of the atmosphere. Approximately halfway along the link path a rain gauge from the KNMI operational network is located. Finally, data is available from several commercial microwave links in the vicinity of the experimental setup, as well as from the KNMI weather radars. We report on the first results from this experiment, collected during the Summer and Fall of 2014.

Structuring and extracting knowledge for the support of hypothesis generation in molecular biology

PubMed Central

Roos, Marco; Marshall, M Scott; Gibson, Andrew P; Schuemie, Martijn; Meij, Edgar; Katrenko, Sophia; van Hage, Willem Robert; Krommydas, Konstantinos; Adriaans, Pieter W

2009-01-01

Background Hypothesis generation in molecular and cellular biology is an empirical process in which knowledge derived from prior experiments is distilled into a comprehensible model. The requirement of automated support is exemplified by the difficulty of considering all relevant facts that are contained in the millions of documents available from PubMed. Semantic Web provides tools for sharing prior knowledge, while information retrieval and information extraction techniques enable its extraction from literature. Their combination makes prior knowledge available for computational analysis and inference. While some tools provide complete solutions that limit the control over the modeling and extraction processes, we seek a methodology that supports control by the experimenter over these critical processes. Results We describe progress towards automated support for the generation of biomolecular hypotheses. Semantic Web technologies are used to structure and store knowledge, while a workflow extracts knowledge from text. We designed minimal proto-ontologies in OWL for capturing different aspects of a text mining experiment: the biological hypothesis, text and documents, text mining, and workflow provenance. The models fit a methodology that allows focus on the requirements of a single experiment while supporting reuse and posterior analysis of extracted knowledge from multiple experiments. Our workflow is composed of services from the 'Adaptive Information Disclosure Application' (AIDA) toolkit as well as a few others. The output is a semantic model with putative biological relations, with each relation linked to the corresponding evidence. Conclusion We demonstrated a 'do-it-yourself' approach for structuring and extracting knowledge in the context of experimental research on biomolecular mechanisms. The methodology can be used to bootstrap the construction of semantically rich biological models using the results of knowledge extraction processes. Models specific to particular experiments can be constructed that, in turn, link with other semantic models, creating a web of knowledge that spans experiments. Mapping mechanisms can link to other knowledge resources such as OBO ontologies or SKOS vocabularies. AIDA Web Services can be used to design personalized knowledge extraction procedures. In our example experiment, we found three proteins (NF-Kappa B, p21, and Bax) potentially playing a role in the interplay between nutrients and epigenetic gene regulation. PMID:19796406

Randomized test of an implementation intention-based tool to reduce stress-induced eating.

PubMed

O'Connor, Daryl B; Armitage, Christopher J; Ferguson, Eamonn

2015-06-01

Stress may indirectly contribute to disease (e.g. cardiovascular disease, cancer) by producing deleterious changes to diet. The purpose of this study was to test the effectiveness of a stress management support (SMS) tool to reduce stress-related unhealthy snacking and to promote stress-related healthy snacking. Participants were randomized to complete a SMS tool with instruction to link stressful situations with healthy snack alternatives (experimental) or a SMS tool without a linking instruction (control). On-line daily reports of stressors and snacking were completed for 7 days. Daily stressors were associated with unhealthy snack consumption in the control condition but not in the experimental condition. Participants highly motivated towards healthy eating consumed a greater number of healthy snacks in the experimental condition on stressful days compared to participants in the experimental condition with low and mean levels of motivation. This tool is an effective, theory driven, intervention that helps to protect against stress-induced high-calorie snack consumption.

Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools

PubMed Central

Sud, Manish; Fahy, Eoin; Cotter, Dawn; Azam, Kenan; Vadivelu, Ilango; Burant, Charles; Edison, Arthur; Fiehn, Oliver; Higashi, Richard; Nair, K. Sreekumaran; Sumner, Susan; Subramaniam, Shankar

2016-01-01

The Metabolomics Workbench, available at www.metabolomicsworkbench.org, is a public repository for metabolomics metadata and experimental data spanning various species and experimental platforms, metabolite standards, metabolite structures, protocols, tutorials, and training material and other educational resources. It provides a computational platform to integrate, analyze, track, deposit and disseminate large volumes of heterogeneous data from a wide variety of metabolomics studies including mass spectrometry (MS) and nuclear magnetic resonance spectrometry (NMR) data spanning over 20 different species covering all the major taxonomic categories including humans and other mammals, plants, insects, invertebrates and microorganisms. Additionally, a number of protocols are provided for a range of metabolite classes, sample types, and both MS and NMR-based studies, along with a metabolite structure database. The metabolites characterized in the studies available on the Metabolomics Workbench are linked to chemical structures in the metabolite structure database to facilitate comparative analysis across studies. The Metabolomics Workbench, part of the data coordinating effort of the National Institute of Health (NIH) Common Fund's Metabolomics Program, provides data from the Common Fund's Metabolomics Resource Cores, metabolite standards, and analysis tools to the wider metabolomics community and seeks data depositions from metabolomics researchers across the world. PMID:26467476

Developing descriptors to predict mechanical properties of nanotubes.

PubMed

Borders, Tammie L; Fonseca, Alexandre F; Zhang, Hengji; Cho, Kyeongjae; Rusinko, Andrew

2013-04-22

Descriptors and quantitative structure property relationships (QSPR) were investigated for mechanical property prediction of carbon nanotubes (CNTs). 78 molecular dynamics (MD) simulations were carried out, and 20 descriptors were calculated to build quantitative structure property relationships (QSPRs) for Young's modulus and Poisson's ratio in two separate analyses: vacancy only and vacancy plus methyl functionalization. In the first analysis, C(N2)/C(T) (number of non-sp2 hybridized carbons per the total carbons) and chiral angle were identified as critical descriptors for both Young's modulus and Poisson's ratio. Further analysis and literature findings indicate the effect of chiral angle is negligible at larger CNT radii for both properties. Raman spectroscopy can be used to measure C(N2)/C(T), providing a direct link between experimental and computational results. Poisson's ratio approaches two different limiting values as CNT radii increases: 0.23-0.25 for chiral and armchair CNTs and 0.10 for zigzag CNTs (surface defects <3%). In the second analysis, the critical descriptors were C(N2)/C(T), chiral angle, and M(N)/C(T) (number of methyl groups per total carbons). These results imply new types of defects can be represented as a new descriptor in QSPR models. Finally, results are qualified and quantified against experimental data.

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.

Link and Network Layers Design for Ultra-High-Speed Terahertz-Band Communications Networks

DTIC Science & Technology

2017-01-01

throughput, and identify the optimal parameter values for their design (Sec. 6.2.3). Moreover, we validate and test the scheme with experimental data obtained...LINK AND NETWORK LAYERS DESIGN FOR ULTRA-HIGH- SPEED TERAHERTZ-BAND COMMUNICATIONS NETWORKS STATE UNIVERSITY OF NEW YORK (SUNY) AT BUFFALO JANUARY...TYPE FINAL TECHNICAL REPORT 3. DATES COVERED (From - To) FEB 2015 – SEP 2016 4. TITLE AND SUBTITLE LINK AND NETWORK LAYERS DESIGN FOR ULTRA-HIGH

The data sharing advantage in astrophysics

NASA Astrophysics Data System (ADS)

Dorch, Bertil F.; Drachen, Thea M.; Ellegaard, Ole

2016-10-01

We present here evidence for the existence of a citation advantage within astrophysics for papers that link to data. Using simple measures based on publication data from NASA Astrophysics Data System we find a citation advantage for papers with links to data receiving on the average significantly more citations per paper than papers without links to data. Furthermore, using INSPEC and Web of Science databases we investigate whether either papers of an experimental or theoretical nature display different citation behavior.

Detection of serum antibodies against Ehrlichia risticii in Potomac horse fever by enzyme-linked immunosorbent assay.

PubMed

Dutta, S K; Rice, R M; Hughes, T D; Savage, P K; Myrup, A C

1987-01-01

An indirect enzyme-linked immunosorbent assay (ELISA) was developed which was specific and sensitive in detecting antibodies to Ehrlichia risticii in Potomac horse fever (PHF). The ELISA antibody titers were correlated with the indirect fluorescent antibody (IFA) titers. E. risticii propagated in human histiocyte culture was purified on renografin gradient and the band of the organisms at a density of 1.182 g/ml was used as antigen. ELISA antibody titers were determined through computer assisted analysis, the observed antibody titers were derived by serial serum dilutions and using a resultant standard curve the predicted antibody titers were obtained from a single serum dilution. The standard curve had a correlation coefficient of 0.8975. The observed and predicted antibody titers were in good agreement, as the respective titers fell within a two-fold range. There was a good correlation between ELISA and IFA test results, but the ELISA titers were several times higher. In experimental infections of horses produced with the infected equine whole blood and the Ehrlichia infected macrophage culture, the antibodies were first detected in two weeks and one week postinoculation (PI), respectively. In both cases the titers reached a peak in about 4 weeks PI with a mean titer of 1:16558 and 1:4030, respectively. The antibody titers of the convalescent sera of field cases of PHF were comparatively lower than the experimentally infected horses.

Study of strong turbulence effects for optical wireless links

NASA Astrophysics Data System (ADS)

Yuksel, Heba; Meric, Hasim; Kunter, Fulya

2012-10-01

Strong turbulence measurements that are taken using real time optical wireless experimental setups are valuable when studying the effects of turbulence regimes on a propagating optical beam. In any kind of FSO system, for us to know the strength of the turbulence thus the refractive index structure constant, is beneficial for having an optimum bandwidth of communication. Even if the FSO Link is placed very well-high-above the ground just to have weak enough turbulence effects, there can be severe atmospheric conditions that can change the turbulence regime. Having a successful theory that will cover all regimes will give us the chance of directly processing the image in existing or using an additional hardware thus deciding on the optimum bandwidth of the communication line at firsthand. For this purpose, Strong Turbulence data has been collected using an outdoor optical wireless setup placed about 85 centimeters above the ground with an acceptable declination and a path length of about 250 meters inducing strong turbulence to the propagating beam. Variations of turbulence strength estimation methods as well as frame image analysis techniques are then been applied to the experimental data in order to study the effects of different parameters on the result. Such strong turbulence data is compared with existing weak and intermediate turbulence data. Aperture Averaging Factor for different turbulence regimes is also investigated.

Self-replenishing ability of cross-linked low surface energy polymer films investigated by a complementary experimental-simulation approach

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

Esteves, A. C. C., E-mail: a.c.c.esteves@tue.nl, E-mail: g.dewith@tue.nl; Lyakhova, K.; Riel, J. M. van

2014-03-28

Nowadays, many self-healing strategies are available for recovering mechanical damage of bulk polymeric materials. The recovery of surface-dependent functionalities on polymer films is, however, equally important and has been less investigated. In this work we study the ability of low surface energy cross-linked poly(ester urethane) networks containing perfluorinated dangling chains to self-replenish their surface, after being submitted to repeated surface damage. For this purpose we used a combined experimental-simulation approach. Experimentally, the cross-linked films were intentionally damaged by cryo-microtoming to remove top layers and create new surfaces which were characterized by water Contact Angle measurements and X-Ray Photoelectron Spectroscopy. Themore » same systems were simultaneously represented by a Dissipative Particles Dynamics simulation method, where the damage was modeled by removing the top film layers in the simulation box and replacing it by new “air” beads. The influence of different experimental parameters, such as the concentration of the low surface energy component and the molecular mobility span of the dangling chains, on the surface recovery is discussed. The combined approach reveals important details of the self-replenishing ability of damaged polymer films such as the occurrence of multiple-healing events, the self-replenishing efficiency, and the minimum “healing agent” concentration for a maximum recovery.« less

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

The Role of Margin in Link Design and Optimization

NASA Technical Reports Server (NTRS)

Cheung, K.

2015-01-01

Link analysis is a system engineering process in the design, development, and operation of communication systems and networks. Link models that are mathematical abstractions representing the useful signal power and the undesirable noise and attenuation effects (including weather effects if the signal path transverses through the atmosphere) that are integrated into the link budget calculation that provides the estimates of signal power and noise power at the receiver. Then the link margin is applied which attempts to counteract the fluctuations of the signal and noise power to ensure reliable data delivery from transmitter to receiver. (Link margin is dictated by the link margin policy or requirements.) A simple link budgeting approach assumes link parameters to be deterministic values typically adopted a rule-of-thumb policy of 3 dB link margin. This policy works for most S- and X-band links due to their insensitivity to weather effects. But for higher frequency links like Ka-band, Ku-band, and optical communication links, it is unclear if a 3 dB link margin would guarantee link closure. Statistical link analysis that adopted the 2-sigma or 3-sigma link margin incorporates link uncertainties in the sigma calculation. (The Deep Space Network (DSN) link margin policies are 2-sigma for downlink and 3-sigma for uplink.) The link reliability can therefore be quantified statistically even for higher frequency links. However in the current statistical link analysis approach, link reliability is only expressed as the likelihood of exceeding the signal-to-noise ratio (SNR) threshold that corresponds to a given bit-error-rate (BER) or frame-error-rate (FER) requirement. The method does not provide the true BER or FER estimate of the link with margin, or the required signalto-noise ratio (SNR) that would meet the BER or FER requirement in the statistical sense. In this paper, we perform in-depth analysis on the relationship between BER/FER requirement, operating SNR, and coding performance curve, in the case when the channel coherence time of link fluctuation is comparable or larger than the time duration of a codeword. We compute the "true" SNR design point that would meet the BER/FER requirement by taking into account the fluctuation of signal power and noise power at the receiver, and the shape of the coding performance curve. This analysis yields a number of valuable insights on the design choices of coding scheme and link margin for the reliable data delivery of a communication system - space and ground. We illustrate the aforementioned analysis using a number of standard NASA error-correcting codes.

SignaLink 2 – a signaling pathway resource with multi-layered regulatory networks

PubMed Central

2013-01-01

Background Signaling networks in eukaryotes are made up of upstream and downstream subnetworks. The upstream subnetwork contains the intertwined network of signaling pathways, while the downstream regulatory part contains transcription factors and their binding sites on the DNA as well as microRNAs and their mRNA targets. Currently, most signaling and regulatory databases contain only a subsection of this network, making comprehensive analyses highly time-consuming and dependent on specific data handling expertise. The need for detailed mapping of signaling systems is also supported by the fact that several drug development failures were caused by undiscovered cross-talk or regulatory effects of drug targets. We previously created a uniformly curated signaling pathway resource, SignaLink, to facilitate the analysis of pathway cross-talks. Here, we present SignaLink 2, which significantly extends the coverage and applications of its predecessor. Description We developed a novel concept to integrate and utilize different subsections (i.e., layers) of the signaling network. The multi-layered (onion-like) database structure is made up of signaling pathways, their pathway regulators (e.g., scaffold and endocytotic proteins) and modifier enzymes (e.g., phosphatases, ubiquitin ligases), as well as transcriptional and post-transcriptional regulators of all of these components. The user-friendly website allows the interactive exploration of how each signaling protein is regulated. The customizable download page enables the analysis of any user-specified part of the signaling network. Compared to other signaling resources, distinctive features of SignaLink 2 are the following: 1) it involves experimental data not only from humans but from two invertebrate model organisms, C. elegans and D. melanogaster; 2) combines manual curation with large-scale datasets; 3) provides confidence scores for each interaction; 4) operates a customizable download page with multiple file formats (e.g., BioPAX, Cytoscape, SBML). Non-profit users can access SignaLink 2 free of charge at http://SignaLink.org. Conclusions With SignaLink 2 as a single resource, users can effectively analyze signaling pathways, scaffold proteins, modifier enzymes, transcription factors and miRNAs that are important in the regulation of signaling processes. This integrated resource allows the systems-level examination of how cross-talks and signaling flow are regulated, as well as provide data for cross-species comparisons and drug discovery analyses. PMID:23331499

SignaLink 2 - a signaling pathway resource with multi-layered regulatory networks.

PubMed

Fazekas, Dávid; Koltai, Mihály; Türei, Dénes; Módos, Dezső; Pálfy, Máté; Dúl, Zoltán; Zsákai, Lilian; Szalay-Bekő, Máté; Lenti, Katalin; Farkas, Illés J; Vellai, Tibor; Csermely, Péter; Korcsmáros, Tamás

2013-01-18

Signaling networks in eukaryotes are made up of upstream and downstream subnetworks. The upstream subnetwork contains the intertwined network of signaling pathways, while the downstream regulatory part contains transcription factors and their binding sites on the DNA as well as microRNAs and their mRNA targets. Currently, most signaling and regulatory databases contain only a subsection of this network, making comprehensive analyses highly time-consuming and dependent on specific data handling expertise. The need for detailed mapping of signaling systems is also supported by the fact that several drug development failures were caused by undiscovered cross-talk or regulatory effects of drug targets. We previously created a uniformly curated signaling pathway resource, SignaLink, to facilitate the analysis of pathway cross-talks. Here, we present SignaLink 2, which significantly extends the coverage and applications of its predecessor. We developed a novel concept to integrate and utilize different subsections (i.e., layers) of the signaling network. The multi-layered (onion-like) database structure is made up of signaling pathways, their pathway regulators (e.g., scaffold and endocytotic proteins) and modifier enzymes (e.g., phosphatases, ubiquitin ligases), as well as transcriptional and post-transcriptional regulators of all of these components. The user-friendly website allows the interactive exploration of how each signaling protein is regulated. The customizable download page enables the analysis of any user-specified part of the signaling network. Compared to other signaling resources, distinctive features of SignaLink 2 are the following: 1) it involves experimental data not only from humans but from two invertebrate model organisms, C. elegans and D. melanogaster; 2) combines manual curation with large-scale datasets; 3) provides confidence scores for each interaction; 4) operates a customizable download page with multiple file formats (e.g., BioPAX, Cytoscape, SBML). Non-profit users can access SignaLink 2 free of charge at http://SignaLink.org. With SignaLink 2 as a single resource, users can effectively analyze signaling pathways, scaffold proteins, modifier enzymes, transcription factors and miRNAs that are important in the regulation of signaling processes. This integrated resource allows the systems-level examination of how cross-talks and signaling flow are regulated, as well as provide data for cross-species comparisons and drug discovery analyses.

Racial discrimination and cortisol output: A meta-analysis.

PubMed

Korous, Kevin M; Causadias, José M; Casper, Deborah M

2017-11-01

Although the relation between stress and physiology is well documented, attempts at understanding the link between racial discrimination and cortisol output, specifically, have produced mixed results, likely due to study characteristics such as racial/ethnic composition of the samples (e.g., African American, Latino), measures of discrimination, and research design (e.g., cross-sectional, experimental). To estimate the overall association between racial discrimination and cortisol output among racial/ethnic minority individuals and to determine if the association between racial discrimination and cortisol output is moderated by age, race/ethnicity, type of discrimination measure, sex, and research design. Using a random effects model, the overall effect size based on k = 16 studies (19% unpublished) and N = 1506 participants was r¯ = 0.040, 95% CI = -0.038 to 0.117. Studies were conducted predominantly in the U.S. (81%). Notably, experimental studies (r¯ = 0.267) exhibited larger effect sizes compared to non-experimental studies (r¯ = -0.007). Age, race/ethnicity, type of discrimination measure, and sex did not moderate the effect sizes. This meta-analysis provides evidence that the measurement of the association between racial discrimination and cortisol is complex, and it offers valuable insight regarding methods and designs that can inform future research on this topic. Limitations and future directions are discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Nonlinear analysis of pupillary dynamics.

PubMed

Onorati, Francesco; Mainardi, Luca Tommaso; Sirca, Fabiola; Russo, Vincenzo; Barbieri, Riccardo

2016-02-01

Pupil size reflects autonomic response to different environmental and behavioral stimuli, and its dynamics have been linked to other autonomic correlates such as cardiac and respiratory rhythms. The aim of this study is to assess the nonlinear characteristics of pupil size of 25 normal subjects who participated in a psychophysiological experimental protocol with four experimental conditions, namely “baseline”, “anger”, “joy”, and “sadness”. Nonlinear measures, such as sample entropy, correlation dimension, and largest Lyapunov exponent, were computed on reconstructed signals of spontaneous fluctuations of pupil dilation. Nonparametric statistical tests were performed on surrogate data to verify that the nonlinear measures are an intrinsic characteristic of the signals. We then developed and applied a piecewise linear regression model to detrended fluctuation analysis (DFA). Two joinpoints and three scaling intervals were identified: slope α0, at slow time scales, represents a persistent nonstationary long-range correlation, whereas α1 and α2, at middle and fast time scales, respectively, represent long-range power-law correlations, similarly to DFA applied to heart rate variability signals. Of the computed complexity measures, α0 showed statistically significant differences among experimental conditions (p<0.001). Our results suggest that (a) pupil size at constant light condition is characterized by nonlinear dynamics, (b) three well-defined and distinct long-memory processes exist at different time scales, and (c) autonomic stimulation is partially reflected in nonlinear dynamics. (c) autonomic stimulation is partially reflected in nonlinear dynamics.

Revealing Structural Details of SiCO Ceramics with GIPAW Calculations of Model Structures and Analysis of Experimental 29Si Nuclear Magnetic Resonance Spectroscopy

NASA Astrophysics Data System (ADS)

Nimmo, John; Kroll, Peter

2015-03-01

The occurrence of the various SiCxO4-x (1 <=x <=4) mixed tetrahedra in silicon oxycarbide (SiCO) is often quantified by means of experimental 29Si nuclear magnetic resonance. The structural centers are assigned to individual peaks in the spectrum, which can be integrated to give the relative populations. Using a recently-developed method, we show that is is also possible to recover information on the connectivity of these tetrahedra. By combining a huge library of model structures an GIPAW calculations, we show that simple relations exist between the Si-O-Si linking angles and the 29Si NMR chemical shift. In this work, we perform detailed analyses of SiCO 29Si NMR spectra available in literature. We extract angular distributions in agreement with the experimental X-ray and neutron diffraction data. Furthermore, in glasses with large amounts of so-called ``free'' carbon, we observe a significant portion of the {Si}O4 tetrahedra which have disproportionately large angles. These angles indicate the presence of internal SiO2 surfaces or cages-like voids, similar to those found in zeolites or clathrates. This analysis suggests that in SiCO, the ``free'' carbon is incorporated into these voids, which produces strain on the bonding angles of the surrounding host glass.

Children's Sleep Regulation Is Linked to Mothers' Sleep-Related Childhood Experiences

ERIC Educational Resources Information Center

Aviezer, Ora; Scher, Anat

2013-01-01

The present research explored how mothers' own childhood experiences are linked to their perceptions of their children's sleep regulation. It focused on collective sleeping; a practice used in the past in the Israeli kibbutz, and used a quasi-experimental research design to examine whether mothers who were raised in collective sleeping…

DTN routing in body sensor networks with dynamic postural partitioning.

PubMed

Quwaider, Muhannad; Biswas, Subir

2010-11-01

This paper presents novel store-and-forward packet routing algorithms for Wireless Body Area Networks ( WBAN ) with frequent postural partitioning. A prototype WBAN has been constructed for experimentally characterizing on-body topology disconnections in the presence of ultra short range radio links, unpredictable RF attenuation, and human postural mobility. On-body DTN routing protocols are then developed using a stochastic link cost formulation, capturing multi-scale topological localities in human postural movements. Performance of the proposed protocols are evaluated experimentally and via simulation, and are compared with a number of existing single-copy DTN routing protocols and an on-body packet flooding mechanism that serves as a performance benchmark with delay lower-bound. It is shown that via multi-scale modeling of the spatio-temporal locality of on-body link disconnection patterns, the proposed algorithms can provide better routing performance compared to a number of existing probabilistic, opportunistic, and utility-based DTN routing protocols in the literature.

Structure Determination of Cisplatin-Amino Acid Analogues by Infrared Multiple Photon Dissociation Action Spectroscopy

NASA Astrophysics Data System (ADS)

He, Chenchen; Bao, Xun; Zhu, Yanlong; Strobehn, Stephen; Kimutai, Bett; Nei, Y.-W.; Chow, C. S.; Rodgers, M. T.; Gao, Juehan; Oomens, J.

2015-06-01

To gain a better understanding of the binding mechanism and assist in the optimization of relevant drug and chemical probe design, both experimental and theoretical studies were performed on a series of amino acid-linked cisplatin derivatives, including glycine-, lysine-, and ornithine-linked cisplatin, Gplatin, Kplatin, and Oplatin, respectively. Cisplatin, the first FDA-approved platinum-based anticancer drug, has been widely used in cancer chemotherapy. Its pharmacological mechanism has been identified as its ability to coordinate to genomic DNA, and guanine is its major target. In previous reports, cisplatin was successfully utilized as a chemical probe to detect solvent accessible sites in ribosomal RNA (rRNA). Among the amino-acid-linked cisplatin derivatives, Oplatin exhibits preference for adenine over guanine. The mechanism behind its different selectivity compared to cisplatin may relate to its potential of forming a hydrogen bond between the carboxylate group in Pt (II) complex and the 6-amino moiety of adenosine stabilizes A-Oplatin products. Tandem mass spectrometry analysis also indicates that different coordination sites of Oplatin on adenosine affect glycosidic bond stability. Infrared multiple photon dissociation (IRMPD) action spectroscopy experiments were performed on all three amino acid-linked cisplatin to characterize their structures. An extensive theoretical study has been performed on Gplatin to guide the selection of the most effective theory and basis set based on its geometric information. The results for Gplatin provide the foundation for characterization of the more complex amino acid-linked cisplatin derivatives, Oplatin and Kplatin. Structural and energetic information elucidated for these compounds, particularly Oplatin reveal the reason for its alternative selectivity compared to cisplatin.

SAR11 bacteria linked to ocean anoxia and nitrogen loss

NASA Astrophysics Data System (ADS)

Tsementzi, Despina; Wu, Jieying; Deutsch, Samuel; Nath, Sangeeta; Rodriguez-R, Luis M.; Burns, Andrew S.; Ranjan, Piyush; Sarode, Neha; Malmstrom, Rex R.; Padilla, Cory C.; Stone, Benjamin K.; Bristow, Laura A.; Larsen, Morten; Glass, Jennifer B.; Thamdrup, Bo; Woyke, Tanja; Konstantinidis, Konstantinos T.; Stewart, Frank J.

2016-08-01

Bacteria of the SAR11 clade constitute up to one half of all microbial cells in the oxygen-rich surface ocean. SAR11 bacteria are also abundant in oxygen minimum zones (OMZs), where oxygen falls below detection and anaerobic microbes have vital roles in converting bioavailable nitrogen to N2 gas. Anaerobic metabolism has not yet been observed in SAR11, and it remains unknown how these bacteria contribute to OMZ biogeochemical cycling. Here, genomic analysis of single cells from the world’s largest OMZ revealed previously uncharacterized SAR11 lineages with adaptations for life without oxygen, including genes for respiratory nitrate reductases (Nar). SAR11 nar genes were experimentally verified to encode proteins catalysing the nitrite-producing first step of denitrification and constituted ~40% of OMZ nar transcripts, with transcription peaking in the anoxic zone of maximum nitrate reduction activity. These results link SAR11 to pathways of ocean nitrogen loss, redefining the ecological niche of Earth’s most abundant organismal group.

SAR11 bacteria linked to ocean anoxia and nitrogen loss.

PubMed

Tsementzi, Despina; Wu, Jieying; Deutsch, Samuel; Nath, Sangeeta; Rodriguez-R, Luis M; Burns, Andrew S; Ranjan, Piyush; Sarode, Neha; Malmstrom, Rex R; Padilla, Cory C; Stone, Benjamin K; Bristow, Laura A; Larsen, Morten; Glass, Jennifer B; Thamdrup, Bo; Woyke, Tanja; Konstantinidis, Konstantinos T; Stewart, Frank J

2016-08-11

Bacteria of the SAR11 clade constitute up to one half of all microbial cells in the oxygen-rich surface ocean. SAR11 bacteria are also abundant in oxygen minimum zones (OMZs), where oxygen falls below detection and anaerobic microbes have vital roles in converting bioavailable nitrogen to N2 gas. Anaerobic metabolism has not yet been observed in SAR11, and it remains unknown how these bacteria contribute to OMZ biogeochemical cycling. Here, genomic analysis of single cells from the world's largest OMZ revealed previously uncharacterized SAR11 lineages with adaptations for life without oxygen, including genes for respiratory nitrate reductases (Nar). SAR11 nar genes were experimentally verified to encode proteins catalysing the nitrite-producing first step of denitrification and constituted ~40% of OMZ nar transcripts, with transcription peaking in the anoxic zone of maximum nitrate reduction activity. These results link SAR11 to pathways of ocean nitrogen loss, redefining the ecological niche of Earth's most abundant organismal group.

A time to search: finding the meaning of variable activation energy.

PubMed

Vyazovkin, Sergey

2016-07-28

This review deals with the phenomenon of variable activation energy frequently observed when studying the kinetics in the liquid or solid phase. This phenomenon commonly manifests itself through nonlinear Arrhenius plots or dependencies of the activation energy on conversion computed by isoconversional methods. Variable activation energy signifies a multi-step process and has a meaning of a collective parameter linked to the activation energies of individual steps. It is demonstrated that by using appropriate models of the processes, the link can be established in algebraic form. This allows one to analyze experimentally observed dependencies of the activation energy in a quantitative fashion and, as a result, to obtain activation energies of individual steps, to evaluate and predict other important parameters of the process, and generally to gain deeper kinetic and mechanistic insights. This review provides multiple examples of such analysis as applied to the processes of crosslinking polymerization, crystallization and melting of polymers, gelation, and solid-solid morphological and glass transitions. The use of appropriate computational techniques is discussed as well.

SAR11 bacteria linked to ocean anoxia and nitrogen loss

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

Tsementzi, Despina; Wu, Jieying; Deutsch, Samuel

Bacteria of the SAR11 clade constitute up to one half of all microbial cells in the oxygen-rich surface ocean. SAR11 bacteria are also abundant in oxygen minimum zones (OMZs), where oxygen falls below detection and anaerobic microbes have vital roles in converting bioavailable nitrogen to N 2 gas. Anaerobic metabolism has not yet been observed in SAR11, and it remains unknown how these bacteria contribute to OMZ biogeochemical cycling. Here in this paper, genomic analysis of single cells from the world's largest OMZ revealed previously uncharacterized SAR11 lineages with adaptations for life without oxygen, including genes for respiratory nitrate reductasesmore » (Nar). SAR11 nar genes were experimentally verified to encode proteins catalysing the nitrite-producing first step of denitrification and constituted ~40% of OMZ nar transcripts, with transcription peaking in the anoxic zone of maximum nitrate reduction activity. Finally, these results link SAR11 to pathways of ocean nitrogen loss, redefining the ecological niche of Earth's most abundant organismal group.« less

A Cohesive Zone Approach for Fatigue-Driven Delamination Analysis in Composite Materials

NASA Astrophysics Data System (ADS)

Amiri-Rad, Ahmad; Mashayekhi, Mohammad

2017-08-01

A new model for prediction of fatigue-driven delamination in laminated composites is proposed using cohesive interface elements. The presented model provides a link between cohesive elements damage evolution rate and crack growth rate of Paris law. This is beneficial since no additional material parameters are required and the well-known Paris law constants are used. The link between the cohesive zone method and fracture mechanics is achieved without use of effective length which has led to more accurate results. The problem of unknown failure path in calculation of the energy release rate is solved by imposing a condition on the damage model which leads to completely vertical failure path. A global measure of energy release rate is used for the whole cohesive zone which is computationally more efficient compared to previous similar models. The performance of the proposed model is investigated by simulation of well-known delamination tests and comparison against experimental data of the literature.

SAR11 bacteria linked to ocean anoxia and nitrogen loss

DOE PAGES

Tsementzi, Despina; Wu, Jieying; Deutsch, Samuel; ...

2016-08-03

Bacteria of the SAR11 clade constitute up to one half of all microbial cells in the oxygen-rich surface ocean. SAR11 bacteria are also abundant in oxygen minimum zones (OMZs), where oxygen falls below detection and anaerobic microbes have vital roles in converting bioavailable nitrogen to N 2 gas. Anaerobic metabolism has not yet been observed in SAR11, and it remains unknown how these bacteria contribute to OMZ biogeochemical cycling. Here in this paper, genomic analysis of single cells from the world's largest OMZ revealed previously uncharacterized SAR11 lineages with adaptations for life without oxygen, including genes for respiratory nitrate reductasesmore » (Nar). SAR11 nar genes were experimentally verified to encode proteins catalysing the nitrite-producing first step of denitrification and constituted ~40% of OMZ nar transcripts, with transcription peaking in the anoxic zone of maximum nitrate reduction activity. Finally, these results link SAR11 to pathways of ocean nitrogen loss, redefining the ecological niche of Earth's most abundant organismal group.« less

Historical Links between Latin American Psychology and Pedagogy in Experimentation

ERIC Educational Resources Information Center

Arias, Walter L.

2014-01-01

This work sets out historical information about the development of Latin American psychology over the base of education. It reviews the contribution from education to Latin American psychology, and especially, the creation of experimental psychology laboratories in schools and educational and psychopedagogical institutions, where experimental…

Performance of adaptive DD-OFDM multicore fiber links and its relation with intercore crosstalk.

PubMed

Alves, Tiago M F; Luís, Ruben S; Puttnam, Benjamin J; Cartaxo, Adolfo V T; Awaji, Yoshinari; Wada, Naoya

2017-07-10

Adaptive direct-detection (DD) orthogonal frequency-division multiplexing (OFDM) is proposed to guarantee signal quality over time in weakly-coupled homogenous multicore fiber (MCFs) links impaired by stochastic intercore crosstalk (ICXT). For the first time, the received electrical power of the ICXT and the performance of the adaptive DD-OFDM MCF link are experimentally monitored quasi-simultaneously over a 210 hour period. Experimental results show that the time evolution of the error vector magnitude due to the ICXT can be suitably estimated from the normalized power of the detected crosstalk. The detected crosstalk results from the beating between the carrier in the test core and ICXT originating from the carrier and modulated signal from interfering core. The results show that the operation of DD-OFDM systems employing fixed modulation can be severely impaired by the presence of ICXT that may unpredictable vary in both power and frequency. The system may suffer from deleterious impact of moderate ICXT levels over a time duration of several hours or from peak ICXT levels occurring over a number of minutes. Such power fluctuations can lead to large variations in bit error ratio (BER) for static modulation schemes. Here, we show that BER fluctuations may be minimized by the use of adaptive modulation techniques and that in particular, the adaptive OFDM is a viable solution to guarantee link quality in MCF-based systems. An experimental model of an adaptive DD-OFDM MCF link shows an average throughput of 12 Gb/s that represents a reduction of only 9% compared to the maximum throughput measured without ICXT and an improvement of 23% relative to throughput obtained with static modulation.

Different types of interactions of links in artificial and natural ecosystems under anthropogenic pressure

NASA Astrophysics Data System (ADS)

Somova, Lydia; Pisman, Tamara; Mikheeva, Galina; Pechurkin, Nickolay

The life of organisms in an ecosystem depends not only on abiotic factors, but also on the interaction of organisms in which they come with each other. The study of mechanisms of the bioregulation based on ecological - biochemical interactions of ecosystem links is necessary to know the ecosystem development, its stability, survival of ecosystem organisms. It is of high importance as for the creation of artificial ecosystems, and also for the study of natural ecosystems under anthropogenic pressure on them. To create well-functioning ecosystems is necessary to study and consider the basic types of relationships between organisms. The basic types of interactions between organisms have been studied with simple terrestrial and water ecosystems. 1. The interaction of microbiocenoses and plants were studied in experiments with agrocenoses. Microbiocenosis proposed for increase of productivity of plants and for obtaining ecologically pure production of plants has been created taking into account mutual relationships between species of microorganisms. 2. The experimental model of the atmosphere closed «autotroph - heterotroph» system in which heterotrophic link was the mixed population of yeasts (Candida utilis and Candida guilliermondii) was studied. The algae Chlorella vulgaris was used as an autotroph link. It was shown, that the competition result for heterotrophic link depended on strategy of populations of yeast in relation to a substrate and oxygen utilization. 3. As a result of experimental and theoretical modelling of a competition of algae Chlorella vulgaris and Scenedesmus quadricauda at continuous cultivation, the impossibility of their coexistence in the conditions of limitation on nitrogen was shown. 4. Pray-predator interactions between algae (Chlorella vulgaris, Scenedesmus quadricauda) and invertebrates (Paramecium caudatum, Brachionus plicatilis) were studied in experimental closed ecosystem. This work was partly supported by the Russian Foundation for Basic Research, project No.13-06-00060

Lexical Link Analysis (LLA) Application: Improving Web Service to Defense Acquisition Visibility Environment (DAVE)

DTIC Science & Technology

2015-05-01

1 LEXICAL LINK ANALYSIS (LLA) APPLICATION: IMPROVING WEB SERVICE TO DEFENSE ACQUISITION VISIBILITY ENVIRONMENT(DAVE) May 13-14, 2015 Dr. Ying...REPORT DATE MAY 2015 2. REPORT TYPE 3. DATES COVERED 00-00-2015 to 00-00-2015 4. TITLE AND SUBTITLE Lexical Link Analysis (LLA) Application...Making 3 2 1 3 L L A Methods • Lexical Link Analysis (LLA) Core – LLA Reports and Visualizations • Collaborative Learning Agents (CLA) for

GPS-MBA: Computational Analysis of MHC Class II Epitopes in Type 1 Diabetes

PubMed Central

Ren, Jian; Ma, Chuang; Gao, Tianshun; Zhou, Yanhong; Yang, Qing; Xue, Yu

2012-01-01

As a severe chronic metabolic disease and autoimmune disorder, type 1 diabetes (T1D) affects millions of people world-wide. Recent advances in antigen-based immunotherapy have provided a great opportunity for further treating T1D with a high degree of selectivity. It is reported that MHC class II I-Ag7 in the non-obese diabetic (NOD) mouse and human HLA-DQ8 are strongly linked to susceptibility to T1D. Thus, the identification of new I-Ag7 and HLA-DQ8 epitopes would be of great help to further experimental and biomedical manipulation efforts. In this study, a novel GPS-MBA (MHC Binding Analyzer) software package was developed for the prediction of I-Ag7 and HLA-DQ8 epitopes. Using experimentally identified epitopes as the training data sets, a previously developed GPS (Group-based Prediction System) algorithm was adopted and improved. By extensive evaluation and comparison, the GPS-MBA performance was found to be much better than other tools of this type. With this powerful tool, we predicted a number of potentially new I-Ag7 and HLA-DQ8 epitopes. Furthermore, we designed a T1D epitope database (TEDB) for all of the experimentally identified and predicted T1D-associated epitopes. Taken together, this computational prediction result and analysis provides a starting point for further experimental considerations, and GPS-MBA is demonstrated to be a useful tool for generating starting information for experimentalists. The GPS-MBA is freely accessible for academic researchers at: http://mba.biocuckoo.org. PMID:22479466

GeneMesh: a web-based microarray analysis tool for relating differentially expressed genes to MeSH terms.

PubMed

Jani, Saurin D; Argraves, Gary L; Barth, Jeremy L; Argraves, W Scott

2010-04-01

An important objective of DNA microarray-based gene expression experimentation is determining inter-relationships that exist between differentially expressed genes and biological processes, molecular functions, cellular components, signaling pathways, physiologic processes and diseases. Here we describe GeneMesh, a web-based program that facilitates analysis of DNA microarray gene expression data. GeneMesh relates genes in a query set to categories available in the Medical Subject Headings (MeSH) hierarchical index. The interface enables hypothesis driven relational analysis to a specific MeSH subcategory (e.g., Cardiovascular System, Genetic Processes, Immune System Diseases etc.) or unbiased relational analysis to broader MeSH categories (e.g., Anatomy, Biological Sciences, Disease etc.). Genes found associated with a given MeSH category are dynamically linked to facilitate tabular and graphical depiction of Entrez Gene information, Gene Ontology information, KEGG metabolic pathway diagrams and intermolecular interaction information. Expression intensity values of groups of genes that cluster in relation to a given MeSH category, gene ontology or pathway can be displayed as heat maps of Z score-normalized values. GeneMesh operates on gene expression data derived from a number of commercial microarray platforms including Affymetrix, Agilent and Illumina. GeneMesh is a versatile web-based tool for testing and developing new hypotheses through relating genes in a query set (e.g., differentially expressed genes from a DNA microarray experiment) to descriptors making up the hierarchical structure of the National Library of Medicine controlled vocabulary thesaurus, MeSH. The system further enhances the discovery process by providing links between sets of genes associated with a given MeSH category to a rich set of html linked tabular and graphic information including Entrez Gene summaries, gene ontologies, intermolecular interactions, overlays of genes onto KEGG pathway diagrams and heatmaps of expression intensity values. GeneMesh is freely available online at http://proteogenomics.musc.edu/genemesh/.

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)].

Link prediction with node clustering coefficient

NASA Astrophysics Data System (ADS)

Wu, Zhihao; Lin, Youfang; Wang, Jing; Gregory, Steve

2016-06-01

Predicting missing links in incomplete complex networks efficiently and accurately is still a challenging problem. The recently proposed Cannistrai-Alanis-Ravai (CAR) index shows the power of local link/triangle information in improving link-prediction accuracy. Inspired by the idea of employing local link/triangle information, we propose a new similarity index with more local structure information. In our method, local link/triangle structure information can be conveyed by clustering coefficient of common-neighbors directly. The reason why clustering coefficient has good effectiveness in estimating the contribution of a common-neighbor is that it employs links existing between neighbors of a common-neighbor and these links have the same structural position with the candidate link to this common-neighbor. In our experiments, three estimators: precision, AUP and AUC are used to evaluate the accuracy of link prediction algorithms. Experimental results on ten tested networks drawn from various fields show that our new index is more effective in predicting missing links than CAR index, especially for networks with low correlation between number of common-neighbors and number of links between common-neighbors.

An experimental study on digital predistortion for radio-over-fiber links

NASA Astrophysics Data System (ADS)

Vieira, Luis C.; Gomes, Nathan J.; Nkansah, Anthony

2010-12-01

Radio-over-fiber (RoF) has been proposed as an enabling technology for broadband networks, such as WiMAX and WiFi. Besides the inherent high bandwidth and reliability of RoF systems, they also allow the reduction of installation and maintenance cost of the remote antenna units (RAUs) and improvement in the coverage area of the base station/access point. However, the nonlinear distortion of the optical link, which stems mainly from the laser diode, may impose serious limitations on the system performance, especially when high PAPR, wideband signals are used. Thus, distortion compensation is a key issue in order to facilitate the application of the RoF technology for broadband networks. In this work, digital predistortion for directly modulated RoF links is experimentally investigated. A memory-polynomial- based predistorter model is identified from measurements of the baseband OFDM input-output signals and through the use of an indirect learning architecture. Then, a predistorted signal is generated and fed to the RoF link for comparing its output with that of the non-predistorted one. As a result of this compensation technique, an improvement of the static link linearity and the output constellation diagram has been found, with an EVM reduction of 1.73 %.

Frequency-tuning input-shaped manifold-based switching control for underactuated space robot equipped with flexible appendages

NASA Astrophysics Data System (ADS)

Kojima, Hirohisa; Ieda, Shoko; Kasai, Shinya

2014-08-01

Underactuated control problems, such as the control of a space robot without actuators on the main body, have been widely investigated. However, few studies have examined attitude control problems of underactuated space robots equipped with a flexible appendage, such as solar panels. In order to suppress vibration in flexible appendages, a zero-vibration input-shaping technique was applied to the link motion of an underactuated planar space robot. However, because the vibrational frequency depends on the link angles, simple input-shaping control methods cannot sufficiently suppress the vibration. In this paper, the dependency of the vibrational frequency on the link angles is measured experimentally, and the time-delay interval of the input shaper is then tuned based on the frequency estimated from the link angles. The proposed control method is referred to as frequency-tuning input-shaped manifold-based switching control (frequency-tuning IS-MBSC). The experimental results reveal that frequency-tuning IS-MBSC is capable of controlling the link angles and the main body attitude to maintain the target angles and that the vibration suppression performance of the proposed frequency-tuning IS-MBSC is better than that of a non-tuning IS-MBSC, which does not take the frequency variation into consideration.

Fractional viscoelasticity in fractal and non-fractal media: Theory, experimental validation, and uncertainty analysis

NASA Astrophysics Data System (ADS)

Mashayekhi, Somayeh; Miles, Paul; Hussaini, M. Yousuff; Oates, William S.

2018-02-01

In this paper, fractional and non-fractional viscoelastic models for elastomeric materials are derived and analyzed in comparison to experimental results. The viscoelastic models are derived by expanding thermodynamic balance equations for both fractal and non-fractal media. The order of the fractional time derivative is shown to strongly affect the accuracy of the viscoelastic constitutive predictions. Model validation uses experimental data describing viscoelasticity of the dielectric elastomer Very High Bond (VHB) 4910. Since these materials are known for their broad applications in smart structures, it is important to characterize and accurately predict their behavior across a large range of time scales. Whereas integer order viscoelastic models can yield reasonable agreement with data, the model parameters often lack robustness in prediction at different deformation rates. Alternatively, fractional order models of viscoelasticity provide an alternative framework to more accurately quantify complex rate-dependent behavior. Prior research that has considered fractional order viscoelasticity lacks experimental validation and contains limited links between viscoelastic theory and fractional order derivatives. To address these issues, we use fractional order operators to experimentally validate fractional and non-fractional viscoelastic models in elastomeric solids using Bayesian uncertainty quantification. The fractional order model is found to be advantageous as predictions are significantly more accurate than integer order viscoelastic models for deformation rates spanning four orders of magnitude.

A flight investigation of simulated data-link communications during single-pilot IFR flight. Volume 1: Experimental design and initial test

NASA Technical Reports Server (NTRS)

Parker, J. F., Jr.; Duffy, J. W.; Christensen, D. G.

1981-01-01

A Flight Data Console simulation of a digital communication link to replace the current voice communication system used in air traffic control (ATC) was developed. The study determined how a digital communications system reduces cockpit workload, improve, flight proficiency, and is acceptable to general aviation pilots. It is shown that instrument flight, including approach and landing, can be accomplished by using a digital data link system for ATC communication.

Land mobile satellite propagation results

NASA Technical Reports Server (NTRS)

Nicholas, David C.

1988-01-01

During the Fall of 1987 a land mobile satellite demonstration using the MARECS B2 satellite at 26 degrees W was performed. While all the data have not been digested, some observations are in order. First, the system worked remarkably well for the margins indicated. Second, when the system worked poorly, the experimenters could almost always identify terrain or other obstacles causing blockage. Third, the forward link seems relatively more reliable than the return link, and occasional return link problems occured which have not been entirely explained.

Research on teaching reform and practice of applied optics design experiment

NASA Astrophysics Data System (ADS)

Geng, Tao; Tong, Chengguo; Zhang, Tao; Lu, Cunlian; Meng, Ting; Zhang, Yang; Wang, Ran; Sun, Weimin; Liu, Zhihai; Yang, Jun

2017-08-01

It is an important way to effectively improve applied optics experimental teaching effect and motivate the undergraduates' practice ability and creativity by means of scientific and systematic setting teaching contents and link. Based on the research and analysis of applied optics experiment teaching present condition at home and abroad, this paper aims to solve the existed problems and deficiencies during the experiment teaching in our university, and also puts forward some reform ideas and practice method from several aspects such as teaching thought, teaching content and mode, examination and evaluation and so on. Simultaneously, this paper also gives some suggestions on the future course development.

An update on the effects of playing violent video games.

PubMed

Anderson, Craig A

2004-02-01

This article presents a brief overview of existing research on the effects of exposure to violent video games. An updated meta-analysis reveals that exposure to violent video games is significantly linked to increases in aggressive behaviour, aggressive cognition, aggressive affect, and cardiovascular arousal, and to decreases in helping behaviour. Experimental studies reveal this linkage to be causal. Correlational studies reveal a linkage to serious, real-world types of aggression. Methodologically weaker studies yielded smaller effect sizes than methodologically stronger studies, suggesting that previous meta-analytic studies of violent video games underestimate the true magnitude of observed deleterious effects on behaviour, cognition, and affect.

Self-match based on polling scheme for passive optical network monitoring

NASA Astrophysics Data System (ADS)

Zhang, Xuan; Guo, Hao; Jia, Xinhong; Liao, Qinghua

2018-06-01

We propose a self-match based on polling scheme for passive optical network monitoring. Each end-user is equipped with an optical matcher that exploits only the specific length patchcord and two different fiber Bragg gratings with 100% reflectivity. The simple and low-cost scheme can greatly simplify the final recognition processing of the network link status and reduce the sensitivity of the photodetector. We analyze the time-domain relation between reflected pulses and establish the calculation model to evaluate the false alarm rate. The feasibility of the proposed scheme and the validity of the time-domain relation analysis are experimentally demonstrated.

A frequency control method for regulating wireless power to implantable devices.

PubMed

Ping Si; Hu, A P; Malpas, S; Budgett, D

2008-03-01

This paper presents a method to regulate the power transferred over a wireless link by adjusting the resonant operating frequency of the primary converter. A significant advantage of this method is that effective power regulation is maintained under variations in load, coupling and circuit parameters. This is particularly important when the wireless supply is used to power implanted medical devices where substantial coupling variations between internal and external systems is expected. The operating frequency is changed dynamically by altering the effective tuning capacitance through soft switched phase control. A thorough analysis of the proposed system has been undertaken, and experimental results verify its functionality.

Few-mode fiber based distributed curvature sensor through quasi-single-mode Brillouin frequency shift.

PubMed

Wu, Hao; Wang, Ruoxu; Liu, Deming; Fu, Songnian; Zhao, Can; Wei, Huifeng; Tong, Weijun; Shum, Perry Ping; Tang, Ming

2016-04-01

We proposed and demonstrated a few-mode fiber (FMF) based optical-fiber sensor for distributed curvature measurement through quasi-single-mode Brillouin frequency shift (BFS). By central-alignment splicing FMF and single-mode fiber (SMF) with a fusion taper, a SMF-components-compatible distributed curvature sensor based on FMF is realized using the conventional Brillouin optical time-domain analysis system. The distributed BFS change induced by bending in FMF has been theoretically and experimentally investigated. The precise BFS response to the curvature along the fiber link has been calibrated. A proof-of-concept experiment is implemented to validate its effectiveness in distributed curvature measurement.

A numerical analysis of high-temperature heat pipe startup from the frozen state

NASA Technical Reports Server (NTRS)

Cao, Y.; Faghri, A.

1993-01-01

Continuum and rarefied vapor flows co-exist along the heat pipe length for most of the startup period. A two-region model is proposed in which the vapor flow in the continuum region is modeled by the compressible Navier-Stokes equations, and the vapor flow in the rarefied region is simulated by a self-diffusion model. The two vapor regions are linked with appropriate boundary conditions, and heat pipe wail, wick, and vapor flow are solved as a conjugate problem. The numerical solutions for the entire heat pipe startup process from the frozen state are compared with the corresponding experimental data with good agreement.

Trust from the past: Bayesian Personalized Ranking based Link Prediction in Knowledge Graphs

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

Zhang, Baichuan; Choudhury, Sutanay; Al-Hasan, Mohammad

2016-02-01

Estimating the confidence for a link is a critical task for Knowledge Graph construction. Link prediction, or predicting the likelihood of a link in a knowledge graph based on prior state is a key research direction within this area. We propose a Latent Feature Embedding based link recommendation model for prediction task and utilize Bayesian Personalized Ranking based optimization technique for learning models for each predicate. Experimental results on large-scale knowledge bases such as YAGO2 show that our approach achieves substantially higher performance than several state-of-art approaches. Furthermore, we also study the performance of the link prediction algorithm in termsmore » of topological properties of the Knowledge Graph and present a linear regression model to reason about its expected level of accuracy.« less

Comparison of beam position calculation methods for application in digital acquisition systems

NASA Astrophysics Data System (ADS)

Reiter, A.; Singh, R.

2018-05-01

Different approaches to the data analysis of beam position monitors in hadron accelerators are compared adopting the perspective of an analog-to-digital converter in a sampling acquisition system. Special emphasis is given to position uncertainty and robustness against bias and interference that may be encountered in an accelerator environment. In a time-domain analysis of data in the presence of statistical noise, the position calculation based on the difference-over-sum method with algorithms like signal integral or power can be interpreted as a least-squares analysis of a corresponding fit function. This link to the least-squares method is exploited in the evaluation of analysis properties and in the calculation of position uncertainty. In an analytical model and experimental evaluations the positions derived from a straight line fit or equivalently the standard deviation are found to be the most robust and to offer the least variance. The measured position uncertainty is consistent with the model prediction in our experiment, and the results of tune measurements improve significantly.

Scleral fibroblast response to experimental glaucoma in mice

PubMed Central

Tezel, Gülgün; Cone-Kimball, Elizabeth; Steinhart, Matthew R.; Jefferys, Joan; Pease, Mary E.; Quigley, Harry A.

2016-01-01

Purpose To study the detailed cellular and molecular changes in the mouse sclera subjected to experimental glaucoma. Methods Three strains of mice underwent experimental bead-injection glaucoma and were euthanized at 3 days and 1, 3, and 6 weeks. Scleral protein expression was analyzed with liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) using 16O/18O labeling for quantification in 1- and 6-week tissues. Sclera protein samples were also analyzed with immunoblotting with specific antibodies to selected proteins. The proportion of proliferating scleral fibroblasts was quantified with Ki67 and 4’,6-diamidino-2-phenylindole (DAPI) labeling, and selected proteins were studied with immunohistochemistry. Results Proteomic analysis showed increases in molecules involved in integrin-linked kinase signaling and actin cytoskeleton signaling pathways at 1 and 6 weeks after experimental glaucoma. The peripapillary scleral region had more fibroblasts than equatorial sclera (p=0.001, n=217, multivariable regression models). There was a sixfold increase in proliferating fibroblasts in the experimental glaucoma sclera at 1 week and a threefold rise at 3 and 6 weeks (p=0.0005, univariate regression). Immunoblots confirmed increases for myosin, spectrin, and actinin at 1 week after glaucoma. Thrombospondin-1 (TSP-1), HINT1, vimentin, actinin, and α-smooth muscle actin were increased according to immunohistochemistry. Conclusions Scleral fibroblasts in experimental mouse glaucoma show increases in actin cytoskeleton and integrin-related signaling, increases in cell division, and features compatible with myofibroblast transition. PMID:26900327

Control of neutral particle fueling and exhaust by plasma edge topology optimization in Wendelstein 7-X and HSX

NASA Astrophysics Data System (ADS)

Stephey, Laurie

2016-10-01

Comparative experiments at the HSX and Wendelstein 7-X stellarators are being performed. At W7-X it was shown that fine control of the edge magnetic structure in W7-X is a feasible actuator to control global particle confinement. During the startup campaign of W7-X, the edge magnetic structure is defined by five poloidal limiters. Inside of the last closed flux surface in the standard magnetic configuration, the 5/6 resonance and corresponding magnetic island are located directly inside of the plasma source region. Inward movement of the island in a predominantly electron-root transport regime has been found to increase the effective helium confinement time τp* He, a critical metric for plasma purity control in future burning plasmas, by a factor of two. The experimental analysis is supported by fully 3-D fluid plasma and kinetic neutral modeling using the EMC3-EIRENE code and will be compared to these experimental results from both devices. A single reservoir, single species particle balance will be extracted from experimental measurements aided by the fully 3-D modeling analysis from EMC3-EIRENE to quantify the causal link established above based on measured parameters. At HSX, similar investigations to those performed at W7-X are ongoing. HSX has substantial flexibility in both its edge magnetic configuration and also in edge connection lengths via limiter insertion. Both are being examined to study any resulting changes global particle confinement and provide insight into the physics of the underlying mechanism. Together with the results from W7-X, both experiments will provide information on the link between the plasma edge topology and the global particle confinement. This work was supported in part by the U.S. Department of Energy under Grants DE-SC0014210, DE-FG02-93ER54222, DE-AC05-00OR22725, DOE LANS Contract DE-AC52- 06NA25396, and within the EUROfusion Consortium under Euratom Grant No 633053.

Comparative Effects of Computer-Based Concept Maps, Refutational Texts, and Expository Texts on Science Learning

ERIC Educational Resources Information Center

Adesope, Olusola O.; Cavagnetto, Andy; Hunsu, Nathaniel J.; Anguiano, Carlos; Lloyd, Joshua

2017-01-01

This study used a between-subjects experimental design to examine the effects of three different computer-based instructional strategies (concept map, refutation text, and expository scientific text) on science learning. Concept maps are node-link diagrams that show concepts as nodes and relationships among the concepts as labeled links.…

Polymers and Cross-Linking: A CORE Experiment to Help Students Think on the Submicroscopic Level

ERIC Educational Resources Information Center

Bruce, Mitchell R. M.; Bruce, Alice E.; Avargil, Shirly; Amar, Francois G.; Wemyss, Thomas M.; Flood, Virginia J.

2016-01-01

The Polymers and Cross-Linking experiment is presented via a new three phase learning cycle: CORE (Chemical Observations, Representations, Experimentation), which is designed to model productive chemical inquiry and to promote a deeper understanding about the chemistry operating at the submicroscopic level. The experiment is built on two familiar…

The Keyword Method of Vocabulary Acquisition: An Experimental Evaluation.

ERIC Educational Resources Information Center

Griffith, Douglas

The keyword method of vocabulary acquisition is a two-step mnemonic technique for learning vocabulary terms. The first step, the acoustic link, generates a keyword based on the sound of the foreign word. The second step, the imagery link, ties the keyword to the meaning of the item to be learned, via an interactive visual image or other…

Mechanical Design of High Lift Systems for High Aspect Ratio Swept Wings

NASA Technical Reports Server (NTRS)

Rudolph, Peter K. C.

1998-01-01

The NASA Ames Research Center is working to develop a methodology for the optimization and design of the high lift system for future subsonic airliners with the involvement of two partners. Aerodynamic analysis methods for two dimensional and three dimensional wing performance with flaps and slats deployed are being developed through a grant with the aeronautical department of the University of California Davis, and a flap and slat mechanism design procedure is being developed through a contract with PKCR, Inc., of Seattle, WA. This report documents the work that has been completed in the contract with PKCR on mechanism design. Flap mechanism designs have been completed for seven (7) different mechanisms with a total of twelve (12) different layouts all for a common single slotted flap configuration. The seven mechanisms are as follows: Simple Hinge, Upside Down/Upright Four Bar Linkage (two layouts), Upside Down Four Bar Linkages (three versions), Airbus A330/340 Link/Track Mechanism, Airbus A320 Link/Track Mechanism (two layouts), Boeing Link/Track Mechanism (two layouts), and Boeing 767 Hinged Beam Four Bar Linkage. In addition, a single layout has been made to investigate the growth potential from a single slotted flap to a vane/main double slotted flap using the Boeing Link/Track Mechanism. All layouts show Fowler motion and gap progression of the flap from stowed to a fully deployed position, and evaluations based on spanwise continuity, fairing size and number, complexity, reliability and maintainability and weight as well as Fowler motion and gap progression are presented. For slat design, the options have been limited to mechanisms for a shallow leading edge slat. Three (3) different layouts are presented for maximum slat angles of 20 deg, 15 deg and 1O deg all mechanized with a rack and pinion drive similar to that on the Boeing 757 airplane. Based on the work of Ljungstroem in Sweden, this type of slat design appears to shift the lift curve so that higher lift is achieved with the deployed slat with no increase in angle of attack. The layouts demonstrate that these slat systems can be designed with no need for slave links, and an experimental test program is outlined to experimentally validate the lift characteristics of the shallow slat.

Heat Capacity of B. Mori Silk Fibroin Based on the Vibrational-Motion of Poly(amino acid)s.

NASA Astrophysics Data System (ADS)

Pyda, Marek; Hu, Xiao; Cebe, Peggy

2009-03-01

Bombyx mori silk fibroin heat capacities with and without water have been determined based on the vibrational motions of poly(amino acid)s and water, using the Advanced Thermal Analysis System (ATHAS) Data Bank. The heat capacities, Cp, of dry silk and silk-water were linked to their vibrational spectra based on the group and skeletal vibration contributions. For dry silk, the experimental and calculated Cp agree to better than ±3% between 200 K and 435 K. The heat capacity of the solid silk-water system, below the glass transition, was estimated from a sum of linear combinations of the molar fractions of the vibrational heat capacities of dry silk and glassy water. Calculations are compared to experimental data obtained from calorimetric methods, using hermetic and non-hermetic pans. The approach presented allows one to predict the low temperature vibrational heat capacity for dry silk and for the silk-water system down to zero kelvin, and, together with an extension to higher temperatures, above the glass transition. This can be used as a reference baseline for quantitative thermal analysis of this biomaterial..

The Missing Link: The Use of Link Words and Phrases as a Link to Manuscript Quality

ERIC Educational Resources Information Center

Onwuegbuzie, Anthony J.

2016-01-01

In this article, I provide a typology of transition words/phrases. This typology comprises 12 dimensions of link words/phrases that capture 277 link words/phrases. Using QDA Miner, WordStat, and SPSS--a computer-assisted mixed methods data analysis software, content analysis software, and statistical software, respectively--I analyzed 74…

Experimental demonstration of real-time adaptively modulated DDO-OFDM systems with a high spectral efficiency up to 5.76bit/s/Hz transmission over SMF links.

PubMed

Chen, Ming; He, Jing; Tang, Jin; Wu, Xian; Chen, Lin

2014-07-28

In this paper, a FPGAs-based real-time adaptively modulated 256/64/16QAM-encoded base-band OFDM transceiver with a high spectral efficiency up to 5.76bit/s/Hz is successfully developed, and experimentally demonstrated in a simple intensity-modulated direct-detection optical communication system. Experimental results show that it is feasible to transmit a raw signal bit rate of 7.19Gbps adaptively modulated real-time optical OFDM signal over 20km and 50km single mode fibers (SMFs). The performance comparison between real-time and off-line digital signal processing is performed, and the results show that there is a negligible power penalty. In addition, to obtain the best transmission performance, direct-current (DC) bias voltage for MZM and launch power into optical fiber links are explored in the real-time optical OFDM systems.

A Review of Experimental Evidence Linking Neurotoxic Organophosphorus Compounds and Inflammation

PubMed Central

Banks, Christopher N.; Lein, Pamela J.

2012-01-01

Organophosphorus (OP) nerve agents and pesticides inhibit acetylcholinesterase (AChE), and this is thought to be a primary mechanism mediating the neurotoxicity of these compounds. However, a number of observations suggest that mechanisms other than or in addition to AChE inhibition contribute to OP neurotoxicity. There is significant experimental evidence that acute OP intoxication elicits a robust inflammatory response, and emerging evidence suggests that chronic repeated low-level OP exposure also upregulates inflammatory mediators. A critical question that is just beginning to be addressed experimentally is the pathophysiologic relevance of inflammation in either acute or chronic OP intoxication. The goal of this article is to provide a brief review of the current status of our knowledge linking inflammation to OP intoxication, and to discuss the implications of these findings in the context of therapeutic and diagnostic approaches to OP neurotoxicity. PMID:22342984

Prediction of multi-target networks of neuroprotective compounds with entropy indices and synthesis, assay, and theoretical study of new asymmetric 1,2-rasagiline carbamates.

PubMed

Romero Durán, Francisco J; Alonso, Nerea; Caamaño, Olga; García-Mera, Xerardo; Yañez, Matilde; Prado-Prado, Francisco J; González-Díaz, Humberto

2014-09-24

In a multi-target complex network, the links (L(ij)) represent the interactions between the drug (d(i)) and the target (t(j)), characterized by different experimental measures (K(i), K(m), IC50, etc.) obtained in pharmacological assays under diverse boundary conditions (c(j)). In this work, we handle Shannon entropy measures for developing a model encompassing a multi-target network of neuroprotective/neurotoxic compounds reported in the CHEMBL database. The model predicts correctly >8300 experimental outcomes with Accuracy, Specificity, and Sensitivity above 80%-90% on training and external validation series. Indeed, the model can calculate different outcomes for >30 experimental measures in >400 different experimental protocolsin relation with >150 molecular and cellular targets on 11 different organisms (including human). Hereafter, we reported by the first time the synthesis, characterization, and experimental assays of a new series of chiral 1,2-rasagiline carbamate derivatives not reported in previous works. The experimental tests included: (1) assay in absence of neurotoxic agents; (2) in the presence of glutamate; and (3) in the presence of H2O2. Lastly, we used the new Assessing Links with Moving Averages (ALMA)-entropy model to predict possible outcomes for the new compounds in a high number of pharmacological tests not carried out experimentally.

Mastitomics, the integrated omics of bovine milk in an experimental model of Streptococcus uberis mastitis: 3. Untargeted metabolomics.

PubMed

Thomas, Funmilola Clara; Mudaliar, Manikhandan; Tassi, Riccardo; McNeilly, Tom N; Burchmore, Richard; Burgess, Karl; Herzyk, Pawel; Zadoks, Ruth N; Eckersall, P David

2016-08-16

Intramammary infection leading to bovine mastitis is the leading disease problem affecting dairy cows and has marked effects on the milk produced by infected udder quarters. An experimental model of Streptococcus uberis mastitis has previously been investigated for clinical, immunological and pathophysiological alteration in milk, and has been the subject of peptidomic and quantitative proteomic investigation. The same sample set has now been investigated with a metabolomics approach using liquid chromatography and mass spectrometry. The analysis revealed over 3000 chromatographic peaks, of which 690 were putatively annotated with a metabolite. Hierarchical clustering analysis and principal component analysis demonstrated that metabolite changes due to S. uberis infection were maximal at 81 hours post challenge with metabolites in the milk from the resolution phase at 312 hours post challenge being closest to the pre-challenge samples. Metabolic pathway analysis revealed that the majority of the metabolites mapped to carbohydrate and nucleotide metabolism show a decreasing trend in concentration up to 81 hours post-challenge whereas an increasing trend was found in lipid metabolites and di-, tri- and tetra-peptides up to the same time point. The increase in these peptides coincides with an increase in larger peptides found in the previous peptidomic analysis and is likely to be due to protease degradation of milk proteins. Components of bile acid metabolism, linked to the FXR pathway regulating inflammation, were also increased. Metabolomic analysis of the response in milk during mastitis provides an essential component to the full understanding of the mammary gland's response to infection.

An efficient transmission power control scheme for temperature variation in wireless sensor networks.

PubMed

Lee, Jungwook; Chung, Kwangsue

2011-01-01

Wireless sensor networks collect data from several nodes dispersed at remote sites. Sensor nodes can be installed in harsh environments such as deserts, cities, and indoors, where the link quality changes considerably over time. Particularly, changes in transmission power may be caused by temperature, humidity, and other factors. In order to compensate for link quality changes, existing schemes detect the link quality changes between nodes and control transmission power through a series of feedback processes, but these approaches can cause heavy overhead with the additional control packets needed. In this paper, the change of the link quality according to temperature is examined through empirical experimentation. A new power control scheme combining both temperature-aware link quality compensation and a closed-loop feedback process to adapt to link quality changes is proposed. We prove that the proposed scheme effectively adapts the transmission power to the changing link quality with less control overhead and energy consumption.

Comparative investigation of thermal and mechanical properties of cross-linked epoxy polymers with different curing agents by molecular dynamics simulation.

PubMed

Jeyranpour, F; Alahyarizadeh, Gh; Arab, B

2015-11-01

Molecular dynamics (MD) simulations were carried out to predict the thermal and mechanical properties of the cross-linked epoxy system composed of DGEBA resin and the curing agent TETA. To investigate the effects of curing agents, a comprehensive and comparative study was also performed on the thermal and mechanical properties of DGEBA/TETA and DGEBA/DETDA epoxy systems such as density, glass transition temperature (Tg), coefficient of thermal expansion (CTE) and elastic properties of different cross-linking densities and different temperatures. The results indicated that the glass transition temperature of DGEBA/TETA system calculated through density-temperature data, ∼ 385-395 °K, for the epoxy system with the cross-linking density of 62.5% has a better agreement with the experimental value (Tg, ∼ 400 °K) in comparison to the value calculated through the variation of cell volume in terms of temperature, 430-440 °K. They also indicated that CTE related parameters and elastic properties including Young, Bulk, and shear's moduli, and Poisson's ratio have a relative agreement with the experimental results. Comparison between the thermal and mechanical properties of epoxy systems of DGEBA/TETA and DGEBA/DETDA showed that the DGEBA/DETDA has a higher Tg in all cross linking densities than that of DGEBA/TETA, while higher mechanical properties was observed in the case of DGEBA/TETA in almost all cross linking densities. Copyright © 2015 Elsevier Inc. All rights reserved.

Inversion of left-right asymmetry alters performance of Xenopus tadpoles in nonlateralized cognitive tasks.

PubMed

Blackiston, Douglas J; Levin, Michael

2013-08-01

Left-right behavioural biases are well documented across the animal kingdom, and handedness has long been associated with cognitive performance. However, the relationship between body laterality and cognitive ability is poorly understood. The embryonic pathways dictating normal left-right patterning have been molecularly dissected in model vertebrates, and numerous genetic and pharmacological treatments now facilitate experimental randomization or reversal of the left-right axis in these animals. Several recent studies showed a link between brain asymmetry and strongly lateralized behaviours such as eye use preference. However, links between laterality of the body and performance on cognitive tasks utilizing nonlateralized cues remain unknown. Xenopus tadpoles are an established model for the study of early left-right patterning, and protocols were recently developed to quantitatively evaluate learning and memory in these animals. Using an automated testing and training platform, we tested wild-type, left-right-randomized and left-right-reversed tadpoles for their ability to learn colour cues in an automated assay. Our results indicate that animals with either randomization or reversal of somatic left-right patterning learned more slowly than wild-type siblings, although all groups were able to reach the same performance optimum given enough training sessions. These results are the first analysis of the link between body laterality and learning of nonlateralized cues, and they position the Xenopus tadpole as an attractive and tractable model for future studies of the links between asymmetry of the body, lateralization of the brain and behaviour.

Wrinkling of solidifying polymeric coatings

NASA Astrophysics Data System (ADS)

Basu, Soumendra Kumar

2005-07-01

In coatings, wrinkles are viewed as defects or as desired features for low gloss, and texture. In either case, discovering the origin of wrinkles and the conditions that lead to their formation is important. This research examines what wrinkling requires and proposes a mechanism to explain the observations. All curing wrinkling coatings contain multi-functional reactants. Upon curing, all develop a depth-wise gradient in solidification that result in a cross-linked elastic skin atop a viscous bottom layer. It is hypothesized that compressive stress develops in the skin when liquid below diffuses up into the skin. High enough compressive stress buckles the skin to produce wrinkles. The hypothesis is substantiated by experimental and theoretical evidences. Effects of various application and compositional parameters on wrinkle size in a liquid-applied acrylic coating and a powder-applied epoxy coating were examined. All three components, namely resin, cross-linker and catalyst blocked with at least equimolar volatile blocker, proved to be required for wrinkling. The wrinkling phenomenon was modeled with a theory that accounts for gradient generation, cross-linking reaction and skinning; predictions compared well with observations. Two-layer non-curing coatings that have a stiff elastic layer atop a complaint elastic bottom layer wrinkled when the top layer is compressed. The top layer was compressed by either moisture absorption or differential thermal expansion. Experimental observations compared well with predictions from a theory based on force balance in multilayer systems subjected to differential contraction or expansion. A model based on the Flory-Rehner free energy of a constrained cross-linked gel was constructed that predicts the compressive stress generated in a coating when it absorbs solvent. Linear stability analysis predicts that when a compressed elastic layer is attached atop a viscous layer, it is always unstable to buckles whose wavelength exceeds a critical value; more cross-linking and poor solvent produce higher wavelength, lower amplitude wrinkles. When a compressed elastic layer is attached atop an elastic layer and subjected to more than a critical compressive stress, it is unstable to intermediate wavelengths of buckling; better solvent, higher ratio of bottom-to-top layer thickness, and lower bottom layer modulus produce higher wavelength, higher amplitude wrinkles.

Systematic Comparison of Reverse Phase and Hydrophilic Interaction Liquid Chromatography Platforms for the Analysis of N-linked Glycans

PubMed Central

Walker, S. Hunter; Carlisle, Brandon C.; Muddiman, David C.

2013-01-01

Due to the hydrophilic nature of glycans, reverse phase chromatography has not been widely used as a glycomic separation technique coupled to mass spectrometry. Other approaches such as hydrophilic interaction chromatography and porous graphitized carbon chromatography are often employed, though these strategies frequently suffer from decreased chromatographic resolution, long equilibration times, indefinite retention, and column bleed. Herein, it is shown that through an efficient hydrazone formation derivatization of N-linked glycans (∼4 hr of additional sample preparation time which is carried out in parallel), numerous experimental and practical advantages are gained when analyzing the glycans by online reverse phase chromatography. These benefits include an increased number of glycans detected, increased peak capacity of the separation, and the ability to analyze glycans on the identical liquid chromatography-mass spectrometry platform commonly used for proteomic analyses. The data presented show that separation of derivatized N-linked glycans by reverse phase chromatography significantly out-performs traditional separation of native or derivatized glycans by hydrophilic interaction chromatography. Furthermore, the movement to a more ubiquitous separation technique will afford numerous research groups the opportunity to analyze both proteomic and glycomic samples on the same platform with minimal time and physical change between experiments, increasing the efficiency of ‘multi-omic’ biological approaches. PMID:22954204

Simultaneous backward data transmission and power harvesting in an ultrasonic transcutaneous energy transfer link employing acoustically dependent electric impedance modulation.

PubMed

Ozeri, Shaul; Shmilovitz, Doron

2014-09-01

The advancement and miniaturization of body implanted medical devices pose several challenges to Ultrasonic Transcutaneous Energy Transfer (UTET), such as the need to reduce the size of the piezoelectric resonator, and the need to maximize the UTET link power-transfer efficiency. Accordingly, the same piezoelectric resonator that is used for energy harvesting at the body implant, may also be used for ultrasonic backward data transfer, for instance, through impedance modulation. This paper presents physical considerations and design guidelines of the body implanted transducer of a UTET link with impedance modulation for a backward data transfer. The acoustic matching design procedure was based on the 2×2 transfer matrix chain analysis, in addition to the Krimholtz Leedom and Matthaei KLM transmission line model. The UTET power transfer was carried out at a frequency of 765 kHz, continuous wave (CW) mode. The backward data transfer was attained by inserting a 9% load resistance variation around its matched value (550 Ohm), resulting in a 12% increase in the acoustic reflection coefficient. A backward data transmission rate of 1200 bits/s was experimentally demonstrated using amplitude shift keying, simultaneously with an acoustic power transfer of 20 mW to the implant. Copyright © 2014 Elsevier B.V. All rights reserved.

Transmembrane Domains of Attraction on the TSH Receptor

PubMed Central

Ali, M. Rejwan; Mezei, Mihaly; Davies, Terry F.

2015-01-01

The TSH receptor (TSHR) has the propensity to form dimers and oligomers. Our data using ectodomain-truncated TSHRs indicated that the predominant interfaces for oligomerization reside in the transmembrane (TM) domain. To map the potentially interacting residues, we first performed in silico studies of the TSHR transmembrane domain using a homology model and using Brownian dynamics (BD). The cluster of dimer conformations obtained from BD analysis indicated that TM1 made contact with TM4 and two residues in TM2 made contact with TM5. To confirm the proximity of these contact residues, we then generated cysteine mutants at all six contact residues predicted by the BD analysis and performed cysteine cross-linking studies. These results showed that the predicted helices in the protomer were indeed involved in proximity interactions. Furthermore, an alternative experimental approach, receptor truncation experiments and LH receptor sequence substitution experiments, identified TM1 harboring a major region involved in TSHR oligomerization, in agreement with the conclusion from the cross-linking studies. Point mutations of the predicted interacting residues did not yield a substantial decrease in oligomerization, unlike the truncation of the TM1, so we concluded that constitutive oligomerization must involve interfaces forming domains of attraction in a cooperative manner that is not dominated by interactions between specific residues. PMID:25406938

Cyrface: An interface from Cytoscape to R that provides a user interface to R packages.

PubMed

Gonçalves, Emanuel; Mirlach, Franz; Saez-Rodriguez, Julio

2013-01-01

There is an increasing number of software packages to analyse biological experimental data in the R environment. In particular, Bioconductor, a repository of curated R packages, is one of the most comprehensive resources for bioinformatics and biostatistics. The use of these packages is increasing, but it requires a basic understanding of the R language, as well as the syntax of the specific package used. The availability of user graphical interfaces for these packages would decrease the learning curve and broaden their application. Here, we present a Cytoscape app termed Cyrface that allows Cytoscape apps to connect to any function and package developed in R. Cyrface can be used to run R packages from within the Cytoscape environment making use of a graphical user interface. Moreover, it can link R packages with the capabilities of Cytoscape and its apps, in particular network visualization and analysis. Cyrface's utility has been demonstrated for two Bioconductor packages ( CellNOptR and DrugVsDisease), and here we further illustrate its usage by implementing a workflow of data analysis and visualization. Download links, installation instructions and user guides can be accessed from the Cyrface's homepage ( http://www.ebi.ac.uk/saezrodriguez/cyrface/) and from the Cytoscape app store ( http://apps.cytoscape.org/apps/cyrface).

Experimental demonstration of beaconless beam displacement tracking for an orbital angular momentum multiplexed free-space optical link.

PubMed

Li, Long; Zhang, Runzhou; Xie, Guodong; Ren, Yongxiong; Zhao, Zhe; Wang, Zhe; Liu, Cong; Song, Haoqian; Pang, Kai; Bock, Robert; Tur, Moshe; Willner, Alan E

2018-05-15

In this Letter, we experimentally demonstrate beaconless beam displacement tracking for free-space optical communication link multiplexing multiple orbital angular momentum (OAM) beams, where the data-carrying OAM beams are used for position detection. 400 Gbit/s data transmission is demonstrated under emulated lateral displacement of up to ±10  mm with power penalties of less than 3 dB for all channels. Channel crosstalk is reduced by the beam tracking system to below -18  dB. Moreover, we investigate using a Gaussian beacon for beam displacement tracking, and achieve similar channel crosstalk and power penalties, compared with using the beaconless beam tracking.

Felix Bloch, Nuclear Induction, Bloch Equations, Bloch Theorem, Bloch

Science.gov Websites

the homemade Stanford cyclotron for the first experimental determination of the energy distribution of they had been using slightly different techniques to achieve experimental results. So they decided to Sciences; Felix Bloch - pages 34 - 71 Top Some links on this page may take you to non-federal websites

MARINE NEWS - GRIDDED and VECTOR DATA

Science.gov Websites

Great Lakes. Experimental gridded data and graphical imagery is now routinely produced at most WFOs. It gusts; weather; and wave height by December 2004. Gridded forecasts from the other non-continental U.S (PNG) format. Links to NDFD Data: Example of NDFD Graphical Imagery (experimental) NDFD GRIB2 data via

Demolishing the Competition: The Longitudinal Link between Competitive Video Games, Competitive Gambling, and Aggression

ERIC Educational Resources Information Center

Adachi, Paul J. C.; Willoughby, Teena

2013-01-01

The majority of research on the link between video games and aggression has focused on the violent content in games. In contrast, recent experimental research suggests that it is video game competition, not violence, that has the greatest effect on aggression in the short-term. However, no researchers have examined the long-term relationship…

Multiple Linking in Equating and Random Scale Drift. Research Report. ETS RR-11-46

ERIC Educational Resources Information Center

Guo, Hongwen; Liu, Jinghua; Dorans, Neil; Feigenbaum, Miriam

2011-01-01

Maintaining score stability is crucial for an ongoing testing program that administers several tests per year over many years. One way to stall the drift of the score scale is to use an equating design with multiple links. In this study, we use the operational and experimental SAT® data collected from 44 administrations to investigate the effect…

Fulfilling the Potential of NYC-2. Linking the Neighborhood Youth Corps and MA-JOBS Program into a Sequential Training-Employment Model.

ERIC Educational Resources Information Center

Lorber, Fred; Feifer, Irwin

Although Neighborhood Youth Corps (NYC) training is conducted either in NYC centers, governmental and non-profit agencies or private industry, there is no commitment for employment after training. The Mobilization for Youth-Experimental Manpower Laboratory (MFY-EML) is exploring the feasibility of linking NYC to other government manpower training…

Link Analysis in the Mission Planning Lab

NASA Technical Reports Server (NTRS)

McCarthy, Jessica A.; Cervantes, Benjamin W.; Daugherty, Sarah C.; Arroyo, Felipe; Mago, Divyang

2011-01-01

The legacy communications link analysis software currently used at Wallops Flight Facility involves processes that are different for command destruct, radar, and telemetry. There is a clear advantage to developing an easy-to-use tool that combines all the processes in one application. Link Analysis in the Mission Planning Lab (MPL) uses custom software and algorithms integrated with Analytical Graphics Inc. Satellite Toolkit (AGI STK). The MPL link analysis tool uses pre/post-mission data to conduct a dynamic link analysis between ground assets and the launch vehicle. Just as the legacy methods do, the MPL link analysis tool calculates signal strength and signal- to-noise according to the accepted processes for command destruct, radar, and telemetry assets. Graphs and other custom data are generated rapidly in formats for reports and presentations. STK is used for analysis as well as to depict plume angles and antenna gain patterns in 3D. The MPL has developed two interfaces with the STK software (see figure). The first interface is an HTML utility, which was developed in Visual Basic to enhance analysis for plume modeling and to offer a more user friendly, flexible tool. A graphical user interface (GUI) written in MATLAB (see figure upper right-hand corner) is also used to quickly depict link budget information for multiple ground assets. This new method yields a dramatic decrease in the time it takes to provide launch managers with the required link budgets to make critical pre-mission decisions. The software code used for these two custom utilities is a product of NASA's MPL.

Morphology and dynamics of explosive vents

NASA Astrophysics Data System (ADS)

Gisler, Galen R.; Galland, Olivier; Haug, Øystein T.

2014-05-01

Eruptive processes in nature produce a wide variety of morphologies, including cone sheets, dykes, sills, and pipes. The choice of a particular eruptive style is determined partly by local inhomogeneities, and partly by the gross overall properties of the country rock and the physical properties of the eruptive fluid. In this study we report on experimental and numerical designed to capture a range of morphologies in an eruptive system. Using dimensional analysis we link the experimental and numerical work together and draw implications for field studies. Our experimental work uses silica flour in a Hele-Shaw cell, with air as the eruptive fluid. A phase diagram demonstrates a separation between two distinct morphologies, with vertical structures occurring at high pressure or low depth of fill and diagonal ones at low pressure or high depth of fill. In the numerical work the eruptive fluid is a mixture of basaltic magma, supercritical water, and carbon dioxide, and the ambient material is a fill of basalt with varying material properties. In the numerical work we see three distinct morphologies: vertical pipes are produced at high pressures and softer backgrounds, diagonal pipes at lower pressures and stiffer backgrounds, while horizontal sills are produced in intermediate regimes.

Diversity of Knot Solitons in Liquid Crystals Manifested by Linking of Preimages in Torons and Hopfions

NASA Astrophysics Data System (ADS)

Ackerman, Paul J.; Smalyukh, Ivan I.

2017-01-01

Topological solitons are knots in continuous physical fields classified by nonzero Hopf index values. Despite arising in theories that span many branches of physics, from elementary particles to condensed matter and cosmology, they remain experimentally elusive and poorly understood. We introduce a method of experimental and numerical analysis of such localized structures in liquid crystals that, similar to the mathematical Hopf maps, relates all points of the medium's order parameter space to their closed-loop preimages within the three-dimensional solitons. We uncover a surprisingly large diversity of naturally occurring and laser-generated topologically nontrivial solitons with differently knotted nematic fields, which previously have not been realized in theories and experiments alike. We discuss the implications of the liquid crystal's nonpolar nature on the knot soliton topology and how the medium's chirality, confinement, and elastic anisotropy help to overcome the constraints of the Hobart-Derrick theorem, yielding static three-dimensional solitons without or with additional defects. Our findings will establish chiral nematics as a model system for experimental exploration of topological solitons and may impinge on understanding of such nonsingular field configurations in other branches of physics, as well as may lead to technological applications.

Microphysics of liquid complex plasmas in equilibrium and non-equilibrium systems

NASA Astrophysics Data System (ADS)

Piel, Alexander; Block, Dietmar; Melzer, André; Mulsow, Matthias; Schablinski, Jan; Schella, André; Wieben, Frank; Wilms, Jochen

2018-05-01

The dynamic evolution of the microscopic structure of solid and liquid phases of complex plasmas is studied experimentally and by means of molecular dynamics (MD) simulations. In small finite systems, the cooperative motion can be described in terms of discrete modes. These modes are studied with different experimental approaches. Using diffuse scattered laser light, applying laser tweezer forces to individual particles, and periodic laser pulses, the excitation of modes is investigated. The instantaneous normal mode analysis of experimental data from two-dimensional liquid clusters gives access to the local dynamics of the liquid phase. Our investigations shed light on the role of compressional and shear modes as well as the determination of diffusion constants and melting temperatures in finite systems. Special attention is paid to hydrodynamic situations with a stationary inhomogeneous dust flow. MD simulations allow to study the collective motion in the shell of nearest neighbors, which can be linked to smooth and sudden changes of the macroscopic flow. Finally, the observed micro-motion in all situations above allows to shed light on the preference of shear-like over compressional motion in terms of a minimized potential energy and a dynamic incompressibility.

Visual and Auditory Components in the Perception of Asynchronous Audiovisual Speech

PubMed Central

Alcalá-Quintana, Rocío

2015-01-01

Research on asynchronous audiovisual speech perception manipulates experimental conditions to observe their effects on synchrony judgments. Probabilistic models establish a link between the sensory and decisional processes underlying such judgments and the observed data, via interpretable parameters that allow testing hypotheses and making inferences about how experimental manipulations affect such processes. Two models of this type have recently been proposed, one based on independent channels and the other using a Bayesian approach. Both models are fitted here to a common data set, with a subsequent analysis of the interpretation they provide about how experimental manipulations affected the processes underlying perceived synchrony. The data consist of synchrony judgments as a function of audiovisual offset in a speech stimulus, under four within-subjects manipulations of the quality of the visual component. The Bayesian model could not accommodate asymmetric data, was rejected by goodness-of-fit statistics for 8/16 observers, and was found to be nonidentifiable, which renders uninterpretable parameter estimates. The independent-channels model captured asymmetric data, was rejected for only 1/16 observers, and identified how sensory and decisional processes mediating asynchronous audiovisual speech perception are affected by manipulations that only alter the quality of the visual component of the speech signal. PMID:27551361

Quantum Experiments and Graphs: Multiparty States as Coherent Superpositions of Perfect Matchings.

PubMed

Krenn, Mario; Gu, Xuemei; Zeilinger, Anton

2017-12-15

We show a surprising link between experimental setups to realize high-dimensional multipartite quantum states and graph theory. In these setups, the paths of photons are identified such that the photon-source information is never created. We find that each of these setups corresponds to an undirected graph, and every undirected graph corresponds to an experimental setup. Every term in the emerging quantum superposition corresponds to a perfect matching in the graph. Calculating the final quantum state is in the #P-complete complexity class, thus it cannot be done efficiently. To strengthen the link further, theorems from graph theory-such as Hall's marriage problem-are rephrased in the language of pair creation in quantum experiments. We show explicitly how this link allows one to answer questions about quantum experiments (such as which classes of entangled states can be created) with graph theoretical methods, and how to potentially simulate properties of graphs and networks with quantum experiments (such as critical exponents and phase transitions).

Experimental Myocardial Infarction Upregulates Circulating Fibroblast Growth Factor-23.

PubMed

Andrukhova, Olena; Slavic, Svetlana; Odörfer, Kathrin I; Erben, Reinhold G

2015-10-01

Myocardial infarction (MI) is a major cause of death worldwide. Epidemiological studies have linked vitamin D deficiency to MI incidence. Because fibroblast growth factor-23 (FGF23) is a master regulator of vitamin D hormone production and has been shown to be associated with cardiac hypertrophy per se, we explored the hypothesis that FGF23 may be a previously unrecognized pathophysiological factor causally linked to progression of cardiac dysfunction post-MI. Here, we show that circulating intact Fgf23 was profoundly elevated, whereas serum vitamin D hormone levels were suppressed, after induction of experimental MI in rat and mouse models, independent of changes in serum soluble Klotho or serum parathyroid hormone. Both skeletal and cardiac expression of Fgf23 was increased after MI. Although the molecular link between the cardiac lesion and circulating Fgf23 concentrations remains to be identified, our study has uncovered a novel heart-bone-kidney axis that may have important clinical implications and may inaugurate the new field of cardio-osteology. © 2015 American Society for Bone and Mineral Research.

Communication: Appearance of undershoots in start-up shear: Experimental findings captured by tumbling-snake dynamics

NASA Astrophysics Data System (ADS)

Stephanou, Pavlos S.; Schweizer, Thomas; Kröger, Martin

2017-04-01

Our experimental data unambiguously show (i) a damping behavior (the appearance of an undershoot following the overshoot) in the transient shear viscosity of a concentrated polymeric solution, and (ii) the absence of a corresponding behavior in the transient normal stress coefficients. Both trends are shown to be quantitatively captured by the bead-link chain kinetic theory for concentrated polymer solutions and entangled polymer melts proposed by Curtiss and Bird, supplemented by a non-constant link tension coefficient that we relate to the nematic order parameter. The observed phenomena are attributed to the tumbling behavior of the links, triggered by rotational fluctuations, on top of reptation. Using model parameters deduced from stationary data, we calculate the transient behavior of the stress tensor for this "tumbling-snake" model after startup of shear flow efficiently via simple Brownian dynamics. The unaltered method is capable of handling arbitrary homogeneous flows and has the promising capacity to improve our understanding of the transient behavior of concentrated polymer solutions.

Quantum Experiments and Graphs: Multiparty States as Coherent Superpositions of Perfect Matchings

NASA Astrophysics Data System (ADS)

Krenn, Mario; Gu, Xuemei; Zeilinger, Anton

2017-12-01

We show a surprising link between experimental setups to realize high-dimensional multipartite quantum states and graph theory. In these setups, the paths of photons are identified such that the photon-source information is never created. We find that each of these setups corresponds to an undirected graph, and every undirected graph corresponds to an experimental setup. Every term in the emerging quantum superposition corresponds to a perfect matching in the graph. Calculating the final quantum state is in the #P-complete complexity class, thus it cannot be done efficiently. To strengthen the link further, theorems from graph theory—such as Hall's marriage problem—are rephrased in the language of pair creation in quantum experiments. We show explicitly how this link allows one to answer questions about quantum experiments (such as which classes of entangled states can be created) with graph theoretical methods, and how to potentially simulate properties of graphs and networks with quantum experiments (such as critical exponents and phase transitions).

Simultaneous transfer of optical frequency and time over 306 km long-haul optical fibre link

NASA Astrophysics Data System (ADS)

Hucl, Vaclav; Cizek, Martin; Pravdova, Lenka; Rerucha, Simon; Hrabina, Jan; Mikel, Bretislav; Smotlacha, Vladimir; Vojtech, Josef; Lazar, Josef; Cip, Ondrej

2016-12-01

Optical fibre links for distributing optical frequencies and time stamps were researched and experimentally tested in the past fifteen years. They have been used mainly for stability comparison of experimental optical clocks. But recent development puts demands on a technology transfer from laboratory experiments to the real industry. The remote calibration of interrogators of Fibre Bragg Grating strain sensory networks is one of important examples. The first step of the adoption the time and frequency broadcasting should be the drop-out free long-term operation of this technology between research laboratories connected via long-haul fibre links. We present a 306 km long-haul optical fibre link between the cities of Prague and Brno in the Czech Republic where a coherent transfer of stable optical frequency and a stable time signal has been firstly demonstrated. The link between ISI CAS Brno and CESNET Prague uses an internet communication fibre where a window of 1540-1546 nm is dedicated for the coherent transfer and 1PPS signal. The link is equipped with 6 bidirectional EDFA amplifiers. The optical frequency standard based on the highly-coherent laser Koheras Adjustik working at 1540.5 nm and stabilized with a saturation absorption spectroscopy technique was used for the coherent wave transfer. The suppression of the Doppler shift induced by the optical fibre was based on an accoustooptical modulator with a servo-loop including a fast PID controller processing the beat-note frequency given by mixing of the Adjustik laser (Brno) and the reflected frequency of this laser from the far end of 306 km long-haul fibre link (Prague). We verified the Doppler shift suppression for the coherent wave with a measuring method analysing the transport delay of the 1PPS signal.

Analysis of opioid efficacy, tolerance, addiction and dependence from cell culture to human

PubMed Central

Morgan, Michael M; Christie, MacDonald J

2011-01-01

Opioid agonists are the most effective treatment for pain, but their use is limited by side effects, tolerance and fears of addiction and dependence. A major goal of opioid research is to develop agonists that have high analgesic efficacy and a low profile for side effects, tolerance, addiction and dependence. Unfortunately, there is a serious lack of experimental data comparing the degree to which different opioids produce these effects in humans. In contrast, a wide range of experimental techniques from heterologous expression systems to behaviour assessment in whole animals have been developed to study these problems. The objective of this review is to describe and evaluate these techniques as they are used to study opioid efficacy, tolerance, addiction and dependence. LINKED ARTICLES This article is part of a themed issue on Translational Neuropharmacology. To view the other articles in this issue visit http://dx.doi.org/10.1111/bph.2011.164.issue-4 PMID:21434879

Experimental investigation of optimum beam size for FSO uplink

NASA Astrophysics Data System (ADS)

Kaushal, Hemani; Kaddoum, Georges; Jain, Virander Kumar; Kar, Subrat

2017-10-01

In this paper, the effect of transmitter beam size on the performance of free space optical (FSO) communication has been determined experimentally. Irradiance profile for varying turbulence strength is obtained using optical turbulence generating (OTG) chamber inside laboratory environment. Based on the results, an optimum beam size is investigated using the semi-analytical method. Moreover, the combined effects of atmospheric scintillation and beam wander induced pointing errors are considered in order to determine the optimum beam size that minimizes the bit error rate (BER) of the system for a fixed transmitter power and link length. The results show that the optimum beam size for FSO uplink depends upon Fried parameter and outer scale of the turbulence. Further, it is observed that the optimum beam size increases with the increase in zenith angle but has negligible effect with the increase in fade threshold level at low turbulence levels and has a marginal effect at high turbulence levels. Finally, the obtained outcome is useful for FSO system design and BER performance analysis.

Optimization of glibenclamide tablet composition through the combined use of differential scanning calorimetry and D-optimal mixture experimental design.

PubMed

Mura, P; Furlanetto, S; Cirri, M; Maestrelli, F; Marras, A M; Pinzauti, S

2005-02-07

A systematic analysis of the influence of different proportions of excipients on the stability of a solid dosage form was carried out. In particular, a d-optimal mixture experimental design was applied for the evaluation of glibenclamide compatibility in tablet formulations, consisting of four classic excipients (natrosol as binding agent, stearic acid as lubricant, sorbitol as diluent and cross-linked polyvinylpyrrolidone as disintegrant). The goal was to find the mixture component proportions which correspond to the optimal drug melting parameters, i.e. its maximum stability, using differential scanning calorimetry (DSC) to quickly obtain information about possible interactions among the formulation components. The absolute value of the difference between the melting peak temperature of pure drug endotherm and that in each analysed mixture and the absolute value of the difference between the enthalpy of the pure glibenclamide melting peak and that of its melting peak in the different analyzed mixtures, were chosen as indexes of the drug-excipient interaction degree.

Adaptive Strategies for Controls of Flexible Arms. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Yuan, Bau-San

1989-01-01

An adaptive controller for a modern manipulator has been designed based on asymptotical stability via the Lyapunov criterion with the output error between the system and a reference model used as the actuating control signal. Computer simulations were carried out to test the design. The combination of the adaptive controller and a system vibration and mode shape estimator show that the flexible arm should move along a pre-defined trajectory with high-speed motion and fast vibration setting time. An existing computer-controlled prototype two link manipulator, RALF (Robotic Arm, Large Flexible), with a parallel mechanism driven by hydraulic actuators was used to verify the mathematical analysis. The experimental results illustrate that assumed modes found from finite element techniques can be used to derive the equations of motion with acceptable accuracy. The robust adaptive (modal) control is implemented to compensate for unmodelled modes and nonlinearities and is compared with the joint feedback control in additional experiments. Preliminary results show promise for the experimental control algorithm.

Life in the laboratory: public responses to experimental biology.

PubMed

Turney, J

1995-04-01

Present-day public attitudes to biological manipulation are ambivalent, many surveys show. This paper explores evidence of earlier attitudes to experimental biology, before survey data exists, by examining published responses in the press to the idea that biologists would 'create life'. This remarkable claim achieved wide currency in the early years of this century, particularly linked to the work of two prototypical 'visible scientists': Jacques Loeb and Alexis Carrel. Analysis of press responses to accounts of their work reveals deep disquiet about its possible implications, at a time when science and technology in general were regarded very positively. The evidence is augmented by studying commentary on a Presidential Address by Edward Schafer to the British Association meeting of 1912. It is concluded that feelings of ambivalence toward the manipulative power of biology are apparent at a very early stage in the development of modern biology, and that this makes it implausible that more recent manifestations of such ambivalence can be ascribed to some generalized 'anti-science' sentiment which has gathered strength in recent years.

A novel method linking neural connectivity to behavioral fluctuations: Behavior-regressed connectivity.

PubMed

Passaro, Antony D; Vettel, Jean M; McDaniel, Jonathan; Lawhern, Vernon; Franaszczuk, Piotr J; Gordon, Stephen M

2017-03-01

During an experimental session, behavioral performance fluctuates, yet most neuroimaging analyses of functional connectivity derive a single connectivity pattern. These conventional connectivity approaches assume that since the underlying behavior of the task remains constant, the connectivity pattern is also constant. We introduce a novel method, behavior-regressed connectivity (BRC), to directly examine behavioral fluctuations within an experimental session and capture their relationship to changes in functional connectivity. This method employs the weighted phase lag index (WPLI) applied to a window of trials with a weighting function. Using two datasets, the BRC results are compared to conventional connectivity results during two time windows: the one second before stimulus onset to identify predictive relationships, and the one second after onset to capture task-dependent relationships. In both tasks, we replicate the expected results for the conventional connectivity analysis, and extend our understanding of the brain-behavior relationship using the BRC analysis, demonstrating subject-specific BRC maps that correspond to both positive and negative relationships with behavior. Comparison with Existing Method(s): Conventional connectivity analyses assume a consistent relationship between behaviors and functional connectivity, but the BRC method examines performance variability within an experimental session to understand dynamic connectivity and transient behavior. The BRC approach examines connectivity as it covaries with behavior to complement the knowledge of underlying neural activity derived from conventional connectivity analyses. Within this framework, BRC may be implemented for the purpose of understanding performance variability both within and between participants. Published by Elsevier B.V.

Analysis of the behavior of a wiper blade around the reversal in consideration of dynamic and static friction

NASA Astrophysics Data System (ADS)

Unno, M.; Shibata, A.; Yabuno, H.; Yanagisawa, D.; Nakano, T.

2017-04-01

Reducing noise generated by automobile windshield wipers during reversals is a desirable feature. For this purpose, details of the behavior of the wiper blade need to be ascertained. In this study, we present theoretical and experimental clarification of this behavior during reversals. Using simulation algorithms to consider exactly the effects of dynamic and static friction, we determined theoretical predictions for the vibrational response caused by friction and the response frequency and compared these results with experimental ones obtained from a mock-up incorporating an actual wiper blade. We introduce an analytical link model with two degrees of freedom and consider two types of states at the blade tip. In the stick and the slip states, static friction and dynamic friction, respectively, act on the blade tip. In the theoretical approach, the static friction is expressed by a set-valued function. The transition between the two states is repeated and an evaluation of an exact transition time leads to an accurate prediction of the behavior of the wiper system. In the analysis, the slack variable method is used to find the exact transition time. Assuming low blade speeds during reversal, a parameter study indicates that the blade tip transitions between slip and stick states and the frequency of the vibration caused by this transitions is close to the natural frequency of the neck of the wiper blade. The theoretical predictions are in good agreement with experimental observations.

An innovative experimental sequence on electromagnetic induction and eddy currents based on video analysis and cheap data acquisition

NASA Astrophysics Data System (ADS)

Bonanno, A.; Bozzo, G.; Sapia, P.

2017-11-01

In this work, we present a coherent sequence of experiments on electromagnetic (EM) induction and eddy currents, appropriate for university undergraduate students, based on a magnet falling through a drilled aluminum disk. The sequence, leveraging on the didactical interplay between the EM and mechanical aspects of the experiments, allows us to exploit the students’ awareness of mechanics to elicit their comprehension of EM phenomena. The proposed experiments feature two kinds of measurements: (i) kinematic measurements (performed by means of high-speed video analysis) give information on the system’s kinematics and, via appropriate numerical data processing, allow us to get dynamic information, in particular on energy dissipation; (ii) induced electromagnetic field (EMF) measurements (by using a homemade multi-coil sensor connected to a cheap data acquisition system) allow us to quantitatively determine the inductive effects of the moving magnet on its neighborhood. The comparison between experimental results and the predictions from an appropriate theoretical model (of the dissipative coupling between the moving magnet and the conducting disk) offers many educational hints on relevant topics related to EM induction, such as Maxwell’s displacement current, magnetic field flux variation, and the conceptual link between induced EMF and induced currents. Moreover, the didactical activity gives students the opportunity to be trained in video analysis, data acquisition and numerical data processing.

The Role of Prosocialness and Trust in the Consumption of Water as a Limited Resource.

PubMed

Cuadrado, Esther; Tabernero, Carmen; García, Rocío; Luque, Bárbara; Seibert, Jan

2017-01-01

This research analyzes the role of prosocialness and trust in the use of water as a limited resource under situations of competition or cooperation. For this purpose, 107 participants played the role of farmers and made decisions about irrigating their fields in the web-based multiplayer game Irrigania. Before the simulation exercise, participants' prosocialness and trust levels were evaluated and they were randomly assigned to an experimental condition (competition or cooperation). Repeated measures analysis, using the 10 fields and the experimental conditions as factors, showed that, in the cooperation condition, farmers and their villages used a less selfish strategy to cultivate their fields, which produced greater benefits. Under competition, benefits to farmers and their villages were reduced over time. Mediational analysis shows that the selfish irrigation strategy fully mediated the relationship between prosocialness and accumulated profits; prosocial individuals choose less selfish irrigation strategies and, in turn, accumulated more benefit. Moreover, moderation analysis shows that trust moderated the link between prosocialness and water use strategy by strengthening the negative effect of prosocialness on selection of selfish strategies. The implications of these results highlight the importance of promoting the necessary trust to develop prosocial strategies in collectives; therefore, the efficacy of interventions, such as the creation of cooperative educational contexts or organization of collective actions with groups affected by water scarcity, are discussed.

Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools.

PubMed

Sud, Manish; Fahy, Eoin; Cotter, Dawn; Azam, Kenan; Vadivelu, Ilango; Burant, Charles; Edison, Arthur; Fiehn, Oliver; Higashi, Richard; Nair, K Sreekumaran; Sumner, Susan; Subramaniam, Shankar

2016-01-04

The Metabolomics Workbench, available at www.metabolomicsworkbench.org, is a public repository for metabolomics metadata and experimental data spanning various species and experimental platforms, metabolite standards, metabolite structures, protocols, tutorials, and training material and other educational resources. It provides a computational platform to integrate, analyze, track, deposit and disseminate large volumes of heterogeneous data from a wide variety of metabolomics studies including mass spectrometry (MS) and nuclear magnetic resonance spectrometry (NMR) data spanning over 20 different species covering all the major taxonomic categories including humans and other mammals, plants, insects, invertebrates and microorganisms. Additionally, a number of protocols are provided for a range of metabolite classes, sample types, and both MS and NMR-based studies, along with a metabolite structure database. The metabolites characterized in the studies available on the Metabolomics Workbench are linked to chemical structures in the metabolite structure database to facilitate comparative analysis across studies. The Metabolomics Workbench, part of the data coordinating effort of the National Institute of Health (NIH) Common Fund's Metabolomics Program, provides data from the Common Fund's Metabolomics Resource Cores, metabolite standards, and analysis tools to the wider metabolomics community and seeks data depositions from metabolomics researchers across the world. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

A computational proposal for designing structured RNA pools for in vitro selection of RNAs.

PubMed

Kim, Namhee; Gan, Hin Hark; Schlick, Tamar

2007-04-01

Although in vitro selection technology is a versatile experimental tool for discovering novel synthetic RNA molecules, finding complex RNA molecules is difficult because most RNAs identified from random sequence pools are simple motifs, consistent with recent computational analysis of such sequence pools. Thus, enriching in vitro selection pools with complex structures could increase the probability of discovering novel RNAs. Here we develop an approach for engineering sequence pools that links RNA sequence space regions with corresponding structural distributions via a "mixing matrix" approach combined with a graph theory analysis. We define five classes of mixing matrices motivated by covariance mutations in RNA; these constructs define nucleotide transition rates and are applied to chosen starting sequences to yield specific nonrandom pools. We examine the coverage of sequence space as a function of the mixing matrix and starting sequence via clustering analysis. We show that, in contrast to random sequences, which are associated only with a local region of sequence space, our designed pools, including a structured pool for GTP aptamers, can target specific motifs. It follows that experimental synthesis of designed pools can benefit from using optimized starting sequences, mixing matrices, and pool fractions associated with each of our constructed pools as a guide. Automation of our approach could provide practical tools for pool design applications for in vitro selection of RNAs and related problems.

The Role of Prosocialness and Trust in the Consumption of Water as a Limited Resource

PubMed Central

Cuadrado, Esther; Tabernero, Carmen; García, Rocío; Luque, Bárbara; Seibert, Jan

2017-01-01

This research analyzes the role of prosocialness and trust in the use of water as a limited resource under situations of competition or cooperation. For this purpose, 107 participants played the role of farmers and made decisions about irrigating their fields in the web-based multiplayer game Irrigania. Before the simulation exercise, participants’ prosocialness and trust levels were evaluated and they were randomly assigned to an experimental condition (competition or cooperation). Repeated measures analysis, using the 10 fields and the experimental conditions as factors, showed that, in the cooperation condition, farmers and their villages used a less selfish strategy to cultivate their fields, which produced greater benefits. Under competition, benefits to farmers and their villages were reduced over time. Mediational analysis shows that the selfish irrigation strategy fully mediated the relationship between prosocialness and accumulated profits; prosocial individuals choose less selfish irrigation strategies and, in turn, accumulated more benefit. Moreover, moderation analysis shows that trust moderated the link between prosocialness and water use strategy by strengthening the negative effect of prosocialness on selection of selfish strategies. The implications of these results highlight the importance of promoting the necessary trust to develop prosocial strategies in collectives; therefore, the efficacy of interventions, such as the creation of cooperative educational contexts or organization of collective actions with groups affected by water scarcity, are discussed. PMID:28533760

Interactive system for geomagnetic data analysis

NASA Astrophysics Data System (ADS)

Solovev, Igor

2017-10-01

The paper suggests the methods for analyzing geomagnetic field variations, which are implemented in "Aurora" software system for complex analysis of geophysical parameters. The software system allows one to perform a detailed magnetic data analysis. The methods allow one to estimate the intensity of geomagnetic perturbations and to allocate increased geomagnetic activity periods. The software system is publicly available (http://aurorasa.ikir.ru:8580, http://www.ikir.ru:8280/lsaserver/MagneticPage.jsp). This research was supported by the Russian Science Foundation (Project No. 14-11-00194).

Nonequilibrium Chromosome Looping via Molecular Slip Links

NASA Astrophysics Data System (ADS)

Brackley, C. A.; Johnson, J.; Michieletto, D.; Morozov, A. N.; Nicodemi, M.; Cook, P. R.; Marenduzzo, D.

2017-09-01

We propose a model for the formation of chromatin loops based on the diffusive sliding of molecular slip links. These mimic the behavior of molecules like cohesin, which, along with the CTCF protein, stabilize loops which contribute to organizing the genome. By combining 3D Brownian dynamics simulations and 1D exactly solvable nonequilibrium models, we show that diffusive sliding is sufficient to account for the strong bias in favor of convergent CTCF-mediated chromosome loops observed experimentally. We also find that the diffusive motion of multiple slip links along chromatin is rectified by an intriguing ratchet effect that arises if slip links bind to the chromatin at a preferred "loading site." This emergent collective behavior favors the extrusion of loops which are much larger than the ones formed by single slip links.

Full-duplex bidirectional transmission of 10-Gb/s millimeter-wave QPSK signal in E-band optical wireless link.

PubMed

Fang, Yuan; Yu, Jianjun; Chi, Nan; Xiao, Jiangnan

2014-01-27

We experimentally demonstrated full-duplex bidirectional transmission of 10-Gb/s millimeter-wave (mm-wave) quadrature phase shift keying (QPSK) signal in E-band (71-76 GHz and 81-86 GHz) optical wireless link. Single-mode fibers (SMF) are connected at both sides of the antenna for uplink and downlink which realize 40-km SMF and 2-m wireless link for bidirectional transmission simultaneously. We utilized multi-level modulation format and coherent detection in such E-band optical wireless link for the first time. Mm-wave QPSK signal is generated by photonic technique to increase spectrum efficiency and received signal is coherently detected to improve receiver sensitivity. After the coherent detection, digital signal processing is utilized to compensate impairments of devices and transmission link.

Electronic Equalization of Multikilometer 10-Gb/s Multimode Fiber Links: Mode-Coupling Effects

NASA Astrophysics Data System (ADS)

Balemarthy, Kasyapa; Polley, Arup; Ralph, Stephen E.

2006-12-01

This paper investigates the ability of electronic equalization to compensate for modal dispersion in the presence of mode coupling in multimode fibers (MMFs) at 10 Gb/s. Using a new time-domain experimental method, mode coupling is quantified in MMF. These results, together with a comprehensive link model, allow to determine the impact of mode coupling on the performance of MMF. The equalizer performance on links from 300 m to 8 km is quantified with and without modal coupling. It is shown that the mode-coupling effects are influenced by the specific index profile and increase the equalizer penalty by as much as 1 dBo for 1-km links and 2.3 dBo for 2-km links when using a standard model of fiber profiles at 1310 nm.

Impact of observational incompleteness on the structural properties of protein interaction networks

NASA Astrophysics Data System (ADS)

Kuhnt, Mathias; Glauche, Ingmar; Greiner, Martin

2007-01-01

The observed structure of protein interaction networks is corrupted by many false positive/negative links. This observational incompleteness is abstracted as random link removal and a specific, experimentally motivated (spoke) link rearrangement. Their impact on the structural properties of gene-duplication-and-mutation network models is studied. For the degree distribution a curve collapse is found, showing no sensitive dependence on the link removal/rearrangement strengths and disallowing a quantitative extraction of model parameters. The spoke link rearrangement process moves other structural observables, like degree correlations, cluster coefficient and motif frequencies, closer to their counterparts extracted from the yeast data. This underlines the importance to take a precise modeling of the observational incompleteness into account when network structure models are to be quantitatively compared to data.

Hekate: Software Suite for the Mass Spectrometric Analysis and Three-Dimensional Visualization of Cross-Linked Protein Samples

PubMed Central

2013-01-01

Chemical cross-linking of proteins combined with mass spectrometry provides an attractive and novel method for the analysis of native protein structures and protein complexes. Analysis of the data however is complex. Only a small number of cross-linked peptides are produced during sample preparation and must be identified against a background of more abundant native peptides. To facilitate the search and identification of cross-linked peptides, we have developed a novel software suite, named Hekate. Hekate is a suite of tools that address the challenges involved in analyzing protein cross-linking experiments when combined with mass spectrometry. The software is an integrated pipeline for the automation of the data analysis workflow and provides a novel scoring system based on principles of linear peptide analysis. In addition, it provides a tool for the visualization of identified cross-links using three-dimensional models, which is particularly useful when combining chemical cross-linking with other structural techniques. Hekate was validated by the comparative analysis of cytochrome c (bovine heart) against previously reported data.1 Further validation was carried out on known structural elements of DNA polymerase III, the catalytic α-subunit of the Escherichia coli DNA replisome along with new insight into the previously uncharacterized C-terminal domain of the protein. PMID:24010795

Thermal tolerance in the keystone species Daphnia magna-a candidate gene and an outlier analysis approach.

PubMed

Jansen, M; Geerts, A N; Rago, A; Spanier, K I; Denis, C; De Meester, L; Orsini, L

2017-04-01

Changes in temperature have occurred throughout Earth's history. However, current warming trends exacerbated by human activities impose severe and rapid loss of biodiversity. Although understanding the mechanisms orchestrating organismal response to climate change is important, remarkably few studies document their role in nature. This is because only few systems enable the combined analysis of genetic and plastic responses to environmental change over long time spans. Here, we characterize genetic and plastic responses to temperature increase in the aquatic keystone grazer Daphnia magna combining a candidate gene and an outlier analysis approach. We capitalize on the short generation time of our species, facilitating experimental evolution, and the production of dormant eggs enabling the analysis of long-term response to environmental change through a resurrection ecology approach. We quantify plasticity in the expression of 35 candidate genes in D. magna populations resurrected from a lake that experienced changes in average temperature over the past century and from experimental populations differing in thermal tolerance isolated from a selection experiment. By measuring expression in multiple genotypes from each of these populations in control and heat treatments, we assess plastic responses to extreme temperature events. By measuring evolutionary changes in gene expression between warm- and cold-adapted populations, we assess evolutionary response to temperature changes. Evolutionary response to temperature increase is also assessed via an outlier analysis using EST-linked microsatellite loci. This study provides the first insights into the role of plasticity and genetic adaptation in orchestrating adaptive responses to environmental change in D. magna. © 2017 John Wiley & Sons Ltd.

NetGen: a novel network-based probabilistic generative model for gene set functional enrichment analysis.

PubMed

Sun, Duanchen; Liu, Yinliang; Zhang, Xiang-Sun; Wu, Ling-Yun

2017-09-21

High-throughput experimental techniques have been dramatically improved and widely applied in the past decades. However, biological interpretation of the high-throughput experimental results, such as differential expression gene sets derived from microarray or RNA-seq experiments, is still a challenging task. Gene Ontology (GO) is commonly used in the functional enrichment studies. The GO terms identified via current functional enrichment analysis tools often contain direct parent or descendant terms in the GO hierarchical structure. Highly redundant terms make users difficult to analyze the underlying biological processes. In this paper, a novel network-based probabilistic generative model, NetGen, was proposed to perform the functional enrichment analysis. An additional protein-protein interaction (PPI) network was explicitly used to assist the identification of significantly enriched GO terms. NetGen achieved a superior performance than the existing methods in the simulation studies. The effectiveness of NetGen was explored further on four real datasets. Notably, several GO terms which were not directly linked with the active gene list for each disease were identified. These terms were closely related to the corresponding diseases when accessed to the curated literatures. NetGen has been implemented in the R package CopTea publicly available at GitHub ( http://github.com/wulingyun/CopTea/ ). Our procedure leads to a more reasonable and interpretable result of the functional enrichment analysis. As a novel term combination-based functional enrichment analysis method, NetGen is complementary to current individual term-based methods, and can help to explore the underlying pathogenesis of complex diseases.

Vibration fatigue using modal decomposition

NASA Astrophysics Data System (ADS)

Mršnik, Matjaž; Slavič, Janko; Boltežar, Miha

2018-01-01

Vibration-fatigue analysis deals with the material fatigue of flexible structures operating close to natural frequencies. Based on the uniaxial stress response, calculated in the frequency domain, the high-cycle fatigue model using the S-N curve material data and the Palmgren-Miner hypothesis of damage accumulation is applied. The multiaxial criterion is used to obtain the equivalent uniaxial stress response followed by the spectral moment approach to the cycle-amplitude probability density estimation. The vibration-fatigue analysis relates the fatigue analysis in the frequency domain to the structural dynamics. However, once the stress response within a node is obtained, the physical model of the structure dictating that response is discarded and does not propagate through the fatigue-analysis procedure. The structural model can be used to evaluate how specific dynamic properties (e.g., damping, modal shapes) affect the damage intensity. A new approach based on modal decomposition is presented in this research that directly links the fatigue-damage intensity with the dynamic properties of the system. It thus offers a valuable insight into how different modes of vibration contribute to the total damage to the material. A numerical study was performed showing good agreement between results obtained using the newly presented approach with those obtained using the classical method, especially with regards to the distribution of damage intensity and critical point location. The presented approach also offers orders of magnitude faster calculation in comparison with the conventional procedure. Furthermore, it can be applied in a straightforward way to strain experimental modal analysis results, taking advantage of experimentally measured strains.

The mass-action law based algorithm for cost-effective approach for cancer drug discovery and development.

PubMed

Chou, Ting-Chao

2011-01-01

The mass-action law based system analysis via mathematical induction and deduction lead to the generalized theory and algorithm that allows computerized simulation of dose-effect dynamics with small size experiments using a small number of data points in vitro, in animals, and in humans. The median-effect equation of the mass-action law deduced from over 300 mechanism specific-equations has been shown to be the unified theory that serves as the common-link for complicated biomedical systems. After using the median-effect principle as the common denominator, its applications are mechanism-independent, drug unit-independent, and dynamic order-independent; and can be used generally for single drug analysis or for multiple drug combinations in constant-ratio or non-constant ratios. Since the "median" is the common link and universal reference point in biological systems, these general enabling lead to computerized quantitative bio-informatics for econo-green bio-research in broad disciplines. Specific applications of the theory, especially relevant to drug discovery, drug combination, and clinical trials, have been cited or illustrated in terms of algorithms, experimental design and computerized simulation for data analysis. Lessons learned from cancer research during the past fifty years provide a valuable opportunity to reflect, and to improve the conventional divergent approach and to introduce a new convergent avenue, based on the mass-action law principle, for the efficient cancer drug discovery and the low-cost drug development.

The mass-action law based algorithm for cost-effective approach for cancer drug discovery and development

PubMed Central

Chou, Ting-Chao

2011-01-01

The mass-action law based system analysis via mathematical induction and deduction lead to the generalized theory and algorithm that allows computerized simulation of dose-effect dynamics with small size experiments using a small number of data points in vitro, in animals, and in humans. The median-effect equation of the mass-action law deduced from over 300 mechanism specific-equations has been shown to be the unified theory that serves as the common-link for complicated biomedical systems. After using the median-effect principle as the common denominator, its applications are mechanism-independent, drug unit-independent, and dynamic order-independent; and can be used generally for single drug analysis or for multiple drug combinations in constant-ratio or non-constant ratios. Since the “median” is the common link and universal reference point in biological systems, these general enabling lead to computerized quantitative bio-informatics for econo-green bio-research in broad disciplines. Specific applications of the theory, especially relevant to drug discovery, drug combination, and clinical trials, have been cited or illustrated in terms of algorithms, experimental design and computerized simulation for data analysis. Lessons learned from cancer research during the past fifty years provide a valuable opportunity to reflect, and to improve the conventional divergent approach and to introduce a new convergent avenue, based on the mass-action law principle, for the efficient cancer drug discovery and the low-cost drug development. PMID:22016837

Channel CAT: A Tactical Link Analysis Tool

DTIC Science & Technology

1997-09-01

NAVAL POSTGRADUATE SCHOOL Monterey, California THESIS CHANNEL CAT : A TACTICAL LINK ANALYSIS TOOL by Michael Glenn Coleman September 1997 Thesis...REPORT TYPE AND DATES COVERED September 1997 Master’s Thesis 4. TITLE AND SUBTITLE CHANNEL CAT : A TACTICAL LINK ANALYSIS TOOL 5. FUNDING NUMBERS 6...tool, the Channel Capacity Analysis Tool (Channel CAT ), designed to provide an automated tool for the anlysis of design decisions in developing client

Influence of ionizing radiation on the mechanical properties of BisGMA/TEGDMA based experimental resin

NASA Astrophysics Data System (ADS)

LMP, Campos; Boaro, LC; LKG, Santos; Parra, DF; Lugão, AB

2015-10-01

Dental restorative composites are activated by visible light and the polymerization process, known as direct technique, is initiated by absorbing light in a specific wavelength range (450-500 nm). However this technique presented some disadvantages. If light is not inserted correctly, layers uncured can cause countless damage to restoration, especially with regard to mechanical properties. A clinical alternative used to reduce the shortcomings of direct application is the use of composite resins for indirect application. These composites are adaptations of resins prepared for direct use, with differences mainly in the healing process. Besides the traditional photoactivation, indirect application composites may be submitted to particular curing conditions, such as a slow curing rate, heating, vacuum, and inert-gas pressure leading to an oxygen-free environment. However few studies have been conducted on the process of post-curing by ionizing radiation at low doses. On this sense the purpose of this study was to evaluate possible interactions of ionizing radiation in the post-curing process of the experimental composites based on BisGMA/TEGDMA filled with silica Aerosil OX-50 silanized. Characterization of the experimental composites was performed by thermogravimetry analysis, infrared spectroscopy, elastic modulus and flexural strength. Statistical analysis of results was calculated by one-way ANOVA/Tukey's test. Cross-linking of the polymeric matrix caused by ionizing radiation, influenced the thermal stability of irradiated specimens. FTIR analysis showed that the ionizing radiation induced a post-cure reaction in the specimens. The irradiation dose influenced directly the mechanical properties that showed a strong positive correlation between flexural strength and irradiation and between modulus strength and irradiation.

A 10-Gbit/s EML link using detuned narrowband optical filtering.

PubMed

Ebrahimi, P; Jones, R; Wang, Y; Yan, L; Mader, T; Paniccia, M; Willner, A E; Paraschis, L

2007-08-20

In this paper, the effects of asymmetric narrowband optical filtering are investigated in a 10-Gbit/s optical communication link using integrated electro-absorption modulated lasers (EML). We investigate the effect of EML chirp on link performance as well as the optimal filter bandwidth and wavelength detuning. We show that both the phase response and the spectral narrowing of the filter will enable a longer distance transmission by interacting with the EML transient chirp and compensating for the fiber chromatic dispersion. Experimentally, an 8.75-GHz filter is shown to improve the link distance by 40 km from 65 to 105 km, when transmitting over standard single mode fiber.

Investigation and evaluation of shuttle/GPS navigation system

NASA Technical Reports Server (NTRS)

Nilsen, P. W.

1977-01-01

Iterative procedures were used to analyze the performance of two preliminary shuttle/GPS navigation system configurations: an early OFT experimental system and a more sophisticated system which consolidates several separate navigation functions thus permitting net cost savings from decreased shuttle avionics weight and power consumption, and from reduced ground data processing. The GPS system can provide on-orbit navigation accuracy an order of magnitude better than the baseline system, with very adequate link margins. The worst-case link margin is 4.3 dB. This link margin accounts for shuttle RF circuit losses which were minimized under the constraints of program schedule and environmental limitations. Implicit in the link analyses are the location trade-offs for preamplifiers and antennas.

Mass spectrometric analysis of O-linked oligosaccharides from various recombinant expression systems.

PubMed

Kenny, Diarmuid T; Gaunitz, Stefan; Hayes, Catherine A; Gustafsson, Anki; Sjöblom, Magnus; Holgersson, Jan; Karlsson, Niclas G

2013-01-01

Analysis of O-linked glycosylation is one of the main challenges during structural validation of recombinant glycoproteins. With methods available for N-linked glycosylation in regard to oligosaccharide analysis as well as glycopeptide mapping, there are still challenges for O-linked glycan analysis. Here, we present mass spectrometric methodology for O-linked oligosaccharides released by reductive β-elimination. Using LC-MS and LC-MS(2) with graphitized carbon columns, oligosaccharides are analyzed without derivatization. This approach provides a high-throughput method for screening during clonal selection, as well as product structure verification, without impairing sequencing ability. The protocols are exemplified by analysis of glycoproteins from mammalian cell cultures (CHO cells) as well as insect cells and yeast. The data shows that the method can be successfully applied to both neutral and acidic O-linked oligosaccharides, where sialic acid, hexuronic acid, and sulfate are common substituents. Further characterization of O-glycans can be achieved using permethylation. Permethylation of O-linked oligosaccharides followed by direct infusion into the mass spectrometer provide information about oligosaccharide composition, and subsequent MS (n) experiments can be carried out to elucidate oligosaccharide structure including linkage information and sequence.

Plant Rho-type (Rop) GTPase-dependent activation of receptor-like cytoplasmic kinases in vitro.

PubMed

Dorjgotov, Dulguun; Jurca, Manuela E; Fodor-Dunai, Csilla; Szucs, Attila; Otvös, Krisztina; Klement, Eva; Bíró, Judit; Fehér, Attila

2009-04-02

Plants have evolved distinct mechanisms to link Rho-type (Rop) GTPases to downstream signaling pathways as compared to other eukaryotes. Here, experimental data are provided that members of the Medicago, as well as Arabidopsis, receptor-like cytoplasmic kinase family (RLCK Class VI) were strongly and specifically activated by GTP-bound Rop GTPases in vitro. Deletion analysis indicated that the residues implicated in the interaction might be distributed on various parts of the kinases. Using a chimaeric Rop GTPase protein, the importance of the Rho-insert region in kinase activation could also be verified. These data strengthen the possibility that RLCKs may serve as Rop GTPase effectors in planta.

Navigator Accuracy Requirements for Prospective Motion Correction

PubMed Central

Maclaren, Julian; Speck, Oliver; Stucht, Daniel; Schulze, Peter; Hennig, Jürgen; Zaitsev, Maxim

2010-01-01

Prospective motion correction in MR imaging is becoming increasingly popular to prevent the image artefacts that result from subject motion. Navigator information is used to update the position of the imaging volume before every spin excitation so that lines of acquired k-space data are consistent. Errors in the navigator information, however, result in residual errors in each k-space line. This paper presents an analysis linking noise in the tracking system to the power of the resulting image artefacts. An expression is formulated for the required navigator accuracy based on the properties of the imaged object and the desired resolution. Analytical results are compared with computer simulations and experimental data. PMID:19918892

14 CFR 21.195 - Experimental certificates: Aircraft to be used for market surveys, sales demonstrations, and...

Code of Federal Regulations, 2010 CFR

2010-01-01

... used for market surveys, sales demonstrations, and customer crew training. 21.195 Section 21.195... be used for market surveys, sales demonstrations, and customer crew training. Link to an amendment... States may apply for an experimental certificate for an aircraft that is to be used for market surveys...

Samuel C.C. Ting, the J/psi Particle (Charm), and the Alpha Magnetic

Science.gov Websites

discoveries provided the first experimental evidence for a fourth quark, "charm," that theoretical Reader , December 1965 Experimental Observation of a Heavy Particle J; Physical Review Letters, Vol. 33 -- Eyewitness, PBS Top Some links on this page may take you to non-federal websites. Their policies may differ

Experimental Study of Short-Term Training in Social Cognition in Pre-Schoolers

ERIC Educational Resources Information Center

Houssa, Marine; Nader-Grosbois, Nathalie; Jacobs, Emilie

2014-01-01

Using an experimental approach, our study examined the differentiated effects on pre-schoolers' social cognition of two short-term social information processing (SIP) and Theory of Mind (ToM) training sessions dealing with emotions and beliefs. The links between ToM, SIP, and social adjustment or externalizing behavior were examined. 47…

Beneficial impact of exercise and obesity interventions on erectile function and its risk factors.

PubMed

Hannan, Johanna L; Maio, M Tina; Komolova, Marina; Adams, Michael A

2009-03-01

Erectile dysfunction (ED) is a multifaceted disease involving cardiovascular, metabolic, and hormonal factors and affects over 100 million men worldwide. ED has been shown to be a harbinger of underlying cardiovascular diseases (CVD), as there are common risk factors (aging, hypertension, obesity) and mechanistic basis. To provide an update on clinical and experimental evidence regarding the impact of lifestyle modifications, such as exercise and diet, with respect to changes in erectile function. Published evidence regarding the impact of aging, hypertension, and obesity on ED and CVD, as well as new experimental data linking obesity and diminished erectile responses. We reviewed the literature regarding common risk factors of ED and CVD, particularly involving obesity, as well as performed new analysis on the findings of other experimental studies involving diet and exercise interventions. Physical inactivity negatively impacts on erectile function, and experimental and clinical exercise interventions have been shown to improve sexual responses and overall cardiovascular health. Mediterranean-style diets and a reduction in caloric intake have been found to improve erectile function in men with the aspects of the metabolic syndrome. In addition, both clinical and experimental studies have confirmed that combining the two interventions provides additional benefit to erectile function, likely via reduced metabolic disturbances (e.g., inflammatory markers, insulin resistance), decreased visceral adipose tissue, and improvement in vascular function (e.g., increased endothelial function). Lifestyle modifications provide significant benefits to vascular health and erectile function in a population that is increasingly aged and more obese.

Cross-Linking Studies of Lysozyme Nucleation

NASA Technical Reports Server (NTRS)

Forsythe, Elizabeth; Pusey, Marc

2000-01-01

Tetragonal chicken egg white crystals consist of 4(sub 3) helices running in alternating directions, the helix rows having a two fold symmetry with each other. The unit cell consists of one complete tetrameric turn from each of two adjacent helices (an octamer). PBC analysis indicates that the helix intermolecular bonds are the strongest in the crystal, therefore likely formed first. AFM analysis of the (110) surface shows only complete helices, no half steps or bisected helices being found, while AFM line scans to measure the growth step increments show that they are multiples of the 4(sub 3) helix tetramer dimensions. This supports our thesis that the growth units are in fact multiples of the four molecule 4(sub 3) helix unit, the "average" growth unit size for the (110) face being an octamer (two turns about the helix) and the (101) growth unit averaging about the size of a hexamer. In an effort to better understand the species involved in the crystal nucleation and growth process, we have initiated an experimental program to study the species formed in solution compared to what is found in the crystal through covalent cross-linking studies. These experiments use the heterobifunctional cross-linking agent aminoethyl-4-azidonitroanaline (AEANA). An aliphatic amine at one end is covalently attached to the protein by a carbodiimide-mediated reaction, and a photo reactive group at the other can be used to initiate crosslinking. Modifications to the parent structure can be used to alter the distance between the two reactive groups and thus the cross-linking agents "reach". In practice, the cross-linking agent is first coupled to the asp101 side chain through the amine group. Asp101 lies within the active site cleft, and previous work with fluorescent probes had shown that derivatives at this site still crystallize in the tetragonal space group. This was also found to be the case with the AEANA derivative, which gave red tetragonal crystals. The protein now has a reactive group that can be photoactivated at a specific point in the nucleation or crystal growth process to "capture" protein molecules bound within reach of the crosslinking agent. If those bound protein molecules have a defined geometric relationship with the capturing molecule, such as would be found in a crystal, then the photoreacted cross-linking site should be consistent. Random protein interactions, typical of an amorphous precipitate or interaction, would show a random cross-linking reaction. The results of these and other experiments will be presented.

Economic Opportunities and Gender Differences in Human Capital: Experimental Evidence for India. NBER Working Paper No. 16021

ERIC Educational Resources Information Center

Jensen, Robert T.

2010-01-01

Gender differences in health and education are a concern for a number of developing countries. While standard theory predicts human capital should respond to market returns, social norms (e.g., disapproval of women working outside the home) may weaken or even sever this link for girls. Though many studies have examined the link between women's…

Individual differences in implicit learning abilities and impulsive behavior in the context of Internet addiction and Internet Gaming Disorder under the consideration of gender.

PubMed

Sariyska, Rayna; Lachmann, Bernd; Markett, Sebastian; Reuter, Martin; Montag, Christian

2017-06-01

•Higher Internet addiction scores were linked to deficient implicit learning.•This association was found in two independent groups of male (excessive) gamers.•Online Gaming addiction was linked to higher risk-taking in healthy participants.•Implicit learning and risk-taking were assessed, using an experimental task.

Using link analysis to explore the impact of the physical environment on pharmacist tasks.

PubMed

Lester, Corey A; Chui, Michelle A

2016-01-01

National community pharmacy organizations have been redesigning pharmacies to better facilitate direct patient care. However, evidence suggests that changing the physical layout of a pharmacy prior to understanding how the environment impacts pharmacists' work may not achieve the desired benefits. This study describes an objective method to understanding how the physical layout of the pharmacy may affect how pharmacists perform tasks. Link analysis is a systems engineering method used to describe the influence of the physical environment on task completion. This study used a secondary data set of field notes collected from 9 h of direct observation in one mass-merchandise community pharmacy in the U.S. State, Wisconsin. A node is an individual location in the environment. A link is the movement between two nodes. Tasks were inventoried and task themes identified. The mean, minimum, and maximum number of links needed to complete each task were then determined and used to construct a link table. A link diagram is a graphical display showing the links in conjunction with the physical layout of the pharmacy. A total of 92 unique tasks were identified resulting in 221 links. Tasks were sorted into five themes: patient care activities, insurance issues, verifying prescriptions, filling prescriptions, and other. Insurance issues required the greatest number of links with a mean of 4.75. Verifying prescriptions and performing patient care were the most commonly performed tasks with 36 and 30 unique task occurrences, respectively. Link analysis provides an objective method for identifying how a pharmacist interacts with the physical environment to complete tasks. This method provides designers with useful information to target interventions to improve the effectiveness of pharmacist work. Analysis beyond link analysis should be considered for large scale system redesign. Copyright © 2015 Elsevier Inc. All rights reserved.

Compact resonator on leather for nonradiative inductive power transfer and far-field data links

NASA Astrophysics Data System (ADS)

Monti, G.; Corchia, L.; De Benedetto, E.; Tarricone, L.

2016-06-01

In this paper, a wearable resonator suitable to be used for both power and data transmission is presented. The basic element is a complementary split ring resonator that has been optimized to operate both as a dipole-like antenna at 2.45 GHz and as the receiver of a resonant energy link operating at 915 MHz when coupled with an identical external resonator connected to a power source. Experimental data referring to a prototype fabricated by using a conductive adhesive fabric on a leather substrate are reported and discussed. With regard to the wireless resonant energy link (WREL), it is demonstrated that at 915 MHz, the RF-to-RF power transfer efficiency of the link is approximately 78.1%. As for the performance obtained when the resonator is used as an antenna, a gain of approximately -0.43 dB was obtained. Additionally, the performance of the proposed link when connected to a Power Management Unit (PMU) that converts the radio frequency (RF) energy received by the wearable resonator into DC energy that can be directly used for recharging a thin-film battery was also investigated. Experimental tests were performed in order to evaluate both the total efficiency of the wireless charger (i.e., the WREL link connected to the PMU) and the time necessary to recharge a THINERGY MEC201 battery. The obtained results demonstrate the feasibility of using the proposed WREL for implementing a battery charger; in particular, by providing an input power higher than 8 dBm, the time necessary to recharge the considered thin-film battery is shorter than 38 min.

LinkedOmics: analyzing multi-omics data within and across 32 cancer types.

PubMed

Vasaikar, Suhas V; Straub, Peter; Wang, Jing; Zhang, Bing

2018-01-04

The LinkedOmics database contains multi-omics data and clinical data for 32 cancer types and a total of 11 158 patients from The Cancer Genome Atlas (TCGA) project. It is also the first multi-omics database that integrates mass spectrometry (MS)-based global proteomics data generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) on selected TCGA tumor samples. In total, LinkedOmics has more than a billion data points. To allow comprehensive analysis of these data, we developed three analysis modules in the LinkedOmics web application. The LinkFinder module allows flexible exploration of associations between a molecular or clinical attribute of interest and all other attributes, providing the opportunity to analyze and visualize associations between billions of attribute pairs for each cancer cohort. The LinkCompare module enables easy comparison of the associations identified by LinkFinder, which is particularly useful in multi-omics and pan-cancer analyses. The LinkInterpreter module transforms identified associations into biological understanding through pathway and network analysis. Using five case studies, we demonstrate that LinkedOmics provides a unique platform for biologists and clinicians to access, analyze and compare cancer multi-omics data within and across tumor types. LinkedOmics is freely available at http://www.linkedomics.org. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Collision-induced dissociative chemical cross-linking reagents and methodology: Applications to protein structural characterization using tandem mass spectrometry analysis.

PubMed

Soderblom, Erik J; Goshe, Michael B

2006-12-01

Chemical cross-linking combined with mass spectrometry is a viable approach to study the low-resolution structure of protein and protein complexes. However, unambiguous identification of the residues involved in a cross-link remains analytically challenging. To enable a more effective analysis across various MS platforms, we have developed a novel set of collision-induced dissociative cross-linking reagents and methodology for chemical cross-linking experiments using tandem mass spectrometry (CID-CXL-MS/MS). These reagents incorporate a single gas-phase cleavable bond within their linker region that can be selectively fragmented within the in-source region of the mass spectrometer, enabling independent MS/MS analysis for each peptide. Initial design concepts were characterized using a synthesized cross-linked peptide complex. Following verification and subsequent optimization of cross-linked peptide complex dissociation, our reagents were applied to homodimeric glutathione S-transferase and monomeric bovine serum albumin. Cross-linked residues identified by our CID-CXL-MS/MS method were in agreement with published crystal structures and previous cross-linking studies using conventional approaches. Common LC/MS/MS acquisition approaches such as data-dependent acquisition experiments using ion trap mass spectrometers and product ion spectral analysis using SEQUEST were shown to be compatible with our CID-CXL-MS/MS reagents, obviating the requirement for high resolution and high mass accuracy measurements to identify both intra- and interpeptide cross-links.

Investigation into response characteristics of the chitosan gel artificial muscle

NASA Astrophysics Data System (ADS)

Zhao, Gang; Yang, Junjie; Wang, Yujian; Zhao, Honghao; Fu, Yu; Zhang, Guangli; Yu, Shuqin; Wu, Yuda; Wei, Chengye; Liu, Xuxiong; Wang, Zhijie

2018-01-01

Bionic artificial muscle made from chitosan gel is an emerging type of the ionic electro active polymer with advantages of large deformation, low cost and environmental protection etc, which leads to a research focus and wide application in the fields of bionic engineering and intelligence material recently. In this paper, effects and improvement mechanisms of the direct casting and genipin cross-linking processes on response speed properties of the chitosan gel artificial muscle (CGAM) were mainly studied. Based on in-depth analysis of the CGAM response mechanism, a platform was built for testing the response performance of the CGAM, then its equivalent circuit and mathematical models were also established. Furthermore, control experiments were carried out to test and analyze several performances of the CGAM on response speed, electrical conductivity, mechanical properties and microstructure with different control variables. The experimental results illustrated that the CGAM assembled by direct casting enabled its electric actuating membrane and non-metallic electrode membrane tightly attached together with low contact resistance, which dramatically promoted the electrical conductivity of the CGAM resulting in nearly doubled response speed. Besides, different concentrations of genipin were adopted to cross-link the CGAM actuating membranes, and then it was found that the response speed of the uncross-linked CGAM was fast in the initial stage, but as time increased, it declined rapidly with poor steadiness. While there was no obvious decrease over time on the response speed of the CGAM cross-linked with low genipin concentration. Namely, its stability was getting better and better. In addition, the response speed of the CGAM cross-linked with low concentration of genipin was roughly the same as uncross-linked CGAM, which was quicker than that of high concentration. In this work, its internal mechanisms, feasible assembly technique and green modification method were provided to further explore the practical applications significantly.

The Role of the NASA Global Hawk Link Module as an Information Nexus For Atmospheric Mapping Missions

NASA Technical Reports Server (NTRS)

Sullivan, D. V.

2015-01-01

The Link Module described in this paper was developed for the NASA Uninhabited Aerial System (UAS) Global Hawk Pacific Mission (GloPAC) Airborne Science Campaign; four flights of 30 hour duration, supporting the Aura Validation Experiment (AVE). It was used again during the Genesis and Rapid Intensification Processes (GRIP) experiment, a NASA Earth Science field experiment to better understand how tropical storms form and develop into major hurricanes. In these missions, the Link Module negotiated all communication over the high bandwidth Ku satellite link, archived all the science data from onboard experiments in a spatially enabled database, routed command and control of the instruments from the Global Hawk Operations Center, and re-transmitted select data sets directly to experimenters control and analysis systems. The availability of aggregated information from collections of sensors, and remote control capabilities, in real-time, is revolutionizing the way Airborne Science is being conducted. The Link Module NG now being flown in support of the NASA Earth Venture missions, the Hurricane and Severe Storm Sentinel (HS3) mission, and Airborne Tropical Tropopause Experiment (A TTREX) mission, has advanced data fusion technologies that are further advancing the Scientific productivity, flexibility and robustness of these systems. On-the-fly traffic shaping has been developed to allow the high definition video, used for critical flight control segments, to dynamically allocate variable bandwidth on demand. Historically, the Link Module evolved from the instrument and communication interface controller used by NASA's Pathfinder and Pathfinder plus solar powered UAS's in the late 1990' s. It later was expanded for use in the AIRDAS four channel scanner flown on the NASA Altus UAS, and then again to a module in the AMS twelve channel multispectral scanner flying on the NASA (Predator-b) Ikhana UAS. The current system is the answer to the challenges imposed by extremely long duration UASs, with on-board multi-instrument (>= 12) Sensor Webs.

Chromium (VI) ion adsorption by grafted cross-linked chitosan beads in aqueous solution - a mathematical and statistical modeling study.

PubMed

Igberase, E; Osifo, P; Ofomaja, A

2017-12-01

Chitosan outstanding qualities and efficient way of binding metal ions even to near zero concentration is the major reason for special attention. Modification of chitosan allows the polymer to be applied in numerous field of research. Depending on the modification techniques, chitosan possesses increased adsorption capacity. In this study chitosan beads (CS) were formulated from chitosan flakes, the beads were cross-linked with glutaraldehyde and thereafter grafted with ethyldiaminetetraacetic acid. The stability and amine concentration of the beads were determined. The chemical functionalities of the beads were obtained by Fourier transform infrared spectroscopy, X-ray diffraction and thermogravimetric analysis (TGA). However, in the adsorption studies with Cr(VI), the number of runs in the experiment was obtained by response surface methodology (RSM), and the maximum adsorption capacity (Q m ) from each run was determined from the Langmuir model. The results of the experiment showed that the non-modified beads were soluble at pH 1-4 and insoluble at pH 5, while the modified beads were insoluble at pH 1-6. The amine concentration of CS, CCS and grafted cross-linked chitosan beads (GCCS) were 4.4, 3.8 and 5.0 mmol/g, respectively. The point of zero charge (pH PZC ) of GCCS was found to be 4.4. The quadratic model was significant and adequate in describing the experimental data. The difference between experimental and predicted Q m was negligible. From the design matrix and results, increased Q m was achieved at pH 5, contact time 70 min, temperature 45°C, adsorbent dosage 5 g and initial concentration 70 mg/l. The desorption of the beads loaded with Cr(VI) was successful with 0.5 M HCl eluant and contact time of 180 min, leading to cost minimization.

Monitoring and Research of the Colorado River Ecosystem: When Is Enough Enough?

NASA Astrophysics Data System (ADS)

Schmidt, J. C.

2014-12-01

The Glen Canyon Dam Adaptive Management Program (GCDAMP) is a well-funded ( $10 million/yr.) river rehabilitation program with long-term monitoring and research focused on 400 km of the Colorado River in Glen, Marble, and Grand Canyons downstream from Lake Powell. More than 15 years of substantive science concerning hydrology, hydraulics, sediment transport, geomorphology, aquatic and fish ecology, riparian ecology, and socio-economics has yielded significant insights that guide experimental river management initiatives, such as a new protocol to annually release sediment-triggered controlled floods; administratively called the High Flow Experimental Protocol (HFEP). Implementation of the HFEP requires nearly real-time monitoring of sediment delivery from key sand producing tributaries, transport in and calculation of sand mass balance in segments of the Colorado River, and defined uncertainty of those processes and conditions (see: http://www.gcmrc.gov/). The HFEP aims to rebuild sandbars within the active channel, but many stakeholders remain focused on other aquatic ecosystem, riparian ecosystem, archaeological resources, or cultural values that are linked in complex ways to active channel conditions. Tension exists within the GCDAMP about how funding is allocated for innovative data collection, analysis, and publication strategies that allow implementation of the HFEP, and to also measure derivative resource conditions about which some stakeholders have concern. Monitoring and research initiatives that attempt to incorporate traditional cultural values also have high uncertainty when resource condition is linked with the simple implementation paradigm of the HFEP. Thus, the GCDAMP is faced with the complex challenge of allocating sufficient resources to monitor active channel processes and characteristics, resolve remaining scientific uncertainties, and develop new strategies for incorporating science insights into engineering and policy decisions, while also monitoring terrestrial resources supported by stakeholders but only indirectly linked with dam operations. The challenge of balancing these scientific and adaptive management objectives is substantial.

Spectral analysis of coniferous foliage and possible links to soil chemistry: are spectral chlorophyll indices related to forest floor dissolved organic C and N?

PubMed

Albrechtova, Jana; Seidl, Zdenek; Aitkenhead-Peterson, Jacqueline; Lhotáková, Zuzana; Rock, Barrett N; Alexander, Jess E; Malenovský, Zbynek; McDowell, William H

2008-10-15

Dissolved organic matter in soils can be predicted from forest floor C:N ratio, which in turn is related to foliar chemistry. Little is known about the linkages between foliar constituents such as chlorophylls, lignin, and cellulose and the concentrations of water-extractable forest floor dissolved organic carbon and dissolved organic nitrogen. Lignin and cellulose are not mobile in foliage and thus may be indicative of growing conditions during prior years, while chlorophylls respond more rapidly to the current physiological status of a tree and reflect nutrient availability. The aim of this study was to examine potential links among spectral foliar data, and the organic C and N of forest soils. Two coniferous species (red spruce and balsam fir) were studied in the White Mountains of New Hampshire, USA. Six trees of each species were sampled at 5 watersheds (2 in the Hubbard Brook Experimental Forest, 3 in the Bartlett Experimental Forest). We hypothesized that in a coniferous forest, chemistry of old foliage would better predict the chemical composition of the forest floor litter layer than younger foliage, which is the more physiologically active and the most likely to be captured by remote sensing of the canopy. Contrary to our expectations, chlorophyll concentration of young needles proved to be most tightly linked to soil properties, in particular water-extractable dissolved organic carbon. Spectral indices related to the chlorophyll content of needles could be used to predict variation in forest floor dissolved organic carbon and dissolved organic nitrogen. Strong correlations were found between optical spectral indices based on chlorophyll absorption and forest floor dissolved organic carbon, with higher foliage chlorophyll content corresponding to lower forest floor dissolved organic carbon. The mechanisms behind these correlations are uncertain and need further investigation. However, the direction of the linkage from soil to tree via nutrient availability is hypothesized based on negative correlations found between foliar N and forest floor dissolved organic carbon.

Experimental evaluation of open-loop UpLink Power Control using ACTS

NASA Technical Reports Server (NTRS)

Dissanayake, Asoka

1995-01-01

The present investigation deals with the implementation of open-loop up-link power control using a beacon signal in the down-link frequency band as the control parameter. A power control system was developed and tested using the ACTS satellite. ACTS carries beacon signals in both up- and down-link bands with which the relationship between the up- and down-link fading can be established. A power controlled carrier was transmitted to the ACTS satellite from a NASA operated ground station and the transponded signal was received at COMSAT Laboratories using a terminal that was routinely used to monitor the two ACTS beacon signals. The experiment ran for a period of approximately six months and the collected data were used to evaluate the performance of the power control system. A brief review of propagation factors involved in estimating the up-link fade using a beacon signal in the down-link band are presented. The power controller design and the experiment configuration are discussed. Results of the experiment are discussed.

Media Reports of Links between MMR and Autism: A Discourse Analysis

ERIC Educational Resources Information Center

O'Dell, Lindsay; Brownlow, Charlotte

2005-01-01

This paper details an analysis of BBC reporting of the proposed links between MMR and autism. The study aimed to identify main issues arising from the media reports into the link between MMR and the development of autism, and how these contribute to common understandings about people with autism. The study employed a form of discourse analysis to…

Real-time observations of lithium battery reactions-operando neutron diffraction analysis during practical operation.

PubMed

Taminato, Sou; Yonemura, Masao; Shiotani, Shinya; Kamiyama, Takashi; Torii, Shuki; Nagao, Miki; Ishikawa, Yoshihisa; Mori, Kazuhiro; Fukunaga, Toshiharu; Onodera, Yohei; Naka, Takahiro; Morishima, Makoto; Ukyo, Yoshio; Adipranoto, Dyah Sulistyanintyas; Arai, Hajime; Uchimoto, Yoshiharu; Ogumi, Zempachi; Suzuki, Kota; Hirayama, Masaaki; Kanno, Ryoji

2016-06-30

Among the energy storage devices for applications in electric vehicles and stationary uses, lithium batteries typically deliver high performance. However, there is still a missing link between the engineering developments for large-scale batteries and the fundamental science of each battery component. Elucidating reaction mechanisms under practical operation is crucial for future battery technology. Here, we report an operando diffraction technique that uses high-intensity neutrons to detect reactions in non-equilibrium states driven by high-current operation in commercial 18650 cells. The experimental system comprising a time-of-flight diffractometer with automated Rietveld analysis was developed to collect and analyse diffraction data produced by sequential charge and discharge processes. Furthermore, observations under high current drain revealed inhomogeneous reactions, a structural relaxation after discharge, and a shift in the lithium concentration ranges with cycling in the electrode matrix. The technique provides valuable information required for the development of advanced batteries.

A didactic proposal about Rutherford backscattering spectrometry with theoretic, experimental, simulation and application activities

NASA Astrophysics Data System (ADS)

Corni, Federico; Michelini, Marisa

2018-01-01

Rutherford backscattering spectrometry is a nuclear analysis technique widely used for materials science investigation. Despite the strict technical requirements to perform the data acquisition, the interpretation of a spectrum is within the reach of general physics students. The main phenomena occurring during a collision between helium ions—with energy of a few MeV—and matter are: elastic nuclear collision, elastic scattering, and, in the case of non-surface collision, ion stopping. To interpret these phenomena, we use classical physics models: material point elastic collision, unscreened Coulomb scattering, and inelastic energy loss of ions with electrons, respectively. We present the educational proposal for Rutherford backscattering spectrometry, within the framework of the model of educational reconstruction, following a rationale that links basic physics concepts with quantities for spectra analysis. This contribution offers the opportunity to design didactic specific interventions suitable for undergraduate and secondary school students.

Building quantitative, three-dimensional atlases of gene expression and morphology at cellular resolution.

PubMed

Knowles, David W; Biggin, Mark D

2013-01-01

Animals comprise dynamic three-dimensional arrays of cells that express gene products in intricate spatial and temporal patterns that determine cellular differentiation and morphogenesis. A rigorous understanding of these developmental processes requires automated methods that quantitatively record and analyze complex morphologies and their associated patterns of gene expression at cellular resolution. Here we summarize light microscopy-based approaches to establish permanent, quantitative datasets-atlases-that record this information. We focus on experiments that capture data for whole embryos or large areas of tissue in three dimensions, often at multiple time points. We compare and contrast the advantages and limitations of different methods and highlight some of the discoveries made. We emphasize the need for interdisciplinary collaborations and integrated experimental pipelines that link sample preparation, image acquisition, image analysis, database design, visualization, and quantitative analysis. Copyright © 2013 Wiley Periodicals, Inc.

A spectroscopic and computational study of Al(III) complexes in sodium cryolite melts: ionic composition in a wide range of cryolite ratios.

PubMed

Nazmutdinov, Renat R; Zinkicheva, Tamara T; Vassiliev, Sergey Yu; Glukhov, Dmitri V; Tsirlina, Galina A; Probst, Michael

2010-04-01

The structure of sodium cryolite melts was studied using Raman spectroscopy and quantum chemical calculations performed at the density functional theory level. The existence of bridged forms in the melts was argued first from the analysis of experimental Raman spectra. In the quantum chemical modelling emphasis was put on the construction of potential energy surfaces describing the formation/dissociation of certain complex species. Effects of the ionic environment were found to play a crucial role in the energetics of model processes. The structure of the simplest possible polymeric forms involving two Al centres linked through F atoms ("dimers") was thoroughly investigated. The calculated equilibrium constants and model Raman spectra yield additional evidence in favour of the dimers. This agrees with a self-consistent analysis of a series of Raman spectra for a wide range of the melt composition. Copyright 2010. Published by Elsevier B.V.

Motif enrichment tool.

PubMed

Blatti, Charles; Sinha, Saurabh

2014-07-01

The Motif Enrichment Tool (MET) provides an online interface that enables users to find major transcriptional regulators of their gene sets of interest. MET searches the appropriate regulatory region around each gene and identifies which transcription factor DNA-binding specificities (motifs) are statistically overrepresented. Motif enrichment analysis is currently available for many metazoan species including human, mouse, fruit fly, planaria and flowering plants. MET also leverages high-throughput experimental data such as ChIP-seq and DNase-seq from ENCODE and ModENCODE to identify the regulatory targets of a transcription factor with greater precision. The results from MET are produced in real time and are linked to a genome browser for easy follow-up analysis. Use of the web tool is free and open to all, and there is no login requirement. ADDRESS: http://veda.cs.uiuc.edu/MET/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Real-time observations of lithium battery reactions—operando neutron diffraction analysis during practical operation

PubMed Central

Taminato, Sou; Yonemura, Masao; Shiotani, Shinya; Kamiyama, Takashi; Torii, Shuki; Nagao, Miki; Ishikawa, Yoshihisa; Mori, Kazuhiro; Fukunaga, Toshiharu; Onodera, Yohei; Naka, Takahiro; Morishima, Makoto; Ukyo, Yoshio; Adipranoto, Dyah Sulistyanintyas; Arai, Hajime; Uchimoto, Yoshiharu; Ogumi, Zempachi; Suzuki, Kota; Hirayama, Masaaki; Kanno, Ryoji

2016-01-01

Among the energy storage devices for applications in electric vehicles and stationary uses, lithium batteries typically deliver high performance. However, there is still a missing link between the engineering developments for large-scale batteries and the fundamental science of each battery component. Elucidating reaction mechanisms under practical operation is crucial for future battery technology. Here, we report an operando diffraction technique that uses high-intensity neutrons to detect reactions in non-equilibrium states driven by high-current operation in commercial 18650 cells. The experimental system comprising a time-of-flight diffractometer with automated Rietveld analysis was developed to collect and analyse diffraction data produced by sequential charge and discharge processes. Furthermore, observations under high current drain revealed inhomogeneous reactions, a structural relaxation after discharge, and a shift in the lithium concentration ranges with cycling in the electrode matrix. The technique provides valuable information required for the development of advanced batteries. PMID:27357605

Calibration and analysis of genome-based models for microbial ecology.

PubMed

Louca, Stilianos; Doebeli, Michael

2015-10-16

Microbial ecosystem modeling is complicated by the large number of unknown parameters and the lack of appropriate calibration tools. Here we present a novel computational framework for modeling microbial ecosystems, which combines genome-based model construction with statistical analysis and calibration to experimental data. Using this framework, we examined the dynamics of a community of Escherichia coli strains that emerged in laboratory evolution experiments, during which an ancestral strain diversified into two coexisting ecotypes. We constructed a microbial community model comprising the ancestral and the evolved strains, which we calibrated using separate monoculture experiments. Simulations reproduced the successional dynamics in the evolution experiments, and pathway activation patterns observed in microarray transcript profiles. Our approach yielded detailed insights into the metabolic processes that drove bacterial diversification, involving acetate cross-feeding and competition for organic carbon and oxygen. Our framework provides a missing link towards a data-driven mechanistic microbial ecology.

Computational knowledge integration in biopharmaceutical research.

PubMed

Ficenec, David; Osborne, Mark; Pradines, Joel; Richards, Dan; Felciano, Ramon; Cho, Raymond J; Chen, Richard O; Liefeld, Ted; Owen, James; Ruttenberg, Alan; Reich, Christian; Horvath, Joseph; Clark, Tim

2003-09-01

An initiative to increase biopharmaceutical research productivity by capturing, sharing and computationally integrating proprietary scientific discoveries with public knowledge is described. This initiative involves both organisational process change and multiple interoperating software systems. The software components rely on mutually supporting integration techniques. These include a richly structured ontology, statistical analysis of experimental data against stored conclusions, natural language processing of public literature, secure document repositories with lightweight metadata, web services integration, enterprise web portals and relational databases. This approach has already begun to increase scientific productivity in our enterprise by creating an organisational memory (OM) of internal research findings, accessible on the web. Through bringing together these components it has also been possible to construct a very large and expanding repository of biological pathway information linked to this repository of findings which is extremely useful in analysis of DNA microarray data. This repository, in turn, enables our research paradigm to be shifted towards more comprehensive systems-based understandings of drug action.

Flow Structures within a Helicopter Rotor Hub Wake

NASA Astrophysics Data System (ADS)

Elbing, Brian; Reich, David; Schmitz, Sven

2015-11-01

A scaled model of a notional helicopter rotor hub was tested in the 48'' Garfield Thomas Water Tunnel at the Applied Research Laboratory Penn State. The measurement suite included total hub drag and wake velocity measurements (LDV, PIV, stereo-PIV) at three downstream locations. The main objective was to understand the spatiotemporal evolution of the unsteady wake between the rotor hub and the nominal location of the empennage (tail). Initial analysis of the data revealed prominent two- and four-per-revolution fluid structures linked to geometric hub features persisting into the wake far-field. In addition, a six-per-revolution fluid structure was observed in the far-field, which is unexpected due to the lack of any hub feature with the corresponding symmetry. This suggests a nonlinear interaction is occurring within the wake to generate these structures. This presentation will provide an overview of the experimental data and analysis with particular emphasis on these six-per-revolution structures.

Structural and conformational determinants of macrocycle cell permeability.

PubMed

Over, Björn; Matsson, Pär; Tyrchan, Christian; Artursson, Per; Doak, Bradley C; Foley, Michael A; Hilgendorf, Constanze; Johnston, Stephen E; Lee, Maurice D; Lewis, Richard J; McCarren, Patrick; Muncipinto, Giovanni; Norinder, Ulf; Perry, Matthew W D; Duvall, Jeremy R; Kihlberg, Jan

2016-12-01

Macrocycles are of increasing interest as chemical probes and drugs for intractable targets like protein-protein interactions, but the determinants of their cell permeability and oral absorption are poorly understood. To enable rational design of cell-permeable macrocycles, we generated an extensive data set under consistent experimental conditions for more than 200 non-peptidic, de novo-designed macrocycles from the Broad Institute's diversity-oriented screening collection. This revealed how specific functional groups, substituents and molecular properties impact cell permeability. Analysis of energy-minimized structures for stereo- and regioisomeric sets provided fundamental insight into how dynamic, intramolecular interactions in the 3D conformations of macrocycles may be linked to physicochemical properties and permeability. Combined use of quantitative structure-permeability modeling and the procedure for conformational analysis now, for the first time, provides chemists with a rational approach to design cell-permeable non-peptidic macrocycles with potential for oral absorption.

Efficient moving target analysis for inverse synthetic aperture radar images via joint speeded-up robust features and regular moment

NASA Astrophysics Data System (ADS)

Yang, Hongxin; Su, Fulin

2018-01-01

We propose a moving target analysis algorithm using speeded-up robust features (SURF) and regular moment in inverse synthetic aperture radar (ISAR) image sequences. In our study, we first extract interest points from ISAR image sequences by SURF. Different from traditional feature point extraction methods, SURF-based feature points are invariant to scattering intensity, target rotation, and image size. Then, we employ a bilateral feature registering model to match these feature points. The feature registering scheme can not only search the isotropic feature points to link the image sequences but also reduce the error matching pairs. After that, the target centroid is detected by regular moment. Consequently, a cost function based on correlation coefficient is adopted to analyze the motion information. Experimental results based on simulated and real data validate the effectiveness and practicability of the proposed method.

Solidarity.com: is there a link between offline behavior and online donations?

PubMed

Eller, Anja

2008-10-01

Solidarity websites, such as The Hunger Site, where people can donate food at no financial cost and minimal effort, have become immensely popular and effective since 1999. These new forms of philanthropy are characterized by wide participation and direct assistance and feedback. The present longitudinal, quasi-experimental study aimed to examine whether online solidarity can be predicted by offline contact with, attitudes about, and altruistic behavior tendencies towards a population in need, asylum seekers. Fifty-seven university students completed two surveys, separated by 1 year. Prior to T1, only 9% of respondents had visited solidarity websites, while at T2 47% reported clicking. Multiple regression analysis showed that T2 visits to solidarity websites were (negatively) predicted by T1 quantity of contact, and marginally, by T1 general evaluation of asylum seekers. These long-term, offline-to-online effects are intriguing, although there were no effects of offline contact quality and altruistic behavior tendencies. Future research should further investigate the causal direction between offline and online behavior and the factors that might influence the link between offline and online attitudes and behavior.

Controlled manipulation of elastomers with radiation: Insights from multiquantum nuclear-magnetic-resonance data and mechanical measurements

NASA Astrophysics Data System (ADS)

Maiti, A.; Weisgraber, T.; Dinh, L. N.; Gee, R. H.; Wilson, T.; Chinn, S.; Maxwell, R. S.

2011-03-01

Filled and cross-linked elastomeric rubbers are versatile network materials with a multitude of applications ranging from artificial organs and biomedical devices to cushions, coatings, adhesives, interconnects, and seismic-isolation, thermal, and electrical barriers. External factors such as mechanical stress, temperature fluctuations, or radiation are known to create chemical changes in such materials that can directly affect the molecular weight distribution (MWD) of the polymer between cross-links and alter the structural and mechanical properties. From a materials science point of view it is highly desirable to understand, affect, and manipulate such property changes in a controlled manner. Unfortunately, that has not yet been possible due to the lack of experimental characterization of such networks under controlled environments. In this work we expose a known rubber material to controlled dosages of γ radiation and utilize a newly developed multiquantum nuclear-magnetic-resonance technique to characterize the MWD as a function of radiation. We show that such data along with mechanical stress-strain measurements are amenable to accurate analysis by simple network models and yield important insights into radiation-induced molecular-level processes.

A defined role for multiple Fanconi anemia gene products in DNA-damage-associated ubiquitination.

PubMed

Tan, Winnie; Deans, Andrew J

2017-06-01

Fanconi anemia (FA) is an inherited blood disorder that causes bone marrow failure and high predisposition to cancers. The FA pathway guards the cell's genome stability by orchestrating the repair of interstrand cross-linking during the S phase of the cell cycle, preventing the chromosomal instability that is a key event in bone marrow failure syndrome. Central to the FA pathway is loss of monoubiquitinated forms of the Fanconi proteins FANCI and FANCD2, a process that is normally mediated by a "core complex" of seven other Fanconi proteins. Each protein, when mutated, can cause FA. The FA core-complex-catalyzed reaction is critical for signaling DNA cross-link damage such as that induced by chemotherapies. Here, we present a perspective on the current understanding of FANCI and FANCD2 monoubiquitination-mediated DNA repair. Our recent biochemical reconstitution of the monoubiquitination (and deubiquitination) reactions creates a paradigm for understanding FA. Further biochemical analysis will create new opportunities to address the leukemic phenotype of FA patients. Copyright © 2017 ISEH - International Society for Experimental Hematology. Published by Elsevier Inc. All rights reserved.

OntoPop: An Ontology Population System for the Semantic Web

NASA Astrophysics Data System (ADS)

Thongkrau, Theerayut; Lalitrojwong, Pattarachai

The development of ontology at the instance level requires the extraction of the terms defining the instances from various data sources. These instances then are linked to the concepts of the ontology, and relationships are created between these instances for the next step. However, before establishing links among data, ontology engineers must classify terms or instances from a web document into an ontology concept. The tool for help ontology engineer in this task is called ontology population. The present research is not suitable for ontology development applications, such as long time processing or analyzing large or noisy data sets. OntoPop system introduces a methodology to solve these problems, which comprises two parts. First, we select meaningful features from syntactic relations, which can produce more significant features than any other method. Second, we differentiate feature meaning and reduce noise based on latent semantic analysis. Experimental evaluation demonstrates that the OntoPop works well, significantly out-performing the accuracy of 49.64%, a learning accuracy of 76.93%, and executes time of 5.46 second/instance.

Identification of the transcriptional regulators by expression profiling infected with hepatitis B virus.

PubMed

Chai, Xiaoqiang; Han, Yanan; Yang, Jian; Zhao, Xianxian; Liu, Yewang; Hou, Xugang; Tang, Yiheng; Zhao, Shirong; Li, Xiao

2016-02-01

The molecular pathogenesis of infection by hepatitis B virus with human is extremely complex and heterogeneous. To date the molecular information is not clearly defined despite intensive research efforts. Thus, studies aimed at transcription and regulation during virus infection or combined researches of those already known to be beneficial are needed. With the purpose of identifying the transcriptional regulators related to infection of hepatitis B virus in gene level, the gene expression profiles from some normal individuals and hepatitis B patients were analyzed in our study. In this work, the differential expressed genes were selected primarily. The several genes among those were validated in an independent set by qRT-PCR. Then the differentially co-expression analysis was conducted to identify differentially co-expressed links and differential co-expressed genes. Next, the analysis of the regulatory impact factors was performed through mapping the links and regulatory data. In order to give a further insight to these regulators, the co-expression gene modules were identified using a threshold-based hierarchical clustering method. Incidentally, the construction of the regulatory network was generated using the computer software. A total of 137,284 differentially co-expressed links and 780 differential co-expressed genes were identified. These co-expressed genes were significantly enriched inflammatory response. The results of regulatory impact factors revealed several crucial regulators related to hepatocellular carcinoma and other high-rank regulators. Meanwhile, more than one hundred co-expression gene modules were identified using clustering method. In our study, some important transcriptional regulators were identified using a computational method, which may enhance the understanding of disease mechanisms and lead to an improved treatment of hepatitis B. However, further experimental studies are required to confirm these findings. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Automated Assignment of MS/MS Cleavable Cross-Links in Protein 3D-Structure Analysis

NASA Astrophysics Data System (ADS)

Götze, Michael; Pettelkau, Jens; Fritzsche, Romy; Ihling, Christian H.; Schäfer, Mathias; Sinz, Andrea

2015-01-01

CID-MS/MS cleavable cross-linkers hold an enormous potential for an automated analysis of cross-linked products, which is essential for conducting structural proteomics studies. The created characteristic fragment ion patterns can easily be used for an automated assignment and discrimination of cross-linked products. To date, there are only a few software solutions available that make use of these properties, but none allows for an automated analysis of cleavable cross-linked products. The MeroX software fills this gap and presents a powerful tool for protein 3D-structure analysis in combination with MS/MS cleavable cross-linkers. We show that MeroX allows an automatic screening of characteristic fragment ions, considering static and variable peptide modifications, and effectively scores different types of cross-links. No manual input is required for a correct assignment of cross-links and false discovery rates are calculated. The self-explanatory graphical user interface of MeroX provides easy access for an automated cross-link search platform that is compatible with commonly used data file formats, enabling analysis of data originating from different instruments. The combination of an MS/MS cleavable cross-linker with a dedicated software tool for data analysis provides an automated workflow for 3D-structure analysis of proteins. MeroX is available at www.StavroX.com .

Orbital-angular-momentum-multiplexed free-space optical communication link using transmitter lenses.

PubMed

Li, Long; Xie, Guodong; Ren, Yongxiong; Ahmed, Nisar; Huang, Hao; Zhao, Zhe; Liao, Peicheng; Lavery, Martin P J; Yan, Yan; Bao, ChangJing; Wang, Zhe; Willner, Asher J; Ashrafi, Nima; Ashrafi, Solyman; Tur, Moshe; Willner, Alan E

2016-03-10

In this paper, we explore the potential benefits and limitations of using transmitter lenses in an orbital-angular-momentum (OAM)-multiplexed free-space optical (FSO) communication link. Both simulation and experimental results indicate that within certain transmission distances, using lenses at the transmitter to focus OAM beams could reduce power loss in OAM-based FSO links and that this improvement might be more significant for higher-order OAM beams. Moreover, the use of transmitter lenses could enhance system tolerance to angular error between transmitter and receiver, but they might degrade tolerance to lateral displacement.

Lethality to leukemia cell lines of DNA interstrand cross-links generated by Cloretazine derived alkylating species

PubMed Central

Penketh, Philip G.; Baumann, Raymond P.; Ishiguro, Kimiko; Shyam, Krishnamurthy; Seow, Helen A.; Sartorelli, Alan C.

2010-01-01

Cloretazine [1, 2-bis(methylsulfonyl)-1-(2-chloroethyl)-2-[(methylamino)carbonyl]-hydrazine; VNP40101M; 101M] is a relatively new prodrug with activity in elderly acute myelogenous leukemia patients. Its therapeutic action is due largely to the production of 1-(3-cytosinyl),2-(1-guanyl)ethane cross-links (G-C ethane cross-links) in DNA. The number of cross-links produced in three experimental leukemia lines (L1210, U937 and HL-60) were fewer than 10 per genome at their respective LC50 concentrations. Only 1 in approximately 20,000 90CE molecules produce a cross-link in the AGT (O6-alkylguanine-DNA alkyltransferase) negative L1210 and U937 cell lines and 1 in 400,000 in the AGT positive HL-60 cell line. PMID:18479747

Novel α-L-arabinofuranosidase from Cellulomonas fimi ATCC 484 and its substrate-specificity analysis with the aid of computer.

PubMed

Yang, Ying; Zhang, Lujia; Guo, Mingrong; Sun, Jiaqi; Matsukawa, Shingo; Xie, Jingli; Wei, Dongzhi

2015-04-15

In the process of gene mining for novel α-L-arabinofuranosidases (AFs), the gene Celf_3321 from Cellulomonas fimi ATCC 484 encodes an AF, termed as AbfCelf, with potent activity, 19.4 U/mg under the optimum condition, pH 6.0 and 40 °C. AbfCelf can hydrolyze α-1,5-linked oligosaccharides, sugar beet arabinan, linear 1,5-α-arabinan, and wheat flour arabinoxylan, which is partly different from some previously well-characterized GH 51 AFs. The traditional substrate-specificity analysis for AFs is labor-consuming and money costing, because the substrates include over 30 kinds of various 4-nitrophenol (PNP)-glycosides, oligosaccharides, and polysaccharides. Hence, a preliminary structure and mechanism based method was applied for substrate-specificity analysis. The binding energy (ΔG, kcal/mol) obtained by docking suggested the reaction possibility and coincided with the experimental results. AbfA crystal 1QW9 was used to test the rationality of docking method in simulating the interaction between enzyme and substrate, as well the credibility of the substrate-specificity analysis method in silico.

A Missing Link in Suggestibility Research: What Is Known About the Behavior of Field Interviewers in Unstructured Interviews With Young Children?

ERIC Educational Resources Information Center

Gilstrap, Livia L.

2004-01-01

Despite suggestibility researchers' focus on adult behaviors that distort children's reports, whether behaviors examined in experimental work are used in the field is unknown. The current study presents a mutually exclusive and exhaustive hierarchical coding system that reflects interview questioning behaviors of concern in experimental work. The…

Role of disulfide cross-linking of mutant SOD1 in the formation of inclusion-body-like structures.

PubMed

Roberts, Brittany L T; Patel, Kinaree; Brown, Hilda H; Borchelt, David R

2012-01-01

Pathologic aggregates of superoxide dismutase 1 (SOD1) harboring mutations linked to familial amyotrophic lateral sclerosis (fALS) have been shown to contain aberrant intermolecular disulfide cross-links. In prior studies, we observed that intermolecular bonding was not necessary in the formation of detergent- insoluble SOD1 complexes by mutant SOD1, but we were unable to assess whether this type of bonding may be important for pathologic inclusion formation. In the present study, we visually assess the formation of large inclusions by fusing mutant SOD1 to yellow fluorescent protein (YFP). Experimental constructs possessing mutations at all cysteine residues in SOD1 (sites 6, 57, 111, and 146 to F,S,Y,R or G,S,Y,R, respectively) were shown to maintain a high propensity of inclusion formation despite the inability to form disulfide cross-links. Interestingly, although aggregates form when all cysteines were mutated, double mutants of the ALS mutation C6G with an experimental mutation C111S exhibited low aggregation propensity. Overall, this study is an extension of previous work demonstrating that cysteine residues in mutant SOD1 play a role in modulating aggregation and that intermolecular disulfide bonds are not required to produce large intracellular inclusion-like structures.

Does footprint depth correlate with foot motion and pressure?

PubMed Central

Bates, K. T.; Savage, R.; Pataky, T. C.; Morse, S. A.; Webster, E.; Falkingham, P. L.; Ren, L.; Qian, Z.; Collins, D.; Bennett, M. R.; McClymont, J.; Crompton, R. H.

2013-01-01

Footprints are the most direct source of evidence about locomotor biomechanics in extinct vertebrates. One of the principal suppositions underpinning biomechanical inferences is that footprint geometry correlates with dynamic foot pressure, which, in turn, is linked with overall limb motion of the trackmaker. In this study, we perform the first quantitative test of this long-standing assumption, using topological statistical analysis of plantar pressures and experimental and computer-simulated footprints. In computer-simulated footprints, the relative distribution of depth differed from the distribution of both peak and pressure impulse in all simulations. Analysis of footprint samples with common loading inputs and similar depths reveals that only shallow footprints lack significant topological differences between depth and pressure distributions. Topological comparison of plantar pressures and experimental beach footprints demonstrates that geometry is highly dependent on overall print depth; deeper footprints are characterized by greater relative forefoot, and particularly toe, depth than shallow footprints. The highlighted difference between ‘shallow’ and ‘deep’ footprints clearly emphasizes the need to understand variation in foot mechanics across different degrees of substrate compliance. Overall, our results indicate that extreme caution is required when applying the ‘depth equals pressure’ paradigm to hominin footprints, and by extension, those of other extant and extinct tetrapods. PMID:23516064

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

DOE PAGES

King, Zachary A.; Lu, Justin; Drager, Andreas; ...

2015-10-17

In this study, genome-scale metabolic models are mathematically structured knowledge bases that can be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can generate and test hypotheses when integrated with experimental data. To maximize the value of these models, centralized repositories of high-quality models must be established, models must adhere to established standards and model components must be linked to relevant databases. Tools for model visualization further enhance their utility. To meet these needs, we present BiGG Models (http://bigg.ucsd.edu), a completely redesigned Biochemical, Genetic and Genomic knowledge base. BiGG Models contains more than 75 high-quality, manually-curated genome-scalemore » metabolic models. On the website, users can browse, search and visualize models. BiGG Models connects genome-scale models to genome annotations and external databases. Reaction and metabolite identifiers have been standardized across models to conform to community standards and enable rapid comparison across models. Furthermore, BiGG Models provides a comprehensive application programming interface for accessing BiGG Models with modeling and analysis tools. As a resource for highly curated, standardized and accessible models of metabolism, BiGG Models will facilitate diverse systems biology studies and support knowledge-based analysis of diverse experimental data.« less

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

PubMed Central

King, Zachary A.; Lu, Justin; Dräger, Andreas; Miller, Philip; Federowicz, Stephen; Lerman, Joshua A.; Ebrahim, Ali; Palsson, Bernhard O.; Lewis, Nathan E.

2016-01-01

Genome-scale metabolic models are mathematically-structured knowledge bases that can be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can generate and test hypotheses when integrated with experimental data. To maximize the value of these models, centralized repositories of high-quality models must be established, models must adhere to established standards and model components must be linked to relevant databases. Tools for model visualization further enhance their utility. To meet these needs, we present BiGG Models (http://bigg.ucsd.edu), a completely redesigned Biochemical, Genetic and Genomic knowledge base. BiGG Models contains more than 75 high-quality, manually-curated genome-scale metabolic models. On the website, users can browse, search and visualize models. BiGG Models connects genome-scale models to genome annotations and external databases. Reaction and metabolite identifiers have been standardized across models to conform to community standards and enable rapid comparison across models. Furthermore, BiGG Models provides a comprehensive application programming interface for accessing BiGG Models with modeling and analysis tools. As a resource for highly curated, standardized and accessible models of metabolism, BiGG Models will facilitate diverse systems biology studies and support knowledge-based analysis of diverse experimental data. PMID:26476456

Refractivity variations and propagation at Ultra High Frequency

NASA Astrophysics Data System (ADS)

Alam, I.; Najam-Ul-Islam, M.; Mujahid, U.; Shah, S. A. A.; Ul Haq, Rizwan

Present framework is established to deal with the refractivity variations normally affected the radio waves propagation at different frequencies, ranges and different environments. To deal such kind of effects, many researchers proposed several methodologies. One method is to use the parameters from meteorology to investigate these effects of variations in refractivity on propagation. These variations are region specific and we have selected a region of one kilometer height over the English Channel. We have constructed different modified refractivity profiles based on the local meteorological data. We have recorded more than 48 million received signal strength from a communication links of 50 km operating at 2015 MHz in the Ultra High Frequency band giving path loss between transmitting and receiving stations of the experimental setup. We have used parabolic wave equation method to simulate an hourly value of signal strength and compared the obtained simulated loss to the experimental loss. The analysis is made to compute refractivity distribution of standard (STD) and ITU (International Telecommunication Union) refractivity profiles for various evaporation ducts. It is found that a standard refractivity profile is better than the ITU refractivity profiles for the region at 2015 MHz. Further, it is inferred from the analysis of results that 10 m evaporation duct height is the dominant among all evaporation duct heights considered in the research.

Workshop on High-Field NMR and Biological Applications

NASA Astrophysics Data System (ADS)

Scientists at the Pacific Northwest Laboratory have been working toward the establishment of a new Molecular Science Research Center (MSRC). The primary scientific thrust of this new research center is in the areas of theoretical chemistry, chemical dynamics, surface and interfacial science, and studies on the structure and interactions of biological macromolecules. The MSRC will provide important new capabilities for studies on the structure of biological macromolecules. The MSRC program includes several types of advanced spectroscopic techniques for molecular structure analysis, and a theory and modeling laboratory for molecular mechanics/dynamics calculations and graphics. It is the goal to closely integrate experimental and theoretical studies on macromolecular structure, and to join these research efforts with those of the molecular biological programs to provide new insights into the structure/function relationships of biological macromolecules. One of the areas of structural biology on which initial efforts in the MSRC will be focused is the application of high field, 2-D NMR to the study of biological macromolecules. First, there is interest in obtaining 3-D structural information on large proteins and oligonucleotides. Second, one of the primary objectives is to closely link theoretical approaches to molecular structure analysis with the results obtained in experimental research using NMR and other spectroscopies.

The influence of simulator input conditions on the wear of total knee replacements: An experimental and computational study

PubMed Central

Brockett, Claire L; Abdelgaied, Abdellatif; Haythornthwaite, Tony; Hardaker, Catherine; Fisher, John; Jennings, Louise M

2016-01-01

Advancements in knee replacement design, material and sterilisation processes have provided improved clinical results. However, surface wear of the polyethylene leading to osteolysis is still considered the longer-term risk factor. Experimental wear simulation is an established method for evaluating the wear performance of total joint replacements. The aim of this study was to investigate the influence of simulation input conditions, specifically input kinematic magnitudes, waveforms and directions of motion and position of the femoral centre of rotation, on the wear performance of a fixed-bearing total knee replacement through a combined experimental and computational approach. Studies were completed using conventional and moderately cross-linked polyethylene to determine whether the influence of these simulation input conditions varied with material. The position of the femoral centre of rotation and the input kinematics were shown to have a significant influence on the wear rates. Similar trends were shown for both the conventional and moderately cross-linked polyethylene materials, although lower wear rates were found for the moderately cross-linked polyethylene due to the higher level of cross-linking. The most important factor influencing the wear was the position of the relative contact point at the femoral component and tibial insert interface. This was dependent on the combination of input displacement magnitudes, waveforms, direction of motion and femoral centre of rotation. This study provides further evidence that in order to study variables such as design and material in total knee replacement, it is important to carefully control knee simulation conditions. This can be more effectively achieved through the use of displacement control simulation. PMID:27160561

An experimental, theoretical and event-driven computational study of narrow vibrofluidised granular materials

NASA Astrophysics Data System (ADS)

Thornton, Anthony; Windows-Yule, Kit; Parker, David; Luding, Stefan

2017-06-01

We review simulations, experiments and a theoretical treatment of vertically vibrated granular media. The systems considered are confined in narrow quasi-two-dimensional and quasi-one-dimensional (column) geometries, where the vertical extension of the container is much larger than one or both horizontal lengths. The additional geometric constraint present in the column setup frustrates the convection state that is normally observed in wider geometries. We start by showing that the Event Driven (ED) simulation method is able to accurately reproduce the previously experimentally determined phase-diagram for vibrofludised granular materials. We then review two papers that used ED simulations to study narrow quasi-one-dimensional systems revealing a new phenomenon: collective oscillations of the grains with a characteristic frequency that is much lower than the frequency of energy injection. Theoretical work was then undertaken that is able to accurately predict the frequency of such an oscillation and Positron Emission Particle Tracking (PEPT) experiments were undertaken to provide the first experimental evidence of this new phenomenon. Finally, we briefly discuss ongoing work to create an open-source version of this ED via its integration in the existing open-source package MercuryDPM (http://MercuryDPM.org); which has many advanced features that are not found in other codes.

Purification and characterization of a novel polysaccharide-peptide complex from Clinacanthus nutans Lindau leaves.

PubMed

Huang, Danmin; Li, Yunhong; Cui, Fengjie; Chen, Jun; Sun, Jiamin

2016-02-10

A novel polysaccharide-peptide complex CNP-1-2 with molecular weight of 9.17 × 10(4) Da was obtained from Clinacanthus nutans Lindau leaves by hot water extraction, ethanol precipitation, and purification with Superdex 200 and DEAE-Sepharose Fast Flow column chromatography. CNP-1-2 exhibited the highest growth inhibitory effect on human gastric cancer cells SGC-7901 with inhibition ratio of 92.34% and stimulated activation of macrophages with NO secretion level of 47.53 μmol/L among the polysaccharide fractions. CNP-1-2 comprised approximately 87.25% carbohydrate and 9.37% protein. Monosaccharide analysis suggested that CNP-1-2 was composed of L-rhamnose, l-arabinose, D-mannose, D-glucose and D-galactose with a molar ratio of 1.30:1.00:2.56:4.95:5.09. Methylation analysis, FT-IR, and (1)H NMR spectroscopy analysis revealed that CNP-1-2 might have a backbone consisting of 1,4-linked Glcp, 1,3-linked Glcp, 1,3-linked Manp, 1,4-linked Galp, 1,2,6-linked Galp and 1,2,6-linked Galp. Its side chain might be composed of 1-linked Araf, 1,6-linked Galp and 1-linked Rhap residues. AFM (atomic force micrograph) analysis revealed that CNP-1-2 had the molecular aggregation along with branched and entangled structure. Copyright © 2015 Elsevier Ltd. All rights reserved.

Computational advances towards linking BOLD and behavior.

PubMed

Serences, John T; Saproo, Sameer

2012-03-01

Traditionally, fMRI studies have focused on analyzing the mean response amplitude within a cortical area. However, the mean response is blind to many important patterns of cortical modulation, which severely limits the formulation and evaluation of linking hypotheses between neural activity, BOLD responses, and behavior. More recently, multivariate pattern classification analysis (MVPA) has been applied to fMRI data to evaluate the information content of spatially distributed activation patterns. This approach has been remarkably successful at detecting the presence of specific information in targeted brain regions, and provides an extremely flexible means of extracting that information without a precise generative model for the underlying neural activity. However, this flexibility comes at a cost: since MVPA relies on pooling information across voxels that are selective for many different stimulus attributes, it is difficult to infer how specific sub-sets of tuned neurons are modulated by an experimental manipulation. In contrast, recently developed encoding models can produce more precise estimates of feature-selective tuning functions, and can support the creation of explicit linking hypotheses between neural activity and behavior. Although these encoding models depend on strong - and often untested - assumptions about the response properties of underlying neural generators, they also provide a unique opportunity to evaluate population-level computational theories of perception and cognition that have previously been difficult to assess using either single-unit recording or conventional neuroimaging techniques. Copyright © 2011. Published by Elsevier Ltd.

Quantitative structure-activity relationship analysis of substituted arylazo pyridone dyes in photocatalytic system: Experimental and theoretical study.

PubMed

Dostanić, J; Lončarević, D; Zlatar, M; Vlahović, F; Jovanović, D M

2016-10-05

A series of arylazo pyridone dyes was synthesized by changing the type of the substituent group in the diazo moiety, ranging from strong electron-donating to strong electron-withdrawing groups. The structural and electronic properties of the investigated dyes was calculated at the M062X/6-31+G(d,p) level of theory. The observed good linear correlations between atomic charges and Hammett σp constants provided a basis to discuss the transmission of electronic substituent effects through a dye framework. The reactivity of synthesized dyes was tested through their decolorization efficiency in TiO2 photocatalytic system (Degussa P-25). Quantitative structure-activity relationship analysis revealed a strong correlation between reactivity of investigated dyes and Hammett substituent constants. The reaction was facilitated by electron-withdrawing groups, and retarded by electron-donating ones. Quantum mechanical calculations was used in order to describe the mechanism of the photocatalytic oxidation reactions of investigated dyes and interpret their reactivities within the framework of the Density Functional Theory (DFT). According to DFT based reactivity descriptors, i.e. Fukui functions and local softness, the active site moves from azo nitrogen atom linked to benzene ring to pyridone carbon atom linked to azo bond, going from dyes with electron-donating groups to dyes with electron-withdrawing groups. Copyright © 2016 Elsevier B.V. All rights reserved.

The NIF LinkOut broker: a web resource to facilitate federated data integration using NCBI identifiers.

PubMed

Marenco, Luis; Ascoli, Giorgio A; Martone, Maryann E; Shepherd, Gordon M; Miller, Perry L

2008-09-01

This paper describes the NIF LinkOut Broker (NLB) that has been built as part of the Neuroscience Information Framework (NIF) project. The NLB is designed to coordinate the assembly of links to neuroscience information items (e.g., experimental data, knowledge bases, and software tools) that are (1) accessible via the Web, and (2) related to entries in the National Center for Biotechnology Information's (NCBI's) Entrez system. The NLB collects these links from each resource and passes them to the NCBI which incorporates them into its Entrez LinkOut service. In this way, an Entrez user looking at a specific Entrez entry can LinkOut directly to related neuroscience information. The information stored in the NLB can also be utilized in other ways. A second approach, which is operational on a pilot basis, is for the NLB Web server to create dynamically its own Web page of LinkOut links for each NCBI identifier in the NLB database. This approach can allow other resources (in addition to the NCBI Entrez) to LinkOut to related neuroscience information. The paper describes the current NLB system and discusses certain design issues that arose during its implementation.

The NIF LinkOut Broker: A Web Resource to Facilitate Federated Data Integration using NCBI Identifiers

PubMed Central

Ascoli, Giorgio A.; Martone, Maryann E.; Shepherd, Gordon M.; Miller, Perry L.

2009-01-01

This paper describes the NIF LinkOut Broker (NLB) that has been built as part of the Neuroscience Information Framework (NIF) project. The NLB is designed to coordinate the assembly of links to neuroscience information items (e.g., experimental data, knowledge bases, and software tools) that are (1) accessible via the Web, and (2) related to entries in the National Center for Biotechnology Information’s (NCBI’s) Entrez system. The NLB collects these links from each resource and passes them to the NCBI which incorporates them into its Entrez LinkOut service. In this way, an Entrez user looking at a specific Entrez entry can LinkOut directly to related neuroscience information. The information stored in the NLB can also be utilized in other ways. A second approach, which is operational on a pilot basis, is for the NLB Web server to create dynamically its own Web page of LinkOut links for each NCBI identifier in the NLB database. This approach can allow other resources (in addition to the NCBI Entrez) to LinkOut to related neuroscience information. The paper describes the current NLB system and discusses certain design issues that arose during its implementation. PMID:18975149

Crosstalk mitigation using pilot assisted least square algorithm in OFDM-carrying orbital angular momentum multiplexed free-space-optical communication links.

PubMed

Sun, Tengfen; Liu, Minwen; Li, Yingchun; Wang, Min

2017-10-16

In this paper, we experimentally investigate the performance of crosstalk mitigation for 16-ary quadrature amplitude modulation orthogonal frequency division multiplexing (16QAM-OFDM) signals carrying orbital angular momentum (OAM) multiplexed free-space-optical communication (FSO) links using the pilot assisted Least Square (LS) algorithm. At the demodulating spatial light modulators (SLMs), we launch the distorted phase holograms which have the information of atmospheric turbulence obeying the modified Hill spectrum. And crosstalk can be introduced by these holograms with the experimental verification. The pilot assisted LS algorithm can efficiently improve the quality of system performance, the points of constellations get closer to the reference points and around two orders of magnitude improvement of bit-error rate (BER) is obtained.

A novel multilayer model for missing link prediction and future link forecasting in dynamic complex networks

NASA Astrophysics Data System (ADS)

Yasami, Yasser; Safaei, Farshad

2018-02-01

The traditional complex network theory is particularly focused on network models in which all network constituents are dealt with equivalently, while fail to consider the supplementary information related to the dynamic properties of the network interactions. This is a main constraint leading to incorrect descriptions of some real-world phenomena or incomplete capturing the details of certain real-life problems. To cope with the problem, this paper addresses the multilayer aspects of dynamic complex networks by analyzing the properties of intrinsically multilayered co-authorship networks, DBLP and Astro Physics, and presenting a novel multilayer model of dynamic complex networks. The model examines the layers evolution (layers birth/death process and lifetime) throughout the network evolution. Particularly, this paper models the evolution of each node's membership in different layers by an Infinite Factorial Hidden Markov Model considering feature cascade, and thereby formulates the link generation process for intra-layer and inter-layer links. Although adjacency matrixes are useful to describe the traditional single-layer networks, such a representation is not sufficient to describe and analyze the multilayer dynamic networks. This paper also extends a generalized mathematical infrastructure to address the problems issued by multilayer complex networks. The model inference is performed using some Markov Chain Monte Carlo sampling strategies, given synthetic and real complex networks data. Experimental results indicate a tremendous improvement in the performance of the proposed multilayer model in terms of sensitivity, specificity, positive and negative predictive values, positive and negative likelihood ratios, F1-score, Matthews correlation coefficient, and accuracy for two important applications of missing link prediction and future link forecasting. The experimental results also indicate the strong predictivepower of the proposed model for the application of cascade prediction in terms of accuracy.

New Markov-Shannon Entropy models to assess connectivity quality in complex networks: from molecular to cellular pathway, Parasite-Host, Neural, Industry, and Legal-Social networks.

PubMed

Riera-Fernández, Pablo; Munteanu, Cristian R; Escobar, Manuel; Prado-Prado, Francisco; Martín-Romalde, Raquel; Pereira, David; Villalba, Karen; Duardo-Sánchez, Aliuska; González-Díaz, Humberto

2012-01-21

Graph and Complex Network theory is expanding its application to different levels of matter organization such as molecular, biological, technological, and social networks. A network is a set of items, usually called nodes, with connections between them, which are called links or edges. There are many different experimental and/or theoretical methods to assign node-node links depending on the type of network we want to construct. Unfortunately, the use of a method for experimental reevaluation of the entire network is very expensive in terms of time and resources; thus the development of cheaper theoretical methods is of major importance. In addition, different methods to link nodes in the same type of network are not totally accurate in such a way that they do not always coincide. In this sense, the development of computational methods useful to evaluate connectivity quality in complex networks (a posteriori of network assemble) is a goal of major interest. In this work, we report for the first time a new method to calculate numerical quality scores S(L(ij)) for network links L(ij) (connectivity) based on the Markov-Shannon Entropy indices of order k-th (θ(k)) for network nodes. The algorithm may be summarized as follows: (i) first, the θ(k)(j) values are calculated for all j-th nodes in a complex network already constructed; (ii) A Linear Discriminant Analysis (LDA) is used to seek a linear equation that discriminates connected or linked (L(ij)=1) pairs of nodes experimentally confirmed from non-linked ones (L(ij)=0); (iii) the new model is validated with external series of pairs of nodes; (iv) the equation obtained is used to re-evaluate the connectivity quality of the network, connecting/disconnecting nodes based on the quality scores calculated with the new connectivity function. This method was used to study different types of large networks. The linear models obtained produced the following results in terms of overall accuracy for network reconstruction: Metabolic networks (72.3%), Parasite-Host networks (93.3%), CoCoMac brain cortex co-activation network (89.6%), NW Spain fasciolosis spreading network (97.2%), Spanish financial law network (89.9%) and World trade network for Intelligent & Active Food Packaging (92.8%). In order to seek these models, we studied an average of 55,388 pairs of nodes in each model and a total of 332,326 pairs of nodes in all models. Finally, this method was used to solve a more complicated problem. A model was developed to score the connectivity quality in the Drug-Target network of US FDA approved drugs. In this last model the θ(k) values were calculated for three types of molecular networks representing different levels of organization: drug molecular graphs (atom-atom bonds), protein residue networks (amino acid interactions), and drug-target network (compound-protein binding). The overall accuracy of this model was 76.3%. This work opens a new door to the computational reevaluation of network connectivity quality (collation) for complex systems in molecular, biomedical, technological, and legal-social sciences as well as in world trade and industry. Copyright © 2011 Elsevier Ltd. All rights reserved.

A Multiscale Virtual Fabrication and Lattice Modeling Approach for the Fatigue Performance Prediction of Asphalt Concrete

NASA Astrophysics Data System (ADS)

Dehghan Banadaki, Arash

Predicting the ultimate performance of asphalt concrete under realistic loading conditions is the main key to developing better-performing materials, designing long-lasting pavements, and performing reliable lifecycle analysis for pavements. The fatigue performance of asphalt concrete depends on the mechanical properties of the constituent materials, namely asphalt binder and aggregate. This dependent link between performance and mechanical properties is extremely complex, and experimental techniques often are used to try to characterize the performance of hot mix asphalt. However, given the seemingly uncountable number of mixture designs and loading conditions, it is simply not economical to try to understand and characterize the material behavior solely by experimentation. It is well known that analytical and computational modeling methods can be combined with experimental techniques to reduce the costs associated with understanding and characterizing the mechanical behavior of the constituent materials. This study aims to develop a multiscale micromechanical lattice-based model to predict cracking in asphalt concrete using component material properties. The proposed algorithm, while capturing different phenomena for different scales, also minimizes the need for laboratory experiments. The developed methodology builds on a previously developed lattice model and the viscoelastic continuum damage model to link the component material properties to the mixture fatigue performance. The resulting lattice model is applied to predict the dynamic modulus mastercurves for different scales. A framework for capturing the so-called structuralization effects is introduced that significantly improves the accuracy of the modulus prediction. Furthermore, air voids are added to the model to help capture this important micromechanical feature that affects the fatigue performance of asphalt concrete as well as the modulus value. The effects of rate dependency are captured by implementing the viscoelastic fracture criterion. In the end, an efficient cyclic loading framework is developed to evaluate the damage accumulation in the material that is caused by long-sustained cyclic loads.

Transient Modulations of Neural Responses to Heartbeats Covary with Bodily Self-Consciousness.

PubMed

Park, Hyeong-Dong; Bernasconi, Fosco; Bello-Ruiz, Javier; Pfeiffer, Christian; Salomon, Roy; Blanke, Olaf

2016-08-10

Recent research has investigated self-consciousness associated with the multisensory processing of bodily signals (e.g., somatosensory, visual, vestibular signals), a notion referred to as bodily self-consciousness, and these studies have shown that the manipulation of bodily inputs induces changes in bodily self-consciousness such as self-identification. Another line of research has highlighted the importance of signals from the inside of the body (e.g., visceral signals) and proposed that neural representations of internal bodily signals underlie self-consciousness, which to date has been based on philosophical inquiry, clinical case studies, and behavioral studies. Here, we investigated the relationship of bodily self-consciousness with the neural processing of internal bodily signals. By combining electrical neuroimaging, analysis of peripheral physiological signals, and virtual reality technology in humans, we show that transient modulations of neural responses to heartbeats in the posterior cingulate cortex covary with changes in bodily self-consciousness induced by the full-body illusion. Additional analyses excluded that measured basic cardiorespiratory parameters or interoceptive sensitivity traits could account for this finding. These neurophysiological data link experimentally the cortical mapping of the internal body to self-consciousness. What are the brain mechanisms of self-consciousness? Prominent views propose that the neural processing associated with signals from the internal organs (such as the heart and the lung) plays a critical role in self-consciousness. Although this hypothesis dates back to influential views in philosophy and psychology (e.g., William James), definitive experimental evidence supporting this idea is lacking despite its recent impact in neuroscience. In the present study, we show that posterior cingulate activities responding to heartbeat signals covary with changes in participants' conscious self-identification with a body that were manipulated experimentally using virtual reality technology. Our finding provides important neural evidence about the long-standing proposal that self-consciousness is linked to the cortical processing of internal bodily signals. Copyright © 2016 the authors 0270-6474/16/368453-08$15.00/0.

Model of rotary-actuated flexible beam with notch filter vibration suppression controller and torque feedforward load compensation controller

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

Bills, K.C.; Kress, R.L.; Kwon, D.S.

1994-12-31

This paper describes ORNL`s development of an environment for the simulation of robotic manipulators. Simulation includes the modeling of kinematics, dynamics, sensors, actuators, control systems, operators, and environments. Models will be used for manipulator design, proposal evaluation, control system design and analysis, graphical preview of proposed motions, safety system development, and training. Of particular interest is the development of models for robotic manipulators having at least one flexible link. As a first application, models have been developed for the Pacific Northwest Laboratory`s Flexible Beam Test Bed (PNL FBTB), which is a 1-Degree-of-Freedom, flexible arm with a hydraulic base actuator. ORNLmore » transferred control algorithms developed for the PNL FBTB to controlling IGRIP models. A robust notch filter is running in IGRIP controlling a full dynamics model of the PNL test bed. Model results provide a reasonable match to the experimental results (quantitative results are being determined) and can run on ORNL`s Onyx machine in approximately realtime. The flexible beam is modeled as six rigid sections with torsional springs between each segment. The spring constants were adjusted to match the physical response of the flexible beam model to the experimental results. The controller is able to improve performance on the model similar to the improvement seen on the experimental system. Some differences are apparent, most notably because the IGRIP model presently uses a different trajectory planner than the one used by ORNL on the PNL test bed. In the future, the trajectory planner will be modified so that the experiments and models are the same. The successful completion of this work provides the ability to link C code with IGRIP, thus allowing controllers to be developed, tested, and tuned in simulation and then ported directly to hardware systems using the C language.« less

Physiological and Psychological Predictors of Short-Term Disability in Workers with a History of Low Back Pain: A Longitudinal Study

PubMed Central

Dubois, Jean-Daniel; Cantin, Vincent; Piché, Mathieu; Descarreaux, Martin

2016-01-01

Despite an elusive pathophysiology, common characteristics are often observed in individuals with chronic low back pain (LBP). These include psychological symptoms, altered pain perception, altered pain modulation and altered muscle activation. These factors have been explored as possible determinants of disability, either separately or in cross-sectional studies, but were never assessed in a single longitudinal study. Therefore, the objective was to determine the relative contribution of psychological and neurophysiological factors to future disability in individuals with past LBP. The study included two experimental sessions (baseline and six months later) to assess cutaneous heat pain and pain tolerance thresholds, pain inhibition, as well as trunk muscle activation. Both sessions included the completion of validated questionnaires to determine clinical pain, disability, pain catastrophizing, fear-avoidance beliefs and pain vigilance. One hundred workers with a history of LBP and 19 healthy individuals took part in the first experimental session. The second experimental session was exclusively conducted on workers with a history of LBP (77/100). Correlation analyses between initial measures and disability at six months were conducted, and measures significantly associated with disability were used in multiple regression analyses. A first regression analysis showed that psychological symptoms contributed unique variance to future disability (R2 = 0.093, p = .009). To control for the fluctuating nature of LBP, a hierarchical regression was conducted while controlling for clinical pain at six months (R2 = 0.213, p < .001) where pain inhibition contributed unique variance in the second step of the regression (R2 change = 0.094, p = .005). These results indicate that pain inhibition processes may constitute potential targets for treatment to alleviate future disability in individuals with past or present LBP. Then again, the link between psychological symptoms and pain inhibition needs to be clarified as both of these factors are linked together and influence disability in their own way. PMID:27783666

Experimental demonstration of bidirectional up to 40 Gbit/s QPSK coherent free-space optical communication link over ∼1 km

NASA Astrophysics Data System (ADS)

Feng, Xianglian; Wu, Zhihang; Wang, Tianshu; Zhang, Peng; Li, Xiaoyan; Jiang, Huilin; Su, Yuwei; He, Hongwei; Wang, Xiaoyan; Gao, Shiming

2018-03-01

Advanced multi-level modulation formats have shown their great potential in high-speed and high-spectral-efficiency optical communications. Using quadrature phase-shift keying (QPSK) modulation format for free-space optical (FSO) communication, a bidirectional high-speed FSO transmission link with the bit rates of up to 40 Gbit/s over ∼1 km, between two buildings in the campus of Changchun University of Science and Technology, Changchun, China, is experimentally demonstrated cooperating by capture and tracking systems. The eye-diagrams and constellation diagrams of the transmitted QPSK signals are clearly observed. By comparing the bit error rate (BER) curves before and after transmission, one can find that the receiving powers are both less than -16.5 dBm for the forward and backward transmissions of the bidirectional 20, 30, and 40 Gbit/s FSO links, and their power penalties due to the phase fluctuation of the atmospheric channel are both less than 2.6 dB, at the BER of 3.8 ×10-3.

Investigation of the Vortex States of Sr2RuO4-Ru Eutectic Microplates Using DC-SQUIDs

NASA Astrophysics Data System (ADS)

Sakuma, Daisuke; Nago, Yusuke; Ishiguro, Ryosuke; Kashiwaya, Satoshi; Nomura, Shintaro; Kono, Kimitoshi; Maeno, Yoshiteru; Takayanagi, Hideaki

2017-11-01

We investigated the magnetic properties of a Sr2RuO4-Ru eutectic microplate containing a single Ru-inclusion using micrometer-sized DC-SQUIDs (direct-current superconducting quantum interference devices). A phase frustration at the interface between chiral p-wave superconducting Sr2RuO4 and s-wave superconducting Ru is expected to cause novel magnetic vortex states such as the spontaneous Ru-center vortex under zero magnetic field [as reported by H. Kaneyasu and M. Sigrist, J. Phys. Soc. Jpn. 79, 053706 (2010)]. Our experimental results show no positive evidence for such a spontaneous vortex state. However, in an applied field, an abrupt change in the magnetic flux distribution was observed at a superconducting transition of Ru. The flux distribution is clarified by comparing our experimental results with electromagnetic field simulations in our sample geometry. We discuss the transition of the vortex states and the superconducting coupling at the Sr2RuO4/Ru interface.

An integrated computational approach can classify VHL missense mutations according to risk of clear cell renal carcinoma

PubMed Central

Gossage, Lucy; Pires, Douglas E. V.; Olivera-Nappa, Álvaro; Asenjo, Juan; Bycroft, Mark; Blundell, Tom L.; Eisen, Tim

2014-01-01

Mutations in the von Hippel–Lindau (VHL) gene are pathogenic in VHL disease, congenital polycythaemia and clear cell renal carcinoma (ccRCC). pVHL forms a ternary complex with elongin C and elongin B, critical for pVHL stability and function, which interacts with Cullin-2 and RING-box protein 1 to target hypoxia-inducible factor for polyubiquitination and proteasomal degradation. We describe a comprehensive database of missense VHL mutations linked to experimental and clinical data. We use predictions from in silico tools to link the functional effects of missense VHL mutations to phenotype. The risk of ccRCC in VHL disease is linked to the degree of destabilization resulting from missense mutations. An optimized binary classification system (symphony), which integrates predictions from five in silico methods, can predict the risk of ccRCC associated with VHL missense mutations with high sensitivity and specificity. We use symphony to generate predictions for risk of ccRCC for all possible VHL missense mutations and present these predictions, in association with clinical and experimental data, in a publically available, searchable web server. PMID:24969085

Space-division-multiplexed transmission of 3x3 multiple-input multiple-output wireless signals over conventional graded-index multimode fiber.

PubMed

Lei, Yi; Li, Jianqiang; Fan, Yuting; Yu, Dawei; Fu, Songnian; Yin, Feifei; Dai, Yitang; Xu, Kun

2016-12-12

In this paper, we experimentally demonstrate space-division-multiplexed (SDM) transmission of IEEE 802.11ac-compliant 3-spatial-stream WLAN signals over 3 spatial modes of conventional 50um graded-index (GI) multimode fiber (MMF) employing non-mode-selective 3D-waveguide photonic lantern. Two kinds of scenarios, including fiber-only transmission and fiber-wireless hybrid transmission, were investigated by measuring error vector magnitude (EVM) performance for each stream and condition number (CN) of the channel matrix. The experimental results show that, SDM-based MMF link could offer a CN< 20dB well-conditioned MIMO channel over up to 1km fiber length within 0-6GHz, achieving as low as 2.38%, 2.97% and 2.11% EVM performance for 1km MMF link at 2.4GHz, 5.8GHz, and 200m MMF link followed by 1m air distance at 2.7GHz, respectively. These results indicate the possibility to distribute wireless MIMO signals over existing in-building commercially-available MMFs with enormous cost-saving.

Mixed-Isotope Labeling with LC-IMS-MS for Characterization of Protein–Protein Interactions by Chemical Cross-Linking

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

Merkley, Eric D.; Baker, Erin S.; Crowell, Kevin L.

2013-02-20

Chemical cross-linking of proteins followed by proteolysis and mass spectrometric analysis of the resulting cross-linked peptides can provide insights into protein structure and protein-protein interactions. However, cross-linked peptides are by necessity of low stoichometry and have different physicochemical properties than linear peptides, routine unambiguous identification of the cross-linked peptides has remained difficult. To address this challenge, we demonstrated the use of liquid chromatography and ion mobility separations coupled with mass spectrometry in combination with a heavy-isotope labeling method. The combination of mixed-isotope cross-linking and ion mobility provided unique and easily interpretable spectral multiplet features for the intermolecular cross-linked peptides. Applicationmore » of the method to two different homodimeric proteins - SrfN, a virulence factor from Salmonella Typhimurium and SO_2176, a protein of unknown function from Shewanella oneidensis- revealed several cross-linked peptides from both proteins that were identified with a low false discovery rate (estimated using a decoy approach). A greater number of cross-linked peptides were identified using ion mobility drift time information in the analysis than when the data were summed across the drift time dimension before analysis. The identified cross-linked peptides migrated more quickly in the ion mobility drift tube than the unmodified peptides.« less

Hydrologic Controls on In-Stream Optical Dissolved Organic Matter Characteristics in an Old-Growth Forest of the Oregon Cascades

NASA Astrophysics Data System (ADS)

Lajtha, K.; Lee, B. S.

2015-12-01

Dissolved organic matter (DOM) is a critical component of the carbon cycle linking terrestrial and aquatic ecosystems, yet DOM composition representative of DOM sources at headwater catchments in the western U.S is poorly understood. This study examined the effect of forest management history and hydrologic patterns on DOM chemistry at nine experimental watersheds located in the H.J. Andrews Long Term Ecological Research Experimental Forest of the Oregon Cascades. Stream water samples representing a three-week composite of each watershed were collected between May 2013 and February 2015 (32 events). DOM chemistry was characterized by examining UV and fluorescent properties of stream samples. Specific UV absorbance at 254 nm (SUVA254; Weishaar et al. 2003), generally indicative of aromaticity, showed the lowest value at the high elevation clear-cut site (watershed 6, 1,030 m) and the highest value at the low elevation clear-cut site (watershed 10, 680 m) throughout the study period. DOM fluorescent components, identified by this study using a multivariate statistical model, Parallel Factor Analysis (PARAFAC), did not differ significantly among experimental watersheds with varying forest management history. However, a protein-like DOM component exhibited temporal variations. Correlation analysis between the protein-like DOM and hydrologic patterns indicate that stream water during dry seasons come from protein-rich groundwater sources. This study shows UV and fluorescent spectroscopy DOM characterization is a viable finger printing method to detect DOM sources in pristine headwater streams at the western Cascades of Oregon where characterization of the stream water source with low DOC and DON concentrations is difficult.

The effect of IDS (immediate dentin sealing) on dentin bond strength under various thermocycling periods

PubMed Central

Leesungbok, Richard; Lee, Sang-Min; Park, Su-Jung; Lee, Suk-Won; Lee, Do Yun; Im, Byung-Jin

2015-01-01

PURPOSE The purpose of this study was to find out the effect of immediate dentin sealing (IDS) on bond strength of ceramic restoration under various thermocycling periods with DBA (dentin bonding agent system). MATERIALS AND METHODS Fifty freshly extracted human mandibular third molars were divided into 5 groups (1 control and 4 experimental groups) of 10 teeth. We removed enamel layer of sound teeth and embedded them which will proceed to be IDS, using All Bond II. A thermocycling was applied to experimental groups for 1, 2, 7, 14 days respectively and was not applied to control group. IPS Empress II for ceramic was acid-etched with ceramic etchant (9.5% HF) and silane was applied. Each ceramic disc was bonded to specimens with Duo-link, dual curable resin cement by means of light curing for 100 seconds. After the cementation procedures, shear bond strength measurement and SEM analysis of the fractured surface were done. The data were analyzed with a one-way ANOVA and Tukey multiple comparison test (α=.05). RESULTS There were no statistically significant differences between 4 experimental groups and control group, however the mean value started to decrease in group 7d, and group 14d showed the lowest mean bond strength in all groups. Also, group 7d and 14d showed distinct exposed dentin and collapsed hybrid layer was observed in SEM analysis. CONCLUSION In the present study, it can be concluded that ceramic restorations like a laminate veneer restoration should be bonded using resin cement within one week after IDS procedure. PMID:26140174

CD-Based Indices for Link Prediction in Complex Network.

PubMed

Wang, Tao; Wang, Hongjue; Wang, Xiaoxia

2016-01-01

Lots of similarity-based algorithms have been designed to deal with the problem of link prediction in the past decade. In order to improve prediction accuracy, a novel cosine similarity index CD based on distance between nodes and cosine value between vectors is proposed in this paper. Firstly, node coordinate matrix can be obtained by node distances which are different from distance matrix and row vectors of the matrix are regarded as coordinates of nodes. Then, cosine value between node coordinates is used as their similarity index. A local community density index LD is also proposed. Then, a series of CD-based indices include CD-LD-k, CD*LD-k, CD-k and CDI are presented and applied in ten real networks. Experimental results demonstrate the effectiveness of CD-based indices. The effects of network clustering coefficient and assortative coefficient on prediction accuracy of indices are analyzed. CD-LD-k and CD*LD-k can improve prediction accuracy without considering the assortative coefficient of network is negative or positive. According to analysis of relative precision of each method on each network, CD-LD-k and CD*LD-k indices have excellent average performance and robustness. CD and CD-k indices perform better on positive assortative networks than on negative assortative networks. For negative assortative networks, we improve and refine CD index, referred as CDI index, combining the advantages of CD index and evolutionary mechanism of the network model BA. Experimental results reveal that CDI index can increase prediction accuracy of CD on negative assortative networks.

Neural Dynamics as Sampling: A Model for Stochastic Computation in Recurrent Networks of Spiking Neurons

PubMed Central

Buesing, Lars; Bill, Johannes; Nessler, Bernhard; Maass, Wolfgang

2011-01-01

The organization of computations in networks of spiking neurons in the brain is still largely unknown, in particular in view of the inherently stochastic features of their firing activity and the experimentally observed trial-to-trial variability of neural systems in the brain. In principle there exists a powerful computational framework for stochastic computations, probabilistic inference by sampling, which can explain a large number of macroscopic experimental data in neuroscience and cognitive science. But it has turned out to be surprisingly difficult to create a link between these abstract models for stochastic computations and more detailed models of the dynamics of networks of spiking neurons. Here we create such a link and show that under some conditions the stochastic firing activity of networks of spiking neurons can be interpreted as probabilistic inference via Markov chain Monte Carlo (MCMC) sampling. Since common methods for MCMC sampling in distributed systems, such as Gibbs sampling, are inconsistent with the dynamics of spiking neurons, we introduce a different approach based on non-reversible Markov chains that is able to reflect inherent temporal processes of spiking neuronal activity through a suitable choice of random variables. We propose a neural network model and show by a rigorous theoretical analysis that its neural activity implements MCMC sampling of a given distribution, both for the case of discrete and continuous time. This provides a step towards closing the gap between abstract functional models of cortical computation and more detailed models of networks of spiking neurons. PMID:22096452

CD-Based Indices for Link Prediction in Complex Network

PubMed Central

Wang, Tao; Wang, Hongjue; Wang, Xiaoxia

2016-01-01

Lots of similarity-based algorithms have been designed to deal with the problem of link prediction in the past decade. In order to improve prediction accuracy, a novel cosine similarity index CD based on distance between nodes and cosine value between vectors is proposed in this paper. Firstly, node coordinate matrix can be obtained by node distances which are different from distance matrix and row vectors of the matrix are regarded as coordinates of nodes. Then, cosine value between node coordinates is used as their similarity index. A local community density index LD is also proposed. Then, a series of CD-based indices include CD-LD-k, CD*LD-k, CD-k and CDI are presented and applied in ten real networks. Experimental results demonstrate the effectiveness of CD-based indices. The effects of network clustering coefficient and assortative coefficient on prediction accuracy of indices are analyzed. CD-LD-k and CD*LD-k can improve prediction accuracy without considering the assortative coefficient of network is negative or positive. According to analysis of relative precision of each method on each network, CD-LD-k and CD*LD-k indices have excellent average performance and robustness. CD and CD-k indices perform better on positive assortative networks than on negative assortative networks. For negative assortative networks, we improve and refine CD index, referred as CDI index, combining the advantages of CD index and evolutionary mechanism of the network model BA. Experimental results reveal that CDI index can increase prediction accuracy of CD on negative assortative networks. PMID:26752405

Pressure-constrained, reduced-DOF, interconnected parallel manipulators with applications to space suit design

NASA Astrophysics Data System (ADS)

Jacobs, Shane Earl

This dissertation presents the concept of a Morphing Upper Torso, an innovative pressure suit design that incorporates robotic elements to enable a resizable, highly mobile and easy to don/doff spacesuit. The torso is modeled as a system of interconnected, pressure-constrained, reduced-DOF, wire-actuated parallel manipulators, that enable the dimensions of the suit to be reconfigured to match the wearer. The kinematics, dynamics and control of wire-actuated manipulators are derived and simulated, along with the Jacobian transforms, which relate the total twist vector of the system to the vector of actuator velocities. Tools are developed that allow calculation of the workspace for both single and interconnected reduced-DOF robots of this type, using knowledge of the link lengths. The forward kinematics and statics equations are combined and solved to produce the pose of the platforms along with the link tensions. These tools allow analysis of the full Morphing Upper Torso design, in which the back hatch of a rear-entry torso is interconnected with the waist ring, helmet ring and two scye bearings. Half-scale and full-scale experimental models are used along with analytical models to examine the feasibility of this novel space suit concept. The analytical and experimental results demonstrate that the torso could be expanded to facilitate donning and doffng, and then contracted to match different wearer's body dimensions. Using the system of interconnected parallel manipulators, suit components can be accurately repositioned to different desired configurations. The demonstrated feasibility of the Morphing Upper Torso concept makes it an exciting candidate for inclusion in a future planetary suit architecture.

Hybrid coexpression link similarity graph clustering for mining biological modules from multiple gene expression datasets.

PubMed

Salem, Saeed; Ozcaglar, Cagri

2014-01-01

Advances in genomic technologies have enabled the accumulation of vast amount of genomic data, including gene expression data for multiple species under various biological and environmental conditions. Integration of these gene expression datasets is a promising strategy to alleviate the challenges of protein functional annotation and biological module discovery based on a single gene expression data, which suffers from spurious coexpression. We propose a joint mining algorithm that constructs a weighted hybrid similarity graph whose nodes are the coexpression links. The weight of an edge between two coexpression links in this hybrid graph is a linear combination of the topological similarities and co-appearance similarities of the corresponding two coexpression links. Clustering the weighted hybrid similarity graph yields recurrent coexpression link clusters (modules). Experimental results on Human gene expression datasets show that the reported modules are functionally homogeneous as evident by their enrichment with biological process GO terms and KEGG pathways.

Advanced optical fiber communication systems

NASA Astrophysics Data System (ADS)

Kazovsky, Leonid G.

1994-03-01

Our research is focused on three major aspects of advanced optical fiber communication systems: dynamic wavelength division multiplexing (WDM) networks, fiber nonlinearities, and high dynamic range coherent analog optical links. In the area of WDM networks, we have designed and implemented two high-speed interface boards and measured their throughput and latency. Furthermore, we designed and constructed an experimental PSK/ASK transceiver that simultaneously transmits packet-switched ASK data and circuit-switched PSK data on the same optical carrier. In the area of fiber nonlinearities, we investigated the theoretical impact of modulation frequency on cross-phase modulation (XPM) in dispersive fibers. In the area of high dynamic range coherent analog optical links, we developed theoretical expressions for the RF power transfer ratio (or RF power gain) and the noise figure (NF) of angle-modulated links. We then compared the RF power gains and noise figures of these links to that of an intensity modulated direct detection (DD) link.

Theorising and testing environmental pathways to behaviour change: natural experimental study of the perception and use of new infrastructure to promote walking and cycling in local communities

PubMed Central

Panter, Jenna; Ogilvie, David

2015-01-01

Objective Some studies have assessed the effectiveness of environmental interventions to promote physical activity, but few have examined how such interventions work. We investigated the environmental mechanisms linking an infrastructural intervention with behaviour change. Design Natural experimental study. Setting Three UK municipalities (Southampton, Cardiff and Kenilworth). Participants Adults living within 5 km of new walking and cycling infrastructure. Intervention Construction or improvement of walking and cycling routes. Exposure to the intervention was defined in terms of residential proximity. Outcome measures Questionnaires at baseline and 2-year follow-up assessed perceptions of the supportiveness of the environment, use of the new infrastructure, and walking and cycling behaviours. Analysis proceeded via factor analysis of perceptions of the physical environment (step 1) and regression analysis to identify plausible pathways involving physical and social environmental mediators and refine the intervention theory (step 2) to a final path analysis to test the model (step 3). Results Participants who lived near and used the new routes reported improvements in their perceptions of provision and safety. However, path analysis (step 3, n=967) showed that the effects of the intervention on changes in time spent walking and cycling were largely (90%) explained by a simple causal pathway involving use of the new routes, and other pathways involving changes in environmental cognitions explained only a small proportion of the effect. Conclusions Physical improvement of the environment itself was the key to the effectiveness of the intervention, and seeking to change people's perceptions may be of limited value. Studies of how interventions lead to population behaviour change should complement those concerned with estimating their effects in supporting valid causal inference. PMID:26338837

Alcohol consumption and the intention to engage in unprotected sex: systematic review and meta-analysis of experimental studies.

PubMed

Rehm, Jürgen; Shield, Kevin D; Joharchi, Narges; Shuper, Paul A

2012-01-01

To review and analyse in experimentally controlled studies the impact of alcohol consumption on intentions to engage in unprotected sex. To draw conclusions with respect to the question of whether alcohol has an independent effect on the incidence of human immunodeficiency virus (HIV) and other sexually transmitted infections (STIs). A systematic review and meta-analysis of randomized controlled studies examined the association between blood alcohol content (BAC) and self-perceived likelihood of using a condom during intercourse. The systematic review and meta-analysis were conducted according to internationally standardized protocols (Preferred Reporting Items for Systematic Reviews and Meta-Analyses: PRISMA). The meta-analysis included an estimate of the dose-response effect, tests for publication bias and sensitivity analyses. Of the 12 studies included in the quantitative synthesis, our pooled analysis indicated that an increase in BAC of 0.1 mg/ml resulted in an increase of 5.0% (95% CI: 2.8-7.1%) in the indicated likelihood (indicated by a Likert scale) of engaging in unprotected sex. After adjusting for potential publication bias, this estimate dropped to 2.9% (95% CI: 2.0-3.9%). Thus, the larger the alcohol intake and the subsequent level of BAC, the higher the intentions to engage in unsafe sex. The main results were homogeneous, persisted in sensitivity analyses and after correction for publication bias. Alcohol use is an independent risk factor for intentions to engage in unprotected sex, and as risky sex intentions have been shown to be linked to actual risk behavior, the role of alcohol consumption in the transmission of HIV and other STIs may be of public health importance. © 2011 The Authors, Addiction © 2011 Society for the Study of Addiction.

Link prediction based on local weighted paths for complex networks

NASA Astrophysics Data System (ADS)

Yao, Yabing; Zhang, Ruisheng; Yang, Fan; Yuan, Yongna; Hu, Rongjing; Zhao, Zhili

As a significant problem in complex networks, link prediction aims to find the missing and future links between two unconnected nodes by estimating the existence likelihood of potential links. It plays an important role in understanding the evolution mechanism of networks and has broad applications in practice. In order to improve prediction performance, a variety of structural similarity-based methods that rely on different topological features have been put forward. As one topological feature, the path information between node pairs is utilized to calculate the node similarity. However, many path-dependent methods neglect the different contributions of paths for a pair of nodes. In this paper, a local weighted path (LWP) index is proposed to differentiate the contributions between paths. The LWP index considers the effect of the link degrees of intermediate links and the connectivity influence of intermediate nodes on paths to quantify the path weight in the prediction procedure. The experimental results on 12 real-world networks show that the LWP index outperforms other seven prediction baselines.

The effect of cross linking density on the mechanical properties and structure of the epoxy polymers: molecular dynamics simulation.

PubMed

Shokuhfar, Ali; Arab, Behrouz

2013-09-01

Recently, great attention has been focused on using epoxy polymers in different fields such as aerospace, automotive, biotechnology, and electronics, owing to their superior properties. In this study, the classical molecular dynamics (MD) was used to simulate the cross linking of diglycidyl ether of bisphenol-A (DGEBA) with diethylenetriamine (DETA) curing agent, and to study the behavior of resulted epoxy polymer with different conversion rates. The constant-strain (static) approach was then applied to calculate the mechanical properties (Bulk, shear and Young's moduli, elastic stiffness constants, and Poisson's ratio) of the uncured and cross-linked systems. Estimated material properties were found to be in good agreement with experimental observations. Moreover, the dependency of mechanical properties on the cross linking density was investigated and revealed improvements in the mechanical properties with increasing the cross linking density. The radial distribution function (RDF) was also used to study the evolution of local structures of the simulated systems as a function of cross linking density.

A constructionist review of morality and emotions: no evidence for specific links between moral content and discrete emotions.

PubMed

Cameron, C Daryl; Lindquist, Kristen A; Gray, Kurt

2015-11-01

Morality and emotions are linked, but what is the nature of their correspondence? Many "whole number" accounts posit specific correspondences between moral content and discrete emotions, such that harm is linked to anger, and purity is linked to disgust. A review of the literature provides little support for these specific morality-emotion links. Moreover, any apparent specificity may arise from global features shared between morality and emotion, such as affect and conceptual content. These findings are consistent with a constructionist perspective of the mind, which argues against a whole number of discrete and domain-specific mental mechanisms underlying morality and emotion. Instead, constructionism emphasizes the flexible combination of basic and domain-general ingredients such as core affect and conceptualization in creating the experience of moral judgments and discrete emotions. The implications of constructionism in moral psychology are discussed, and we propose an experimental framework for rigorously testing morality-emotion links. © 2015 by the Society for Personality and Social Psychology, Inc.

Understanding Complexity and Self-Organization in a Defense Program Management Organization (Experimental Design)

DTIC Science & Technology

2016-03-18

SPONSORED REPORT SERIES Understanding Complexity and Self - Organization in a Defense Program Management Organization (Experimental Design...experiment will examine the decision-making process within the program office and the self - organization of key program office personnel based upon formal...and informal communications links. Additionally, we are interested in the effects of this self - organizing process on the organization’s shared

Longitudinal analysis of the group A Streptococcus transcriptome in experimental pharyngitis in cynomolgus macaques.

PubMed

Virtaneva, Kimmo; Porcella, Stephen F; Graham, Morag R; Ireland, Robin M; Johnson, Claire A; Ricklefs, Stacy M; Babar, Imran; Parkins, Larye D; Romero, Romina A; Corn, G Judson; Gardner, Don J; Bailey, John R; Parnell, Michael J; Musser, James M

2005-06-21

Identification of the genetic events that contribute to host-pathogen interactions is important for understanding the natural history of infectious diseases and developing therapeutics. Transcriptome studies conducted on pathogens have been central to this goal in recent years. However, most of these investigations have focused on specific end points or disease phases, rather than analysis of the entire time course of infection. To gain a more complete understanding of how bacterial gene expression changes over time in a primate host, the transcriptome of group A Streptococcus (GAS) was analyzed during an 86-day infection protocol in 20 cynomolgus macaques with experimental pharyngitis. The study used 260 custom Affymetrix (Santa Clara, CA) chips, and data were confirmed by TaqMan analysis. Colonization, acute, and asymptomatic phases of disease were identified. Successful colonization and severe inflammation were significantly correlated with an early onset of superantigen gene expression. The differential expression of two-component regulators covR and spy0680 (M1_spy0874) was significantly associated with GAS colony-forming units, inflammation, and phases of disease. Prophage virulence gene expression and prophage induction occurred predominantly during high pathogen cell densities and acute inflammation. We discovered that temporal changes in the GAS transcriptome were integrally linked to the phase of clinical disease and host-defense response. Knowledge of the gene expression patterns characterizing each phase of pathogen-host interaction provides avenues for targeted investigation of proven and putative virulence factors and genes of unknown function and will assist vaccine research.

Lexical Link Analysis Application: Improving Web Service to Acquisition Visibility Portal Phase II

DTIC Science & Technology

2014-04-30

bäÉîÉåíÜ=^ååì~ä=^Åèìáëáíáçå= oÉëÉ~êÅÜ=póãéçëáìã= qÜìêëÇ~ó=pÉëëáçåë= sçäìãÉ=ff= = Lexical Link Analysis Application: Improving Web Service to...DATE 30 APR 2014 2. REPORT TYPE 3. DATES COVERED 00-00-2014 to 00-00-2014 4. TITLE AND SUBTITLE Lexical Link Analysis Application: Improving...vocabulary or lexicon, to describe the attributes and surrounding environment of the system. Lexical Link Analysis (LLA) is a form of text mining in which

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

Nour, Ali, E-mail: ali.nour@polymtl.ca; Hydro Quebec, Montreal, Quebec, H2L 4P5; Massicotte, Bruno

This study is aimed at proposing a simple analytical model to investigate the post-cracking behaviour of FRC panels, using an arbitrary tension softening, stress crack opening diagram, as the input. A new relationship that links the crack opening to the panel deflection is proposed. Due to the stochastic nature of material properties, the random fibre distribution, and other uncertainties that are involved in concrete mix, this relationship is developed from the analysis of beams having the same thickness using the Monte Carlo simulation (MCS) technique. The softening diagrams obtained from direct tensile tests are used as the input for themore » calculation, in a deterministic way, of the mean load displacement response of round panels. A good agreement is found between the model predictions and the experimental results.« less

Analysis of crystallization data in the Protein Data Bank

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

Kirkwood, Jobie; Hargreaves, David; O’Keefe, Simon

In a large-scale study using data from the Protein Data Bank, some of the many reported findings regarding the crystallization of proteins were investigated. The Protein Data Bank (PDB) is the largest available repository of solved protein structures and contains a wealth of information on successful crystallization. Many centres have used their own experimental data to draw conclusions about proteins and the conditions in which they crystallize. Here, data from the PDB were used to reanalyse some of these results. The most successful crystallization reagents were identified, the link between solution pH and the isoelectric point of the protein wasmore » investigated and the possibility of predicting whether a protein will crystallize was explored.« less

Estimating the effect of gang membership on nonviolent and violent delinquency: a counterfactual analysis.

PubMed

Barnes, J C; Beaver, Kevin M; Miller, J Mitchell

2010-01-01

This study reconsiders the well-known link between gang membership and criminal involvement. Recently developed analytical techniques enabled the approximation of an experimental design to determine whether gang members, after being matched with similarly situated nongang members, exhibited greater involvement in nonviolent and violent delinquency. Findings indicated that while gang membership is a function of self-selection, selection effects alone do not account for the greater involvement in delinquency exhibited by gang members. After propensity score matching was employed, gang members maintained a greater involvement in both nonviolent and violent delinquency when measured cross-sectionally, but only violent delinquency when measured longitudinally. Additional analyses using inverse probability of treatment weights reaffirmed these conclusions. © 2010 Wiley-Liss, Inc.

Design and evaluation of an oral multiparticulate system for dual delivery of amoxicillin and Lactobacillus acidophilus.

PubMed

Govender, Mershen; Choonara, Yahya E; van Vuuren, Sandy; Kumar, Pradeep; du Toit, Lisa C; Pillay, Viness

2016-09-01

A delayed-release dual delivery system for amoxicillin and the probiotic Lactobacillus acidophilus was developed and evaluated. Statistical optimization of a cross-linked denatured ovalbumin protective matrix was first synthesized using a Box-Behnken experimental design prior to encapsulation with glyceryl monostereate. The encapsulated ovalbumin matrix was thereafter incorporated with amoxicillin in a gastro-resistant capsule. In vitro characterization and stability analysis of the ovalbumin and encapsulated components were also performed Results: Protection of L. acidophilus probiotic against the bactericidal effects of amoxicillin within the dual formulation was determined. The dual formulation in this study proved effective and provides insight into current microbiome research to identify, classify and use functional healthy bacteria to develop novel probiotic delivery technologies.

Spectrum of 100-kyr glacial cycle: Orbital inclination, not eccentricity

PubMed Central

Muller, Richard A.; MacDonald, Gordon J.

1997-01-01

Spectral analysis of climate data shows a strong narrow peak with period ≈100 kyr, attributed by the Milankovitch theory to changes in the eccentricity of the earth’s orbit. The narrowness of the peak does suggest an astronomical origin; however the shape of the peak is incompatible with both linear and nonlinear models that attribute the cycle to eccentricity or (equivalently) to the envelope of the precession. In contrast, the orbital inclination parameter gives a good match to both the spectrum and bispectrum of the climate data. Extraterrestrial accretion from meteoroids or interplanetary dust is proposed as a mechanism that could link inclination to climate, and experimental tests are described that could prove or disprove this hypothesis. PMID:11607741

Scaling laws and size effects for amorphous crystallization kinetics: Constraints imposed by nucleation and growth specificities.

PubMed

Descamps, Marc; Willart, Jean-François

2018-05-05

In the present paper we review different aspects of the crystallization of amorphous compounds in relation to specificities of the nucleation and growth rates. Its main purpose is: i) to underline the interest of a scaling analysis of recrystallization kinetics to identify similarities or disparities of experimental kinetic regimes. ii) to highlight the intrinsic link between the nucleation rate and growth rate with a temperature dependent characteristic transformation time τ(T), and a characteristic size ξ(T). The consequences on the influence of the sample size on kinetics of crystallization is considered. The significance of size effect and confinement for amorphous stabilization in the pharmaceutical sciences is discussed. Copyright © 2018. Published by Elsevier B.V.

Modeling spatial competition for light in plant populations with the porous medium equation.

PubMed

Beyer, Robert; Etard, Octave; Cournède, Paul-Henry; Laurent-Gengoux, Pascal

2015-02-01

We consider a plant's local leaf area index as a spatially continuous variable, subject to particular reaction-diffusion dynamics of allocation, senescence and spatial propagation. The latter notably incorporates the plant's tendency to form new leaves in bright rather than shaded locations. Applying a generalized Beer-Lambert law allows to link existing foliage to production dynamics. The approach allows for inter-individual variability and competition for light while maintaining robustness-a key weakness of comparable existing models. The analysis of the single plant case leads to a significant simplification of the system's key equation when transforming it into the well studied porous medium equation. Confronting the theoretical model to experimental data of sugar beet populations, differing in configuration density, demonstrates its accuracy.

The neurogenetic frontier--lessons from misbehaving zebrafish.

PubMed

Burgess, Harold A; Granato, Michael

2008-11-01

One of the central questions in neuroscience is how refined patterns of connectivity in the brain generate and monitor behavior. Genetic mutations can influence neural circuits by disrupting differentiation or maintenance of component neuronal cells or by altering functional patterns of nervous system connectivity. Mutagenesis screens therefore have the potential to reveal not only the molecular underpinnings of brain development and function, but to illuminate the cellular basis of behavior. Practical considerations make the zebrafish an organism of choice for undertaking forward genetic analysis of behavior. The powerful array of experimental tools at the disposal of the zebrafish researcher makes it possible to link molecular function to neuronal properties that underlie behavior. This review focuses on specific challenges to isolating and analyzing behavioral mutants in zebrafish.

The neurogenetic frontier—lessons from misbehaving zebrafish

PubMed Central

Granato, Michael

2008-01-01

One of the central questions in neuroscience is how refined patterns of connectivity in the brain generate and monitor behavior. Genetic mutations can influence neural circuits by disrupting differentiation or maintenance of component neuronal cells or by altering functional patterns of nervous system connectivity. Mutagenesis screens therefore have the potential to reveal not only the molecular underpinnings of brain development and function, but to illuminate the cellular basis of behavior. Practical considerations make the zebrafish an organism of choice for undertaking forward genetic analysis of behavior. The powerful array of experimental tools at the disposal of the zebrafish researcher makes it possible to link molecular function to neuronal properties that underlie behavior. This review focuses on specific challenges to isolating and analyzing behavioral mutants in zebrafish. PMID:18836206

Range image segmentation using Zernike moment-based generalized edge detector

NASA Technical Reports Server (NTRS)

Ghosal, S.; Mehrotra, R.

1992-01-01

The authors proposed a novel Zernike moment-based generalized step edge detection method which can be used for segmenting range and intensity images. A generalized step edge detector is developed to identify different kinds of edges in range images. These edge maps are thinned and linked to provide final segmentation. A generalized edge is modeled in terms of five parameters: orientation, two slopes, one step jump at the location of the edge, and the background gray level. Two complex and two real Zernike moment-based masks are required to determine all these parameters of the edge model. Theoretical noise analysis is performed to show that these operators are quite noise tolerant. Experimental results are included to demonstrate edge-based segmentation technique.

Experimental study and numerical simulation of the salinity effect on water-freezing point and ice-melting rate

NASA Astrophysics Data System (ADS)

Qin, N.; Wu, Y.; Wang, H. W.; Wang, Y. Y.

2017-12-01

In this paper, based on the background of snowmelt de-icing tools, we studied the effect of salt on freezing point and melting rate of ice through laboratory test and FLUENT numerical simulation analysis. It was confirmed that the freezing point is inversely proportional to the salt solid content, and with the salt solid content increasing, the freezing process of salt water gradually accepts the curing rule of non-crystal solids. At the same temperature, an increase in the salt solid content, the ice melting rate increase by the empirical formula linking the melting time with temperature and salt content. The theoretical aspects of solid/fluid transformation are discussed in detail.

Localization/delocalization of charges in bay-linked perylene bisimides.

PubMed

Jiang, Wei; Xiao, Chengyi; Hao, Linxiao; Wang, Zhaohui; Ceymann, Harald; Lambert, Christoph; Di Motta, Simone; Negri, Fabrizia

2012-05-29

The copper-mediated Ullmann coupling of 1,7-dibromoperylene bisimides afforded structurally perfect singly-linked perylene bisimide (PBI) arrays, whilst the homo-coupling of 1,12-dibromoperylene bisimides gave doubly-linked and triply-linked diperylene bisimides. The interactions of three bay-linked diperylene bisimides that differed in their linkage (singly, doubly, and triply) were investigated in their neutral and reduced forms (mono-anion to tetra-anion). UV/Vis absorption and fluorescence spectroscopy revealed different degrees of interaction, which was explained by exciton coupling and conjugation effects. The electrochemical properties and spectroelectrochemistry also showed quite-different degrees of PBI interactions in the reduced mixed-valence species, which was apparent by the observation of CT bands. The interpretation of the experimental findings was supported by spin-restricted and -unrestricted DFT and time-dependent TD-DFT calculations with the long-range-corrected CAM-B3LYP functional. Accordingly, the degree of interaction in both the neutral and reduced forms of the bay-linked PBIs was qualitatively in the order doubly linked

A flight test design for studying airborne applications of air to ground duplex data link communications

NASA Technical Reports Server (NTRS)

Scanlon, Charles H.

1988-01-01

The Automatic En Route Air Traffic Control (AERA) and the Advanced Automated System (AAS) of the NAS plan, call for utilization of data links for such items as computer generated flight clearances, enroute minimum safe altitude warnings, sector probes, out of conformance check, automated flight services, and flow management of advisories. A major technical challenge remaining is the integration, flight testing, and validation of data link equipment and procedures in the aircraft cockpit. The flight test organizational chart, was designed to have the airplane side of data link experiments implemented in the NASA Langley Research Center (LaRC) experimental Boeing 737 airplane. This design would enable investigations into implementation of data link equipment and pilot interface, operations, and procedures. The illustrated ground system consists of a work station with links to a national weather database and a data link transceiver system. The data link transceiver system could be a Mode-S transponder, ACARS, AVSAT, or another type of radio system such as the military type HF data link. The airborne system was designed so that a data link transceiver, workstation, and touch panel could be interfaced with an input output processor to the aircraft system bus and thus have communications access to other digital airplane systems.

Balancing the pros and cons of GMOs: socio-scientific argumentation in pre-service teacher education

NASA Astrophysics Data System (ADS)

Cinici, Ayhan

2016-07-01

This study investigates the role of the discursive process in the act of scientific knowledge building. Specifically, it links scientific knowledge building to risk perception of Genetically Modified Organisms (GMOs). To this end, this study designed and implemented a three-stage argumentation programme giving pre-service teachers (PSTs) the opportunity to consider, discuss and construct shared decisions about GMOs. The study involved 101 third-year PSTs from two different classes, randomly divided into control and experimental groups. The study utilised both quantitative and qualitative methods. During the quantitative phase, researchers administered a pre- and post-intervention scale to measure both groups' risk perception of GMOs. During the qualitative phase, data were collected from the experimental group alone through individual and group reports and an open-ended questionnaire. T-test results showed a statistically significant difference between the experimental and control groups' risk perception of GMOs. Qualitative analysis also revealed differences, for example, in PSTs' weighing of the pros and cons of scientific research demonstrating positive results of GMOs. In addition, PSTs' acceptance of GMOs increased. Consequently, this study suggests that developing familiarity with scientific enterprise may play an effective role in adopting a scientific perspective as well as a more balanced risk perception of GMOs.

Bimorph Silk Microsheets with Programmable Actuating Behavior: Experimental Analysis and Computer Simulations.

PubMed

Ye, Chunhong; Nikolov, Svetoslav V; Geryak, Ren D; Calabrese, Rossella; Ankner, John F; Alexeev, Alexander; Kaplan, David L; Tsukruk, Vladimir V

2016-07-13

Microscaled self-rolling construct sheets from silk protein material have been fabricated, containing a silk bimorph composed of silk ionomers as an active layer and cross-linked silk β-sheet as the passive layer. The programmable morphology was experimentally explored along with a computational simulation to understand the mechanism of shape reconfiguration. The neutron reflectivity shows that the active silk ionomers layer undergoes remarkable swelling (eight times increase in thickness) after deprotonation while the passive silk β-sheet retains constant volume under the same conditions and supports the bimorph construct. This selective swelling within the silk-on-silk bimorph microsheets generates strong interfacial stress between layers and out-of-plane forces, which trigger autonomous self-rolling into various 3D constructs such as cylindrical and helical tubules. The experimental observations and computational modeling confirmed the role of interfacial stresses and allow programming the morphology of the 3D constructs with particular design. We demonstrated that the biaxial stress distribution over the 2D planar films depends upon the lateral dimensions, thickness and the aspect ratio of the microsheets. The results allow the fine-tuning of autonomous shape transformations for the further design of complex micro-origami constructs and the silk based rolling/unrolling structures provide a promising platform for polymer-based biomimetic devices for implant applications.

Illusory conjunctions reflect the time course of the attentional blink.

PubMed

Botella, Juan; Privado, Jesús; de Liaño, Beatriz Gil-Gómez; Suero, Manuel

2011-07-01

Illusory conjunctions in the time domain are binding errors for features from stimuli presented sequentially but in the same spatial position. A similar experimental paradigm is employed for the attentional blink (AB), an impairment of performance for the second of two targets when it is presented 200-500 msec after the first target. The analysis of errors along the time course of the AB allows the testing of models of illusory conjunctions. In an experiment, observers identified one (control condition) or two (experimental condition) letters in a specified color, so that illusory conjunctions in each response could be linked to specific positions in the series. Two items in the target colors (red and white, embedded in distractors of different colors) were employed in four conditions defined according to whether both targets were in the same or different colors. Besides the U-shaped function for hits, the errors were analyzed by calculating several response parameters reflecting characteristics such as the average position of the responses or the attentional suppression during the blink. The several error parameters cluster in two time courses, as would be expected from prevailing models of the AB. Furthermore, the results match the predictions from Botella, Barriopedro, and Suero's (Journal of Experimental Psychology: Human Perception and Performance, 27, 1452-1467, 2001) model for illusory conjunctions.

Forensic Signature Detection of Yersinia Pestis Culturing Practices Across Institutions Using a Bayesian Network

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

Webb-Robertson, Bobbie-Jo M.; Corley, Courtney D.; McCue, Lee Ann

The field of bioforensics is focused on the analysis of evidence from a biocrime. Existing laboratory analyses can identify the specific strain of an organism in the evidence, as well signatures of the specific culture batch of organisms, such as low-frequency contaminants or indicators of growth and processing methods. To link these disparate types of physical data to potential suspects, investigators may need to identify institutions or individuals whose access to strains and culturing practices match those identified from the evidence. In this work we present a Bayesian statistical network to fuse different types of analytical measurements that predict themore » production environment of a Yersinia pestis sample under investigation with automated test processing of scientific publications to identify institutions with a history of growing Y. pestis under similar conditions. Furthermore, the textual and experimental signatures were evaluated recursively to determine the overall sensitivity of the network across all levels of false positives. We illustrate that institutions associated with several specific culturing practices can be accurately selected based on the experimental signature from only a few analytical measurements. These findings demonstrate that similar Bayesian networks can be generated generically for many organisms of interest and their deployment is not prohibitive due to either computational or experimental factors.« less

Water age and stream solute dynamics at the Hubbard Brook Experimental Forest (US)

NASA Astrophysics Data System (ADS)

Botter, Gianluca; Benettin, Paolo; McGuire, Kevin; Rinaldo, Andrea

2016-04-01

The contribution discusses experimental and modeling results from a headwater catchment at the Hubbard Brook Experimental Forest (New Hampshire, USA) to explore the link between stream solute dynamics and water age. A theoretical framework based on water age dynamics, which represents a general basis for characterizing solute transport at the catchment scale, is used to model both conservative and weathering-derived solutes. Based on the available information about the hydrology of the site, an integrated transport model was developed and used to estimate the relevant hydrochemical fluxes. The model was designed to reproduce the deuterium content of streamflow and allowed for the estimate of catchment water storage and dynamic travel time distributions (TTDs). Within this framework, dissolved silicon and sodium concentration in streamflow were simulated by implementing first-order chemical kinetics based explicitly on dynamic TTD, thus upscaling local geochemical processes to catchment scale. Our results highlight the key role of water stored within the subsoil glacial material in both the short-term and long-term solute circulation at Hubbard Brook. The analysis of the results provided by the calibrated model allowed a robust estimate of the emerging concentration-discharge relationship, streamflow age distributions (including the fraction of event water) and storage size, and their evolution in time due to hydrologic variability.

Violent media and hostile appraisals: A meta-analytic review.

PubMed

Bushman, Brad J

2016-11-01

Hostile people tend to view the world as a hostile place. Although there are individual differences in hostile world-views, situational factors can also play a role. For example, scenes of violence in the mass media might influence people to view the world as a hostile place. This meta-analysis aggregates, for the first time, all studies that have investigated the link between exposure to violent media and hostile appraisals (e.g., perceiving the ambiguous actions by others as aggressive actions). This meta-analysis included 37 independent studies involving 10,410 participants. The results showed a "small" to "moderate" sized average correlation between exposure to violent media and hostile appraisals (r +  = .20, 95%CI = .14, .26). Significant correlations were found in experimental, cross-sectional, and longitudinal studies, indicating a triangulation of evidence. Effects were not correlated with participant gender. Effects were also stable over time. However, the link between exposure to violent media and hostile appraisals was positively related to age, perhaps because violent media can have cumulative effects over time. There was no evidence of publication bias. The findings from this meta-analysis are consistent with the General Aggression Model (e.g., Anderson, & Bushman, 2002; Annual Review of Psychology 53:27-51). These results compliment those from previous meta-analyses showing that violent media can increase aggressive thoughts, angry feelings, physiological arousal, and aggressive behavior. These findings also have practical significance, because people who view the world in a hostile manner are more likely to behave aggressively themselves. Aggr. Behav. 42:605-613, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Life hassles and delusional ideation: Scoping the potential role of cognitive and affective mediators.

PubMed

Kingston, Cara; Schuurmans-Stekhoven, James

2016-12-01

An intertemporal association between major psychological stress and subsequent delusion formation has been established by others. The current study explores (1) whether the stress from life hassles predicts delusional ideation and (2) if so, do self-criticism, self-reassurance, and positive and negative affectivity (PA and NA, respectively) mediate this link. This paper thus aimed to scope-out viable psychological processes involved in the formation of stress-induced delusions. A cross-sectional survey using a non-clinical community sample. Responses (N = 251) to an online community survey were tested via a nonparametric bootstrap sampling approach to examine the effects of multiple mediators. Self-criticism and NA appear to mediate a connection found between life hassles and delusions. A second mediation analysis found that life hassles positively predicts NA directly and indirectly (via self-criticism). NA in turn predicted delusional tendencies. Life events had direct statistical effects on delusions in all models. Neither PA nor self-reassurance mediated the stress-delusion link. Self-criticism and NA seem to be viable mediators worth contemplating when elaborating upon the connection between life hassles and delusions. Compared to self-criticism, NA appears to be the intervening variable most proximal to delusions and explains more variance. Even if these cross-sectional results were interpreted as causative, life hassles and delusions remained directly interconnected in all mediation models (suggesting much of the association remains unexplained). Although the results are theory-consistent, investigations using longitudinal, known-group, and experimental methods are now warranted to establish causation and possible feedback loops - especially from delusion to life hassles. Self-criticism and negative affectivity (NA) mediate the link between stressful life events and delusions suggesting they might actively elicit delusional ideation, whereas self-reassurance and PA (although negatively associated with life hassles) have no unique predictive link to delusions. This study offers initial evidence that NA and self-criticism may be viable clinical intervention targets for early psychosis-sufferers under stress - especially for medically non-compliant and marginal (where drug treatment is not clinically indicated) cases. The clinical efficacy of alleviating self-criticism and/or negative emotional processes in those displaying early psychosis or at high risk appear worthy of exploration using both practice-based case studies and formal experimental research methods. © 2016 The British Psychological Society.

A 400 Gbps/100 m free-space optical link

NASA Astrophysics Data System (ADS)

Lin, Chun-Yu; Lu, Hai-Han; Ho, Chun-Ming; Cheng, Ming-Te; Huang, Sheng-Jhe; Wang, Yun-Chieh; Chi, Jing-Kai

2017-02-01

A 400 Gbps/100 m free-space optical (FSO) link with dense-wavelength-division-multiplexing (DWDM)/space-division-multiplexing (SDM) techniques and a doublet lens scheme is proposed. To the best of our knowledge, this is the first time that a link adopting DWDM and SDM techniques and a doublet lens scheme has demonstrated a 400 Gbps/100 m FSO link. The experimental results show that the free-space transmission rate is significantly enhanced by the DWDM and SDM techniques, and the free-space transmission distance is greatly increased by the doublet lens scheme. A 16-channel FSO link with a total transmission rate of 400 Gbps (25 Gbps/λ  ×  16 λ  =  400 Gbps) over a 100 m free-space link is successfully demonstrated. Such a 400 Gbps/100 m DWDM/SDM FSO link provides the advantages of optical wireless communications for high transmission rates and long transmission distances, which is very useful for high-speed and long-haul light-based WiFi (LiFi) applications.

Aggregation of Lens Crystallins in an In Vivo Hyperbaric Oxygen Guinea Pig Model of Nuclear Cataract: Dynamic Light-Scattering and HPLC Analysis

PubMed Central

Simpanya, M. Francis; Ansari, Rafat R.; Suh, Kwang I.; Leverenz, Victor R.; Giblin, Frank J.

2006-01-01

Purpose The role of oxygen in the formation of lens high-molecular-weight (HMW) protein aggregates during the development of human nuclear cataract is not well understood. The purpose of this study was to investigate lens crystallin aggregate formation in hyperbaric oxygen (HBO)–treated guinea pigs by using in vivo and in vitro methods. Methods Guinea pigs were treated three times weekly for 7 months with HBO, and lens crystallin aggregation was investigated in vivo with the use of dynamic light-scattering (DLS) and in vitro by HPLC analysis of water-insoluble (WI) proteins. DLS measurements were made every 0.1 mm across the 4.5- to 5.0-mm optical axis of the guinea pig lens. Results The average apparent diameter of proteins in the nucleus (the central region) of lenses of HBO-treated animals was nearly twice that of the control animals (P < 0.001). Size distribution analysis conducted at one selected point in the nucleus and cortex (the outer periphery of the lens) after dividing the proteins into small-diameter and large-diameter groups, showed in the O2-treated nucleus a threefold increase in intensity (P < 0.001) and a doubling in apparent size (P = 0.03) of large-diameter aggregate proteins, compared with the same control group. No significant changes in apparent protein diameter were detected in the O2-treated cortex, compared with the control. The average diameter of protein aggregates at the single selected location in the O2-treated nucleus was estimated to be 150 nm, a size capable of scattering light and similar to the size of aggregates found in human nuclear cataracts. HPLC analysis indicated that one half of the experimental nuclear WI protein fraction (that had been dissolved in guanidine) consisted of disulfide cross-linked 150- to 1000-kDa aggregates, not present in the control. HPLC-isolated aggregates contained αA-, β-, γ-, and ζ-crystallins, but not αB-crystallin, which is devoid of −SH groups and thus does not participate in disulfide cross-linking. All ζ-crystallin present in the nuclear WI fraction appeared to be there as a result of disulfide cross-linking. Conclusions The results indicate that molecular oxygen in vivo can induce the cross-linking of guinea pig lens nuclear crystallins into large disulfide-bonded aggregates capable of scattering light. A similar process may be involved in the formation of human nuclear cataract. PMID:16303961

Modeling the Structure of Helical Assemblies with Experimental Constraints in Rosetta.

PubMed

André, Ingemar

2018-01-01

Determining high-resolution structures of proteins with helical symmetry can be challenging due to limitations in experimental data. In such instances, structure-based protein simulations driven by experimental data can provide a valuable approach for building models of helical assemblies. This chapter describes how the Rosetta macromolecular package can be used to model homomeric protein assemblies with helical symmetry in a range of modeling scenarios including energy refinement, symmetrical docking, comparative modeling, and de novo structure prediction. Data-guided structure modeling of helical assemblies with experimental information from electron density, X-ray fiber diffraction, solid-state NMR, and chemical cross-linking mass spectrometry is also described.

DFB laser - External modulator fiber optic delay line for radar applications

NASA Astrophysics Data System (ADS)

Newberg, I. L.; Gee, C. M.; Thurmond, G. D.; Yen, H. W.

1989-09-01

A new application of a long fiber-optic delay line as a radar repeater in a radar test set is described. The experimental 31.6-kilometer fiber-optic link includes an external modulator operating with a distributed-feedback laser and low-loss single-mode fiber matched to the laser wavelength to obtain low dispersion for achieving large bandwidth-length performance. The successful tests, in which pulse compression peak sidelobe measurements are used to confirm the link RF phase linearity and SNR performance, show that fiber-optic links can meet the stringent phase and noise requirements of modern radars at high microwave frequencies.

Handbook for the estimation of microwave propagation effects: Link calculations for earth-space paths (path loss and noise estimation)

NASA Technical Reports Server (NTRS)

Crane, R. K.; Blood, D. W.

1979-01-01

A single model for a standard of comparison for other models when dealing with rain attenuation problems in system design and experimentation is proposed. Refinements to the Global Rain Production Model are incorporated. Path loss and noise estimation procedures as the basic input to systems design for earth-to-space microwave links operating at frequencies from 1 to 300 GHz are provided. Topics covered include gaseous absorption, attenuation by rain, ionospheric and tropospheric scintillation, low elevation angle effects, radome attenuation, diversity schemes, link calculation, and receiver noise emission by atmospheric gases, rain, and antenna contributions.

Hopf-link topological nodal-loop semimetals

NASA Astrophysics Data System (ADS)

Zhou, Yao; Xiong, Feng; Wan, Xiangang; An, Jin

2018-04-01

We construct a generic two-band model which can describe topological semimetals with multiple closed nodal loops. All the existing multi-nodal-loop semimetals, including the nodal-net, nodal-chain, and Hopf-link states, can be examined within the same framework. Based on a two-nodal-loop model, the corresponding drumhead surface states for these topologically different bulk states are studied and compared with each other. The connection of our model with Hopf insulators is also discussed. Furthermore, to identify experimentally these topologically different semimetal states, especially to distinguish the Hopf-link from unlinked ones, we also investigate their Landau levels. It is found that the Hopf-link state can be characterized by the existence of a quadruply degenerate zero-energy Landau band, regardless of the direction of the magnetic field.

LinkWinds: An Approach to Visual Data Analysis

NASA Technical Reports Server (NTRS)

Jacobson, Allan S.

1992-01-01

The Linked Windows Interactive Data System (LinkWinds) is a prototype visual data exploration and analysis system resulting from a NASA/JPL program of research into graphical methods for rapidly accessing, displaying and analyzing large multivariate multidisciplinary datasets. It is an integrated multi-application execution environment allowing the dynamic interconnection of multiple windows containing visual displays and/or controls through a data-linking paradigm. This paradigm, which results in a system much like a graphical spreadsheet, is not only a powerful method for organizing large amounts of data for analysis, but provides a highly intuitive, easy to learn user interface on top of the traditional graphical user interface.

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.

Andrew Norman | NREL

Science.gov Websites

MOCVD grown InP-based materials and a LINK project involving TEM studies of non-planar and localized . M. Jones, Appl. Phys. Lett. 93 (2008) 123505. "Theoretical and experimental examination of the

Active Semi-Supervised Community Detection Based on Must-Link and Cannot-Link Constraints

PubMed Central

Cheng, Jianjun; Leng, Mingwei; Li, Longjie; Zhou, Hanhai; Chen, Xiaoyun

2014-01-01

Community structure detection is of great importance because it can help in discovering the relationship between the function and the topology structure of a network. Many community detection algorithms have been proposed, but how to incorporate the prior knowledge in the detection process remains a challenging problem. In this paper, we propose a semi-supervised community detection algorithm, which makes full utilization of the must-link and cannot-link constraints to guide the process of community detection and thereby extracts high-quality community structures from networks. To acquire the high-quality must-link and cannot-link constraints, we also propose a semi-supervised component generation algorithm based on active learning, which actively selects nodes with maximum utility for the proposed semi-supervised community detection algorithm step by step, and then generates the must-link and cannot-link constraints by accessing a noiseless oracle. Extensive experiments were carried out, and the experimental results show that the introduction of active learning into the problem of community detection makes a success. Our proposed method can extract high-quality community structures from networks, and significantly outperforms other comparison methods. PMID:25329660

Flexible robot control: Modeling and experiments

NASA Technical Reports Server (NTRS)

Oppenheim, Irving J.; Shimoyama, Isao

1989-01-01

Described here is a model and its use in experimental studies of flexible manipulators. The analytical model uses the equivalent of Rayleigh's method to approximate the displaced shape of a flexible link as the static elastic displacement which would occur under end rotations as applied at the joints. The generalized coordinates are thereby expressly compatible with joint motions and rotations in serial link manipulators, because the amplitude variables are simply the end rotations between the flexible link and the chord connecting the end points. The equations for the system dynamics are quite simple and can readily be formulated for the multi-link, three-dimensional case. When the flexible links possess mass and (polar moment of) inertia which are small compared to the concentrated mass and inertia at the joints, the analytical model is exact and displays the additional advantage of reduction in system dimension for the governing equations. Four series of pilot tests have been completed. Studies on a planar single-link system were conducted at Carnegie-Mellon University, and tests conducted at Toshiba Corporation on a planar two-link system were then incorporated into the study. A single link system under three-dimensional motion, displaying biaxial flexure, was then tested at Carnegie-Mellon.

A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry.

PubMed

Chavez, Juan D; Eng, Jimmy K; Schweppe, Devin K; Cilia, Michelle; Rivera, Keith; Zhong, Xuefei; Wu, Xia; Allen, Terrence; Khurgel, Moshe; Kumar, Akhilesh; Lampropoulos, Athanasios; Larsson, Mårten; Maity, Shuvadeep; Morozov, Yaroslav; Pathmasiri, Wimal; Perez-Neut, Mathew; Pineyro-Ruiz, Coriness; Polina, Elizabeth; Post, Stephanie; Rider, Mark; Tokmina-Roszyk, Dorota; Tyson, Katherine; Vieira Parrine Sant'Ana, Debora; Bruce, James E

2016-01-01

Chemical cross-linking mass spectrometry (XL-MS) provides protein structural information by identifying covalently linked proximal amino acid residues on protein surfaces. The information gained by this technique is complementary to other structural biology methods such as x-ray crystallography, NMR and cryo-electron microscopy[1]. The extension of traditional quantitative proteomics methods with chemical cross-linking can provide information on the structural dynamics of protein structures and protein complexes. The identification and quantitation of cross-linked peptides remains challenging for the general community, requiring specialized expertise ultimately limiting more widespread adoption of the technique. We describe a general method for targeted quantitative mass spectrometric analysis of cross-linked peptide pairs. We report the adaptation of the widely used, open source software package Skyline, for the analysis of quantitative XL-MS data as a means for data analysis and sharing of methods. We demonstrate the utility and robustness of the method with a cross-laboratory study and present data that is supported by and validates previously published data on quantified cross-linked peptide pairs. This advance provides an easy to use resource so that any lab with access to a LC-MS system capable of performing targeted quantitative analysis can quickly and accurately measure dynamic changes in protein structure and protein interactions.

Modeling Protein Excited-state Structures from "Over-length" Chemical Cross-links.

PubMed

Ding, Yue-He; Gong, Zhou; Dong, Xu; Liu, Kan; Liu, Zhu; Liu, Chao; He, Si-Min; Dong, Meng-Qiu; Tang, Chun

2017-01-27

Chemical cross-linking coupled with mass spectroscopy (CXMS) provides proximity information for the cross-linked residues and is used increasingly for modeling protein structures. However, experimentally identified cross-links are sometimes incompatible with the known structure of a protein, as the distance calculated between the cross-linked residues far exceeds the maximum length of the cross-linker. The discrepancies may persist even after eliminating potentially false cross-links and excluding intermolecular ones. Thus the "over-length" cross-links may arise from alternative excited-state conformation of the protein. Here we present a method and associated software DynaXL for visualizing the ensemble structures of multidomain proteins based on intramolecular cross-links identified by mass spectrometry with high confidence. Representing the cross-linkers and cross-linking reactions explicitly, we show that the protein excited-state structure can be modeled with as few as two over-length cross-links. We demonstrate the generality of our method with three systems: calmodulin, enzyme I, and glutamine-binding protein, and we show that these proteins alternate between different conformations for interacting with other proteins and ligands. Taken together, the over-length chemical cross-links contain valuable information about protein dynamics, and our findings here illustrate the relationship between dynamic domain movement and protein function. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

30S(α , p) Thermonuclear Reaction Rate from Experimental Level Structure of 34Ar

NASA Astrophysics Data System (ADS)

Kahl, D.; Chen, A. A.; Kubono, S.; Yamaguchi, H.; Binh, D. N.; Chen, J.; Cherubini, S.; Duy, N. N.; Hashimoto, T.; Hayakawa, S.; Iwasa, N.; Jung, H. S.; Kato, S.; Kwon, Y. K.; Nishimura, S.; Ota, S.; Setoodehnia, K.; Teranishi, T.; Tokieda, H.; Yamada, T.; Yun, C. C.; Zhang, L. Y.

Type I X-ray bursts are the most frequent thermonuclear explosions in the galaxy. Owing to their recurrence from known astronomical objects, burst morphology is extensively documented, and they are modeled very successfully as neutron-deficient, thermonuclear runaway on the surface of accreting neutron stars. While reaction networks include hundreds of isotopes and thousands of nuclear processes, only a small subset appear to play a pivotal role. One such reaction is the 30S(α , p) reaction, which is believed to be a crucial link in the explosive helium burning which is responsible for the large energy flux. However, very little experimental information is available concerning the cross section itself, nor the 34Ar compound nucleus at the relevant energies. We performed the first study of the entrance channel via 30S alpha resonant elastic scattering using a state-of-the-art, low-energy, 30S radioactive ion beam. The measurement was performed in inverse kinematics using a newly-developed active target. An R-matrix analysis of the excitation function reveals previously unknown resonances, including their quantum properties of spin, parity, width, and energy.

Predicting properties of gas and solid streams by intrinsic kinetics of fast pyrolysis of wood

DOE PAGES

Klinger, Jordan; Bar-Ziv, Ezra; Shonnard, David; ...

2015-12-12

Pyrolysis has the potential to create a biocrude oil from biomass sources that can be used as fuel or as feedstock for subsequent upgrading to hydrocarbon fuels or other chemicals. The product distribution/composition, however, is linked to the biomass source. This work investigates the products formed from pyrolysis of woody biomass with a previously developed chemical kinetics model. Different woody feedstocks reported in prior literature are placed on a common basis (moisture, ash, fixed carbon free) and normalized by initial elemental composition through ultimate analysis. Observed product distributions over the full devolatilization range are explored, reconstructed by the model, andmore » verified with independent experimental data collected with a microwave-assisted pyrolysis system. These trends include production of permanent gas (CO, CO 2), char, and condensable (oil, water) species. Elementary compositions of these streams are also investigated. As a result, close agreement between literature data, model predictions, and independent experimental data indicate that the proposed model/method is able to predict the ideal distribution from fast pyrolysis given reaction temperature, residence time, and feedstock composition.« less

Generation and analysis of correlated pairs of photons on board a nanosatellite

NASA Astrophysics Data System (ADS)

Chandrasekara, R.; Tang, Z.; Tan, Y. C.; Cheng, C.; Sha, L.; Hiang, G. C.; Oi, D.; Ling, A.

2016-10-01

Progress in quantum computers and their threat to conventional public key infrastructure is driving new forms of encryption. Quantum Key Distribution (QKD) using entangled photons is a promising approach. A global QKD network can be achieved using satellites equipped with optical links. Despite numerous proposals, actual experimental work demonstrating relevant entanglement technology in space is limited due to the prohibitive cost of traditional satellite development. To make progress, we have designed a photon pair source that can operate on modular spacecraft called CubeSats. We report the in-orbit operation of the photon pair source on board an orbiting CubeSat and demonstrate pair generation and polarisation correlation under space conditions. The in-orbit polarisation correlations are compatible with ground-based tests, validating our design. This successful demonstration is a major experimental milestone towards a space-based quantum network. Our approach provides a cost-effective method for proving the space-worthiness of critical components used in entangled photon technology. We expect that it will also accelerate efforts to probe the overlap between quantum and relativistic models of physics.

Speaker gender identification based on majority vote classifiers

NASA Astrophysics Data System (ADS)

Mezghani, Eya; Charfeddine, Maha; Nicolas, Henri; Ben Amar, Chokri

2017-03-01

Speaker gender identification is considered among the most important tools in several multimedia applications namely in automatic speech recognition, interactive voice response systems and audio browsing systems. Gender identification systems performance is closely linked to the selected feature set and the employed classification model. Typical techniques are based on selecting the best performing classification method or searching optimum tuning of one classifier parameters through experimentation. In this paper, we consider a relevant and rich set of features involving pitch, MFCCs as well as other temporal and frequency-domain descriptors. Five classification models including decision tree, discriminant analysis, nave Bayes, support vector machine and k-nearest neighbor was experimented. The three best perming classifiers among the five ones will contribute by majority voting between their scores. Experimentations were performed on three different datasets spoken in three languages: English, German and Arabic in order to validate language independency of the proposed scheme. Results confirm that the presented system has reached a satisfying accuracy rate and promising classification performance thanks to the discriminating abilities and diversity of the used features combined with mid-level statistics.

Biosorption of Cd(II) and Cs(I) from aqueous solution by live and dead cells of Saccharomyces carlsbergensis PTCC 5051.

PubMed

Sayyadi, Shayan; Ahmady-Asbchin, Salman; Kamali, Kasra

2018-02-01

The biosorption characteristics of Cd(II) and Cs(I) using live and dead cells of Saccharomyces carlsbergensis PTCC 5051 as biosorbents have been investigated in the present research. The influence of different experimental parameters such as initial pH (pHi), shaking rate, sorption time and initial metal concentration was evaluated. The optimum pH was obtained as 4 for Cd(II) and 7 for Cs(I). The experimental adsorption data were fitted to the Langmuir linear equation adsorption model. The highest metal uptake values of 0.593 and 0.473 mmol g -1 were calculated for Cd(II) and Cs(I), respectively. The results of Fourier transform infrared analysis suggested the involvement of amine, carboxyl and hydroxyl groups during the biosorption process and also indicated that more functional groups were involved in the biosorption process of live adsorbents, compared with those linked to dead biomass. The results showed that the biomass of S. carlsbergensis PTCC 5051 is a suitable biosorbent for the removal of Cd(II) and Cs(I) from the aqueous solutions.

13C CPMAS NMR studies and DFT calculations of triterpene xylosides isolated from Actaea racemosa

NASA Astrophysics Data System (ADS)

Jamróz, Marta K.; Paradowska, Katarzyna; Gliński, Jan A.; Wawer, Iwona

2011-05-01

13C CPMAS NMR spectra of four triterpene glycosides: cimigenol xyloside ( 1), 26-deoxyactein ( 2), cimicifugoside H-1 ( 3) and 24-acethylhydroshengmanol xyloside ( 4) were recorded and analyzed to characterize their solid-state structure. Experimental data were supported by theoretical calculations of NMR shielding constants with the GIAO/6-31G**-su1 approach. A number of methods for the conformational search and a number of functionals for the DFT calculations were applied to ( 1). The best method was proven to be MMFF or MMFFAQ for the conformational search and the PBE1PBE functional for the DFT calculations. Extra calculations simulating C16 dbnd O⋯HOH hydrogen bond yield the isotropic shielding closer to the experimental solid-state value. For all the compounds CP kinetics parameters were calculated using either the I-S or the I-I*-S model. The analysis of CP kinetics data for methyl groups revealed differences in the T2 time constant for two methyl groups (C29 and C30) linked at C4.

Adsorption of Emerging Munitions Contaminants on Cellulose Surface: A Combined Theoretical and Experimental Investigation.

PubMed

Shukla, Manoj K; Poda, Aimee

2016-06-01

This manuscript reports results of an integrated theoretical and experimental investigation of adsorption of two emerging contaminants (DNAN and FOX-7) and legacy compound TNT on cellulose surface. Cellulose was modeled as trimeric form of the linear chain of 1 → 4 linked of β-D-glucopyranos in (4)C1 chair conformation. Geometries of modeled cellulose, munitions compounds and their complexes were optimized at the M06-2X functional level of Density Functional Theory using the 6-31G(d,p) basis set in gas phase and in water solution. The effect of water solution was modeled using the CPCM approach. Nature of potential energy surfaces was ascertained through harmonic vibrational frequency analysis. Interaction energies were corrected for basis set superposition error and the 6-311G(d,p) basis set was used. Molecular electrostatic potential mapping was performed to understand the reactivity of the investigated systems. It was predicted that adsorbates will be weakly adsorbed on the cellulose surface in water solution than in the gas phase.

Applicability of ELISA-based Determination of Pesticides for Groundwater Quality Monitoring

NASA Astrophysics Data System (ADS)

Tsuchihara, Takeo; Yoshimoto, Shuhei; Ishida, Satoshi; Imaizumi, Masayuki

The principals and procedures of ELISA (Enzyme-linked Immunosorbent Assay)-based determination of pesticides (Fenitrothion) in environmental samples were reviewed, and the applicability of the ELISA method for groundwater quality monitoring were validated through the experimental tracer tests in soil columns and the field test in Okinoerabu Island. The test results showed that the ELISA method could be useful not only for screening but also for quantitative analysis of pesticides. In the experimental tracer tests in soil columns, the retardation of pesticides leaching compared with conservative tracers were observed. In the field test, the contamination of the pesticide was detected in groundwater samples in Okinoerabu Island, even though the targeted pesticide was considered to be applied to the upland field 4 months ago. In order to investigate the transport and fate of pesticides in groundwater taking into account retardation from the field to groundwater table and the residue in groundwater, continuous observations of pesticides in groundwater are in a strong need, and the ELISA method is applicable to the long-term quality groundwater monitoring.

Antagonistic autoregulation speeds up a homogeneous response in Escherichia coli.

PubMed

Rodrigo, Guillermo; Bajic, Djordje; Elola, Ignacio; Poyatos, Juan F

2016-10-31

By integrating positive and negative feedback loops, biological systems establish intricate gene expression patterns linked to multistability, pulsing, and oscillations. This depends on the specific characteristics of each interlinked feedback, and thus one would expect additional expression programs to be found. Here, we investigate one such program associated with an antagonistic positive and negative transcriptional autoregulatory motif derived from the multiple antibiotic resistance (mar) system of Escherichia coli. We studied the dynamics of the system by combining a predictive mathematical model with high-resolution experimental measures of the response both at the population and single-cell level. We show that in this motif the weak positive autoregulation does not slow down but rather enhances response speedup in combination with a strong negative feedback loop. This balance of feedback strengths anticipates a homogeneous population phenotype, which we corroborate experimentally. Theoretical analysis also emphasized the specific molecular properties that determine the dynamics of the mar phenotype. More broadly, response acceleration could provide a rationale for the presence of weak positive feedbacks in other biological scenarios exhibiting these interlinked regulatory architectures.

Inter-satellite links for satellite autonomous integrity monitoring

NASA Astrophysics Data System (ADS)

Rodríguez-Pérez, Irma; García-Serrano, Cristina; Catalán Catalán, Carlos; García, Alvaro Mozo; Tavella, Patrizia; Galleani, Lorenzo; Amarillo, Francisco

2011-01-01

A new integrity monitoring mechanisms to be implemented on-board on a GNSS taking advantage of inter-satellite links has been introduced. This is based on accurate range and Doppler measurements not affected neither by atmospheric delays nor ground local degradation (multipath and interference). By a linear combination of the Inter-Satellite Links Observables, appropriate observables for both satellite orbits and clock monitoring are obtained and by the proposed algorithms it is possible to reduce the time-to-alarm and the probability of undetected satellite anomalies.Several test cases have been run to assess the performances of the new orbit and clock monitoring algorithms in front of a complete scenario (satellite-to-satellite and satellite-to-ground links) and in a satellite-only scenario. The results of this experimentation campaign demonstrate that the Orbit Monitoring Algorithm is able to detect orbital feared events when the position error at the worst user location is still under acceptable limits. For instance, an unplanned manoeuvre in the along-track direction is detected (with a probability of false alarm equals to 5 × 10-9) when the position error at the worst user location is 18 cm. The experimentation also reveals that the clock monitoring algorithm is able to detect phase jumps, frequency jumps and instability degradation on the clocks but the latency of detection as well as the detection performances strongly depends on the noise added by the clock measurement system.

A Multiscale Model for the Quasi-Static Thermo-Plastic Behavior of Highly Cross-Linked Glassy Polymers

DOE PAGES

Vu-Bac, N.; Bessa, M. A.; Rabczuk, Timon; ...

2015-09-10

In this paper, we present experimentally validated molecular dynamics predictions of the quasi- static yield and post-yield behavior for a highly cross-linked epoxy polymer under gen- eral stress states and for different temperatures. In addition, a hierarchical multiscale model is presented where the nano-scale simulations obtained from molecular dynamics were homogenized to a continuum thermoplastic constitutive model for the epoxy that can be used to describe the macroscopic behavior of the material. Three major conclusions were achieved: (1) the yield surfaces generated from the nano-scale model for different temperatures agree well with the paraboloid yield crite- rion, supporting previous macroscopicmore » experimental observations; (2) rescaling of the entire yield surfaces to the quasi-static case is possible by considering Argon’s theoretical predictions for pure compression of the polymer at absolute zero temperature; (3) nano- scale simulations can be used for an experimentally-free calibration of macroscopic con- tinuum models, opening new avenues for the design of materials and structures through multi-scale simulations that provide structure-property-performance relationships.« less

Promoting resilience in youth from divorced families: lessons learned from experimental trials of the New Beginnings Program.

PubMed

Wolchik, Sharlene A; Schenck, Clorinda E; Sandler, Irwin N

2009-12-01

This article focuses on the contributions that the program of research on the New Beginnings Program (NBP) has made to understanding pathways to resilience in youth who experience parental divorce. First, the research demonstrating that divorce increases risk for mental health, physical health, and social adaptation problems is reviewed. Next, theory and research linking social environmental-level and youth-level modifiable risk factors and resilience resources to youth's postdivorce adjustment are presented. The conceptual framework underlying the NBP and the risk factors and resilience resources targeted in this program are described next. The short-term and long-term results of two experimental, randomized efficacy trials of the NBP and moderators and mediators of its effects are then presented. Analyses that examine whether youth self-systems beliefs account for the links between program-induced changes in family-level resilience resources and positive long-term program on adaptation outcomes are presented and how experimental trials can be used to further theories of resilience for youth facing adversities is discussed. The final section describes directions for future research on the NBP.

Promoting Resilience in Youth from Divorced Families: Lessons Learned from Experimental Trials of the New Beginnings Program

PubMed Central

Wolchik, Sharlene A.; Schenck, Clorinda E.; Sandler, Irwin N.

2009-01-01

This article focuses on the contributions that the program of research on the New Beginnings Program (NBP) has made to understanding pathways to resilience in youth who experience parental divorce. First, the research demonstrating that divorce increases risk for mental health, physical health and social adaptation problems is reviewed. Next, theory and research linking social environmental-level and youth-level modifiable risk factors and resilience resources to youth’s post-divorce adjustment are presented. The conceptual framework underlying the NBP and the risk factors and resilience resources targeted in this program are described next. The short-term and long-term results of two experimental, randomized efficacy trials of the NBP and moderators and mediators of its effects are then presented. Analyses that examine whether youth self-systems beliefs account for the links between program-induced changes in family-level resilience resources and positive long-term program on adaptation outcomes are presented and how experimental trials can be used to further theories of resilience for youth facing adversities is discussed. The final section describes directions for future research on the NBP. PMID:19807862

Wallops Low Elevation Link Analysis for the Constellation Launch/Ascent Links

NASA Technical Reports Server (NTRS)

Cheung, Keith; Ho, C.; Kantak, A.; Lee, C.; Tye, R.; Richards, E.; Sham, C.; Schlesinger, A.; Barritt, B.

2011-01-01

To execute the President's Vision for Space Exploration, the Constellation Program (CxP) was formed to build the next generation spacecraft Orion and launch vehicles Ares, to transport human and cargo to International Space Station (ISS), moon, and Mars. This paper focuses on the detailed link analysis for Orion/Ares s launch and ascent links with Wallops 11.3m antenna (1) Orion's Dissimilar Voice link: 10.24 Kbps, 2-way (2) Ares Developmental Flight Instrument link, 20 Mbps, downlink. Three launch trajectories are considered: TD7-E, F (Feb), and G (Aug). In certain launch scenarios, the critical events of main engine cutoff (MECO) and Separation occur during the low elevation regime of WFF s downrange -- less than 5 degree elevation angle. The goal of the study is to access if there is enough link margins for WFF to track the DV and DFI links.

Alexei Abrikosov and Superconductivity

Science.gov Websites

Superconducting Cuprates Based on Experimental Evidence, , DOE Technical Report Download Adobe PDF Reader Some links on this page may take you to non-federal websites. Their policies may differ from this site

Michael Levitt and Computational Biology

Science.gov Websites

molecular structures, compute structural changes, refine experimental structure, model enzyme catalysis and (May 2004) Top Some links on this page may take you to non-federal websites. Their policies may differ

77 FR 27097 - Sunshine Act Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-08

... Experimental Amateur-Built Aircraft. NEWS MEDIA CONTACT: Telephone: (202) 314-6100. The press and public may.... The public may view the meeting via a live or archived webcast by accessing a link under ``News...

Linking Well-Tempered Metadynamics Simulations with Experiments

PubMed Central

Barducci, Alessandro; Bonomi, Massimiliano; Parrinello, Michele

2010-01-01

Abstract Linking experiments with the atomistic resolution provided by molecular dynamics simulations can shed light on the structure and dynamics of protein-disordered states. The sampling limitations of classical molecular dynamics can be overcome using metadynamics, which is based on the introduction of a history-dependent bias on a small number of suitably chosen collective variables. Even if such bias distorts the probability distribution of the other degrees of freedom, the equilibrium Boltzmann distribution can be reconstructed using a recently developed reweighting algorithm. Quantitative comparison with experimental data is thus possible. Here we show the potential of this combined approach by characterizing the conformational ensemble explored by a 13-residue helix-forming peptide by means of a well-tempered metadynamics/parallel tempering approach and comparing the reconstructed nuclear magnetic resonance scalar couplings with experimental data. PMID:20441734

What can experimental geobiology tell us about mass extinctions, past, present and future?

NASA Astrophysics Data System (ADS)

Bond, David

2017-04-01

We know more than ever about the causes and consequences of Earth's greatest mass extinctions thanks to much improved resolution in the fossil record, dating, and proxies for palaeoenvironmental change. Despite much progress, there is no consensus on what drives ecosystems to collapse. The realisation that Earth is again facing stresses implicated in its past crises (e.g. proximal kill mechanisms such as global warming, ocean acidification and anoxia) has intensified research on the ultimate cause(s) of extinctions (e.g. large igneous provinces and bolide impacts). However, the links between proximal kill mechanisms and their drivers remains poorly understood. Here I evaluate environmental factors implicated in major episodes of species extinctions and explores the mechanistic links by which they did their damage. Experimental geobiology is beginning to unlock the secrets of past crises by examining responses of species to change. Reduced pH, for instance alters the efficacy of fishes' chemical receptors, leaving them less equipped to detect prey, predators and mates - invoking "death-by-celibacy" scenarios. Elevated atmospheric CO2 induces hypercapnic stress (as well as being the root cause of ocean acidification). Prolonged exposure to anoxia causes death without selectivity. Global warming induces a multitude of stresses, primarily linked to increased metabolic rate according to the Q10 law. Experimental geobiologists and Earth scientists could together unravel the causes of past extinctions, better inform understanding of the modern crisis and our approach to the future.

Development of Compositionally Graded Metallic Glass Alloys with Desirable Properties

DTIC Science & Technology

2016-06-01

individual study . Include participation in conferences, workshops, and seminars not listed under major activities. At OSU, one graduate student ...best glass former in a fraction of the experimental time of previous study , which identified similar compositions of Cu57.6Zr32.4Ti10,13 and...years, several experimental and computational studies have suggested a direct link between the population of shear transformation zones (STZs

Experimentally Estimated Impacts of School Vouchers on College Enrollment and Degree Attainment. Program on Education Policy and Governance Working Papers Series. PEPG 15-01

ERIC Educational Resources Information Center

Chingos, Matthew M.; Peterson, Paul E.

2015-01-01

We provide the first experimental estimates of the long-term impacts of a voucher to attend private school by linking data from a privately sponsored voucher initiative in New York City, which awarded the scholarships by lottery to low-income families, to administrative records on college enrollment and degree attainment. We find no significant…