An experimental approach to the fundamental principles of hemodynamics.

PubMed

Pontiga, Francisco; Gaytán, Susana P

2005-09-01

An experimental model has been developed to give students hands-on experience with the fundamental laws of hemodynamics. The proposed experimental setup is of simple construction but permits the precise measurements of physical variables involved in the experience. The model consists in a series of experiments where different basic phenomena are quantitatively investigated, such as the pressure drop in a long straight vessel and in an obstructed vessel, the transition from laminar to turbulent flow, the association of vessels in vascular networks, or the generation of a critical stenosis. Through these experiments, students acquire a direct appreciation of the importance of the parameters involved in the relationship between pressure and flow rate, thus facilitating the comprehension of more complex problems in hemodynamics.

Computational modeling of RNA 3D structures, with the aid of experimental restraints

PubMed Central

Magnus, Marcin; Matelska, Dorota; Łach, Grzegorz; Chojnowski, Grzegorz; Boniecki, Michal J; Purta, Elzbieta; Dawson, Wayne; Dunin-Horkawicz, Stanislaw; Bujnicki, Janusz M

2014-01-01

In addition to mRNAs whose primary function is transmission of genetic information from DNA to proteins, numerous other classes of RNA molecules exist, which are involved in a variety of functions, such as catalyzing biochemical reactions or performing regulatory roles. In analogy to proteins, the function of RNAs depends on their structure and dynamics, which are largely determined by the ribonucleotide sequence. Experimental determination of high-resolution RNA structures is both laborious and difficult, and therefore, the majority of known RNAs remain structurally uncharacterized. To address this problem, computational structure prediction methods were developed that simulate either the physical process of RNA structure formation (“Greek science” approach) or utilize information derived from known structures of other RNA molecules (“Babylonian science” approach). All computational methods suffer from various limitations that make them generally unreliable for structure prediction of long RNA sequences. However, in many cases, the limitations of computational and experimental methods can be overcome by combining these two complementary approaches with each other. In this work, we review computational approaches for RNA structure prediction, with emphasis on implementations (particular programs) that can utilize restraints derived from experimental analyses. We also list experimental approaches, whose results can be relatively easily used by computational methods. Finally, we describe case studies where computational and experimental analyses were successfully combined to determine RNA structures that would remain out of reach for each of these approaches applied separately. PMID:24785264

A multiscale-based approach for composite materials with embedded PZT filaments for energy harvesting

NASA Astrophysics Data System (ADS)

El-Etriby, Ahmed E.; Abdel-Meguid, Mohamed E.; Hatem, Tarek M.; Bahei-El-Din, Yehia A.

2014-03-01

Ambient vibrations are major source of wasted energy, exploiting properly such vibration can be converted to valuable energy and harvested to power up devices, i.e. electronic devices. Accordingly, energy harvesting using smart structures with active piezoelectric ceramics has gained wide interest over the past few years as a method for converting such wasted energy. This paper provides numerical and experimental analysis of piezoelectric fiber based composites for energy harvesting applications proposing a multi-scale modeling approach coupled with experimental verification. The multi-scale approach suggested to predict the behavior of piezoelectric fiber-based composites use micromechanical model based on Transformation Field Analysis (TFA) to calculate the overall material properties of electrically active composite structure. Capitalizing on the calculated properties, single-phase analysis of a homogeneous structure is conducted using finite element method. The experimental work approach involves running dynamic tests on piezoelectric fiber-based composites to simulate mechanical vibrations experienced by a subway train floor tiles. Experimental results agree well with the numerical results both for static and dynamic tests.

Teaching Grade 5 Life Science with a Case Study Approach

ERIC Educational Resources Information Center

Olgun, Ozlem Sila; Adali, Belgin

2008-01-01

The main purpose of this study was to investigate the effects of a case study approach on students' achievement and attitudes towards viruses, bacteria, fungi, and protista. Fifth-grade students (N = 88) from two different classes were involved in the study. One intact class was assigned as the experimental group, whereas the other intact class…

Intergration of system identification and robust controller designs for flexible structures in space

NASA Technical Reports Server (NTRS)

Juang, Jer-Nan; Lew, Jiann-Shiun

1990-01-01

An approach is developed using experimental data to identify a reduced-order model and its model error for a robust controller design. There are three steps involved in the approach. First, an approximately balanced model is identified using the Eigensystem Realization Algorithm, which is an identification algorithm. Second, the model error is calculated and described in frequency domain in terms of the H(infinity) norm. Third, a pole placement technique in combination with a H(infinity) control method is applied to design a controller for the considered system. A set experimental data from an existing setup, namely the Mini-Mast system, is used to illustrate and verify the approach.

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

Noe, F; Diadone, Isabella; Lollmann, Marc

There is a gap between kinetic experiment and simulation in their views of the dynamics of complex biomolecular systems. Whereas experiments typically reveal only a few readily discernible exponential relaxations, simulations often indicate complex multistate behavior. Here, a theoretical framework is presented that reconciles these two approaches. The central concept is dynamical fingerprints which contain peaks at the time scales of the dynamical processes involved with amplitudes determined by the experimental observable. Fingerprints can be generated from both experimental and simulation data, and their comparison by matching peaks permits assignment of structural changes present in the simulation to experimentally observedmore » relaxation processes. The approach is applied here to a test case interpreting single molecule fluorescence correlation spectroscopy experiments on a set of fluorescent peptides with molecular dynamics simulations. The peptides exhibit complex kinetics shown to be consistent with the apparent simplicity of the experimental data. Moreover, the fingerprint approach can be used to design new experiments with site-specific labels that optimally probe specific dynamical processes in the molecule under investigation.« less

Mathematical Science Course

ERIC Educational Resources Information Center

Woof, K. R.

1975-01-01

Describes an experimental type of science course which involves theoretical and practical approaches to scientific topics by using mathematics to develop and explain scientific problems and theory. Gives an example of such a course applied to the teaching of physical anthropology. (MLH)

Prolonged sleep restriction induces changes in pathways involved in cholesterol metabolism and inflammatory responses.

PubMed

Aho, Vilma; Ollila, Hanna M; Kronholm, Erkki; Bondia-Pons, Isabel; Soininen, Pasi; Kangas, Antti J; Hilvo, Mika; Seppälä, Ilkka; Kettunen, Johannes; Oikonen, Mervi; Raitoharju, Emma; Hyötyläinen, Tuulia; Kähönen, Mika; Viikari, Jorma S A; Härmä, Mikko; Sallinen, Mikael; Olkkonen, Vesa M; Alenius, Harri; Jauhiainen, Matti; Paunio, Tiina; Lehtimäki, Terho; Salomaa, Veikko; Orešič, Matej; Raitakari, Olli T; Ala-Korpela, Mika; Porkka-Heiskanen, Tarja

2016-04-22

Sleep loss and insufficient sleep are risk factors for cardiometabolic diseases, but data on how insufficient sleep contributes to these diseases are scarce. These questions were addressed using two approaches: an experimental, partial sleep restriction study (14 cases and 7 control subjects) with objective verification of sleep amount, and two independent epidemiological cohorts (altogether 2739 individuals) with questions of sleep insufficiency. In both approaches, blood transcriptome and serum metabolome were analysed. Sleep loss decreased the expression of genes encoding cholesterol transporters and increased expression in pathways involved in inflammatory responses in both paradigms. Metabolomic analyses revealed lower circulating large HDL in the population cohorts among subjects reporting insufficient sleep, while circulating LDL decreased in the experimental sleep restriction study. These findings suggest that prolonged sleep deprivation modifies inflammatory and cholesterol pathways at the level of gene expression and serum lipoproteins, inducing changes toward potentially higher risk for cardiometabolic diseases.

The Development of Animal Behavior: From Lorenz to Neural Nets

NASA Astrophysics Data System (ADS)

Bolhuis, Johan J.

In the study of behavioral development both causal and functional approaches have been used, and they often overlap. The concept of ontogenetic adaptations suggests that each developmental phase involves unique adaptations to the environment of the developing animal. The functional concept of optimal outbreeding has led to further experimental evidence and theoretical models concerning the role of sexual imprinting in the evolutionary process of sexual selection. From a causal perspective it has been proposed that behavioral ontogeny involves the development of various kinds of perceptual, motor, and central mechanisms and the formation of connections among them. This framework has been tested for a number of complex behavior systems such as hunger and dustbathing. Imprinting is often seen as a model system for behavioral development in general. Recent advances in imprinting research have been the result of an interdisciplinary effort involving ethology, neuroscience, and experimental psychology, with a continual interplay between these approaches. The imprinting results are consistent with Lorenz' early intuitive suggestions and are also reflected in the architecture of recent neural net models.

A Sub-filter Scale Noise Equation far Hybrid LES Simulations

NASA Technical Reports Server (NTRS)

Goldstein, Marvin E.

2006-01-01

Hybrid LES/subscale modeling approaches have an important advantage over the current noise prediction methods in that they only involve modeling of the relatively universal subscale motion and not the configuration dependent larger scale turbulence . Previous hybrid approaches use approximate statistical techniques or extrapolation methods to obtain the requisite information about the sub-filter scale motion. An alternative approach would be to adopt the modeling techniques used in the current noise prediction methods and determine the unknown stresses from experimental data. The present paper derives an equation for predicting the sub scale sound from information that can be obtained with currently available experimental procedures. The resulting prediction method would then be intermediate between the current noise prediction codes and previously proposed hybrid techniques.

Reducing emotional reasoning: an experimental manipulation in individuals with fear of spiders.

PubMed

Lommen, Miriam J J; Engelhard, Iris M; van den Hout, Marcel A; Arntz, Arnoud

2013-01-01

Emotional reasoning involves the tendency to use subjective responses to make erroneous inferences about situations (e.g., "If I feel anxious, there must be danger") and has been implicated in various anxiety disorders. The aim of this study of individuals with fear of spiders was to test whether computerised experimental training, compared to control training, would decrease emotional reasoning, reduce fear-related danger beliefs, and increase approach behaviour towards a fear-relevant stimulus. Effects were assessed shortly after the experimental manipulation and one day later. Results showed that the manipulation significantly decreased emotional reasoning in the experimental condition, not in the control condition, and resulted in lower danger estimates of a spider, which was maintained up to one day later. No differences in approach behaviour towards the spider were found. Reducing emotional reasoning may ultimately help patients with anxiety disorders attend more to objective situational information to correct erroneous danger beliefs.

Demonstrations of Extraterrestrial Life Detection Techniques in the High School Biology Laboratory

ERIC Educational Resources Information Center

Saltinski, Ronald

1969-01-01

Discusses the experimental procedures and equipment for exobiology projects at the high school level. An interdisciplinary approach involving electronic equipment and micro-biological laboratory techniques is used. Photographs and diagrams of equipment are included. Bibliography. (LC)

A Three-Dimensional Approach and Open Source Structure for the Design and Experimentation of Teaching-Learning Sequences: The Case of Friction

ERIC Educational Resources Information Center

Besson, Ugo; Borghi, Lidia; De Ambrosis, Anna; Mascheretti, Paolo

2010-01-01

We have developed a teaching-learning sequence (TLS) on friction based on a preliminary study involving three dimensions: an analysis of didactic research on the topic, an overview of usual approaches, and a critical analysis of the subject, considered also in its historical development. We found that mostly the usual presentations do not take…

Determination of excitation profile and dielectric function spatial nonuniformity in porous silicon by using WKB approach.

PubMed

He, Wei; Yurkevich, Igor V; Canham, Leigh T; Loni, Armando; Kaplan, Andrey

2014-11-03

We develop an analytical model based on the WKB approach to evaluate the experimental results of the femtosecond pump-probe measurements of the transmittance and reflectance obtained on thin membranes of porous silicon. The model allows us to retrieve a pump-induced nonuniform complex dielectric function change along the membrane depth. We show that the model fitting to the experimental data requires a minimal number of fitting parameters while still complying with the restriction imposed by the Kramers-Kronig relation. The developed model has a broad range of applications for experimental data analysis and practical implementation in the design of devices involving a spatially nonuniform dielectric function, such as in biosensing, wave-guiding, solar energy harvesting, photonics and electro-optical devices.

Three-dimensional broadband omnidirectional acoustic ground cloak

NASA Astrophysics Data System (ADS)

Zigoneanu, Lucian; Popa, Bogdan-Ioan; Cummer, Steven A.

2014-04-01

The control of sound propagation and reflection has always been the goal of engineers involved in the design of acoustic systems. A recent design approach based on coordinate transformations, which is applicable to many physical systems, together with the development of a new class of engineered materials called metamaterials, has opened the road to the unconstrained control of sound. However, the ideal material parameters prescribed by this methodology are complex and challenging to obtain experimentally, even using metamaterial design approaches. Not surprisingly, experimental demonstration of devices obtained using transformation acoustics is difficult, and has been implemented only in two-dimensional configurations. Here, we demonstrate the design and experimental characterization of an almost perfect three-dimensional, broadband, and, most importantly, omnidirectional acoustic device that renders a region of space three wavelengths in diameter invisible to sound.

The Intersection of Theory and Application in Elucidating Pattern Formation in Developmental Biology

PubMed Central

Othmer, Hans G.; Painter, Kevin; Umulis, David; Xue, Chuan

2009-01-01

We discuss theoretical and experimental approaches to three distinct developmental systems that illustrate how theory can influence experimental work and vice-versa. The chosen systems – Drosophila melanogaster, bacterial pattern formation, and pigmentation patterns – illustrate the fundamental physical processes of signaling, growth and cell division, and cell movement involved in pattern formation and development. These systems exemplify the current state of theoretical and experimental understanding of how these processes produce the observed patterns, and illustrate how theoretical and experimental approaches can interact to lead to a better understanding of development. As John Bonner said long ago ‘We have arrived at the stage where models are useful to suggest experiments, and the facts of the experiments in turn lead to new and improved models that suggest new experiments. By this rocking back and forth between the reality of experimental facts and the dream world of hypotheses, we can move slowly toward a satisfactory solution of the major problems of developmental biology.’ PMID:19844610

Orbital Energy Levels in Molecular Hydrogen. A Simple Approach.

ERIC Educational Resources Information Center

Willis, Christopher J.

1988-01-01

Described are the energetics involved in the formation of molecular hydrogen using concepts that should be familiar to students beginning the study of molecular orbital theory. Emphasized are experimental data on ionization energies. Included are two-electron atomic and molecular systems. (CW)

MODELING A MIXTURE: PBPK/PD APPROACHES FOR PREDICTING CHEMICAL INTERACTIONS.

EPA Science Inventory

Since environmental chemical exposures generally involve multiple chemicals, there are both regulatory and scientific drivers to develop methods to predict outcomes of these exposures. Even using efficient statistical and experimental designs, it is not possible to test in vivo a...

R1 autonomic nervous system in acute kidney injury.

PubMed

Hering, Dagmara; Winklewski, Pawel J

2017-02-01

Acute kidney injury (AKI) is a rapid loss of kidney function resulting in accumulation of end metabolic products and associated abnormalities in fluid, electrolyte and acid-base homeostasis. The pathophysiology of AKI is complex and multifactorial involving numerous vascular, tubular and inflammatory pathways. Neurohumoral activation with heightened activity of the sympathetic nervous system and renin-angiotensin-aldosterone system play a critical role in this scenario. Inflammation and/or local renal ischaemia are underlying mechanisms triggering renal tissue hypoxia and resultant renal microcirculation dysfunction; a common feature of AKI occurring in numerous clinical conditions leading to a high morbidity and mortality rate. The contribution of renal nerves to the pathogenesis of AKI has been extensively demonstrated in a series of experimental models over the past decades. While this has led to better knowledge of the pathogenesis of human AKI, therapeutic approaches to improve patient outcomes are scarce. Restoration of autonomic regulatory function with vagal nerve stimulation resulting in anti-inflammatory effects and modulation of centrally-mediated mechanisms could be of clinical relevance. Evidence from experimental studies suggests that a therapeutic splenic ultrasound approach may prevent AKI via activation of the cholinergic anti-inflammatory pathway. This review briefly summarizes renal nerve anatomy, basic insights into neural control of renal function in the physiological state and the involvement of the autonomic nervous system in the pathophysiology of AKI chiefly due to sepsis, cardiopulmonary bypass and ischaemia/reperfusion experimental model. Finally, potentially preventive experimental pre-clinical approaches for the treatment of AKI aimed at sympathetic inhibition and/or parasympathetic stimulation are presented. © 2016 John Wiley & Sons Australia, Ltd.

An Integrated Constraint Programming Approach to Scheduling Sports Leagues with Divisional and Round-robin Tournaments

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

Carlsson, Mats; Johansson, Mikael; Larson, Jeffrey

Previous approaches for scheduling a league with round-robin and divisional tournaments involved decomposing the problem into easier subproblems. This approach, used to schedule the top Swedish handball league Elitserien, reduces the problem complexity but can result in suboptimal schedules. This paper presents an integrated constraint programming model that allows to perform the scheduling in a single step. Particular attention is given to identifying implied and symmetry-breaking constraints that reduce the computational complexity significantly. The experimental evaluation of the integrated approach takes considerably less computational effort than the previous approach.

New advances in the statistical parton distributions approach

NASA Astrophysics Data System (ADS)

Soffer, Jacques; Bourrely, Claude

2016-03-01

The quantum statistical parton distributions approach proposed more than one decade ago is revisited by considering a larger set of recent and accurate Deep Inelastic Scattering experimental results. It enables us to improve the description of the data by means of a new determination of the parton distributions. This global next-to-leading order QCD analysis leads to a good description of several structure functions, involving unpolarized parton distributions and helicity distributions, in terms of a rather small number of free parameters. There are many serious challenging issues. The predictions of this theoretical approach will be tested for single-jet production and charge asymmetry in W± production in p¯p and pp collisions up to LHC energies, using recent data and also for forthcoming experimental results. Presented by J. So.er at POETIC 2015

Understanding healthcare innovation systems: the Stockholm region case.

PubMed

Larisch, Lisa-Marie; Amer-Wåhlin, Isis; Hidefjäll, Patrik

2016-11-21

Purpose There is an increasing interest in understanding how innovation processes can address current challenges in healthcare. The purpose of this paper is to analyze the wider socio-economic context and conditions for such innovation processes in the Stockholm region, using the functional dynamics approach to innovation systems (ISs). Design/methodology/approach The analysis is based on triangulation using data from 16 in-depth interviews, two workshops, and additional documents. Using the functional dynamics approach, critical structural and functional components of the healthcare IS were analyzed. Findings The analysis revealed several mechanisms blocking innovation processes such as fragmentation, lack of clear leadership, as well as insufficient involvement of patients and healthcare professionals. Furthermore, innovation is expected to occur linearly as a result of research. Restrictive rules for collaboration with industry, reimbursement, and procurement mechanisms limit entrepreneurial experimentation, commercialization, and spread of innovations. Research limitations/implications In this study, the authors analyzed how certain functions of the functional dynamics approach to ISs related to each other. The authors grouped knowledge creation, resource mobilization, and legitimacy as they jointly constitute conditions for needs articulation and entrepreneurial experimentation. The economic effects of entrepreneurial experimentation and needs articulation are mainly determined by the stage of market formation and existence of positive externalities. Social implications Stronger user involvement; a joint innovation strategy for healthcare, academia, and industry; and institutional reform are necessary to remove blocking mechanisms that today prevent innovation from occurring. Originality/value This study is the first to provide an analysis of the system of innovation in healthcare using a functional dynamics approach, which has evolved as a tool for public policy making. A better understanding of ISs in general, and in healthcare in particular, may provide the basis for designing and evaluating innovation policy.

A Quantitative Systems Pharmacology Approach to Infer Pathways Involved in Complex Disease Phenotypes.

PubMed

Schurdak, Mark E; Pei, Fen; Lezon, Timothy R; Carlisle, Diane; Friedlander, Robert; Taylor, D Lansing; Stern, Andrew M

2018-01-01

Designing effective therapeutic strategies for complex diseases such as cancer and neurodegeneration that involve tissue context-specific interactions among multiple gene products presents a major challenge for precision medicine. Safe and selective pharmacological modulation of individual molecular entities associated with a disease often fails to provide efficacy in the clinic. Thus, development of optimized therapeutic strategies for individual patients with complex diseases requires a more comprehensive, systems-level understanding of disease progression. Quantitative systems pharmacology (QSP) is an approach to drug discovery that integrates computational and experimental methods to understand the molecular pathogenesis of a disease at the systems level more completely. Described here is the chemogenomic component of QSP for the inference of biological pathways involved in the modulation of the disease phenotype. The approach involves testing sets of compounds of diverse mechanisms of action in a disease-relevant phenotypic assay, and using the mechanistic information known for the active compounds, to infer pathways and networks associated with the phenotype. The example used here is for monogenic Huntington's disease (HD), which due to the pleiotropic nature of the mutant phenotype has a complex pathogenesis. The overall approach, however, is applicable to any complex disease.

Experimental design matters for statistical analysis: how to handle blocking.

PubMed

Jensen, Signe M; Schaarschmidt, Frank; Onofri, Andrea; Ritz, Christian

2018-03-01

Nowadays, evaluation of the effects of pesticides often relies on experimental designs that involve multiple concentrations of the pesticide of interest or multiple pesticides at specific comparable concentrations and, possibly, secondary factors of interest. Unfortunately, the experimental design is often more or less neglected when analysing data. Two data examples were analysed using different modelling strategies. First, in a randomized complete block design, mean heights of maize treated with a herbicide and one of several adjuvants were compared. Second, translocation of an insecticide applied to maize as a seed treatment was evaluated using incomplete data from an unbalanced design with several layers of hierarchical sampling. Extensive simulations were carried out to further substantiate the effects of different modelling strategies. It was shown that results from suboptimal approaches (two-sample t-tests and ordinary ANOVA assuming independent observations) may be both quantitatively and qualitatively different from the results obtained using an appropriate linear mixed model. The simulations demonstrated that the different approaches may lead to differences in coverage percentages of confidence intervals and type 1 error rates, confirming that misleading conclusions can easily happen when an inappropriate statistical approach is chosen. To ensure that experimental data are summarized appropriately, avoiding misleading conclusions, the experimental design should duly be reflected in the choice of statistical approaches and models. We recommend that author guidelines should explicitly point out that authors need to indicate how the statistical analysis reflects the experimental design. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

On the Learning of Mathematics Through Conversation.

ERIC Educational Resources Information Center

Haroutunian-Gordan, Sophie; Tartakoff, David S.

1996-01-01

Describes an experimental mathematics course involving an interpretive discussion approach in which students and instructors work together to develop questions about the meaning of mathematical, philosophical, and musical texts. Appendix contains a cluster of questions for Euclid's proof of the infinity of prime numbers. (MKR)

Frustration, Failure, and a "Meaningful" Lab Experience for Adult Nonscience Majors

ERIC Educational Resources Information Center

Fryshman, Bernard

1974-01-01

Describes an open-ended research approach used in an attempt to develop an appreciation of experimental science. The research project involved such topics as "properties of lead,""reasons for lead additives in gasoline," and "the effect of lead on health." (GS)

MULTI-SENSOR REPORTER CELL TECHNOLOGY TO ASSESS HAZARD INVOLVING ENDOCRINE SIGNALING PATHWAYS

EPA Science Inventory

Results will define an experimental approach that can be used in a high-throughput format to evaluate the response of hormone signaling pathways and networks to individual chemicals or mixtures. The assay also will have application across species and would significantly reduce...

Experimental modal analysis of the fuselage panels of an Aero Commander aircraft

NASA Technical Reports Server (NTRS)

Geisler, D.

1981-01-01

The reduction of interior noise in light aircraft was investigated with emphasis the thin fuselage sidewall. The approach used is theoretical and involves modeling of the sidewall panels and stiffeners. Experimental data obtained from tests investigating the effects of mass and stiffness treatments to the sidewalls are presented. The dynamic characteristics of treated panels are contrasted with the untreated sidewall panels using experimental modal analysis techniques. The results include the natural frequencies, modal dampling, and mode shapes of selected panels. Frequency response functions, data relating to the global fuselage response, and acoustic response are also presented.

Thermogravimetric analysis for rapid assessment of moisture diffusivity in polydisperse powder and thin film matrices.

PubMed

Thirunathan, Praveena; Arnz, Patrik; Husny, Joeska; Gianfrancesco, Alessandro; Perdana, Jimmy

2018-03-01

Accurate description of moisture diffusivity is key to precisely understand and predict moisture transfer behaviour in a matrix. Unfortunately, measuring moisture diffusivity is not trivial, especially at low moisture values and/or elevated temperatures. This paper presents a novel experimental procedure to accurately measure moisture diffusivity based on thermogravimetric approach. The procedure is capable to measure diffusivity even at elevated temperatures (>70°C) and low moisture values (>1%). Diffusivity was extracted from experimental data based on "regular regime approach". The approach was tailored to determine diffusivity from thin film and from poly-dispersed powdered samples. Subsequently, measured diffusivity was validated by comparing to available literature data, showing good agreement. Ability of this approach to accurately measure diffusivity at a wider range of temperatures provides better insight on temperature dependency of diffusivity. Thus, this approach can be crucial to ensure good accuracy of moisture transfer description/prediction especially when involving elevated temperatures. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Effect of Visual Information on the Manual Approach and Landing

NASA Technical Reports Server (NTRS)

Wewerinke, P. H.

1982-01-01

The effect of visual information in combination with basic display information on the approach performance. A pre-experimental model analysis was performed in terms of the optimal control model. The resulting aircraft approach performance predictions were compared with the results of a moving base simulator program. The results illustrate that the model provides a meaningful description of the visual (scene) perception process involved in the complex (multi-variable, time varying) manual approach task with a useful predictive capability. The theoretical framework was shown to allow a straight-forward investigation of the complex interaction of a variety of task variables.

Interplay of stereoelectronic and enviromental effects in tuning the structural and magnetic properties of a prototypical spin probe: further insights from a first principle dynamical approach.

PubMed

Pavone, Michele; Cimino, Paola; De Angelis, Filippo; Barone, Vincenzo

2006-04-05

The nitrogen isotropic hyperfine coupling constant (hcc) and the g tensor of a prototypical spin probe (di-tert-butyl nitroxide, DTBN) in aqueous solution have been investigated by means of an integrated computational approach including Car-Parrinello molecular dynamics and quantum mechanical calculations involving a discrete-continuum embedding. The quantitative agreement between computed and experimental parameters fully validates our integrated approach. Decoupling of the structural, dynamical, and environmental contributions acting onto the spectral observables allows an unbiased judgment of the role played by different effects in determining the overall experimental observables and highlights the importance of finite-temperature vibrational averaging. Together with their intrinsic interest, our results pave the route toward more reliable interpretations of EPR parameters of complex systems of biological and technological relevance.

Informed Consent in Research with Children: A Piagetian Approach.

ERIC Educational Resources Information Center

Nichols, Irene A.; Shauffer, Carole B.

The ethical codes for experimentation adopted by most professional organizations include references to the requirement that subjects be given at least minimal information about their involvement in research, but are generally silent on the necessity of ascertaining whether or not subjects sufficiently comprehend the information given. For moral,…

Pigeons ("Columba Livia") Approach Nash Equilibrium in Experimental Matching Pennies Competitions

ERIC Educational Resources Information Center

Sanabria, Federico; Thrailkill, Eric

2009-01-01

The game of Matching Pennies (MP), a simplified version of the more popular Rock, Papers, Scissors, schematically represents competitions between organisms with incentives to predict each other's behavior. Optimal performance in iterated MP competitions involves the production of random choice patterns and the detection of nonrandomness in the…

Investigation of Proprioceptor Stimulation.

ERIC Educational Resources Information Center

Caukins, Sivan E.; And Others

A research proposal to study the effect of multisensory teaching methods in first-grade reading is presented. The focus is on sex differences in learning and in multisensory approaches to teaching. The project will involve 10 experimental and 10 control first-grade classes in several Southern California schools. Both groups will be given IQ,…

A Vocational Approach to Written Communications. Final Report.

ERIC Educational Resources Information Center

Hutkin, Ronald M., Comp.

Students' cognitive and affective development in achieving written communication objectives in the context of the world of work were compared with the same objectives placed in a liberal arts context. The research project involved four groups of students at Platte Technical Community College. Two experimental groups completed the cognitive…

Can Reflection Boost Competences Development in Organizations?

ERIC Educational Resources Information Center

Nansubuga, Florence; Munene, John C.; Ntayi, Joseph M.

2015-01-01

Purpose: The purpose of this paper is to examine the gaps in some existing competence frameworks and investigate the power of reflection on one's behavior to improve the process of the competences development. Design/methodology/approach: The authors used a correlational design and a quasi-experimental non-equivalent group design involving a…

An Application of Latent Variable Structural Equation Modeling for Experimental Research in Educational Technology

ERIC Educational Resources Information Center

Lee, Hyeon Woo

2011-01-01

As the technology-enriched learning environments and theoretical constructs involved in instructional design become more sophisticated and complex, a need arises for equally sophisticated analytic methods to research these environments, theories, and models. Thus, this paper illustrates a comprehensive approach for analyzing data arising from…

Early-life effects on adult physical activity: Concepts, relevance, and experimental approaches

USDA-ARS?s Scientific Manuscript database

Locomotion is a defining characteristic of animal life and plays a crucial role in most behaviors. Locomotion involves physical activity, which can have far-reaching effects on physiology and neurobiology, both acutely and chronically. In human populations and in laboratory rodents, higher levels of...

First Steps in Computational Systems Biology: A Practical Session in Metabolic Modeling and Simulation

ERIC Educational Resources Information Center

Reyes-Palomares, Armando; Sanchez-Jimenez, Francisca; Medina, Miguel Angel

2009-01-01

A comprehensive understanding of biological functions requires new systemic perspectives, such as those provided by systems biology. Systems biology approaches are hypothesis-driven and involve iterative rounds of model building, prediction, experimentation, model refinement, and development. Developments in computer science are allowing for ever…

Traditional Dyeing--An Educational Approach

ERIC Educational Resources Information Center

Alves, H.; Manhita, A.; Dias, C. Barrocas; Ferreira, T.

2014-01-01

This paper describes a mini-project developed with 10th grade Portuguese students where, by using an experimental activity involving the use of natural dyes to colour wool, students acquired a better understanding of the concepts and relationship between the colour, the electromagnetic spectrum, and chemical bonding. As demonstrated by the results…

Attributing Responsibility for Child Maltreatment when Domestic Violence Is Present

ERIC Educational Resources Information Center

Landsman, Miriam J.; Hartley, Carolyn Copps

2007-01-01

Objective: The purpose of this study was to examine factors that influence how child welfare workers attribute responsibility for child maltreatment and child safety in cases involving domestic violence. Methods: The study used a factorial survey approach, combining elements of survey research with an experimental design. Case vignettes were…

The Study of a Simple Redox Reaction as an Experimental Approach to Chemical Kinetics.

ERIC Educational Resources Information Center

Elias, Horst; Zipp, Arden P.

1988-01-01

Recommends using iodide ions and peroxodisulfate ions for studying rate laws instead of the standard iodine clock for kinetic study. Presents the methodology and a discussion of the kinetics involved for a laboratory experiment for a high school or introductory college course. (ML)

Studies of oscillatory combustion and fuel vaporization

NASA Technical Reports Server (NTRS)

Borman, G. L.; Myers, P. S.; Uyehara, O. A.

1972-01-01

Research projects involving oscillatory combustion and fuel vaporization are reported. Comparisons of experimental and theoretical droplet vaporization histories under ambient conditions such that the droplet may approach its thermodynamic critical point are presented. Experimental data on instantaneous heat transfer from a gas to a solid surface under conditions of oscillatory pressure with comparisons to an unsteady one-dimensional model are analyzed. Droplet size and velocity distribution in a spray as obtained by use of a double flash fluorescent method were investigated.

Effects of stakeholder involvement in river management

NASA Astrophysics Data System (ADS)

Buchecker, M.; Menzel, S.

2012-04-01

In the last decades, in many parts of Europe involving local stakeholders or the local public in river management has become a standard procedure. For many decision makers, the purpose of involving other interest groups is limited to achieving a sufficient local acceptance of the project, and accordingly they adopt minimal forms of involvement. Theoretical literature and first empirical studies, however, suggest that stakeholder involvement can have, if done in appropriate quality, have much more far-reaching benefits for a sustainable river management such as a better consensus, social learning and social capital building. But there is so far only little reliable evidence that and under which conditions such benefits or effects in fact result from stakeholder involvement processes. The reason for this is that such involvement processes represent very complex social interventions, and all"affordable"effect measurement methods have their weaknesses. In our project we wanted to find out which were the really robust social effects of stakeholder involvement in river management. We therefore evaluated a number of real Swiss case studies of participatory river management using three different approaches of effect measurements: a quasi-experimental approach using repeated standardized measurement of stakeholders' attitudes, a qualitative long-term ex-post measurement approach based on interviews with stakeholders of five participatory river projects, and a comparative analysis approach based on data of residents effect assessments of participatory river planning gathered in a Swiss national survey. The analysis of all three evaluation studies confirmed that stakeholder involvement in river management projects have substantive social effects. The comparison of the results of the three measurement approaches revealed that social learning and acceptance building were the most robust effects of stakeholder involvement, as they were confirmed by all the three measurement approaches. Social capital building, however, was not found to be a relevant effect in the long-term qualitative ex-post measurement of stakeholder processes in river management. The data suggested that social capital was "only" maintained or reproduced by the involvement process. The results will be discussed, and implications for the practice as well as for future research will be drawn.

Gene Function Hypotheses for the Campylobacter jejuni Glycome Generated by a Logic-Based Approach

PubMed Central

Sternberg, Michael J.E.; Tamaddoni-Nezhad, Alireza; Lesk, Victor I.; Kay, Emily; Hitchen, Paul G.; Cootes, Adrian; van Alphen, Lieke B.; Lamoureux, Marc P.; Jarrell, Harold C.; Rawlings, Christopher J.; Soo, Evelyn C.; Szymanski, Christine M.; Dell, Anne; Wren, Brendan W.; Muggleton, Stephen H.

2013-01-01

Increasingly, experimental data on biological systems are obtained from several sources and computational approaches are required to integrate this information and derive models for the function of the system. Here, we demonstrate the power of a logic-based machine learning approach to propose hypotheses for gene function integrating information from two diverse experimental approaches. Specifically, we use inductive logic programming that automatically proposes hypotheses explaining the empirical data with respect to logically encoded background knowledge. We study the capsular polysaccharide biosynthetic pathway of the major human gastrointestinal pathogen Campylobacter jejuni. We consider several key steps in the formation of capsular polysaccharide consisting of 15 genes of which 8 have assigned function, and we explore the extent to which functions can be hypothesised for the remaining 7. Two sources of experimental data provide the information for learning—the results of knockout experiments on the genes involved in capsule formation and the absence/presence of capsule genes in a multitude of strains of different serotypes. The machine learning uses the pathway structure as background knowledge. We propose assignments of specific genes to five previously unassigned reaction steps. For four of these steps, there was an unambiguous optimal assignment of gene to reaction, and to the fifth, there were three candidate genes. Several of these assignments were consistent with additional experimental results. We therefore show that the logic-based methodology provides a robust strategy to integrate results from different experimental approaches and propose hypotheses for the behaviour of a biological system. PMID:23103756

Gene function hypotheses for the Campylobacter jejuni glycome generated by a logic-based approach.

PubMed

Sternberg, Michael J E; Tamaddoni-Nezhad, Alireza; Lesk, Victor I; Kay, Emily; Hitchen, Paul G; Cootes, Adrian; van Alphen, Lieke B; Lamoureux, Marc P; Jarrell, Harold C; Rawlings, Christopher J; Soo, Evelyn C; Szymanski, Christine M; Dell, Anne; Wren, Brendan W; Muggleton, Stephen H

2013-01-09

Increasingly, experimental data on biological systems are obtained from several sources and computational approaches are required to integrate this information and derive models for the function of the system. Here, we demonstrate the power of a logic-based machine learning approach to propose hypotheses for gene function integrating information from two diverse experimental approaches. Specifically, we use inductive logic programming that automatically proposes hypotheses explaining the empirical data with respect to logically encoded background knowledge. We study the capsular polysaccharide biosynthetic pathway of the major human gastrointestinal pathogen Campylobacter jejuni. We consider several key steps in the formation of capsular polysaccharide consisting of 15 genes of which 8 have assigned function, and we explore the extent to which functions can be hypothesised for the remaining 7. Two sources of experimental data provide the information for learning-the results of knockout experiments on the genes involved in capsule formation and the absence/presence of capsule genes in a multitude of strains of different serotypes. The machine learning uses the pathway structure as background knowledge. We propose assignments of specific genes to five previously unassigned reaction steps. For four of these steps, there was an unambiguous optimal assignment of gene to reaction, and to the fifth, there were three candidate genes. Several of these assignments were consistent with additional experimental results. We therefore show that the logic-based methodology provides a robust strategy to integrate results from different experimental approaches and propose hypotheses for the behaviour of a biological system. Copyright © 2012 Elsevier Ltd. All rights reserved.

Current views on HIV-1 latency, persistence, and cure.

PubMed

Melkova, Zora; Shankaran, Prakash; Madlenakova, Michaela; Bodor, Josef

2017-01-01

HIV-1 infection cannot be cured as it persists in latently infected cells that are targeted neither by the immune system nor by available therapeutic approaches. Consequently, a lifelong therapy suppressing only the actively replicating virus is necessary. The latent reservoir has been defined and characterized in various experimental models and in human patients, allowing research and development of approaches targeting individual steps critical for HIV-1 latency establishment, maintenance, and reactivation. However, additional mechanisms and processes driving the remaining low-level HIV-1 replication in the presence of the suppressive therapy still remain to be identified and targeted. Current approaches toward HIV-1 cure involve namely attempts to reactivate and purge HIV latently infected cells (so-called "shock and kill" strategy), as well as approaches involving gene therapy and/or gene editing and stem cell transplantation aiming at generation of cells resistant to HIV-1. This review summarizes current views and concepts underlying different approaches aiming at functional or sterilizing cure of HIV-1 infection.

Behavioural Differences between Single Scandinavian Brown Bears (Ursus arctos) and Females with Dependent Young When Experimentally Approached by Humans

PubMed Central

Sahlén, Veronica; Ordiz, Andrés; Swenson, Jon E.; Støen, Ole Gunnar

2015-01-01

Carnivore-human encounters that result in human injury present a conservation and management challenge and it is therefore important to understand under what conditions such incidents occur. Females with cubs are often involved when humans are injured by brown bears Ursus arctos. In Scandinavia, this is particularly true for unarmed recreational forest users. Our aim was to document behavioural differences between single bears and females with cubs in order to develop recommendations to minimize the risk of injuries to recreational forest users. We documented the reactions of GPS-collared females with cubs and single brown bears to experimental approaches by humans to 50 m from the bear on 42 and 108 occasions, respectively. The majority of females with cubs (95%) and single bears (89%) left when approached. Bears that left were passed at shorter distances and were in more open areas than those that stayed. Both groups had similar flight initiation distances, which were longer for bears that were active at the time of the disturbance. Females with cubs selected more open habitat than single bears, also for the new site they selected following disturbance. Females with cubs, particularly active females with cubs of the year, moved greater distances and spent more time active following the approach. Females with cubs and single bears were seen or heard in 26% and 14% of the approaches, respectively. None of the bears displayed any aggressive behaviour during the approaches. Females with cubs selected more open habitat, perhaps predisposing them to encountering people that are not involved in hunting activities, which might be the primary explanation why females with cubs are most frequently involved when unarmed people are injured by bears in Scandinavia. To mitigate injury risks, one must consider factors that bring bears closer to human activity in the first place. PMID:25830333

A metadata approach for clinical data management in translational genomics studies in breast cancer.

PubMed

Papatheodorou, Irene; Crichton, Charles; Morris, Lorna; Maccallum, Peter; Davies, Jim; Brenton, James D; Caldas, Carlos

2009-11-30

In molecular profiling studies of cancer patients, experimental and clinical data are combined in order to understand the clinical heterogeneity of the disease: clinical information for each subject needs to be linked to tumour samples, macromolecules extracted, and experimental results. This may involve the integration of clinical data sets from several different sources: these data sets may employ different data definitions and some may be incomplete. In this work we employ semantic web techniques developed within the CancerGrid project, in particular the use of metadata elements and logic-based inference to annotate heterogeneous clinical information, integrate and query it. We show how this integration can be achieved automatically, following the declaration of appropriate metadata elements for each clinical data set; we demonstrate the practicality of this approach through application to experimental results and clinical data from five hospitals in the UK and Canada, undertaken as part of the METABRIC project (Molecular Taxonomy of Breast Cancer International Consortium). We describe a metadata approach for managing similarities and differences in clinical datasets in a standardized way that uses Common Data Elements (CDEs). We apply and evaluate the approach by integrating the five different clinical datasets of METABRIC.

Experimental study designs to improve the evaluation of road mitigation measures for wildlife.

PubMed

Rytwinski, Trina; van der Ree, Rodney; Cunnington, Glenn M; Fahrig, Lenore; Findlay, C Scott; Houlahan, Jeff; Jaeger, Jochen A G; Soanes, Kylie; van der Grift, Edgar A

2015-05-01

An experimental approach to road mitigation that maximizes inferential power is essential to ensure that mitigation is both ecologically-effective and cost-effective. Here, we set out the need for and standards of using an experimental approach to road mitigation, in order to improve knowledge of the influence of mitigation measures on wildlife populations. We point out two key areas that need to be considered when conducting mitigation experiments. First, researchers need to get involved at the earliest stage of the road or mitigation project to ensure the necessary planning and funds are available for conducting a high quality experiment. Second, experimentation will generate new knowledge about the parameters that influence mitigation effectiveness, which ultimately allows better prediction for future road mitigation projects. We identify seven key questions about mitigation structures (i.e., wildlife crossing structures and fencing) that remain largely or entirely unanswered at the population-level: (1) Does a given crossing structure work? What type and size of crossing structures should we use? (2) How many crossing structures should we build? (3) Is it more effective to install a small number of large-sized crossing structures or a large number of small-sized crossing structures? (4) How much barrier fencing is needed for a given length of road? (5) Do we need funnel fencing to lead animals to crossing structures, and how long does such fencing have to be? (6) How should we manage/manipulate the environment in the area around the crossing structures and fencing? (7) Where should we place crossing structures and barrier fencing? We provide experimental approaches to answering each of them using example Before-After-Control-Impact (BACI) study designs for two stages in the road/mitigation project where researchers may become involved: (1) at the beginning of a road/mitigation project, and (2) after the mitigation has been constructed; highlighting real case studies when available. Copyright © 2015 Elsevier Ltd. All rights reserved.

Novel image processing approach to detect malaria

NASA Astrophysics Data System (ADS)

Mas, David; Ferrer, Belen; Cojoc, Dan; Finaurini, Sara; Mico, Vicente; Garcia, Javier; Zalevsky, Zeev

2015-09-01

In this paper we present a novel image processing algorithm providing good preliminary capabilities for in vitro detection of malaria. The proposed concept is based upon analysis of the temporal variation of each pixel. Changes in dark pixels mean that inter cellular activity happened, indicating the presence of the malaria parasite inside the cell. Preliminary experimental results involving analysis of red blood cells being either healthy or infected with malaria parasites, validated the potential benefit of the proposed numerical approach.

Towards a quantum internet

NASA Astrophysics Data System (ADS)

Dür, Wolfgang; Lamprecht, Raphael; Heusler, Stefan

2017-07-01

A long-range quantum communication network is among the most promising applications of emerging quantum technologies. We discuss the potential of such a quantum internet for the secure transmission of classical and quantum information, as well as theoretical and experimental approaches and recent advances to realize them. We illustrate the involved concepts such as error correction, teleportation or quantum repeaters and consider an approach to this topic based on catchy visualizations as a context-based, modern treatment of quantum theory at high school.

IR-IR Conformation Specific Spectroscopy of Na+(Glucose) Adducts

NASA Astrophysics Data System (ADS)

Voss, Jonathan M.; Kregel, Steven J.; Fischer, Kaitlyn C.; Garand, Etienne

2018-01-01

We report an IR-IR double resonance study of the structural landscape present in the Na+(glucose) complex. Our experimental approach involves minimal modifications to a typical IR predissociation setup, and can be carried out via ion-dip or isomer-burning methods, providing additional flexibility to suit different experimental needs. In the current study, the single-laser IR predissociation spectrum of Na+(glucose), which clearly indicates contributions from multiple structures, was experimentally disentangled to reveal the presence of three α-conformers and five β-conformers. Comparisons with calculations show that these eight conformations correspond to the lowest energy gas-phase structures with distinctive Na+ coordination. [Figure not available: see fulltext.

Animal experimentation in Japan: regulatory processes and application for microbiological studies.

PubMed

Takahashi-Omoe, H; Omoe, K

2007-07-01

We have conducted animal experimentation as a highly effective technique in biological studies. Also in microbiological studies, we have used experimentation to prevent and treat many infectious diseases in humans and animals. In Japan, the 'Law for the Humane Treatment and Management of Animals', which covers the consideration of the three R principles, refinement, replacement and reduction for an international humane approach to animal experimentation came into effect in June 2006. Looking towards the straightforward operation of the law in animal experimentation, three government ministries established new basic guidelines for experimentation performed in their jurisdictional research and testing facilities. For future microbiological studies involving animals in Japan, we need to perform animal experiments according to the basic guidelines in association with overseas management systems. In this report, we discussed essential actions for the management of animal experimentation in microbiological studies in Japan.

Analysis of DNA replication associated chromatin decondensation: in vivo assay for understanding chromatin remodeling mechanisms of selected proteins.

PubMed

Borysov, Sergiy; Bryant, Victoria L; Alexandrow, Mark G

2015-01-01

Of critical importance to many of the events underlying transcriptional control of gene expression are modifications to core and linker histones that regulate the accessibility of trans-acting factors to the DNA substrate within the context of chromatin. Likewise, control over the initiation of DNA replication, as well as the ability of the replication machinery to proceed during elongation through the multiple levels of chromatin condensation that are likely to be encountered, is known to involve the creation of chromatin accessibility. In the latter case, chromatin access will likely need to be a transient event so as to prevent total genomic unraveling of the chromatin that would be deleterious to cells. While there are many molecular and biochemical approaches in use to study histone changes and their relationship to transcription and chromatin accessibility, few techniques exist that allow a molecular dissection of the events underlying DNA replication control as it pertains to chromatin changes and accessibility. Here, we outline a novel experimental strategy for addressing the ability of specific proteins to induce large-scale chromatin unfolding (decondensation) in vivo upon site-specific targeting to an engineered locus. Our laboratory has used this powerful system in novel ways to directly address the ability of DNA replication proteins to create chromatin accessibility, and have incorporated modifications to the basic approach that allow for a molecular genetic analysis of the mechanisms and associated factors involved in causing chromatin decondensation by a protein of interest. Alternative approaches involving co-expression of other proteins (competitors or stimulators), concurrent drug treatments, and analysis of co-localizing histone modifications are also addressed, all of which are illustrative of the utility of this experimental system for extending basic findings to physiologically relevant mechanisms. Although used by our group to analyze mechanisms underlying DNA replication associated chromatin accessibility, this unique and powerful experimental system has the propensity to be a valuable tool for understanding chromatin remodeling mechanisms orchestrated by other cellular processes such as DNA repair, recombination, mitotic chromosome condensation, or other chromosome dynamics involving chromatin alterations and accessibility.

Why Traditional Expository Teaching-Learning Approaches May Founder? An Experimental Examination of Neural Networks in Biology Learning

ERIC Educational Resources Information Center

Lee, Jun-Ki; Kwon, Yong-Ju

2011-01-01

Using functional magnetic resonance imaging (fMRI), this study investigates and discusses neurological explanations for, and the educational implications of, the neural network activations involved in hypothesis-generating and hypothesis-understanding for biology education. Two sets of task paradigms about biological phenomena were designed:…

Young People and Caregivers' Perceptions of an Intervention Program for Children Who Deliberately Light Fires

ERIC Educational Resources Information Center

Lambie, Ian; Seymour, Fred; Popaduk, Tanya

2012-01-01

A significant number of children and adolescents engage in deliberate fire setting, beyond the scope of curiosity and experimentation. Interventions developed to respond to the needs of such fire setters generally involve educational and/or psychosocial approaches. Research evaluating the effectiveness of these interventions is dominated by…

Elucidating unconscious processing with instrumental hypnosis

PubMed Central

Landry, Mathieu; Appourchaux, Krystèle; Raz, Amir

2014-01-01

Most researchers leverage bottom-up suppression to unlock the underlying mechanisms of unconscious processing. However, a top-down approach – for example via hypnotic suggestion – paves the road to experimental innovation and complementary data that afford new scientific insights concerning attention and the unconscious. Drawing from a reliable taxonomy that differentiates subliminal and preconscious processing, we outline how an experimental trajectory that champions top-down suppression techniques, such as those practiced in hypnosis, is uniquely poised to further contextualize and refine our scientific understanding of unconscious processing. Examining subliminal and preconscious methods, we demonstrate how instrumental hypnosis provides a reliable adjunct that supplements contemporary approaches. Specifically, we provide an integrative synthesis of the advantages and shortcomings that accompany a top-down approach to probe the unconscious mind. Our account provides a larger framework for complementing the results from core studies involving prevailing subliminal and preconscious techniques. PMID:25120504

Modeling of short channel MOS transistors

NASA Technical Reports Server (NTRS)

Lin, H. C.; Kokalis, D. P.; Bandy, W. R.

1976-01-01

Higher frequency response in MOS technology can be obtained by shortening the channel length. One approach for doing this involves an employment of higher resolution lithography technology. A second approach makes use of a double-diffused MOS transistor (DMOS). It is pointed out that the ordinary method of modeling the transistors used in both approaches is not accurate. An investigation is conducted of the questions which have to be considered for DMOS modeling. The modeling of a short channel MOS transistor is discussed, taking into account the derivation of the threshold voltage equation. Excellent agreement between theoretical and experimental data shows the accuracy of the described modeling approach.

Optimum Tolerance Design Using Component-Amount and Mixture-Amount Experiments

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

Piepel, Gregory F.; Ozler, Cenk; Sehirlioglu, Ali Kemal

2013-08-01

One type of tolerance design problem involves optimizing component and assembly tolerances to minimize the total cost (sum of manufacturing cost and quality loss). Previous literature recommended using traditional response surface (RS) designs and models to solve this type of tolerance design problem. In this article, component-amount (CA) and mixture-amount (MA) approaches are proposed as more appropriate for solving this type of tolerance design problem. The advantages of the CA and MA approaches over the RS approach are discussed. Reasons for choosing between the CA and MA approaches are also discussed. The CA and MA approaches (experimental design, response modeling,more » and optimization) are illustrated using real examples.« less

Simple analysis of scattering data with the Ornstein-Zernike equation

NASA Astrophysics Data System (ADS)

Kats, E. I.; Muratov, A. R.

2018-01-01

In this paper we propose and explore a method of analysis of the scattering experimental data for uniform liquidlike systems. In our pragmatic approach we are not trying to introduce by hands an artificial small parameter to work out a perturbation theory with respect to the known results, e.g., for hard spheres or sticky hard spheres (all the more that in the agreement with the notorious Landau statement, there is no physical small parameter for liquids). Instead of it being guided by the experimental data we are solving the Ornstein-Zernike equation with a trial (variational) form of the interparticle interaction potential. To find all needed correlation functions this variational input is iterated numerically to satisfy the Ornstein-Zernike equation supplemented by a closure relation. Our method is developed for spherically symmetric scattering objects, and our numeric code is written for such a case. However, it can be extended (at the expense of more involved computations and a larger amount of required experimental input information) for nonspherical particles. What is important for our approach is that it is sufficient to know experimental data in a relatively narrow range of the scattering wave vectors (q ) to compute the static structure factor in a much broader range of q . We illustrate by a few model and real experimental examples of the x-ray and neutron scattering data how the approach works.

Mapping soil types from multispectral scanner data.

NASA Technical Reports Server (NTRS)

Kristof, S. J.; Zachary, A. L.

1971-01-01

Multispectral remote sensing and computer-implemented pattern recognition techniques were used for automatic ?mapping' of soil types. This approach involves subjective selection of a set of reference samples from a gray-level display of spectral variations which was generated by a computer. Each resolution element is then classified using a maximum likelihood ratio. Output is a computer printout on which the researcher assigns a different symbol to each class. Four soil test areas in Indiana were experimentally examined using this approach, and partially successful results were obtained.

Toward Predictive Theories of Nuclear Reactions Across the Isotopic Chart: Web Report

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

Escher, J. E.; Blackmon, J.; Elster, C.

Recent years have seen exciting new developments and progress in nuclear structure theory, reaction theory, and experimental techniques, that allow us to move towards a description of exotic systems and environments, setting the stage for new discoveries. The purpose of the 5-week program was to bring together physicists from the low-energy nuclear structure and reaction communities to identify avenues for achieving reliable and predictive descriptions of reactions involving nuclei across the isotopic chart. The 4-day embedded workshop focused on connecting theory developments to experimental advances and data needs for astrophysics and other applications. Nuclear theory must address phenomena from laboratorymore » experiments to stellar environments, from stable nuclei to weakly-bound and exotic isotopes. Expanding the reach of theory to these regimes requires a comprehensive understanding of the reaction mechanisms involved as well as detailed knowledge of nuclear structure. A recurring theme throughout the program was the desire to produce reliable predictions rooted in either ab initio or microscopic approaches. At the same time it was recognized that some applications involving heavy nuclei away from stability, e.g. those involving fi ssion fragments, may need to rely on simple parameterizations of incomplete data for the foreseeable future. The goal here, however, is to subsequently improve and refine the descriptions, moving to phenomenological, then microscopic approaches. There was overarching consensus that future work should also focus on reliable estimates of errors in theoretical descriptions.« less

On the consistency among different approaches for nuclear track scanning and data processing

NASA Astrophysics Data System (ADS)

Inozemtsev, K. O.; Kushin, V. V.; Kodaira, S.; Shurshakov, V. A.

2018-04-01

The article describes various approaches for space radiation track measurement using CR-39™ detector (Tastrak). The results of comparing different methods for track scanning and data processing are presented. Basic algorithms for determination of track parameters are described. Every approach involves individual set of measured track parameters. For two sets, track scanning is sufficient in the plane of detector surface (2-D measurement), third set requires scanning in the additional projection (3-D measurement). An experimental comparison of considered techniques was made with the use of accelerated heavy ions Ar, Fe and Kr.

Assessing health risks of synthetic vitreous fibers: an integrative approach.

PubMed

McClellan, R O

1994-12-01

This paper reviews a tiered approach to acquiring information from multiple experimental systems to understand and assess the potential human health risks of exposure to airborne synthetic fibers. The approach is grounded in the now widely accepted research-risk assessment-risk management paradigm. It involves the acquisition of information that will provide mechanistic linkages within the exposure-dose-response paradigm. It advocates the use of the inhalation route of exposure for developing relevant information for assessing human health risks and calls attention to serious problems encountered using nonphysiologic routes of administration to assess human health risks.

Combined non-parametric and parametric approach for identification of time-variant systems

NASA Astrophysics Data System (ADS)

Dziedziech, Kajetan; Czop, Piotr; Staszewski, Wieslaw J.; Uhl, Tadeusz

2018-03-01

Identification of systems, structures and machines with variable physical parameters is a challenging task especially when time-varying vibration modes are involved. The paper proposes a new combined, two-step - i.e. non-parametric and parametric - modelling approach in order to determine time-varying vibration modes based on input-output measurements. Single-degree-of-freedom (SDOF) vibration modes from multi-degree-of-freedom (MDOF) non-parametric system representation are extracted in the first step with the use of time-frequency wavelet-based filters. The second step involves time-varying parametric representation of extracted modes with the use of recursive linear autoregressive-moving-average with exogenous inputs (ARMAX) models. The combined approach is demonstrated using system identification analysis based on the experimental mass-varying MDOF frame-like structure subjected to random excitation. The results show that the proposed combined method correctly captures the dynamics of the analysed structure, using minimum a priori information on the model.

Nature plus nurture: the triggering of multiple sclerosis.

PubMed

Wekerle, Hartmut

2015-01-01

Recent clinical and experimental studies indicate that multiple sclerosis develops as consequence of a failed interplay between genetic ("nature") and environmental ("nurture") factors. A large number of risk genes favour an autoimmune response against the body's own brain matter. New experimental data indicate that the actual trigger of this attack is however provided by an interaction of brain-specific immune cells with components of the regular commensal gut flora, the intestinal microbiota. This concept opens the way for new therapeutic approaches involving modulation of the microbiota by dietary or antibiotic regimens.

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.

Second-order sliding mode control with experimental application.

PubMed

Eker, Ilyas

2010-07-01

In this article, a second-order sliding mode control (2-SMC) is proposed for second-order uncertain plants using equivalent control approach to improve the performance of control systems. A Proportional + Integral + Derivative (PID) sliding surface is used for the sliding mode. The sliding mode control law is derived using direct Lyapunov stability approach and asymptotic stability is proved theoretically. The performance of the closed-loop system is analysed through an experimental application to an electromechanical plant to show the feasibility and effectiveness of the proposed second-order sliding mode control and factors involved in the design. The second-order plant parameters are experimentally determined using input-output measured data. The results of the experimental application are presented to make a quantitative comparison with the traditional (first-order) sliding mode control (SMC) and PID control. It is demonstrated that the proposed 2-SMC system improves the performance of the closed-loop system with better tracking specifications in the case of external disturbances, better behavior of the output and faster convergence of the sliding surface while maintaining the stability. 2010 ISA. Published by Elsevier Ltd. All rights reserved.

Studying technology use as social practice: the untapped potential of ethnography

PubMed Central

2011-01-01

Information and communications technologies (ICTs) in healthcare are often introduced with expectations of higher-quality, more efficient, and safer care. Many fail to meet these expectations. We argue here that the well-documented failures of ICTs in healthcare are partly attributable to the philosophical foundations of much health informatics research. Positivistic assumptions underpinning the design, implementation and evaluation of ICTs (in particular the notion that technology X has an impact which can be measured and reproduced in new settings), and the deterministic experimental and quasi-experimental study designs which follow from these assumptions, have inherent limitations when ICTs are part of complex social practices involving multiple human actors. We suggest that while experimental and quasi-experimental studies have an important place in health informatics research overall, ethnography is the preferred methodological approach for studying ICTs introduced into complex social systems. But for ethnographic approaches to be accepted and used to their full potential, many in the health informatics community will need to revisit their philosophical assumptions about what counts as research rigor. PMID:21521535

Three-Level Analysis of Single-Case Experimental Data: Empirical Validation

ERIC Educational Resources Information Center

Moeyaert, Mariola; Ugille, Maaike; Ferron, John M.; Beretvas, S. Natasha; Van den Noortgate, Wim

2014-01-01

One approach for combining single-case data involves use of multilevel modeling. In this article, the authors use a Monte Carlo simulation study to inform applied researchers under which realistic conditions the three-level model is appropriate. The authors vary the value of the immediate treatment effect and the treatment's effect on the time…

Cross-National Impacts of Public-Private Partnerships on Equitable Student Achievement: A Quasi-Experimental Assessment Using PISA 2009

ERIC Educational Resources Information Center

Baum, Donald Rey

2013-01-01

Public-private partnerships are being increasingly supported and advocated for, ideologically and financially, as an approach to educational reform in many countries across the world. Proponents suggest that non-state involvement in the education sector has the potential to bolster international Education for All efforts, improve school…

The Role of Community Book Club in Changing Literacy Practices

ERIC Educational Resources Information Center

Dail, Alanna Rochelle; McGee, Lea M.; Edwards, Patricia A.

2009-01-01

Community Book Club began as an experimental approach intended to combine professional development for teachers and family literacy for the parents of the preschoolers involved in an Early Reading First project. We collected data on 11 book club meetings over a 2-year time period. Meetings were held at local churches and at each meeting,…

The Rosetta video approach: An overview and lessons learned so far

NASA Astrophysics Data System (ADS)

Zender, J.; Schwehm, G.; Wilke, M.

2008-01-01

After an interplanetary cruise of 10 years, the Rosetta spacecraft and Philae lander, will arrive in 2014 at comet Churyomov-Gerasimenkov. All involved parties are aware of the knowledge decrease during these years and the potential complications that might arise during problem resolution before or during cometary operations. The Rosetta Science Operations Center (RSOC) supports the Rosetta orbiter experimenters in the preservation of their knowledge. The author will present the overall efforts that are done within the RSOC team to ensure the preservation of the existing information—address databases, documentation, etc.—but will emphasis on the effort to preserve existing experience using a video approach. The video approach included the visit of all orbiter experimenter teams for several days, executing interviews with engineers, technicians and scientists. During the interviews a table of content with attached keywords was generated. The final video was transferred into a computer readable form and connected with the table of content. We will present the methodology that was used to prepare and execute the interviews, to prepare the final video material and the storage and structure of the table of content and keyword. The experimenter interviews at their home institutes and the follow-up work are finished. The feedback we received so far from experimenters and the lessons learned from the interview team will be presented. In the meantime, the approach is continued during the Rosetta commissioning and interviews are executed after each instrument commissioning slot. The author will give an outlook of potential further usage of this approach.

Challenges in structural approaches to cell modeling

PubMed Central

Im, Wonpil; Liang, Jie; Olson, Arthur; Zhou, Huan-Xiang; Vajda, Sandor; Vakser, Ilya A.

2016-01-01

Computational modeling is essential for structural characterization of biomolecular mechanisms across the broad spectrum of scales. Adequate understanding of biomolecular mechanisms inherently involves our ability to model them. Structural modeling of individual biomolecules and their interactions has been rapidly progressing. However, in terms of the broader picture, the focus is shifting toward larger systems, up to the level of a cell. Such modeling involves a more dynamic and realistic representation of the interactomes in vivo, in a crowded cellular environment, as well as membranes and membrane proteins, and other cellular components. Structural modeling of a cell complements computational approaches to cellular mechanisms based on differential equations, graph models, and other techniques to model biological networks, imaging data, etc. Structural modeling along with other computational and experimental approaches will provide a fundamental understanding of life at the molecular level and lead to important applications to biology and medicine. A cross section of diverse approaches presented in this review illustrates the developing shift from the structural modeling of individual molecules to that of cell biology. Studies in several related areas are covered: biological networks; automated construction of three-dimensional cell models using experimental data; modeling of protein complexes; prediction of non-specific and transient protein interactions; thermodynamic and kinetic effects of crowding; cellular membrane modeling; and modeling of chromosomes. The review presents an expert opinion on the current state-of-the-art in these various aspects of structural modeling in cellular biology, and the prospects of future developments in this emerging field. PMID:27255863

[Experimental psychological research on the level of pretensions in alcoholics taking the sex factor into account].

PubMed

Meerzon, M M

1987-01-01

An experimental psychological study has involved 50 males and 53 females with Stage I-II alcoholism during their first hospitalization. The studied patients presented an extravert-neurotic type of personality degradation. Abnormalities of motivational activity in an experimental situation of choice were characterized by a very low level of pretensions in male alcoholics and the maximum level of pretensions in female alcoholics. An analysis of intellectual productivity of the patients has indicated a low intellectual output and inability of the rational utilization of the intellectual potential. In view of the heterogeneity of affective disturbances in men and women, the author recommends a differential psychotherapeutical approach to alcoholic patients of different sex.

IR-IR Conformation Specific Spectroscopy of Na +(Glucose) Adducts

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

Voss, Jonathan M.; Kregel, Steven J.; Fischer, Kaitlyn C.

Here in this paper we report an IR-IR double resonance study of the structural landscape present in the Na +(glucose) complex. Our experimental approach involves minimal modifications to a typical IR predissociation setup, and can be carried out via ion-dip or isomer-burning methods, providing additional flexibility to suit different experimental needs. In the current study, the single-laser IR predissociation spectrum of Na +(glucose), which clearly indicates contributions from multiple structures, was experimentally disentangled to reveal the presence of three α-conformers and five β-conformers. Comparisons with calculations show that these eight conformations correspond to the lowest energy gas-phase structures with distinctivemore » Na+ coordination.« less

IR-IR Conformation Specific Spectroscopy of Na +(Glucose) Adducts

DOE PAGES

Voss, Jonathan M.; Kregel, Steven J.; Fischer, Kaitlyn C.; ...

2017-09-27

Here in this paper we report an IR-IR double resonance study of the structural landscape present in the Na +(glucose) complex. Our experimental approach involves minimal modifications to a typical IR predissociation setup, and can be carried out via ion-dip or isomer-burning methods, providing additional flexibility to suit different experimental needs. In the current study, the single-laser IR predissociation spectrum of Na +(glucose), which clearly indicates contributions from multiple structures, was experimentally disentangled to reveal the presence of three α-conformers and five β-conformers. Comparisons with calculations show that these eight conformations correspond to the lowest energy gas-phase structures with distinctivemore » Na+ coordination.« less

Characterizing Fracturing of Clay-Rich Lower Watrous Rock: From Laboratory Experiments to Nonlocal Damage-Based Simulations

NASA Astrophysics Data System (ADS)

Guy, N.; Seyedi, D. M.; Hild, F.

2018-06-01

The work presented herein aims at characterizing and modeling fracturing (i.e., initiation and propagation of cracks) in a clay-rich rock. The analysis is based on two experimental campaigns. The first one relies on a probabilistic analysis of crack initiation considering Brazilian and three-point flexural tests. The second one involves digital image correlation to characterize crack propagation. A nonlocal damage model based on stress regularization is used for the simulations. Two thresholds both based on regularized stress fields are considered. They are determined from the experimental campaigns performed on Lower Watrous rock. The results obtained with the proposed approach are favorably compared with the experimental results.

Parametric study of closed wet cooling tower thermal performance

NASA Astrophysics Data System (ADS)

Qasim, S. M.; Hayder, M. J.

2017-08-01

The present study involves experimental and theoretical analysis to evaluate the thermal performance of modified Closed Wet Cooling Tower (CWCT). The experimental study includes: design, manufacture and testing prototype of a modified counter flow forced draft CWCT. The modification based on addition packing to the conventional CWCT. A series of experiments was carried out at different operational parameters. In view of energy analysis, the thermal performance parameters of the tower are: cooling range, tower approach, cooling capacity, thermal efficiency, heat and mass transfer coefficients. The theoretical study included develops Artificial Neural Network (ANN) models to predicting various thermal performance parameters of the tower. Utilizing experimental data for training and testing, the models simulated by multi-layer back propagation algorithm for varying all operational parameters stated in experimental test.

Compelled body weight shift approach in rehabilitation of individuals with chronic stroke.

PubMed

Aruin, Alexander S; Rao, Noel; Sharma, Asha; Chaudhuri, Gouri

2012-01-01

This study was designed to evaluate the effectiveness of the compelled body weight shift (CBWS) therapy approach in the rehabilitation of individuals with chronic stroke. CBWS involves a forced shift of body weight toward a person's affected side by means of a shoe insert that establishes a lift of the nonaffected lower extremity. Eighteen individuals with chronic, unilateral stroke (mean age 57.7 ± 11.9 years, with a range of 35-75 years; mean time since stroke 6.7 ± 3.9 years, with a range of 1.1-14.1 years) who showed asymmetrical stance were randomly divided into 2 groups: the experimental group received 6 weeks of physical therapy combined with CBWS therapy, and the control group received only physical therapy. Both groups underwent a battery of identical tests (Fugl-Meyer Assessment, Berg Balance Scale, weight bearing, and gait velocity) before the start of the rehabilitation intervention, following its completion, and 3 months after the end of therapy. After the intervention, weight bearing on the affected side (measured with the Balance Master) increased in the experimental group to a larger degree compared to the control group (9.7% vs 6.4%). Similarly, gait velocity increased 10.5% in the experimental group compared to the control group. Improvements in weight bearing and gait velocity were maintained in the experimental group after the 3-month retention period. The study outcome revealed that a 6-week intervention involving CBWS therapy could result in a long-lasting improvement of the symmetry of weight bearing and velocity of gait in individuals with chronic stroke.

The impact of genetically modified crops on soil microbial communities.

PubMed

Giovannetti, Manuela; Sbrana, Cristiana; Turrini, Alessandra

2005-01-01

Genetically modified (GM) plants represent a potential benefit for environmentally friendly agriculture and human health. Though, poor knowledge is available on potential hazards posed by unintended modifications occurring during genetic manipulation. The increasing amount of reports on ecological risks and benefits of GM plants stresses the need for experimental works aimed at evaluating the impact of GM crops on natural and agro-ecosystems. Major environmental risks associated with GM crops include their potential impact on non-target soil microorganisms playing a fundamental role in crop residues degradation and in biogeochemical cycles. Recent works assessed the effects of GM crops on soil microbial communities on the basis of case-by-case studies, using multimodal experimental approaches involving different target and non-target organisms. Experimental evidences discussed in this review confirm that a precautionary approach should be adopted, by taking into account the risks associated with the unpredictability of transformation events, of their pleiotropic effects and of the fate of transgenes in natural and agro-ecosystems, weighing benefits against costs.

The Experimental Measurement of Local and Bulk Oxygen Transport Resistances in the Catalyst Layer of Proton Exchange Membrane Fuel Cells.

PubMed

Wang, Chao; Cheng, Xiaojing; Lu, Jiabin; Shen, Shuiyun; Yan, Xiaohui; Yin, Jiewei; Wei, Guanghua; Zhang, Junliang

2017-12-07

Remarkable progress has been made in reducing the cathodic Pt loading of PEMFCs; however, a huge performance loss appears at high current densities, indicating the existence of a large oxygen transport resistance associated with the ultralow Pt loading catalyst layer. To reduce the Pt loading without sacrificing cell performance, it is essential to illuminate the oxygen transport mechanism in the catalyst layer. Toward this goal, an experimental approach to measure the oxygen transport resistance in catalyst layers is proposed and realized for the first time in this study. The measuring approach involves a dual-layer catalyst layer design, which consists of a dummy catalyst layer and a practical catalyst layer, followed by changing the thickness of dummy layer to respectively quantify the local and bulk resistances via limiting current measurements combined with linear extrapolation. The experimental results clearly reveal that the local resistance dominates the total resistance in the catalyst layer.

Computational Biorheology of Human Blood Flow in Health and Disease

PubMed Central

Fedosov, Dmitry A.; Dao, Ming; Karniadakis, George Em; Suresh, Subra

2014-01-01

Hematologic disorders arising from infectious diseases, hereditary factors and environmental influences can lead to, and can be influenced by, significant changes in the shape, mechanical and physical properties of red blood cells (RBCs), and the biorheology of blood flow. Hence, modeling of hematologic disorders should take into account the multiphase nature of blood flow, especially in arterioles and capillaries. We present here an overview of a general computational framework based on dissipative particle dynamics (DPD) which has broad applicability in cell biophysics with implications for diagnostics, therapeutics and drug efficacy assessments for a wide variety of human diseases. This computational approach, validated by independent experimental results, is capable of modeling the biorheology of whole blood and its individual components during blood flow so as to investigate cell mechanistic processes in health and disease. DPD is a Lagrangian method that can be derived from systematic coarse-graining of molecular dynamics but can scale efficiently up to arterioles and can also be used to model RBCs down to the spectrin level. We start from experimental measurements of a single RBC to extract the relevant biophysical parameters, using single-cell measurements involving such methods as optical tweezers, atomic force microscopy and micropipette aspiration, and cell-population experiments involving microfluidic devices. We then use these validated RBC models to predict the biorheological behavior of whole blood in healthy or pathological states, and compare the simulations with experimental results involving apparent viscosity and other relevant parameters. While the approach discussed here is sufficiently general to address a broad spectrum of hematologic disorders including certain types of cancer, this paper specifically deals with results obtained using this computational framework for blood flow in malaria and sickle cell anemia. PMID:24419829

Experimentally-induced maternal hypothyroidism alters crucial enzyme activities in the frontal cortex and hippocampus of the offspring rat.

PubMed

Koromilas, Christos; Tsakiris, Stylianos; Kalafatakis, Konstantinos; Zarros, Apostolos; Stolakis, Vasileios; Kimpizi, Despoina; Bimpis, Alexios; Tsagianni, Anastasia; Liapi, Charis

2015-02-01

Thyroid hormone insufficiency during neurodevelopment can result into significant structural and functional changes within the developing central nervous system (CNS), and is associated with the establishment of serious cognitive impairment and neuropsychiatric symptomatology. The aim of the present study was to shed more light on the effects of gestational and/or lactational maternal exposure to propylthiouracil (PTU)-induced hypothyroidism as a multilevel experimental approach to the study of hypothyroidism-induced changes on crucial brain enzyme activities of 21-day-old Wistar rat offspring in a brain region-specific manner. This experimental approach has been recently developed and characterized by the authors based on neurochemical analyses performed on newborn and 21-day-old rat offspring whole brain homogenates; as a continuum to this effort, the current study focused on two CNS regions of major significance for cognitive development: the frontal cortex and the hippocampus. Maternal exposure to PTU in the drinking water during gestation and/or lactation resulted into changes in the activities of acetylcholinesterase and two important adenosinetriphosphatases (Na(+),K(+)- and Mg(2+)-ATPase), that seemed to take place in a CNS-region-specific manner and that were dependent upon the PTU-exposure timeframe followed. As these findings are analyzed and compared to the available literature, they: (i) highlight the variability involved in the changes of the aforementioned enzymatic parameters in the studied CNS regions (attributed to both the different neuroanatomical composition and the thyroid-hormone-dependent neurodevelopmental growth/differentiation patterns of the latter), (ii) reveal important information with regards to the neurochemical mechanisms that could be involved in the way clinical hypothyroidism could affect optimal neurodevelopment and, ultimately, cognitive function, as well as (iii) underline the need for the adoption of more consistent approaches towards the experimental simulation of congenital and early-age-occurring hypothyroidism.

1D quantum simulation using a solid state platform

NASA Astrophysics Data System (ADS)

Kirkendall, Megan; Irvin, Patrick; Huang, Mengchen; Levy, Jeremy; Lee, Hyungwoo; Eom, Chang-Beom

Understanding the properties of large quantum systems can be challenging both theoretically and numerically. One experimental approach-quantum simulation-involves mapping a quantum system of interest onto a physical system that is programmable and experimentally accessible. A tremendous amount of work has been performed with quantum simulators formed from optical lattices; by contrast, solid-state platforms have had only limited success. Our experimental approach to quantum simulation takes advantage of nanoscale control of a metal-insulator transition at the interface between two insulating complex oxide materials. This system naturally exhibits a wide variety of ground states (e.g., ferromagnetic, superconducting) and can be configured into a variety of complex geometries. We will describe initial experiments that explore the magnetotransport properties of one-dimensional superlattices with spatial periods as small as 4 nm, comparable to the Fermi wavelength. The results demonstrate the potential of this solid-state quantum simulation approach, and also provide empirical constraints for physical models that describe the underlying oxide material properties. We gratefully acknowledge financial support from AFOSR (FA9550-12-1- 0057 (JL), FA9550-10-1-0524 (JL) and FA9550-12-1-0342 (CBE)), ONR N00014-15-1-2847 (JL), and NSF DMR-1234096 (CBE).

Examining the relationship between psychosocial and behavioral proxies for future consumption behavior: self-reported impact and bidding behavior in an experimental auction study on cigarette labeling

PubMed Central

Rousu, Matthew C.; Thrasher, James F.

2014-01-01

Experimental and observational research often involves asking consumers to self-report the impact of some proposed option. Because self-reported responses involve no consequence to the respondent for falsely revealing how he or she feels about an issue, self-reports may be subject to social desirability and other influences that bias responses in important ways. In this article, we analyzed data from an experiment on the impact of cigarette packaging and pack warnings, comparing smokers’ self-reported impact (four-item scale) and the bids they placed in experimental auctions to estimate differences in demand. The results were consistent across methods; however, the estimated effect size associated with different warning labels was two times greater for the four-item self-reported response scale when compared to the change in demand as indicated by auction bids. Our study provides evidence that self-reported psychosocial responses provide a valid proxy for behavioral change as reflected by experimental auction bidding behavior. More research is needed to better understand the advantages and disadvantages of behavioral economic methods and traditional self-report approaches to evaluating health behavior change interventions. PMID:24399267

Highlighting the Need for Systems-Level Experimental Characterization of Plant Metabolic Enzymes.

PubMed

Engqvist, Martin K M

2016-01-01

The biology of living organisms is determined by the action and interaction of a large number of individual gene products, each with specific functions. Discovering and annotating the function of gene products is key to our understanding of these organisms. Controlled experiments and bioinformatic predictions both contribute to functional gene annotation. For most species it is difficult to gain an overview of what portion of gene annotations are based on experiments and what portion represent predictions. Here, I survey the current state of experimental knowledge of enzymes and metabolism in Arabidopsis thaliana as well as eleven economically important crops and forestry trees - with a particular focus on reactions involving organic acids in central metabolism. I illustrate the limited availability of experimental data for functional annotation of enzymes in most of these species. Many enzymes involved in metabolism of citrate, malate, fumarate, lactate, and glycolate in crops and forestry trees have not been characterized. Furthermore, enzymes involved in key biosynthetic pathways which shape important traits in crops and forestry trees have not been characterized. I argue for the development of novel high-throughput platforms with which limited functional characterization of gene products can be performed quickly and relatively cheaply. I refer to this approach as systems-level experimental characterization. The data collected from such platforms would form a layer intermediate between bioinformatic gene function predictions and in-depth experimental studies of these functions. Such a data layer would greatly aid in the pursuit of understanding a multiplicity of biological processes in living organisms.

Dry deposition models for radionuclides dispersed in air: a new approach for deposition velocity evaluation schema

NASA Astrophysics Data System (ADS)

Giardina, M.; Buffa, P.; Cervone, A.; De Rosa, F.; Lombardo, C.; Casamirra, M.

2017-11-01

In the framework of a National Research Program funded by the Italian Minister of Economic Development, the Department of Energy, Information Engineering and Mathematical Models (DEIM) of Palermo University and ENEA Research Centre of Bologna, Italy are performing several research activities to study physical models and mathematical approaches aimed at investigating dry deposition mechanisms of radioactive pollutants. On the basis of such studies, a new approach to evaluate the dry deposition velocity for particles is proposed. Comparisons with some literature experimental data show that the proposed dry deposition scheme can capture the main phenomena involved in the dry deposition process successfully.

Generators of the brainstem auditory evoked potential in cat. I. An experimental approach to their identification.

PubMed

Melcher, J R; Knudson, I M; Fullerton, B C; Guinan, J J; Norris, B E; Kiang, N Y

1996-04-01

This paper is the first in a series aimed at identifying the cellular generators of the brainstem auditory evoked potential (BAEP) in cats. The approach involves (1) developing experimental procedures for making small selective lesions and determining the corresponding changes in BAEP waveforms, (2) identifying brainstem regions involved in BAEP generation by examining the effects of lesions on the BAEP and (3) identifying specific cell populations involved by combining the lesion results with electrophysiological and anatomical information from other kinds of studies. We created lesions in the lower brainstem by injecting kainic acid which is generally toxic for neuronal cell bodies but not for axons and terminals. This first paper describes the justifications for using kainic acid, explains the associated problems, and develops a methodology that addresses the main difficulties. The issues and aspects of the specific methods are generally applicable to physiological and anatomical studies using any neurotoxin, as well as to the present BAEP study. The methods chosen involved (1) measuring the BAEP at regular intervals until it reached a post-injection steady state and perfusing the animals with fixative shortly after the last BAEP recordings were made, (2) using objective criteria to distinguish injection-related BAEP changes from unrelated ones, (3) making control injections to identify effects not due to kainic acid toxicity, (4) verifying the anatomical and functional integrity of axons in lesioned regions, and (5) examining injected brainstems microscopically for cell loss and cellular abnormalities indicating dysfunction. This combination of methods enabled us to identify BAEP changes which are clearly correlated with lesion locations.

Optimal decentralized feedback control for a truss structure

NASA Technical Reports Server (NTRS)

Cagle, A.; Ozguner, U.

1989-01-01

One approach to the decentralized control of large flexible space structures involves the design of controllers for the substructures of large systems and their subsequent application to the entire coupled system. This approach is presently developed for the case of active vibration damping on an experimental large struss structure. The isolated boundary loading method is used to define component models by FEM; component controllers are designed using an interlocking control concept which minimizes the motion of the boundary nodes, thereby reducing the exchange of mechanical disturbances among components.

What Is Mathematical Modelling? Exploring Prospective Teachers' Use of Experiments to Connect Mathematics to the Study of Motion

ERIC Educational Resources Information Center

Carrejo, David J.; Marshall, Jill

2007-01-01

This paper focuses on the construction, development, and use of mathematical models by prospective science and mathematics teachers enrolled in a university physics course. By studying their involvement in an inquiry-based, experimental approach to learning kinematics, we address a fundamental question about the meaning and role of abstraction in…

The Effects of Using Concept Mapping for Improving Advanced Level Biology Students' Lower- and Higher-Order Cognitive Skills

ERIC Educational Resources Information Center

Bramwell-Lalor, Sharon; Rainford, Marcia

2014-01-01

This paper reports on teachers' use of concept mapping as an alternative assessment strategy in advanced level biology classes and its effects on students' cognitive skills on selected biology concepts. Using a mixed methods approach, the study employed a pre-test/post-test quasi-experimental design involving 156 students and 8 teachers from…

Mental Models for Mechanical Comprehension. A Review of Literature.

DTIC Science & Technology

1986-06-01

the mental models that people use to understand and solve problems involving mechanics and motion. Method The existing psychological literature on...have been used to investigate mental models. The constructionist school is concerned with how mental models are formed. The information-processing...school uses the experimental methods of modern cognitive psychology to investigate mental structures. The componential approach attempts to meld the

From Structure to Function: A Comprehensive Compendium of Tools to Unveil Protein Domains and Understand Their Role in Cytokinesis.

PubMed

Rincon, Sergio A; Paoletti, Anne

2016-01-01

Unveiling the function of a novel protein is a challenging task that requires careful experimental design. Yeast cytokinesis is a conserved process that involves modular structural and regulatory proteins. For such proteins, an important step is to identify their domains and structural organization. Here we briefly discuss a collection of methods commonly used for sequence alignment and prediction of protein structure that represent powerful tools for the identification homologous domains and design of structure-function approaches to test experimentally the function of multi-domain proteins such as those implicated in yeast cytokinesis.

Bounding the Set of Classical Correlations of a Many-Body System

NASA Astrophysics Data System (ADS)

Fadel, Matteo; Tura, Jordi

2017-12-01

We present a method to certify the presence of Bell correlations in experimentally observed statistics, and to obtain new Bell inequalities. Our approach is based on relaxing the conditions defining the set of correlations obeying a local hidden variable model, yielding a convergent hierarchy of semidefinite programs (SDP's). Because the size of these SDP's is independent of the number of parties involved, this technique allows us to characterize correlations in many-body systems. As an example, we illustrate our method with the experimental data presented in Science 352, 441 (2016), 10.1126/science.aad8665.

Using Separable Nonnegative Matrix Factorization Techniques for the Analysis of Time-Resolved Raman Spectra

NASA Astrophysics Data System (ADS)

Luce, R.; Hildebrandt, P.; Kuhlmann, U.; Liesen, J.

2016-09-01

The key challenge of time-resolved Raman spectroscopy is the identification of the constituent species and the analysis of the kinetics of the underlying reaction network. In this work we present an integral approach that allows for determining both the component spectra and the rate constants simultaneously from a series of vibrational spectra. It is based on an algorithm for non-negative matrix factorization which is applied to the experimental data set following a few pre-processing steps. As a prerequisite for physically unambiguous solutions, each component spectrum must include one vibrational band that does not significantly interfere with vibrational bands of other species. The approach is applied to synthetic "experimental" spectra derived from model systems comprising a set of species with component spectra differing with respect to their degree of spectral interferences and signal-to-noise ratios. In each case, the species involved are connected via monomolecular reaction pathways. The potential and limitations of the approach for recovering the respective rate constants and component spectra are discussed.

Probing nanoscale ion dynamics in ultrathin films of polymerized ionic liquids by broadband dielectric spectroscopy

NASA Astrophysics Data System (ADS)

Sangoro, Joshua; Heres, Maximilian; Cosby, Tyler

Continuous progress in energy storage and conversion technologies necessitates novel experimental approaches that can provide fundamental insights regarding the impact of reduced dimensions on the functional properties of materials. In this talk, a nondestructive experimental approach to probe nanoscale ion dynamics in ultrathin films of polymerized ionic liquids over a broad frequency range spanning over six orders of magnitude by broadband dielectric spectroscopy will be presented. The approach involves using an electrode configuration with lithographically patterned silica nanostructures, which allow for an air gap between the confined ion conductor and one of the electrodes. It is observed that the characteristic ion dynamics rates significantly slow down with decreasing film thicknesses above the calorimetric glass transition of the bulk polymer. However, the mean rates remain bulk-like at lower temperatures. These results highlight the increasing influence of the polymer/substrate interactions with decreasing film thickness on ion dynamics. The authors gratefully acknowledge the National Science Foundation for financial support through the Polymers Program award DMR-1508394.

An experimental approach towards the development of an in vitro cortical-thalamic co-culture model.

PubMed

Kanagasabapathi, Thirukumaran T; Massobrio, Paolo; Tedesco, Mariateresa; Martinoia, Sergio; Wadman, Wytse J; Decré, Michel M J

2011-01-01

In this paper, we propose an experimental approach to develop an in vitro dissociated cortical-thalamic co-culture model using a dual compartment neurofluidic device. The device has two compartments separated by 10 μm wide and 3 μm high microchannels. The microchannels provide a physical isolation of neurons allowing only neurites to grow between the compartments. Long-term viable co-culture was maintained in the compartmented device, neurite growth through the microchannels was verified using immunofluorescence staining, and electrophysiological recordings from the co-culture system was investigated. Preliminary analysis of spontaneous activities from the co-culture shows a distinctively different firing pattern associated with cultures of individual cell types and further analysis is proposed for a deeper understanding of the dynamics involved in the network connectivity in such a co-culture system.

Identification of material properties of orthotropic composite plate using experimental frequency response function data

NASA Astrophysics Data System (ADS)

Tam, Jun Hui; Ong, Zhi Chao; Ismail, Zubaidah; Ang, Bee Chin; Khoo, Shin Yee

2018-05-01

The demand for composite materials is increasing due to their great superiority in material properties, e.g., lightweight, high strength and high corrosion resistance. As a result, the invention of composite materials of diverse properties is becoming prevalent, and thus, leading to the development of material identification methods for composite materials. Conventional identification methods are destructive, time-consuming and costly. Therefore, an accurate identification approach is proposed to circumvent these drawbacks, involving the use of Frequency Response Function (FRF) error function defined by the correlation discrepancy between experimental and Finite-Element generated FRFs. A square E-glass epoxy composite plate is investigated under several different configurations of boundary conditions. It is notable that the experimental FRFs are used as the correlation reference, such that, during computation, the predicted FRFs are continuously updated with reference to the experimental FRFs until achieving a solution. The final identified elastic properties, namely in-plane elastic moduli, Ex and Ey, in-plane shear modulus, Gxy, and major Poisson's ratio, vxy of the composite plate are subsequently compared to the benchmark parameters as well as with those obtained using modal-based approach. As compared to the modal-based approach, the proposed method is found to have yielded relatively better results. This can be explained by the direct employment of raw data in the proposed method that avoids errors that might incur during the stage of modal extraction.

Experimental confirmation of a PDE-based approach to design of feedback controls

NASA Technical Reports Server (NTRS)

Banks, H. T.; Smith, Ralph C.; Brown, D. E.; Silcox, R. J.; Metcalf, Vern L.

1995-01-01

Issues regarding the experimental implementation of partial differential equation based controllers are discussed in this work. While the motivating application involves the reduction of vibration levels for a circular plate through excitation of surface-mounted piezoceramic patches, the general techniques described here will extend to a variety of applications. The initial step is the development of a PDE model which accurately captures the physics of the underlying process. This model is then discretized to yield a vector-valued initial value problem. Optimal control theory is used to determine continuous-time voltages to the patches, and the approximations needed to facilitate discrete time implementation are addressed. Finally, experimental results demonstrating the control of both transient and steady state vibrations through these techniques are presented.

Thermochemical Modeling of Nonequilibrium Oxygen Flows

NASA Astrophysics Data System (ADS)

Neitzel, Kevin Joseph

The development of hypersonic vehicles leans heavily on computational simulation due to the high enthalpy flow conditions that are expensive and technically challenging to replicate experimentally. The accuracy of the nonequilibrium modeling in the computer simulations dictates the design margin that is required for the thermal protection system and flight dynamics. Previous hypersonic vehicles, such as Apollo and the Space Shuttle, were primarily concerned with re-entry TPS design. The strong flow conditions of re-entry, involving Mach numbers of 25, quickly dissociate the oxygen molecules in air. Sustained flight, hypersonic vehicles will be designed to operate in Mach number ranges of 5 to 10. The oxygen molecules will not quickly dissociate and will play an important role in the flow field behavior. The development of nonequilibrium models of oxygen is crucial for limiting modeling uncertainty. Thermochemical nonequilibrium modeling is investigated for oxygen flows. Specifically, the vibrational relaxation and dissociation behavior that dominate the nonequilibrium physics in this flight regime are studied in detail. The widely used two-temperature (2T) approach is compared to the higher fidelity and more computationally expensive state-to-state (STS) approach. This dissertation utilizes a wide range of rate sources, including newly available STS rates, to conduct a comprehensive study of modeling approaches for hypersonic nonequilibrium thermochemical modeling. Additionally, the physical accuracy of the computational methods are assessed by comparing the numerical results with available experimental data. The numerical results and experimental measurements present strong nonequilibrium, and even non-Boltzmann behavior in the vibrational energy mode for the sustained hypersonic flight regime. The STS approach is able to better capture the behavior observed in the experimental data, especially for stronger nonequilibrium conditions. Additionally, a reduced order model (ROM) modification to the 2T model is developed to improve the capability of the 2T approach framework.

Toward the understanding of hydration phenomena in aqueous electrolytes from the interplay of theory, molecular simulation, and experiment

DOE PAGES

Chialvo, Ariel A.; Vlcek, Lukas

2015-05-22

We confront the microstructural analysis of aqueous electrolytes and present a detailed account of the fundamentals underlying the neutron scattering with isotopic substitution (NDIS) approach for the experimental determination of ion coordination numbers in systems involving both halides anions and oxyanions. We place particular emphasis on the frequently overlooked ion-pairing phenomenon, identify its microstructural signature in the neutron-weighted distribution functions, and suggest novel techniques to deal with either the estimation of the ion-pairing magnitude or the correction of its effects on the experimentally measured coordination numbers. We illustrate the underlying ideas by applying these new developments to the interpretation ofmore » four NDIS test-cases via molecular simulation, as convenient dry runs for the actual scattering experiments, for representative aqueous electrolyte solutions at ambient conditions involving metal halides and nitrates.« less

Exciton coupling in molecular crystals

NASA Technical Reports Server (NTRS)

Ake, R. L.

1976-01-01

The implications of perfect exciton coupling and molecular vibrations were investigated, as well as the effect they have on the lifetime of singlet and triplet excitons coupled in a limiting geometry. Crystalline bibenzyl, Cl4Hl4, provided a situation in which these mechanisms involving exciton coupling can be studied in the limit of perfect coupling between units due to the crystal's geometry. This geometry leads to a coupling between the two halves of the molecule resulting in a splitting of the molecular excited states. The study reported involves an experimental spectroscopic approach and begins with the purification of the bibenzyl. The principal experimental apparatus was an emission spectrometer. A closed cycle cryogenic system was used to vary the temperature of the sample between 20 K and 300 K. The desired results are the temperature-dependent emission spectra of the bibenzyl; in addition, the lifetimes and quantum yields measured at each temperature reveal the effect of competing radiationless processes.

Understanding ocean acidification impacts on organismal to ecological scales

USGS Publications Warehouse

Andersson, Andreas J; Kline, David I; Edmunds, Peter J; Archer, Stephen D; Bednaršek, Nina; Carpenter, Robert C; Chadsey, Meg; Goldstein, Philip; Grottoli, Andrea G.; Hurst, Thomas P; King, Andrew L; Kübler, Janet E.; Kuffner, Ilsa B.; Mackey, Katherine R M; Menge, Bruce A.; Paytan, Adina; Riebesell, Ulf; Schnetzer, Astrid; Warner, Mark E; Zimmerman, Richard C

2015-01-01

Ocean acidification (OA) research seeks to understand how marine ecosystems and global elemental cycles will respond to changes in seawater carbonate chemistry in combination with other environmental perturbations such as warming, eutrophication, and deoxygenation. Here, we discuss the effectiveness and limitations of current research approaches used to address this goal. A diverse combination of approaches is essential to decipher the consequences of OA to marine organisms, communities, and ecosystems. Consequently, the benefits and limitations of each approach must be considered carefully. Major research challenges involve experimentally addressing the effects of OA in the context of large natural variability in seawater carbonate system parameters and other interactive variables, integrating the results from different research approaches, and scaling results across different temporal and spatial scales.

How experimental biology and ecology can support evidence-based decision-making in conservation: avoiding pitfalls and enabling application.

PubMed

Cooke, Steven J; Birnie-Gauvin, Kim; Lennox, Robert J; Taylor, Jessica J; Rytwinski, Trina; Rummer, Jodie L; Franklin, Craig E; Bennett, Joseph R; Haddaway, Neal R

2017-01-01

Policy development and management decisions should be based upon the best available evidence. In recent years, approaches to evidence synthesis, originating in the medical realm (such as systematic reviews), have been applied to conservation to promote evidence-based conservation and environmental management. Systematic reviews involve a critical appraisal of evidence, but studies that lack the necessary rigour (e.g. experimental, technical and analytical aspects) to justify their conclusions are typically excluded from systematic reviews or down-weighted in terms of their influence. One of the strengths of conservation physiology is the reliance on experimental approaches that help to more clearly establish cause-and-effect relationships. Indeed, experimental biology and ecology have much to offer in terms of building the evidence base that is needed to inform policy and management options related to pressing issues such as enacting endangered species recovery plans or evaluating the effectiveness of conservation interventions. Here, we identify a number of pitfalls that can prevent experimental findings from being relevant to conservation or would lead to their exclusion or down-weighting during critical appraisal in a systematic review. We conclude that conservation physiology is well positioned to support evidence-based conservation, provided that experimental designs are robust and that conservation physiologists understand the nuances associated with informing decision-making processes so that they can be more relevant.

How experimental biology and ecology can support evidence-based decision-making in conservation: avoiding pitfalls and enabling application

PubMed Central

Birnie-Gauvin, Kim; Lennox, Robert J.; Taylor, Jessica J.; Rytwinski, Trina; Rummer, Jodie L.; Franklin, Craig E.; Bennett, Joseph R.; Haddaway, Neal R.

2017-01-01

Abstract Policy development and management decisions should be based upon the best available evidence. In recent years, approaches to evidence synthesis, originating in the medical realm (such as systematic reviews), have been applied to conservation to promote evidence-based conservation and environmental management. Systematic reviews involve a critical appraisal of evidence, but studies that lack the necessary rigour (e.g. experimental, technical and analytical aspects) to justify their conclusions are typically excluded from systematic reviews or down-weighted in terms of their influence. One of the strengths of conservation physiology is the reliance on experimental approaches that help to more clearly establish cause-and-effect relationships. Indeed, experimental biology and ecology have much to offer in terms of building the evidence base that is needed to inform policy and management options related to pressing issues such as enacting endangered species recovery plans or evaluating the effectiveness of conservation interventions. Here, we identify a number of pitfalls that can prevent experimental findings from being relevant to conservation or would lead to their exclusion or down-weighting during critical appraisal in a systematic review. We conclude that conservation physiology is well positioned to support evidence-based conservation, provided that experimental designs are robust and that conservation physiologists understand the nuances associated with informing decision-making processes so that they can be more relevant. PMID:28835842

Visualizing complex processes using a cognitive-mapping tool to support the learning of clinical reasoning.

PubMed

Wu, Bian; Wang, Minhong; Grotzer, Tina A; Liu, Jun; Johnson, Janice M

2016-08-22

Practical experience with clinical cases has played an important role in supporting the learning of clinical reasoning. However, learning through practical experience involves complex processes difficult to be captured by students. This study aimed to examine the effects of a computer-based cognitive-mapping approach that helps students to externalize the reasoning process and the knowledge underlying the reasoning process when they work with clinical cases. A comparison between the cognitive-mapping approach and the verbal-text approach was made by analyzing their effects on learning outcomes. Fifty-two third-year or higher students from two medical schools participated in the study. Students in the experimental group used the computer-base cognitive-mapping approach, while the control group used the verbal-text approach, to make sense of their thinking and actions when they worked with four simulated cases over 4 weeks. For each case, students in both groups reported their reasoning process (involving data capture, hypotheses formulation, and reasoning with justifications) and the underlying knowledge (involving identified concepts and the relationships between the concepts) using the given approach. The learning products (cognitive maps or verbal text) revealed that students in the cognitive-mapping group outperformed those in the verbal-text group in the reasoning process, but not in making sense of the knowledge underlying the reasoning process. No significant differences were found in a knowledge posttest between the two groups. The computer-based cognitive-mapping approach has shown a promising advantage over the verbal-text approach in improving students' reasoning performance. Further studies are needed to examine the effects of the cognitive-mapping approach in improving the construction of subject-matter knowledge on the basis of practical experience.

Challenges in structural approaches to cell modeling.

PubMed

Im, Wonpil; Liang, Jie; Olson, Arthur; Zhou, Huan-Xiang; Vajda, Sandor; Vakser, Ilya A

2016-07-31

Computational modeling is essential for structural characterization of biomolecular mechanisms across the broad spectrum of scales. Adequate understanding of biomolecular mechanisms inherently involves our ability to model them. Structural modeling of individual biomolecules and their interactions has been rapidly progressing. However, in terms of the broader picture, the focus is shifting toward larger systems, up to the level of a cell. Such modeling involves a more dynamic and realistic representation of the interactomes in vivo, in a crowded cellular environment, as well as membranes and membrane proteins, and other cellular components. Structural modeling of a cell complements computational approaches to cellular mechanisms based on differential equations, graph models, and other techniques to model biological networks, imaging data, etc. Structural modeling along with other computational and experimental approaches will provide a fundamental understanding of life at the molecular level and lead to important applications to biology and medicine. A cross section of diverse approaches presented in this review illustrates the developing shift from the structural modeling of individual molecules to that of cell biology. Studies in several related areas are covered: biological networks; automated construction of three-dimensional cell models using experimental data; modeling of protein complexes; prediction of non-specific and transient protein interactions; thermodynamic and kinetic effects of crowding; cellular membrane modeling; and modeling of chromosomes. The review presents an expert opinion on the current state-of-the-art in these various aspects of structural modeling in cellular biology, and the prospects of future developments in this emerging field. Copyright © 2016 Elsevier Ltd. All rights reserved.

The feasibility of an efficient drug design method with high-performance computers.

PubMed

Yamashita, Takefumi; Ueda, Akihiko; Mitsui, Takashi; Tomonaga, Atsushi; Matsumoto, Shunji; Kodama, Tatsuhiko; Fujitani, Hideaki

2015-01-01

In this study, we propose a supercomputer-assisted drug design approach involving all-atom molecular dynamics (MD)-based binding free energy prediction after the traditional design/selection step. Because this prediction is more accurate than the empirical binding affinity scoring of the traditional approach, the compounds selected by the MD-based prediction should be better drug candidates. In this study, we discuss the applicability of the new approach using two examples. Although the MD-based binding free energy prediction has a huge computational cost, it is feasible with the latest 10 petaflop-scale computer. The supercomputer-assisted drug design approach also involves two important feedback procedures: The first feedback is generated from the MD-based binding free energy prediction step to the drug design step. While the experimental feedback usually provides binding affinities of tens of compounds at one time, the supercomputer allows us to simultaneously obtain the binding free energies of hundreds of compounds. Because the number of calculated binding free energies is sufficiently large, the compounds can be classified into different categories whose properties will aid in the design of the next generation of drug candidates. The second feedback, which occurs from the experiments to the MD simulations, is important to validate the simulation parameters. To demonstrate this, we compare the binding free energies calculated with various force fields to the experimental ones. The results indicate that the prediction will not be very successful, if we use an inaccurate force field. By improving/validating such simulation parameters, the next prediction can be made more accurate.

A Look Inside HIV Resistance through Retroviral Protease Interaction Maps

PubMed Central

Kontijevskis, Aleksejs; Prusis, Peteris; Petrovska, Ramona; Yahorava, Sviatlana; Mutulis, Felikss; Mutule, Ilze; Komorowski, Jan; Wikberg, Jarl E. S

2007-01-01

Retroviruses affect a large number of species, from fish and birds to mammals and humans, with global socioeconomic negative impacts. Here the authors report and experimentally validate a novel approach for the analysis of the molecular networks that are involved in the recognition of substrates by retroviral proteases. Using multivariate analysis of the sequence-based physiochemical descriptions of 61 retroviral proteases comprising wild-type proteases, natural mutants, and drug-resistant forms of proteases from nine different viral species in relation to their ability to cleave 299 substrates, the authors mapped the physicochemical properties and cross-dependencies of the amino acids of the proteases and their substrates, which revealed a complex molecular interaction network of substrate recognition and cleavage. The approach allowed a detailed analysis of the molecular–chemical mechanisms involved in substrate cleavage by retroviral proteases. PMID:17352531

Compelled Body-Weight Shift Approach in Rehabilitation of Individuals with Chronic Stroke

PubMed Central

Aruin, Alexander S.; Rao, Noel; Sharma, Asha; Chaudhuri, Gouri

2013-01-01

Purpose To evaluate the effectiveness of the Compelled Body Weight Shift (CBWS) therapy approach in the rehabilitation of individuals with chronic stroke. CBWS involves a forced shift of body weight towards a person’s affected side by means of a shoe insert that establishes a lift of the non-affected lower extremity. Method Eighteen individuals with chronic, unilateral stroke (mean age 57.7 ± 11.9 years, with a range of 35–75 years, mean time since stroke 6.7±3.9 years with a range of 1.1–14.1 years) who showed asymmetrical stance were randomly divided into two groups: the experimental group received a six-week physical therapy combined with CBWS therapy and the control group received only physical therapy. Both groups underwent a battery of identical tests (Fugl-Meyer assessment, Berg Balance Scale, weight bearing, and gait velocity) before the start of the rehabilitation intervention, following its completion, and three months after the end of therapy. Results After the intervention, weight bearing on the affected side (measured with the Balance Master®) increased in the experimental group to a larger degree compared to the control group (9.7% vs. 6.4%). Similarly, gait velocity increased 10.5% in the experimental group compared to the control group. Improvements in weight bearing and gait velocity were maintained in the experimental group after the three month retention period. Conclusion The study outcome revealed that a six-week intervention involving CBWS therapy could result in a long-lasting improvement of the symmetry of weight bearing and velocity of gait in individuals with chronic stroke. PMID:23192720

Ischemic compression and joint mobilisation for the treatment of nonspecific myofascial foot pain: findings from two quasi-experimental before-and-after studies.

PubMed

Hains, Guy; Boucher, Pierre B; Lamy, Anne-Marie

2015-03-01

The aim of this study was to evaluate the efficacy of myofascial therapy involving ischemic compression on trigger points in combination with mobilization therapy on patients with chronic nonspecific foot pain. Two quasi-experimental before-and-after studies involving two different baseline states. Foot pain patients at a private clinic were divided into two separate cohorts: A, custom orthotic users; and B, non-users. In Study A, 31 users received 15 experimental treatments consisting of ischemic compressions on trigger points and mobilization of articulations through the foot immediately after study enrollment. In study B, ten non-users were prescribed a soft prefabricated insole and were monitored for five weeks before subsequently receiving 15 experimental treatments after the initial five-week delay. The Foot Function Index (FFI) and patients' perceived improvement score (PIS) on a scale from 0% to 100%. The Study A group (n=31) maintained a significant reduction in the FFI at all three follow-up evaluations. Mean improvement from baseline in FFI was 47%, 49% and 56% at 0, 1 and 6 months, respectively, post-treatment. Mean PIS was 58%, 57%, and 58%, again at 0, 1 and 6 months post-treatment. For the Study B group, mean improvement in FFI was only 19% after the monitoring period, and 64% after the experimental treatment period. Mean PIS was 31% after monitoring, and 78% after experimental treatment. In repeated measures analyses, experimental treatment was associated with a significant main effect in both of these before-and after studies (all P values<0.01). Combined treatment involving ischemic compression and joint mobilization for chronic foot pain is associated with significant improvements in functional and self-perceived improvement immediately and at up to six-months post-treatment. Further validation of this treatment approach within a randomized controlled trial is needed.

Planetary atmospheric physics and solar physics research

NASA Technical Reports Server (NTRS)

1973-01-01

An overview is presented on current and planned research activities in the major areas of solar physics, planetary atmospheres, and space astronomy. The approach to these unsolved problems involves experimental techniques, theoretical analysis, and the use of computers to analyze the data from space experiments. The point is made that the research program is characterized by each activity interacting with the other activities in the laboratory.

Biodiversity and hypervirulence of Listeria monocytogenes.

PubMed

Grad, Yonatan H; Fortune, Sarah M

2016-03-01

The integration of large, well-sampled collections of bacterial isolates with genomics and experimental methods provides opportunities for 'top-down' discovery of the genetic basis of phenotypes of interest. In a new report, the authors apply this approach to investigate the heterogeneity in manifestations of disease caused by Listeria monocytogenes and demonstrate that a previously uncharacterized cellobiose PTS system is involved in central nervous system infection.

Altered interaction with environmental reinforcers in major depressive disorder: Relationship to anhedonia.

PubMed

Szczepanik, Joanna E; Furey, Maura L; Nugent, Allison C; Henter, Ioline D; Zarate, Carlos A; Lejuez, Carl W

2017-10-01

Anhedonia-defined as loss of interest or pleasure-is one of two core symptoms of major depressive disorder (MDD). Anhedonia may involve decreased enjoyment of potentially rewarding activities and decreased motivation to engage in such activities. Increased engagement with reinforcers-activities with the potential to be positive experiences-is a frequent target of cognitive-behavioral therapies. Nevertheless, how environmental reinforcers are perceived, and how decisions to approach or avoid them are made by individuals with MDD, is largely unknown. We developed an experimental Behavioral Approach Motivation Paradigm to study how activities are evaluated and approached in MDD. Twenty-one MDD participants and 23 healthy controls performed an experimental task that rated activity words for their hedonic value, then engaged in an approach-avoidance joystick task with each individual's unique set of 'liked' and 'disliked' activity words. A negative correlation was observed between anhedonia and the number of 'liked' activities across participants. No significant difference between approach and avoidance behavior was found in direct comparisons between healthy controls and MDD participants; however, weaker avoidance and greater approach toward 'disliked' activities was found in MDD participants. This suggests negative bias in selecting environmental opportunities, potentially further compromising access to hedonic experiences in MDD. Copyright © 2017. Published by Elsevier Ltd.

Altered interaction with environmental reinforcers in major depressive disorder: Relationship to anhedonia

PubMed Central

Szczepanik, Joanna E.; Furey, Maura L.; Nugent, Allison C.; Henter, Ioline D.; Zarate, Carlos A.; Lejuez, Carl W.

2017-01-01

Anhedonia—defined as loss of interest or pleasure—is one of two core symptoms of major depressive disorder (MDD). Anhedonia may involve decreased enjoyment of potentially rewarding activities and decreased motivation to engage in such activities. Increased engagement with reinforcers—activities with the potential to be positive experiences—is a frequent target of cognitive-behavioral therapies. Nevertheless, how environmental reinforcers are perceived, and how decisions to approach or avoid them are made by individuals with MDD, is largely unknown. We developed an experimental Behavioral Approach Motivation Paradigm to study how activities are evaluated and approached in MDD. Twenty-one MDD participants and 23 healthy controls performed an experimental task that rated activity words for their hedonic value, then engaged in an approach-avoidance joystick task with each individual’s unique set of ‘liked’ and ‘disliked’ activity words. A negative correlation was observed between anhedonia and the number of ‘liked’ activities across participants. No significant difference between approach and avoidance behavior was found in direct comparisons between healthy controls and MDD participants; however, weaker avoidance and greater approach toward ‘disliked’ activities was found in MDD participants. This suggests negative bias in selecting environmental opportunities, potentially further compromising access to hedonic experiences in MDD. PMID:28806614

Automated Analysis of siRNA Screens of Virus Infected Cells Based on Immunofluorescence Microscopy

NASA Astrophysics Data System (ADS)

Matula, Petr; Kumar, Anil; Wörz, Ilka; Harder, Nathalie; Erfle, Holger; Bartenschlager, Ralf; Eils, Roland; Rohr, Karl

We present an image analysis approach as part of a high-throughput microscopy screening system based on cell arrays for the identification of genes involved in Hepatitis C and Dengue virus replication. Our approach comprises: cell nucleus segmentation, quantification of virus replication level in cells, localization of regions with transfected cells, cell classification by infection status, and quality assessment of an experiment. The approach is fully automatic and has been successfully applied to a large number of cell array images from screening experiments. The experimental results show a good agreement with the expected behavior of positive as well as negative controls and encourage the application to screens from further high-throughput experiments.

View-Invariant Gait Recognition Through Genetic Template Segmentation

NASA Astrophysics Data System (ADS)

Isaac, Ebenezer R. H. P.; Elias, Susan; Rajagopalan, Srinivasan; Easwarakumar, K. S.

2017-08-01

Template-based model-free approach provides by far the most successful solution to the gait recognition problem in literature. Recent work discusses how isolating the head and leg portion of the template increase the performance of a gait recognition system making it robust against covariates like clothing and carrying conditions. However, most involve a manual definition of the boundaries. The method we propose, the genetic template segmentation (GTS), employs the genetic algorithm to automate the boundary selection process. This method was tested on the GEI, GEnI and AEI templates. GEI seems to exhibit the best result when segmented with our approach. Experimental results depict that our approach significantly outperforms the existing implementations of view-invariant gait recognition.

A theoretical approach for analyzing the restabilization of wakes

NASA Astrophysics Data System (ADS)

Hill, D. C.

1992-04-01

Recently reported experimental results demonstrate that restabilization of the low-Reynolds-number flow past a circular cylinder can be achieved by the placement of a smaller cylinder in the wake of the first at particular locations. Traditional numerical procedures for modeling such phenomena are computationally expensive. An approach is presented here in which the properties of the adjoint solutions to the linearized equations of motion are exploited to map quickly the best positions for the small cylinder's placement. Comparisons with experiment and previous computations are favorable. The approach is shown to be applicable to general flows, illustrating how strongly control mechanisms that involve sources of momentum couple to unstable (or stable) modes of the system.

Frequency Response Function Expansion for Unmeasured Translation and Rotation Dofs for Impedance Modelling Applications

NASA Astrophysics Data System (ADS)

Avitabile, P.; O'Callahan, J.

2003-07-01

Inclusion of rotational effects is critical for the accuracy of the predicted system characteristics, in almost all system modelling studies. However, experimentally derived information for the description of one or more of the components for the system will generally not have any rotational effects included in the description of the component. The lack of rotational effects has long affected the results from any system model development whether using a modal-based approach or an impedance-based approach. Several new expansion processes are described herein for the development of FRFs needed for impedance-based system models. These techniques expand experimentally derived mode shapes, residual modes from the modal parameter estimation process and FRFs directly to allow for the inclusion of the necessary rotational dof. The FRFs involving translational to rotational dofs are developed as well as the rotational to rotational dof. Examples are provided to show the use of these techniques.

Modeling the Hydration Layer around Proteins: Applications to Small- and Wide-Angle X-Ray Scattering

PubMed Central

Virtanen, Jouko Juhani; Makowski, Lee; Sosnick, Tobin R.; Freed, Karl F.

2011-01-01

Small-/wide-angle x-ray scattering (SWAXS) experiments can aid in determining the structures of proteins and protein complexes, but success requires accurate computational treatment of solvation. We compare two methods by which to calculate SWAXS patterns. The first approach uses all-atom explicit-solvent molecular dynamics (MD) simulations. The second, far less computationally expensive method involves prediction of the hydration density around a protein using our new HyPred solvation model, which is applied without the need for additional MD simulations. The SWAXS patterns obtained from the HyPred model compare well to both experimental data and the patterns predicted by the MD simulations. Both approaches exhibit advantages over existing methods for analyzing SWAXS data. The close correspondence between calculated and observed SWAXS patterns provides strong experimental support for the description of hydration implicit in the HyPred model. PMID:22004761

A systematic approach for finding the objective function and active constraints for dynamic flux balance analysis.

PubMed

Nikdel, Ali; Braatz, Richard D; Budman, Hector M

2018-05-01

Dynamic flux balance analysis (DFBA) has become an instrumental modeling tool for describing the dynamic behavior of bioprocesses. DFBA involves the maximization of a biologically meaningful objective subject to kinetic constraints on the rate of consumption/production of metabolites. In this paper, we propose a systematic data-based approach for finding both the biological objective function and a minimum set of active constraints necessary for matching the model predictions to the experimental data. The proposed algorithm accounts for the errors in the experiments and eliminates the need for ad hoc choices of objective function and constraints as done in previous studies. The method is illustrated for two cases: (1) for in silico (simulated) data generated by a mathematical model for Escherichia coli and (2) for actual experimental data collected from the batch fermentation of Bordetella Pertussis (whooping cough).

Biogenic amines and aggression: experimental approaches in crustaceans.

PubMed

Huber, R; Orzeszyna, M; Pokorny, N; Kravitz, E A

1997-01-01

This review summarizes our experimental approaches attempting to link amines and their metabolites to aggression in crustaceans. The results demonstrate (i) that agonistic behavior in crustaceans can be quantified, (ii) that the amines themselves have telling and subtle effects on the fighting behavior of animals, (iii) that pharmacological interventions are possible that might allow a biochemical dissection of the underlying mechanisms involved in processes like decision making in these animals, and (iv) that selective metabolites of amines are excreted in the urine of lobsters where they may serve behavioral roles. Many of the studies presented here are preliminary. Nonetheless, we believe the results are provocative and nicely complement previous detailed physiological, morphological and biochemical studies exploring the roles of amines in aggression in crustaceans. We expect that the continued use of this invertebrate model system will allow us to gain considerable insight into, and understanding of, the role served by biogenic amines in a complex behavioral process like aggression.

Predictions of Cockpit Simulator Experimental Outcome Using System Models

NASA Technical Reports Server (NTRS)

Sorensen, J. A.; Goka, T.

1984-01-01

This study involved predicting the outcome of a cockpit simulator experiment where pilots used cockpit displays of traffic information (CDTI) to establish and maintain in-trail spacing behind a lead aircraft during approach. The experiments were run on the NASA Ames Research Center multicab cockpit simulator facility. Prior to the experiments, a mathematical model of the pilot/aircraft/CDTI flight system was developed which included relative in-trail and vertical dynamics between aircraft in the approach string. This model was used to construct a digital simulation of the string dynamics including response to initial position errors. The model was then used to predict the outcome of the in-trail following cockpit simulator experiments. Outcome included performance and sensitivity to different separation criteria. The experimental results were then used to evaluate the model and its prediction accuracy. Lessons learned in this modeling and prediction study are noted.

Scalable architecture for a room temperature solid-state quantum information processor.

PubMed

Yao, N Y; Jiang, L; Gorshkov, A V; Maurer, P C; Giedke, G; Cirac, J I; Lukin, M D

2012-04-24

The realization of a scalable quantum information processor has emerged over the past decade as one of the central challenges at the interface of fundamental science and engineering. Here we propose and analyse an architecture for a scalable, solid-state quantum information processor capable of operating at room temperature. Our approach is based on recent experimental advances involving nitrogen-vacancy colour centres in diamond. In particular, we demonstrate that the multiple challenges associated with operation at ambient temperature, individual addressing at the nanoscale, strong qubit coupling, robustness against disorder and low decoherence rates can be simultaneously achieved under realistic, experimentally relevant conditions. The architecture uses a novel approach to quantum information transfer and includes a hierarchy of control at successive length scales. Moreover, it alleviates the stringent constraints currently limiting the realization of scalable quantum processors and will provide fundamental insights into the physics of non-equilibrium many-body quantum systems.

Composing problem solvers for simulation experimentation: a case study on steady state estimation.

PubMed

Leye, Stefan; Ewald, Roland; Uhrmacher, Adelinde M

2014-01-01

Simulation experiments involve various sub-tasks, e.g., parameter optimization, simulation execution, or output data analysis. Many algorithms can be applied to such tasks, but their performance depends on the given problem. Steady state estimation in systems biology is a typical example for this: several estimators have been proposed, each with its own (dis-)advantages. Experimenters, therefore, must choose from the available options, even though they may not be aware of the consequences. To support those users, we propose a general scheme to aggregate such algorithms to so-called synthetic problem solvers, which exploit algorithm differences to improve overall performance. Our approach subsumes various aggregation mechanisms, supports automatic configuration from training data (e.g., via ensemble learning or portfolio selection), and extends the plugin system of the open source modeling and simulation framework James II. We show the benefits of our approach by applying it to steady state estimation for cell-biological models.

Comparison of peer-tutoring learning model through problem-solving approach and traditional learning model on the cognitive ability of grade 10 students at SMKN 13 Bandung on the topic of Stoichiometry

NASA Astrophysics Data System (ADS)

Hayat, A. Z.; Wahyu, W.; Kurnia

2018-05-01

This study aims to find out the improvement of cognitive ability of students on the implementation of cooperative learning model of peer-tutoring by using problem-solving approach. The research method used is mix method of Sequential Explanatory strategy and pretest post-test non-equivalent control group design. The participants involved in this study were 68 grade 10 students of Vocational High School in Bandung that consisted of 34 samples of experimental class and 34 samples of control class. The instruments used include written test and questionnaires. The improvement of cognitive ability of students was calculated using the N- gain formula. Differences of two average scores were calculated using t-test at significant level of α = 0.05. The result of study shows that the improvement of cognitive ability in experimental class was significantly different compared to the improvement in the control class at significant level of α = 0.05. The improvement of cognitive ability in experimental class is higher than in control class.

Real-time control systems: feedback, scheduling and robustness

NASA Astrophysics Data System (ADS)

Simon, Daniel; Seuret, Alexandre; Sename, Olivier

2017-08-01

The efficient control of real-time distributed systems, where continuous components are governed through digital devices and communication networks, needs a careful examination of the constraints arising from the different involved domains inside co-design approaches. Thanks to the robustness of feedback control, both new control methodologies and slackened real-time scheduling schemes are proposed beyond the frontiers between these traditionally separated fields. A methodology to design robust aperiodic controllers is provided, where the sampling interval is considered as a control variable of the system. Promising experimental results are provided to show the feasibility and robustness of the approach.

Applying Knowledge of Enzyme Biochemistry to the Prediction of Functional Sites for Aiding Drug Discovery.

PubMed

Pai, Priyadarshini P; Mondal, Sukanta

2017-01-01

Enzymes are biological catalysts that play an important role in determining the patterns of chemical transformations pertaining to life. Many milestones have been achieved in unraveling the mechanisms in which the enzymes orchestrate various cellular processes using experimental and computational approaches. Experimental studies generating nearly all possible mutations of target enzymes have been aided by rapid computational approaches aiming at enzyme functional classification, understanding domain organization, functional site identification. The functional architecture, essentially, is involved in binding or interaction with ligands including substrates, products, cofactors, inhibitors, providing for their function, such as in catalysis, ligand mediated cell signaling, allosteric regulation and post-translational modifications. With the increasing availability of enzyme information and advances in algorithm development, computational approaches have now become more capable of providing precise inputs for enzyme engineering, and in the process also making it more efficient. This has led to interesting findings, especially in aberrant enzyme interactions, such as hostpathogen interactions in infection, neurodegenerative diseases, cancer and diabetes. This review aims to summarize in retrospection - the mined knowledge, vivid perspectives and challenging strides in using available experimentally validated enzyme information for characterization. An analytical outlook is presented on the scope of exploring future directions. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Advantages of mixing bioinformatics and visualization approaches for analyzing sRNA-mediated regulatory bacterial networks

PubMed Central

Bourqui, Romain; Benchimol, William; Gaspin, Christine; Sirand-Pugnet, Pascal; Uricaru, Raluca; Dutour, Isabelle

2015-01-01

The revolution in high-throughput sequencing technologies has enabled the acquisition of gigabytes of RNA sequences in many different conditions and has highlighted an unexpected number of small RNAs (sRNAs) in bacteria. Ongoing exploitation of these data enables numerous applications for investigating bacterial transacting sRNA-mediated regulation networks. Focusing on sRNAs that regulate mRNA translation in trans, recent works have noted several sRNA-based regulatory pathways that are essential for key cellular processes. Although the number of known bacterial sRNAs is increasing, the experimental validation of their interactions with mRNA targets remains challenging and involves expensive and time-consuming experimental strategies. Hence, bioinformatics is crucial for selecting and prioritizing candidates before designing any experimental work. However, current software for target prediction produces a prohibitive number of candidates because of the lack of biological knowledge regarding the rules governing sRNA–mRNA interactions. Therefore, there is a real need to develop new approaches to help biologists focus on the most promising predicted sRNA–mRNA interactions. In this perspective, this review aims at presenting the advantages of mixing bioinformatics and visualization approaches for analyzing predicted sRNA-mediated regulatory bacterial networks. PMID:25477348

Advantages of mixing bioinformatics and visualization approaches for analyzing sRNA-mediated regulatory bacterial networks.

PubMed

Thébault, Patricia; Bourqui, Romain; Benchimol, William; Gaspin, Christine; Sirand-Pugnet, Pascal; Uricaru, Raluca; Dutour, Isabelle

2015-09-01

The revolution in high-throughput sequencing technologies has enabled the acquisition of gigabytes of RNA sequences in many different conditions and has highlighted an unexpected number of small RNAs (sRNAs) in bacteria. Ongoing exploitation of these data enables numerous applications for investigating bacterial transacting sRNA-mediated regulation networks. Focusing on sRNAs that regulate mRNA translation in trans, recent works have noted several sRNA-based regulatory pathways that are essential for key cellular processes. Although the number of known bacterial sRNAs is increasing, the experimental validation of their interactions with mRNA targets remains challenging and involves expensive and time-consuming experimental strategies. Hence, bioinformatics is crucial for selecting and prioritizing candidates before designing any experimental work. However, current software for target prediction produces a prohibitive number of candidates because of the lack of biological knowledge regarding the rules governing sRNA-mRNA interactions. Therefore, there is a real need to develop new approaches to help biologists focus on the most promising predicted sRNA-mRNA interactions. In this perspective, this review aims at presenting the advantages of mixing bioinformatics and visualization approaches for analyzing predicted sRNA-mediated regulatory bacterial networks. © The Author 2014. Published by Oxford University Press.

Adaptive restoration of river terrace vegetation through iterative experiments

USGS Publications Warehouse

Dela Cruz, Michelle P.; Beauchamp, Vanessa B.; Shafroth, Patrick B.; Decker, Cheryl E.; O’Neil, Aviva

2014-01-01

Restoration projects can involve a high degree of uncertainty and risk, which can ultimately result in failure. An adaptive restoration approach can reduce uncertainty through controlled, replicated experiments designed to test specific hypotheses and alternative management approaches. Key components of adaptive restoration include willingness of project managers to accept the risk inherent in experimentation, interest of researchers, availability of funding for experimentation and monitoring, and ability to restore sites as iterative experiments where results from early efforts can inform the design of later phases. This paper highlights an ongoing adaptive restoration project at Zion National Park (ZNP), aimed at reducing the cover of exotic annual Bromus on riparian terraces, and revegetating these areas with native plant species. Rather than using a trial-and-error approach, ZNP staff partnered with academic, government, and private-sector collaborators to conduct small-scale experiments to explicitly address uncertainties concerning biomass removal of annual bromes, herbicide application rates and timing, and effective seeding methods for native species. Adaptive restoration has succeeded at ZNP because managers accept the risk inherent in experimentation and ZNP personnel are committed to continue these projects over a several-year period. Techniques that result in exotic annual Bromus removal and restoration of native plant species at ZNP can be used as a starting point for adaptive restoration projects elsewhere in the region.

A highly efficient approach to protein interactome mapping based on collaborative filtering framework.

PubMed

Luo, Xin; You, Zhuhong; Zhou, Mengchu; Li, Shuai; Leung, Hareton; Xia, Yunni; Zhu, Qingsheng

2015-01-09

The comprehensive mapping of protein-protein interactions (PPIs) is highly desired for one to gain deep insights into both fundamental cell biology processes and the pathology of diseases. Finely-set small-scale experiments are not only very expensive but also inefficient to identify numerous interactomes despite their high accuracy. High-throughput screening techniques enable efficient identification of PPIs; yet the desire to further extract useful knowledge from these data leads to the problem of binary interactome mapping. Network topology-based approaches prove to be highly efficient in addressing this problem; however, their performance deteriorates significantly on sparse putative PPI networks. Motivated by the success of collaborative filtering (CF)-based approaches to the problem of personalized-recommendation on large, sparse rating matrices, this work aims at implementing a highly efficient CF-based approach to binary interactome mapping. To achieve this, we first propose a CF framework for it. Under this framework, we model the given data into an interactome weight matrix, where the feature-vectors of involved proteins are extracted. With them, we design the rescaled cosine coefficient to model the inter-neighborhood similarity among involved proteins, for taking the mapping process. Experimental results on three large, sparse datasets demonstrate that the proposed approach outperforms several sophisticated topology-based approaches significantly.

A Highly Efficient Approach to Protein Interactome Mapping Based on Collaborative Filtering Framework

PubMed Central

Luo, Xin; You, Zhuhong; Zhou, Mengchu; Li, Shuai; Leung, Hareton; Xia, Yunni; Zhu, Qingsheng

2015-01-01

The comprehensive mapping of protein-protein interactions (PPIs) is highly desired for one to gain deep insights into both fundamental cell biology processes and the pathology of diseases. Finely-set small-scale experiments are not only very expensive but also inefficient to identify numerous interactomes despite their high accuracy. High-throughput screening techniques enable efficient identification of PPIs; yet the desire to further extract useful knowledge from these data leads to the problem of binary interactome mapping. Network topology-based approaches prove to be highly efficient in addressing this problem; however, their performance deteriorates significantly on sparse putative PPI networks. Motivated by the success of collaborative filtering (CF)-based approaches to the problem of personalized-recommendation on large, sparse rating matrices, this work aims at implementing a highly efficient CF-based approach to binary interactome mapping. To achieve this, we first propose a CF framework for it. Under this framework, we model the given data into an interactome weight matrix, where the feature-vectors of involved proteins are extracted. With them, we design the rescaled cosine coefficient to model the inter-neighborhood similarity among involved proteins, for taking the mapping process. Experimental results on three large, sparse datasets demonstrate that the proposed approach outperforms several sophisticated topology-based approaches significantly. PMID:25572661

A Highly Efficient Approach to Protein Interactome Mapping Based on Collaborative Filtering Framework

NASA Astrophysics Data System (ADS)

Luo, Xin; You, Zhuhong; Zhou, Mengchu; Li, Shuai; Leung, Hareton; Xia, Yunni; Zhu, Qingsheng

2015-01-01

The comprehensive mapping of protein-protein interactions (PPIs) is highly desired for one to gain deep insights into both fundamental cell biology processes and the pathology of diseases. Finely-set small-scale experiments are not only very expensive but also inefficient to identify numerous interactomes despite their high accuracy. High-throughput screening techniques enable efficient identification of PPIs; yet the desire to further extract useful knowledge from these data leads to the problem of binary interactome mapping. Network topology-based approaches prove to be highly efficient in addressing this problem; however, their performance deteriorates significantly on sparse putative PPI networks. Motivated by the success of collaborative filtering (CF)-based approaches to the problem of personalized-recommendation on large, sparse rating matrices, this work aims at implementing a highly efficient CF-based approach to binary interactome mapping. To achieve this, we first propose a CF framework for it. Under this framework, we model the given data into an interactome weight matrix, where the feature-vectors of involved proteins are extracted. With them, we design the rescaled cosine coefficient to model the inter-neighborhood similarity among involved proteins, for taking the mapping process. Experimental results on three large, sparse datasets demonstrate that the proposed approach outperforms several sophisticated topology-based approaches significantly.

Poly(ADP-ribose) polymerase inhibition reveals a potential mechanism to promote neuroprotection and treat neuropathic pain.

PubMed

Komirishetty, Prashanth; Areti, Aparna; Gogoi, Ranadeep; Sistla, Ramakrishna; Kumar, Ashutosh

2016-10-01

Neuropathic pain is triggered by the lesions to peripheral nerves which alter their structure and function. Neuroprotective approaches that limit the pathological changes and improve the behavioral outcome have been well explained in different experimental models of neuropathy but translation of such strategies to clinics has been disappointing. Experimental evidences revealed the role of free radicals, especially peroxynitrite after the nerve injury. They provoke oxidative DNA damage and consequent over-activation of the poly(ADP-ribose) polymerase (PARP) upregulates pro-inflammatory pathways, causing bioenergetic crisis and neuronal death. Along with these changes, it causes mitochondrial dysfunction leading to neuronal apoptosis. In related preclinical studies agents that neutralize the free radicals and pharmacological inhibitors of PARP have shown benefits in treating experimental neuropathy. This article reviews the involvement of PARP over-activation in trauma induced neuropathy and therapeutic significance of PARP inhibitors in the experimental neuropathy and neuropathic pain.

Solar energy program evaluation: an introduction

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

deLeon, P.

The Program Evaluation Methodology provides an overview of the practice and methodology of program evaluation and defines more precisely the evaluation techniques and methodologies that would be most appropriate to government organizations which are actively involved in the research, development, and commercialization of solar energy systems. Formal evaluation cannot be treated as a single methodological approach for assessing a program. There are four basic types of evaluation designs - the pre-experimental design; the quasi-experimental design based on time series; the quasi-experimental design based on comparison groups; and the true experimental design. This report is organized to first introduce the rolemore » and issues of evaluation. This is to provide a set of issues to organize the subsequent sections detailing the national solar energy programs. Then, these two themes are integrated by examining the evaluation strategies and methodologies tailored to fit the particular needs of the various individual solar energy programs. (MCW)« less

The effective molarity (EM)--a computational approach.

PubMed

Karaman, Rafik

2010-08-01

The effective molarity (EM) for 12 intramolecular S(N)2 processes involving the formation of substituted aziridines and substituted epoxides were computed using ab initio and DFT calculation methods. Strong correlation was found between the calculated effective molarity and the experimentally determined values. This result could open a door for obtaining EM values for intramolecular processes that are difficult to be experimentally provided. Furthermore, the calculation results reveal that the driving forces for ring-closing reactions in the two different systems are proximity orientation of the nucleophile to the electrophile and the ground strain energies of the products and the reactants. Copyright 2010 Elsevier Inc. All rights reserved.

Application of experimental design in geothermal resources assessment of Ciwidey-Patuha, West Java, Indonesia

NASA Astrophysics Data System (ADS)

Ashat, Ali; Pratama, Heru Berian

2017-12-01

The successful Ciwidey-Patuha geothermal field size assessment required integration data analysis of all aspects to determined optimum capacity to be installed. Resources assessment involve significant uncertainty of subsurface information and multiple development scenarios from these field. Therefore, this paper applied the application of experimental design approach to the geothermal numerical simulation of Ciwidey-Patuha to generate probabilistic resource assessment result. This process assesses the impact of evaluated parameters affecting resources and interacting between these parameters. This methodology have been successfully estimated the maximum resources with polynomial function covering the entire range of possible values of important reservoir parameters.

Engineering and simulation of life science Spacelab experiments

NASA Technical Reports Server (NTRS)

Bush, B.; Rummel, J.; Johnston, R. S.

1977-01-01

Approaches to the planning and realization of Spacelab life sciences experiments, which may involve as many as 16 Space Shuttle missions and 100 tests, are discussed. In particular, a Spacelab simulation program, designed to evaluate problems associated with the use of live animal specimens, the constraints imposed by zero gravity on equipment operation, training of investigators and data management, is described. The simulated facility approximates the hardware and support systems of a current European Space Agency Spacelab model. Preparations necessary for the experimental program, such as crew activity plans, payload documentation and inflight experimental procedures are developed; health problems of the crew, including human/animal microbial contamination, are also assessed.

An evaluation of the strategic approach to the rehabilitation of traumatic brain injury (TBI) patients

PubMed Central

Tomaszewski, Wiesław; Mańko, Grzegorz

2011-01-01

Summary Background The objective of our study was to evaluate a goal-driven strategic plan for the step-by-step rehabilitation of traumatic brain injury (TBI) patients, with effectiveness measured in terms of quality of life, as compared to patients treated according to a standard, progressive rehabilitation program. Material/Methods We studied 40 patients after TBI awakened from a long-term coma. The patients were divided into two equal groups: a control group (n=20) involving patients treated before the introduction of the strategic approach, and an experimental group (n=20) involving patients rehabilitated under the strategic approach. In evaluating the effectiveness of rehabilitation we used a structured interview with clinical observation and a scale for assessing the quality of life of patients after TBI. Results The deterioration in the quality of life of TBI patients is mainly related to difficulties in satisfying physiological needs, self-care, reduced mobility and disorders of cognitive, regulatory, and social functions. In both groups, the feature most susceptible to rehabilitation related change was movement, while the least susceptible functions were associated with the use of different means of transport. This change is significantly greater in persons in the experimental group, as compared to controls. Conclusions We found that a rehabilitation program controlled by a strategic plan, with the cooperation of the patient, is more effective in improving the quality of life, as the patient is more self-motivated to individually designed objectives. PMID:21873948

Learning styles and approaches to learning mathematics of students majoring in elementary education: a three-year study.

PubMed

Alkhateeb, Haitham M; Mji, Andile

2009-10-01

The goal of this 3-yr. study was to explore the learning styles and approaches to learning mathematics of elementary education majors. Two questionnaires, the Learning Style Inventory and the Approaches to Learning Mathematics Questionnaire, were administered to 149 women and 32 men (M = 20.1 yr., SD. = 2.1; range = 18-31). All were in their first or second years of college and enrolled in Mathematics for Elementary School Teachers at a Midwestern U.S. university. Results on the Learning Style Inventory indicated that a majority scored as either Accommodators, i.e., they primarily followed learning modes involving Active Experimentation and Concrete Experience, or as Divergers, i.e., approaching learning by focusing on Concrete Experience and Reflective Observation. A weak but statistically significant association was observed on the Approaches questionnaire between the Surface Approach and Reflective Observation.

Using experimental and computational energy equilibration to understand hierarchical self-assembly of Fmoc-dipeptide amphiphiles.

PubMed

Sasselli, I R; Pappas, C G; Matthews, E; Wang, T; Hunt, N T; Ulijn, R V; Tuttle, T

2016-10-12

Despite progress, a fundamental understanding of the relationships between the molecular structure and self-assembly configuration of Fmoc-dipeptides is still in its infancy. In this work, we provide a combined experimental and computational approach that makes use of free energy equilibration of a number of related Fmoc-dipeptides to arrive at an atomistic model of Fmoc-threonine-phenylalanine-amide (Fmoc-TF-NH 2 ) which forms twisted fibres. By using dynamic peptide libraries where closely related dipeptide sequences are dynamically exchanged to eventually favour the formation of the thermodynamically most stable configuration, the relative importance of C-terminus modifications (amide versus methyl ester) and contributions of aliphatic versus aromatic amino acids (phenylalanine F vs. leucine L) is determined (F > L and NH 2 > OMe). The approach enables a comparative interpretation of spectroscopic data, which can then be used to aid the construction of the atomistic model of the most stable structure (Fmoc-TF-NH 2 ). The comparison of the relative stabilities of the models using molecular dynamic simulations and the correlation with experimental data using dynamic peptide libraries and a range of spectroscopy methods (FTIR, CD, fluorescence) allow for the determination of the nanostructure with atomistic resolution. The final model obtained through this process is able to reproduce the experimentally observed formation of intertwining fibres for Fmoc-TF-NH 2 , providing information of the interactions involved in the hierarchical supramolecular self-assembly. The developed methodology and approach should be of general use for the characterization of supramolecular structures.

Development of an electron paramagnetic resonance methodology for studying the photo-generation of reactive species in semiconductor nano-particle assembled films

NASA Astrophysics Data System (ADS)

Twardoch, Marek; Messai, Youcef; Vileno, Bertrand; Hoarau, Yannick; Mekki, Djamel E.; Felix, Olivier; Turek, Philippe; Weiss, Jean; Decher, Gero; Martel, David

2018-06-01

An experimental approach involving electron paramagnetic resonance is proposed for studying photo-generated reactive species in semiconductor nano-particle-based films deposited on the internal wall of glass capillaries. This methodology is applied here to nano-TiO2 and allows a semi-quantitative analysis of the kinetic evolutions of radical production using a spin scavenger probe.

Development and Experimental Verification of Surface Effects in a Fluidic Model

DTIC Science & Technology

2006-01-01

FROM A HE PLASMA INSIDE A POLYSTYRENE MICROCHANNEL. 43 FIGURE 30: THE EMISSION SPECTRA FROM A MIXED HEXAFLUOROETHYLENE/HE PLASMA INSIDE THE...MICROCHANNEL 47 FIGURE 35: THE ADSORPTION OF GLUCOSE OXIDASE TO DIFFERENT POLYMER SURFACES WAS SHOWN TO HAVE A SIGNIFICANT EFFECT ON ELECTROOSMOTIC FLOW...approach involves neglecting non-ideal (convective-diffusive) effects 5 by assuming well- mixed protein in contact with an idealized surface. Coupled

Powder compaction in systems of bimodal distribution

NASA Technical Reports Server (NTRS)

Chattopadhyay, A. K.; Whittemore, O. J., Jr.

1973-01-01

The compaction of mixtures involving different particle sizes is discussed. The various stages of the compaction process include the rearrangement of particles, the filling of the interstices of the large particles by the smaller ones, and the change in particle size and shape upon further densification through the application of pressure. Experimental approaches and equipment used for compacting material are discussed together with the theoretical relations of the compacting process.

Multiple-labelling immunoEM using different sizes of colloidal gold: alternative approaches to test for differential distribution and colocalization in subcellular structures.

PubMed

Mayhew, Terry M; Lucocq, John M

2011-03-01

Various methods for quantifying cellular immunogold labelling on transmission electron microscope thin sections are currently available. All rely on sound random sampling principles and are applicable to single immunolabelling across compartments within a given cell type or between different experimental groups of cells. Although methods are also available to test for colocalization in double/triple immunogold labelling studies, so far, these have relied on making multiple measurements of gold particle densities in defined areas or of inter-particle nearest neighbour distances. Here, we present alternative two-step approaches to codistribution and colocalization assessment that merely require raw counts of gold particles in distinct cellular compartments. For assessing codistribution over aggregate compartments, initial statistical evaluation involves combining contingency table and chi-squared analyses to provide predicted gold particle distributions. The observed and predicted distributions allow testing of the appropriate null hypothesis, namely, that there is no difference in the distribution patterns of proteins labelled by different sizes of gold particle. In short, the null hypothesis is that of colocalization. The approach for assessing colabelling recognises that, on thin sections, a compartment is made up of a set of sectional images (profiles) of cognate structures. The approach involves identifying two groups of compartmental profiles that are unlabelled and labelled for one gold marker size. The proportions in each group that are also labelled for the second gold marker size are then compared. Statistical analysis now uses a 2 × 2 contingency table combined with the Fisher exact probability test. Having identified double labelling, the profiles can be analysed further in order to identify characteristic features that might account for the double labelling. In each case, the approach is illustrated using synthetic and/or experimental datasets and can be refined to correct observed labelling patterns to specific labelling patterns. These simple and efficient approaches should be of more immediate utility to those interested in codistribution and colocalization in multiple immunogold labelling investigations.

Experimental quantum annealing: case study involving the graph isomorphism problem.

PubMed

Zick, Kenneth M; Shehab, Omar; French, Matthew

2015-06-08

Quantum annealing is a proposed combinatorial optimization technique meant to exploit quantum mechanical effects such as tunneling and entanglement. Real-world quantum annealing-based solvers require a combination of annealing and classical pre- and post-processing; at this early stage, little is known about how to partition and optimize the processing. This article presents an experimental case study of quantum annealing and some of the factors involved in real-world solvers, using a 504-qubit D-Wave Two machine and the graph isomorphism problem. To illustrate the role of classical pre-processing, a compact Hamiltonian is presented that enables a reduced Ising model for each problem instance. On random N-vertex graphs, the median number of variables is reduced from N(2) to fewer than N log2 N and solvable graph sizes increase from N = 5 to N = 13. Additionally, error correction via classical post-processing majority voting is evaluated. While the solution times are not competitive with classical approaches to graph isomorphism, the enhanced solver ultimately classified correctly every problem that was mapped to the processor and demonstrated clear advantages over the baseline approach. The results shed some light on the nature of real-world quantum annealing and the associated hybrid classical-quantum solvers.

Experimental quantum annealing: case study involving the graph isomorphism problem

PubMed Central

Zick, Kenneth M.; Shehab, Omar; French, Matthew

2015-01-01

Quantum annealing is a proposed combinatorial optimization technique meant to exploit quantum mechanical effects such as tunneling and entanglement. Real-world quantum annealing-based solvers require a combination of annealing and classical pre- and post-processing; at this early stage, little is known about how to partition and optimize the processing. This article presents an experimental case study of quantum annealing and some of the factors involved in real-world solvers, using a 504-qubit D-Wave Two machine and the graph isomorphism problem. To illustrate the role of classical pre-processing, a compact Hamiltonian is presented that enables a reduced Ising model for each problem instance. On random N-vertex graphs, the median number of variables is reduced from N2 to fewer than N log2 N and solvable graph sizes increase from N = 5 to N = 13. Additionally, error correction via classical post-processing majority voting is evaluated. While the solution times are not competitive with classical approaches to graph isomorphism, the enhanced solver ultimately classified correctly every problem that was mapped to the processor and demonstrated clear advantages over the baseline approach. The results shed some light on the nature of real-world quantum annealing and the associated hybrid classical-quantum solvers. PMID:26053973

Blinded interpretation of study results can feasibly and effectively diminish interpretation bias.

PubMed

Järvinen, Teppo L N; Sihvonen, Raine; Bhandari, Mohit; Sprague, Sheila; Malmivaara, Antti; Paavola, Mika; Schünemann, Holger J; Guyatt, Gordon H

2014-07-01

Controversial and misleading interpretation of data from randomized trials is common. How to avoid misleading interpretation has received little attention. Herein, we describe two applications of an approach that involves blinded interpretation of the results by study investigators. The approach involves developing two interpretations of the results on the basis of a blinded review of the primary outcome data (experimental treatment A compared with control treatment B). One interpretation assumes that A is the experimental intervention and another assumes that A is the control. After agreeing that there will be no further changes, the investigators record their decisions and sign the resulting document. The randomization code is then broken, the correct interpretation chosen, and the manuscript finalized. Review of the document by an external authority before finalization can provide another safeguard against interpretation bias. We found the blinded preparation of a summary of data interpretation described in this article practical, efficient, and useful. Blinded data interpretation may decrease the frequency of misleading data interpretation. Widespread adoption of blinded data interpretation would be greatly facilitated were it added to the minimum set of recommendations outlining proper conduct of randomized controlled trials (eg, the Consolidated Standards of Reporting Trials statement). Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Machine learning–enabled identification of material phase transitions based on experimental data: Exploring collective dynamics in ferroelectric relaxors

DOE PAGES

Li, Linglong; Yang, Yaodong; Zhang, Dawei; ...

2018-03-30

Exploration of phase transitions and construction of associated phase diagrams are of fundamental importance for condensed matter physics and materials science alike, and remain the focus of extensive research for both theoretical and experimental studies. For the latter, comprehensive studies involving scattering, thermodynamics, and modeling are typically required. We present a new approach to data mining multiple realizations of collective dynamics, measured through piezoelectric relaxation studies, to identify the onset of a structural phase transition in nanometer-scale volumes, that is, the probed volume of an atomic force microscope tip. Machine learning is used to analyze the multidimensional data sets describingmore » relaxation to voltage and thermal stimuli, producing the temperature-bias phase diagram for a relaxor crystal without the need to measure (or know) the order parameter. The suitability of the approach to determine the phase diagram is shown with simulations based on a two-dimensional Ising model. Finally, these results indicate that machine learning approaches can be used to determine phase transitions in ferroelectrics, providing a general, statistically significant, and robust approach toward determining the presence of critical regimes and phase boundaries.« less

Contactless and pose invariant biometric identification using hand surface.

PubMed

Kanhangad, Vivek; Kumar, Ajay; Zhang, David

2011-05-01

This paper presents a novel approach for hand matching that achieves significantly improved performance even in the presence of large hand pose variations. The proposed method utilizes a 3-D digitizer to simultaneously acquire intensity and range images of the user's hand presented to the system in an arbitrary pose. The approach involves determination of the orientation of the hand in 3-D space followed by pose normalization of the acquired 3-D and 2-D hand images. Multimodal (2-D as well as 3-D) palmprint and hand geometry features, which are simultaneously extracted from the user's pose normalized textured 3-D hand, are used for matching. Individual matching scores are then combined using a new dynamic fusion strategy. Our experimental results on the database of 114 subjects with significant pose variations yielded encouraging results. Consistent (across various hand features considered) performance improvement achieved with the pose correction demonstrates the usefulness of the proposed approach for hand based biometric systems with unconstrained and contact-free imaging. The experimental results also suggest that the dynamic fusion approach employed in this work helps to achieve performance improvement of 60% (in terms of EER) over the case when matching scores are combined using the weighted sum rule.

Machine learning–enabled identification of material phase transitions based on experimental data: Exploring collective dynamics in ferroelectric relaxors

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

Li, Linglong; Yang, Yaodong; Zhang, Dawei

Exploration of phase transitions and construction of associated phase diagrams are of fundamental importance for condensed matter physics and materials science alike, and remain the focus of extensive research for both theoretical and experimental studies. For the latter, comprehensive studies involving scattering, thermodynamics, and modeling are typically required. We present a new approach to data mining multiple realizations of collective dynamics, measured through piezoelectric relaxation studies, to identify the onset of a structural phase transition in nanometer-scale volumes, that is, the probed volume of an atomic force microscope tip. Machine learning is used to analyze the multidimensional data sets describingmore » relaxation to voltage and thermal stimuli, producing the temperature-bias phase diagram for a relaxor crystal without the need to measure (or know) the order parameter. The suitability of the approach to determine the phase diagram is shown with simulations based on a two-dimensional Ising model. Finally, these results indicate that machine learning approaches can be used to determine phase transitions in ferroelectrics, providing a general, statistically significant, and robust approach toward determining the presence of critical regimes and phase boundaries.« less

Style follows content: on the microgenesis of art perception.

PubMed

Augustin, M Dorothee; Leder, Helmut; Hutzler, Florian; Carbon, Claus-Christian

2008-05-01

Despite fruitful research in experimental aesthetics, the dynamics of aesthetics, i.e., the processes involved in art perception, have received little attention. Concerning representational art, two aspects seem most important in this respect: style and content. In two experiments, we examined the dynamics of processing of style and content by means of the microgenetic approach. This approach systematically varies perceptual conditions to find out about the stages involved in the formation of percepts--their microgenesis. Participants gave similarity ratings for pairs of pictures that were fully crossed in style (artist) and content (motif). Presentation times were systematically varied between 10, 50, 202 and 3000 ms (Experiment 1) plus unlimited presentation time (Experiment 2). While effects of content were present at all presentation times, effects of style were traceable from 50 ms onwards. The results show clear differences in the microgenesis of style and content, suggesting that in art perception style follows content.

Numerical modeling of experimental observations on gas formation and multi-phase flow of carbon dioxide in subsurface formations

NASA Astrophysics Data System (ADS)

Pawar, R.; Dash, Z.; Sakaki, T.; Plampin, M. R.; Lassen, R. N.; Illangasekare, T. H.; Zyvoloski, G.

2011-12-01

One of the concerns related to geologic CO2 sequestration is potential leakage of CO2 and its subsequent migration to shallow groundwater resources leading to geochemical impacts. Developing approaches to monitor CO2 migration in shallow aquifer and mitigate leakage impacts will require improving our understanding of gas phase formation and multi-phase flow subsequent to CO2 leakage in shallow aquifers. We are utilizing an integrated approach combining laboratory experiments and numerical simulations to characterize the multi-phase flow of CO2 in shallow aquifers. The laboratory experiments involve a series of highly controlled experiments in which CO2 dissolved water is injected in homogeneous and heterogeneous soil columns and tanks. The experimental results are used to study the effects of soil properties, temperature, pressure gradients and heterogeneities on gas formation and migration. We utilize the Finite Element Heat and Mass (FEHM) simulator (Zyvoloski et al, 2010) to numerically model the experimental results. The numerical models capture the physics of CO2 exsolution, multi-phase fluid flow as well as sand heterogeneity. Experimental observations of pressure, temperature and gas saturations are used to develop and constrain conceptual models for CO2 gas-phase formation and multi-phase CO2 flow in porous media. This talk will provide details of development of conceptual models based on experimental observation, development of numerical models for laboratory experiments and modelling results.

Plastic Biliary Stent Occlusion: Factors Involved and Possible Preventive Approaches

PubMed Central

Donelli, Gianfranco; Guaglianone, Emilio; Di Rosa, Roberta; Fiocca, Fausto; Basoli, Antonio

2007-01-01

Endoscopic biliary stenting is today the most common palliative treatment for patients suffering from obstructive jaundice associated with malignant hepatobiliary tumors or benign strictures. However, recurrent jaundice, with or without cholangitis, is a major complication of a biliary endoprosthesis insertion. Thus, stent removal and replacement with a new one frequently occurs as a consequence of device blockage caused by microbial biofilm growth and biliary sludge accumulation in the lumen. Factors and mechanisms involved in plastic stent clogging arising from epidemiological, clinical and experimental data, as well as the possible strategies to prevent biliary stent failure, will be reviewed and discussed. PMID:17456835

An integrated runtime and compile-time approach for parallelizing structured and block structured applications

NASA Technical Reports Server (NTRS)

Agrawal, Gagan; Sussman, Alan; Saltz, Joel

1993-01-01

Scientific and engineering applications often involve structured meshes. These meshes may be nested (for multigrid codes) and/or irregularly coupled (called multiblock or irregularly coupled regular mesh problems). A combined runtime and compile-time approach for parallelizing these applications on distributed memory parallel machines in an efficient and machine-independent fashion was described. A runtime library which can be used to port these applications on distributed memory machines was designed and implemented. The library is currently implemented on several different systems. To further ease the task of application programmers, methods were developed for integrating this runtime library with compilers for HPK-like parallel programming languages. How this runtime library was integrated with the Fortran 90D compiler being developed at Syracuse University is discussed. Experimental results to demonstrate the efficacy of our approach are presented. A multiblock Navier-Stokes solver template and a multigrid code were experimented with. Our experimental results show that our primitives have low runtime communication overheads. Further, the compiler parallelized codes perform within 20 percent of the code parallelized by manually inserting calls to the runtime library.

Using Separable Nonnegative Matrix Factorization Techniques for the Analysis of Time-Resolved Raman Spectra.

PubMed

Luce, Robert; Hildebrandt, Peter; Kuhlmann, Uwe; Liesen, Jörg

2016-09-01

The key challenge of time-resolved Raman spectroscopy is the identification of the constituent species and the analysis of the kinetics of the underlying reaction network. In this work we present an integral approach that allows for determining both the component spectra and the rate constants simultaneously from a series of vibrational spectra. It is based on an algorithm for nonnegative matrix factorization that is applied to the experimental data set following a few pre-processing steps. As a prerequisite for physically unambiguous solutions, each component spectrum must include one vibrational band that does not significantly interfere with the vibrational bands of other species. The approach is applied to synthetic "experimental" spectra derived from model systems comprising a set of species with component spectra differing with respect to their degree of spectral interferences and signal-to-noise ratios. In each case, the species involved are connected via monomolecular reaction pathways. The potential and limitations of the approach for recovering the respective rate constants and component spectra are discussed. © The Author(s) 2016.

A statistical approach to optimizing concrete mixture design.

PubMed

Ahmad, Shamsad; Alghamdi, Saeid A

2014-01-01

A step-by-step statistical approach is proposed to obtain optimum proportioning of concrete mixtures using the data obtained through a statistically planned experimental program. The utility of the proposed approach for optimizing the design of concrete mixture is illustrated considering a typical case in which trial mixtures were considered according to a full factorial experiment design involving three factors and their three levels (3(3)). A total of 27 concrete mixtures with three replicates (81 specimens) were considered by varying the levels of key factors affecting compressive strength of concrete, namely, water/cementitious materials ratio (0.38, 0.43, and 0.48), cementitious materials content (350, 375, and 400 kg/m(3)), and fine/total aggregate ratio (0.35, 0.40, and 0.45). The experimental data were utilized to carry out analysis of variance (ANOVA) and to develop a polynomial regression model for compressive strength in terms of the three design factors considered in this study. The developed statistical model was used to show how optimization of concrete mixtures can be carried out with different possible options.

A Statistical Approach to Optimizing Concrete Mixture Design

PubMed Central

Alghamdi, Saeid A.

2014-01-01

A step-by-step statistical approach is proposed to obtain optimum proportioning of concrete mixtures using the data obtained through a statistically planned experimental program. The utility of the proposed approach for optimizing the design of concrete mixture is illustrated considering a typical case in which trial mixtures were considered according to a full factorial experiment design involving three factors and their three levels (33). A total of 27 concrete mixtures with three replicates (81 specimens) were considered by varying the levels of key factors affecting compressive strength of concrete, namely, water/cementitious materials ratio (0.38, 0.43, and 0.48), cementitious materials content (350, 375, and 400 kg/m3), and fine/total aggregate ratio (0.35, 0.40, and 0.45). The experimental data were utilized to carry out analysis of variance (ANOVA) and to develop a polynomial regression model for compressive strength in terms of the three design factors considered in this study. The developed statistical model was used to show how optimization of concrete mixtures can be carried out with different possible options. PMID:24688405

A multi-state fragment charge difference approach for diabatic states in electron transfer: Extension and automation

NASA Astrophysics Data System (ADS)

Yang, Chou-Hsun; Hsu, Chao-Ping

2013-10-01

The electron transfer (ET) rate prediction requires the electronic coupling values. The Generalized Mulliken-Hush (GMH) and Fragment Charge Difference (FCD) schemes have been useful approaches to calculate ET coupling from an excited state calculation. In their typical form, both methods use two eigenstates in forming the target charge-localized diabatic states. For problems involve three or four states, a direct generalization is possible, but it is necessary to pick and assign the locally excited or charge-transfer states involved. In this work, we generalize the 3-state scheme for a multi-state FCD without the need of manual pick or assignment for the states. In this scheme, the diabatic states are obtained separately in the charge-transfer or neutral excited subspaces, defined by their eigenvalues in the fragment charge-difference matrix. In each subspace, the Hamiltonians are diagonalized, and there exist off-diagonal Hamiltonian matrix elements between different subspaces, particularly the charge-transfer and neutral excited diabatic states. The ET coupling values are obtained as the corresponding off-diagonal Hamiltonian matrix elements. A similar multi-state GMH scheme can also be developed. We test the new multi-state schemes for the performance in systems that have been studied using more than two states with FCD or GMH. We found that the multi-state approach yields much better charge-localized states in these systems. We further test for the dependence on the number of state included in the calculation of ET couplings. The final coupling values are converged when the number of state included is increased. In one system where experimental value is available, the multi-state FCD coupling value agrees better with the previous experimental result. We found that the multi-state GMH and FCD are useful when the original two-state approach fails.

Experimental Investigation of Gas/Slag/Matte/Tridymite Equilibria in the Cu-Fe-O-S-Si System in Controlled Atmospheres: Development of Technique

NASA Astrophysics Data System (ADS)

Fallah-Mehrjardi, Ata; Hidayat, Taufiq; Hayes, Peter C.; Jak, Evgueni

2017-12-01

The majority of primary pyrometallurgical copper making processes involve the formation of two immiscible liquid phases, i.e., matte product and the slag phase. There are significant gaps and discrepancies in the phase equilibria data of the slag and the matte systems due to issues and difficulties in performing the experiments and phase analysis. The present study aims to develop an improved experimental methodology for accurate characterisation of gas/slag/matte/tridymite equilibria in the Cu-Fe-O-S-Si system under controlled atmospheres. The experiments involve high-temperature equilibration of synthetic mixtures on silica substrates in CO/CO2/SO2/Ar atmospheres, rapid quenching of samples into water, and direct composition measurement of the equilibrium phases using Electron Probe X-ray Microanalysis (EPMA). A four-point-test procedure was applied to ensure the achievement of equilibrium, which included the following: (i) investigation of equilibration as a function of time, (ii) assessment of phase homogeneity, (iii) confirmation of equilibrium by approaching from different starting conditions, and (iv) systematic analysis of the reactions specific to the system. An iterative improved experimental methodology was developed using this four-point-test approach to characterize the complex multi-component, multi-phase equilibria with high accuracy and precision. The present study is a part of a broader overall research program on the characterisation of the multi-component (Cu-Fe-O-S-Si-Al-Ca-Mg), multi-phase (gas/slag/matte/metal/solids) systems with minor elements (Pb, Zn, As, Bi, Sn, Sb, Ag, and Au).

Single molecule experimentation in biological physics: exploring the living component of soft condensed matter one molecule at a time.

PubMed

Harriman, O L J; Leake, M C

2011-12-21

The soft matter of biological systems consists of mesoscopic length scale building blocks, composed of a variety of different types of biological molecules. Most single biological molecules are so small that 1 billion would fit on the full-stop at the end of this sentence, but collectively they carry out the vital activities in living cells whose length scale is at least three orders of magnitude greater. Typically, the number of molecules involved in any given cellular process at any one time is relatively small, and so real physiological events may often be dominated by stochastics and fluctuation behaviour at levels comparable to thermal noise, and are generally heterogeneous in nature. This challenging combination of heterogeneity and stochasticity is best investigated experimentally at the level of single molecules, as opposed to more conventional bulk ensemble-average techniques. In recent years, the use of such molecular experimental approaches has become significantly more widespread in research laboratories around the world. In this review we discuss recent experimental approaches in biological physics which can be applied to investigate the living component of soft condensed matter to a precision of a single molecule. © 2011 IOP Publishing Ltd Printed in the UK & the USA

A latent discriminative model-based approach for classification of imaginary motor tasks from EEG data.

PubMed

Saa, Jaime F Delgado; Çetin, Müjdat

2012-04-01

We consider the problem of classification of imaginary motor tasks from electroencephalography (EEG) data for brain-computer interfaces (BCIs) and propose a new approach based on hidden conditional random fields (HCRFs). HCRFs are discriminative graphical models that are attractive for this problem because they (1) exploit the temporal structure of EEG; (2) include latent variables that can be used to model different brain states in the signal; and (3) involve learned statistical models matched to the classification task, avoiding some of the limitations of generative models. Our approach involves spatial filtering of the EEG signals and estimation of power spectra based on autoregressive modeling of temporal segments of the EEG signals. Given this time-frequency representation, we select certain frequency bands that are known to be associated with execution of motor tasks. These selected features constitute the data that are fed to the HCRF, parameters of which are learned from training data. Inference algorithms on the HCRFs are used for the classification of motor tasks. We experimentally compare this approach to the best performing methods in BCI competition IV as well as a number of more recent methods and observe that our proposed method yields better classification accuracy.

Composition of web services using Markov decision processes and dynamic programming.

PubMed

Uc-Cetina, Víctor; Moo-Mena, Francisco; Hernandez-Ucan, Rafael

2015-01-01

We propose a Markov decision process model for solving the Web service composition (WSC) problem. Iterative policy evaluation, value iteration, and policy iteration algorithms are used to experimentally validate our approach, with artificial and real data. The experimental results show the reliability of the model and the methods employed, with policy iteration being the best one in terms of the minimum number of iterations needed to estimate an optimal policy, with the highest Quality of Service attributes. Our experimental work shows how the solution of a WSC problem involving a set of 100,000 individual Web services and where a valid composition requiring the selection of 1,000 services from the available set can be computed in the worst case in less than 200 seconds, using an Intel Core i5 computer with 6 GB RAM. Moreover, a real WSC problem involving only 7 individual Web services requires less than 0.08 seconds, using the same computational power. Finally, a comparison with two popular reinforcement learning algorithms, sarsa and Q-learning, shows that these algorithms require one or two orders of magnitude and more time than policy iteration, iterative policy evaluation, and value iteration to handle WSC problems of the same complexity.

Optical analysis of laser systems using interferometry

NASA Astrophysics Data System (ADS)

Viswanathan, V. K.; Liberman, I.; Lawrence, G.; Seery, B. D.

1980-06-01

It is noted that previous approaches of predicting focal spot parameters involved the digitization of interference patterns of the optical components and propagation of the complex amplitude and phase of the wave front throughout the system. The present paper describes an approach in which the computational procedure is extended to produce computer plots of the final emerging wave front. It is shown that this enables direct comparison with the experimentally produced wave front of the total system and makes possible the optical analysis, design, and possible optimization of laser systems. A description is given of the computational procedure and the Twyman-Green and Smartt IR interferometers constructed to verify this approach. Finally, consideration is given to the implications of the results.

Computer Aided Enzyme Design and Catalytic Concepts

PubMed Central

Frushicheva, Maria P.; Mills, Matthew J. L.; Schopf, Patrick; Singh, Manoj K.; Warshel, Arieh

2014-01-01

Gaining a deeper understanding of enzyme catalysis is of great practical and fundamental importance. Over the years it has become clear that despite advances made in experimental mutational studies, a quantitative understanding of enzyme catalysis will not be possible without the use of computer modeling approaches. While we believe that electrostatic preorganization is by far the most important catalytic factor, convincing the wider scientific community of this may require the demonstration of effective rational enzyme design. Here we make the point that the main current advances in enzyme design are basically advances in directed evolution and that computer aided enzyme design must involve approaches that can reproduce catalysis in well-defined test cases. Such an approach is provided by the empirical valence bond method. PMID:24814389

Games as Tools to Address Conservation Conflicts.

PubMed

Redpath, Steve M; Keane, Aidan; Andrén, Henrik; Baynham-Herd, Zachary; Bunnefeld, Nils; Duthie, A Bradley; Frank, Jens; Garcia, Claude A; Månsson, Johan; Nilsson, Lovisa; Pollard, Chris R J; Rakotonarivo, O Sarobidy; Salk, Carl F; Travers, Henry

2018-06-01

Conservation conflicts represent complex multilayered problems that are challenging to study. We explore the utility of theoretical, experimental, and constructivist approaches to games to help to understand and manage these challenges. We show how these approaches can help to develop theory, understand patterns in conflict, and highlight potentially effective management solutions. The choice of approach should be guided by the research question and by whether the focus is on testing hypotheses, predicting behaviour, or engaging stakeholders. Games provide an exciting opportunity to help to unravel the complexity in conflicts, while researchers need an awareness of the limitations and ethical constraints involved. Given the opportunities, this field will benefit from greater investment and development. Copyright © 2018 Elsevier Ltd. All rights reserved.

A Model Based Approach to Increase the Part Accuracy in Robot Based Incremental Sheet Metal Forming

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

Meier, Horst; Laurischkat, Roman; Zhu Junhong

One main influence on the dimensional accuracy in robot based incremental sheet metal forming results from the compliance of the involved robot structures. Compared to conventional machine tools the low stiffness of the robot's kinematic results in a significant deviation of the planned tool path and therefore in a shape of insufficient quality. To predict and compensate these deviations offline, a model based approach, consisting of a finite element approach, to simulate the sheet forming, and a multi body system, modeling the compliant robot structure, has been developed. This paper describes the implementation and experimental verification of the multi bodymore » system model and its included compensation method.« less

A processing centre for the CNES CE-GPS experimentation

NASA Technical Reports Server (NTRS)

Suard, Norbert; Durand, Jean-Claude

1994-01-01

CNES is involved in a GPS (Global Positioning System) geostationary overlay experimentation. The purpose of this experimentation is to test various new techniques in order to select the optimal station synchronization method, as well as the geostationary spacecraft orbitography method. These new techniques are needed to develop the Ranging GPS Integrity Channel services. The CNES experimentation includes three transmitting/receiving ground stations (manufactured by IN-SNEC), one INMARSAT 2 C/L band transponder and a processing center named STE (Station de Traitements de l'Experimentation). Not all the techniques to be tested are implemented, but the experimental system has to include several functions; part of the future system simulation functions, such as a servo-loop function, and in particular a data collection function providing for rapid monitoring of system operation, analysis of existing ground station processes, and several weeks of data coverage for other scientific studies. This paper discusses system architecture and some criteria used in its design, as well as the monitoring function, the approach used to develop a low-cost and short-life processing center in collaboration with a CNES sub-contractor (ATTDATAID), and some results.

Influence of Cultural, Organizational, and Automation Capability on Human Automation Trust: A Case Study of Auto-GCAS Experimental Test Pilots

NASA Technical Reports Server (NTRS)

Koltai, Kolina; Ho, Nhut; Masequesmay, Gina; Niedober, David; Skoog, Mark; Cacanindin, Artemio; Johnson, Walter; Lyons, Joseph

2014-01-01

This paper discusses a case study that examined the influence of cultural, organizational and automation capability upon human trust in, and reliance on, automation. In particular, this paper focuses on the design and application of an extended case study methodology, and on the foundational lessons revealed by it. Experimental test pilots involved in the research and development of the US Air Force's newly developed Automatic Ground Collision Avoidance System served as the context for this examination. An eclectic, multi-pronged approach was designed to conduct this case study, and proved effective in addressing the challenges associated with the case's politically sensitive and military environment. Key results indicate that the system design was in alignment with pilot culture and organizational mission, indicating the potential for appropriate trust development in operational pilots. These include the low-vulnerability/ high risk nature of the pilot profession, automation transparency and suspicion, system reputation, and the setup of and communications among organizations involved in the system development.

Experimental and computational fluid dynamic studies of mixing for complex oral health products

NASA Astrophysics Data System (ADS)

Garcia, Marti Cortada; Mazzei, Luca; Angeli, Panagiota

2015-11-01

Mixing high viscous non-Newtonian fluids is common in the consumer health industry. Sometimes this process is empirical and involves many pilot plants trials which are product specific. The first step to study the mixing process is to build on knowledge on the rheology of the fluids involved. In this research a systematic approach is used to validate the rheology of two liquids: glycerol and a gel formed by polyethylene glycol and carbopol. Initially, the constitutive equation is determined which relates the viscosity of the fluids with temperature, shear rate, and concentration. The key variable for the validation is the power required for mixing, which can be obtained both from CFD and experimentally using a stirred tank and impeller of well-defined geometries at different impeller speeds. A good agreement between the two values indicates a successful validation of the rheology and allows the CFD model to be used for the study of mixing in the complex vessel geometries and increased sizes encountered during scale up.

Visualization and Analysis of MiRNA-Targets Interactions Networks.

PubMed

León, Luis E; Calligaris, Sebastián D

2017-01-01

MicroRNAs are a class of small, noncoding RNA molecules of 21-25 nucleotides in length that regulate the gene expression by base-pairing with the target mRNAs, mainly leading to down-regulation or repression of the target genes. MicroRNAs are involved in diverse regulatory pathways in normal and pathological conditions. In this context, it is highly important to identify the targets of specific microRNA in order to understand the mechanism of its regulation and consequently its involvement in disease. However, the microRNA target identification is experimentally laborious and time-consuming. The in silico prediction of microRNA targets is an extremely useful approach because you can identify potential mRNA targets, reduce the number of possibilities and then, validate a few microRNA-mRNA interactions in an in vitro experimental model. In this chapter, we describe, in a simple way, bioinformatics guidelines to use miRWalk database and Cytoscape software for analyzing microRNA-mRNA interactions through their visualization as a network.

Avalanching strain dynamics during the hydriding phase transformation in individual palladium nanoparticles

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

Ulvestad, A.; Welland, M. J.; Collins, S. S. E.

2015-12-11

Phase transitions in reactive environments are crucially important in energy and information storage, catalysis and sensors. Nanostructuring active particles can yield faster charging/ discharging kinetics, increased lifespan and record catalytic activities. However, establishing the causal link between structure and function is challenging for nanoparticles, as ensemble measurements convolve intrinsic single-particle properties with sample diversity. Here we study the hydriding phase transformation in individual palladium nanocubes in situ using coherent X-ray diffractive imaging. The phase transformation dynamics, which involve the nucleation and propagation of a hydrogen-rich region, are dependent on absolute time (aging) and involve intermittent dynamics (avalanching). A hydrogen-rich surfacemore » layer dominates the crystal strain in the hydrogen-poor phase, while strain inversion occurs at the cube corners in the hydrogen-rich phase. A three-dimensional phase-field model is used to interpret the experimental results. In conclusion, our experimental and theoretical approach provides a general framework for designing and optimizing phase transformations for single nanocrystals in reactive environments.« less

A surprising role for conformational entropy in protein function

PubMed Central

Wand, A. Joshua; Moorman, Veronica R.; Harpole, Kyle W.

2014-01-01

Formation of high-affinity complexes is critical for the majority of enzymatic reactions involving proteins. The creation of the family of Michaelis and other intermediate complexes during catalysis clearly involves a complicated manifold of interactions that are diverse and complex. Indeed, computing the energetics of interactions between proteins and small molecule ligands using molecular structure alone remains a grand challenge. One of the most difficult contributions to the free energy of protein-ligand complexes to experimentally access is that due to changes in protein conformational entropy. Fortunately, recent advances in solution nuclear magnetic resonance (NMR) relaxation methods have enabled the use of measures-of-motion between conformational states of a protein as a proxy for conformational entropy. This review briefly summarizes the experimental approaches currently employed to characterize fast internal motion in proteins, how this information is used to gain insight into conformational entropy, what has been learned and what the future may hold for this emerging view of protein function. PMID:23478875

Differences in Risk Aversion between Young and Older Adults.

PubMed

Albert, Steven M; Duffy, John

2012-01-15

Research on decision-making strategies among younger and older adults suggests that older adults may be more risk averse than younger people in the case of potential losses. These results mostly come from experimental studies involving gambling paradigms. Since these paradigms involve substantial demands on memory and learning, differences in risk aversion or other features of decision-making attributed to age may in fact reflect age-related declines in cognitive abilities. In the current study, older and younger adults completed a simpler, paired lottery choice task used in the experimental economics literature to elicit risk aversion. A similar approach was used to elicit participants' discount rates. The older adult group was more risk averse than younger adults (p < .05) and also had a higher discount rate (15.6-21.0% vs. 10.3-15.5%, p < .01), indicating lower expected utility from future income. Risk aversion and implied discount rates were weakly correlated. It may be valuable to investigate developmental changes in neural correlates of decision-making across the lifespan.

Differences in Risk Aversion between Young and Older Adults

PubMed Central

Albert, Steven M.; Duffy, John

2013-01-01

Research on decision-making strategies among younger and older adults suggests that older adults may be more risk averse than younger people in the case of potential losses. These results mostly come from experimental studies involving gambling paradigms. Since these paradigms involve substantial demands on memory and learning, differences in risk aversion or other features of decision-making attributed to age may in fact reflect age-related declines in cognitive abilities. In the current study, older and younger adults completed a simpler, paired lottery choice task used in the experimental economics literature to elicit risk aversion. A similar approach was used to elicit participants' discount rates. The older adult group was more risk averse than younger adults (p < .05) and also had a higher discount rate (15.6-21.0% vs. 10.3-15.5%, p < .01), indicating lower expected utility from future income. Risk aversion and implied discount rates were weakly correlated. It may be valuable to investigate developmental changes in neural correlates of decision-making across the lifespan. PMID:24319671

Avalanching strain dynamics during the hydriding phase transformation in individual palladium nanoparticles

NASA Astrophysics Data System (ADS)

Ulvestad, A.; Welland, M. J.; Collins, S. S. E.; Harder, R.; Maxey, E.; Wingert, J.; Singer, A.; Hy, S.; Mulvaney, P.; Zapol, P.; Shpyrko, O. G.

2015-12-01

Phase transitions in reactive environments are crucially important in energy and information storage, catalysis and sensors. Nanostructuring active particles can yield faster charging/discharging kinetics, increased lifespan and record catalytic activities. However, establishing the causal link between structure and function is challenging for nanoparticles, as ensemble measurements convolve intrinsic single-particle properties with sample diversity. Here we study the hydriding phase transformation in individual palladium nanocubes in situ using coherent X-ray diffractive imaging. The phase transformation dynamics, which involve the nucleation and propagation of a hydrogen-rich region, are dependent on absolute time (aging) and involve intermittent dynamics (avalanching). A hydrogen-rich surface layer dominates the crystal strain in the hydrogen-poor phase, while strain inversion occurs at the cube corners in the hydrogen-rich phase. A three-dimensional phase-field model is used to interpret the experimental results. Our experimental and theoretical approach provides a general framework for designing and optimizing phase transformations for single nanocrystals in reactive environments.

Avalanching strain dynamics during the hydriding phase transformation in individual palladium nanoparticles

PubMed Central

Ulvestad, A.; Welland, M. J.; Collins, S. S. E.; Harder, R.; Maxey, E.; Wingert, J.; Singer, A.; Hy, S.; Mulvaney, P.; Zapol, P.; Shpyrko, O. G.

2015-01-01

Phase transitions in reactive environments are crucially important in energy and information storage, catalysis and sensors. Nanostructuring active particles can yield faster charging/discharging kinetics, increased lifespan and record catalytic activities. However, establishing the causal link between structure and function is challenging for nanoparticles, as ensemble measurements convolve intrinsic single-particle properties with sample diversity. Here we study the hydriding phase transformation in individual palladium nanocubes in situ using coherent X-ray diffractive imaging. The phase transformation dynamics, which involve the nucleation and propagation of a hydrogen-rich region, are dependent on absolute time (aging) and involve intermittent dynamics (avalanching). A hydrogen-rich surface layer dominates the crystal strain in the hydrogen-poor phase, while strain inversion occurs at the cube corners in the hydrogen-rich phase. A three-dimensional phase-field model is used to interpret the experimental results. Our experimental and theoretical approach provides a general framework for designing and optimizing phase transformations for single nanocrystals in reactive environments. PMID:26655832

The Biophysics of Infection.

PubMed

Leake, Mark C

2016-01-01

Our understanding of the processes involved in infection has grown enormously in the past decade due in part to emerging methods of biophysics. This new insight has been enabled through advances in interdisciplinary experimental technologies and theoretical methods at the cutting-edge interface of the life and physical sciences. For example, this has involved several state-of-the-art biophysical tools used in conjunction with molecular and cell biology approaches, which enable investigation of infection in living cells. There are also new, emerging interfacial science tools which enable significant improvements to the resolution of quantitative measurements both in space and time. These include single-molecule biophysics methods and super-resolution microscopy approaches. These new technological tools in particular have underpinned much new understanding of dynamic processes of infection at a molecular length scale. Also, there are many valuable advances made recently in theoretical approaches of biophysics which enable advances in predictive modelling to generate new understanding of infection. Here, I discuss these advances, and take stock on our knowledge of the biophysics of infection and discuss where future advances may lead.

Digital phased array beamforming using single-bit delta-sigma conversion with non-uniform oversampling.

PubMed

Kozak, M; Karaman, M

2001-07-01

Digital beamforming based on oversampled delta-sigma (delta sigma) analog-to-digital (A/D) conversion can reduce the overall cost, size, and power consumption of phased array front-end processing. The signal resampling involved in dynamic delta sigma beamforming, however, disrupts synchronization between the modulators and demodulator, causing significant degradation in the signal-to-noise ratio. As a solution to this, we have explored a new digital beamforming approach based on non-uniform oversampling delta sigma A/D conversion. Using this approach, the echo signals received by the transducer array are sampled at time instants determined by the beamforming timing and then digitized by single-bit delta sigma A/D conversion prior to the coherent beam summation. The timing information involves a non-uniform sampling scheme employing different clocks at each array channel. The delta sigma coded beamsums obtained by adding the delayed 1-bit coded RF echo signals are then processed through a decimation filter to produce final beamforming outputs. The performance and validity of the proposed beamforming approach are assessed by means of emulations using experimental raw RF data.

Synthesis and Labeling of RNA In Vitro

PubMed Central

Huang, Chao; Yu, Yi-Tao

2013-01-01

This unit discusses several methods for generating large amounts of uniformly labeled, end-labeled, and site-specifically labeled RNAs in vitro. The methods involve a number of experimental procedures, including RNA transcription, 5′ dephosphorylation and rephosphorylation, 3′ terminal nucleotide addition (via ligation), site-specific RNase H cleavage directed by 2′-O-methyl RNA-DNA chimeras, and 2-piece splint ligation. The applications of these RNA radiolabeling approaches are also discussed. PMID:23547015

Principles of cancer prevention.

PubMed

Meyskens, Frank L; Tully, Patricia

2005-11-01

To summarize the scientific principles underlying cancer prevention. Articles, text books, personal communications, and experience. The scientific basis of cancer prevention is complex and involves experimental and epidemiologic approaches and clinical trials. As more information becomes available regarding proven and potential cancer-prevention strategies, oncology nurses are regularly called upon to guide patients and others in making choices regarding preventative options. It is important for oncology nurses to stay abreast of this growing body of knowledge.

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

DTIC Science & Technology

2010-04-01

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

A new experimental method for determining local airloads on rotor blades in forward flight

NASA Astrophysics Data System (ADS)

Berton, E.; Maresca, C.; Favier, D.

This paper presents a new approach for determining local airloads on helicopter rotor blade sections in forward flight. The method is based on the momentum equation in which all the terms are expressed by means of the velocity field measured by a laser Doppler velocimeter. The relative magnitude of the different terms involved in the momentum and Bernoulli equations is estimated and the results are encouraging.

Dynamic analysis for shuttle design verification

NASA Technical Reports Server (NTRS)

Fralich, R. W.; Green, C. E.; Rheinfurth, M. H.

1972-01-01

Two approaches that are used for determining the modes and frequencies of space shuttle structures are discussed. The first method, direct numerical analysis, involves finite element mathematical modeling of the space shuttle structure in order to use computer programs for dynamic structural analysis. The second method utilizes modal-coupling techniques of experimental verification made by vibrating only spacecraft components and by deducing modes and frequencies of the complete vehicle from results obtained in the component tests.

Hepatic injury due to combined choline-deprivation and thioacetamide administration: an experimental approach to liver diseases.

PubMed

Al-Humadi, Hussam; Theocharis, Stamatios; Dontas, Ismene; Stolakis, Vasileios; Zarros, Apostolos; Kyriakaki, Argyro; Al-Saigh, Rafal; Liapi, Charis

2012-12-01

The induction of prolonged choline-deprivation (CD) in rats receiving thioacetamide (TAA) is an experimental approach of mild hepatotoxicity that could resemble commonly presented cases in clinical practice (in which states of malnutrition and/or alcoholism are complicated by the development of other liver-associated diseases). The present study aimed to investigate the time-dependent effects of a 30-, a 60- and a 90-day dietary CD and/or TAA administration on the adult rat liver histopathology and the serum markers of hepatic functional integrity. Rats were divided into four main groups: (a) control, (b) CD, (c) TAA and (d) CD + TAA. Dietary CD was provoked through the administration of choline-deficient diet, while TAA administration was performed ad libitum through the drinking water (300 mg/l of drinking water). Histological examination of the CD + TAA liver sections revealed micro- and macro-vesicular steatosis with degeneration and primary fibrosis at day 30, to extensive steatosis and fibrosis at day 90. Steatosis was mostly of the macrovesicular type, involving all zones of the lobule, while inflammatory infiltrate consisted of foci of acute and chronic inflammatory cells randomly distributed in the lobule. These changes were accompanied by gradually increasing mitotic activity, as well as by a constantly high alpha-smooth muscle actin immunohistochemical staining. The determination of hepatocellular injury markers such as the serum enzyme levels' of alanine aminotransferase and aspartate aminotransferase demonstrated a decrease at day 30 (they returned to control levels at days 60 and 90). However, the determination of those serum enzymes used for the assessment of cholestatic liver injury (gamma-glutamyltransferase, alkaline phosphatase) revealed a constant (time-independent) statistically-significant increase versus control values. Long-term combined dietary CD and TAA administration could be a more realistic experimental approach to human liver diseases involving severe steatosis, fibrosis, stellate cell activation and significant regenerative hepatocellular response.

Experimental investigation of a four-qubit linear-optical quantum logic circuit

NASA Astrophysics Data System (ADS)

Stárek, R.; Mičuda, M.; Miková, M.; Straka, I.; Dušek, M.; Ježek, M.; Fiurášek, J.

2016-09-01

We experimentally demonstrate and characterize a four-qubit linear-optical quantum logic circuit. Our robust and versatile scheme exploits encoding of two qubits into polarization and path degrees of single photons and involves two crossed inherently stable interferometers. This approach allows us to design a complex quantum logic circuit that combines a genuine four-qubit C3Z gate and several two-qubit and single-qubit gates. The C3Z gate introduces a sign flip if and only if all four qubits are in the computational state |1>. We verify high-fidelity performance of this central four-qubit gate using Hofmann bounds on quantum gate fidelity and Monte Carlo fidelity sampling. We also experimentally demonstrate that the quantum logic circuit can generate genuine multipartite entanglement and we certify the entanglement with the use of suitably tailored entanglement witnesses.

Modeling of coherent ultrafast magneto-optical experiments: Light-induced molecular mean-field model

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

Hinschberger, Y.; Hervieux, P.-A.

2015-12-28

We present calculations which aim to describe coherent ultrafast magneto-optical effects observed in time-resolved pump-probe experiments. Our approach is based on a nonlinear semi-classical Drude-Voigt model and is used to interpret experiments performed on nickel ferromagnetic thin film. Within this framework, a phenomenological light-induced coherent molecular mean-field depending on the polarizations of the pump and probe pulses is proposed whose microscopic origin is related to a spin-orbit coupling involving the electron spins of the material sample and the electric field of the laser pulses. Theoretical predictions are compared to available experimental data. The model successfully reproduces the observed experimental trendsmore » and gives meaningful insight into the understanding of magneto-optical rotation behavior in the ultrafast regime. Theoretical predictions for further experimental studies are also proposed.« less

Experimental investigation of a four-qubit linear-optical quantum logic circuit.

PubMed

Stárek, R; Mičuda, M; Miková, M; Straka, I; Dušek, M; Ježek, M; Fiurášek, J

2016-09-20

We experimentally demonstrate and characterize a four-qubit linear-optical quantum logic circuit. Our robust and versatile scheme exploits encoding of two qubits into polarization and path degrees of single photons and involves two crossed inherently stable interferometers. This approach allows us to design a complex quantum logic circuit that combines a genuine four-qubit C(3)Z gate and several two-qubit and single-qubit gates. The C(3)Z gate introduces a sign flip if and only if all four qubits are in the computational state |1〉. We verify high-fidelity performance of this central four-qubit gate using Hofmann bounds on quantum gate fidelity and Monte Carlo fidelity sampling. We also experimentally demonstrate that the quantum logic circuit can generate genuine multipartite entanglement and we certify the entanglement with the use of suitably tailored entanglement witnesses.

[Prediction of the molecular response to pertubations from single cell measurements].

PubMed

Remacle, Françoise; Levine, Raphael D

2014-12-01

The response of protein signalization networks to perturbations is analysed from single cell measurements. This experimental approach allows characterizing the fluctuations in protein expression levels from cell to cell. The analysis is based on an information theoretic approach grounded in thermodynamics leading to a quantitative version of Le Chatelier principle which allows to predict the molecular response. Two systems are investigated: human macrophages subjected to lipopolysaccharide challenge, analogous to the immune response against Gram-negative bacteria and the response of the proteins involved in the mTOR signalizing network of GBM cancer cells to changes in partial oxygen pressure. © 2014 médecine/sciences – Inserm.

A new approach of watermarking technique by means multichannel wavelet functions

NASA Astrophysics Data System (ADS)

Agreste, Santa; Puccio, Luigia

2012-12-01

The digital piracy involving images, music, movies, books, and so on, is a legal problem that has not found a solution. Therefore it becomes crucial to create and to develop methods and numerical algorithms in order to solve the copyright problems. In this paper we focus the attention on a new approach of watermarking technique applied to digital color images. Our aim is to describe the realized watermarking algorithm based on multichannel wavelet functions with multiplicity r = 3, called MCWM 1.0. We report a large experimentation and some important numerical results in order to show the robustness of the proposed algorithm to geometrical attacks.

Management of impulse control disorders in Parkinson's disease: Controversies and future approaches.

PubMed

Samuel, Michael; Rodriguez-Oroz, Maria; Antonini, Angelo; Brotchie, Jonathan M; Ray Chaudhuri, Kallol; Brown, Richard G; Galpern, Wendy R; Nirenberg, Melissa J; Okun, Michael S; Lang, Anthony E

2015-02-01

Impulse control disorders in Parkinson's disease are a group of impulsive behaviors most often associated with dopaminergic treatment. Presently, there is a lack of high quality evidence available to guide their management. This manuscript reviews current management strategies, before concentrating on the concept of dopamine agonist withdrawal syndrome and its implications for the management of impulse control disorders. Further, we focus on controversies, including the role of more recently available anti-parkinsonian drugs, and potential future approaches involving routes of drug delivery, nonpharmacological treatments (such as cognitive behavioral therapy and deep brain stimulation), and other as yet experimental strategies. © 2015 International Parkinson and Movement Disorder Society.

Impulse Control Disorders in Parkinson’s Disease:Management, Controversies, and Potential Approaches

PubMed Central

Samuel, M; Rodriguez-Oroz, M; Antonini, A; Brotchie, JM; Ray Chaudhuri, K; Brown, RG; Galpern, WR; Nirenberg, MJ; Okun, MS; Lang, AE

2016-01-01

Impulse control disorders in Parkinson’s disease are a group of impulsive behaviors most often associated with dopaminergic treatment. Presently, there is a lack of high quality evidence available to guide their management. This manuscript reviews current management strategies, before concentrating on the concept of dopamine agonist withdrawal syndrome and its implications for the management of impulse control disorders. Further, we focus on controversies including the role of more recently available anti-parkinsonian drugs, and potential future approaches involving routes of drug delivery, non-pharmacological treatments (such as cognitive behaviour therapy and deep brain stimulation), and other as yet experimental strategies. PMID:25607799

Ribosome profiling reveals the what, when, where and how of protein synthesis.

PubMed

Brar, Gloria A; Weissman, Jonathan S

2015-11-01

Ribosome profiling, which involves the deep sequencing of ribosome-protected mRNA fragments, is a powerful tool for globally monitoring translation in vivo. The method has facilitated discovery of the regulation of gene expression underlying diverse and complex biological processes, of important aspects of the mechanism of protein synthesis, and even of new proteins, by providing a systematic approach for experimental annotation of coding regions. Here, we introduce the methodology of ribosome profiling and discuss examples in which this approach has been a key factor in guiding biological discovery, including its prominent role in identifying thousands of novel translated short open reading frames and alternative translation products.

Refined approach for quantification of in vivo ischemia-reperfusion injury in the mouse heart

PubMed Central

Medway, Debra J.; Schulz-Menger, Jeanette; Schneider, Jurgen E.; Neubauer, Stefan; Lygate, Craig A.

2009-01-01

Cardiac ischemia-reperfusion experiments in the mouse are important in vivo models of human disease. Infarct size is a particularly important scientific readout as virtually all cardiocirculatory pathways are affected by it. Therefore, such measurements must be exact and valid. The histological analysis, however, remains technically challenging, and the resulting quality is often unsatisfactory. For this report we have scrutinized each step involved in standard double-staining histology. We have tested published approaches and challenged their practicality. As a result, we propose an improved and streamlined protocol, which consistently yields high-quality histology, thereby minimizing experimental noise and group sizes. PMID:19820193

In-plane and cross-plane thermal conductivity in La2-xSrxCuO4

NASA Astrophysics Data System (ADS)

Kumari, Anita; Gupta, Anushri; Verma, Sanjeev K.; Indu, B. D.

2018-05-01

The problem of heat transport anisotropy in layered cuprate high temperature superconductors (HTS) has been investigated in terms of a-, b-, c- axis thermal conductivity. Various inadequacies involved due to dispersion and violation of Matthessien's rule in the Callaway's model have been removed with the help of life time approach of quantum many body theory of scattering mechanisms. Based on this approach the thermal conductivity of La1.98Sr0.02CuO4 and La1.96Sr0.04CuO4 samples has been numerically estimated and the observed results are found in good agreement with experimental observations.

Fast and simple acquisition of solid-state 14N NMR spectra with signal enhancement via population transfer.

PubMed

O'Dell, Luke A; Schurko, Robert W

2009-05-20

A new approach for the acquisition of static, wideline (14)N NMR powder patterns is outlined. The method involves the use of frequency-swept pulses which serve two simultaneous functions: (1) broad-band excitation of magnetization and (2) signal enhancement via population transfer. The signal enhancement mechanism is described using numerical simulations and confirmed experimentally. This approach, which we call DEISM (Direct Enhancement of Integer Spin Magnetization), allows high-quality (14)N spectra to be acquired at intermediate field strengths in an uncomplicated way and in a fraction of the time required for previously reported methods.

From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity.

PubMed

Cristescu, Melania E

2014-10-01

DNA-based species identification, known as barcoding, transformed the traditional approach to the study of biodiversity science. The field is transitioning from barcoding individuals to metabarcoding communities. This revolution involves new sequencing technologies, bioinformatics pipelines, computational infrastructure, and experimental designs. In this dynamic genomics landscape, metabarcoding studies remain insular and biodiversity estimates depend on the particular methods used. In this opinion article, I discuss the need for a coordinated advancement of DNA-based species identification that integrates taxonomic and barcoding information. Such an approach would facilitate access to almost 3 centuries of taxonomic knowledge and 1 decade of building repository barcodes. Conservation projects are time sensitive, research funding is becoming restricted, and informed decisions depend on our ability to embrace integrative approaches to biodiversity science. Copyright © 2014 Elsevier Ltd. All rights reserved.

[Cognitive experimental approach to anxiety disorders].

PubMed

Azaïs, F

1995-01-01

Cognitive psychology is proposing a functional model to explain the mental organisation leading to emotional disorders. Among these disorders, anxiety spectrum represents a domain in which this model seems to be interesting for an efficient and comprehensive approach of the pathology. Number of behavioral or cognitive psychotherapeutic methods are relating to these cognitive references, but the theorical concepts of cognitive "shemata" or cognitive "processes" evoked to describe mental functioning in anxiety need an experimental approach for a better rational understanding. Cognitive function as perception, attention or memory can be explored in this domaine in an efficient way, allowing a more precise study of each stage of information processing. The cognitive model proposed in the psychopathology of anxiety suggests that anxious subjects are characterized by biases in processing of emotionally valenced information. This hypothesis suggests functional interference in information processing in these subjects, leading to an anxious response to the most of different stimuli. Experimental approach permit to explore this hypothesis, using many tasks for testing different cognitive dysfunction evoked in the anxious cognitive organisation. Impairments revealed in anxiety disorders seem to result from specific biases in threat-related information processing, involving several stages of cognitive processes. Semantic interference, attentional bias, implicit memory bias and priming effect are the most often disorders observed in anxious pathology, like simple phobia, generalised anxiety, panic disorder or post-traumatic stress disorder. These results suggest a top-down organisation of information processing in anxious subjects, who tend to detect, perceive and label many situations as threatening experience. The processes of reasoning and elaboration are consequently impaired in their adaptative function to threat, leading to the anxious response observed in clinical condition. The cognitive, behavioral and emotional components of this anxious reaction maintain the stressful experience for the subject, in which the self cognitive competence remain pathologically decreased. Cognitive psychology proposes an interesting model for the understanding of anxiety, in a domain in which subjectivity could benefit from an experimental approach.(ABSTRACT TRUNCATED AT 400 WORDS)

Statistical Methods for Proteomic Biomarker Discovery based on Feature Extraction or Functional Modeling Approaches.

PubMed

Morris, Jeffrey S

2012-01-01

In recent years, developments in molecular biotechnology have led to the increased promise of detecting and validating biomarkers, or molecular markers that relate to various biological or medical outcomes. Proteomics, the direct study of proteins in biological samples, plays an important role in the biomarker discovery process. These technologies produce complex, high dimensional functional and image data that present many analytical challenges that must be addressed properly for effective comparative proteomics studies that can yield potential biomarkers. Specific challenges include experimental design, preprocessing, feature extraction, and statistical analysis accounting for the inherent multiple testing issues. This paper reviews various computational aspects of comparative proteomic studies, and summarizes contributions I along with numerous collaborators have made. First, there is an overview of comparative proteomics technologies, followed by a discussion of important experimental design and preprocessing issues that must be considered before statistical analysis can be done. Next, the two key approaches to analyzing proteomics data, feature extraction and functional modeling, are described. Feature extraction involves detection and quantification of discrete features like peaks or spots that theoretically correspond to different proteins in the sample. After an overview of the feature extraction approach, specific methods for mass spectrometry ( Cromwell ) and 2D gel electrophoresis ( Pinnacle ) are described. The functional modeling approach involves modeling the proteomic data in their entirety as functions or images. A general discussion of the approach is followed by the presentation of a specific method that can be applied, wavelet-based functional mixed models, and its extensions. All methods are illustrated by application to two example proteomic data sets, one from mass spectrometry and one from 2D gel electrophoresis. While the specific methods presented are applied to two specific proteomic technologies, MALDI-TOF and 2D gel electrophoresis, these methods and the other principles discussed in the paper apply much more broadly to other expression proteomics technologies.

Dual-domain mass-transfer parameters from electrical hysteresis: theory and analytical approach applied to laboratory, synthetic streambed, and groundwater experiments

USGS Publications Warehouse

Briggs, Martin A.; Day-Lewis, Frederick D.; Ong, John B.; Harvey, Judson W.; Lane, John W.

2014-01-01

Models of dual-domain mass transfer (DDMT) are used to explain anomalous aquifer transport behavior such as the slow release of contamination and solute tracer tailing. Traditional tracer experiments to characterize DDMT are performed at the flow path scale (meters), which inherently incorporates heterogeneous exchange processes; hence, estimated “effective” parameters are sensitive to experimental design (i.e., duration and injection velocity). Recently, electrical geophysical methods have been used to aid in the inference of DDMT parameters because, unlike traditional fluid sampling, electrical methods can directly sense less-mobile solute dynamics and can target specific points along subsurface flow paths. Here we propose an analytical framework for graphical parameter inference based on a simple petrophysical model explaining the hysteretic relation between measurements of bulk and fluid conductivity arising in the presence of DDMT at the local scale. Analysis is graphical and involves visual inspection of hysteresis patterns to (1) determine the size of paired mobile and less-mobile porosities and (2) identify the exchange rate coefficient through simple curve fitting. We demonstrate the approach using laboratory column experimental data, synthetic streambed experimental data, and field tracer-test data. Results from the analytical approach compare favorably with results from calibration of numerical models and also independent measurements of mobile and less-mobile porosity. We show that localized electrical hysteresis patterns resulting from diffusive exchange are independent of injection velocity, indicating that repeatable parameters can be extracted under varied experimental designs, and these parameters represent the true intrinsic properties of specific volumes of porous media of aquifers and hyporheic zones.

Dual-domain mass-transfer parameters from electrical hysteresis: Theory and analytical approach applied to laboratory, synthetic streambed, and groundwater experiments

NASA Astrophysics Data System (ADS)

Briggs, Martin A.; Day-Lewis, Frederick D.; Ong, John B.; Harvey, Judson W.; Lane, John W.

2014-10-01

Models of dual-domain mass transfer (DDMT) are used to explain anomalous aquifer transport behavior such as the slow release of contamination and solute tracer tailing. Traditional tracer experiments to characterize DDMT are performed at the flow path scale (meters), which inherently incorporates heterogeneous exchange processes; hence, estimated "effective" parameters are sensitive to experimental design (i.e., duration and injection velocity). Recently, electrical geophysical methods have been used to aid in the inference of DDMT parameters because, unlike traditional fluid sampling, electrical methods can directly sense less-mobile solute dynamics and can target specific points along subsurface flow paths. Here we propose an analytical framework for graphical parameter inference based on a simple petrophysical model explaining the hysteretic relation between measurements of bulk and fluid conductivity arising in the presence of DDMT at the local scale. Analysis is graphical and involves visual inspection of hysteresis patterns to (1) determine the size of paired mobile and less-mobile porosities and (2) identify the exchange rate coefficient through simple curve fitting. We demonstrate the approach using laboratory column experimental data, synthetic streambed experimental data, and field tracer-test data. Results from the analytical approach compare favorably with results from calibration of numerical models and also independent measurements of mobile and less-mobile porosity. We show that localized electrical hysteresis patterns resulting from diffusive exchange are independent of injection velocity, indicating that repeatable parameters can be extracted under varied experimental designs, and these parameters represent the true intrinsic properties of specific volumes of porous media of aquifers and hyporheic zones.

Variation in teenage mothers' experiences of child care and other components of welfare reform: selection processes and developmental consequences.

PubMed

Yoshikawa, H; Rosman, E A; Hsueh, J

2001-01-01

Developmental evaluations of the current wave of welfare reform programs present challenges with regard to (1) assessing child outcomes; (2) accounting for heterogeneity among low-income families in both baseline characteristics and involvement in self-sufficiency activities and supports, and (3) development of alternatives to experimental approaches to causal inference. This study (N = 1,079) addresses these challenges by examining effects on 4- to 6-year-old children of different patterns of child care, self-sufficiency activities, and other service utilization indicators among experimental-group mothers in a 16-site welfare reform program. Outcomes in areas of cognitive ability and behavior problems were investigated. The study identified seven subgroups of participants engaging in different patterns of service utilization and activity involvement. A two-stage simultaneous equation methodology was used to account for selection, and effects on child cognitive ability of participation in specific patterns of services and activities were found. For example, children of mothers characterized by high levels of involvement in center-based child care, education, and job training showed higher levels of cognitive ability than children of mothers in groups characterized by high involvement in center-based care and education, or center-based care and job training. In addition, children of mothers in groups with high levels of involvement in any of these activities showed higher levels of cognitive ability than those with low levels of involvement. The bulk of selection effects occurred through site-level differences, rather than family-level socio-economic status or maternal depression indicators. Implications for welfare reform program and policy concerns are discussed.

Quasiparticles and charge transfer at the two surfaces of the honeycomb iridate Na2IrO3

NASA Astrophysics Data System (ADS)

Moreschini, L.; Lo Vecchio, I.; Breznay, N. P.; Moser, S.; Ulstrup, S.; Koch, R.; Wirjo, J.; Jozwiak, C.; Kim, K. S.; Rotenberg, E.; Bostwick, A.; Analytis, J. G.; Lanzara, A.

2017-10-01

Direct experimental investigations of the low-energy electronic structure of the Na2IrO3 iridate insulator are sparse and draw two conflicting pictures. One relies on flat bands and a clear gap, the other involves dispersive states approaching the Fermi level, pointing to surface metallicity. Here, by a combination of angle-resolved photoemission, photoemission electron microscopy, and x-ray absorption, we show that the correct picture is more complex and involves an anomalous band, arising from charge transfer from Na atoms to Ir-derived states. Bulk quasiparticles do exist, but in one of the two possible surface terminations the charge transfer is smaller and they remain elusive.

Preventing Substance Abuse among Black and Hispanic Adolescent Girls: Results from a Computer-Delivered, Mother-Daughter Intervention Approach

PubMed Central

Schinke, Steven P.; Fang, Lin; Cole, Kristin C. A.

2010-01-01

This 2008 study involved 546 Black- and Hispanic-American adolescent girls and their mothers from New York, New Jersey, and Connecticut. Participants provided self-report data. Analysis of covariance indicated that the experimental intervention reduced risk factors, improved protective factors, and lowered girls' alcohol use and their future intentions to use substances. The study supports the value of computer-based and gender-specific interventions that involve girls and mothers. Future work needs to replicate and strengthen study results. Research support came from the National Institute on Drug Abuse within the National Institutes of Health of the United States Public Health Service. PMID:21190404

Relevance of advanced nuclear fusion research: Breakthroughs and obstructions

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

Coppi, Bruno, E-mail: coppi@mit.edu

2016-03-25

An in depth understanding of the collective modes that can be excited in a wide range of high-energy plasmas is necessary to advance nuclear fusion research in parallel with other fields that include space and astrophysics in particular. Important achievements are shown to have resulted from implementing programs based on this reality, maintaining a tight connection with different areas of investigations. This involves the undertaking of a plurality of experimental approaches aimed at understanding the physics of fusion burning plasmas. At present, the most advanced among these is the Ignitor experiment involving international cooperation, that is designed to investigate burningmore » plasma regimes near ignition for the first time.« less

Semi-empirical quantum evaluation of peptide - MHC class II binding

NASA Astrophysics Data System (ADS)

González, Ronald; Suárez, Carlos F.; Bohórquez, Hugo J.; Patarroyo, Manuel A.; Patarroyo, Manuel E.

2017-01-01

Peptide presentation by the major histocompatibility complex (MHC) is a key process for triggering a specific immune response. Studying peptide-MHC (pMHC) binding from a structural-based approach has potential for reducing the costs of investigation into vaccine development. This study involved using two semi-empirical quantum chemistry methods (PM7 and FMO-DFTB) for computing the binding energies of peptides bonded to HLA-DR1 and HLA-DR2. We found that key stabilising water molecules involved in the peptide binding mechanism were required for finding high correlation with IC50 experimental values. Our proposal is computationally non-intensive, and is a reliable alternative for studying pMHC binding interactions.

Overview of research on Bombyx mori microRNA

PubMed Central

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

2014-01-01

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

MHD processes in the outer heliosphere

NASA Technical Reports Server (NTRS)

Burlaga, L. F.

1984-01-01

The magnetic field measurements from Voyager and the magnetohydrodynamic (MHD) processes in the outer heliosphere are reviewed. A bibliography of the experimental and theoretical work concerning magnetic fields and plasmas observed in the outer heliosphere is given. Emphasis in this review is on basic concepts and dynamical processes involving the magnetic field. The theory that serves to explain and unify the interplanetary magnetic field and plasma observations is magnetohydrodynamics. Basic physical processes and observations that relate directly to solutions of the MHD equations are emphasized, but obtaining solutions of this complex system of equations involves various assumptions and approximations. The spatial and temporal complexity of the outer heliosphere and some approaches for dealing with this complexity are discussed.

Therapeutic interventions in sepsis: current and anticipated pharmacological agents

PubMed Central

Shukla, Prashant; Rao, G Madhava; Pandey, Gitu; Sharma, Shweta; Mittapelly, Naresh; Shegokar, Ranjita; Mishra, Prabhat Ranjan

2014-01-01

Sepsis is a clinical syndrome characterized by a multisystem response to a pathogenic assault due to underlying infection that involves a combination of interconnected biochemical, cellular and organ–organ interactive networks. After the withdrawal of recombinant human-activated protein C (rAPC), researchers and physicians have continued to search for new therapeutic approaches and targets against sepsis, effective in both hypo- and hyperinflammatory states. Currently, statins are being evaluated as a viable option in clinical trials. Many agents that have shown favourable results in experimental sepsis are not clinically effective or have not been clinically evaluated. Apart from developing new therapeutic molecules, there is great scope for for developing a variety of drug delivery strategies, such as nanoparticulate carriers and phospholipid-based systems. These nanoparticulate carriers neutralize intracorporeal LPS as well as deliver therapeutic agents to targeted tissues and subcellular locations. Here, we review and critically discuss the present status and new experimental and clinical approaches for therapeutic intervention in sepsis. PMID:24977655

Convenient yet not a convenience sample: Jury pools as experimental subject pools.

PubMed

Murray, Gregg R; Rugeley, Cynthia R; Mitchell, Dona-Gene; Mondak, Jeffery J

2013-01-01

Scholars greatly benefit from access to convenient, inexpensive data sources. Many researchers rely on student subject pools, a practice that raises concern about the "college sophomore problem," or the possibility that findings from student subjects do not generalize beyond the campus. As an accessible, low cost, and heterogeneous data source, some researchers have used subjects recruited from jury pools, which are drawn from randomly-selected citizens required by law to appear for jury duty. In this paper, we discuss the strengths and weaknesses of this approach. First, we review pragmatic considerations involving access to jury pools, substantive content, the administration of survey-experiments, and the financial costs and benefits of this approach. Next, we present evidence regarding the quality of jury pool samples in terms of response rates, diversity, and representativeness. We conclude that jury pools, given proper attention to their limitations, offer an attractive addition to the viable sources of experimental data. Copyright © 2012 Elsevier Inc. All rights reserved.

Wave Manipulation in Metamaterials: A LEGO® Bricks Enabled Platform

NASA Astrophysics Data System (ADS)

Celli, Paolo; Gonella, Stefano

In this work, we show how simple, reconfigurable arrangements of LEGO® bricks can be turned into the building blocks of an experimental platform for the investigation of wave phenomena in metamaterial architectures. The approach involves the assembly of reconfigurable specimens consisting of patterns of bricks on a baseplate and the use of a 3D laser vibrometer to reconstruct global and local wave features. The ability to seamlessly transition between different topologies makes this an effective approach for rapid experimental verification and proof of concept in the arena of mechanical metamaterials engineering. The intuitive nature of the brick-and-baseplate assembly paradigm can also be leveraged to implement families of intuitive lab demonstrations with significant didactic and scientific outreach potential. The versatility of the platform is tested through a series of experiments that illustrate a variety of wave manipulation effects, such as waveguiding and seismic isolation, both in periodic and disordered topologies. We acknowledge the support of the National Science Foundation (Grant CMMI-1266089).

A community-based health education analysis of an infectous disease control program in Nigeria.

PubMed

Adeyanju, O M

1987-01-01

This descriptive study utilized the strategy of primary health care in program development-especially a community-based health education intervention approach-in the control of guinea-worm in rural communities of Nigeria. Two closely related rural communities in two states served as target groups. Committee system approach, nominal group process, interview methods, audio-visual aids, and health care volunteer trainingship were the educational strategies employed in a control and experimental set up. The PRECEDE model was applied in the analysis. Results show a significant control action on guinea-worm infestation in the experimental community and a tremendous achievement in preventive health education interventions through organized community participation/involvement and ultimate self-reliance and individual responsibility. A positive increase in health knowledge and attitude examined through interview method, and observable changes in health behavior were noticed. Wells were provided, drinking water treated, while personal and community health promotion strategies were encouraged by all. The study has shown the effectiveness/efficacy of a community-based effort facilitated by a health educator.

Smoothing spline analysis of variance models: A new tool for the analysis of cyclic biomechanical data.

PubMed

Helwig, Nathaniel E; Shorter, K Alex; Ma, Ping; Hsiao-Wecksler, Elizabeth T

2016-10-03

Cyclic biomechanical data are commonplace in orthopedic, rehabilitation, and sports research, where the goal is to understand and compare biomechanical differences between experimental conditions and/or subject populations. A common approach to analyzing cyclic biomechanical data involves averaging the biomechanical signals across cycle replications, and then comparing mean differences at specific points of the cycle. This pointwise analysis approach ignores the functional nature of the data, which can hinder one׳s ability to find subtle differences between experimental conditions and/or subject populations. To overcome this limitation, we propose using mixed-effects smoothing spline analysis of variance (SSANOVA) to analyze differences in cyclic biomechanical data. The SSANOVA framework makes it possible to decompose the estimated function into the portion that is common across groups (i.e., the average cycle, AC) and the portion that differs across groups (i.e., the contrast cycle, CC). By partitioning the signal in such a manner, we can obtain estimates of the CC differences (CCDs), which are the functions directly describing group differences in the cyclic biomechanical data. Using both simulated and experimental data, we illustrate the benefits of using SSANOVA models to analyze differences in noisy biomechanical (gait) signals collected from multiple locations (joints) of subjects participating in different experimental conditions. Using Bayesian confidence intervals, the SSANOVA results can be used in clinical and research settings to reliably quantify biomechanical differences between experimental conditions and/or subject populations. Copyright © 2016 Elsevier Ltd. All rights reserved.

Determination and prediction of the magnetic anisotropy of Mn ions.

PubMed

Duboc, Carole

2016-10-24

This tutorial is dedicated to the investigation of magnetic anisotropy using both electron paramagnetic resonance (EPR) spectroscopy for its experimental determination and quantum chemistry for its theoretical prediction. Such an approach could lead to the definition of magneto-structural correlation essential for the rational design of complexes with targeted magnetic properties or for the identification of unknown reactive metallic species involved in catalysis. To illustrate this combined approach the high spin Mn II , Mn III and Mn IV ions have been taken as specific examples. The first part deals with the analysis of the EPR experiments as a function of the ions under investigation and the conditions of the measurements, specifically: (i) EPR spectra recorded under high vs. low frequency conditions with respect to magnetic anisotropy, (ii) EPR spectra of non-integer (Kramers) vs. integer (non-Kramers) spin states and (iii) mono- vs. multi-frequency EPR spectra. In the second part, two main quantum chemical approaches, which have proven their capability to predict magnetic anisotropy, are described. More importantly, these calculations give access to the different contributions of zero field splitting, key information for the full understanding of magnetic anisotropy. The last part demonstrates that such a combined experimental and theoretical approach allows for the definition of magneto-structural correlations.

Microgravity

NASA Image and Video Library

2004-04-15

The M512 Materials Processing Facility (MPF) with the M518 Multipurpose Electric Facility (MEF) tested and demonstrated a facility approach for materials process experimentation in space. It also provided a basic apparatus and a common interface for a group of metallic and nonmetallic materials experiments. The MPF consisted of a vacuum work chamber and associated mechanical and electrical controls. The M518 Multipurpose Electric Furnace (MEF) was an electric furnace system in which solidification, crystal growth, and other experiments involving phase changes were performed.

16 CFR 1702.10 - Human experimental data involving the testing of human subjects.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 16 Commercial Practices 2 2011-01-01 2011-01-01 false Human experimental data involving the testing of human subjects. 1702.10 Section 1702.10 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION... PACKAGING ACT REQUIREMENTS; PETITION PROCEDURES AND REQUIREMENTS § 1702.10 Human experimental data involving...

16 CFR 1702.10 - Human experimental data involving the testing of human subjects.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 16 Commercial Practices 2 2012-01-01 2012-01-01 false Human experimental data involving the testing of human subjects. 1702.10 Section 1702.10 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION... PACKAGING ACT REQUIREMENTS; PETITION PROCEDURES AND REQUIREMENTS § 1702.10 Human experimental data involving...

16 CFR 1702.10 - Human experimental data involving the testing of human subjects.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 16 Commercial Practices 2 2014-01-01 2014-01-01 false Human experimental data involving the testing of human subjects. 1702.10 Section 1702.10 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION... PACKAGING ACT REQUIREMENTS; PETITION PROCEDURES AND REQUIREMENTS § 1702.10 Human experimental data involving...

16 CFR 1702.10 - Human experimental data involving the testing of human subjects.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 16 Commercial Practices 2 2010-01-01 2010-01-01 false Human experimental data involving the testing of human subjects. 1702.10 Section 1702.10 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION... PACKAGING ACT REQUIREMENTS; PETITION PROCEDURES AND REQUIREMENTS § 1702.10 Human experimental data involving...

Utilization of the Building-Block Approach in Structural Mechanics Research

NASA Technical Reports Server (NTRS)

Rouse, Marshall; Jegley, Dawn C.; McGowan, David M.; Bush, Harold G.; Waters, W. Allen

2005-01-01

In the last 20 years NASA has worked in collaboration with industry to develop enabling technologies needed to make aircraft safer and more affordable, extend their lifetime, improve their reliability, better understand their behavior, and reduce their weight. To support these efforts, research programs starting with ideas and culminating in full-scale structural testing were conducted at the NASA Langley Research Center. Each program contained development efforts that (a) started with selecting the material system and manufacturing approach; (b) moved on to experimentation and analysis of small samples to characterize the system and quantify behavior in the presence of defects like damage and imperfections; (c) progressed on to examining larger structures to examine buckling behavior, combined loadings, and built-up structures; and (d) finally moved to complicated subcomponents and full-scale components. Each step along the way was supported by detailed analysis, including tool development, to prove that the behavior of these structures was well-understood and predictable. This approach for developing technology became known as the "building-block" approach. In the Advanced Composites Technology Program and the High Speed Research Program the building-block approach was used to develop a true understanding of the response of the structures involved through experimentation and analysis. The philosophy that if the structural response couldn't be accurately predicted, it wasn't really understood, was critical to the progression of these programs. To this end, analytical techniques including closed-form and finite elements were employed and experimentation used to verify assumptions at each step along the way. This paper presents a discussion of the utilization of the building-block approach described previously in structural mechanics research and development programs at NASA Langley Research Center. Specific examples that illustrate the use of this approach are included from recent research and development programs for both subsonic and supersonic transports.

Recursive Bayesian recurrent neural networks for time-series modeling.

PubMed

Mirikitani, Derrick T; Nikolaev, Nikolay

2010-02-01

This paper develops a probabilistic approach to recursive second-order training of recurrent neural networks (RNNs) for improved time-series modeling. A general recursive Bayesian Levenberg-Marquardt algorithm is derived to sequentially update the weights and the covariance (Hessian) matrix. The main strengths of the approach are a principled handling of the regularization hyperparameters that leads to better generalization, and stable numerical performance. The framework involves the adaptation of a noise hyperparameter and local weight prior hyperparameters, which represent the noise in the data and the uncertainties in the model parameters. Experimental investigations using artificial and real-world data sets show that RNNs equipped with the proposed approach outperform standard real-time recurrent learning and extended Kalman training algorithms for recurrent networks, as well as other contemporary nonlinear neural models, on time-series modeling.

Linking definitions, mechanisms, and modeling of drought-induced tree death.

PubMed

Anderegg, William R L; Berry, Joseph A; Field, Christopher B

2012-12-01

Tree death from drought and heat stress is a critical and uncertain component in forest ecosystem responses to a changing climate. Recent research has illuminated how tree mortality is a complex cascade of changes involving interconnected plant systems over multiple timescales. Explicit consideration of the definitions, dynamics, and temporal and biological scales of tree mortality research can guide experimental and modeling approaches. In this review, we draw on the medical literature concerning human death to propose a water resource-based approach to tree mortality that considers the tree as a complex organism with a distinct growth strategy. This approach provides insight into mortality mechanisms at the tree and landscape scales and presents promising avenues into modeling tree death from drought and temperature stress. Copyright © 2012 Elsevier Ltd. All rights reserved.

Deformation in Micro Roll Forming of Bipolar Plate

NASA Astrophysics Data System (ADS)

Zhang, P.; Pereira, M.; Rolfe, B.; Daniel, W.; Weiss, M.

2017-09-01

Micro roll forming is a new processing technology to produce bipolar plates for Proton Exchange Membrane Fuel Cells (PEMFC) from thin stainless steel foil. To gain a better understanding of the deformation of the material in this process, numerical studies are necessary before experimental implementation. In general, solid elements with several layers through the material thickness are required to analyse material thinning in processes where the deformation mode is that of bending combined with tension, but this results in high computational costs. This pure solid element approach is especially time-consuming when analysing roll forming processes which generally involves feeding a long strip through a number of successive roll stands. In an attempt to develop a more efficient modelling approach without sacrificing accuracy, two solutions are numerically analysed with ABAQUS/Explicit in this paper. In the first, a small patch of solid elements over the strip width and in the centre of the “pre-cut” sheet is coupled with shell elements while in the second approach pure shell elements are used to discretize the full sheet. In the first approach, the shell element enables accounting for the effect of material being held in the roll stands on material flow while solid elements can be applied to analyse material thinning in a small discrete area of the sheet. Experimental micro roll forming trials are performed to prove that the coupling of solid and shell elements can give acceptable model accuracy while using shell elements alone is shown to result in major deviations between numerical and experimental results.

Pharmacotherapy in Generalized Anxiety Disorder: Novel Experimental Medicine Models and Emerging Drug Targets.

PubMed

Baldwin, David S; Hou, Ruihua; Gordon, Robert; Huneke, Nathan T M; Garner, Matthew

2017-04-01

Many pharmacological and psychological approaches have been found efficacious in patients with generalized anxiety disorder (GAD), but many treatment-seeking patients will not respond and others will relapse despite continuing with interventions that initially had beneficial effects. Other patients will respond but then stop treatment early because of untoward effects such as sexual dysfunction, drowsiness, and weight gain. There is much scope for the development of novel approaches that could have greater overall effectiveness or acceptability than currently available interventions or that have particular effectiveness in specific clinical subgroups. 'Experimental medicine' studies in healthy volunteers model disease states and represent a proof-of-concept approach for the development of novel therapeutic interventions: they determine whether to proceed to pivotal efficacy studies and so can reduce delays in translating innovations into clinical practice. Investigations in healthy volunteers challenged with the inhalation of air 'enriched' with 7.5% carbon dioxide (CO 2 ) indicate this technique provides a validated and robust experimental medicine model, mirroring the subjective, autonomic, and cognitive features of GAD. The anxiety response during CO 2 challenge probably involves both central noradrenergic neurotransmission and effects on acid-base sensitive receptors and so may stimulate development of novel agents targeted at central chemosensors. Increasing awareness of the potential role of altered cytokine balance in anxiety and the interplay of cytokines with monoaminergic mechanisms may also encourage the investigation of novel agents with modulating effects on immunological profiles. Although seemingly disparate, these two approaches to treatment development may pivot on a shared mechanism in exerting anxiolytic-like effects through pharmacological effects on acid-sensing ion channels.

Applications of asymptotic confidence intervals with continuity corrections for asymmetric comparisons in noninferiority trials.

PubMed

Soulakova, Julia N; Bright, Brianna C

2013-01-01

A large-sample problem of illustrating noninferiority of an experimental treatment over a referent treatment for binary outcomes is considered. The methods of illustrating noninferiority involve constructing the lower two-sided confidence bound for the difference between binomial proportions corresponding to the experimental and referent treatments and comparing it with the negative value of the noninferiority margin. The three considered methods, Anbar, Falk-Koch, and Reduced Falk-Koch, handle the comparison in an asymmetric way, that is, only the referent proportion out of the two, experimental and referent, is directly involved in the expression for the variance of the difference between two sample proportions. Five continuity corrections (including zero) are considered with respect to each approach. The key properties of the corresponding methods are evaluated via simulations. First, the uncorrected two-sided confidence intervals can, potentially, have smaller coverage probability than the nominal level even for moderately large sample sizes, for example, 150 per group. Next, the 15 testing methods are discussed in terms of their Type I error rate and power. In the settings with a relatively small referent proportion (about 0.4 or smaller), the Anbar approach with Yates' continuity correction is recommended for balanced designs and the Falk-Koch method with Yates' correction is recommended for unbalanced designs. For relatively moderate (about 0.6) and large (about 0.8 or greater) referent proportion, the uncorrected Reduced Falk-Koch method is recommended, although in this case, all methods tend to be over-conservative. These results are expected to be used in the design stage of a noninferiority study when asymmetric comparisons are envisioned. Copyright © 2013 John Wiley & Sons, Ltd.

Inelastic neutron scattering of large molecular systems: The case of the original benzylic amide [2]catenane

NASA Astrophysics Data System (ADS)

Caciuffo, Roberto; Esposti, Alessandra Degli; Deleuze, Michael S.; Leigh, David A.; Murphy, Aden; Paci, Barbara; Parker, Stewart F.; Zerbetto, Francesco

1998-12-01

The inelastic neutron scattering (INS) spectrum of the original benzylic amide [2]catenane is recorded and simulated by a semiempirical quantum chemical procedure coupled with the most comprehensive approach available to date, the CLIMAX program. The successful simulation of the spectrum indicates that the modified neglect of differential overlap (MNDO) model can reproduce the intramolecular vibrations of a molecular system as large as a catenane (136 atoms). Because of the computational costs involved and some numerical instabilities, a less expensive approach is attempted which involves the molecular mechanics-based calculation of the INS response in terms of the most basic formulation for the scattering activity. The encouraging results obtained validate the less computationally intensive procedure and allow its extension to the calculation of the INS spectrum for a second, theoretical, co-conformer, which, although structurally and energetically reasonable, is not, in fact, found in the solid state. The second structure was produced by a Monte Carlo simulated annealing method run in the conformational space (a procedure that would have been prohibitively expensive at the semiempirical level) and is characterized by a higher degree of intramolecular hydrogen bonding than the x-ray structure. The two alternative structures yield different simulated spectra, only one of which, the authentic one, is compatible with the experimental data. Comparison of the two simulated and experimental spectra affords the identification of an inelastic neutron scattering spectral signature of the correct hydrogen bonding motif in the region slightly above 700 cm-1. The study illustrates that combinations of simulated INS data and experimental results can be successfully used to discriminate between different proposed structures or possible hydrogen bonding motifs in large functional molecular systems.

Electrical stimulation of the insular cortex as a novel target for the relief of refractory pain: An experimental approach in rodents.

PubMed

Dimov, Luiz Fabio; Toniolo, Elaine Flamia; Alonso-Matielo, Heloísa; de Andrade, Daniel Ciampi; Garcia-Larrea, Luis; Ballester, Gerson; Teixeira, Manoel Jacobsen; Dale, Camila Squarzoni

2018-07-02

Cortical electrical stimulation (CES) has shown to be an effective therapeutic alternative for neuropathic pain refractory to pharmacological treatment. The primary motor cortex(M1) was the main cortical target used in the vast majority of both invasive and non-invasive studies. Despite positive results M1-based approaches still fail to relieve pain in a significant proportion of individuals. It has been advocated that the direct stimulation of cortical areas directly implicated in the central integration of pain could increase the efficacy of analgesic brain stimulation. Here, we evaluated the behavioral effects of electrical stimulation of the insular cortex (ESI) on pain sensitivity in an experimental rat model of peripheral neuropathy, and have described the pathways involved. Animals underwent chronic constriction of the sciatic nerve in the right hind limb and had concentric electrodes implanted in the posterior dysranular insular cortex. Mechanical nociception responses were evaluated before and at the end of a 15-min session of ESI (60Hz, 210μs, 1V). ESI reversed mechanical hypersensitivity in the paw contralateral to the brain hemisphere stimulated, without inducing motor impairment in the open-field test. Pharmacological blockade of μ-opioid (MOR) or type 1-cannabinoid receptors (CB1R) abolished ESI-induced antinociceptive effects. Evaluation of CB1R and MOR spatial expression demonstrated differential modulation of CB1R and MOR in the periaqueductal gray matter (PAG) of ESI-treated rats in sub-areas involved in pain processing/modulation. These results indicate that ESI induces antinociception by functionally modulating opioid and cannabinoid systems in the PAG pain circuitry in rats with experimentally induced neuropathic pain. Copyright © 2017 Elsevier B.V. All rights reserved.

Developing students’ learning achievement and experimental skills on buoyancy and the involvement of Newton’s third law through experimental sets

NASA Astrophysics Data System (ADS)

Chokchai, Jaewijarn; Khanti, Toedtanya; Sura, Wuttiprom

2017-09-01

The purposes of this research were: to construct packages of operations on buoyancy and the involvement of Newton’s third law, to enhance achievement score of students on buoyancy and the involvement of Newton’s third law, to enhance experimental skills on buoyancy and the involvement of Newton’s third law and to evaluate students’ attitude towards the packages of operations on buoyancy and the involvement of Newton’s third law using inquiry method. The samples were 42 grade 11 students in academic year 2016 at Hatyaiwittayalai School, Hatyai, Songkhla. The research method was one group pretest-posttest design. The research tools consisted of experimental set on buoyancy and the involvement of Newton’s third law, the learning achievement test on buoyancy and the involvement of Newton’s third law and the students’ attitude questionnaires. The experimental skills of most students was in a good level . The satisfaction of most students was in a good level. The research showed the learning achievement after instruction higher than that before instruction using experimental set at the significant level of 0.05 and the class average normalized gain is in the medium gain

Propriomuscular coding of kinaesthetic sensation. Experimental approach and mathematical modelling.

PubMed

Gilhodes, J C; Coiton, Y; Roll, J P; Ans, B

1993-01-01

The role of propriomuscular information in kinaesthetic sensation was studied. Experiments were carried out on human subjects in whom kinaesthetic illusions were induced by applying tendon vibration with a variable frequency. Six patterns of frequency modulation were used, four of which had an arbitrary form and the other two mimicked natural Ia discharges. The results show that the shape of the illusory movements recorded depended on the type of vibratory pattern used. A mathematical model for the propriomuscular information decoding process is proposed. It takes into account both the agonist and antagonist muscle spindle populations as sources of kinaesthetic information and is based on the assumption that position and velocity information are additively combined. The experimental data show a good fit with the theoretical data obtained by means of model simulation, thus validating our initial hypothesis. Various aspects of the experimental results and the hypotheses involved in the model are discussed.

Towards optimal experimental tests on the reality of the quantum state

NASA Astrophysics Data System (ADS)

Knee, George C.

2017-02-01

The Barrett-Cavalcanti-Lal-Maroney (BCLM) argument stands as the most effective means of demonstrating the reality of the quantum state. Its advantages include being derived from very few assumptions, and a robustness to experimental error. Finding the best way to implement the argument experimentally is an open problem, however, and involves cleverly choosing sets of states and measurements. I show that techniques from convex optimisation theory can be leveraged to numerically search for these sets, which then form a recipe for experiments that allow for the strongest statements about the ontology of the wavefunction to be made. The optimisation approach presented is versatile, efficient and can take account of the finite errors present in any real experiment. I find significantly improved low-cardinality sets which are guaranteed partially optimal for a BCLM test in low Hilbert space dimension. I further show that mixed states can be more optimal than pure states.

Investigation of the Thermomechanical Response of Shape Memory Alloy Hybrid Composite Beams

NASA Technical Reports Server (NTRS)

Davis, Brian A.

2005-01-01

Previous work at NASA Langley Research Center (LaRC) involved fabrication and testing of composite beams with embedded, pre-strained shape memory alloy (SMA) ribbons. That study also provided comparison of experimental results with numerical predictions from a research code making use of a new thermoelastic model for shape memory alloy hybrid composite (SMAHC) structures. The previous work showed qualitative validation of the numerical model. However, deficiencies in the experimental-numerical correlation were noted and hypotheses for the discrepancies were given for further investigation. The goal of this work is to refine the experimental measurement and numerical modeling approaches in order to better understand the discrepancies, improve the correlation between prediction and measurement, and provide rigorous quantitative validation of the numerical model. Thermal buckling, post-buckling, and random responses to thermal and inertial (base acceleration) loads are studied. Excellent agreement is achieved between the predicted and measured results, thereby quantitatively validating the numerical tool.

Experimental investigation of a four-qubit linear-optical quantum logic circuit

PubMed Central

Stárek, R.; Mičuda, M.; Miková, M.; Straka, I.; Dušek, M.; Ježek, M.; Fiurášek, J.

2016-01-01

We experimentally demonstrate and characterize a four-qubit linear-optical quantum logic circuit. Our robust and versatile scheme exploits encoding of two qubits into polarization and path degrees of single photons and involves two crossed inherently stable interferometers. This approach allows us to design a complex quantum logic circuit that combines a genuine four-qubit C3Z gate and several two-qubit and single-qubit gates. The C3Z gate introduces a sign flip if and only if all four qubits are in the computational state |1〉. We verify high-fidelity performance of this central four-qubit gate using Hofmann bounds on quantum gate fidelity and Monte Carlo fidelity sampling. We also experimentally demonstrate that the quantum logic circuit can generate genuine multipartite entanglement and we certify the entanglement with the use of suitably tailored entanglement witnesses. PMID:27647176

Efficient modeling of vector hysteresis using a novel Hopfield neural network implementation of Stoner–Wohlfarth-like operators

PubMed Central

Adly, Amr A.; Abd-El-Hafiz, Salwa K.

2012-01-01

Incorporation of hysteresis models in electromagnetic analysis approaches is indispensable to accurate field computation in complex magnetic media. Throughout those computations, vector nature and computational efficiency of such models become especially crucial when sophisticated geometries requiring massive sub-region discretization are involved. Recently, an efficient vector Preisach-type hysteresis model constructed from only two scalar models having orthogonally coupled elementary operators has been proposed. This paper presents a novel Hopfield neural network approach for the implementation of Stoner–Wohlfarth-like operators that could lead to a significant enhancement in the computational efficiency of the aforementioned model. Advantages of this approach stem from the non-rectangular nature of these operators that substantially minimizes the number of operators needed to achieve an accurate vector hysteresis model. Details of the proposed approach, its identification and experimental testing are presented in the paper. PMID:25685446

How much does participatory flood management contribute to stakeholders' social capacity building? Empirical findings based on a triangulation of three evaluation approaches

NASA Astrophysics Data System (ADS)

Buchecker, M.; Menzel, S.; Home, R.

2013-06-01

Recent literature suggests that dialogic forms of risk communication are more effective to build stakeholders' hazard-related social capacities. In spite of the high theoretical expectations, there is a lack of univocal empirical evidence on the relevance of these effects. This is mainly due to the methodological limitations of the existing evaluation approaches. In our paper we aim at eliciting the contribution of participatory river revitalisation projects on stakeholders' social capacity building by triangulating the findings of three evaluation studies that were based on different approaches: a field-experimental, a qualitative long-term ex-post and a cross-sectional household survey approach. The results revealed that social learning and avoiding the loss of trust were more relevant benefits of participatory flood management than acceptance building. The results suggest that stakeholder involvements should be more explicitly designed as tools for long-term social learning.

Adaptive coded aperture imaging in the infrared: towards a practical implementation

NASA Astrophysics Data System (ADS)

Slinger, Chris W.; Gilholm, Kevin; Gordon, Neil; McNie, Mark; Payne, Doug; Ridley, Kevin; Strens, Malcolm; Todd, Mike; De Villiers, Geoff; Watson, Philip; Wilson, Rebecca; Dyer, Gavin; Eismann, Mike; Meola, Joe; Rogers, Stanley

2008-08-01

An earlier paper [1] discussed the merits of adaptive coded apertures for use as lensless imaging systems in the thermal infrared and visible. It was shown how diffractive (rather than the more conventional geometric) coding could be used, and that 2D intensity measurements from multiple mask patterns could be combined and decoded to yield enhanced imagery. Initial experimental results in the visible band were presented. Unfortunately, radiosity calculations, also presented in that paper, indicated that the signal to noise performance of systems using this approach was likely to be compromised, especially in the infrared. This paper will discuss how such limitations can be overcome, and some of the tradeoffs involved. Experimental results showing tracking and imaging performance of these modified, diffractive, adaptive coded aperture systems in the visible and infrared will be presented. The subpixel imaging and tracking performance is compared to that of conventional imaging systems and shown to be superior. System size, weight and cost calculations indicate that the coded aperture approach, employing novel photonic MOEMS micro-shutter architectures, has significant merits for a given level of performance in the MWIR when compared to more conventional imaging approaches.

Deciphering Epithelial–Mesenchymal Transition Regulatory Networks in Cancer through Computational Approaches

PubMed Central

Burger, Gerhard A.; Danen, Erik H. J.; Beltman, Joost B.

2017-01-01

Epithelial–mesenchymal transition (EMT), the process by which epithelial cells can convert into motile mesenchymal cells, plays an important role in development and wound healing but is also involved in cancer progression. It is increasingly recognized that EMT is a dynamic process involving multiple intermediate or “hybrid” phenotypes rather than an “all-or-none” process. However, the role of EMT in various cancer hallmarks, including metastasis, is debated. Given the complexity of EMT regulation, computational modeling has proven to be an invaluable tool for cancer research, i.e., to resolve apparent conflicts in experimental data and to guide experiments by generating testable hypotheses. In this review, we provide an overview of computational modeling efforts that have been applied to regulation of EMT in the context of cancer progression and its associated tumor characteristics. Moreover, we identify possibilities to bridge different modeling approaches and point out outstanding questions in which computational modeling can contribute to advance our understanding of pathological EMT. PMID:28824874

2n-emission from 205Pb* nucleus using clusterization approach at Ebeam˜14-20 MeV

NASA Astrophysics Data System (ADS)

Kaur, Amandeep; Sandhu, Kiran; Sharma, Manoj Kumar

2016-05-01

The dynamics involved in n-induced reaction with 204Pb target is analyzed and the decay of the composite system 205Pb* is governed within the collective clusterization approach of the Dynamical Cluster-decay Model (DCM). The experimental data for 2n-evaporation channel is available for neutron energy range of 14-20 MeV and is addressed by optimizing the only parameter of the model, the neck-length parameter (ΔR). The calculations are done by taking the quadrupole (β2) deformations of the decaying fragments and the calculated 2n-emission cross-sections find nice agreement with available data. An effort is made to study the role of level density parameter in the decay of hot-rotating nucleus, and the mass dependence in level density parameter is exercised for the first time in DCM based calculations. It is to be noted that the effect of deformation, temperature and angular momentum etc. is studied to extract better description of the dynamics involved.

The Eratosthenes Project: the reproduction of a historical experiment as a resource for the inclusion of Astronomy concepts in High School

NASA Astrophysics Data System (ADS)

de Jesus Santos, Antônio José; Voelzke, Marcos Rincon; Teixeira de Araújo, Mauro Sérgio

2012-12-01

This investigation was about an educational approach based on the History of Science and experimentation involving scientific concepts in the area of Astronomy, highlighting the reproduction of the original experiment performed by Eratosthenes in the third century B.C., designed to measure the Earth radius. It was found that the realized activities contributed significantly to the success of High School students from two public schools of Sergipe - the State College State Secretary Francisco Rosa Santos in Aracaju, Sergipe and the Federal Institute, campus of São Cristov - since these activities had aroused the students' interest for the construction of new scientific knowledge, and they improved their comprehension of some aspects related to Science and Astronomy in particular, as its empirical character and its historical development, therefore immersed in a specific social, economic and cultural context. The approach allowed for a greater involvement of participating students and it improved student-teacher relationship. The evaluations identified that a significant learning of the discussed concepts involving Physics and Astronomy had occurred, such as latitude, longitude, equinox, solstice, midday sun, among other concepts treated in an interdisciplinary manner with other disciplines such as Geography, History and Mathematics.

A comparison of online versus face-to-face teaching delivery in statistics instruction for undergraduate health science students.

PubMed

Lu, Fletcher; Lemonde, Manon

2013-12-01

The objective of this study was to assess if online teaching delivery produces comparable student test performance as the traditional face-to-face approach irrespective of academic aptitude. This study involves a quasi-experimental comparison of student performance in an undergraduate health science statistics course partitioned in two ways. The first partition involves one group of students taught with a traditional face-to-face classroom approach and the other through a completely online instructional approach. The second partition of the subjects categorized the academic aptitude of the students into groups of higher and lower academically performing based on their assignment grades during the course. Controls that were placed on the study to reduce the possibility of confounding variables were: the same instructor taught both groups covering the same subject information, using the same assessment methods and delivered over the same period of time. The results of this study indicate that online teaching delivery is as effective as a traditional face-to-face approach in terms of producing comparable student test performance but only if the student is academically higher performing. For academically lower performing students, the online delivery method produced significantly poorer student test results compared to those lower performing students taught in a traditional face-to-face environment.

A Gaussian Approximation Approach for Value of Information Analysis.

PubMed

Jalal, Hawre; Alarid-Escudero, Fernando

2018-02-01

Most decisions are associated with uncertainty. Value of information (VOI) analysis quantifies the opportunity loss associated with choosing a suboptimal intervention based on current imperfect information. VOI can inform the value of collecting additional information, resource allocation, research prioritization, and future research designs. However, in practice, VOI remains underused due to many conceptual and computational challenges associated with its application. Expected value of sample information (EVSI) is rooted in Bayesian statistical decision theory and measures the value of information from a finite sample. The past few years have witnessed a dramatic growth in computationally efficient methods to calculate EVSI, including metamodeling. However, little research has been done to simplify the experimental data collection step inherent to all EVSI computations, especially for correlated model parameters. This article proposes a general Gaussian approximation (GA) of the traditional Bayesian updating approach based on the original work by Raiffa and Schlaifer to compute EVSI. The proposed approach uses a single probabilistic sensitivity analysis (PSA) data set and involves 2 steps: 1) a linear metamodel step to compute the EVSI on the preposterior distributions and 2) a GA step to compute the preposterior distribution of the parameters of interest. The proposed approach is efficient and can be applied for a wide range of data collection designs involving multiple non-Gaussian parameters and unbalanced study designs. Our approach is particularly useful when the parameters of an economic evaluation are correlated or interact.

Composition of Web Services Using Markov Decision Processes and Dynamic Programming

PubMed Central

Uc-Cetina, Víctor; Moo-Mena, Francisco; Hernandez-Ucan, Rafael

2015-01-01

We propose a Markov decision process model for solving the Web service composition (WSC) problem. Iterative policy evaluation, value iteration, and policy iteration algorithms are used to experimentally validate our approach, with artificial and real data. The experimental results show the reliability of the model and the methods employed, with policy iteration being the best one in terms of the minimum number of iterations needed to estimate an optimal policy, with the highest Quality of Service attributes. Our experimental work shows how the solution of a WSC problem involving a set of 100,000 individual Web services and where a valid composition requiring the selection of 1,000 services from the available set can be computed in the worst case in less than 200 seconds, using an Intel Core i5 computer with 6 GB RAM. Moreover, a real WSC problem involving only 7 individual Web services requires less than 0.08 seconds, using the same computational power. Finally, a comparison with two popular reinforcement learning algorithms, sarsa and Q-learning, shows that these algorithms require one or two orders of magnitude and more time than policy iteration, iterative policy evaluation, and value iteration to handle WSC problems of the same complexity. PMID:25874247

The NASA Ames 16-Inch Shock Tunnel Nozzle Simulations and Experimental Comparison

NASA Technical Reports Server (NTRS)

TokarcikPolsky, S.; Papadopoulos, P.; Venkatapathy, E.; Delwert, G. S.; Edwards, Thomas A. (Technical Monitor)

1995-01-01

The 16-Inch Shock Tunnel at NASA Ames Research Center is a unique test facility used for hypersonic propulsion testing. To provide information necessary to understand the hypersonic testing of the combustor model, computational simulations of the facility nozzle were performed and results are compared with available experimental data, namely static pressure along the nozzle walls and pitot pressure at the exit of the nozzle section. Both quasi-one-dimensional and axisymmetric approaches were used to study the numerous modeling issues involved. The facility nozzle flow was examined for three hypersonic test conditions, and the computational results are presented in detail. The effects of variations in reservoir conditions, boundary layer growth, and parameters of numerical modeling are explored.

Synthesis, characterization and relativistic DFT studies of fac-Re(CO)3(isonicotinic acid)2Cl complex

NASA Astrophysics Data System (ADS)

Zúñiga, César; Oyarzún, Diego P.; Martin-Transaco, Rudy; Yáñez-S, Mauricio; Tello, Alejandra; Fuentealba, Mauricio; Cantero-López, Plinio; Arratia-Pérez, Ramiro

2017-11-01

In this work, new fac-Re(CO)3(PyCOOH)2Cl from isonicotinic acid ligand has been prepared. The complex was characterized by structural (single-crystal X-ray diffraction), elemental analysis and spectroscopic (FTIR, NMR, UV-vis spectroscopy) methods. DFT and TDDFT calculations were performed to obtain the electronic transitions involved in their UV-Vis spectrum. The excitation energies agree with the experimental results. The TDDFT calculations suggest that experimental mixed absorption bands at 270 and 314 nm could be assigned to (MLCT-LLCT)/MLCT transitions. Natural Bond Orbitals (NBO) approach has enabled studying the effects of bonding interactions. E(2) energies confirm the occurrence of ICT (Intra-molecular Charge Transfer) within the molecule.

Combined experimental and ab initio study of the electronic structure of narrow-diameter single-wall carbon nanotubes with predominant (6,4),(6,5) chirality

NASA Astrophysics Data System (ADS)

de Blauwe, K.; Mowbray, D. J.; Miyata, Y.; Ayala, P.; Shiozawa, H.; Rubio, A.; Hoffmann, P.; Kataura, H.; Pichler, T.

2010-09-01

Narrow diameter tubes and especially (6,5) tubes with a diameter of 0.75 nm are currently one of the most studied carbon nanotubes because their unique optical and especially luminescence response makes them exceptionally suited for biomedical applications. Here we report on a detailed analysis of the electronic structure of nanotubes with (6,5) and (6,4) chiralities using a combined experimental and theoretical approach. From high-energy spectroscopy involving x-ray absorption and photoemission spectroscopy the detailed valence- and conduction-band response of these narrow diameter tubes is studied. The observed electronic structure is in sound agreement with state of the art ab initio calculations using density-functional theory.

Statistical process control in nursing research.

PubMed

Polit, Denise F; Chaboyer, Wendy

2012-02-01

In intervention studies in which randomization to groups is not possible, researchers typically use quasi-experimental designs. Time series designs are strong quasi-experimental designs but are seldom used, perhaps because of technical and analytic hurdles. Statistical process control (SPC) is an alternative analytic approach to testing hypotheses about intervention effects using data collected over time. SPC, like traditional statistical methods, is a tool for understanding variation and involves the construction of control charts that distinguish between normal, random fluctuations (common cause variation), and statistically significant special cause variation that can result from an innovation. The purpose of this article is to provide an overview of SPC and to illustrate its use in a study of a nursing practice improvement intervention. Copyright © 2011 Wiley Periodicals, Inc.

Control of flexible beams using a free-free active truss

NASA Technical Reports Server (NTRS)

Clark, W. W.; Kimiavi, B.; Robertshaw, H. H.

1989-01-01

An analytical and experimental study involving controlling flexible beams using a free-free active truss is presented. This work extends previous work in controlling flexible continua with active trusses which were configured with fixed-free boundary conditions. The following describes the Lagrangian approach used to derive the equations of motion for the active truss and the beams attached to it. A partial-state feedback control law is derived for this system based on a full-state feedback Linear Quadratic Regulator method. The analytical model is examined via numerical simulations and the results are compared to a similar experimental apparatus described herein. The results show that control of a flexible continua is possible with a free-free active truss.

A Discounting Framework for Choice With Delayed and Probabilistic Rewards

PubMed Central

Green, Leonard; Myerson, Joel

2005-01-01

When choosing between delayed or uncertain outcomes, individuals discount the value of such outcomes on the basis of the expected time to or the likelihood of their occurrence. In an integrative review of the expanding experimental literature on discounting, the authors show that although the same form of hyperbola-like function describes discounting of both delayed and probabilistic outcomes, a variety of recent findings are inconsistent with a single-process account. The authors also review studies that compare discounting in different populations and discuss the theoretical and practical implications of the findings. The present effort illustrates the value of studying choice involving both delayed and probabilistic outcomes within a general discounting framework that uses similar experimental procedures and a common analytical approach. PMID:15367080

A tradeoff study of determine the optimum approach to a wash/rinse capability to support future space flight

NASA Technical Reports Server (NTRS)

Wilson, D. A.

1976-01-01

Specific requirements for a wash/rinse capability to support Spacelab biological experimentation and to identify various concepts for achieving this capability were determined. This included the examination of current state-of-the-art and emerging technology designs that would meet the wash/rinse requirements. Once several concepts were identified, including the disposable utensils, tools and gloves or other possible alternatives, a tradeoff analysis involving system cost, weight, volume utilization, functional performance, maintainability, reliability, power utilization, safety, complexity, etc., was performed so as to determine an optimum approach for achieving a wash/rinse capability to support future space flights. Missions of varying crew size and durations were considered.

On-orbit cryogenic fluid transfer

NASA Technical Reports Server (NTRS)

Aydelott, J. C.; Gille, J. P.; Eberhardt, R. N.

1984-01-01

A number of future NASA and DOD missions have been identified that will require, or could benefit from resupply of cryogenic liquids in orbit. The most promising approach for accomplishing cryogenic fluid transfer in the weightlessness environment of space is to use the thermodynamic filling technique. This approach involves initially reducing the receiver tank temperature by using several charge hold vent cycles followed by filling the tank without venting. Martin Marietta Denver Aerospace, under contract to the NASA Lewis Research Center, is currently developing analytical models to describe the on orbit cryogenic fluid transfer process. A detailed design of a shuttle attached experimental facility, which will provide the data necessary to verify the analytical models, is also being performed.

Optimization of an innovative approach involving mechanical activation and acid digestion for the extraction of lithium from lepidolite

NASA Astrophysics Data System (ADS)

Vieceli, Nathália; Nogueira, Carlos A.; Pereira, Manuel F. C.; Durão, Fernando O.; Guimarães, Carlos; Margarido, Fernanda

2018-01-01

The recovery of lithium from hard rock minerals has received increased attention given the high demand for this element. Therefore, this study optimized an innovative process, which does not require a high-temperature calcination step, for lithium extraction from lepidolite. Mechanical activation and acid digestion were suggested as crucial process parameters, and experimental design and response-surface methodology were applied to model and optimize the proposed lithium extraction process. The promoting effect of amorphization and the formation of lithium sulfate hydrate on lithium extraction yield were assessed. Several factor combinations led to extraction yields that exceeded 90%, indicating that the proposed process is an effective approach for lithium recovery.

Investigating Student Perceptions of the Chemistry Laboratory and Their Approaches to Learning in the Laboratory

NASA Astrophysics Data System (ADS)

Berger, Spencer Granett

This dissertation explores student perceptions of the instructional chemistry laboratory and the approaches students take when learning in the laboratory environment. To measure student perceptions of the chemistry laboratory, a survey instrument was developed. 413 students responded to the survey during the Fall 2011 semester. Students' perception of the usefulness of the laboratory in helping them learn chemistry in high school was related to several factors regarding their experiences in high school chemistry. Students' perception of the usefulness of the laboratory in helping them learn chemistry in college was also measured. Reasons students provided for the usefulness of the laboratory were categorized. To characterize approaches to learning in the laboratory, students were interviewed midway through semester (N=18). The interviews were used to create a framework describing learning approaches that students use in the laboratory environment. Students were categorized into three levels: students who view the laboratory as a requirement, students who believe that the laboratory augments their understanding, and students who view the laboratory as an important part of science. These categories describe the types of strategies students used when conducting experiments. To further explore the relationship between students' perception of the laboratory and their approaches to learning, two case studies are described. These case studies involve interviews in the beginning and end of the semester. In the interviews, students reflect on what they have learned in the laboratory and describe their perceptions of the laboratory environment. In order to encourage students to adopt higher-level approaches to learning in the laboratory, a metacognitive intervention was created. The intervention involved supplementary questions that students would answer while completing laboratory experiments. The questions were designed to encourage students to think critically about the laboratory procedures. In order to test the effects of the intervention, an experimental group (N=87) completed these supplementary questions during two laboratory experiments while a control group (N=84) performed the same experiments without these additional questions. The effects of the intervention on laboratory exam performance were measured. Students in the experimental group had a higher average on the laboratory exam than students in the control group.

Multi-scale modelling of elastic moduli of trabecular bone

PubMed Central

Hamed, Elham; Jasiuk, Iwona; Yoo, Andrew; Lee, YikHan; Liszka, Tadeusz

2012-01-01

We model trabecular bone as a nanocomposite material with hierarchical structure and predict its elastic properties at different structural scales. The analysis involves a bottom-up multi-scale approach, starting with nanoscale (mineralized collagen fibril) and moving up the scales to sub-microscale (single lamella), microscale (single trabecula) and mesoscale (trabecular bone) levels. Continuum micromechanics methods, composite materials laminate theory and finite-element methods are used in the analysis. Good agreement is found between theoretical and experimental results. PMID:22279160

Toward a therapy for mitochondrial disease

PubMed Central

Viscomi, Carlo

2016-01-01

Mitochondrial disorders are a group of genetic diseases affecting the energy-converting process of oxidative phosphorylation. The extreme variability of symptoms, organ involvement, and clinical course represent a challenge to the development of effective therapeutic interventions. However, new possibilities have recently been emerging from studies in model organisms and awaiting verification in humans. I will discuss here the most promising experimental approaches and the challenges we face to translate them into the clinics. The current clinical trials will also be briefly reviewed. PMID:27911730

The development of low temperature curing adhesives

NASA Technical Reports Server (NTRS)

Green, H. E.; Sutherland, J. D.; Hom, J. M.; Sheppard, C. H.

1975-01-01

An approach for the development of a practical low temperature (293 K-311 K/68 F-100 F) curing adhesive system based on a family of amide/ester resins was studied and demonstrated. The work was conducted on resin optimization and adhesive compounding studies. An improved preparative method was demonstrated which involved the reaction of an amine-alcohol precursor, in a DMF solution with acid chloride. Experimental studies indicated that an adhesive formulation containing aluminum powder provided the best performance when used in conjunction with a commercial primer.

Age-related macular degeneration

PubMed Central

Querques, Giuseppe; Avellis, Fernando Onofrio; Querques, Lea; Bandello, Francesco; Souied, Eric H

2011-01-01

Clinical question: Is there any new knowledge about the pathogenesis and treatment of age-related macular degeneration (AMD)? Results: We now understand better the biochemical and pathological pathways involved in the genesis of AMD. Treatment of exudative AMD is based on intravitreal injection of new antivascular endothelial growth factor drugs for which there does not yet exist a unique recognized strategy of administration. No therapies are actually available for atrophic AMD, despite some experimental new pharmacological approaches. Implementation: strategy of administration, safety of intravitreal injection PMID:21654887

Evaluation of variable selection methods for random forests and omics data sets.

PubMed

Degenhardt, Frauke; Seifert, Stephan; Szymczak, Silke

2017-10-16

Machine learning methods and in particular random forests are promising approaches for prediction based on high dimensional omics data sets. They provide variable importance measures to rank predictors according to their predictive power. If building a prediction model is the main goal of a study, often a minimal set of variables with good prediction performance is selected. However, if the objective is the identification of involved variables to find active networks and pathways, approaches that aim to select all relevant variables should be preferred. We evaluated several variable selection procedures based on simulated data as well as publicly available experimental methylation and gene expression data. Our comparison included the Boruta algorithm, the Vita method, recurrent relative variable importance, a permutation approach and its parametric variant (Altmann) as well as recursive feature elimination (RFE). In our simulation studies, Boruta was the most powerful approach, followed closely by the Vita method. Both approaches demonstrated similar stability in variable selection, while Vita was the most robust approach under a pure null model without any predictor variables related to the outcome. In the analysis of the different experimental data sets, Vita demonstrated slightly better stability in variable selection and was less computationally intensive than Boruta.In conclusion, we recommend the Boruta and Vita approaches for the analysis of high-dimensional data sets. Vita is considerably faster than Boruta and thus more suitable for large data sets, but only Boruta can also be applied in low-dimensional settings. © The Author 2017. Published by Oxford University Press.

Sound transmission in the chest under surface excitation - An experimental and computational study with diagnostic applications

PubMed Central

Peng, Ying; Dai, Zoujun; Mansy, Hansen A.; Sandler, Richard H.; Balk, Robert A; Royston, Thomas. J

2014-01-01

Chest physical examination often includes performing chest percussion, which involves introducing sound stimulus to the chest wall and detecting an audible change. This approach relies on observations that underlying acoustic transmission, coupling, and resonance patterns can be altered by chest structure changes due to pathologies. More accurate detection and quantification of these acoustic alterations may provide further useful diagnostic information. To elucidate the physical processes involved, a realistic computer model of sound transmission in the chest is helpful. In the present study, a computational model was developed and validated by comparing its predictions with results from animal and human experiments which involved applying acoustic excitation to the anterior chest while detecting skin vibrations at the posterior chest. To investigate the effect of pathology on sound transmission, the computational model was used to simulate the effects of pneumothorax on sounds introduced at the anterior chest and detected at the posterior. Model predictions and experimental results showed similar trends. The model also predicted wave patterns inside the chest, which may be used to assess results of elastography measurements. Future animal and human tests may expand the predictive power of the model to include acoustic behavior for a wider range of pulmonary conditions. PMID:25001497

Detection of multiple damages employing best achievable eigenvectors under Bayesian inference

NASA Astrophysics Data System (ADS)

Prajapat, Kanta; Ray-Chaudhuri, Samit

2018-05-01

A novel approach is presented in this work to localize simultaneously multiple damaged elements in a structure along with the estimation of damage severity for each of the damaged elements. For detection of damaged elements, a best achievable eigenvector based formulation has been derived. To deal with noisy data, Bayesian inference is employed in the formulation wherein the likelihood of the Bayesian algorithm is formed on the basis of errors between the best achievable eigenvectors and the measured modes. In this approach, the most probable damage locations are evaluated under Bayesian inference by generating combinations of various possible damaged elements. Once damage locations are identified, damage severities are estimated using a Bayesian inference Markov chain Monte Carlo simulation. The efficiency of the proposed approach has been demonstrated by carrying out a numerical study involving a 12-story shear building. It has been found from this study that damage scenarios involving as low as 10% loss of stiffness in multiple elements are accurately determined (localized and severities quantified) even when 2% noise contaminated modal data are utilized. Further, this study introduces a term parameter impact (evaluated based on sensitivity of modal parameters towards structural parameters) to decide the suitability of selecting a particular mode, if some idea about the damaged elements are available. It has been demonstrated here that the accuracy and efficiency of the Bayesian quantification algorithm increases if damage localization is carried out a-priori. An experimental study involving a laboratory scale shear building and different stiffness modification scenarios shows that the proposed approach is efficient enough to localize the stories with stiffness modification.

Identification of Conserved and Potentially Regulatory Small RNAs in Heterocystous Cyanobacteria.

PubMed

Brenes-Álvarez, Manuel; Olmedo-Verd, Elvira; Vioque, Agustín; Muro-Pastor, Alicia M

2016-01-01

Small RNAs (sRNAs) are a growing class of non-protein-coding transcripts that participate in the regulation of virtually every aspect of bacterial physiology. Heterocystous cyanobacteria are a group of photosynthetic organisms that exhibit multicellular behavior and developmental alternatives involving specific transcriptomes exclusive of a given physiological condition or even a cell type. In the context of our ongoing effort to understand developmental decisions in these organisms we have undertaken an approach to the global identification of sRNAs. Using differential RNA-Seq we have previously identified transcriptional start sites for the model heterocystous cyanobacterium Nostoc sp. PCC 7120. Here we combine this dataset with a prediction of Rho-independent transcriptional terminators and an analysis of phylogenetic conservation of potential sRNAs among 89 available cyanobacterial genomes. In contrast to predictive genome-wide approaches, the use of an experimental dataset comprising all active transcriptional start sites (differential RNA-Seq) facilitates the identification of bona fide sRNAs. The output of our approach is a dataset of predicted potential sRNAs in Nostoc sp. PCC 7120, with different degrees of phylogenetic conservation across the 89 cyanobacterial genomes analyzed. Previously described sRNAs appear among the predicted sRNAs, demonstrating the performance of the algorithm. In addition, new predicted sRNAs are now identified that can be involved in regulation of different aspects of cyanobacterial physiology, including adaptation to nitrogen stress, the condition that triggers differentiation of heterocysts (specialized nitrogen-fixing cells). Transcription of several predicted sRNAs that appear exclusively in the genomes of heterocystous cyanobacteria is experimentally verified by Northern blot. Cell-specific transcription of one of these sRNAs, NsiR8 (nitrogen stress-induced RNA 8), in developing heterocysts is also demonstrated.

A comprehensive approach to identify reliable reference gene candidates to investigate the link between alcoholism and endocrinology in Sprague-Dawley rats.

PubMed

Taki, Faten A; Abdel-Rahman, Abdel A; Zhang, Baohong

2014-01-01

Gender and hormonal differences are often correlated with alcohol dependence and related complications like addiction and breast cancer. Estrogen (E2) is an important sex hormone because it serves as a key protein involved in organism level signaling pathways. Alcoholism has been reported to affect estrogen receptor signaling; however, identifying the players involved in such multi-faceted syndrome is complex and requires an interdisciplinary approach. In many situations, preliminary investigations included a straight forward, yet informative biotechniques such as gene expression analyses using quantitative real time PCR (qRT-PCR). The validity of qRT-PCR-based conclusions is affected by the choice of reliable internal controls. With this in mind, we compiled a list of 15 commonly used housekeeping genes (HKGs) as potential reference gene candidates in rat biological models. A comprehensive comparison among 5 statistical approaches (geNorm, dCt method, NormFinder, BestKeeper, and RefFinder) was performed to identify the minimal number as well the most stable reference genes required for reliable normalization in experimental rat groups that comprised sham operated (SO), ovariectomized rats in the absence (OVX) or presence of E2 (OVXE2). These rat groups were subdivided into subgroups that received alcohol in liquid diet or isocalroic control liquid diet for 12 weeks. Our results showed that U87, 5S rRNA, GAPDH, and U5a were the most reliable gene candidates for reference genes in heart and brain tissue. However, different gene stability ranking was specific for each tissue input combination. The present preliminary findings highlight the variability in reference gene rankings across different experimental conditions and analytic methods and constitute a fundamental step for gene expression assays.

Optimal bioprocess design through a gene regulatory network - growth kinetic hybrid model: Towards Replacing Monod kinetics.

PubMed

Tsipa, Argyro; Koutinas, Michalis; Usaku, Chonlatep; Mantalaris, Athanasios

2018-05-02

Currently, design and optimisation of biotechnological bioprocesses is performed either through exhaustive experimentation and/or with the use of empirical, unstructured growth kinetics models. Whereas, elaborate systems biology approaches have been recently explored, mixed-substrate utilisation is predominantly ignored despite its significance in enhancing bioprocess performance. Herein, bioprocess optimisation for an industrially-relevant bioremediation process involving a mixture of highly toxic substrates, m-xylene and toluene, was achieved through application of a novel experimental-modelling gene regulatory network - growth kinetic (GRN-GK) hybrid framework. The GRN model described the TOL and ortho-cleavage pathways in Pseudomonas putida mt-2 and captured the transcriptional kinetics expression patterns of the promoters. The GRN model informed the formulation of the growth kinetics model replacing the empirical and unstructured Monod kinetics. The GRN-GK framework's predictive capability and potential as a systematic optimal bioprocess design tool, was demonstrated by effectively predicting bioprocess performance, which was in agreement with experimental values, when compared to four commonly used models that deviated significantly from the experimental values. Significantly, a fed-batch biodegradation process was designed and optimised through the model-based control of TOL Pr promoter expression resulting in 61% and 60% enhanced pollutant removal and biomass formation, respectively, compared to the batch process. This provides strong evidence of model-based bioprocess optimisation at the gene level, rendering the GRN-GK framework as a novel and applicable approach to optimal bioprocess design. Finally, model analysis using global sensitivity analysis (GSA) suggests an alternative, systematic approach for model-driven strain modification for synthetic biology and metabolic engineering applications. Copyright © 2018. Published by Elsevier Inc.

Human Visual System as a Double-Slit Single Photon Interference Sensor: A Comparison between Modellistic and Biophysical Tests

PubMed Central

Pizzi, Rita; Wang, Rui; Rossetti, Danilo

2016-01-01

This paper describes a computational approach to the theoretical problems involved in the Young's single-photon double-slit experiment, focusing on a simulation of this experiment in the absence of measuring devices. Specifically, the human visual system is used in place of a photomultiplier or similar apparatus. Beginning with the assumption that the human eye perceives light in the presence of very few photons, we measure human eye performance as a sensor in a double-slit one-photon-at-a-time experimental setup. To interpret the results, we implement a simulation algorithm and compare its results with those of human subjects under identical experimental conditions. In order to evaluate the perceptive parameters exactly, which vary depending on the light conditions and on the subject’s sensitivity, we first review the existing literature on the biophysics of the human eye in the presence of a dim light source, and then use the known values of the experimental variables to set the parameters of the computational simulation. The results of the simulation and their comparison with the experiment involving human subjects are reported and discussed. It is found that, while the computer simulation indicates that the human eye has the capacity to detect the corpuscular nature of photons under these conditions, this was not observed in practice. The possible reasons for the difference between theoretical prediction and experimental results are discussed. PMID:26816029

Coordinated photomorphogenic UV-B signaling network captured by mathematical modeling.

PubMed

Ouyang, Xinhao; Huang, Xi; Jin, Xiao; Chen, Zheng; Yang, Panyu; Ge, Hao; Li, Shigui; Deng, Xing Wang

2014-08-05

Long-wavelength and low-fluence UV-B light is an informational signal known to induce photomorphogenic development in plants. Using the model plant Arabidopsis thaliana, a variety of factors involved in UV-B-specific signaling have been experimentally characterized over the past decade, including the UV-B light receptor UV resistance locus 8; the positive regulators constitutive photomorphogenesis 1 and elongated hypocotyl 5; and the negative regulators cullin4, repressor of UV-B photomorphogenesis 1 (RUP1), and RUP2. Individual genetic and molecular studies have revealed that these proteins function in either positive or negative regulatory capacities for the sufficient and balanced transduction of photomorphogenic UV-B signal. Less is known, however, regarding how these signaling events are systematically linked. In our study, we use a systems biology approach to investigate the dynamic behaviors and correlations of multiple signaling components involved in Arabidopsis UV-B-induced photomorphogenesis. We define a mathematical representation of photomorphogenic UV-B signaling at a temporal scale. Supplemented with experimental validation, our computational modeling demonstrates the functional interaction that occurs among different protein complexes in early and prolonged response to photomorphogenic UV-B.

Protein kinase Cβ as a therapeutic target stabilizing blood–brain barrier disruption in experimental autoimmune encephalomyelitis

PubMed Central

Lanz, Tobias V.; Becker, Simon; Osswald, Matthias; Bittner, Stefan; Schuhmann, Michael K.; Opitz, Christiane A.; Gaikwad, Sadanand; Wiestler, Benedikt; Litzenburger, Ulrike M.; Sahm, Felix; Ott, Martina; Iwantscheff, Simeon; Grabitz, Carl; Mittelbronn, Michel; von Deimling, Andreas; Winkler, Frank; Meuth, Sven G.; Wick, Wolfgang; Platten, Michael

2013-01-01

Disruption of the blood–brain barrier (BBB) is a hallmark of acute inflammatory lesions in multiple sclerosis (MS) and its animal model experimental autoimmune encephalomyelitis. This disruption may precede and facilitate the infiltration of encephalitogenic T cells. The signaling events that lead to this BBB disruption are incompletely understood but appear to involve dysregulation of tight-junction proteins such as claudins. Pharmacological interventions aiming at stabilizing the BBB in MS might have therapeutic potential. Here, we show that the orally available small molecule LY-317615, a synthetic bisindolylmaleimide and inhibitor of protein kinase Cβ, which is clinically under investigation for the treatment of cancer, suppresses the transmigration of activated T cells through an inflamed endothelial cell barrier, where it leads to the induction of the tight-junction molecules zona occludens-1, claudin 3, and claudin 5 and other pathways critically involved in transendothelial leukocyte migration. Treatment of mice with ongoing experimental autoimmune encephalomyelitis with LY-317615 ameliorates inflammation, demyelination, axonal damage, and clinical symptoms. Although LY-317615 dose-dependently suppresses T-cell proliferation and cytokine production independent of antigen specificity, its therapeutic effect is abrogated in a mouse model requiring pertussis toxin. This abrogation indicates that the anti-inflammatory and clinical efficacy is mainly mediated by stabilization of the BBB, thus suppressing the transmigration of encephalitogenic T cells. Collectively, our data suggest the involvement of endothelial protein kinase Cβ in stabilizing the BBB in autoimmune neuroinflammation and imply a therapeutic potential of BBB-targeting agents such as LY-317615 as therapeutic approaches for MS. PMID:23959874

Spatial awareness comparisons between large-screen, integrated pictorial displays and conventional EFIS displays during simulated landing approaches

NASA Technical Reports Server (NTRS)

Parrish, Russell V.; Busquets, Anthony M.; Williams, Steven P.; Nold, Dean E.

1994-01-01

An extensive simulation study was performed to determine and compare the spatial awareness of commercial airline pilots on simulated landing approaches using conventional flight displays with their awareness using advanced pictorial 'pathway in the sky' displays. Sixteen commercial airline pilots repeatedly made simulated complex microwave landing system approaches to closely spaced parallel runways with an extremely short final segment. Scenarios involving conflicting traffic situation assessments and recoveries from flight path offset conditions were used to assess spatial awareness (own ship position relative the the desired flight route, the runway, and other traffic) with the various display formats. The situation assessment tools are presented, as well as the experimental designs and the results. The results demonstrate that the integrated pictorial displays substantially increase spatial awareness over conventional electronic flight information systems display formats.

Modeling of scale-dependent bacterial growth by chemical kinetics approach.

PubMed

Martínez, Haydee; Sánchez, Joaquín; Cruz, José-Manuel; Ayala, Guadalupe; Rivera, Marco; Buhse, Thomas

2014-01-01

We applied the so-called chemical kinetics approach to complex bacterial growth patterns that were dependent on the liquid-surface-area-to-volume ratio (SA/V) of the bacterial cultures. The kinetic modeling was based on current experimental knowledge in terms of autocatalytic bacterial growth, its inhibition by the metabolite CO2, and the relief of inhibition through the physical escape of the inhibitor. The model quantitatively reproduces kinetic data of SA/V-dependent bacterial growth and can discriminate between differences in the growth dynamics of enteropathogenic E. coli, E. coli JM83, and Salmonella typhimurium on one hand and Vibrio cholerae on the other hand. Furthermore, the data fitting procedures allowed predictions about the velocities of the involved key processes and the potential behavior in an open-flow bacterial chemostat, revealing an oscillatory approach to the stationary states.

Effect of primary and secondary parameters on analytical estimation of effective thermal conductivity of two phase materials using unit cell approach

NASA Astrophysics Data System (ADS)

S, Chidambara Raja; P, Karthikeyan; Kumaraswamidhas, L. A.; M, Ramu

2018-05-01

Most of the thermal design systems involve two phase materials and analysis of such systems requires detailed understanding of the thermal characteristics of the two phase material. This article aimed to develop geometry dependent unit cell approach model by considering the effects of all primary parameters (conductivity ratio and concentration) and secondary parameters (geometry, contact resistance, natural convection, Knudsen and radiation) for the estimation of effective thermal conductivity of two-phase materials. The analytical equations have been formulated based on isotherm approach for 2-D and 3-D spatially periodic medium. The developed models are validated with standard models and suited for all kind of operating conditions. The results have shown substantial improvement compared to the existing models and are in good agreement with the experimental data.

Efficient video-equipped fire detection approach for automatic fire alarm systems

NASA Astrophysics Data System (ADS)

Kang, Myeongsu; Tung, Truong Xuan; Kim, Jong-Myon

2013-01-01

This paper proposes an efficient four-stage approach that automatically detects fire using video capabilities. In the first stage, an approximate median method is used to detect video frame regions involving motion. In the second stage, a fuzzy c-means-based clustering algorithm is employed to extract candidate regions of fire from all of the movement-containing regions. In the third stage, a gray level co-occurrence matrix is used to extract texture parameters by tracking red-colored objects in the candidate regions. These texture features are, subsequently, used as inputs of a back-propagation neural network to distinguish between fire and nonfire. Experimental results indicate that the proposed four-stage approach outperforms other fire detection algorithms in terms of consistently increasing the accuracy of fire detection in both indoor and outdoor test videos.

A simple approach to polymer mixture miscibility.

PubMed

Higgins, Julia S; Lipson, Jane E G; White, Ronald P

2010-03-13

Polymeric mixtures are important materials, but the control and understanding of mixing behaviour poses problems. The original Flory-Huggins theoretical approach, using a lattice model to compute the statistical thermodynamics, provides the basic understanding of the thermodynamic processes involved but is deficient in describing most real systems, and has little or no predictive capability. We have developed an approach using a lattice integral equation theory, and in this paper we demonstrate that this not only describes well the literature data on polymer mixtures but allows new insights into the behaviour of polymers and their mixtures. The characteristic parameters obtained by fitting the data have been successfully shown to be transferable from one dataset to another, to be able to correctly predict behaviour outside the experimental range of the original data and to allow meaningful comparisons to be made between different polymer mixtures.

Experimental search for high-temperature ferroelectric perovskites guided by two-step machine learning.

PubMed

Balachandran, Prasanna V; Kowalski, Benjamin; Sehirlioglu, Alp; Lookman, Turab

2018-04-26

Experimental search for high-temperature ferroelectric perovskites is a challenging task due to the vast chemical space and lack of predictive guidelines. Here, we demonstrate a two-step machine learning approach to guide experiments in search of xBi[Formula: see text]O 3 -(1 - x)PbTiO 3 -based perovskites with high ferroelectric Curie temperature. These involve classification learning to screen for compositions in the perovskite structures, and regression coupled to active learning to identify promising perovskites for synthesis and feedback. The problem is challenging because the search space is vast, spanning ~61,500 compositions and only 167 are experimentally studied. Furthermore, not every composition can be synthesized in the perovskite phase. In this work, we predict x, y, Me', and Me″ such that the resulting compositions have both high Curie temperature and form in the perovskite structure. Outcomes from both successful and failed experiments then iteratively refine the machine learning models via an active learning loop. Our approach finds six perovskites out of ten compositions synthesized, including three previously unexplored {Me'Me″} pairs, with 0.2Bi(Fe 0.12 Co 0.88 )O 3 -0.8PbTiO 3 showing the highest measured Curie temperature of 898 K among them.

Boolean network inference from time series data incorporating prior biological knowledge.

PubMed

Haider, Saad; Pal, Ranadip

2012-01-01

Numerous approaches exist for modeling of genetic regulatory networks (GRNs) but the low sampling rates often employed in biological studies prevents the inference of detailed models from experimental data. In this paper, we analyze the issues involved in estimating a model of a GRN from single cell line time series data with limited time points. We present an inference approach for a Boolean Network (BN) model of a GRN from limited transcriptomic or proteomic time series data based on prior biological knowledge of connectivity, constraints on attractor structure and robust design. We applied our inference approach to 6 time point transcriptomic data on Human Mammary Epithelial Cell line (HMEC) after application of Epidermal Growth Factor (EGF) and generated a BN with a plausible biological structure satisfying the data. We further defined and applied a similarity measure to compare synthetic BNs and BNs generated through the proposed approach constructed from transitions of various paths of the synthetic BNs. We have also compared the performance of our algorithm with two existing BN inference algorithms. Through theoretical analysis and simulations, we showed the rarity of arriving at a BN from limited time series data with plausible biological structure using random connectivity and absence of structure in data. The framework when applied to experimental data and data generated from synthetic BNs were able to estimate BNs with high similarity scores. Comparison with existing BN inference algorithms showed the better performance of our proposed algorithm for limited time series data. The proposed framework can also be applied to optimize the connectivity of a GRN from experimental data when the prior biological knowledge on regulators is limited or not unique.

Process simulation and dynamic control for marine oily wastewater treatment using UV irradiation.

PubMed

Jing, Liang; Chen, Bing; Zhang, Baiyu; Li, Pu

2015-09-15

UV irradiation and advanced oxidation processes have been recently regarded as promising solutions in removing polycyclic aromatic hydrocarbons (PAHs) from marine oily wastewater. However, such treatment methods are generally not sufficiently understood in terms of reaction mechanisms, process simulation and process control. These deficiencies can drastically hinder their application in shipping and offshore petroleum industries which produce bilge/ballast water and produced water as the main streams of marine oily wastewater. In this study, the factorial design of experiment was carried out to investigate the degradation mechanism of a typical PAH, namely naphthalene, under UV irradiation in seawater. Based on the experimental results, a three-layer feed-forward artificial neural network simulation model was developed to simulate the treatment process and to forecast the removal performance. A simulation-based dynamic mixed integer nonlinear programming (SDMINP) approach was then proposed to intelligently control the treatment process by integrating the developed simulation model, genetic algorithm and multi-stage programming. The applicability and effectiveness of the developed approach were further tested though a case study. The experimental results showed that the influences of fluence rate and temperature on the removal of naphthalene were greater than those of salinity and initial concentration. The developed simulation model could well predict the UV-induced removal process under varying conditions. The case study suggested that the SDMINP approach, with the aid of the multi-stage control strategy, was able to significantly reduce treatment cost when comparing to the traditional single-stage process optimization. The developed approach and its concept/framework have high potential of applicability in other environmental fields where a treatment process is involved and experimentation and modeling are used for process simulation and control. Copyright © 2015 Elsevier Ltd. All rights reserved.

A Magic-Angle Spinning NMR Method for the Site-Specific Measurement of Proton Chemical-Shift Anisotropy in Biological and Organic Solids.

PubMed

Hou, Guangjin; Gupta, Rupal; Polenova, Tatyana; Vega, Alexander J

2014-02-01

Proton chemical shifts are a rich probe of structure and hydrogen bonding environments in organic and biological molecules. Until recently, measurements of 1 H chemical shift tensors have been restricted to either solid systems with sparse proton sites or were based on the indirect determination of anisotropic tensor components from cross-relaxation and liquid-crystal experiments. We have introduced an MAS approach that permits site-resolved determination of CSA tensors of protons forming chemical bonds with labeled spin-1/2 nuclei in fully protonated solids with multiple sites, including organic molecules and proteins. This approach, originally introduced for the measurements of chemical shift tensors of amide protons, is based on three RN -symmetry based experiments, from which the principal components of the 1 H CS tensor can be reliably extracted by simultaneous triple fit of the data. In this article, we expand our approach to a much more challenging system involving aliphatic and aromatic protons. We start with a review of the prior work on experimental-NMR and computational-quantum-chemical approaches for the measurements of 1 H chemical shift tensors and for relating these to the electronic structures. We then present our experimental results on U- 13 C, 15 N-labeled histdine demonstrating that 1 H chemical shift tensors can be reliably determined for the 1 H 15 N and 1 H 13 C spin pairs in cationic and neutral forms of histidine. Finally, we demonstrate that the experimental 1 H(C) and 1 H(N) chemical shift tensors are in agreement with Density Functional Theory calculations, therefore establishing the usefulness of our method for characterization of structure and hydrogen bonding environment in organic and biological solids.

Single particle fluorescence: a simple experimental approach to evaluate coincidence effects.

PubMed

Wu, Xihong; Omenetto, Nicoló; Smith, Benjamin W; Winefordner, James D

2007-07-01

Real-time characterization of the chemical and physical properties of individual aerosol particles is an important issue in environmental studies. A well-established way of accomplishing this task relies on the use of laser-induced fluorescence or laser ionization mass spectrometry. We describe here a simple approach aimed at experimentally verifying that single particles are indeed addressed. The approach has been tested with a system consisting of a series of aerodynamic lenses to form a beam of dye-doped particles aerosolized from a solution of known concentration with a medical nebulizer. Two independent spectral detection channels simultaneously measure the fluorescence signals generated in two different spectral regions by the passage of a mixture of two dye-doped particles through a focused laser beam in a vacuum chamber. Coincidence effects, arising from the simultaneous observation of both fluorescence emissions, can then be directly observed. Both dual-color fluorescence and pulse height distribution have been analyzed. As expected, the probability of single- or multiple-particle interaction strongly depends on the particle flux in the chamber, which is related to the concentration of particles in the nebulized solution. In our case, to achieve a two-particle coincidence smaller than 10%, a particle concentration lower than 1.2x10(5) particles/mL is required. Moreover, it was found that the experimental observations are in agreement with a simple mathematical model based on Poisson statistics. Although the results obtained refer to particle concentrations in solution, our approach can equally be applicable to experiments involving direct air sampling, provided that the number density of particles in air can be measured a priori, e.g., with a particle counter.

Discovery of Intramolecular Signal Transduction Network Based on a New Protein Dynamics Model of Energy Dissipation

PubMed Central

Ma, Cheng-Wei; Xiu, Zhi-Long; Zeng, An-Ping

2012-01-01

A novel approach to reveal intramolecular signal transduction network is proposed in this work. To this end, a new algorithm of network construction is developed, which is based on a new protein dynamics model of energy dissipation. A key feature of this approach is that direction information is specified after inferring protein residue-residue interaction network involved in the process of signal transduction. This enables fundamental analysis of the regulation hierarchy and identification of regulation hubs of the signaling network. A well-studied allosteric enzyme, E. coli aspartokinase III, is used as a model system to demonstrate the new method. Comparison with experimental results shows that the new approach is able to predict all the sites that have been experimentally proved to desensitize allosteric regulation of the enzyme. In addition, the signal transduction network shows a clear preference for specific structural regions, secondary structural types and residue conservation. Occurrence of super-hubs in the network indicates that allosteric regulation tends to gather residues with high connection ability to collectively facilitate the signaling process. Furthermore, a new parameter of propagation coefficient is defined to determine the propagation capability of residues within a signal transduction network. In conclusion, the new approach is useful for fundamental understanding of the process of intramolecular signal transduction and thus has significant impact on rational design of novel allosteric proteins. PMID:22363664

Instructional Efficiency of Tutoring in an Outreach Gene Technology Laboratory

NASA Astrophysics Data System (ADS)

Scharfenberg, Franz-Josef; Bogner, Franz X.

2013-06-01

Our research objective focused on examining the instructional efficiency of tutoring as a form of instructional change as opposed to a non-tutoring approach in an outreach laboratory. We designed our laboratory based on cognitive load (CL) theory. Altogether, 269 twelfth-graders participated in our day-long module Genetic Fingerprinting. In a quasi-experimental design, the control group ( n = 121) followed the non-tutoring approach previously used, while the treatment group ( n = 148) followed the newly developed tutoring approach. Each tutor was in charge of two student work groups and recorded the tutoring activities requested by the tutees throughout the day. We measured the students' invested mental effort (as an index of CL), cognitive achievement (in a pre-post-follow-up design), and the students' cooperation in their work groups as well as calculated the student instructional involvement (as a motivational variable). Additionally, we examined which aspects of the hands-on phases were of particular relevance to the students' invested mental effort. Unexpectedly, the combined mental effort and cognitive achievement data indicated that our implemented tutoring approach resulted in a lower instructional efficiency despite the relevance of tutoring for students' mental effort invested during the experimental phases. Most of the tutor assistance was unnecessarily requested for performing the procedural steps and using the equipment. Our results indicate an assistance dilemma and consequently underscore the necessity for effective tutor preparation in outreach laboratories.

Genome-wide prediction and analysis of human tissue-selective genes using microarray expression data

PubMed Central

2013-01-01

Background Understanding how genes are expressed specifically in particular tissues is a fundamental question in developmental biology. Many tissue-specific genes are involved in the pathogenesis of complex human diseases. However, experimental identification of tissue-specific genes is time consuming and difficult. The accurate predictions of tissue-specific gene targets could provide useful information for biomarker development and drug target identification. Results In this study, we have developed a machine learning approach for predicting the human tissue-specific genes using microarray expression data. The lists of known tissue-specific genes for different tissues were collected from UniProt database, and the expression data retrieved from the previously compiled dataset according to the lists were used for input vector encoding. Random Forests (RFs) and Support Vector Machines (SVMs) were used to construct accurate classifiers. The RF classifiers were found to outperform SVM models for tissue-specific gene prediction. The results suggest that the candidate genes for brain or liver specific expression can provide valuable information for further experimental studies. Our approach was also applied for identifying tissue-selective gene targets for different types of tissues. Conclusions A machine learning approach has been developed for accurately identifying the candidate genes for tissue specific/selective expression. The approach provides an efficient way to select some interesting genes for developing new biomedical markers and improve our knowledge of tissue-specific expression. PMID:23369200

Using neighborhood cohesiveness to infer interactions between protein domains.

PubMed

Segura, Joan; Sorzano, C O S; Cuenca-Alba, Jesus; Aloy, Patrick; Carazo, J M

2015-08-01

In recent years, large-scale studies have been undertaken to describe, at least partially, protein-protein interaction maps, or interactomes, for a number of relevant organisms, including human. However, current interactomes provide a somehow limited picture of the molecular details involving protein interactions, mostly because essential experimental information, especially structural data, is lacking. Indeed, the gap between structural and interactomics information is enlarging and thus, for most interactions, key experimental information is missing. We elaborate on the observation that many interactions between proteins involve a pair of their constituent domains and, thus, the knowledge of how protein domains interact adds very significant information to any interactomic analysis. In this work, we describe a novel use of the neighborhood cohesiveness property to infer interactions between protein domains given a protein interaction network. We have shown that some clustering coefficients can be extended to measure a degree of cohesiveness between two sets of nodes within a network. Specifically, we used the meet/min coefficient to measure the proportion of interacting nodes between two sets of nodes and the fraction of common neighbors. This approach extends previous works where homolog coefficients were first defined around network nodes and later around edges. The proposed approach substantially increases both the number of predicted domain-domain interactions as well as its accuracy as compared with current methods. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Incorporating neurophysiological concepts in mathematical thermoregulation models

NASA Astrophysics Data System (ADS)

Kingma, Boris R. M.; Vosselman, M. J.; Frijns, A. J. H.; van Steenhoven, A. A.; van Marken Lichtenbelt, W. D.

2014-01-01

Skin blood flow (SBF) is a key player in human thermoregulation during mild thermal challenges. Various numerical models of SBF regulation exist. However, none explicitly incorporates the neurophysiology of thermal reception. This study tested a new SBF model that is in line with experimental data on thermal reception and the neurophysiological pathways involved in thermoregulatory SBF control. Additionally, a numerical thermoregulation model was used as a platform to test the function of the neurophysiological SBF model for skin temperature simulation. The prediction-error of the SBF-model was quantified by root-mean-squared-residual (RMSR) between simulations and experimental measurement data. Measurement data consisted of SBF (abdomen, forearm, hand), core and skin temperature recordings of young males during three transient thermal challenges (1 development and 2 validation). Additionally, ThermoSEM, a thermoregulation model, was used to simulate body temperatures using the new neurophysiological SBF-model. The RMSR between simulated and measured mean skin temperature was used to validate the model. The neurophysiological model predicted SBF with an accuracy of RMSR < 0.27. Tskin simulation results were within 0.37 °C of the measured mean skin temperature. This study shows that (1) thermal reception and neurophysiological pathways involved in thermoregulatory SBF control can be captured in a mathematical model, and (2) human thermoregulation models can be equipped with SBF control functions that are based on neurophysiology without loss of performance. The neurophysiological approach in modelling thermoregulation is favourable over engineering approaches because it is more in line with the underlying physiology.

Contingency management adapted for African-American adolescents with obesity enhances youth weight loss with caregiver participation: a multiple baseline pilot study.

PubMed

Hartlieb, Kathryn Brogan; Naar, Sylvie; Ledgerwood, David M; Templin, Thomas N; Ellis, Deborah A; Donohue, Bradley; Cunningham, Phillippe B

2015-12-07

Contingency management (CM) interventions, which use operant conditioning principles to encourage completion of target behavioral goals, may be useful for improving adherence to behavioral skills training (BST). Research-to-date has yet to explore CM for weight loss in minority adolescents. To examine the effects of CM in improving adolescent weight loss when added to BST. The study utilized an innovative experimental design that builds upon multiple baseline approaches as recommended by the National Institutes of Health. Six obese African-American youth and their primary caregivers living in Detroit, Michigan, USA. Adolescents received between 4 and 12 weeks of BST during a baseline period and subsequently received CM targeting weight loss. Youth weight. Linear mixed effects modeling was used in the analysis. CM did not directly affect adolescent weight loss above that of BST (p=0.053). However, when caregivers were involved in CM session treatment, contingency management had a positive effect on adolescent weight loss. The estimated weight loss due to CM when caregivers also attended was 0.66 kg/week (p<0.001, [95% CI; -1.96, -0.97]) relative to the baseline trajectory. This study demonstrates application of a novel experimental approach to intervention development and demonstrated the importance of parent involvement when delivering contingency management for minority youth weight loss. Lessons learned from contingency management program implementation are also discussed in order to inform practice.

Rocket Ejector Studies for Application to RBCC Engines: An Integrated Experimental/CFD Approach

NASA Technical Reports Server (NTRS)

Pal, S.; Merkle, C. L.; Anderson, W. E.; Santoro, R. J.

1997-01-01

Recent interest in low cost, reliable access to space has generated increased interest in advanced technology approaches to space transportation systems. A key to the success of such programs lies in the development of advanced propulsion systems capable of achieving the performance and operations goals required for the next generation of space vehicles. One extremely promising approach involves the combination of rocket and air- breathing engines into a rocket-based combined-cycle engine (RBCC). A key element of that engine is the rocket ejector which is utilized in the zero to Mach two operating regime. Studies of RBCC engine concepts are not new and studies dating back thirty years are well documented in the literature. However, studies focused on the rocket ejector mode of the RBCC cycle are lacking. The present investigation utilizes an integrated experimental and computation fluid dynamics (CFD) approach to examine critical rocket ejector performance issues. In particular, the development of a predictive methodology capable of performance prediction is a key objective in order to analyze thermal choking and its control, primary/secondary pressure matching considerations, and effects of nozzle expansion ratio. To achieve this objective, the present study emphasizes obtaining new data using advanced optical diagnostics such as Raman spectroscopy and CFD techniques to investigate mixing in the rocket ejector mode. A new research facility for the study of the rocket ejector mode is described along with the diagnostic approaches to be used. The CFD modeling approach is also described along with preliminary CFD predictions obtained to date.

Descriptive vs. mechanistic network models in plant development in the post-genomic era.

PubMed

Davila-Velderrain, J; Martinez-Garcia, J C; Alvarez-Buylla, E R

2015-01-01

Network modeling is now a widespread practice in systems biology, as well as in integrative genomics, and it constitutes a rich and diverse scientific research field. A conceptually clear understanding of the reasoning behind the main existing modeling approaches, and their associated technical terminologies, is required to avoid confusions and accelerate the transition towards an undeniable necessary more quantitative, multidisciplinary approach to biology. Herein, we focus on two main network-based modeling approaches that are commonly used depending on the information available and the intended goals: inference-based methods and system dynamics approaches. As far as data-based network inference methods are concerned, they enable the discovery of potential functional influences among molecular components. On the other hand, experimentally grounded network dynamical models have been shown to be perfectly suited for the mechanistic study of developmental processes. How do these two perspectives relate to each other? In this chapter, we describe and compare both approaches and then apply them to a given specific developmental module. Along with the step-by-step practical implementation of each approach, we also focus on discussing their respective goals, utility, assumptions, and associated limitations. We use the gene regulatory network (GRN) involved in Arabidopsis thaliana Root Stem Cell Niche patterning as our illustrative example. We show that descriptive models based on functional genomics data can provide important background information consistent with experimentally supported functional relationships integrated in mechanistic GRN models. The rationale of analysis and modeling can be applied to any other well-characterized functional developmental module in multicellular organisms, like plants and animals.

Critical Need for Family-Based, Quasi-Experimental Designs in Integrating Genetic and Social Science Research

PubMed Central

Lahey, Benjamin B.; Turkheimer, Eric; Lichtenstein, Paul

2013-01-01

Researchers have identified environmental risks that predict subsequent psychological and medical problems. Based on these correlational findings, researchers have developed and tested complex developmental models and have examined biological moderating factors (e.g., gene–environment interactions). In this context, we stress the critical need for researchers to use family-based, quasi-experimental designs when trying to integrate genetic and social science research involving environmental variables because these designs rigorously examine causal inferences by testing competing hypotheses. We argue that sibling comparison, offspring of twins or siblings, in vitro fertilization designs, and other genetically informed approaches play a unique role in bridging gaps between basic biological and social science research. We use studies on maternal smoking during pregnancy to exemplify these principles. PMID:23927516

Critical need for family-based, quasi-experimental designs in integrating genetic and social science research.

PubMed

D'Onofrio, Brian M; Lahey, Benjamin B; Turkheimer, Eric; Lichtenstein, Paul

2013-10-01

Researchers have identified environmental risks that predict subsequent psychological and medical problems. Based on these correlational findings, researchers have developed and tested complex developmental models and have examined biological moderating factors (e.g., gene-environment interactions). In this context, we stress the critical need for researchers to use family-based, quasi-experimental designs when trying to integrate genetic and social science research involving environmental variables because these designs rigorously examine causal inferences by testing competing hypotheses. We argue that sibling comparison, offspring of twins or siblings, in vitro fertilization designs, and other genetically informed approaches play a unique role in bridging gaps between basic biological and social science research. We use studies on maternal smoking during pregnancy to exemplify these principles.

Single-ion hydration thermodynamics from clusters to bulk solutions: Recent insights from molecular modeling

DOE PAGES

Vlcek, Lukas; Chialvo, Ariel A.

2016-01-03

The importance of single-ion hydration thermodynamic properties for understanding the driving forces of aqueous electrolyte processes, along with the impossibility of their direct experimental measurement, have prompted a large number of experimental, theoretical, and computational studies aimed at separating the cation and anion contributions. Here we provide an overview of historical approaches based on extrathermodynamic assumptions and more recent computational studies of single-ion hydration in order to evaluate the approximations involved in these methods, quantify their accuracy, reliability, and limitations in the light of the latest developments. Finally, we also offer new insights into the factors that influence the accuracymore » of ion–water interaction models and our views on possible ways to fill this substantial knowledge gap in aqueous physical chemistry.« less

Bayesian experimental design for models with intractable likelihoods.

PubMed

Drovandi, Christopher C; Pettitt, Anthony N

2013-12-01

In this paper we present a methodology for designing experiments for efficiently estimating the parameters of models with computationally intractable likelihoods. The approach combines a commonly used methodology for robust experimental design, based on Markov chain Monte Carlo sampling, with approximate Bayesian computation (ABC) to ensure that no likelihood evaluations are required. The utility function considered for precise parameter estimation is based upon the precision of the ABC posterior distribution, which we form efficiently via the ABC rejection algorithm based on pre-computed model simulations. Our focus is on stochastic models and, in particular, we investigate the methodology for Markov process models of epidemics and macroparasite population evolution. The macroparasite example involves a multivariate process and we assess the loss of information from not observing all variables. © 2013, The International Biometric Society.

Excess thermodynamics of mixtures involving xenon and light linear alkanes by computer simulation.

PubMed

Carvalho, A J Palace; Ramalho, J P Prates; Martins, Luís F G

2007-06-14

Excess molar enthalpies and excess molar volumes as a function of composition for liquid mixtures of xenon + ethane (at 161.40 K), xenon + propane (at 161.40 K) and xenon + n-butane (at 182.34 K) have been obtained by Monte Carlo computer simulations and compared with available experimental data. Simulation conditions were chosen to closely match those of the corresponding experimental results. The TraPPE-UA force field was selected among other force fields to model all the alkanes studied, whereas the one-center Lennard-Jones potential from Bohn et al. was used for xenon. The calculated H(m)(E) and V(m)(E) for all systems are negative, increasing in magnitude as the alkane chain length increases. The results for these systems were compared with experimental data and with other theoretical calculations using the SAFT approach. An excellent agreement between simulation and experimental results was found for xenon + ethane system, whereas for the remaining two systems, some deviations that become progressively more significant as the alkane chain length increases were observed.

Partial wave analysis for folded differential cross sections

NASA Astrophysics Data System (ADS)

Machacek, J. R.; McEachran, R. P.

2018-03-01

The value of modified effective range theory (MERT) and the connection between differential cross sections and phase shifts in low-energy electron scattering has long been recognized. Recent experimental techniques involving magnetically confined beams have introduced the concept of folded differential cross sections (FDCS) where the forward (θ ≤ π/2) and backward scattered (θ ≥ π/2) projectiles are unresolved, that is the value measured at the angle θ is the sum of the signal for particles scattered into the angles θ and π - θ. We have developed an alternative approach to MERT in order to analyse low-energy folded differential cross sections for positrons and electrons. This results in a simplified expression for the FDCS when it is expressed in terms of partial waves and thereby enables one to extract the first few phase shifts from a fit to an experimental FDCS at low energies. Thus, this method predicts forward and backward angle scattering (0 to π) using only experimental FDCS data and can be used to determine the total elastic cross section solely from experimental results at low-energy, which are limited in angular range.

REVIEWS OF TOPICAL PROBLEMS: Universal viscosity growth in metallic melts at megabar pressures: the vitreous state of the Earth's inner core

NASA Astrophysics Data System (ADS)

Brazhkin, Vadim V.; Lyapin, A. G.

2000-05-01

Experimental data on and theoretical models for the viscosity of various types of liquids and melts under pressure are reviewed. Experimentally, the least studied melts are those of metals, whose viscosity is considered to be virtually constant along the melting curve. The authors' new approach to the viscosity of melts involves the measurement of the grain size in solidified samples. Measurements on liquid metals at pressures up to 10 GPa using this method show, contrary to the empirical approach, that the melt viscosity grows considerably along the melting curves. Based on the experimental data and on the critical analysis of current theories, a hypothesis of a universal viscosity behavior is introduced for liquids under pressure. Extrapolating the liquid iron results to the pressures and temperatures at the Earth's core reveals that the Earth's outer core is a very viscous melt with viscosity values ranging from 102 Pa s to 1011 Pa s depending on the depth. The Earth's inner core is presumably an ultraviscous (>1011 Pa s) glass-like liquid — in disagreement with the current idea of a crystalline inner core. The notion of the highly viscous interior of celestial bodies sheds light on many mysteries of planetary geophysics and astronomy. From the analysis of the pressure variation of the melting and glass-transition temperatures, an entirely new concept of a stable metallic vitreous state arises, calling for further experimental and theoretical study.

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

Frame, E.A.

The objectives of this project were: (1) to determine the feasibility of adding a vapor-phase corrosion inhibitor (VCI) component to improve the preservation performance of MIL-L-21260 and (2) to evaluate a less complicated engine preservation procedure. A simultaneous two-phase approach was conducted. Phase 1 involved the formulation and evaluation of experimental VCI oils, while Phase 2 was the evaluation of a simplified engine preservation procedure. VCI oil formulation was conducted by Ronco Laboratory under subcontract. Compatibility of the experimental VCI oils with metal coupons, elastomers, and fuel filters was determined. Effectiveness of the experimental VCI oil was evaluated in amore » 3-year outdoor engine storage test. The engines were preserved using an experimental, simplified preservation procedure. The simplified engine preservation procedure proved to be acceptable as engines stored for 3 years in a very severe environment were judged to have been adequately preserved. Engine oil meeting specification MIL-L-21260 provided satisfactory protection during the 3-year storage test. The experimental VCI oil also provided satisfactory storage protection during this test; however, there was no observable advantage for the VCI oil. The VCI oil had acceptable compatibility with an elastomeric flex ring, metal coupons (except lead), and fuel filters.« less

Improving human activity recognition and its application in early stroke diagnosis.

PubMed

Villar, José R; González, Silvia; Sedano, Javier; Chira, Camelia; Trejo-Gabriel-Galan, Jose M

2015-06-01

The development of efficient stroke-detection methods is of significant importance in today's society due to the effects and impact of stroke on health and economy worldwide. This study focuses on Human Activity Recognition (HAR), which is a key component in developing an early stroke-diagnosis tool. An overview of the proposed global approach able to discriminate normal resting from stroke-related paralysis is detailed. The main contributions include an extension of the Genetic Fuzzy Finite State Machine (GFFSM) method and a new hybrid feature selection (FS) algorithm involving Principal Component Analysis (PCA) and a voting scheme putting the cross-validation results together. Experimental results show that the proposed approach is a well-performing HAR tool that can be successfully embedded in devices.

A Density Functional Approach to Polarizable Models: A Kim-Gordon-Response Density Interaction Potential for Molecular Simulations

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

Tabacchi, G; Hutter, J; Mundy, C

2005-04-07

A combined linear response--frozen electron density model has been implemented in a molecular dynamics scheme derived from an extended Lagrangian formalism. This approach is based on a partition of the electronic charge distribution into a frozen region described by Kim-Gordon theory, and a response contribution determined by the instaneous ionic configuration of the system. The method is free from empirical pair-potentials and the parameterization protocol involves only calculations on properly chosen subsystems. They apply this method to a series of alkali halides in different physical phases and are able to reproduce experimental structural and thermodynamic properties with an accuracy comparablemore » to Kohn-Sham density functional calculations.« less

Neural network approaches versus statistical methods in classification of multisource remote sensing data

NASA Technical Reports Server (NTRS)

Benediktsson, Jon A.; Swain, Philip H.; Ersoy, Okan K.

1990-01-01

Neural network learning procedures and statistical classificaiton methods are applied and compared empirically in classification of multisource remote sensing and geographic data. Statistical multisource classification by means of a method based on Bayesian classification theory is also investigated and modified. The modifications permit control of the influence of the data sources involved in the classification process. Reliability measures are introduced to rank the quality of the data sources. The data sources are then weighted according to these rankings in the statistical multisource classification. Four data sources are used in experiments: Landsat MSS data and three forms of topographic data (elevation, slope, and aspect). Experimental results show that two different approaches have unique advantages and disadvantages in this classification application.

SPR Biosensors in Direct Molecular Fishing: Implications for Protein Interactomics.

PubMed

Florinskaya, Anna; Ershov, Pavel; Mezentsev, Yuri; Kaluzhskiy, Leonid; Yablokov, Evgeniy; Medvedev, Alexei; Ivanov, Alexis

2018-05-18

We have developed an original experimental approach based on the use of surface plasmon resonance (SPR) biosensors, applicable for investigation of potential partners involved in protein⁻protein interactions (PPI) as well as protein⁻peptide or protein⁻small molecule interactions. It is based on combining a SPR biosensor, size exclusion chromatography (SEC), mass spectrometric identification of proteins (LC-MS/MS) and direct molecular fishing employing principles of affinity chromatography for isolation of potential partner proteins from the total lysate of biological samples using immobilized target proteins (or small non-peptide compounds) as ligands. Applicability of this approach has been demonstrated within the frame of the Human Proteome Project (HPP) and PPI regulation by a small non-peptide biologically active compound, isatin.

Plasma Liner Research for MTF at NASA Marshall Space Flight Center

NASA Technical Reports Server (NTRS)

Thio, Y. C. F.; Eskridge, R.; Lee, M.; Martin, A.; Smith, J.; Cassibry, J. T.; Wu, S. T.; Kirkpatrick, R. C.; Knapp, C. E.; Turchi, P. J.;

Data analytics using canonical correlation analysis and Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Rickman, Jeffrey M.; Wang, Yan; Rollett, Anthony D.; Harmer, Martin P.; Compson, Charles

2017-07-01

A canonical correlation analysis is a generic parametric model used in the statistical analysis of data involving interrelated or interdependent input and output variables. It is especially useful in data analytics as a dimensional reduction strategy that simplifies a complex, multidimensional parameter space by identifying a relatively few combinations of variables that are maximally correlated. One shortcoming of the canonical correlation analysis, however, is that it provides only a linear combination of variables that maximizes these correlations. With this in mind, we describe here a versatile, Monte-Carlo based methodology that is useful in identifying non-linear functions of the variables that lead to strong input/output correlations. We demonstrate that our approach leads to a substantial enhancement of correlations, as illustrated by two experimental applications of substantial interest to the materials science community, namely: (1) determining the interdependence of processing and microstructural variables associated with doped polycrystalline aluminas, and (2) relating microstructural decriptors to the electrical and optoelectronic properties of thin-film solar cells based on CuInSe2 absorbers. Finally, we describe how this approach facilitates experimental planning and process control.

Identifying Effective Design Approaches to Allocate Genotypes in Two-Phase Designs: A Case Study in Pelargonium zonale.

PubMed

Molenaar, Heike; Boehm, Robert; Piepho, Hans-Peter

2017-01-01

Robust phenotypic data allow adequate statistical analysis and are crucial for any breeding purpose. Such data is obtained from experiments laid out to best control local variation. Additionally, experiments frequently involve two phases, each contributing environmental sources of variation. For example, in a former experiment we conducted to evaluate production related traits in Pelargonium zonale , there were two consecutive phases, each performed in a different greenhouse. Phase one involved the propagation of the breeding strains to obtain the stem cutting count, and phase two involved the assessment of root formation. The evaluation of the former study raised questions regarding options for improving the experimental layout: (i) Is there a disadvantage to using exactly the same design in both phases? (ii) Instead of generating a separate layout for each phase, can the design be optimized across both phases, such that the mean variance of a pair-wise treatment difference (MVD) can be decreased? To answer these questions, alternative approaches were explored to generate two-phase designs either in phase-wise order (Option 1) or across phases (Option 2). In Option 1 we considered the scenarios (i) using in both phases the same experimental design and (ii) randomizing each phase separately. In Option 2, we considered the scenarios (iii) generating a single design with eight replicates and splitting these among the two phases, (iv) separating the block structure across phases by dummy coding, and (v) design generation with optimal alignment of block units in the two phases. In both options, we considered the same or different block structures in each phase. The designs were evaluated by the MVD obtained by the intra-block analysis and the joint inter-block-intra-block analysis. The smallest MVD was most frequently obtained for designs generated across phases rather than for each phase separately, in particular when both phases of the design were separated with a single pseudo-level. The joint optimization ensured that treatment concurrences were equally balanced across pairs, one of the prerequisites for an efficient design. The proposed alternative approaches can be implemented with any model-based design packages with facilities to formulate linear models for treatment and block structures.

A computational modeling approach for the characterization of mechanical properties of 3D alginate tissue scaffolds.

PubMed

Nair, K; Yan, K C; Sun, W

2008-01-01

Scaffold guided tissue engineering is an innovative approach wherein cells are seeded onto biocompatible and biodegradable materials to form 3-dimensional (3D) constructs that, when implanted in the body facilitate the regeneration of tissue. Tissue scaffolds act as artificial extracellular matrix providing the environment conducive for tissue growth. Characterization of scaffold properties is necessary to understand better the underlying processes involved in controlling cell behavior and formation of functional tissue. We report a computational modeling approach to characterize mechanical properties of 3D gellike biomaterial, specifically, 3D alginate scaffold encapsulated with cells. Alginate inherent nonlinearity and variations arising from minute changes in its concentration and viscosity make experimental evaluation of its mechanical properties a challenging and time consuming task. We developed an in silico model to determine the stress-strain relationship of alginate based scaffolds from experimental data. In particular, we compared the Ogden hyperelastic model to other hyperelastic material models and determined that this model was the most suitable to characterize the nonlinear behavior of alginate. We further propose a mathematical model that represents the alginate material constants in Ogden model as a function of concentrations and viscosity. This study demonstrates the model capability to predict mechanical properties of 3D alginate scaffolds.

Multi-Scale Modeling of the Gamma Radiolysis of Nitrate Solutions.

PubMed

Horne, Gregory P; Donoclift, Thomas A; Sims, Howard E; Orr, Robin M; Pimblott, Simon M

2016-11-17

A multiscale modeling approach has been developed for the extended time scale long-term radiolysis of aqueous systems. The approach uses a combination of stochastic track structure and track chemistry as well as deterministic homogeneous chemistry techniques and involves four key stages: radiation track structure simulation, the subsequent physicochemical processes, nonhomogeneous diffusion-reaction kinetic evolution, and homogeneous bulk chemistry modeling. The first three components model the physical and chemical evolution of an isolated radiation chemical track and provide radiolysis yields, within the extremely low dose isolated track paradigm, as the input parameters for a bulk deterministic chemistry model. This approach to radiation chemical modeling has been tested by comparison with the experimentally observed yield of nitrite from the gamma radiolysis of sodium nitrate solutions. This is a complex radiation chemical system which is strongly dependent on secondary reaction processes. The concentration of nitrite is not just dependent upon the evolution of radiation track chemistry and the scavenging of the hydrated electron and its precursors but also on the subsequent reactions of the products of these scavenging reactions with other water radiolysis products. Without the inclusion of intratrack chemistry, the deterministic component of the multiscale model is unable to correctly predict experimental data, highlighting the importance of intratrack radiation chemistry in the chemical evolution of the irradiated system.

Flight-Test Evaluation of Flutter-Prediction Methods

NASA Technical Reports Server (NTRS)

Lind, RIck; Brenner, Marty

2003-01-01

The flight-test community routinely spends considerable time and money to determine a range of flight conditions, called a flight envelope, within which an aircraft is safe to fly. The cost of determining a flight envelope could be greatly reduced if there were a method of safely and accurately predicting the speed associated with the onset of an instability called flutter. Several methods have been developed with the goal of predicting flutter speeds to improve the efficiency of flight testing. These methods include (1) data-based methods, in which one relies entirely on information obtained from the flight tests and (2) model-based approaches, in which one relies on a combination of flight data and theoretical models. The data-driven methods include one based on extrapolation of damping trends, one that involves an envelope function, one that involves the Zimmerman-Weissenburger flutter margin, and one that involves a discrete-time auto-regressive model. An example of a model-based approach is that of the flutterometer. These methods have all been shown to be theoretically valid and have been demonstrated on simple test cases; however, until now, they have not been thoroughly evaluated in flight tests. An experimental apparatus called the Aerostructures Test Wing (ATW) was developed to test these prediction methods.

Limited Agreement of Independent RNAi Screens for Virus-Required Host Genes Owes More to False-Negative than False-Positive Factors

PubMed Central

Wang, Zhishi; Craven, Mark; Newton, Michael A.; Ahlquist, Paul

2013-01-01

Systematic, genome-wide RNA interference (RNAi) analysis is a powerful approach to identify gene functions that support or modulate selected biological processes. An emerging challenge shared with some other genome-wide approaches is that independent RNAi studies often show limited agreement in their lists of implicated genes. To better understand this, we analyzed four genome-wide RNAi studies that identified host genes involved in influenza virus replication. These studies collectively identified and validated the roles of 614 cell genes, but pair-wise overlap among the four gene lists was only 3% to 15% (average 6.7%). However, a number of functional categories were overrepresented in multiple studies. The pair-wise overlap of these enriched-category lists was high, ∼19%, implying more agreement among studies than apparent at the gene level. Probing this further, we found that the gene lists implicated by independent studies were highly connected in interacting networks by independent functional measures such as protein-protein interactions, at rates significantly higher than predicted by chance. We also developed a general, model-based approach to gauge the effects of false-positive and false-negative factors and to estimate, from a limited number of studies, the total number of genes involved in a process. For influenza virus replication, this novel statistical approach estimates the total number of cell genes involved to be ∼2,800. This and multiple other aspects of our experimental and computational results imply that, when following good quality control practices, the low overlap between studies is primarily due to false negatives rather than false-positive gene identifications. These results and methods have implications for and applications to multiple forms of genome-wide analysis. PMID:24068911

A Multicriteria Decision Making Approach for Estimating the Number of Clusters in a Data Set

PubMed Central

Peng, Yi; Zhang, Yong; Kou, Gang; Shi, Yong

2012-01-01

Determining the number of clusters in a data set is an essential yet difficult step in cluster analysis. Since this task involves more than one criterion, it can be modeled as a multiple criteria decision making (MCDM) problem. This paper proposes a multiple criteria decision making (MCDM)-based approach to estimate the number of clusters for a given data set. In this approach, MCDM methods consider different numbers of clusters as alternatives and the outputs of any clustering algorithm on validity measures as criteria. The proposed method is examined by an experimental study using three MCDM methods, the well-known clustering algorithm–k-means, ten relative measures, and fifteen public-domain UCI machine learning data sets. The results show that MCDM methods work fairly well in estimating the number of clusters in the data and outperform the ten relative measures considered in the study. PMID:22870181

Generation algorithm of craniofacial structure contour in cephalometric images

NASA Astrophysics Data System (ADS)

Mondal, Tanmoy; Jain, Ashish; Sardana, H. K.

2010-02-01

Anatomical structure tracing on cephalograms is a significant way to obtain cephalometric analysis. Computerized cephalometric analysis involves both manual and automatic approaches. The manual approach is limited in accuracy and repeatability. In this paper we have attempted to develop and test a novel method for automatic localization of craniofacial structure based on the detected edges on the region of interest. According to the grey scale feature at the different region of the cephalometric images, an algorithm for obtaining tissue contour is put forward. Using edge detection with specific threshold an improved bidirectional contour tracing approach is proposed by an interactive selection of the starting edge pixels, the tracking process searches repetitively for an edge pixel at the neighborhood of previously searched edge pixel to segment images, and then craniofacial structures are obtained. The effectiveness of the algorithm is demonstrated by the preliminary experimental results obtained with the proposed method.

Statistical mapping of zones of focused groundwater/surface-water exchange using fiber-optic distributed temperature sensing

USGS Publications Warehouse

Mwakanyamale, Kisa; Day-Lewis, Frederick D.; Slater, Lee D.

2013-01-01

Fiber-optic distributed temperature sensing (FO-DTS) increasingly is used to map zones of focused groundwater/surface-water exchange (GWSWE). Previous studies of GWSWE using FO-DTS involved identification of zones of focused GWSWE based on arbitrary cutoffs of FO-DTS time-series statistics (e.g., variance, cross-correlation between temperature and stage, or spectral power). New approaches are needed to extract more quantitative information from large, complex FO-DTS data sets while concurrently providing an assessment of uncertainty associated with mapping zones of focused GSWSE. Toward this end, we present a strategy combining discriminant analysis (DA) and spectral analysis (SA). We demonstrate the approach using field experimental data from a reach of the Columbia River adjacent to the Hanford 300 Area site. Results of the combined SA/DA approach are shown to be superior to previous results from qualitative interpretation of FO-DTS spectra alone.

A review of active learning approaches to experimental design for uncovering biological networks

PubMed Central

2017-01-01

Various types of biological knowledge describe networks of interactions among elementary entities. For example, transcriptional regulatory networks consist of interactions among proteins and genes. Current knowledge about the exact structure of such networks is highly incomplete, and laboratory experiments that manipulate the entities involved are conducted to test hypotheses about these networks. In recent years, various automated approaches to experiment selection have been proposed. Many of these approaches can be characterized as active machine learning algorithms. Active learning is an iterative process in which a model is learned from data, hypotheses are generated from the model to propose informative experiments, and the experiments yield new data that is used to update the model. This review describes the various models, experiment selection strategies, validation techniques, and successful applications described in the literature; highlights common themes and notable distinctions among methods; and identifies likely directions of future research and open problems in the area. PMID:28570593

Energy exchange analysis in droplet dynamics via the Navier-Stokes-Cahn-Hilliard model

NASA Astrophysics Data System (ADS)

Espath, L. F. R.; Sarmiento, A. F.; Vignal, P.; Varga, B. O. N.; Cortes, A. M. A.; Dalcin, L.; Calo, V. M.

2016-06-01

We develop the energy budget equation of the coupled Navier-Stokes-Cahn-Hilliard (NSCH) system. We use the NSCH equations to model the dynamics of liquid droplets in a liquid continuum. Buoyancy effects are accounted for through the Boussinesq assumption. We physically interpret each quantity involved in the energy exchange to further insight into the model. Highly resolved simulations involving density-driven flows and merging of droplets allow us to analyze these energy budgets. In particular, we focus on the energy exchanges when droplets merge, and describe flow features relevant to this phenomenon. By comparing our numerical simulations to analytical predictions and experimental results available in the literature, we conclude that modeling droplet dynamics within the framework of NSCH equations is a sensible approach worth further research.

Neurocognition: the food–brain connection.

PubMed

Hill, James O; Berridge, Kent; Avena, Nicole M; Ziauddeen, Hisham; Alonso-Alonso, Miguel; Allison, David B; Khan, Naiman A; Kelley, Michael

2014-09-01

This article summarizes presentations from “Neurocognition: The Food–Brain Connection” symposium held at the ASN Scientific Sessions and Annual Meeting at Experimental Biology 2014 in San Diego, CA on 28 April 2014. Presenters reviewed research from several disciplines, including neurobiology, neuropsychology, cognitive neuroscience, and nutrition, concerning the role of the brain in food-intake regulation, reward, and addiction. A transdisciplinary approach was taken to evaluate the state of the science regarding addiction models, as well as research gaps and future research necessary to understand neurocircuitry and pathways involved in food-intake control and behavior in humans.

FRAP Analysis: Accounting for Bleaching during Image Capture

PubMed Central

Wu, Jun; Shekhar, Nandini; Lele, Pushkar P.; Lele, Tanmay P.

2012-01-01

The analysis of Fluorescence Recovery After Photobleaching (FRAP) experiments involves mathematical modeling of the fluorescence recovery process. An important feature of FRAP experiments that tends to be ignored in the modeling is that there can be a significant loss of fluorescence due to bleaching during image capture. In this paper, we explicitly include the effects of bleaching during image capture in the model for the recovery process, instead of correcting for the effects of bleaching using reference measurements. Using experimental examples, we demonstrate the usefulness of such an approach in FRAP analysis. PMID:22912750

A Palladium Iodide-Catalyzed Cyclocarbonylation Approach to Thiadiazafluorenones.

PubMed

Veltri, Lucia; Paladino, Veronica; Plastina, Pierluigi; Gabriele, Bartolo

2016-07-15

The first example of an additive cyclocarbonylation process leading to 1-thia-4a,9-diazafluoren-4-ones is reported. This process is based on the reaction of readily available 2-(propynylthio)benzimidazoles with carbon monoxide carried out in EtOH at 100 °C under a 5/2 mixture of CO-CO2 at 70 atm in the presence of the PdI2/KI catalytic system. Experimental evidence suggests a mechanistic pathway involving N-palladation of the substrate followed by CO insertion, triple bond insertion, protonolysis, and isomerization.

Microscale bioprocess optimisation.

PubMed

Micheletti, Martina; Lye, Gary J

2006-12-01

Microscale processing techniques offer the potential to speed up the delivery of new drugs to the market, reducing development costs and increasing patient benefit. These techniques have application across both the chemical and biopharmaceutical sectors. The approach involves the study of individual bioprocess operations at the microlitre scale using either microwell or microfluidic formats. In both cases the aim is to generate quantitative bioprocess information early on, so as to inform bioprocess design and speed translation to the manufacturing scale. Automation can enhance experimental throughput and will facilitate the parallel evaluation of competing biocatalyst and process options.

A building block for hardware belief networks.

PubMed

Behin-Aein, Behtash; Diep, Vinh; Datta, Supriyo

2016-07-21

Belief networks represent a powerful approach to problems involving probabilistic inference, but much of the work in this area is software based utilizing standard deterministic hardware based on the transistor which provides the gain and directionality needed to interconnect billions of them into useful networks. This paper proposes a transistor like device that could provide an analogous building block for probabilistic networks. We present two proof-of-concept examples of belief networks, one reciprocal and one non-reciprocal, implemented using the proposed device which is simulated using experimentally benchmarked models.

Microbial detection method based on sensing molecular hydrogen

NASA Technical Reports Server (NTRS)

Wilkins, J. R.; Stoner, G. E.; Boykin, E. H.

1974-01-01

An approach involving the measurement of hydrogen evolution by test organisms was used to detect and enumerate various members of the Enterobacteriaceae group. The experimental setup for measuring hydrogen evolution consisted of a test tube containing two electrodes plus broth and organisms. The test tube was kept in a water bath at a temperature of 35 C. It is pointed out that the hydrogen-sensing method, coupled with the pressure transducer technique reported by Wilkins (1974) could be used in various experiments in which gas production by microorganisms is being measured.

Report on Physics of Channelization: Theory, Experiment, and Observation

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

Kudrolli, Arshad

2014-05-19

The project involved a study of physical processes that create eroded channel and drainage networks. A particular focus was on how the shape of the channels and the network depended on the nature of the fluid flow. Our approach was to combine theoretical, experimental, and observational studies in close collaboration with Professor Daniel Rothman of the Massachusetts Institute of Technology. Laboratory -scaled experiments were developed and quantitative data on the shape of the pattern and erosion dynamics are obtained with a laser-aided topography technique and fluorescent optical imaging techniques.

Cerebral specialization. [greater performance efficiency for certain mental abilities or processes by one cerebral hemisphere over another

NASA Technical Reports Server (NTRS)

Morris, Robin D.; Hopkins, William D.; Rumbaugh, Duane M.

1991-01-01

The concept of greater performance efficiency for certain mental abilities or processes in one cerebral hemisphere rather than the other is referred to as 'cerebral lateralization'. The experimental paradigm for lateralization research involves the study of patients with one damaged hemisphere, which prevents their performance of a certain task or function; this approach, however, presents many difficulties in extrapolating to brain function in normal patients. Attention is presently given to gender differences in lateralization, cerebral asymmetries in other species, and the evolutionary bases of hemispheric specialization.

Stochastic simulations of fatty-acid proto-cell models

NASA Astrophysics Data System (ADS)

Mavelli, F.; Ruiz-Mirazo, K.

2007-06-01

In this contribution we tackle the problem of simulating the time behavior of self-assembling fatty acid vesicles in different experimental conditions. These systems have been (and are being) explored by various labs as possible precursor models of cellular compartments. By means of our recently developed stochastic simulation platform ('ENVIRONMENT') we are able to reproduce quite satisfactorily experimental data that have been reported on the different growth behavior of this type of proto-cellular systems, depending on the level of osmotic pressure they are under. The work here presented is part of a more general attempt to gain insight into the problem of how self-assembling vesicles (closed bilayer structures) could progressively turn into minimal self-producing and self-reproducing cells: i.e., into interesting candidates for (proto-)biological systems. This involves crossing the traditional gap between in silico and in vitro approaches, as we try to do here, convinced that major adavances in the field require the correct integration of both theoretical and experimental endeavors.

Efficient Modeling and Active Learning Discovery of Biological Responses

PubMed Central

Naik, Armaghan W.; Kangas, Joshua D.; Langmead, Christopher J.; Murphy, Robert F.

2013-01-01

High throughput and high content screening involve determination of the effect of many compounds on a given target. As currently practiced, screening for each new target typically makes little use of information from screens of prior targets. Further, choices of compounds to advance to drug development are made without significant screening against off-target effects. The overall drug development process could be made more effective, as well as less expensive and time consuming, if potential effects of all compounds on all possible targets could be considered, yet the cost of such full experimentation would be prohibitive. In this paper, we describe a potential solution: probabilistic models that can be used to predict results for unmeasured combinations, and active learning algorithms for efficiently selecting which experiments to perform in order to build those models and determining when to stop. Using simulated and experimental data, we show that our approaches can produce powerful predictive models without exhaustive experimentation and can learn them much faster than by selecting experiments at random. PMID:24358322

Drosophila as a screening tool to study human neurodegenerative diseases.

PubMed

Lenz, Sarah; Karsten, Peter; Schulz, Jörg B; Voigt, Aaron

2013-11-01

In an aging society, research involving neurodegenerative disorders is of paramount importance. Over the past few years, research on Alzheimer's and Parkinson's diseases has made tremendous progress. Experimental studies, however, rely mostly on transgenic animal models, preferentially using mice. Although experiments on mice have enormous advantages, they also have some inherent limitations, some of which can be overcome by the use of Drosophila melanogaster as an experimental animal. Among the major advantages of using the fly is its small genome, which can also be modified very easily. The fact that its genome lends itself to diverse alterations (e. g. mutagenesis, transposons) has made the fly a useful organism to perform large-scale and genome-wide screening approaches. This has opened up an entirely new field of experimental research aiming to elucidate genetic interactions and screen for modifiers of disease processes in vivo. Here, we provide a brief overview of how flies can be used to analyze molecular mechanisms underlying human neurodegenerative diseases. © 2013 International Society for Neurochemistry.

A reconfigurable visual-programming library for real-time closed-loop cellular electrophysiology

PubMed Central

Biró, István; Giugliano, Michele

2015-01-01

Most of the software platforms for cellular electrophysiology are limited in terms of flexibility, hardware support, ease of use, or re-configuration and adaptation for non-expert users. Moreover, advanced experimental protocols requiring real-time closed-loop operation to investigate excitability, plasticity, dynamics, are largely inaccessible to users without moderate to substantial computer proficiency. Here we present an approach based on MATLAB/Simulink, exploiting the benefits of LEGO-like visual programming and configuration, combined to a small, but easily extendible library of functional software components. We provide and validate several examples, implementing conventional and more sophisticated experimental protocols such as dynamic-clamp or the combined use of intracellular and extracellular methods, involving closed-loop real-time control. The functionality of each of these examples is demonstrated with relevant experiments. These can be used as a starting point to create and support a larger variety of electrophysiological tools and methods, hopefully extending the range of default techniques and protocols currently employed in experimental labs across the world. PMID:26157385

Design and synthetic considerations of matrix metalloproteinase inhibitors.

PubMed

Skotnicki, J S; Zask, A; Nelson, F C; Albright, J D; Levin, J I

1999-06-30

Experimental evidence confirms that the matrix metalloproteinases (MMPs) play a fundamental role in a wide variety of pathologic conditions that involve connective tissue destruction including osteoarthritis and rheumatoid arthritis, tumor metastasis and angiogenesis, corneal ulceration, multiple sclerosis, periodontal disease, and atherosclerosis. Modulation of MMP regulation is possible at several biochemical sites, but direct inhibition of enzyme action provides a particularly attractive target for therapeutic intervention. Hypotheses concerning inhibition of specific MMP(s) with respect to disease target and/or side-effect profile have emerged. Examples are presented of recent advances in medicinal chemistry approaches to the design of matrix metalloproteinase inhibitors (MMPIs), approaches that address structural requirements and that influence potency, selectivity, and bioavailability. Two important approaches to the design, synthesis, and biological evaluation of MMPIs are highlighted: (1) the invention of alternatives to hydroxamic acid zinc chelators and (2) the construction of nonpeptide scaffolds. One current example in each of these two approaches from our own work is described.

Arabic sign language recognition based on HOG descriptor

NASA Astrophysics Data System (ADS)

Ben Jmaa, Ahmed; Mahdi, Walid; Ben Jemaa, Yousra; Ben Hamadou, Abdelmajid

2017-02-01

We present in this paper a new approach for Arabic sign language (ArSL) alphabet recognition using hand gesture analysis. This analysis consists in extracting a histogram of oriented gradient (HOG) features from a hand image and then using them to generate an SVM Models. Which will be used to recognize the ArSL alphabet in real-time from hand gesture using a Microsoft Kinect camera. Our approach involves three steps: (i) Hand detection and localization using a Microsoft Kinect camera, (ii) hand segmentation and (iii) feature extraction using Arabic alphabet recognition. One each input image first obtained by using a depth sensor, we apply our method based on hand anatomy to segment hand and eliminate all the errors pixels. This approach is invariant to scale, to rotation and to translation of the hand. Some experimental results show the effectiveness of our new approach. Experiment revealed that the proposed ArSL system is able to recognize the ArSL with an accuracy of 90.12%.

Transcriptional Profiling of Midguts Prepared from Trypanosoma/T. congolense-Positive Glossina palpalis palpalis Collected from Two Distinct Cameroonian Foci: Coordinated Signatures of the Midguts’ Remodeling As T. congolense-Supportive Niches

PubMed Central

Tsagmo Ngoune, Jean M.; Njiokou, Flobert; Loriod, Béatrice; Kame-Ngasse, Ginette; Fernandez-Nunez, Nicolas; Rioualen, Claire; van Helden, Jacques; Geiger, Anne

2017-01-01

Our previous transcriptomic analysis of Glossina palpalis gambiensis experimentally infected or not with Trypanosoma brucei gambiense aimed to detect differentially expressed genes (DEGs) associated with infection. Specifically, we selected candidate genes governing tsetse fly vector competence that could be used in the context of an anti-vector strategy, to control human and/or animal trypanosomiasis. The present study aimed to verify whether gene expression in field tsetse flies (G. p. palpalis) is modified in response to natural infection by trypanosomes (T. congolense), as reported when insectary-raised flies (G. p. gambiensis) are experimentally infected with T. b. gambiense. This was achieved using the RNA-seq approach, which identified 524 DEGs in infected vs. non-infected tsetse flies, including 285 downregulated genes and 239 upregulated genes (identified using DESeq2). Several of these genes were highly differentially expressed, with log2 fold change values in the vicinity of either +40 or −40. Downregulated genes were primarily involved in transcription/translation processes, whereas encoded upregulated genes governed amino acid and nucleotide biosynthesis pathways. The BioCyc metabolic pathways associated with infection also revealed that downregulated genes were mainly involved in fly immunity processes. Importantly, our study demonstrates that data on the molecular cross-talk between the host and the parasite (as well as the always present fly microbiome) recorded from an experimental biological model has a counterpart in field flies, which in turn validates the use of experimental host/parasite couples. PMID:28804485

Computational investigation of kinetics of cross-linking reactions in proteins: importance in structure prediction.

PubMed

Bandyopadhyay, Pradipta; Kuntz, Irwin D

2009-01-01

The determination of protein structure using distance constraints is a new and promising field of study. One implementation involves attaching residues of a protein using a cross-linking agent, followed by protease digestion, analysis of the resulting peptides by mass spectroscopy, and finally sequence threading to detect the protein folds. In the present work, we carry out computational modeling of the kinetics of cross-linking reactions in proteins using the master equation approach. The rate constants of the cross-linking reactions are estimated using the pKas and the solvent-accessible surface areas of the residues involved. This model is tested with fibroblast growth factor (FGF) and cytochrome C. It is consistent with the initial experimental rate data for individual lysine residues for cytochrome C. Our model captures all observed cross-links for FGF and almost 90% of the observed cross-links for cytochrome C, although it also predicts cross-links that were not observed experimentally (false positives). However, the analysis of the false positive results is complicated by the fact that experimental detection of cross-links can be difficult and may depend on specific experimental conditions such as pH, ionic strength. Receiver operator characteristic plots showed that our model does a good job in predicting the observed cross-links. Molecular dynamics simulations showed that for cytochrome C, in general, the two lysines come closer for the observed cross-links as compared to the false positive ones. For FGF, no such clear pattern exists. The kinetic model and MD simulation can be used to study proposed cross-linking protocols.

Analysis of transformations of the ultrafast electron transfer photoreaction mechanism in liquid solutions by the rate distribution approach.

PubMed

Kuzmin, Michael G; Soboleva, Irina V

2014-05-01

Representation of the experimental reaction kinetics in the form of rate distribution is shown to be an effective method for the analysis of the mechanisms of these reactions and for comparisons of the kinetics with QC calculations, as well as with the experimental data on the medium mobility. The rate constant distribution function P(k) can be obtained directly from the experimental kinetics N(t) by an inverse Laplace transform. The application of this approach to kinetic data for several excited-state electron transfer reactions reveals the transformations of their rate control factors in the time domain of 1-1000 ps. In neat electron donating solvents two components are observed. The fastest component (k > 1 ps(-1)) was found to be controlled by the fluctuations of the overall electronic coupling matrix element, involving all the reactant molecules, located inside the interior of the solvent shell, rather than for specific pairs of reactant molecules. The slower component (1 > k > 0.1 ps(-1)) is controlled by the medium reorganization (longitudinal relaxation times, τL). A substantial contribution from the non-stationary diffusion controlled reaction is observed in diluted solutions ([Q] < 1 M). No contribution from the long-distance electron transfer (electron tunneling) proposed earlier for the excited-state electron transfer between perylene and tetracyanoethylene in acetonitrile is observed. The rate distribution approach provides a simple and efficient method for the quantitative analysis of the reaction mechanism and transformation of the rate control factors in the course of the reactions.

Mechanism of thermal decomposition of K2FeO4 and BaFeO4: A review

NASA Astrophysics Data System (ADS)

Sharma, Virender K.; Machala, Libor

2016-12-01

This paper presents thermal decomposition of potassium ferrate(VI) (K2FeO4) and barium ferrate(VI) (BaFeO4) in air and nitrogen atmosphere. Mössbauer spectroscopy and nuclear forward scattering (NFS) synchrotron radiation approaches are reviewed to advance understanding of electron-transfer processes involved in reduction of ferrate(VI) to Fe(III) phases. Direct evidences of Fe V and Fe IV as intermediate iron species using the applied techniques are given. Thermal decomposition of K2FeO4 involved Fe V, Fe IV, and K3FeO3 as intermediate species while BaFeO3 (i.e. Fe IV) was the only intermediate species during the decomposition of BaFeO4. Nature of ferrite species, formed as final Fe(III) species, of thermal decomposition of K2FeO4 and BaFeO4 under different conditions are evaluated. Steps of the mechanisms of thermal decomposition of ferrate(VI), which reasonably explained experimental observations of applied approaches in conjunction with thermal and surface techniques, are summarized.

Applications of Automation Methods for Nonlinear Fracture Test Analysis

NASA Technical Reports Server (NTRS)

Allen, Phillip A.; Wells, Douglas N.

2013-01-01

As fracture mechanics material testing evolves, the governing test standards continue to be refined to better reflect the latest understanding of the physics of the fracture processes involved. The traditional format of ASTM fracture testing standards, utilizing equations expressed directly in the text of the standard to assess the experimental result, is self-limiting in the complexity that can be reasonably captured. The use of automated analysis techniques to draw upon a rich, detailed solution database for assessing fracture mechanics tests provides a foundation for a new approach to testing standards that enables routine users to obtain highly reliable assessments of tests involving complex, non-linear fracture behavior. Herein, the case for automating the analysis of tests of surface cracks in tension in the elastic-plastic regime is utilized as an example of how such a database can be generated and implemented for use in the ASTM standards framework. The presented approach forms a bridge between the equation-based fracture testing standards of today and the next generation of standards solving complex problems through analysis automation.

2n-emission from {sup 205}Pb* nucleus using clusterization approach at E{sub beam}∼14-20 MeV

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

Kaur, Amandeep, E-mail: adeepkaur89@gmail.com; Sandhu, Kiran; Sharma, Manoj Kumar, E-mail: msharma@thapar.edu

2016-05-06

The dynamics involved in n-induced reaction with {sup 204}Pb target is analyzed and the decay of the composite system {sup 205}Pb* is governed within the collective clusterization approach of the Dynamical Cluster-decay Model (DCM). The experimental data for 2n-evaporation channel is available for neutron energy range of 14-20 MeV and is addressed by optimizing the only parameter of the model, the neck-length parameter (ΔR). The calculations are done by taking the quadrupole (β{sub 2}) deformations of the decaying fragments and the calculated 2n-emission cross-sections find nice agreement with available data. An effort is made to study the role of levelmore » density parameter in the decay of hot-rotating nucleus, and the mass dependence in level density parameter is exercised for the first time in DCM based calculations. It is to be noted that the effect of deformation, temperature and angular momentum etc. is studied to extract better description of the dynamics involved.« less

How similar are nut-cracking and stone-flaking? A functional approach to percussive technology

PubMed Central

Bril, Blandine; Parry, Ross; Dietrich, Gilles

2015-01-01

Various authors have suggested similarities between tool use in early hominins and chimpanzees. This has been particularly evident in studies of nut-cracking which is considered to be the most complex skill exhibited by wild apes, and has also been interpreted as a precursor of more complex stone-flaking abilities. It has been argued that there is no major qualitative difference between what the chimpanzee does when he cracks a nut and what early hominins did when they detached a flake from a core. In this paper, similarities and differences between skills involved in stone-flaking and nut-cracking are explored through an experimental protocol with human subjects performing both tasks. We suggest that a ‘functional’ approach to percussive action, based on the distinction between functional parameters that characterize each task and parameters that characterize the agent's actions and movements, is a fruitful method for understanding those constraints which need to be mastered to perform each task successfully, and subsequently, the nature of skill involved in both tasks. PMID:26483533

High-Throughput Experimental Approach Capabilities | Materials Science |

Science.gov Websites

NREL High-Throughput Experimental Approach Capabilities High-Throughput Experimental Approach by yellow and is for materials in the upper right sector. NREL's high-throughput experimental ,Te) and oxysulfide sputtering Combi-5: Nitrides and oxynitride sputtering We also have several non

A framework for self-experimentation in personalized health.

PubMed

Karkar, Ravi; Zia, Jasmine; Vilardaga, Roger; Mishra, Sonali R; Fogarty, James; Munson, Sean A; Kientz, Julie A

2016-05-01

To describe an interdisciplinary and methodological framework for applying single case study designs to self-experimentation in personalized health. The authors examine the framework's applicability to various health conditions and present an initial case study with irritable bowel syndrome (IBS). An in-depth literature review was performed to develop the framework and to identify absolute and desired health condition requirements for the application of this framework. The authors developed mobile application prototypes, storyboards, and process flows of the framework using IBS as the case study. The authors conducted three focus groups and an online survey using a human-centered design approach for assessing the framework's feasibility. All 6 focus group participants had a positive view about our framework and volunteered to participate in future studies. Most stated they would trust the results because it was their own data being analyzed. They were most concerned about confounds, nonmeaningful measures, and erroneous assumptions on the timing of trigger effects. Survey respondents (N = 60) were more likely to be adherent to an 8- vs 12-day study length even if it meant lower confidence results. Implementation of the self-experimentation framework in a mobile application appears to be feasible for people with IBS. This framework can likely be applied to other health conditions. Considerations include the learning curve for teaching self-experimentation to non-experts and the challenges involved in operationalizing and customizing study designs. Using mobile technology to guide people through self-experimentation to investigate health questions is a feasible and promising approach to advancing personalized health. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Collected notes from the Benchmarks and Metrics Workshop

NASA Technical Reports Server (NTRS)

Drummond, Mark E.; Kaelbling, Leslie P.; Rosenschein, Stanley J.

1991-01-01

In recent years there has been a proliferation of proposals in the artificial intelligence (AI) literature for integrated agent architectures. Each architecture offers an approach to the general problem of constructing an integrated agent. Unfortunately, the ways in which one architecture might be considered better than another are not always clear. There has been a growing realization that many of the positive and negative aspects of an architecture become apparent only when experimental evaluation is performed and that to progress as a discipline, we must develop rigorous experimental methods. In addition to the intrinsic intellectual interest of experimentation, rigorous performance evaluation of systems is also a crucial practical concern to our research sponsors. DARPA, NASA, and AFOSR (among others) are actively searching for better ways of experimentally evaluating alternative approaches to building intelligent agents. One tool for experimental evaluation involves testing systems on benchmark tasks in order to assess their relative performance. As part of a joint DARPA and NASA funded project, NASA-Ames and Teleos Research are carrying out a research effort to establish a set of benchmark tasks and evaluation metrics by which the performance of agent architectures may be determined. As part of this project, we held a workshop on Benchmarks and Metrics at the NASA Ames Research Center on June 25, 1990. The objective of the workshop was to foster early discussion on this important topic. We did not achieve a consensus, nor did we expect to. Collected here is some of the information that was exchanged at the workshop. Given here is an outline of the workshop, a list of the participants, notes taken on the white-board during open discussions, position papers/notes from some participants, and copies of slides used in the presentations.

Integration of Genome-Scale Modeling and Transcript Profiling Reveals Metabolic Pathways Underlying Light and Temperature Acclimation in Arabidopsis[C][W

PubMed Central

Töpfer, Nadine; Caldana, Camila; Grimbs, Sergio; Willmitzer, Lothar; Fernie, Alisdair R.; Nikoloski, Zoran

2013-01-01

Understanding metabolic acclimation of plants to challenging environmental conditions is essential for dissecting the role of metabolic pathways in growth and survival. As stresses involve simultaneous physiological alterations across all levels of cellular organization, a comprehensive characterization of the role of metabolic pathways in acclimation necessitates integration of genome-scale models with high-throughput data. Here, we present an integrative optimization-based approach, which, by coupling a plant metabolic network model and transcriptomics data, can predict the metabolic pathways affected in a single, carefully controlled experiment. Moreover, we propose three optimization-based indices that characterize different aspects of metabolic pathway behavior in the context of the entire metabolic network. We demonstrate that the proposed approach and indices facilitate quantitative comparisons and characterization of the plant metabolic response under eight different light and/or temperature conditions. The predictions of the metabolic functions involved in metabolic acclimation of Arabidopsis thaliana to the changing conditions are in line with experimental evidence and result in a hypothesis about the role of homocysteine-to-Cys interconversion and Asn biosynthesis. The approach can also be used to reveal the role of particular metabolic pathways in other scenarios, while taking into consideration the entirety of characterized plant metabolism. PMID:23613196

Limitations in electrophysiological model development and validation caused by differences between simulations and experimental protocols.

PubMed

Carro, Jesús; Rodríguez-Matas, José F; Monasterio, Violeta; Pueyo, Esther

2017-10-01

Models of ion channel dynamics are usually built by fitting isolated cell experimental values of individual parameters while neglecting the interaction between them. Another shortcoming regards the estimation of ionic current conductances, which is often based on quantification of Action Potential (AP)-derived markers. Although this procedure reduces the uncertainty in the calculation of conductances, many studies evaluate electrophysiological AP-derived markers from single cell simulations, whereas experimental measurements are obtained from tissue preparations. In this work, we explore the limitations of these approaches to estimate ion channel dynamics and maximum current conductances and how they could be overcome by using multiscale simulations of experimental protocols. Four human ventricular cell models, namely ten Tusscher and Panfilov (2006), Grandi et al. (2010), O'Hara et al. (2011), and Carro et al. (2011), were used. Two problems involving scales from ion channels to tissue were investigated: 1) characterization of L-type calcium voltage-dependent inactivation I Ca,L ; 2) identification of major ionic conductance contributors to steady-state AP markers, including APD 90 , APD 75 , APD 50 , APD 25 , Triangulation and maximal and minimal values of V and dV/dt during the AP (V max , V min , dV/dt max , dV/dt min ). Our results show that: 1) I Ca,L inactivation characteristics differed significantly when calculated from model equations and from simulations reproducing the experimental protocols. 2) Large differences were found in the ionic currents contributors to APD 25 , Triangulation, V max , dV/dt max and dV/dt min between single cells and 1D-tissue. When proposing any new model formulation, or evaluating an existing model, consistency between simulated and experimental data should be verified considering all involved effects and scales. Copyright © 2016 Elsevier Ltd. All rights reserved.

Remote Internet access to advanced analytical facilities: a new approach with Web-based services.

PubMed

Sherry, N; Qin, J; Fuller, M Suominen; Xie, Y; Mola, O; Bauer, M; McIntyre, N S; Maxwell, D; Liu, D; Matias, E; Armstrong, C

2012-09-04

Over the past decade, the increasing availability of the World Wide Web has held out the possibility that the efficiency of scientific measurements could be enhanced in cases where experiments were being conducted at distant facilities. Examples of early successes have included X-ray diffraction (XRD) experimental measurements of protein crystal structures at synchrotrons and access to scanning electron microscopy (SEM) and NMR facilities by users from institutions that do not possess such advanced capabilities. Experimental control, visual contact, and receipt of results has used some form of X forwarding and/or VNC (virtual network computing) software that transfers the screen image of a server at the experimental site to that of the users' home site. A more recent development is a web services platform called Science Studio that provides teams of scientists with secure links to experiments at one or more advanced research facilities. The software provides a widely distributed team with a set of controls and screens to operate, observe, and record essential parts of the experiment. As well, Science Studio provides high speed network access to computing resources to process the large data sets that are often involved in complex experiments. The simple web browser and the rapid transfer of experimental data to a processing site allow efficient use of the facility and assist decision making during the acquisition of the experimental results. The software provides users with a comprehensive overview and record of all parts of the experimental process. A prototype network is described involving X-ray beamlines at two different synchrotrons and an SEM facility. An online parallel processing facility has been developed that analyzes the data in near-real time using stream processing. Science Studio and can be expanded to include many other analytical applications, providing teams of users with rapid access to processed results along with the means for detailed discussion of their significance.

Backward Dependencies and in-Situ wh-Questions as Test Cases on How to Approach Experimental Linguistics Research That Pursues Theoretical Linguistics Questions

PubMed Central

Pablos, Leticia; Doetjes, Jenny; Cheng, Lisa L.-S.

2018-01-01

The empirical study of language is a young field in contemporary linguistics. This being the case, and following a natural development process, the field is currently at a stage where different research methods and experimental approaches are being put into question in terms of their validity. Without pretending to provide an answer with respect to the best way to conduct linguistics related experimental research, in this article we aim at examining the process that researchers follow in the design and implementation of experimental linguistics research with a goal to validate specific theoretical linguistic analyses. First, we discuss the general challenges that experimental work faces in finding a compromise between addressing theoretically relevant questions and being able to implement these questions in a specific controlled experimental paradigm. We discuss the Granularity Mismatch Problem (Poeppel and Embick, 2005) which addresses the challenges that research that is trying to bridge the representations and computations of language and their psycholinguistic/neurolinguistic evidence faces, and the basic assumptions that interdisciplinary research needs to consider due to the different conceptual granularity of the objects under study. To illustrate the practical implications of the points addressed, we compare two approaches to perform linguistic experimental research by reviewing a number of our own studies strongly grounded on theoretically informed questions. First, we show how linguistic phenomena similar at a conceptual level can be tested within the same language using measurement of event-related potentials (ERP) by discussing results from two ERP experiments on the processing of long-distance backward dependencies that involve coreference and negative polarity items respectively in Dutch. Second, we examine how the same linguistic phenomenon can be tested in different languages using reading time measures by discussing the outcome of four self-paced reading experiments on the processing of in-situ wh-questions in Mandarin Chinese and French. Finally, we review the implications that our findings have for the specific theoretical linguistics questions that we originally aimed to address. We conclude with an overview of the general insights that can be gained from the role of structural hierarchy and grammatical constraints in processing and the existing limitations on the generalization of results. PMID:29375417

Backward Dependencies and in-Situ wh-Questions as Test Cases on How to Approach Experimental Linguistics Research That Pursues Theoretical Linguistics Questions.

PubMed

Pablos, Leticia; Doetjes, Jenny; Cheng, Lisa L-S

2017-01-01

The empirical study of language is a young field in contemporary linguistics. This being the case, and following a natural development process, the field is currently at a stage where different research methods and experimental approaches are being put into question in terms of their validity. Without pretending to provide an answer with respect to the best way to conduct linguistics related experimental research, in this article we aim at examining the process that researchers follow in the design and implementation of experimental linguistics research with a goal to validate specific theoretical linguistic analyses. First, we discuss the general challenges that experimental work faces in finding a compromise between addressing theoretically relevant questions and being able to implement these questions in a specific controlled experimental paradigm. We discuss the Granularity Mismatch Problem (Poeppel and Embick, 2005) which addresses the challenges that research that is trying to bridge the representations and computations of language and their psycholinguistic/neurolinguistic evidence faces, and the basic assumptions that interdisciplinary research needs to consider due to the different conceptual granularity of the objects under study. To illustrate the practical implications of the points addressed, we compare two approaches to perform linguistic experimental research by reviewing a number of our own studies strongly grounded on theoretically informed questions. First, we show how linguistic phenomena similar at a conceptual level can be tested within the same language using measurement of event-related potentials (ERP) by discussing results from two ERP experiments on the processing of long-distance backward dependencies that involve coreference and negative polarity items respectively in Dutch. Second, we examine how the same linguistic phenomenon can be tested in different languages using reading time measures by discussing the outcome of four self-paced reading experiments on the processing of in-situ wh -questions in Mandarin Chinese and French. Finally, we review the implications that our findings have for the specific theoretical linguistics questions that we originally aimed to address. We conclude with an overview of the general insights that can be gained from the role of structural hierarchy and grammatical constraints in processing and the existing limitations on the generalization of results.

An ambient assisted living approach in designing domiciliary services combined with innovative technologies for patients with Alzheimer's disease: a case study.

PubMed

Cavallo, Filippo; Aquilano, Michela; Arvati, Marco

2015-02-01

Alzheimer's disease (AD) is one of the most disabling diseases to affect large numbers of elderly people worldwide. Because of the characteristics of this disease, patients with AD require daily assistance from service providers both in nursing homes and at home. Domiciliary assistance has been demonstrated to be cost effective and efficient in the first phase of the disease, helping to slow down the course of the illness, improve the quality of life and care, and extend independence for patients and caregivers. In this context, the aim of this work is to demonstrate the technical effectiveness and acceptability of an innovative domiciliary smart sensor system for providing domiciliary assistance to patients with AD which has been developed with an Ambient Assisted Living (AAL) approach. The design, development, testing, and evaluation of the innovative technological solution were performed by a multidisciplinary team. In all, 15 sociomedical operators and 14 patients with AD were directly involved in defining the end-users' needs and requirements, identifying design principles with acceptability and usability features and evaluating the technological solutions before and after the real experimentation. A modular technological system was produced to help caregivers continuously monitor the health status, safety, and daily activities of patients with AD. During the experimentation, the acceptability, utility, usability, and efficacy of this system were evaluated as quite positive. The experience described in this article demonstrated that AAL technologies are feasible and effective nowadays and can be actively used in assisting patients with AD in their homes. The extensive involvement of caregivers in the experimentation allowed to assess that there is, through the use of the technological system, a proven improvement in care performance and efficiency of care provision by both formal and informal caregivers and consequently an increase in the quality of life of patients, their relatives, and their caregivers. © The Author(s) 2014.

A review of covariate selection for non-experimental comparative effectiveness research.

PubMed

Sauer, Brian C; Brookhart, M Alan; Roy, Jason; VanderWeele, Tyler

2013-11-01

This paper addresses strategies for selecting variables for adjustment in non-experimental comparative effectiveness research and uses causal graphs to illustrate the causal network that relates treatment to outcome. Variables in the causal network take on multiple structural forms. Adjustment for a common cause pathway between treatment and outcome can remove confounding, whereas adjustment for other structural types may increase bias. For this reason, variable selection would ideally be based on an understanding of the causal network; however, the true causal network is rarely known. Therefore, we describe more practical variable selection approaches based on background knowledge when the causal structure is only partially known. These approaches include adjustment for all observed pretreatment variables thought to have some connection to the outcome, all known risk factors for the outcome, and all direct causes of the treatment or the outcome. Empirical approaches, such as forward and backward selection and automatic high-dimensional proxy adjustment, are also discussed. As there is a continuum between knowing and not knowing the causal, structural relations of variables, we recommend addressing variable selection in a practical way that involves a combination of background knowledge and empirical selection and that uses high-dimensional approaches. This empirical approach can be used to select from a set of a priori variables based on the researcher's knowledge to be included in the final analysis or to identify additional variables for consideration. This more limited use of empirically derived variables may reduce confounding while simultaneously reducing the risk of including variables that may increase bias. Copyright © 2013 John Wiley & Sons, Ltd.

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

PubMed Central

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

2014-01-01

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

Redox reaction characteristics of riboflavin: a fluorescence spectroelectrochemical analysis and density functional theory calculation.

PubMed

Chen, Wei; Chen, Jie-Jie; Lu, Rui; Qian, Chen; Li, Wen-Wei; Yu, Han-Qing

2014-08-01

Riboflavin (RF), the primary redox active component of flavin, is involved in many redox processes in biogeochemical systems. Despite of its wide distribution and important roles in environmental remediation, its redox behaviors and reaction mechanisms in hydrophobic sites remain unclear yet. In this study, spectroelectrochemical analysis and density functional theory (DFT) calculation were integrated to explore the redox behaviors of RF in dimethyl sulfoxide (DMSO), which was used to create a hydrophobic environment. Specifically, cyclic voltafluorometry (CVF) and derivative cyclic voltafluorometry (DCVF) were employed to track the RF concentration changing profiles. It was found that the reduction contained a series of proton-coupled electron transfers dependent of potential driving force. In addition to the electron transfer-chemical reaction-electron transfer process, a disproportionation (DISP1) process was also identified to be involved in the reduction. The redox potential and free energy of each step obtained from the DFT calculations further confirmed the mechanisms proposed based on the experimental results. The combination of experimental and theoretical approaches yields a deep insight into the characteristics of RF in environmental remediation and better understanding about the proton-coupled electron transfer mechanisms. Copyright © 2014 Elsevier B.V. All rights reserved.

Study of Lamb Waves for Non-Destructive Testing Behind Screens

NASA Astrophysics Data System (ADS)

Kauffmann, P.; Ploix, M.-A.; Chaix, J.-F.; Gueudré, C.; Corneloup, G.; Baqué, F. AF(; )

2018-01-01

The inspection and control of sodium-cooled fast reactors (SFR) is a major issue for the nuclear industry. Ultrasonic solutions are under study because of the opacity of liquid sodium. In this paper, the use of leaky Lamb waves is considered for non-destructive testing (NDT) on parallel and immersed structures assimilated as plates. The first phase of our approach involved studying the propagation properties of leaky Lamb waves. Equations that model the propagation of Lamb waves in an immersed plate were solved numerically. The phase velocity can be experimentally measured using a two dimensional Fourier transform. The group velocity can be experimentally measured using a short-time Fourier transform technique. Attenuation of leaky Lamb waves is mostly due to the re-emission of energy into the surrounding fluid, and it can be measured by these two techniques.

Uncovering productive morphosyntax in French-learning toddlers: a multidimensional methodology perspective.

PubMed

Barrière, Isabelle; Goyet, Louise; Kresh, Sarah; Legendre, Géraldine; Nazzi, Thierry

2016-09-01

The present study applies a multidimensional methodological approach to the study of the acquisition of morphosyntax. It focuses on evaluating the degree of productivity of an infrequent subject-verb agreement pattern in the early acquisition of French and considers the explanatory role played by factors such as input frequency, semantic transparency of the agreement markers, and perceptual factors in accounting for comprehension of agreement in number (singular vs. plural) in an experimental setting. Results on a pointing task involving pseudo-verbs demonstrate significant comprehension of both singular and plural agreement in children aged 2;6. The experimental results are shown not to reflect input frequency, input marker reliability on its own, or lexically driven knowledge. We conclude that toddlers have knowledge of subject-verb agreement at age 2;6 which is abstract and productive despite its paucity in the input.

Experimental evidence for excess entropy discontinuities in glass-forming solutions.

PubMed

Lienhard, Daniel M; Zobrist, Bernhard; Zuend, Andreas; Krieger, Ulrich K; Peter, Thomas

2012-02-21

Glass transition temperatures T(g) are investigated in aqueous binary and multi-component solutions consisting of citric acid, calcium nitrate (Ca(NO(3))(2)), malonic acid, raffinose, and ammonium bisulfate (NH(4)HSO(4)) using a differential scanning calorimeter. Based on measured glass transition temperatures of binary aqueous mixtures and fitted binary coefficients, the T(g) of multi-component systems can be predicted using mixing rules. However, the experimentally observed T(g) in multi-component solutions show considerable deviations from two theoretical approaches considered. The deviations from these predictions are explained in terms of the molar excess mixing entropy difference between the supercooled liquid and glassy state at T(g). The multi-component mixtures involve contributions to these excess mixing entropies that the mixing rules do not take into account. © 2012 American Institute of Physics

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

Pirojsirikul, Teerapong; Götz, Andreas W.; Weare, John

Green Fluorescent Protein (GFP) is a widely used fluorescent biomarker for the study of biological systems. Our investigation is focused on providing a reliable theoretical description of the GFP chromophore, the photochemical properties of which can be influenced through both the surrounding protein environment and pH levels. In this work we are specifically addressing the effect of an aqueous solvation environment , where a number of experimental measurements have been performed. Our approach is based on a combined quantum mechanics molecular mechanics (QM/MM) methodology, which incorporates high level coupled cluster theory for the analysis of excited states. It also presentsmore » the first application of the newly developed NWChem/AMBER QM/MM interface. Using a systematic approach, which involves comparison of gas phase and aqueous results for different protonation states and conformations, we have resolved existing uncertainties regarding theoretical interpretation of the experimental data. We observe that the impact of aqueous environment on charged states generally results in blue shifts, but the magnitude of the effect is sensitive to charge state and conformation and can be rationalized based on charge movement into the area of higher/lower external electrostatic potentials. At neutral pH levels the experimentally observed absorption signal is most likely coming from the phenol protonated form. Our results also show that the high level coupled description is essential for proper description of excited states of GFP.« less

Statics and dynamics of DNA knotting

NASA Astrophysics Data System (ADS)

Orlandini, Enzo

2018-02-01

Knots and entanglement in polymers and biopolymers such as DNA and proteins constitute a timely topic that spans various scientific disciplines ranging from physics to chemistry, biology and mathematics. Although in the past many advancements have been made in understanding the equilibrium knotting probability and knot complexity of long polymer chains in solutions, many questions have been addressed in recent years by both experimental and theoretical means—for instance, how the knotting probability depends on the quality of the solvent, the elastic properties of the molecule and its degree of confinement. How knots form, evolve and eventually disappear in a fluctuating chain. Are the equilibrium and non-equilibrium properties of knotted molecules affected by the knot swelling/shrinking dynamics? Moreover, thanks to the great advance in nanotechnology and micromanipulation techniques, nowadays knots can be ‘manually’ tied in a single DNA molecule, followed during their motion along the chains, forced to pass through nanopores, or stretched by external forces or elongational flows. All these experimental approaches allow access to new information on the interplay of topology and polymer physics, and this has opened new perspectives in the field. Here, we provide an overview of the current knowledge of this topic, stressing the main results obtained, including the recent developments in experimental and computational approaches. Since almost all experiments on knotting involve DNA, the review will be mainly focused on the topological properties of this fascinating and biologically relevant molecule.

Estimating loop length from CryoEM images at medium resolutions.

PubMed

McKnight, Andrew; Si, Dong; Al Nasr, Kamal; Chernikov, Andrey; Chrisochoides, Nikos; He, Jing

2013-01-01

De novo protein modeling approaches utilize 3-dimensional (3D) images derived from electron cryomicroscopy (CryoEM) experiments. The skeleton connecting two secondary structures such as α-helices represent the loop in the 3D image. The accuracy of the skeleton and of the detected secondary structures are critical in De novo modeling. It is important to measure the length along the skeleton accurately since the length can be used as a constraint in modeling the protein. We have developed a novel computational geometric approach to derive a simplified curve in order to estimate the loop length along the skeleton. The method was tested using fifty simulated density images of helix-loop-helix segments of atomic structures and eighteen experimentally derived density data from Electron Microscopy Data Bank (EMDB). The test using simulated density maps shows that it is possible to estimate within 0.5 Å of the expected length for 48 of the 50 cases. The experiments, involving eighteen experimentally derived CryoEM images, show that twelve cases have error within 2 Å. The tests using both simulated and experimentally derived images show that it is possible for our proposed method to estimate the loop length along the skeleton if the secondary structure elements, such as α-helices, can be detected accurately, and there is a continuous skeleton linking the α-helices.

16 CFR § 1702.10 - Human experimental data involving the testing of human subjects.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 16 Commercial Practices 2 2013-01-01 2013-01-01 false Human experimental data involving the testing of human subjects. § 1702.10 Section § 1702.10 Commercial Practices CONSUMER PRODUCT SAFETY... PREVENTION PACKAGING ACT REQUIREMENTS; PETITION PROCEDURES AND REQUIREMENTS § 1702.10 Human experimental data...

Head Motion Modeling for Human Behavior Analysis in Dyadic Interaction

PubMed Central

Xiao, Bo; Georgiou, Panayiotis; Baucom, Brian; Narayanan, Shrikanth S.

2015-01-01

This paper presents a computational study of head motion in human interaction, notably of its role in conveying interlocutors’ behavioral characteristics. Head motion is physically complex and carries rich information; current modeling approaches based on visual signals, however, are still limited in their ability to adequately capture these important properties. Guided by the methodology of kinesics, we propose a data driven approach to identify typical head motion patterns. The approach follows the steps of first segmenting motion events, then parametrically representing the motion by linear predictive features, and finally generalizing the motion types using Gaussian mixture models. The proposed approach is experimentally validated using video recordings of communication sessions from real couples involved in a couples therapy study. In particular we use the head motion model to classify binarized expert judgments of the interactants’ specific behavioral characteristics where entrainment in head motion is hypothesized to play a role: Acceptance, Blame, Positive, and Negative behavior. We achieve accuracies in the range of 60% to 70% for the various experimental settings and conditions. In addition, we describe a measure of motion similarity between the interaction partners based on the proposed model. We show that the relative change of head motion similarity during the interaction significantly correlates with the expert judgments of the interactants’ behavioral characteristics. These findings demonstrate the effectiveness of the proposed head motion model, and underscore the promise of analyzing human behavioral characteristics through signal processing methods. PMID:26557047

Experiment Design for Nonparametric Models Based On Minimizing Bayes Risk: Application to Voriconazole1

PubMed Central

Bayard, David S.; Neely, Michael

2016-01-01

An experimental design approach is presented for individualized therapy in the special case where the prior information is specified by a nonparametric (NP) population model. Here, a nonparametric model refers to a discrete probability model characterized by a finite set of support points and their associated weights. An important question arises as to how to best design experiments for this type of model. Many experimental design methods are based on Fisher Information or other approaches originally developed for parametric models. While such approaches have been used with some success across various applications, it is interesting to note that they largely fail to address the fundamentally discrete nature of the nonparametric model. Specifically, the problem of identifying an individual from a nonparametric prior is more naturally treated as a problem of classification, i.e., to find a support point that best matches the patient’s behavior. This paper studies the discrete nature of the NP experiment design problem from a classification point of view. Several new insights are provided including the use of Bayes Risk as an information measure, and new alternative methods for experiment design. One particular method, denoted as MMopt (Multiple-Model Optimal), will be examined in detail and shown to require minimal computation while having distinct advantages compared to existing approaches. Several simulated examples, including a case study involving oral voriconazole in children, are given to demonstrate the usefulness of MMopt in pharmacokinetics applications. PMID:27909942

Oligomerization of G protein-coupled receptors: computational methods.

PubMed

Selent, J; Kaczor, A A

2011-01-01

Recent research has unveiled the complexity of mechanisms involved in G protein-coupled receptor (GPCR) functioning in which receptor dimerization/oligomerization may play an important role. Although the first high-resolution X-ray structure for a likely functional chemokine receptor dimer has been deposited in the Protein Data Bank, the interactions and mechanisms of dimer formation are not yet fully understood. In this respect, computational methods play a key role for predicting accurate GPCR complexes. This review outlines computational approaches focusing on sequence- and structure-based methodologies as well as discusses their advantages and limitations. Sequence-based approaches that search for possible protein-protein interfaces in GPCR complexes have been applied with success in several studies, but did not yield always consistent results. Structure-based methodologies are a potent complement to sequence-based approaches. For instance, protein-protein docking is a valuable method especially when guided by experimental constraints. Some disadvantages like limited receptor flexibility and non-consideration of the membrane environment have to be taken into account. Molecular dynamics simulation can overcome these drawbacks giving a detailed description of conformational changes in a native-like membrane. Successful prediction of GPCR complexes using computational approaches combined with experimental efforts may help to understand the role of dimeric/oligomeric GPCR complexes for fine-tuning receptor signaling. Moreover, since such GPCR complexes have attracted interest as potential drug target for diverse diseases, unveiling molecular determinants of dimerization/oligomerization can provide important implications for drug discovery.

Experiment design for nonparametric models based on minimizing Bayes Risk: application to voriconazole¹.

PubMed

Bayard, David S; Neely, Michael

2017-04-01

An experimental design approach is presented for individualized therapy in the special case where the prior information is specified by a nonparametric (NP) population model. Here, a NP model refers to a discrete probability model characterized by a finite set of support points and their associated weights. An important question arises as to how to best design experiments for this type of model. Many experimental design methods are based on Fisher information or other approaches originally developed for parametric models. While such approaches have been used with some success across various applications, it is interesting to note that they largely fail to address the fundamentally discrete nature of the NP model. Specifically, the problem of identifying an individual from a NP prior is more naturally treated as a problem of classification, i.e., to find a support point that best matches the patient's behavior. This paper studies the discrete nature of the NP experiment design problem from a classification point of view. Several new insights are provided including the use of Bayes Risk as an information measure, and new alternative methods for experiment design. One particular method, denoted as MMopt (multiple-model optimal), will be examined in detail and shown to require minimal computation while having distinct advantages compared to existing approaches. Several simulated examples, including a case study involving oral voriconazole in children, are given to demonstrate the usefulness of MMopt in pharmacokinetics applications.

A survey of existing and proposed classical and quantum approaches to the photon mass

NASA Astrophysics Data System (ADS)

Spavieri, G.; Quintero, J.; Gillies, G. T.; Rodríguez, M.

2011-02-01

Over the past twenty years, there have been several careful experimental, observational and phenomenological investigations aimed at searching for and establishing ever tighter bounds on the possible mass of the photon. There are many fascinating and paradoxical physical implications that would arise from the presence of even a very small value for it, and thus such searches have always been well motivated in terms of the new physics that would result. We provide a brief overview of the theoretical background and classical motivations for this work and the early tests of the exactness of Coulomb's law that underlie it. We then go on to address the modern situation, in which quantum physics approaches come to attention. Among them we focus especially on the implications that the Aharonov-Bohm and Aharonov-Casher class of effects have on searches for a photon mass. These arise in several different ways and can lead to experiments that might involve the interaction of magnetic dipoles, electric dipoles, or charged particles with suitable potentials. Still other quantum-based approaches employ measurements of the g-factor of the electron. Plausible target sensitivities for limits on the photon mass as sought by the various quantum approaches are in the range of 10-53 to 10-54 g. Possible experimental arrangements for the associated experiments are discussed. We close with an assessment of the state of the art and a prognosis for future work.

Interdisciplinary research and education at the biology-engineering-computer science interface: a perspective.

PubMed

Tadmor, Brigitta; Tidor, Bruce

2005-09-01

Progress in the life sciences, including genome sequencing and high-throughput experimentation, offers an opportunity for understanding biology and medicine from a systems perspective. This 'new view', which complements the more traditional component-based approach, involves the integration of biological research with approaches from engineering disciplines and computer science. The result is more than a new set of technologies. Rather, it promises a fundamental reconceptualization of the life sciences based on the development of quantitative and predictive models to describe crucial processes. To achieve this change, learning communities are being formed at the interface of the life sciences, engineering and computer science. Through these communities, research and education will be integrated across disciplines and the challenges associated with multidisciplinary team-based science will be addressed.

Analysis of the interaction of a weak normal shock wave with a turbulent boundary layer

NASA Technical Reports Server (NTRS)

Melnik, R. E.; Grossman, B.

1974-01-01

The method of matched asymptotic expansions is used to analyze the interaction of a normal shock wave with an unseparated turbulent boundary layer on a flat surface at transonic speeds. The theory leads to a three-layer description of the interaction in the double limit of Reynolds number approaching infinity and Mach number approaching unity. The interaction involves an outer, inviscid rotational layer, a constant shear-stress wall layer, and a blending region between them. The pressure distribution is obtained from a numerical solution of the outer-layer equations by a mixed-flow relaxation procedure. An analytic solution for the skin friction is determined from the inner-layer equations. The significance of the mathematical model is discussed with reference to existing experimental data.

Reconstructing biochemical pathways from time course data.

PubMed

Srividhya, Jeyaraman; Crampin, Edmund J; McSharry, Patrick E; Schnell, Santiago

2007-03-01

Time series data on biochemical reactions reveal transient behavior, away from chemical equilibrium, and contain information on the dynamic interactions among reacting components. However, this information can be difficult to extract using conventional analysis techniques. We present a new method to infer biochemical pathway mechanisms from time course data using a global nonlinear modeling technique to identify the elementary reaction steps which constitute the pathway. The method involves the generation of a complete dictionary of polynomial basis functions based on the law of mass action. Using these basis functions, there are two approaches to model construction, namely the general to specific and the specific to general approach. We demonstrate that our new methodology reconstructs the chemical reaction steps and connectivity of the glycolytic pathway of Lactococcus lactis from time course experimental data.

Teaching renewable energy using online PBL in investigating its effect on behaviour towards energy conservation among Malaysian students: ANOVA repeated measures approach

NASA Astrophysics Data System (ADS)

Nordin, Norfarah; Samsudin, Mohd Ali; Hadi Harun, Abdul

2017-01-01

This research aimed to investigate whether online problem based learning (PBL) approach to teach renewable energy topic improves students’ behaviour towards energy conservation. A renewable energy online problem based learning (REePBaL) instruction package was developed based on the theory of constructivism and adaptation of the online learning model. This study employed a single group quasi-experimental design to ascertain the changed in students’ behaviour towards energy conservation after underwent the intervention. The study involved 48 secondary school students in a Malaysian public school. ANOVA Repeated Measure technique was employed in order to compare scores of students’ behaviour towards energy conservation before and after the intervention. Based on the finding, students’ behaviour towards energy conservation improved after the intervention.

Quantal diffusion description of multinucleon transfers in heavy-ion collisions

NASA Astrophysics Data System (ADS)

Ayik, S.; Yilmaz, B.; Yilmaz, O.; Umar, A. S.

2018-05-01

Employing the stochastic mean-field (SMF) approach, we develop a quantal diffusion description of the multi-nucleon transfer in heavy-ion collisions at finite impact parameters. The quantal transport coefficients are determined by the occupied single-particle wave functions of the time-dependent Hartree-Fock equations. As a result, the primary fragment mass and charge distribution functions are determined entirely in terms of the mean-field properties. This powerful description does not involve any adjustable parameter, includes the effects of shell structure, and is consistent with the fluctuation-dissipation theorem of the nonequilibrium statistical mechanics. As a first application of the approach, we analyze the fragment mass distribution in 48Ca+ 238U collisions at the center-of-mass energy Ec.m.=193 MeV and compare the calculations with the experimental data.

Computational Intelligence Techniques for Tactile Sensing Systems

PubMed Central

Gastaldo, Paolo; Pinna, Luigi; Seminara, Lucia; Valle, Maurizio; Zunino, Rodolfo

2014-01-01

Tactile sensing helps robots interact with humans and objects effectively in real environments. Piezoelectric polymer sensors provide the functional building blocks of the robotic electronic skin, mainly thanks to their flexibility and suitability for detecting dynamic contact events and for recognizing the touch modality. The paper focuses on the ability of tactile sensing systems to support the challenging recognition of certain qualities/modalities of touch. The research applies novel computational intelligence techniques and a tensor-based approach for the classification of touch modalities; its main results consist in providing a procedure to enhance system generalization ability and architecture for multi-class recognition applications. An experimental campaign involving 70 participants using three different modalities in touching the upper surface of the sensor array was conducted, and confirmed the validity of the approach. PMID:24949646

Master-equation approach to the study of phase-change processes in data storage media

NASA Astrophysics Data System (ADS)

Blyuss, K. B.; Ashwin, P.; Bassom, A. P.; Wright, C. D.

2005-07-01

We study the dynamics of crystallization in phase-change materials using a master-equation approach in which the state of the crystallizing material is described by a cluster size distribution function. A model is developed using the thermodynamics of the processes involved and representing the clusters of size two and greater as a continuum but clusters of size one (monomers) as a separate equation. We present some partial analytical results for the isothermal case and for large cluster sizes, but principally we use numerical simulations to investigate the model. We obtain results that are in good agreement with experimental data and the model appears to be useful for the fast simulation of reading and writing processes in phase-change optical and electrical memories.

Computational intelligence techniques for tactile sensing systems.

PubMed

Gastaldo, Paolo; Pinna, Luigi; Seminara, Lucia; Valle, Maurizio; Zunino, Rodolfo

2014-06-19

Tactile sensing helps robots interact with humans and objects effectively in real environments. Piezoelectric polymer sensors provide the functional building blocks of the robotic electronic skin, mainly thanks to their flexibility and suitability for detecting dynamic contact events and for recognizing the touch modality. The paper focuses on the ability of tactile sensing systems to support the challenging recognition of certain qualities/modalities of touch. The research applies novel computational intelligence techniques and a tensor-based approach for the classification of touch modalities; its main results consist in providing a procedure to enhance system generalization ability and architecture for multi-class recognition applications. An experimental campaign involving 70 participants using three different modalities in touching the upper surface of the sensor array was conducted, and confirmed the validity of the approach.

Facebook study: a little bit unethical but worth it?

PubMed

Kleinsman, John; Buckley, Sue

2015-06-01

Human research involving the use social media raises many of the same issues as medical research. The publication of a paper in June 2014 investigating "emotional contagion" received extensive publicity recently because of the methods used. The approach involved manipulating the "News Feeds" of Facebook users, but the participants were not informed of their involvement in the research and had no opportunity to consent or opt out. Some commentators have argued that although it would have been preferable to obtain informed consent, it was not strictly required because the research was unlikely to cause significant harm and was important. This paper argues that the research was unethical because (i) it should have been overseen by an independent ethics committee or review board and (ii) informed consent could and should have been obtained. Regardless of the importance of any research and irrespective of its likelihood to cause harm, the ethical principles that have evolved since the 1940s should be followed in all instances when experimental research is being carried out on human participants.

Dynamic Nucleation of Supercooled Melts and Measurement of the Surface Tension and Viscosity

NASA Technical Reports Server (NTRS)

Trinh, E. H.; Ohsaka, K.

1999-01-01

We investigate the phenomenon of acoustic pressure-induced nucleation by using a novel approach involving the large amplitude resonant radial oscillations and collapse of a single bubble intentionally injected into a supercooled liquid. Using a combination of previously developed and proven techniques, the bubble is suspended in a fluid host by an ultrasonic field which supplies both the levitation capability as well as the forcing of the radial oscillations. We observe the effects of an increase in pressure (due to bubble collapse) in a region no larger than 100 microns within the supercooled melt to rigorously probe the hypothesis of pressure-induced nucleation of the solid phase. The use of single bubbles operating in narrow temporal and spatial scales will allow the direct and unambiguous correlation between the origin and location of the generation of the disturbance and the location and timing of the nucleation event. In a companion research effort, we are developing novel techniques for the non-contact measurements of the surface tension and viscosity of highly viscous supercooled liquids. Currently used non-invasive methods of surface tension measurement for the case of undercooled liquids generally rely of the quantitative determination of the resonance frequencies of drop shape oscillations, of the dynamics of surface capillary waves, or of the velocity of streaming flows. These methods become quickly ineffective when the liquid viscosity rises to a significant value. An alternate and accurate method which would be applicable to liquids of significant viscosity is therefore needed. We plan to develop such a capability by measuring the equilibrium shape of levitated undercooled melt droplets as they undergo solid-body rotation. The experimental measurement of the characteristic point of transition (bifurcation point) between axisymmetric and two-lobed shapes will be used to calculate the surface tension of the liquid. Such an approach has already been validated through the experimental verification of numerical modeling results. The experimental approach involves levitation, melting, and solidification of undercooled droplets using a hybrid ultrasonic-electrostatic technique in both a gaseous as well as a vacuum environment. A shape relaxation method will be investigated in order to derive a reliable method to measure the viscosity of undercooled melts. The analysis of the monotonic relaxation to equilibrium shape of a drastically deformed and super-critically damped free drop has been used to derive interfacial tension of immiscible liquid combinations where one of the component has high viscosity. A standard approach uses the initial elongation of a droplet through shear flows, but an equivalent method could involve the initial deformation of a drop levitated in a gas by ultrasonic radiation pressure, electric stresses, or even solid body rotation. The dynamic behavior of the free drop relaxing back to equilibrium shape will be modeled, and its characteristic time dependence should provide a quantitative means to evaluate the liquid viscosity.

Pre-recombination quenching of the radiation induced fluorescence as the approach to study kinetics of ion-molecular reactions

NASA Astrophysics Data System (ADS)

Borovkov, V. I.; Ivanishko, I. S.

2011-04-01

This study deals with the geminate ion recombination in the presence of bulk scavengers, that is the so-called scavenger problem, as well as with the effect of the scavenging reaction on the radiation-induced recombination fluorescence. Borovkov and Velizhanin (2004) have proposed a method to determine the rate constant of the bulk reaction between neutral scavengers and one of the geminate ions if the ion-molecular reaction prevented the formation of electronically excited states upon recombination involving a newly formed ion. If such pre-recombination quenching of the radiation-induced fluorescence took place, it manifested itself as a progressive decrease in the decay of the fluorescence intensity. The relative change in the fluorescence decay as caused by the scavengers was believed to be closely related to the kinetics of the scavenging reaction. The goal of the present study is to support this method, both computationally and experimentally because there are two factors, which cast doubt on the intuitively obvious approach to the scavenger problem: spatial correlations between the particles involved and the drift of the charged reagent in the electric field of its geminate partner. Computer simulation of geminate ions recombination with an explicit modeling of the motion trajectories of scavengers has been performed for media of low dielectric permittivity, i.e. for the maximal Coulomb interaction between the ions. The simulation has shown that upon continuous diffusion of the particles involved, the joint effect of the two above factors can be considered as insignificant with a high accuracy. Besides, it is concluded then that the method of pre-recombination quenching could be applied to study parallel and consecutive reactions where the yields of excited states in the reaction pathways are different with the use of very simple analytical relations of the formal chemical kinetics. The conclusion has been confirmed experimentally by the example of the reactions of electron transfer from the diphenylacetylene radical anion to dibromoethane and hexafluorobenzene in n-dodecane solutions.

Reactions of Ground State Nitrogen Atoms N(4S) with Astrochemically-Relevant Molecules on Interstellar Dusts

NASA Astrophysics Data System (ADS)

Krim, Lahouari; Nourry, Sendres

2015-06-01

In the last few years, ambitious programs were launched to probe the interstellar medium always more accurately. One of the major challenges of these missions remains the detection of prebiotic compounds and the understanding of reaction pathways leading to their formation. These complex heterogeneous reactions mainly occur on icy dust grains, and their studies require the coupling of laboratory experiments mimicking the extreme conditions of extreme cold and dilute media. For that purpose, we have developed an original experimental approach that combine the study of heterogeneous reactions (by exposing neutral molecules adsorbed on ice to non-energetic radicals H, OH, N...) and a neon matrix isolation study at very low temperatures, which is of paramount importance to isolate and characterize highly reactive reaction intermediates. Such experimental approach has already provided answers to many questions raised about some astrochemically-relevant reactions occurring in the ground state on the surface of dust grain ices in dense molecular clouds. The aim of this new present work is to show the implication of ground state atomic nitrogen on hydrogen atom abstraction reactions from some astrochemically-relevant species, at very low temperatures (3K-20K), without providing any external energy. Under cryogenic temperatures and with high barrier heights, such reactions involving N(4S) nitrogen atoms should not occur spontaneously and require an initiating energy. However, the detection of some radicals species as byproducts, in our solid samples left in the dark for hours at 10K, proves that hydrogen abstraction reactions involving ground state N(4S) nitrogen atoms may occur in solid phase at cryogenic temperatures. Our results show the efficiency of radical species formation stemming from non-energetic N-atoms and astrochemically-relevant molecules. We will then discuss how such reactions, involving nitrogen atoms in their ground states, might be the first key step towards complex organic molecules production in the interstellar medium.

An atmospheric pressure high-temperature laminar flow reactor for investigation of combustion and related gas phase reaction systems

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

Oßwald, Patrick; Köhler, Markus

A new high-temperature flow reactor experiment utilizing the powerful molecular beam mass spectrometry (MBMS) technique for detailed observation of gas phase kinetics in reacting flows is presented. The reactor design provides a consequent extension of the experimental portfolio of validation experiments for combustion reaction kinetics. Temperatures up to 1800 K are applicable by three individually controlled temperature zones with this atmospheric pressure flow reactor. Detailed speciation data are obtained using the sensitive MBMS technique, providing in situ access to almost all chemical species involved in the combustion process, including highly reactive species such as radicals. Strategies for quantifying the experimentalmore » data are presented alongside a careful analysis of the characterization of the experimental boundary conditions to enable precise numeric reproduction of the experimental results. The general capabilities of this new analytical tool for the investigation of reacting flows are demonstrated for a selected range of conditions, fuels, and applications. A detailed dataset for the well-known gaseous fuels, methane and ethylene, is provided and used to verify the experimental approach. Furthermore, application for liquid fuels and fuel components important for technical combustors like gas turbines and engines is demonstrated. Besides the detailed investigation of novel fuels and fuel components, the wide range of operation conditions gives access to extended combustion topics, such as super rich conditions at high temperature important for gasification processes, or the peroxy chemistry governing the low temperature oxidation regime. These demonstrations are accompanied by a first kinetic modeling approach, examining the opportunities for model validation purposes.« less

A New Two-Step Approach for Hands-On Teaching of Gene Technology: Effects on Students' Activities During Experimentation in an Outreach Gene Technology Lab

NASA Astrophysics Data System (ADS)

Scharfenberg, Franz-Josef; Bogner, Franz X.

2011-08-01

Emphasis on improving higher level biology education continues. A new two-step approach to the experimental phases within an outreach gene technology lab, derived from cognitive load theory, is presented. We compared our approach using a quasi-experimental design with the conventional one-step mode. The difference consisted of additional focused discussions combined with students writing down their ideas (step one) prior to starting any experimental procedure (step two). We monitored students' activities during the experimental phases by continuously videotaping 20 work groups within each approach ( N = 131). Subsequent classification of students' activities yielded 10 categories (with well-fitting intra- and inter-observer scores with respect to reliability). Based on the students' individual time budgets, we evaluated students' roles during experimentation from their prevalent activities (by independently using two cluster analysis methods). Independently of the approach, two common clusters emerged, which we labeled as `all-rounders' and as `passive students', and two clusters specific to each approach: `observers' as well as `high-experimenters' were identified only within the one-step approach whereas under the two-step conditions `managers' and `scribes' were identified. Potential changes in group-leadership style during experimentation are discussed, and conclusions for optimizing science teaching are drawn.

Evidence-based intervention against bullying and cyberbullying: Evaluation of the NoTrap! program in two independent trials.

PubMed

Palladino, Benedetta E; Nocentini, Annalaura; Menesini, Ersilia

2016-01-01

The NoTrap! (Noncadiamointrappola!) program is a school-based intervention, which utilizes a peer-led approach to prevent and combat both traditional bullying and cyberbullying. The aim of the present study was to evaluate the efficacy of the third Edition of the program in accordance with the recent criteria for evidence-based interventions. Towards this aim, two quasi-experimental trials involving adolescents (age M = 14.91, SD = .98) attending their first year at different high schools were conducted. In Trial 1 (control group, n = 171; experimental group, n = 451), latent growth curve models for data from pre-, middle- and post-tests showed that intervention significantly predicted change over time in all the target variables (victimization, bullying, cybervictimization, and cyberbullying). Specifically, target variables were stable for the control group but decreased significantly over time for the experimental group. Long-term effects at the follow up 6 months later were also found. In Trial 2 (control group, n = 227; experimental group, n = 234), the moderating effect of gender was examined and there was a reported decrease in bullying and cyberbullying over time (pre- and post-test) in the experimental group but not the control group, and this decrease was similar for boys and girls. © 2016 Wiley Periodicals, Inc.

Atomic oxygen recombination on quartz at high temperature: experiments and molecular dynamics simulation.

PubMed

Bedra, L; Rutigliano, M; Balat-Pichelin, M; Cacciatore, M

2006-08-15

A joint experimental and theoretical approach has been developed to study oxygen atom recombination on a beta-quartz surface. The experimental MESOX setup has been applied for the direct measurement of the atomic oxygen recombination coefficient gamma at T(S) = 1000 K. The time evolution of the relative atomic oxygen concentration in the cell is described by the diffusion equation because the mean free path of the atoms is less than the characteristic dimension of the reactor. The recombination coefficient gamma is then calculated from the concentration profile obtained by visible spectroscopy. We get an experimental value of gamma = 0.008, which is a factor of about 3 less than the gamma value reported for O recombination over beta-cristobalite. The experimental results are discussed and compared with the semiclassical collision dynamics calculations performed on the same catalytic system aimed at determining the basic features of the surface catalytic activity. Agreement, both qualitative and quantitative, between the experimental and the theoretical recombination coefficients has been found that supports the Eley-Rideal recombination mechanism and gives more evidence of the impact that surface crystallographic variation has on catalytic activity. Also, several interesting aspects concerning the energetics and the mechanism of the surface processes involving the oxygen atoms are pointed out and discussed.

Bifidobacterium breve UCC2003 metabolises the human milk oligosaccharides lacto-N-tetraose and lacto-N-neo-tetraose through overlapping, yet distinct pathways

PubMed Central

James, Kieran; Motherway, Mary O’Connell; Bottacini, Francesca; van Sinderen, Douwe

2016-01-01

In this study, we demonstrate that the prototype B. breve strain UCC2003 possesses specific metabolic pathways for the utilisation of lacto-N-tetraose (LNT) and lacto-N-neotetraose (LNnT), which represent the central moieties of Type I and Type II human milk oligosaccharides (HMOs), respectively. Using a combination of experimental approaches, the enzymatic machinery involved in the metabolism of LNT and LNnT was identified and characterised. Homologs of the key genetic loci involved in the utilisation of these HMO substrates were identified in B. breve, B. bifidum, B. longum subsp. infantis and B. longum subsp. longum using bioinformatic analyses, and were shown to be variably present among other members of the Bifidobacterium genus, with a distinct pattern of conservation among human-associated bifidobacterial species. PMID:27929046

Theoretical and experimental analysis of the reaction mechanism of MrTPS2, a triquinane-forming sesquiterpene synthase from chamomile.

PubMed

Hong, Young J; Irmisch, Sandra; Wang, Selina C; Garms, Stefan; Gershenzon, Jonathan; Zu, Liansuo; Köllner, Tobias G; Tantillo, Dean J

2013-09-27

Terpene synthases, as key enzymes of terpene biosynthesis, have garnered the attention of chemists and biologists for many years. Their carbocationic reaction mechanisms are responsible for the huge variety of terpene structures in nature. These mechanisms are amenable to study by using classical biochemical approaches as well as computational analysis, and in this study we combine quantum-chemical calculations and deuterium-labeling experiments to elucidate the reaction mechanism of a triquinane forming sesquiterpene synthase from chamomile. Our results suggest that the reaction from farnesyl diphosphate to triquinanes proceeds through caryophyllyl and presilphiperfolanyl cations and involves the protonation of a stable (-)-(E)-β-caryophyllene intermediate. A tyrosine residue was identified that appears to be involved in the proton-transfer process. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Precison Muon Physics

NASA Astrophysics Data System (ADS)

Hertzog, David

2013-04-01

The worldwide, vibrant experimental program involving precision measurements with muons will be presented. Recent achievements in this field have greatly improved our knowledge of fundamental parameters: Fermi constant (lifetime), weak-nucleon pseudoscalar coupling (μp capture), Michel decay parameters, and the proton charged radius (Lamb shift). The charged-lepton-violating decay μ->eγ sets new physics limits. Updated Standard Model theory evaluations of the muon anomalous magnetic moment has increased the significance beyond 3 σ for the deviation with respect to experiment. Next-generation experiments are mounting, with ambitious sensitivity goals for the muon-to-electron search approaching 10-17 sensitivity and for a 0.14 ppm determination of g-2. The broad physics reach of these efforts involves atomic, nuclear and particle physics communities. I will select from recent work and outline the most important efforts that are in preparation.

Dynamics of Infection and Spread of Diseases

NASA Astrophysics Data System (ADS)

Zorzenon dos Santos, Rita Maria

2003-03-01

This text summarizes a series of four lectures presented at the PASI on Modern Challenges in Statistical Mechanics. The idea was to give to the students a flavor of the biological aspects involved in the dynamics of infection and the spread of diseases, the complexity of the systems involved, and how we can improve our modeling of such systems by using different approaches in order to get closer to experimental results. In a huge universe of publications about the subject, we restrict the list of references to the ones that may be useful to the students and will lead them to other important work. Therefore, the text should not be taken as a review of the subject, but rather as an introductory text for physicists about the dynamics of infection and spread of diseases and the role of biological physics in this interdisciplinary field.

Bridging the PSI Knowledge Gap: A Multi-Scale Approach

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

Wirth, Brian D.

2015-01-08

Plasma-surface interactions (PSI) pose an immense scientific hurdle in magnetic confinement fusion and our present understanding of PSI in confinement environments is highly inadequate; indeed, a recent Fusion Energy Sciences Advisory Committee report found that 4 out of the 5 top five fusion knowledge gaps were related to PSI. The time is appropriate to develop a concentrated and synergistic science effort that would expand, exploit and integrate the wealth of laboratory ion-beam and plasma research, as well as exciting new computational tools, towards the goal of bridging the PSI knowledge gap. This effort would broadly advance plasma and material sciences,more » while providing critical knowledge towards progress in fusion PSI. This project involves the development of a Science Center focused on a new approach to PSI science; an approach that both exploits access to state-of-the-art PSI experiments and modeling, as well as confinement devices. The organizing principle is to develop synergistic experimental and modeling tools that treat the truly coupled multi-scale aspect of the PSI issues in confinement devices. This is motivated by the simple observation that while typical lab experiments and models allow independent manipulation of controlling variables, the confinement PSI environment is essentially self-determined with few outside controls. This means that processes that may be treated independently in laboratory experiments, because they involve vastly different physical and time scales, will now affect one another in the confinement environment. Also, lab experiments cannot simultaneously match all exposure conditions found in confinement devices typically forcing a linear extrapolation of lab results. At the same time programmatic limitations prevent confinement experiments alone from answering many key PSI questions. The resolution to this problem is to usefully exploit access to PSI science in lab devices, while retooling our thinking from a linear and de-coupled extrapolation to a multi-scale, coupled approach. The PSI Plasma Center consisted of three equal co-centers; one located at the MIT Plasma Science and Fusion Center, one at UC San Diego Center for Energy Research and one at the UC Berkeley Department of Nuclear Engineering, which moved to the University of Tennessee, Knoxville (UTK) with Professor Brian Wirth in July 2010. The Center had three co-directors: Prof. Dennis Whyte led the MIT co-center, the UCSD co-center was led by Dr. Russell Doerner, and Prof. Brian Wirth led the UCB/UTK center. The directors have extensive experience in PSI and material research, and have been internationally recognized in the magnetic fusion, materials and plasma research fields. The co-centers feature keystone PSI experimental and modeling facilities dedicated to PSI science: the DIONISOS/CLASS facility at MIT, the PISCES facility at UCSD, and the state-of-the-art numerical modeling capabilities at UCB/UTK. A collaborative partner in the center is Sandia National Laboratory at Livermore (SNL/CA), which has extensive capabilities with low energy ion beams and surface diagnostics, as well as supporting plasma facilities, including the Tritium Plasma Experiment, all of which significantly augment the Center. Interpretive, continuum material models are available through SNL/CA, UCSD and MIT. The participating institutions of MIT, UCSD, UCB/UTK, SNL/CA and LLNL brought a formidable array of experimental tools and personnel abilities into the PSI Plasma Center. Our work has focused on modeling activities associated with plasma surface interactions that are involved in effects of He and H plasma bombardment on tungsten surfaces. This involved performing computational material modeling of the surface evolution during plasma bombardment using molecular dynamics modeling. The principal outcomes of the research efforts within the combined experimental – modeling PSI center are to provide a knowledgebase of the mechanisms of surface degradation, and the influence of the surface on plasma conditions.« less

Can encouraging substance abuse patients to participate in self-help groups reduce demand for health care? A quasi-experimental study.

PubMed

Humphreys , K; Moos, R

2001-05-01

Twelve-step-oriented inpatient treatment programs emphasize 12-step treatment approaches and the importance of ongoing attendance at 12-step self-help groups more than do cognitive-behavioral (CB) inpatient treatment programs. This study evaluated whether this difference in therapeutic approach leads patients who are treated in 12-step programs to rely less on professionally provided services and more on self-help groups after discharge, thereby reducing long-term health care costs. A prospective, quasi-experimental comparison of 12-step-based (N = 5) and cognitive-behavioral (n = 5) inpatient treatment programs was conducted. These treatments were compared on the degree to which their patients participated in self-help groups, used outpatient and inpatient mental health services, and experienced positive outcomes (e.g., abstinence) in the year following discharge. Using a larger sample from an ongoing research project, 887 male substance-dependent patients from each type of treatment program were matched on pre-intake health care costs (N = 1774). At baseline and 1-year follow-up, patients' involvement in self-help groups (e.g., Alcoholics Anonymous), utilization and costs of mental health services, and clinical outcomes were assessed. Compared with patients treated in CB programs, patients treated in 12-step programs had significantly greater involvement in self-help groups at follow-up. In contrast, patients treated in CB programs averaged almost twice as many outpatient continuing care visits after discharge (22.5 visits) as patients treated in 12-step treatment programs (13.1 visits), and also received significantly more days of inpatient care (17.0 days in CB versus 10.5 in 12-step), resulting in 64% higher annual costs in CB programs ($4729/patient, p < 0.001). Psychiatric and substance abuse outcomes were comparable across treatments, except that 12-step patients had higher rates of abstinence at follow-up (45.7% versus 36.2% for patients from CB programs, p < 0.001). Professional treatment programs that emphasize self-help approaches increase their patients' reliance on cost-free self-help groups and thereby lower subsequent health care costs. Such programs therefore represent a cost-effective approach to promoting recovery from substance abuse.

A procedure for calibration and validation of FE modelling of laser-assisted metal to polymer direct joining

NASA Astrophysics Data System (ADS)

Lambiase, F.; Genna, S.; Kant, R.

2018-01-01

The quality of the joints produced by means of Laser-Assisted Metal to Polymer direct joining (LAMP) is strongly influenced by the temperature field produced during the laser treatment. The main phenomena including the adhesion of the plastic to the metal sheet and the development of bubbles (on the plastic surface) depend on the temperature reached by the polymer at the interface. Such a temperature should be higher than the softening temperature, but lower than the degradation temperature of the polymer. However, the temperature distribution is difficult to be measured by experimental tests since the most polymers (which are transparent to the laser radiation) are often opaque to the infrared wavelength. Thus, infrared analysis involving pyrometers and infrared camera is not suitable for this purpose. On the other hand, thermocouples are difficult to be placed at the interface without influencing the temperature conditions. In this paper, an integrated approach involving both experimental measurements and a Finite Element (FE) model were used to perform such an analysis. LAMP of Polycarbonate and AISI304 stainless steel was performed by means of high power diode laser and the main process parameters i.e. laser power and scanning speed were varied. Comparing the experimental measurements and the FE model prediction of the thermal field, a good correspondence was achieved proving the suitability of the developed model and the proposed calibration procedure to be ready used for process design and optimization.

Determination of minor and trace elements in kidney stones by x-ray fluorescence analysis

NASA Astrophysics Data System (ADS)

Srivastava, Anjali; Heisinger, Brianne J.; Sinha, Vaibhav; Lee, Hyong-Koo; Liu, Xin; Qu, Mingliang; Duan, Xinhui; Leng, Shuai; McCollough, Cynthia H.

2014-03-01

The determination of accurate material composition of a kidney stone is crucial for understanding the formation of the kidney stone as well as for preventive therapeutic strategies. Radiations probing instrumental activation analysis techniques are excellent tools for identification of involved materials present in the kidney stone. In particular, x-ray fluorescence (XRF) can be very useful for the determination of minor and trace materials in the kidney stone. The X-ray fluorescence measurements were performed at the Radiation Measurements and Spectroscopy Laboratory (RMSL) of department of nuclear engineering of Missouri University of Science and Technology and different kidney stones were acquired from the Mayo Clinic, Rochester, Minnesota. Presently, experimental studies in conjunction with analytical techniques were used to determine the exact composition of the kidney stone. A new type of experimental set-up was developed and utilized for XRF analysis of the kidney stone. The correlation of applied radiation source intensity, emission of X-ray spectrum from involving elements and absorption coefficient characteristics were analyzed. To verify the experimental results with analytical calculation, several sets of kidney stones were analyzed using XRF technique. The elements which were identified from this techniques are Silver (Ag), Arsenic (As), Bromine (Br), Chromium (Cr), Copper (Cu), Gallium (Ga), Germanium (Ge), Molybdenum (Mo), Niobium (Nb), Rubidium (Rb), Selenium (Se), Strontium (Sr), Yttrium (Y), Zirconium (Zr). This paper presents a new approach for exact detection of accurate material composition of kidney stone materials using XRF instrumental activation analysis technique.

Experimental and numerical analysis of coastal protection provided by natural ecosystems

NASA Astrophysics Data System (ADS)

Maza, M.; Lara, J. L.; Losada, I. J.; Nepf, H. M.

2016-12-01

The risk of flooding and erosion is increasing for many coastal areas owing to global and regional changes in climate conditions together with increasing exposure and vulnerability. After hurricane Katrina (2005) and Sandy (2012) and the tsunami in Indonesia (2004), coastal managers have become interested in low environmental impact alternatives, or nature-based solutions, to protect the coast. Although capacity for coastal ecosystems to damp flow energy has been widely recognized, they have not been firmly considered in the portfolio of coastal protection options. This is mainly due to the complexity of flow-vegetation interaction and of quantifying the value of coastal protection provided by these ecosystems. This complex problem involves different temporal and spatial scales and disciplines, such as engineering, ecology and economics. This work aims to make a step forward in better understanding the physics involved in flow-vegetation interaction leading to new formulations and parameterizations to address some unsolved questions in literature: the representation of plants and field properties; the influence of wave parameters on the relevant processes; the role of the combined effect of waves and currents and the effect of extreme events on vegetation elements. The three main coastal vegetated ecosystems (seagrasses, saltmarshes and mangroves) are studied with an experimental and numerical approach. Experimental analysis is carried out using mimics and real vegetation, considering different flow and vegetation parameters and characterizing flow energy attenuation for the different scenarios. Numerical simulations are performed using 2-D and 3-D Navier-Stokes models in which the effect of vegetation is implemented and validated. These models are used to extend experimental results by simulating different vegetation distributions and analyzing variables such as high-spatial-resolution free surface and velocity data and forces exerted on vegetation elements.

Design, Construction and Testing of Annular Diffusers for High Speed Civil Transportation Combustor Applications

NASA Technical Reports Server (NTRS)

Okhio, Cyril B.

1996-01-01

A theoretical and an experimental design study of subsonic flow through curved-wall annular diffusers has been initiated under this award in order to establish the most pertinent design parameters and hence performance characteristics for such devices, an the implications of their application in the design of engine components in the aerospace industries. The diffusers under this study are expected to contain appreciable regions of stall and the effects of swirl on their performance are being studied. The experimental work involves the application of Computer Aided Design software tool to the development of a suitable annular diffuse geometry and the subsequent downloading of such data to a CNC machine at Central State University (CSU). Two experimental run segments have been completed so far during FY-95 involving flow visualization and diffuser performance evaluation based on Kinetic Energy Dissipation. The method of calculation of the performance of diffusers based on pressure recovery coefficient has been shown to have some shortcomings and so the kinetic energy dissipation approach has been introduced in the run segment two with some success. The application of the discretized, full Navier Stokes and Continuity equations to the numerical study of the problem described above for the time-mean flow is expected to follow. Various models of turbulence are being evaluated for adoption throughout the study and comparisons would be made with experimental data where they exist. Assessment of diffuser performance based on the dissipated mechanical energy would also be made. The result of the investigations are expected to indicate that more cost effective component design of such devices as diffusers which normally contain complex flows can still be achieved.

Effects of xanthine oxidase inhibition with febuxostat on the development of nephropathy in experimental type 2 diabetes

PubMed Central

Xu, Bei; Schneider, Jennifer; Oyama, Terry T

2016-01-01

Background and Purpose Elevated serum uric acid (UA) is a risk factor for the development of kidney disease. Inhibitors of xanthine oxidase (XOi), an enzyme involved in UA synthesis, have protective effects at early stages of experimental diabetic nephropathy (DN). However, long‐term effects of XOi in models of DN remain to be determined. Experimental Approach The development of albuminuria, renal structure and molecular markers of DN were studied in type 2 diabetic Zucker obese (ZO) rats treated for 18 weeks with the XOi febuxostat and compared with vehicle‐treated ZO rats, ZO rats treated with enalapril or a combination of both agents, and lean Zucker rats without metabolic defects. Results Febuxostat normalized serum UA and attenuated the development of albuminuria, renal structural changes, with no significant effects on BP, metabolic control or systemic markers of oxidative stress (OS). Most of these actions were comparable with those of enalapril. Combination treatment induced marked decreases in BP and was more effective in ameliorating structural changes, expression of profibrotic genes and systemic OS than either monotherapy. Febuxostat attenuated renal protein expression of TGF‐ß, CTGF, collagen 4, mesenchymal markers (FSP1 and vimentin) and a tissue marker of OS nitrotyrosine. Moreover, febuxostat attenuated TGF‐ß‐ and S100B‐induced increased expression of fibrogenic molecules in renal tubular cells in vitro in UA‐free media in an Akt kinase‐dependent manner. Conclusions and Implications Febuxostat is protective and enhances the actions of enalapril in experimental DN. Multiple mechanisms might be involved, such as a reduction of UA, renal OS and inhibition of profibrotic signalling. PMID:27238746

Estimation of hydrogen sulfide emission rates at several wastewater treatment plants through experimental concentration measurements and dispersion modeling.

PubMed

Llavador Colomer, Fernando; Espinós Morató, Héctor; Mantilla Iglesias, Enrique

2012-07-01

The management and operation of wastewater treatment plants (WWTP) usually involve the release into the atmosphere of malodorous substances with the potential to reduce the quality of life of people living nearby. In this type of facility, anaerobic degradation processes contribute to the generation of hydrogen sulfide (H2S), often at quite high concentrations; thus, the presence of this chemical compound in the atmosphere can be a good indicator of the occurrence and intensity of the olfactory impact in a specific area. The present paper describes the experimental and modelling work being carried out by CEAM-UMH in the surroundings of several wastewater treatment plants located in the Valencia Autonomous Community (Spain). This work has permitted the estimation of H2S emission rates at different WWTPs under different environmental and operating conditions. Our methodological approach for analyzing and describing the most relevant aspects of the olfactory impact consisted of several experimental campaigns involving intensive field measurements using passive samplers in the vicinity of several WWTPs, in combination with numerical simulation results from a diagnostic dispersion model. A meteorological tower at each WWTP provided the input values for the dispersion code, ensuring a good fit of the advective component and therefore more confidence in the modelled concentration field in response to environmental conditions. Then, comparisons between simulated and experimental H2S concentrations yielded estimates of the global emission rate for this substance at several WWTPs at different time periods. The results obtained show a certain degree of temporal and spatial (between-plant) variability (possibly due to both operational and environmental conditions). Nevertheless, and more importantly, the results show a high degree of uniformity in the estimates, which consistently stay within the same order of magnitude.

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

Bass, Jay D.

This project is aimed at experimental characterization of the sound velocities, equations of state (EOS), and derived physical and chemical properties of aqueous solutions and carbon dioxide at extreme pressure and temperature conditions relevant to processes occurring in the interior of the Earth. Chemical transport, phase changes (including melting), fluid-solid reactions, and formation of magmatic liquids at convergent plat boundaries are a key motivation for this project. Research in this area has long been limited by the extreme experimental challenges and lack of data under the appropriate pressure-temperature (P-T) conditions. The vast majority of studies of aqueous geochemistry relevant tomore » terrestrial problems of fluid-rock interactions have been conducted at 0.3 GPa or less, and the widely used Helgeson-Kirkham-Flowers equation of state for aqueous species is applicable only at ~ < 0.5 GPa. These limits are unfortunate because fluid flow and reactions plays a central role in many deeper environments. Recent efforts including our own, have resulted in new experimental techniques that now make it possible to investigate properties of homogeneous and heterogeneous equilibria involving aqueous species and minerals over a much broader range of pressure and temperature appropriate for deep crustal and upper mantle processes involving water-rich fluids. We carried out 1) Brillouin scattering measurements of the equations of state and molar volume of water and carbon dioxide to over 10 GPa and 870K using precise resistance heating of samples under pressure in the diamond anvil cell, and 2) the phase diagrams of the water and CO2, and 3) Exploring new experimental approaches, including CO2 laser heating of samples in a diamond cell, to measurements of sound velocities, EOS, and phase relations by Brillouin scattering to far greater pressures and temperatures.« less

Novel method for enumeration of viable Lactobacillus plantarum WCFS1 cells after single-droplet drying.

PubMed

Perdana, Jimmy; Bereschenko, Ludmila; Roghair, Mark; Fox, Martijn B; Boom, Remko M; Kleerebezem, Michiel; Schutyser, Maarten A I

2012-11-01

Survival of probiotic bacteria during drying is not trivial. Survival percentages are very specific for each probiotic strain and can be improved by careful selection of drying conditions and proper drying carrier formulation. An experimental approach is presented, comprising a single-droplet drying method and a subsequent novel screening methodology, to assess the microbial viability within single particles. The drying method involves the drying of a single droplet deposited on a flat, hydrophobic surface under well-defined drying conditions and carrier formulations. Semidried or dried particles were subjected to rehydration, fluorescence staining, and live/dead enumeration using fluorescence microscopy. The novel screening methodology provided accurate survival percentages in line with conventional plating enumeration and was evaluated in single-droplet drying experiments with Lactobacillus plantarum WCFS1 as a model probiotic strain. Parameters such as bulk air temperatures and the carrier matrices (glucose, trehalose, and maltodextrin DE 6) were varied. Following the experimental approach, the influence on the viability as a function of the drying history could be monitored. Finally, the applicability of the novel viability assessment was demonstrated for samples obtained from drying experiments at a larger scale.

Comparison of different options for harvest of a therapeutic protein product from high cell density yeast fermentation broth.

PubMed

Wang, Alice; Lewus, Rachael; Rathore, Anurag S

2006-05-05

Recovery of therapeutic protein from high cell density yeast fermentations at commercial scale is a challenging task. In this study, we investigate and compare three different harvest approaches, namely centrifugation followed by depth filtration, centrifugation followed by filter-aid enhanced depth filtration, and microfiltration. This is achieved by presenting a case study involving recovery of a therapeutic protein from Pichia pastoris fermentation broth. The focus of this study is on performance of the depth filtration and the microfiltration steps. The experimental data has been fitted to the conventional models for cake filtration to evaluate specific cake resistance and cake compressibility. In the case of microfiltration, the experimental data agrees well with flux predicted by shear induced diffusion model. It is shown that, under optimal conditions, all three options can deliver the desired product recovery ( >80%), harvest time ( <15 h including sequential concentration/diafiltration step), and clarification ( <6 NTU). However, the three options differ in terms of process development time required, capital cost, consumable cost, ease of scale-ability and process robustness. It is recommended that these be kept under consideration when making a final decision on a harvesting approach.

Improving of prospective elementary teachers' reasoning: Learning geometry through mathematical investigation

NASA Astrophysics Data System (ADS)

Sumarna, Nana; Sentryo, Izlan

2017-08-01

This research applies mathematical investigation approach in teaching geometry to improve mathematical reasoning abilities of prospective elementary teachers. Mathematical investigation in this study involved non-routine tasks through a mathematical investigation process, namely through a series of activities as an attribute of mathematical investigation. Developing the ability of mathematical reasoning of research subjects obtained through capability of research subjects in the analysis, generalization, synthesis, justify, and resolve non-routine, which is operationally constructed as an indicator of research and is used as a criterion for measuring the ability of mathematical reasoning. Research design using Quasi-Experimental design. Based on this type, the researchers apply a pre-and posttest design, which is divided into two study groups: control group and the treatment group. The number of research subjects were 111 students consisting of 56 students in the experimental group and 55 students in the control group. The conclusion of this study stated that (1) Investigation of mathematics as an approach to learning is able to give a positive response to the increasing ability of mathematical reasoning, and (2) There is no interaction effect of the factors of learning and prior knowledge of mathematics to the increased ability of mathematical reasoning.

Phosphodiesterase Inhibitors as a Therapeutic Approach to Neuroprotection and Repair

PubMed Central

Knott, Eric P.; Assi, Mazen; Rao, Sudheendra N. R.; Ghosh, Mousumi; Pearse, Damien D.

2017-01-01

A wide diversity of perturbations of the central nervous system (CNS) result in structural damage to the neuroarchitecture and cellular defects, which in turn are accompanied by neurological dysfunction and abortive endogenous neurorepair. Altering intracellular signaling pathways involved in inflammation and immune regulation, neural cell death, axon plasticity and remyelination has shown therapeutic benefit in experimental models of neurological disease and trauma. The second messengers, cyclic adenosine monophosphate (cyclic AMP) and cyclic guanosine monophosphate (cyclic GMP), are two such intracellular signaling targets, the elevation of which has produced beneficial cellular effects within a range of CNS pathologies. The only known negative regulators of cyclic nucleotides are a family of enzymes called phosphodiesterases (PDEs) that hydrolyze cyclic nucleotides into adenosine monophosphate (AMP) or guanylate monophosphate (GMP). Herein, we discuss the structure and physiological function as well as the roles PDEs play in pathological processes of the diseased or injured CNS. Further we review the approaches that have been employed therapeutically in experimental paradigms to block PDE expression or activity and in turn elevate cyclic nucleotide levels to mediate neuroprotection or neurorepair as well as discuss both the translational pathway and current limitations in moving new PDE-targeted therapies to the clinic. PMID:28338622

Characterizing new compositions of [001]C relaxor ferroelectric single crystals using a work-energy model

NASA Astrophysics Data System (ADS)

Gallagher, John A.

2016-04-01

The desired operating range of ferroelectric materials with compositions near the morphotropic phase boundary is limited by field induced phase transformations. In [001]C cut and poled relaxor ferroelectric single crystals the mechanically driven ferroelectric rhombohedral to ferroelectric orthorhombic phase transformation is hindered by antagonistic electrical loading. Instability around the phase transformation makes the current experimental technique for characterization of the large field behavior very time consuming. Characterization requires specialized equipment and involves an extensive set of measurements under combined electrical, mechanical, and thermal loads. In this work a mechanism-based model is combined with a more limited set of experiments to obtain the same results. The model utilizes a work-energy criterion that calculates the mechanical work required to induce the transformation and the required electrical work that is removed to reverse the transformation. This is done by defining energy barriers to the transformation. The results of the combined experiment and modeling approach are compared to the fully experimental approach and error is discussed. The model shows excellent predictive capability and is used to substantially reduce the total number of experiments required for characterization. This decreases the time and resources required for characterization of new compositions.

A pattern recognition approach to transistor array parameter variance

NASA Astrophysics Data System (ADS)

da F. Costa, Luciano; Silva, Filipi N.; Comin, Cesar H.

2018-06-01

The properties of semiconductor devices, including bipolar junction transistors (BJTs), are known to vary substantially in terms of their parameters. In this work, an experimental approach, including pattern recognition concepts and methods such as principal component analysis (PCA) and linear discriminant analysis (LDA), was used to experimentally investigate the variation among BJTs belonging to integrated circuits known as transistor arrays. It was shown that a good deal of the devices variance can be captured using only two PCA axes. It was also verified that, though substantially small variation of parameters is observed for BJT from the same array, larger variation arises between BJTs from distinct arrays, suggesting the consideration of device characteristics in more critical analog designs. As a consequence of its supervised nature, LDA was able to provide a substantial separation of the BJT into clusters, corresponding to each transistor array. In addition, the LDA mapping into two dimensions revealed a clear relationship between the considered measurements. Interestingly, a specific mapping suggested by the PCA, involving the total harmonic distortion variation expressed in terms of the average voltage gain, yielded an even better separation between the transistor array clusters. All in all, this work yielded interesting results from both semiconductor engineering and pattern recognition perspectives.

The unsolved puzzle of neuropathogenesis in glutaric aciduria type I.

PubMed

Jafari, Paris; Braissant, Olivier; Bonafé, Luisa; Ballhausen, Diana

2011-12-01

Glutaric aciduria type I (GA-I) is a cerebral organic aciduria caused by deficiency of glutaryl-Co-A dehydrogenase (GCDH). GCDH deficiency leads to accumulation of glutaric acid (GA) and 3-hydroxyglutaric acid (3-OHGA), two metabolites that are believed to be neurotoxic, in brain and body fluids. The disorder usually becomes clinically manifest during a catabolic state (e.g. intercurrent illness) with an acute encephalopathic crisis that results in striatal necrosis and in a permanent dystonic-dyskinetic movement disorder. The results of numerous in vitro and in vivo studies have pointed to three main mechanisms involved in the metabolite-mediated neuronal damage: excitotoxicity, impairment of energy metabolism and oxidative stress. There is evidence that during a metabolic crisis GA and its metabolites are produced endogenously in the CNS and accumulate because of limiting transport mechanisms across the blood-brain barrier. Despite extensive experimental work, the relative contribution of the proposed pathogenic mechanisms remains unclear and specific therapeutic approaches have yet to be developed. Here, we review the experimental evidence and try to delineate possible pathogenetic models and approaches for future studies. Copyright © 2011 Elsevier Inc. All rights reserved.

Novel Method for Enumeration of Viable Lactobacillus plantarum WCFS1 Cells after Single-Droplet Drying

PubMed Central

Perdana, Jimmy; Bereschenko, Ludmila; Roghair, Mark; Fox, Martijn B.; Boom, Remko M.; Kleerebezem, Michiel

2012-01-01

Survival of probiotic bacteria during drying is not trivial. Survival percentages are very specific for each probiotic strain and can be improved by careful selection of drying conditions and proper drying carrier formulation. An experimental approach is presented, comprising a single-droplet drying method and a subsequent novel screening methodology, to assess the microbial viability within single particles. The drying method involves the drying of a single droplet deposited on a flat, hydrophobic surface under well-defined drying conditions and carrier formulations. Semidried or dried particles were subjected to rehydration, fluorescence staining, and live/dead enumeration using fluorescence microscopy. The novel screening methodology provided accurate survival percentages in line with conventional plating enumeration and was evaluated in single-droplet drying experiments with Lactobacillus plantarum WCFS1 as a model probiotic strain. Parameters such as bulk air temperatures and the carrier matrices (glucose, trehalose, and maltodextrin DE 6) were varied. Following the experimental approach, the influence on the viability as a function of the drying history could be monitored. Finally, the applicability of the novel viability assessment was demonstrated for samples obtained from drying experiments at a larger scale. PMID:22983965

Excluded volume and ion-ion correlation effects on the ionic atmosphere around B-DNA: Theory, simulations, and experiments

PubMed Central

Ovanesyan, Zaven; Fenley, Marcia O.; Guerrero-García, Guillermo Iván; Olvera de la Cruz, Mónica

2014-01-01

The ionic atmosphere around a nucleic acid regulates its stability in aqueous salt solutions. One major source of complexity in biological activities involving nucleic acids arises from the strong influence of the surrounding ions and water molecules on their structural and thermodynamic properties. Here, we implement a classical density functional theory for cylindrical polyelectrolytes embedded in aqueous electrolytes containing explicit (neutral hard sphere) water molecules at experimental solvent concentrations. Our approach allows us to include ion correlations as well as solvent and ion excluded volume effects for studying the structural and thermodynamic properties of highly charged cylindrical polyelectrolytes. Several models of size and charge asymmetric mixtures of aqueous electrolytes at physiological concentrations are studied. Our results are in good agreement with Monte Carlo simulations. Our numerical calculations display significant differences in the ion density profiles for the different aqueous electrolyte models studied. However, similar results regarding the excess number of ions adsorbed to the B-DNA molecule are predicted by our theoretical approach for different aqueous electrolyte models. These findings suggest that ion counting experimental data should not be used alone to validate the performance of aqueous DNA-electrolyte models. PMID:25494770

The Results of a Simulator Study to Determine the Effects on Pilot Performance of Two Different Motion Cueing Algorithms and Various Delays, Compensated and Uncompensated

NASA Technical Reports Server (NTRS)

Guo, Li-Wen; Cardullo, Frank M.; Telban, Robert J.; Houck, Jacob A.; Kelly, Lon C.

2003-01-01

A study was conducted employing the Visual Motion Simulator (VMS) at the NASA Langley Research Center, Hampton, Virginia. This study compared two motion cueing algorithms, the NASA adaptive algorithm and a new optimal control based algorithm. Also, the study included the effects of transport delays and the compensation thereof. The delay compensation algorithm employed is one developed by Richard McFarland at NASA Ames Research Center. This paper reports on the analyses of the results of analyzing the experimental data collected from preliminary simulation tests. This series of tests was conducted to evaluate the protocols and the methodology of data analysis in preparation for more comprehensive tests which will be conducted during the spring of 2003. Therefore only three pilots were used. Nevertheless some useful results were obtained. The experimental conditions involved three maneuvers; a straight-in approach with a rotating wind vector, an offset approach with turbulence and gust, and a takeoff with and without an engine failure shortly after liftoff. For each of the maneuvers the two motion conditions were combined with four delay conditions (0, 50, 100 & 200ms), with and without compensation.

Metabolic pathway reconstruction of eugenol to vanillin bioconversion in Aspergillus niger

PubMed Central

Srivastava, Suchita; Luqman, Suaib; Khan, Feroz; Chanotiya, Chandan S; Darokar, Mahendra P

2010-01-01

Identification of missing genes or proteins participating in the metabolic pathways as enzymes are of great interest. One such class of pathway is involved in the eugenol to vanillin bioconversion. Our goal is to develop an integral approach for identifying the topology of a reference or known pathway in other organism. We successfully identify the missing enzymes and then reconstruct the vanillin biosynthetic pathway in Aspergillus niger. The procedure combines enzyme sequence similarity searched through BLAST homology search and orthologs detection through COG & KEGG databases. Conservation of protein domains and motifs was searched through CDD, PFAM & PROSITE databases. Predictions regarding how proteins act in pathway were validated experimentally and also compared with reported data. The bioconversion of vanillin was screened on UV-TLC plates and later confirmed through GC and GC-MS techniques. We applied a procedure for identifying missing enzymes on the basis of conserved functional motifs and later reconstruct the metabolic pathway in target organism. Using the vanillin biosynthetic pathway of Pseudomonas fluorescens as a case study, we indicate how this approach can be used to reconstruct the reference pathway in A. niger and later results were experimentally validated through chromatography and spectroscopy techniques. PMID:20978605

The use of time-averaged 3JHH restrained molecular dynamics (tar-MD) simulations for the conformational analysis of five-membered ring systems: methodology and applications.

PubMed

Hendrickx, Pieter M S; Corzana, Francisco; Depraetere, Stefaan; Tourwé, Dirk A; Augustyns, Koen; Martins, José C

2010-02-01

Because of its presence in many molecules of biological relevance, the conformational analysis of five-membered rings using (3)J(HH) scalar coupling data from NMR is a topic of considerable interest. Typically, conformational analysis involves the use of a well-established mathematical procedure, originally developed by de Leeuw et al., that fits two rigid conformations to the available experimental data. This so-called pseudorotation analysis approach is not without problems, however, as chemically unrealistic conformations are sometimes generated from the data. Here, we present our investigations in the use of time-averaged restrained molecular dynamics simulations as a generic tool to determine the conformations that agree with experimental (3)J(HH) scalar coupling data. For this purpose, a set of six ribose-based molecules has been used as model compounds. The influence of several modeling parameters is assessed and optimized values are proposed. The results obtained with the tar-MD approach are compared to those obtained from the two conformer fitting procedure. Interpretation of the latter is facilitated by the introduction of a fitting error analysis that allows mapping the solution space of the fitting procedure. The relative merits of both methods and the advantages that result from the use of a force field and a time-averaged restraint potential for the experimental data are discussed. When combined, both techniques allow an enhanced understanding of the molecules' conformational behavior and prevent possible overinterpretation. In view of the very reasonable computational burden of a tar-MD simulation for the systems investigated here, the approach should be generally applicable. Copyright 2009 Wiley Periodicals, Inc.

Estimating 3D positions and velocities of projectiles from monocular views.

PubMed

Ribnick, Evan; Atev, Stefan; Papanikolopoulos, Nikolaos P

2009-05-01

In this paper, we consider the problem of localizing a projectile in 3D based on its apparent motion in a stationary monocular view. A thorough theoretical analysis is developed, from which we establish the minimum conditions for the existence of a unique solution. The theoretical results obtained have important implications for applications involving projectile motion. A robust, nonlinear optimization-based formulation is proposed, and the use of a local optimization method is justified by detailed examination of the local convexity structure of the cost function. The potential of this approach is validated by experimental results.

Taguchi Experimental Design for Cleaning PWAs with Ball Grid Arrays

NASA Technical Reports Server (NTRS)

Bonner, J. K.; Mehta, A.; Walton, S.

1997-01-01

Ball grid arrays (BGAs), and other area array packages, are becoming more prominent as a way to increase component pin count while avoiding the manufacturing difficulties inherent in processing quad flat packs (QFPs)...Cleaning printed wiring assemblies (PWAs) with BGA components mounted on the surface is problematic...Currently, a low flash point semi-aqueous material, in conjunction with a batch cleaning unit, is being used to clean PWAs. The approach taken at JPL was to investigate the use of (1) semi-aqueous materials having a high flash point and (2) aqueous cleaning involving a saponifier.

Size-Dependent Materials Properties Toward a Universal Equation

PubMed Central

2010-01-01

Due to the lack of experimental values concerning some material properties at the nanoscale, it is interesting to evaluate this theoretically. Through a “top–down” approach, a universal equation is developed here which is particularly helpful when experiments are difficult to lead on a specific material property. It only requires the knowledge of the surface area to volume ratio of the nanomaterial, its size as well as the statistic (Fermi–Dirac or Bose–Einstein) followed by the particles involved in the considered material property. Comparison between different existing theoretical models and the proposed equation is done. PMID:20596422

Human-computer interaction in multitask situations

NASA Technical Reports Server (NTRS)

Rouse, W. B.

1977-01-01

Human-computer interaction in multitask decisionmaking situations is considered, and it is proposed that humans and computers have overlapping responsibilities. Queueing theory is employed to model this dynamic approach to the allocation of responsibility between human and computer. Results of simulation experiments are used to illustrate the effects of several system variables including number of tasks, mean time between arrivals of action-evoking events, human-computer speed mismatch, probability of computer error, probability of human error, and the level of feedback between human and computer. Current experimental efforts are discussed and the practical issues involved in designing human-computer systems for multitask situations are considered.

Thermal barrier coating life prediction model development

NASA Technical Reports Server (NTRS)

Demasi, J. T.; Sheffler, K. D.

1986-01-01

The objective of this program is to establish a methodology to predict Thermal Barrier Coating (TBC) life on gas turbine engine components. The approach involves experimental life measurement coupled with analytical modeling of relevant degradation modes. The coating being studied is a flight qualified two layer system, designated PWA 264, consisting of a nominal ten mil layer of seven percent yttria partially stabilized zirconia plasma deposited over a nominal five mil layer of low pressure plasma deposited NiCoCrAlY. Thermal barrier coating degradation modes being investigated include: thermomechanical fatigue, oxidation, erosion, hot corrosion, and foreign object damage.

Spectra of conditionalization and typicality in the multiverse

NASA Astrophysics Data System (ADS)

Azhar, Feraz

2016-02-01

An approach to testing theories describing a multiverse, that has gained interest of late, involves comparing theory-generated probability distributions over observables with their experimentally measured values. It is likely that such distributions, were we indeed able to calculate them unambiguously, will assign low probabilities to any such experimental measurements. An alternative to thereby rejecting these theories, is to conditionalize the distributions involved by restricting attention to domains of the multiverse in which we might arise. In order to elicit a crisp prediction, however, one needs to make a further assumption about how typical we are of the chosen domains. In this paper, we investigate interactions between the spectra of available assumptions regarding both conditionalization and typicality, and draw out the effects of these interactions in a concrete setting; namely, on predictions of the total number of species that contribute significantly to dark matter. In particular, for each conditionalization scheme studied, we analyze how correlations between densities of different dark matter species affect the prediction, and explicate the effects of assumptions regarding typicality. We find that the effects of correlations can depend on the conditionalization scheme, and that in each case atypicality can significantly change the prediction. In doing so, we demonstrate the existence of overlaps in the predictions of different "frameworks" consisting of conjunctions of theory, conditionalization scheme and typicality assumption. This conclusion highlights the acute challenges involved in using such tests to identify a preferred framework that aims to describe our observational situation in a multiverse.

Electro-Analytical Study of Material Interfaces Relevant for Chemical Mechanical Planarization and Lithium Ion Batteries

NASA Astrophysics Data System (ADS)

Turk, Michael C.

This dissertation work involves two areas of experimental research, focusing specifically on the applications of electro-analytical techniques for interfacial material characterization. The first area of the work is centered on the evaluation and characterization of material components used for chemical mechanical planarization (CMP) in the fabrication of semiconductor devices. This part also represents the bulk of the projects undertaken for the present dissertation. The other area of research included here involves exploratory electrochemical studies of certain electrolyte and electrode materials for applications in the development of advanced lithium ion secondary batteries. The common element between the two areas of investigation is the technical approach that combines a broad variety of electro-analytical characterization techniques to examine application specific functions of the associated materials and devices. The CMP related projects concentrate on designing and evaluating materials for CMP slurries that would be useful in the processing of copper interconnects for the sub-22 nm technology node. Specifically, ruthenium and cobalt are nontraditional barrier materials currently considered for the new interconnects. The CMP schemes used to process the structures based on these metals involve complex surface chemistries of Ru, Co and Cu (used for wiring lines). The strict requirement of defect-control while maintaining material removal by precisely regulated tribo-corrosion complicates the designs of the CMP slurries needed to process these systems. Since Ru is electrochemically more noble than Cu, the surface regions of Cu assembled in contact with Ru tend to generate defects due to galvanic corrosion in the CMP environment. At the same time, Co is strongly reactive in the typical slurry environment and is prone to developing galvanic corrosion induced by Cu. The present work explores a selected class of alkaline slurry formulations aimed at reducing these galvanic corrosions in chemically controlled low-pressure CMP. The CMP specific functions of the slurry components are characterized in the tribo-electro-analytical approach by using voltammetry, open circuit potential (OCP) measurements and electrochemical impedance spectroscopy (EIS) in the presence as well as in the absence of surface abrasion, both with and without the inclusion of colloidal silica (SiO2) abrasives. The results are used to understand the reaction mechanisms responsible for supporting material removal and corrosion suppression. The project carried out in the area of Li ion batteries (LIBs) uses electro-analytical techniques to probe electrolyte characteristics as well as electrode material performance. The investigation concentrates on optimizing a tactically chosen set of electrolyte compositions for low-to-moderate temperature applications of lithium titanium oxide (LTO), a relatively new anode material for such batteries. For this application, mixtures of non-aqueous carbonate based solvents are studied in combination with lithium perchlorate. The temperature dependent conductivities of the electrolytes are rigorously measured and analyzed using EIS. The experimental considerations and the working principle of this EIS based approach are carefully examined and standardized in the course of this study. These experiments also investigate the effects of temperature variations (below room temperature) on the solid electrolyte interphase (SEI) formation characteristics of LTO in the given electrolytes. This dissertation is organized as follows: Each experimental system and its relevance for practical applications are briefly introduced in each chapter. The experimental approach and the motivation for carrying out the investigation are also noted in that context. The experimental details specific to the particular study are described. This is followed by the results and their discussion, and subsequently, by the specific conclusions drawn from the given set of experiments. A general summary of the obtained results is presented at the end of the dissertation. Possible extensions of the present studies have also been briefly noted there.

Determining the mechanical constitutive properties of metals as a function of strain rate and temperature: A combined experimental and modeling approach

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

I. M. Robertson; A. Beaudoin; J. Lambros

2004-01-05

OAK-135 Development and validation of constitutive models for polycrystalline materials subjected to high strain rate loading over a range of temperatures are needed to predict the response of engineering materials to in-service type conditions (foreign object damage, high-strain rate forging, high-speed sheet forming, deformation behavior during forming, response to extreme conditions, etc.). To account accurately for the complex effects that can occur during extreme and variable loading conditions, requires significant and detailed computational and modeling efforts. These efforts must be closely coupled with precise and targeted experimental measurements that not only verify the predictions of the models, but also providemore » input about the fundamental processes responsible for the macroscopic response. Achieving this coupling between modeling and experimentation is the guiding principle of this program. Specifically, this program seeks to bridge the length scale between discrete dislocation interactions with grain boundaries and continuum models for polycrystalline plasticity. Achieving this goal requires incorporating these complex dislocation-interface interactions into the well-defined behavior of single crystals. Despite the widespread study of metal plasticity, this aspect is not well understood for simple loading conditions, let alone extreme ones. Our experimental approach includes determining the high-strain rate response as a function of strain and temperature with post-mortem characterization of the microstructure, quasi-static testing of pre-deformed material, and direct observation of the dislocation behavior during reloading by using the in situ transmission electron microscope deformation technique. These experiments will provide the basis for development and validation of physically-based constitutive models, which will include dislocation-grain boundary interactions for polycrystalline systems. One aspect of the program will involve the dire ct observation of specific mechanisms of micro-plasticity, as these will indicate the boundary value problem that should be addressed. This focus on the pre-yield region in the quasi-static effort (the elasto-plastic transition) is also a tractable one from an experimental and modeling viewpoint. In addition, our approach will minimize the need to fit model parameters to experimental data to obtain convergence. These are critical steps to reach the primary objective of simulating and modeling material performance under extreme loading conditions. In this annual report, we describe the progress made in the first year of this program.« less

An experimental nonlinear low dynamic stiffness device for shock isolation

NASA Astrophysics Data System (ADS)

Francisco Ledezma-Ramirez, Diego; Ferguson, Neil S.; Brennan, Michael J.; Tang, Bin

2015-07-01

The problem of shock generated vibration is very common in practice and difficult to isolate due to the high levels of excitation involved and its transient nature. If not properly isolated it could lead to large transmitted forces and displacements. Typically, classical shock isolation relies on the use of passive stiffness elements to absorb energy by deformation and some damping mechanism to dissipate residual vibration. The approach of using nonlinear stiffness elements is explored in this paper, focusing in providing an isolation system with low dynamic stiffness. The possibilities of using such a configuration for a shock mount are studied experimentally following previous theoretical models. The model studied considers electromagnets and permanent magnets in order to obtain nonlinear stiffness forces using different voltage configurations. It is found that the stiffness nonlinearities could be advantageous in improving shock isolation in terms of absolute displacement and acceleration response when compared with linear elastic elements.

Seeking maximum linearity of transfer functions

NASA Astrophysics Data System (ADS)

Silva, Filipi N.; Comin, Cesar H.; Costa, Luciano da F.

2016-12-01

Linearity is an important and frequently sought property in electronics and instrumentation. Here, we report a method capable of, given a transfer function (theoretical or derived from some real system), identifying the respective most linear region of operation with a fixed width. This methodology, which is based on least squares regression and systematic consideration of all possible regions, has been illustrated with respect to both an analytical (sigmoid transfer function) and a simple situation involving experimental data of a low-power, one-stage class A transistor current amplifier. Such an approach, which has been addressed in terms of transfer functions derived from experimentally obtained characteristic surface, also yielded contributions such as the estimation of local constants of the device, as opposed to typically considered average values. The reported method and results pave the way to several further applications in other types of devices and systems, intelligent control operation, and other areas such as identifying regions of power law behavior.

A comparative approach for the characterization of a pneumatic piston gauge up to 8 MPa using finite element calculations

NASA Astrophysics Data System (ADS)

Dogra, Sugandha; Singh, Jasveer; Lodh, Abhishek; Dilawar Sharma, Nita; Bandyopadhyay, A. K.

2011-02-01

This paper reports the behavior of a well-characterized pneumatic piston gauge in the pressure range up to 8 MPa through simulation using finite element method (FEM). Experimentally, the effective area of this piston gauge has been estimated by cross-floating to obtain A0 and λ. The FEM technique addresses this problem through simulation and optimization with standard commercial software (ANSYS) where the material properties of the piston and cylinder, dimensional measurements, etc are used as the input parameters. The simulation provides the effective area Ap as a function of pressure in the free deformation mode. From these data, one can estimate Ap versus pressure and thereby Ao and λ. Further, we have carried out a similar theoretical calculation of Ap using the conventional method involving the Dadson's as well as Johnson-Newhall equations. A comparison of these results with the experimental results has been carried out.

Ab initio treatment of ion-induced charge transfer dynamics of isolated 2-deoxy-D-ribose.

PubMed

Bacchus-Montabonel, Marie-Christine

2014-08-21

Modeling-induced radiation damage in biological systems, in particular, in DNA building blocks, is of major concern in cancer therapy studies. Ion-induced charge-transfer dynamics may indeed be involved in proton and hadrontherapy treatments. We have thus performed a theoretical approach of the charge-transfer dynamics in collision of C(4+) ions and protons with isolated 2-deoxy-D-ribose in a wide collision energy range by means of ab initio quantum chemistry molecular methods. The comparison of both projectile ions has been performed with regard to previous theoretical and experimental results. The charge transfer appears markedly less efficient with the 2-deoxy-D-ribose target than that with pyrimidine nucleobases, which would induce an enhancement of the fragmentation process in agreement with experimental measurements. The mechanism has been analyzed with regard to inner orbital excitations, and qualitative tendencies have been pointed out for studies on DNA buiding block damage.

Taking Ockham's razor to enzyme dynamics and catalysis.

PubMed

Glowacki, David R; Harvey, Jeremy N; Mulholland, Adrian J

2012-01-29

The role of protein dynamics in enzyme catalysis is a matter of intense current debate. Enzyme-catalysed reactions that involve significant quantum tunnelling can give rise to experimental kinetic isotope effects with complex temperature dependences, and it has been suggested that standard statistical rate theories, such as transition-state theory, are inadequate for their explanation. Here we introduce aspects of transition-state theory relevant to the study of enzyme reactivity, taking cues from chemical kinetics and dynamics studies of small molecules in the gas phase and in solution--where breakdowns of statistical theories have received significant attention and their origins are relatively better understood. We discuss recent theoretical approaches to understanding enzyme activity and then show how experimental observations for a number of enzymes may be reproduced using a transition-state-theory framework with physically reasonable parameters. Essential to this simple model is the inclusion of multiple conformations with different reactivity.

Learning to Like Exercising: Evaluative Conditioning Changes Automatic Evaluations of Exercising and Influences Subsequent Exercising Behavior.

PubMed

Antoniewicz, Franziska; Brand, Ralf

2016-04-01

This multistudy report used an experimental approach to alter automatic evaluations of exercise (AEE). First, we investigated the plasticity of AEE (study 1). A computerized evaluative conditioning task was developed that altered the AEE of participants in two experimental groups (acquisition of positive/negative associations involving exercising) and a control group (η2 part. = .11). Second, we examined connections between changes in AEE and subsequent exercise behavior (chosen intensity on a bike ergometer; study 2) in individuals that were placed in groups according to their baseline AEE. Group differences in exercise behavior were detected (η2 part. = .29). The effect was driven by the performance of the group with preexisting negative AEE that acquired more positive associations. This illustrates the effect of altered AEE on subsequent exercise behavior and the potential of AEE as a target for exercise intervention.

Autogenic-Feedback Training (AFT) as a preventive method for space motion sickness: Background and experimental design

NASA Technical Reports Server (NTRS)

Cowings, Patricia S.; Toscano, William B.

1993-01-01

Finding an effective treatment for the motion sickness-like symptoms that occur in space has become a high priority for NASA. The background research is reviewed and the experimental design of a formal life sciences shuttle flight experiment designed to prevent space motion sickness in shuttle crew members is presented. This experiment utilizes a behavioral medicine approach to solving this problem. This method, Autogenic-Feedback Training (AFT), involves training subjects to voluntarily control several of their own physiological responses to environmental stressors. AFT has been used reliably to increase tolerance to motion sickness during ground-based tests in over 200 men and women under a variety of conditions that induce motion sickness, and preliminary evidence from space suggests that AFT may be an effective treatment for space motion sickness as well. Proposed changes to this experiment for future manifests are included.

The materials processing research base of the Materials Processing Center. Report for FY 1982

NASA Technical Reports Server (NTRS)

Flemings, M. C.

1983-01-01

The work described, while involving research in the broad field of materials processing, has two common features: the problems are closed related to space precessing of materials and have both practical and fundamental significance. An interesting and important feature of many of the projects is that the interdisciplinary nature of the problem mandates complementary analytical modeling/experimental approaches. An other important aspect of many of the projects is the increasing use of mathematical modeling techniques as one of the research tools. The predictive capability of these models, when tested against measurements, plays a very important role in both the planning of experimental programs and in the rational interpretation of the results. Many of the projects described have a space experiment as their ultimate objective. Mathematical models are proving to be extremely valuable in projecting the findings of ground - based experiments to microgravity conditions.

Chemical reacting flows

NASA Technical Reports Server (NTRS)

Mularz, Edward J.; Sockol, Peter M.

1987-01-01

Future aerospace propulsion concepts involve the combination of liquid or gaseous fuels in a highly turbulent internal air stream. Accurate predictive computer codes which can simulate the fluid mechanics, chemistry, and turbulence combustion interaction of these chemical reacting flows will be a new tool that is needed in the design of these future propulsion concepts. Experimental and code development research is being performed at Lewis to better understand chemical reacting flows with the long term goal of establishing these reliable computer codes. The approach to understanding chemical reacting flows is to look at separate simple parts of this complex phenomena as well as to study the full turbulent reacting flow process. As a result research on the fluid mechanics associated with chemical reacting flows was initiated. The chemistry of fuel-air combustion is also being studied. Finally, the phenomena of turbulence-combustion interaction is being investigated. This presentation will highlight research, both experimental and analytical, in each of these three major areas.

Chemical reacting flows

NASA Technical Reports Server (NTRS)

Mularz, Edward J.; Sockol, Peter M.

1990-01-01

Future aerospace propulsion concepts involve the combustion of liquid or gaseous fuels in a highly turbulent internal airstream. Accurate predictive computer codes which can simulate the fluid mechanics, chemistry, and turbulence-combustion interaction of these chemical reacting flows will be a new tool that is needed in the design of these future propulsion concepts. Experimental and code development research is being performed at LeRC to better understand chemical reacting flows with the long-term goal of establishing these reliable computer codes. Our approach to understand chemical reacting flows is to look at separate, more simple parts of this complex phenomenon as well as to study the full turbulent reacting flow process. As a result, we are engaged in research on the fluid mechanics associated with chemical reacting flows. We are also studying the chemistry of fuel-air combustion. Finally, we are investigating the phenomenon of turbulence-combustion interaction. Research, both experimental and analytical, is highlighted in each of these three major areas.

Performance optimization and validation of ADM1 simulations under anaerobic thermophilic conditions.

PubMed

Atallah, Nabil M; El-Fadel, Mutasem; Ghanimeh, Sophia; Saikaly, Pascal; Abou-Najm, Majdi

2014-12-01

In this study, two experimental sets of data each involving two thermophilic anaerobic digesters treating food waste, were simulated using the Anaerobic Digestion Model No. 1 (ADM1). A sensitivity analysis was conducted, using both data sets of one digester, for parameter optimization based on five measured performance indicators: methane generation, pH, acetate, total COD, ammonia, and an equally weighted combination of the five indicators. The simulation results revealed that while optimization with respect to methane alone, a commonly adopted approach, succeeded in simulating methane experimental results, it predicted other intermediary outputs less accurately. On the other hand, the multi-objective optimization has the advantage of providing better results than methane optimization despite not capturing the intermediary output. The results from the parameter optimization were validated upon their independent application on the data sets of the second digester. Copyright © 2014 Elsevier Ltd. All rights reserved.

A laser based frequency modulated NL-OSL phenomenon

NASA Astrophysics Data System (ADS)

Mishra, D. R.; Bishnoi, A. S.; Soni, Anuj; Rawat, N. S.; Bhatt, B. C.; Kulkarni, M. S.; Babu, D. A. R.

2015-01-01

The detailed theoretical and experimental approach to novel technique of pulse frequency modulated stimulation (PFMS) method has been described for NL-OSL phenomenon. This method involved pulsed frequency modulation with respect to time for fixed pulse width of 532 nm continuous wave (CW)-laser light. The linearly modulated (LM)-, non-linearly (NL)-stimulation profiles have been generated using fast electromagnetic optical shutter. The PFMS parameters have been determined for present experimental setup. The PFMS based LM-, NL-OSL studies have been carried out on dosimetry grade single crystal α-Al2O3:C. The photo ionization cross section of α-Al2O3:C has been found to be ∼9.97 × 10-19 cm2 for 532 nm laser light using PFMS LM-OSL studies under assumption of first order of kinetic. This method of PFMS is found to be a potential alternative to generate different stimulation profiles using CW-light sources.

Processing of pictorial food stimuli in patients with eating disorders--a systematic review.

PubMed

Giel, Katrin Elisabeth; Teufel, Martin; Friederich, Hans-Christoph; Hautzinger, Martin; Enck, Paul; Zipfel, Stephan

2011-03-01

The processing of food cues in eating-disordered patients has recently been increasingly investigated. Outlined is current evidence from pictorial food stimuli studies. PubMed and PsychINFO were searched for quantitative pictorial food stimuli studies investigating healthy controls and expert-diagnosed eating-disordered patients. Patients with eating disorders (ED) demonstrated cue reactivity to food stimuli. Results from functional imaging suggest sensory disengagement and higher emotional involvement while self-reported data and facial EMG revealed that food pictures were perceived as less pleasurable. Different experimental paradigms have demonstrated an attentional bias for food cues in ED. Currently, psychophysiological data is widely inconclusive. Evidence suggests cue reactivity to food pictures in eating-disordered patients. However, the overall picture is inconclusive because methodological problems and the integration of findings from different experimental approaches pose a challenge to the research field. Copyright © 2009 Wiley Periodicals, Inc.

Towards the Physics of Calcium Signalling in Plants

PubMed Central

Vaz Martins, Teresa; Evans, Matthew J.; Woolfenden, Hugh C.; Morris, Richard J.

2013-01-01

Calcium is an abundant element with a wide variety of important roles within cells. Calcium ions are inter- and intra-cellular messengers that are involved in numerous signalling pathways. Fluctuating compartment-specific calcium ion concentrations can lead to localised and even plant-wide oscillations that can regulate downstream events. Understanding the mechanisms that give rise to these complex patterns that vary both in space and time can be challenging, even in cases for which individual components have been identified. Taking a systems biology approach, mathematical and computational techniques can be employed to produce models that recapitulate experimental observations and capture our current understanding of the system. Useful models make novel predictions that can be investigated and falsified experimentally. This review brings together recent work on the modelling of calcium signalling in plants, from the scale of ion channels through to plant-wide responses to external stimuli. Some in silico results that have informed later experiments are highlighted. PMID:27137393

X-ray crystallography, an essential tool for the determination of thermodynamic relationships between crystalline polymorphs.

PubMed

Céolin, R; Rietveld, I-B

2016-01-01

After a short review of the controversies surrounding the discovery of crystalline polymorphism in relation to our present day understanding, the methods of how to solve the stability hierarchy of different polymorphs will be briefly discussed. They involve either theoretical calculations, or, more commonly, experimental methods based on classical thermodynamics. The experimental approach is mainly carried out using heat-exchange data associated to the transition of one form into another. It will be demonstrated that work-related data associated to the phase transition should be taken into account and the role of X-ray crystallography therein will be discussed. X-ray crystallography has become increasingly precise and can nowadays provide specific volumes and their differences as a function of temperature, and also as a function of pressure, humidity, and time. Copyright © 2015 Académie Nationale de Pharmacie. Published by Elsevier Masson SAS. All rights reserved.

Improved Subcell Model for the Prediction of Braided Composite Response

NASA Technical Reports Server (NTRS)

Cater, Christopher R.; Xinran, Xiao; Goldberg, Robert K.; Kohlman, Lee W.

2013-01-01

In this work, the modeling of triaxially braided composites was explored through a semi-analytical discretization. Four unique subcells, each approximated by a "mosaic" stacking of unidirectional composite plies, were modeled through the use of layered-shell elements within the explicit finite element code LS-DYNA. Two subcell discretizations were investigated: a model explicitly capturing pure matrix regions, and a novel model which absorbed pure matrix pockets into neighboring tow plies. The in-plane stiffness properties of both models, computed using bottom-up micromechanics, correlated well to experimental data. The absorbed matrix model, however, was found to best capture out-of- plane flexural properties by comparing numerical simulations of the out-of-plane displacements from single-ply tension tests to experimental full field data. This strong correlation of out-of-plane characteristics supports the current modeling approach as a viable candidate for future work involving impact simulations.

Science, population ecology, and the management of the American black duck

USGS Publications Warehouse

Nichols, J.D.

1991-01-01

This essay deals with the relevance of some of the ideas of Romesburg (1981) to population ecology and management of the American black duck (Anas rubripes). Most investigations dealing with the effects of hunting regulations on black duck populations have used the hypothetico-deductive (H-D) approach of specifying a priori hypotheses and associated deduced predictions. These investigations have not used manipulative experimentation, however, but have involved severely constrained analyses of historical data and have thus produced weak inferences. The 1982 lawsuit over black duck hunting regulations, the current uncertainty about appropriate black duck management actions, and the frequent skirmishes in the published literature of black duck population ecology are natural consequences of these weak inferences. I suggest that we attempt to take advantage of management and other manipulations by treating them as an opportunity to learn something via experimentation, as recommended by Macnab (1983) and Walters (1986).

Stringent homology-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions.

PubMed

Zhou, Hufeng; Gao, Shangzhi; Nguyen, Nam Ninh; Fan, Mengyuan; Jin, Jingjing; Liu, Bing; Zhao, Liang; Xiong, Geng; Tan, Min; Li, Shijun; Wong, Limsoon

2014-04-08

H. sapiens-M. tuberculosis H37Rv protein-protein interaction (PPI) data are essential for understanding the infection mechanism of the formidable pathogen M. tuberculosis H37Rv. Computational prediction is an important strategy to fill the gap in experimental H. sapiens-M. tuberculosis H37Rv PPI data. Homology-based prediction is frequently used in predicting both intra-species and inter-species PPIs. However, some limitations are not properly resolved in several published works that predict eukaryote-prokaryote inter-species PPIs using intra-species template PPIs. We develop a stringent homology-based prediction approach by taking into account (i) differences between eukaryotic and prokaryotic proteins and (ii) differences between inter-species and intra-species PPI interfaces. We compare our stringent homology-based approach to a conventional homology-based approach for predicting host-pathogen PPIs, based on cellular compartment distribution analysis, disease gene list enrichment analysis, pathway enrichment analysis and functional category enrichment analysis. These analyses support the validity of our prediction result, and clearly show that our approach has better performance in predicting H. sapiens-M. tuberculosis H37Rv PPIs. Using our stringent homology-based approach, we have predicted a set of highly plausible H. sapiens-M. tuberculosis H37Rv PPIs which might be useful for many of related studies. Based on our analysis of the H. sapiens-M. tuberculosis H37Rv PPI network predicted by our stringent homology-based approach, we have discovered several interesting properties which are reported here for the first time. We find that both host proteins and pathogen proteins involved in the host-pathogen PPIs tend to be hubs in their own intra-species PPI network. Also, both host and pathogen proteins involved in host-pathogen PPIs tend to have longer primary sequence, tend to have more domains, tend to be more hydrophilic, etc. And the protein domains from both host and pathogen proteins involved in host-pathogen PPIs tend to have lower charge, and tend to be more hydrophilic. Our stringent homology-based prediction approach provides a better strategy in predicting PPIs between eukaryotic hosts and prokaryotic pathogens than a conventional homology-based approach. The properties we have observed from the predicted H. sapiens-M. tuberculosis H37Rv PPI network are useful for understanding inter-species host-pathogen PPI networks and provide novel insights for host-pathogen interaction studies.

A model of the regulatory network involved in the control of the cell cycle and cell differentiation in the Caenorhabditis elegans vulva.

PubMed

Weinstein, Nathan; Ortiz-Gutiérrez, Elizabeth; Muñoz, Stalin; Rosenblueth, David A; Álvarez-Buylla, Elena R; Mendoza, Luis

2015-03-13

There are recent experimental reports on the cross-regulation between molecules involved in the control of the cell cycle and the differentiation of the vulval precursor cells (VPCs) of Caenorhabditis elegans. Such discoveries provide novel clues on how the molecular mechanisms involved in the cell cycle and cell differentiation processes are coordinated during vulval development. Dynamic computational models are helpful to understand the integrated regulatory mechanisms affecting these cellular processes. Here we propose a simplified model of the regulatory network that includes sufficient molecules involved in the control of both the cell cycle and cell differentiation in the C. elegans vulva to recover their dynamic behavior. We first infer both the topology and the update rules of the cell cycle module from an expected time series. Next, we use a symbolic algorithmic approach to find which interactions must be included in the regulatory network. Finally, we use a continuous-time version of the update rules for the cell cycle module to validate the cyclic behavior of the network, as well as to rule out the presence of potential artifacts due to the synchronous updating of the discrete model. We analyze the dynamical behavior of the model for the wild type and several mutants, finding that most of the results are consistent with published experimental results. Our model shows that the regulation of Notch signaling by the cell cycle preserves the potential of the VPCs and the three vulval fates to differentiate and de-differentiate, allowing them to remain completely responsive to the concentration of LIN-3 and lateral signal in the extracellular microenvironment.

Identifying Effective Design Approaches to Allocate Genotypes in Two-Phase Designs: A Case Study in Pelargonium zonale

PubMed Central

Molenaar, Heike; Boehm, Robert; Piepho, Hans-Peter

2018-01-01

Robust phenotypic data allow adequate statistical analysis and are crucial for any breeding purpose. Such data is obtained from experiments laid out to best control local variation. Additionally, experiments frequently involve two phases, each contributing environmental sources of variation. For example, in a former experiment we conducted to evaluate production related traits in Pelargonium zonale, there were two consecutive phases, each performed in a different greenhouse. Phase one involved the propagation of the breeding strains to obtain the stem cutting count, and phase two involved the assessment of root formation. The evaluation of the former study raised questions regarding options for improving the experimental layout: (i) Is there a disadvantage to using exactly the same design in both phases? (ii) Instead of generating a separate layout for each phase, can the design be optimized across both phases, such that the mean variance of a pair-wise treatment difference (MVD) can be decreased? To answer these questions, alternative approaches were explored to generate two-phase designs either in phase-wise order (Option 1) or across phases (Option 2). In Option 1 we considered the scenarios (i) using in both phases the same experimental design and (ii) randomizing each phase separately. In Option 2, we considered the scenarios (iii) generating a single design with eight replicates and splitting these among the two phases, (iv) separating the block structure across phases by dummy coding, and (v) design generation with optimal alignment of block units in the two phases. In both options, we considered the same or different block structures in each phase. The designs were evaluated by the MVD obtained by the intra-block analysis and the joint inter-block–intra-block analysis. The smallest MVD was most frequently obtained for designs generated across phases rather than for each phase separately, in particular when both phases of the design were separated with a single pseudo-level. The joint optimization ensured that treatment concurrences were equally balanced across pairs, one of the prerequisites for an efficient design. The proposed alternative approaches can be implemented with any model-based design packages with facilities to formulate linear models for treatment and block structures. PMID:29354145

Sampling Participants’ Experience in Laboratory Experiments: Complementary Challenges for More Complete Data Collection

PubMed Central

McAuliffe, Alan; McGann, Marek

2016-01-01

Speelman and McGann’s (2013) examination of the uncritical way in which the mean is often used in psychological research raises questions both about the average’s reliability and its validity. In the present paper, we argue that interrogating the validity of the mean involves, amongst other things, a better understanding of the person’s experiences, the meaning of their actions, at the time that the behavior of interest is carried out. Recently emerging approaches within Psychology and Cognitive Science have argued strongly that experience should play a more central role in our examination of behavioral data, but the relationship between experience and behavior remains very poorly understood. We outline some of the history of the science on this fraught relationship, as well as arguing that contemporary methods for studying experience fall into one of two categories. “Wide” approaches tend to incorporate naturalistic behavior settings, but sacrifice accuracy and reliability in behavioral measurement. “Narrow” approaches maintain controlled measurement of behavior, but involve too specific a sampling of experience, which obscures crucial temporal characteristics. We therefore argue for a novel, mid-range sampling technique, that extends Hurlburt’s descriptive experience sampling, and adapts it for the controlled setting of the laboratory. This controlled descriptive experience sampling may be an appropriate tool to help calibrate both the mean and the meaning of an experimental situation with one another. PMID:27242588

Thermal barrier coating life prediction model development, phase 1

NASA Technical Reports Server (NTRS)

Demasi, Jeanine T.; Ortiz, Milton

1989-01-01

The objective of this program was to establish a methodology to predict thermal barrier coating (TBC) life on gas turbine engine components. The approach involved experimental life measurement coupled with analytical modeling of relevant degradation modes. Evaluation of experimental and flight service components indicate the predominant failure mode to be thermomechanical spallation of the ceramic coating layer resulting from propagation of a dominant near interface crack. Examination of fractionally exposed specimens indicated that dominant crack formation results from progressive structural damage in the form of subcritical microcrack link-up. Tests conducted to isolate important life drivers have shown MCrAlY oxidation to significantly affect the rate of damage accumulation. Mechanical property testing has shown the plasma deposited ceramic to exhibit a non-linear stress-strain response, creep and fatigue. The fatigue based life prediction model developed accounts for the unusual ceramic behavior and also incorporates an experimentally determined oxide rate model. The model predicts the growth of this oxide scale to influence the intensity of the mechanic driving force, resulting from cyclic strains and stresses caused by thermally induced and externally imposed mechanical loads.

Sexual risk attitudes and intentions of youth aged 12-14 years: survey comparisons of parent-teen prevention and control groups.

PubMed

Lederman, Regina P; Chan, Wenyaw; Roberts-Gray, Cynthia

2004-01-01

In this study, the authors compared differences in sexual risk attitudes and intentions for three groups of youth (experimental program, n = 90; attention control, n = 80; and nonparticipant control, n = 634) aged 12-14 years. Two student groups participated with their parents in programs focused on strengthening family interaction and prevention of sexual risks, HIV, and adolescent pregnancy. Surveys assessed students' attitudes and intentions regarding early sexual and other health-risk behaviors, family interactions, and perceived parental disapproval of risk behaviors. The authors used general linear modeling to compare results. The experimental prevention program differentiated the total scores of the 3 groups (p < .05). A similar result was obtained for student intentions to avoid sex (p < .01). Pairwise comparisons showed the experimental program group scored higher than the nonparticipant group on total scores (p < .01) and on students' intention to avoid sex (p < .01). The results suggest this novel educational program involving both parents and students offers a promising approach to HIV and teen pregnancy prevention.

A comparison of turbulence models in computing multi-element airfoil flows

NASA Technical Reports Server (NTRS)

Rogers, Stuart E.; Menter, Florian; Durbin, Paul A.; Mansour, Nagi N.

1994-01-01

Four different turbulence models are used to compute the flow over a three-element airfoil configuration. These models are the one-equation Baldwin-Barth model, the one-equation Spalart-Allmaras model, a two-equation k-omega model, and a new one-equation Durbin-Mansour model. The flow is computed using the INS2D two-dimensional incompressible Navier-Stokes solver. An overset Chimera grid approach is utilized. Grid resolution tests are presented, and manual solution-adaptation of the grid was performed. The performance of each of the models is evaluated for test cases involving different angles-of-attack, Reynolds numbers, and flap riggings. The resulting surface pressure coefficients, skin friction, velocity profiles, and lift, drag, and moment coefficients are compared with experimental data. The models produce very similar results in most cases. Excellent agreement between computational and experimental surface pressures was observed, but only moderately good agreement was seen in the velocity profile data. In general, the difference between the predictions of the different models was less than the difference between the computational and experimental data.

Analyzing neural responses with vector fields.

PubMed

Buneo, Christopher A

2011-04-15

Analyzing changes in the shape and scale of single cell response fields is a key component of many neurophysiological studies. Typical analyses of shape change involve correlating firing rates between experimental conditions or "cross-correlating" single cell tuning curves by shifting them with respect to one another and correlating the overlapping data. Such shifting results in a loss of data, making interpretation of the resulting correlation coefficients problematic. The problem is particularly acute for two dimensional response fields, which require shifting along two axes. Here, an alternative method for quantifying response field shape and scale based on correlation of vector field representations is introduced. The merits and limitations of the methods are illustrated using both simulated and experimental data. It is shown that vector correlation provides more information on response field changes than scalar correlation without requiring field shifting and concomitant data loss. An extension of this vector field approach is also demonstrated which can be used to identify the manner in which experimental variables are encoded in studies of neural reference frames. Copyright © 2011 Elsevier B.V. All rights reserved.

Testing theoretical models of magnetic damping using an air track

NASA Astrophysics Data System (ADS)

Vidaurre, Ana; Riera, Jaime; Monsoriu, Juan A.; Giménez, Marcos H.

2008-03-01

Magnetic braking is a long-established application of Lenz's law. A rigorous analysis of the laws governing this problem involves solving Maxwell's equations in a time-dependent situation. Approximate models have been developed to describe different experimental results related to this phenomenon. In this paper we present a new method for the analysis of magnetic braking using a magnet fixed to the glider of an air track. The forces acting on the glider, a result of the eddy currents, can be easily observed and measured. As a consequence of the air track inclination, the glider accelerates at the beginning, although it asymptotically tends towards a uniform rectilinear movement characterized by a terminal speed. This speed depends on the interaction between the magnetic field and the conductivity properties of the air track. Compared with previous related approaches, in our experimental setup the magnet fixed to the glider produces a magnetic braking force which acts continuously, rather than over a short period of time. The experimental results satisfactorily concur with the theoretical models adapted to this configuration.

Blade Surface Pressure Distributions in a Rocket Engine Turbine: Experimental Work With On-Blade Pressure Transducers

NASA Technical Reports Server (NTRS)

Hudson, Susan T.; Zoladz, Thomas F.; Griffin, Lisa W.; Turner, James E. (Technical Monitor)

2000-01-01

Understanding the unsteady aspects of turbine rotor flowfields is critical to successful future turbine designs. A technology program was conducted at NASA's Marshall Space Flight Center to increase the understanding of unsteady environments for rocket engine turbines. The experimental program involved instrumenting turbine rotor blades with surface-mounted high frequency response pressure transducers. The turbine model was then tested to measure the unsteady pressures on the rotor blades. The data obtained from the experimental program is unique in three respects. First, much more unsteady data was obtained (several minutes per set point) than has been possible in the past. Also, two independent unsteady data acquisition systems and fundamental signal processing approaches were used. Finally, an extensive steady performance database existed for the turbine model. This allowed an evaluation of the effect of the on-blade instrumentation on the turbine's performance. This unique data set, the lessons learned for acquiring this type of data, and the improvements made to the data analysis and prediction tools will contribute to future turbine programs such as those for reusable launch vehicles.

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

Groppi, Flavia; Manenti, Simone; Gini, Luigi

In Italy the 'nuclear issue' was for a long time a taboo. A way to approach this theme to make the public more trusting of nuclear issues is to discuss radioactivity and ionizing radiation starting from young students. An experimental activity that involves secondary school students has been developed. The approach is to have students engaged in activities that will allow them to understand how natural radioactivity is a part of our everyday environment. This would include how radiation enters our lives in different ways, to demonstrate that natural radioactive sources found in soil, water, and air contribute to ourmore » exposure to natural ionizing radiation and how this exposure effects human health. Another objective is to develop a new technique for teaching physics which will enhance scientific interest of students in applications of nuclear physics in both environmental and physical sciences.« less

Program in environmental sustainability uses interdisciplinary approach to cross-train students

NASA Astrophysics Data System (ADS)

Arvidson, Raymond E.; Johnson, Sarah S.

The Hewlett Program in Environmental Sustainability, an experimental educational pathway for undergraduate students interested in the study of the environment (http://wundow.wustl.edu/hewlett), is now in its third year at Washington University. About 90% of incoming students have stayed with the program through the first year and about 80% through the second year.The program's objectives and implementation closely follow the recommendations presented in a 1998 Boyer Commission Report on emphasizing and improving undergraduate education at research universities (http://notes.cc.sunysb.edu/Pres/boyer/nsf). A clustered, interdisciplinary approach is used for coursework, with key environmental problems viewed from scientific, political, cultural, and ethical perspectives. Courses are taught by instructors who conduct research in environmental areas. The program's multidisciplinary nature is considered a strong draw for faculty involvement, though retaining faculty is still an issue.

Structural damage continuous monitoring by using a data driven approach based on principal component analysis and cross-correlation analysis

NASA Astrophysics Data System (ADS)

Camacho-Navarro, Jhonatan; Ruiz, Magda; Villamizar, Rodolfo; Mujica, Luis; Moreno-Beltrán, Gustavo; Quiroga, Jabid

2017-05-01

Continuous monitoring for damage detection in structural assessment comprises implementation of low cost equipment and efficient algorithms. This work describes the stages involved in the design of a methodology with high feasibility to be used in continuous damage assessment. Specifically, an algorithm based on a data-driven approach by using principal component analysis and pre-processing acquired signals by means of cross-correlation functions, is discussed. A carbon steel pipe section and a laboratory tower were used as test structures in order to demonstrate the feasibility of the methodology to detect abrupt changes in the structural response when damages occur. Two types of damage cases are studied: crack and leak for each structure, respectively. Experimental results show that the methodology is promising in the continuous monitoring of real structures.

Involvement of the European Confederation of the Soil Science Societies in soil protection policy development

NASA Astrophysics Data System (ADS)

Boivin, Pascal

2017-04-01

The European Confederation of the Soil Science Societies (ECSSS) was founded not only to organize the Eurosoil congress, but also to continuously support and promote the soil causes in the European area. A work is in progress to define the best way to achieve this goal, with integrating voices of the European structures and networks, and the national societies. One of the major objectives is to develop a modern approach of soil protection, including leading experimentations shared with all the members, and active lobbying. Such an approach requires the buildup of an efficient interface with policy makers, stake holders, engineering and science, which should be concretized in a new the dimension of the Eurosoil congress. This communication will sketch the on-going work, with reviewing the perspectives, conditions, strengths, questions and difficulties identified.

Analysis of longitudinal "time series" data in toxicology.

PubMed

Cox, C; Cory-Slechta, D A

1987-02-01

Studies focusing on chronic toxicity or on the time course of toxicant effect often involve repeated measurements or longitudinal observations of endpoints of interest. Experimental design considerations frequently necessitate between-group comparisons of the resulting trends. Typically, procedures such as the repeated-measures analysis of variance have been used for statistical analysis, even though the required assumptions may not be satisfied in some circumstances. This paper describes an alternative analytical approach which summarizes curvilinear trends by fitting cubic orthogonal polynomials to individual profiles of effect. The resulting regression coefficients serve as quantitative descriptors which can be subjected to group significance testing. Randomization tests based on medians are proposed to provide a comparison of treatment and control groups. Examples from the behavioral toxicology literature are considered, and the results are compared to more traditional approaches, such as repeated-measures analysis of variance.

Prediction of the acoustic pressure above periodically uneven facings in industrial workplaces

NASA Astrophysics Data System (ADS)

Ducourneau, J.; Bos, L.; Planeau, V.; Faiz, Adil; Skali Lami, Salah; Nejade, A.

2010-05-01

The aim of this work is to predict sound pressure in front of wall facings based on periodic sound scattering surface profiles. The method involves investigating plane wave reflections randomly incident upon an uneven surface. The waveguide approach is well suited to the geometries usually encountered in industrial workplaces. This method simplifies the profile geometry by using elementary rectangular volumes. The acoustic field in the profile interstices can then be expressed as the superposition of waveguide modes. In past work, walls considered are of infinite dimensions and are subjected to a periodic surface profile in only one direction. We therefore generalise this approach by extending its applicability to "double-periodic" wall facings. Free-field measurements have been taken and the observed agreement between numerical and experimental results supports the validity of the waveguide method.

Single-Molecule Methods for Nucleotide Excision Repair: Building a System to Watch Repair in Real Time.

PubMed

Kong, Muwen; Beckwitt, Emily C; Springall, Luke; Kad, Neil M; Van Houten, Bennett

2017-01-01

Single-molecule approaches to solving biophysical problems are powerful tools that allow static and dynamic real-time observations of specific molecular interactions of interest in the absence of ensemble-averaging effects. Here, we provide detailed protocols for building an experimental system that employs atomic force microscopy and a single-molecule DNA tightrope assay based on oblique angle illumination fluorescence microscopy. Together with approaches for engineering site-specific lesions into DNA substrates, these complementary biophysical techniques are well suited for investigating protein-DNA interactions that involve target-specific DNA-binding proteins, such as those engaged in a variety of DNA repair pathways. In this chapter, we demonstrate the utility of the platform by applying these techniques in the studies of proteins participating in nucleotide excision repair. © 2017 Elsevier Inc. All rights reserved.

Discrimination of dynamical system models for biological and chemical processes.

PubMed

Lorenz, Sönke; Diederichs, Elmar; Telgmann, Regina; Schütte, Christof

2007-06-01

In technical chemistry, systems biology and biotechnology, the construction of predictive models has become an essential step in process design and product optimization. Accurate modelling of the reactions requires detailed knowledge about the processes involved. However, when concerned with the development of new products and production techniques for example, this knowledge often is not available due to the lack of experimental data. Thus, when one has to work with a selection of proposed models, the main tasks of early development is to discriminate these models. In this article, a new statistical approach to model discrimination is described that ranks models wrt. the probability with which they reproduce the given data. The article introduces the new approach, discusses its statistical background, presents numerical techniques for its implementation and illustrates the application to examples from biokinetics.

Lorentz Invariance Violation effects on UHECR propagation: A geometrized approach

NASA Astrophysics Data System (ADS)

Torri, Marco Danilo Claudio; Bertini, Stefano; Giammarchi, Marco; Miramonti, Lino

2018-06-01

We explore the possibility to geometrize the interaction of massive fermions with the quantum structure of space-time, trying to create a theoretical background, in order to explain what some recent experimental results seem to implicate on the propagation of Ultra High Energy Cosmic Rays (UHECR). We will investigate part of the phenomenological implications of this approach on the predicted effect of the UHECR suppression, in fact recent evidences seem to involve the modification of the GZK cut-off phenomenon. The search for an effective theory, which can explain this physical effect, is based on Lorentz Invariance Violation (LIV), which is introduced via Modified Dispersion Relations (MDRs). Furthermore we illustrate that this perspective implies a more general geometry of space-time than the usual Riemannian one, indicating, for example, the opportunity to resort to Finsler theory.

Found in Translation: Applying Lessons from Model Systems to Strigolactone Signaling in Parasitic Plants.

PubMed

Lumba, Shelley; Subha, Asrinus; McCourt, Peter

2017-07-01

Strigolactones (SLs) are small molecules that act as endogenous hormones to regulate plant development as well as exogenous cues that help parasitic plants to infect their hosts. Given that parasitic plants are experimentally challenging systems, researchers are using two approaches to understand how they respond to host-derived SLs. The first involves extrapolating information on SLs from model genetic systems to dissect their roles in parasitic plants. The second uses chemicals to probe SL signaling directly in the parasite Striga hermonthica. These approaches indicate that parasitic plants have co-opted a family of α/β hydrolases to perceive SLs. The importance of this genetic and chemical information cannot be overstated since parasitic plant infestations are major obstacles to food security in the developing world. Copyright © 2017 Elsevier Ltd. All rights reserved.

Exploring how musical rhythm entrains brain activity with electroencephalogram frequency-tagging

PubMed Central

Nozaradan, Sylvie

2014-01-01

The ability to perceive a regular beat in music and synchronize to this beat is a widespread human skill. Fundamental to musical behaviour, beat and meter refer to the perception of periodicities while listening to musical rhythms and often involve spontaneous entrainment to move on these periodicities. Here, we present a novel experimental approach inspired by the frequency-tagging approach to understand the perception and production of rhythmic inputs. This approach is illustrated here by recording the human electroencephalogram responses at beat and meter frequencies elicited in various contexts: mental imagery of meter, spontaneous induction of a beat from rhythmic patterns, multisensory integration and sensorimotor synchronization. Collectively, our observations support the view that entrainment and resonance phenomena subtend the processing of musical rhythms in the human brain. More generally, they highlight the potential of this approach to help us understand the link between the phenomenology of musical beat and meter and the bias towards periodicities arising under certain circumstances in the nervous system. Entrainment to music provides a highly valuable framework to explore general entrainment mechanisms as embodied in the human brain. PMID:25385771

An overview of bioinformatics methods for modeling biological pathways in yeast

PubMed Central

Hou, Jie; Acharya, Lipi; Zhu, Dongxiao

2016-01-01

The advent of high-throughput genomics techniques, along with the completion of genome sequencing projects, identification of protein–protein interactions and reconstruction of genome-scale pathways, has accelerated the development of systems biology research in the yeast organism Saccharomyces cerevisiae. In particular, discovery of biological pathways in yeast has become an important forefront in systems biology, which aims to understand the interactions among molecules within a cell leading to certain cellular processes in response to a specific environment. While the existing theoretical and experimental approaches enable the investigation of well-known pathways involved in metabolism, gene regulation and signal transduction, bioinformatics methods offer new insights into computational modeling of biological pathways. A wide range of computational approaches has been proposed in the past for reconstructing biological pathways from high-throughput datasets. Here we review selected bioinformatics approaches for modeling biological pathways in S. cerevisiae, including metabolic pathways, gene-regulatory pathways and signaling pathways. We start with reviewing the research on biological pathways followed by discussing key biological databases. In addition, several representative computational approaches for modeling biological pathways in yeast are discussed. PMID:26476430

Automated analysis of siRNA screens of cells infected by hepatitis C and dengue viruses based on immunofluorescence microscopy images

NASA Astrophysics Data System (ADS)

Matula, Petr; Kumar, Anil; Wörz, Ilka; Harder, Nathalie; Erfle, Holger; Bartenschlager, Ralf; Eils, Roland; Rohr, Karl

2008-03-01

We present an image analysis approach as part of a high-throughput microscopy siRNA-based screening system using cell arrays for the identification of cellular genes involved in hepatitis C and dengue virus replication. Our approach comprises: cell nucleus segmentation, quantification of virus replication level in the neighborhood of segmented cell nuclei, localization of regions with transfected cells, cell classification by infection status, and quality assessment of an experiment and single images. In particular, we propose a novel approach for the localization of regions of transfected cells within cell array images, which combines model-based circle fitting and grid fitting. By this scheme we integrate information from single cell array images and knowledge from the complete cell arrays. The approach is fully automatic and has been successfully applied to a large number of cell array images from screening experiments. The experimental results show a good agreement with the expected behaviour of positive as well as negative controls and encourage the application to screens from further high-throughput experiments.

Bioinformatics tools for the analysis of NMR metabolomics studies focused on the identification of clinically relevant biomarkers.

PubMed

Puchades-Carrasco, Leonor; Palomino-Schätzlein, Martina; Pérez-Rambla, Clara; Pineda-Lucena, Antonio

2016-05-01

Metabolomics, a systems biology approach focused on the global study of the metabolome, offers a tremendous potential in the analysis of clinical samples. Among other applications, metabolomics enables mapping of biochemical alterations involved in the pathogenesis of diseases, and offers the opportunity to noninvasively identify diagnostic, prognostic and predictive biomarkers that could translate into early therapeutic interventions. Particularly, metabolomics by Nuclear Magnetic Resonance (NMR) has the ability to simultaneously detect and structurally characterize an abundance of metabolic components, even when their identities are unknown. Analysis of the data generated using this experimental approach requires the application of statistical and bioinformatics tools for the correct interpretation of the results. This review focuses on the different steps involved in the metabolomics characterization of biofluids for clinical applications, ranging from the design of the study to the biological interpretation of the results. Particular emphasis is devoted to the specific procedures required for the processing and interpretation of NMR data with a focus on the identification of clinically relevant biomarkers. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Statistical Engineering in Air Traffic Management Research

NASA Technical Reports Server (NTRS)

Wilson, Sara R.

2015-01-01

NASA is working to develop an integrated set of advanced technologies to enable efficient arrival operations in high-density terminal airspace for the Next Generation Air Transportation System. This integrated arrival solution is being validated and verified in laboratories and transitioned to a field prototype for an operational demonstration at a major U.S. airport. Within NASA, this is a collaborative effort between Ames and Langley Research Centers involving a multi-year iterative experimentation process. Designing and analyzing a series of sequential batch computer simulations and human-in-the-loop experiments across multiple facilities and simulation environments involves a number of statistical challenges. Experiments conducted in separate laboratories typically have different limitations and constraints, and can take different approaches with respect to the fundamental principles of statistical design of experiments. This often makes it difficult to compare results from multiple experiments and incorporate findings into the next experiment in the series. A statistical engineering approach is being employed within this project to support risk-informed decision making and maximize the knowledge gained within the available resources. This presentation describes a statistical engineering case study from NASA, highlights statistical challenges, and discusses areas where existing statistical methodology is adapted and extended.

Innovative approaches to bipolar disorder and its treatment

PubMed Central

Cipriani, Andrea; Harmer, Catherine J.; Nobre, Anna C.; Saunders, Kate; Goodwin, Guy M.; Geddes, John R.

2016-01-01

All psychiatric disorders have suffered from a dearth of truly novel pharmacological interventions. In bipolar disorder, lithium remains a mainstay of treatment, six decades since its effects were serendipitously discovered. The lack of progress reflects several factors, including ignorance of the disorder's pathophysiology and the complexities of the clinical phenotype. After reviewing the current status, we discuss some ways forward. First, we highlight the need for a richer characterization of the clinical profile, facilitated by novel devices and new forms of data capture and analysis; such data are already promoting a reevaluation of the phenotype, with an emphasis on mood instability rather than on discrete clinical episodes. Second, experimental medicine can provide early indications of target engagement and therapeutic response, reducing the time, cost, and risk involved in evaluating potential mood stabilizers. Third, genomic data can inform target identification and validation, such as the increasing evidence for involvement of calcium channel genes in bipolar disorder. Finally, new methods and models relevant to bipolar disorder, including stem cells and genetically modified mice, are being used to study key pathways and drug effects. A combination of these approaches has real potential to break the impasse and deliver genuinely new treatments. PMID:27111134

Initiating heavy-atom-based phasing by multi-dimensional molecular replacement.

PubMed

Pedersen, Bjørn Panyella; Gourdon, Pontus; Liu, Xiangyu; Karlsen, Jesper Lykkegaard; Nissen, Poul

2016-03-01

To obtain an electron-density map from a macromolecular crystal the phase problem needs to be solved, which often involves the use of heavy-atom derivative crystals and concomitant heavy-atom substructure determination. This is typically performed by dual-space methods, direct methods or Patterson-based approaches, which however may fail when only poorly diffracting derivative crystals are available. This is often the case for, for example, membrane proteins. Here, an approach for heavy-atom site identification based on a molecular-replacement parameter matrix (MRPM) is presented. It involves an n-dimensional search to test a wide spectrum of molecular-replacement parameters, such as different data sets and search models with different conformations. Results are scored by the ability to identify heavy-atom positions from anomalous difference Fourier maps. The strategy was successfully applied in the determination of a membrane-protein structure, the copper-transporting P-type ATPase CopA, when other methods had failed to determine the heavy-atom substructure. MRPM is well suited to proteins undergoing large conformational changes where multiple search models should be considered, and it enables the identification of weak but correct molecular-replacement solutions with maximum contrast to prime experimental phasing efforts.

Theoretical Estimation of Thermal Effects in Drilling of Woven Carbon Fiber Composite

PubMed Central

Díaz-Álvarez, José; Olmedo, Alvaro; Santiuste, Carlos; Miguélez, María Henar

2014-01-01

Carbon Fiber Reinforced Polymer (CFRPs) composites are extensively used in structural applications due to their attractive properties. Although the components are usually made near net shape, machining processes are needed to achieve dimensional tolerance and assembly requirements. Drilling is a common operation required for further mechanical joining of the components. CFRPs are vulnerable to processing induced damage; mainly delamination, fiber pull-out, and thermal degradation, drilling induced defects being one of the main causes of component rejection during manufacturing processes. Despite the importance of analyzing thermal phenomena involved in the machining of composites, only few authors have focused their attention on this problem, most of them using an experimental approach. The temperature at the workpiece could affect surface quality of the component and its measurement during processing is difficult. The estimation of the amount of heat generated during drilling is important; however, numerical modeling of drilling processes involves a high computational cost. This paper presents a combined approach to thermal analysis of composite drilling, using both an analytical estimation of heat generated during drilling and numerical modeling for heat propagation. Promising results for indirect detection of risk of thermal damage, through the measurement of thrust force and cutting torque, are obtained. PMID:28788685

Initiating heavy-atom-based phasing by multi-dimensional molecular replacement

PubMed Central

Pedersen, Bjørn Panyella; Gourdon, Pontus; Liu, Xiangyu; Karlsen, Jesper Lykkegaard; Nissen, Poul

2016-01-01

To obtain an electron-density map from a macromolecular crystal the phase problem needs to be solved, which often involves the use of heavy-atom derivative crystals and concomitant heavy-atom substructure determination. This is typically performed by dual-space methods, direct methods or Patterson-based approaches, which however may fail when only poorly diffracting derivative crystals are available. This is often the case for, for example, membrane proteins. Here, an approach for heavy-atom site identification based on a molecular-replacement parameter matrix (MRPM) is presented. It involves an n-dimensional search to test a wide spectrum of molecular-replacement parameters, such as different data sets and search models with different conformations. Results are scored by the ability to identify heavy-atom positions from anomalous difference Fourier maps. The strategy was successfully applied in the determination of a membrane-protein structure, the copper-transporting P-type ATPase CopA, when other methods had failed to determine the heavy-atom substructure. MRPM is well suited to proteins undergoing large conformational changes where multiple search models should be considered, and it enables the identification of weak but correct molecular-replacement solutions with maximum contrast to prime experimental phasing efforts. PMID:26960131

Systematic review of the information and communication technology features of web- and mobile-based psychoeducational interventions for depression.

PubMed

Zhao, Danyang; Lustria, Mia Liza A; Hendrickse, Joshua

2017-06-01

To examine the information and communication technology (ICT) features of psychoeducational interventions for depression delivered via the Internet or via mobile technology. Web- and mobile-based psychoeducational intervention studies published from 2004 to 2014 were selected and reviewed by two independent coders. A total of 55 unique studies satisfied the selection criteria. The review revealed a diverse range of ICTs used to support the psychoeducational programs. Most interventions used websites as their main mode of delivery and reported greater use of communication tools compared to effective approaches like tailoring or interactive technologies games, videos, and self-monitoring tools. Many of the studies relied on medium levels of clinician involvement and only a few were entirely self-guided. Programs that reported higher levels of clinician involvement also reported using more communication tools, and reported greater compliance to treatment. Future experimental studies may help unpack the effects of technology features and reveal new ways to automate aspects of clinician input. There is a need to further examine ways ICTs can be optimized to reduce the burden on clinicians whilst enhancing the delivery of proven effective therapeutic approaches. Copyright © 2017 Elsevier B.V. All rights reserved.

The Role of the Calcium-sensing Receptor in Cancer

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

Rodland, Karin D.

2004-03-01

The cell surface calcium receptor (Ca2+ receptor) is a particularly difficult receptor to study because its primary physiological ligand, Ca2+, affects numerous biological processes both within and outside of cells. Because of this, distinguishing effects of extracellular Ca2+ mediated by the Ca2+ receptor from those mediated by other mechanisms is challenging. Certain pharmacological approaches, however, when combined with appropriate experimental designs, can be used to more confidently identify cellular responses regulated by the Ca2+ receptor and select those that might be targeted therapeutically. The Ca2+ receptor on parathyroid cells, because it is the primary mechanism regulating secretion of parathyroid hormonemore » (PTH), is one such target. Calcimimetic compounds, which active this Ca2+ receptor and lower circulating levels of PTH, have been developed for treating hyperparathyroidism. The converse pharmaceutical approach, involving calcilytic compounds that block parathyroid cell Ca2+ receptors and stimulate PTH secretion thereby providing an anabolic therapy for osteoporosis, still awaits clinical validation. Although Ca2+ receptors are expressed throughout the body and in many tissues that are not intimately involved in systemic Ca2+ homeostasis, their physiological and/or pathological significance remains speculative and their value as therapeutic targets is unknown.« less

Applying a palliative care approach in residential care: effects on nurse assistants' work situation.

PubMed

Beck, Ingela; Jakobsson, Ulf; Edberg, Anna-Karin

2015-06-01

The aim was to investigate the effects of an intervention that applies a palliative care approach in residential care upon nurse assistants' level of strain, job satisfaction, and view of leadership. A quasi-experimental, pretest and posttest design was used. Study circles with workshops involving nurse assistants (n = 75) and their superiors (n = 9) focusing on emotional and existential issues in palliative care were evaluated using a questionnaire answered by the nurse assistants at baseline (November 2009), post-intervention (May 2010), and six-month follow-up (November 2010) in comparison with controls (n = 110). Directly after the intervention, the job satisfaction of the nurse assistants decreased and they perceived the leadership more negatively than before the intervention. Six months later, strain as a result of criticism from residents and their superiors and having difficulty in balancing emotional involvement had decreased. The intervention initially seemed to decrease the well-being of the nurse assistants, which could be the result of their increased awareness of the residents' and relatives' needs, in combination with limited support. More emphasis should be placed on the role of leadership when implementing changes in practice.

Optimal experimental design for improving the estimation of growth parameters of Lactobacillus viridescens from data under non-isothermal conditions.

PubMed

Longhi, Daniel Angelo; Martins, Wiaslan Figueiredo; da Silva, Nathália Buss; Carciofi, Bruno Augusto Mattar; de Aragão, Gláucia Maria Falcão; Laurindo, João Borges

2017-01-02

In predictive microbiology, the model parameters have been estimated using the sequential two-step modeling (TSM) approach, in which primary models are fitted to the microbial growth data, and then secondary models are fitted to the primary model parameters to represent their dependence with the environmental variables (e.g., temperature). The Optimal Experimental Design (OED) approach allows reducing the experimental workload and costs, and the improvement of model identifiability because primary and secondary models are fitted simultaneously from non-isothermal data. Lactobacillus viridescens was selected to this study because it is a lactic acid bacterium of great interest to meat products preservation. The objectives of this study were to estimate the growth parameters of L. viridescens in culture medium from TSM and OED approaches and to evaluate both the number of experimental data and the time needed in each approach and the confidence intervals of the model parameters. Experimental data for estimating the model parameters with TSM approach were obtained at six temperatures (total experimental time of 3540h and 196 experimental data of microbial growth). Data for OED approach were obtained from four optimal non-isothermal profiles (total experimental time of 588h and 60 experimental data of microbial growth), two profiles with increasing temperatures (IT) and two with decreasing temperatures (DT). The Baranyi and Roberts primary model and the square root secondary model were used to describe the microbial growth, in which the parameters b and T min (±95% confidence interval) were estimated from the experimental data. The parameters obtained from TSM approach were b=0.0290 (±0.0020) [1/(h 0.5 °C)] and T min =-1.33 (±1.26) [°C], with R 2 =0.986 and RMSE=0.581, and the parameters obtained with the OED approach were b=0.0316 (±0.0013) [1/(h 0.5 °C)] and T min =-0.24 (±0.55) [°C], with R 2 =0.990 and RMSE=0.436. The parameters obtained from OED approach presented smaller confidence intervals and best statistical indexes than those from TSM approach. Besides, less experimental data and time were needed to estimate the model parameters with OED than TSM. Furthermore, the OED model parameters were validated with non-isothermal experimental data with great accuracy. In this way, OED approach is feasible and is a very useful tool to improve the prediction of microbial growth under non-isothermal condition. Copyright © 2016 Elsevier B.V. All rights reserved.

Hume, Mill, Hill, and the Sui Generis Epidemiologic Approach to Causal Inference

PubMed Central

Morabia, Alfredo

2013-01-01

The epidemiologic approach to causal inference (i.e., Hill's viewpoints) consists of evaluating potential causes from the following 2, noncumulative angles: 1) established results from comparative, observational, or experimental epidemiologic studies; and 2) reviews of nonepidemiologic evidence. It does not involve statements of statistical significance. The philosophical roots of Hill's viewpoints are unknown. Superficially, they seem to descend from the ideas of Hume and Mill. Hill's viewpoints, however, use a different kind of evidence and have different purposes than do Hume's rules or Mill's system of logic. In a nutshell, Hume ignores comparative evidence central to Hill's viewpoints. Mill's logic disqualifies as invalid nonexperimental evidence, which forms the bulk of epidemiologic findings reviewed from Hill's viewpoints. The approaches by Hume and Mill cannot corroborate successful implementations of Hill's viewpoints. Besides Hume and Mill, the epidemiologic literature is clueless about a plausible, pre-1965 philosophical origin of Hill's viewpoints. Thus, Hill's viewpoints may be philosophically novel, sui generis, still waiting to be validated and justified. PMID:24071010

An effective biometric discretization approach to extract highly discriminative, informative, and privacy-protective binary representation

NASA Astrophysics Data System (ADS)

Lim, Meng-Hui; Teoh, Andrew Beng Jin

2011-12-01

Biometric discretization derives a binary string for each user based on an ordered set of biometric features. This representative string ought to be discriminative, informative, and privacy protective when it is employed as a cryptographic key in various security applications upon error correction. However, it is commonly believed that satisfying the first and the second criteria simultaneously is not feasible, and a tradeoff between them is always definite. In this article, we propose an effective fixed bit allocation-based discretization approach which involves discriminative feature extraction, discriminative feature selection, unsupervised quantization (quantization that does not utilize class information), and linearly separable subcode (LSSC)-based encoding to fulfill all the ideal properties of a binary representation extracted for cryptographic applications. In addition, we examine a number of discriminative feature-selection measures for discretization and identify the proper way of setting an important feature-selection parameter. Encouraging experimental results vindicate the feasibility of our approach.

A response-time approach to comparing generalized rational and take-the-best models of decision making.

PubMed

Bergert, F Bryan; Nosofsky, Robert M

2007-01-01

The authors develop and test generalized versions of take-the-best (TTB) and rational (RAT) models of multiattribute paired-comparison inference. The generalized models make allowances for subjective attribute weighting, probabilistic orders of attribute inspection, and noisy decision making. A key new test involves a response-time (RT) approach. TTB predicts that RT is determined solely by the expected time required to locate the 1st discriminating attribute, whereas RAT predicts that RT is determined by the difference in summed evidence between the 2 alternatives. Critical test pairs are used that partially decouple these 2 factors. Under conditions in which ideal observer TTB and RAT strategies yield equivalent decisions, both the RT results and the estimated attribute weights suggest that the vast majority of subjects adopted the generalized TTB strategy. The RT approach is also validated in an experimental condition in which use of a RAT strategy is essentially forced upon subjects. (c) 2007 APA, all rights reserved.

Behavioural responses of dogs to asymmetrical tail wagging of a robotic dog replica.

PubMed

Artelle, K A; Dumoulin, L K; Reimchen, T E

2011-03-01

Recent evidence suggests that bilateral asymmetry in the amplitude of tail wagging of domestic dogs (Canis familiaris) is associated with approach (right wag) versus withdrawal (left wag) motivation and may be the by-product of hemispheric dominance. We consider whether such asymmetry in motion of the tail, a crucial appendage in intra-specific communication in all canids, provides visual information to a conspecific leading to differential behaviour. To evaluate this, we experimentally investigated the approach behaviour of free-ranging dogs to the asymmetric tail wagging of a life-size robotic dog replica. Our data, involving 452 separate interactions, showed a significantly greater proportion of dogs approaching the model continuously without stopping when the tail wagged to the left, compared with a right wag, which was more likely to yield stops. While the results indicate that laterality of a wagging tail provides behavioural information to conspecifics, the responses are not readily integrated into the predicted behaviour based on hemispheric dominance.

Identification of Protein–Excipient Interaction Hotspots Using Computational Approaches

PubMed Central

Barata, Teresa S.; Zhang, Cheng; Dalby, Paul A.; Brocchini, Steve; Zloh, Mire

2016-01-01

Protein formulation development relies on the selection of excipients that inhibit protein–protein interactions preventing aggregation. Empirical strategies involve screening many excipient and buffer combinations using force degradation studies. Such methods do not readily provide information on intermolecular interactions responsible for the protective effects of excipients. This study describes a molecular docking approach to screen and rank interactions allowing for the identification of protein–excipient hotspots to aid in the selection of excipients to be experimentally screened. Previously published work with Drosophila Su(dx) was used to develop and validate the computational methodology, which was then used to determine the formulation hotspots for Fab A33. Commonly used excipients were examined and compared to the regions in Fab A33 prone to protein–protein interactions that could lead to aggregation. This approach could provide information on a molecular level about the protective interactions of excipients in protein formulations to aid the more rational development of future formulations. PMID:27258262

Parallel consensual neural networks.

PubMed

Benediktsson, J A; Sveinsson, J R; Ersoy, O K; Swain, P H

1997-01-01

A new type of a neural-network architecture, the parallel consensual neural network (PCNN), is introduced and applied in classification/data fusion of multisource remote sensing and geographic data. The PCNN architecture is based on statistical consensus theory and involves using stage neural networks with transformed input data. The input data are transformed several times and the different transformed data are used as if they were independent inputs. The independent inputs are first classified using the stage neural networks. The output responses from the stage networks are then weighted and combined to make a consensual decision. In this paper, optimization methods are used in order to weight the outputs from the stage networks. Two approaches are proposed to compute the data transforms for the PCNN, one for binary data and another for analog data. The analog approach uses wavelet packets. The experimental results obtained with the proposed approach show that the PCNN outperforms both a conjugate-gradient backpropagation neural network and conventional statistical methods in terms of overall classification accuracy of test data.

The mechanism distinguishability problem in biochemical kinetics: the single-enzyme, single-substrate reaction as a case study.

PubMed

Schnell, Santiago; Chappell, Michael J; Evans, Neil D; Roussel, Marc R

2006-01-01

A theoretical analysis of the distinguishability problem of two rival models of the single enzyme-single substrate reaction, the Michaelis-Menten and Henri mechanisms, is presented. We also outline a general approach for analysing the structural indistinguishability between two mechanisms. The approach involves constructing, if possible, a smooth mapping between the two candidate models. Evans et al. [N.D. Evans, M.J. Chappell, M.J. Chapman, K.R. Godfrey, Structural indistinguishability between uncontrolled (autonomous) nonlinear analytic systems, Automatica 40 (2004) 1947-1953] have shown that if, in addition, either of the mechanisms satisfies a particular criterion then such a transformation always exists when the models are indistinguishable from their experimentally observable outputs. The approach is applied to the single enzyme-single substrate reaction mechanism. In principle, mechanisms can be distinguished using this analysis, but we show that our ability to distinguish mechanistic models depends both on the precise measurements made, and on our knowledge of the system prior to performing the kinetics experiments.

Hume, Mill, Hill, and the sui generis epidemiologic approach to causal inference.

PubMed

Morabia, Alfredo

2013-11-15

The epidemiologic approach to causal inference (i.e., Hill's viewpoints) consists of evaluating potential causes from the following 2, noncumulative angles: 1) established results from comparative, observational, or experimental epidemiologic studies; and 2) reviews of nonepidemiologic evidence. It does not involve statements of statistical significance. The philosophical roots of Hill's viewpoints are unknown. Superficially, they seem to descend from the ideas of Hume and Mill. Hill's viewpoints, however, use a different kind of evidence and have different purposes than do Hume's rules or Mill's system of logic. In a nutshell, Hume ignores comparative evidence central to Hill's viewpoints. Mill's logic disqualifies as invalid nonexperimental evidence, which forms the bulk of epidemiologic findings reviewed from Hill's viewpoints. The approaches by Hume and Mill cannot corroborate successful implementations of Hill's viewpoints. Besides Hume and Mill, the epidemiologic literature is clueless about a plausible, pre-1965 philosophical origin of Hill's viewpoints. Thus, Hill's viewpoints may be philosophically novel, sui generis, still waiting to be validated and justified.

Cell-oriented modeling of angiogenesis.

PubMed

Guidolin, Diego; Rebuffat, Piera; Albertin, Giovanna

2011-01-01

Due to its significant involvement in various physiological and pathological conditions, angiogenesis (the development of new blood vessels from an existing vasculature) represents an important area of the actual biological research and a field in which mathematical modeling proved particularly useful in supporting the experimental work. In this paper, we focus on a specific modeling strategy, known as "cell-centered" approach. This type of mathematical models work at a "mesoscopic scale," assuming the cell as the natural level of abstraction for computational modeling of development. They treat cells phenomenologically, considering their essential behaviors to study how tissue structure and organization emerge from the collective dynamics of multiple cells. The main contributions of the cell-oriented approach to the study of the angiogenic process will be described. From one side, they have generated "basic science understanding" about the process of capillary assembly during development, growth, and pathology. On the other side, models were also developed supporting "applied biomedical research" for the purpose of identifying new therapeutic targets and clinically relevant approaches for either inhibiting or stimulating angiogenesis.

A general approach for sample size calculation for the three-arm 'gold standard' non-inferiority design.

PubMed

Stucke, Kathrin; Kieser, Meinhard

2012-12-10

In the three-arm 'gold standard' non-inferiority design, an experimental treatment, an active reference, and a placebo are compared. This design is becoming increasingly popular, and it is, whenever feasible, recommended for use by regulatory guidelines. We provide a general method to calculate the required sample size for clinical trials performed in this design. As special cases, the situations of continuous, binary, and Poisson distributed outcomes are explored. Taking into account the correlation structure of the involved test statistics, the proposed approach leads to considerable savings in sample size as compared with application of ad hoc methods for all three scale levels. Furthermore, optimal sample size allocation ratios are determined that result in markedly smaller total sample sizes as compared with equal assignment. As optimal allocation makes the active treatment groups larger than the placebo group, implementation of the proposed approach is also desirable from an ethical viewpoint. Copyright © 2012 John Wiley & Sons, Ltd.

Multiplex biomarker approach to cardiovascular diseases.

PubMed

Adamcova, Michaela; Šimko, Fedor

2018-04-12

Personalized medicine is partly based on biomarker-guided diagnostics, therapy and prognosis, which is becoming an unavoidable concept in modern cardiology. However, the clinical significance of single biomarker studies is rather limited. A promising novel approach involves combining multiple markers into a multiplex panel, which could refine the management of a particular patient with cardiovascular pathology. Two principally different assay formats have been developed to facilitate simultaneous quantification of multiple antigens: planar array assays and microbead assays. These approaches may help to better evaluate the complexity and dynamic nature of pathologic processes and offer substantial cost and sample savings compared with traditional enzyme-linked immunosorbent assay (ELISA) measurements. However, a multiplex multimarker approach cannot become a generally disseminated method until analytical problems are solved and further studies confirming improved clinical outcomes are accomplished. These drawbacks underlie the fact that a limited number of systematic studies are available regarding the use of a multiplex biomarker approach in cardiovascular medicine to date. Our perspective underscores the significant potential of the use of the multiplex approach in a wider conceptual framework under the close cooperation of clinical and experimental cardiologists, pathophysiologists and biochemists so that the personalized approach based on standardized multimarker testing may improve the management of various cardiovascular pathologies and become a ubiquitous partner of population-derived evidence-based medicine.

Evaluation of a New Molecular Entity as a Victim of Metabolic Drug-Drug Interactions-an Industry Perspective.

PubMed

Bohnert, Tonika; Patel, Aarti; Templeton, Ian; Chen, Yuan; Lu, Chuang; Lai, George; Leung, Louis; Tse, Susanna; Einolf, Heidi J; Wang, Ying-Hong; Sinz, Michael; Stearns, Ralph; Walsky, Robert; Geng, Wanping; Sudsakorn, Sirimas; Moore, David; He, Ling; Wahlstrom, Jan; Keirns, Jim; Narayanan, Rangaraj; Lang, Dieter; Yang, Xiaoqing

2016-08-01

Under the guidance of the International Consortium for Innovation and Quality in Pharmaceutical Development (IQ), scientists from 20 pharmaceutical companies formed a Victim Drug-Drug Interactions Working Group. This working group has conducted a review of the literature and the practices of each company on the approaches to clearance pathway identification (fCL), estimation of fractional contribution of metabolizing enzyme toward metabolism (fm), along with modeling and simulation-aided strategy in predicting the victim drug-drug interaction (DDI) liability due to modulation of drug metabolizing enzymes. Presented in this perspective are the recommendations from this working group on: 1) strategic and experimental approaches to identify fCL and fm, 2) whether those assessments may be quantitative for certain enzymes (e.g., cytochrome P450, P450, and limited uridine diphosphoglucuronosyltransferase, UGT enzymes) or qualitative (for most of other drug metabolism enzymes), and the impact due to the lack of quantitative information on the latter. Multiple decision trees are presented with stepwise approaches to identify specific enzymes that are involved in the metabolism of a given drug and to aid the prediction and risk assessment of drug as a victim in DDI. Modeling and simulation approaches are also discussed to better predict DDI risk in humans. Variability and parameter sensitivity analysis were emphasized when applying modeling and simulation to capture the differences within the population used and to characterize the parameters that have the most influence on the prediction outcome. Copyright © 2016 by The American Society for Pharmacology and Experimental Therapeutics.

Quantitative biology: where modern biology meets physical sciences.

PubMed

Shekhar, Shashank; Zhu, Lian; Mazutis, Linas; Sgro, Allyson E; Fai, Thomas G; Podolski, Marija

2014-11-05

Quantitative methods and approaches have been playing an increasingly important role in cell biology in recent years. They involve making accurate measurements to test a predefined hypothesis in order to compare experimental data with predictions generated by theoretical models, an approach that has benefited physicists for decades. Building quantitative models in experimental biology not only has led to discoveries of counterintuitive phenomena but has also opened up novel research directions. To make the biological sciences more quantitative, we believe a two-pronged approach needs to be taken. First, graduate training needs to be revamped to ensure biology students are adequately trained in physical and mathematical sciences and vice versa. Second, students of both the biological and the physical sciences need to be provided adequate opportunities for hands-on engagement with the methods and approaches necessary to be able to work at the intersection of the biological and physical sciences. We present the annual Physiology Course organized at the Marine Biological Laboratory (Woods Hole, MA) as a case study for a hands-on training program that gives young scientists the opportunity not only to acquire the tools of quantitative biology but also to develop the necessary thought processes that will enable them to bridge the gap between these disciplines. © 2014 Shekhar, Zhu, Mazutis, Sgro, Fai, and Podolski. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Evaluation of an electricity-free, culture-based approach for detecting typhoidal Salmonella bacteremia during enteric fever in a high burden, resource-limited setting.

PubMed

Andrews, Jason R; Prajapati, Krishna G; Eypper, Elizabeth; Shrestha, Poojan; Shakya, Mila; Pathak, Kamal R; Joshi, Niva; Tiwari, Priyanka; Risal, Manisha; Koirala, Samir; Karkey, Abhilasha; Dongol, Sabina; Wen, Shawn; Smith, Amy B; Maru, Duncan; Basnyat, Buddha; Baker, Stephen; Farrar, Jeremy; Ryan, Edward T; Hohmann, Elizabeth; Arjyal, Amit

2013-01-01

In many rural areas at risk for enteric fever, there are few data on Salmonella enterica serotypes Typhi (S. Typhi) and Paratyphi (S. Paratyphi) incidence, due to limited laboratory capacity for microbiologic culture. Here, we describe an approach that permits recovery of the causative agents of enteric fever in such settings. This approach involves the use of an electricity-free incubator based upon use of phase-change materials. We compared this against conventional blood culture for detection of typhoidal Salmonella. Three hundred and four patients with undifferentiated fever attending the outpatient and emergency departments of a public hospital in the Kathmandu Valley of Nepal were recruited. Conventional blood culture was compared against an electricity-free culture approach. Blood from 66 (21.7%) patients tested positive for a Gram-negative bacterium by at least one of the two methods. Sixty-five (21.4%) patients tested blood culture positive for S. Typhi (30; 9.9%) or S. Paratyphi A (35; 11.5%). From the 65 individuals with culture-confirmed enteric fever, 55 (84.6%) were identified by the conventional blood culture and 60 (92.3%) were identified by the experimental method. Median time-to-positivity was 2 days for both procedures. The experimental approach was falsely positive due to probable skin contaminants in 2 of 239 individuals (0.8%). The percentages of positive and negative agreement for diagnosis of enteric fever were 90.9% (95% CI: 80.0%-97.0%) and 96.0% (92.7%-98.1%), respectively. After initial incubation, Salmonella isolates could be readily recovered from blood culture bottles maintained at room temperature for six months. A simple culture approach based upon a phase-change incubator can be used to isolate agents of enteric fever. This approach could be used as a surveillance tool to assess incidence and drug resistance of the etiologic agents of enteric fever in settings without reliable local access to electricity or local diagnostic microbiology laboratories.

Implicit flux-split Euler schemes for unsteady aerodynamic analysis involving unstructured dynamic meshes

NASA Technical Reports Server (NTRS)

Batina, John T.

1990-01-01

Improved algorithms for the solution of the time-dependent Euler equations are presented for unsteady aerodynamic analysis involving unstructured dynamic meshes. The improvements have been developed recently to the spatial and temporal discretizations used by unstructured grid flow solvers. The spatial discretization involves a flux-split approach which is naturally dissipative and captures shock waves sharply with at most one grid point within the shock structure. The temporal discretization involves an implicit time-integration shceme using a Gauss-Seidel relaxation procedure which is computationally efficient for either steady or unsteady flow problems. For example, very large time steps may be used for rapid convergence to steady state, and the step size for unsteady cases may be selected for temporal accuracy rather than for numerical stability. Steady and unsteady flow results are presented for the NACA 0012 airfoil to demonstrate applications of the new Euler solvers. The unsteady results were obtained for the airfoil pitching harmonically about the quarter chord. The resulting instantaneous pressure distributions and lift and moment coefficients during a cycle of motion compare well with experimental data. The paper presents a description of the Euler solvers along with results and comparisons which assess the capability.

Implicit flux-split Euler schemes for unsteady aerodynamic analysis involving unstructured dynamic meshes

NASA Technical Reports Server (NTRS)

Batina, John T.

1990-01-01

Improved algorithm for the solution of the time-dependent Euler equations are presented for unsteady aerodynamic analysis involving unstructured dynamic meshes. The improvements were developed recently to the spatial and temporal discretizations used by unstructured grid flow solvers. The spatial discretization involves a flux-split approach which is naturally dissipative and captures shock waves sharply with at most one grid point within the shock structure. The temporal discretization involves an implicit time-integration scheme using a Gauss-Seidel relaxation procedure which is computationally efficient for either steady or unsteady flow problems. For example, very large time steps may be used for rapid convergence to steady state, and the step size for unsteady cases may be selected for temporal accuracy rather than for numerical stability. Steady and unsteady flow results are presented for the NACA 0012 airfoil to demonstrate applications of the new Euler solvers. The unsteady results were obtained for the airfoil pitching harmonically about the quarter chord. The resulting instantaneous pressure distributions and lift and moment coefficients during a cycle of motion compare well with experimental data. A description of the Euler solvers is presented along with results and comparisons which assess the capability.

Jacques Loeb, B. F. Skinner, and the legacy of prediction and control

PubMed Central

Hackenberg, Timothy D.

1995-01-01

The biologist Jacques Loeb is an important figure in the history of behavior analysis. Between 1890 and 1915, Loeb championed an approach to experimental biology that would later exert substantial influence on the work of B. F. Skinner and behavior analysis. This paper examines some of these sources of influence, with a particular emphasis on Loeb's firm commitment to prediction and control as fundamental goals of an experimental life science, and how these goals were extended and broadened by Skinner. Both Loeb and Skinner adopted a pragmatic approach to science that put practical control of their subject matter above formal theory testing, both based their research programs on analyses of reproducible units involving the intact organism, and both strongly endorsed technological applications of basic laboratory science. For Loeb, but especially for Skinner, control came to mean something more than mere experimental or technological control for its own sake; it became synonomous with scientific understanding. This view follows from (a) the successful working model of science Loeb and Skinner inherited from Ernst Mach, in which science is viewed as human social activity, and effective practical action is taken as the basis of scientific knowledge, and (b) Skinner's analysis of scientific activity, situated in the world of direct experience and related to practices arranged by scientific verbal communities. From this perspective, prediction and control are human acts that arise from and are maintained by social circumstances in which such acts meet with effective consequences. PMID:22478220

Biomedical discovery acceleration, with applications to craniofacial development.

PubMed

Leach, Sonia M; Tipney, Hannah; Feng, Weiguo; Baumgartner, William A; Kasliwal, Priyanka; Schuyler, Ronald P; Williams, Trevor; Spritz, Richard A; Hunter, Lawrence

2009-03-01

The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning, and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or using biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data. An implementation of this approach, called the Hanalyzer, is demonstrated on a large-scale gene expression array dataset relevant to craniofacial development. The use of the tool was critical in the creation of hypotheses regarding the roles of four genes never previously characterized as involved in craniofacial development; each of these hypotheses was validated by further experimental work.

IR, Raman and Vibrational Optical Activity Spectra of Methyl Glycidate in Chloroform and Water: The Clusters-in-a-Liquid Solvation Model.

PubMed

Xu, Yunjie; Perera, Angelo Shehan; Cheramy, Joseph; Merten, Christian; Thomas, Javix

2018-05-16

Solvent effects, in particular those involving water as the solvent, are of significant interest to chemistry and physics communities. IR, vibrational circular dichroism (VCD), Raman, and Raman optical activity (ROA) spectra of methyl glycidate in two very different solvents, namely CCl4 and water, have been measured experimentally and simulated theoretically. While the observed spectra in CCl4 could be well modelled using the polarizable continuum model for the solvent, the situation is much different in water. The experimental VCD spectrum of methyl glycidate in water reveals strong induced VCD signatures in the water bending region, indicating the presence of the relatively long-lived methyl glycidate-watern complexes. We applied the clusters-in-a-liquid approach to identify the dominant methyl glycidate-water1,2 complexes which are the long-lived species responsible for all the spectra observed in water. We examined the influences of solvent dielectric environment and the hydrogen-bonding interactions on the conformational distribution of methyl glycidate. The geometry optimizations, frequency calculations, IR, VCD, Raman and ROA intensity calculations were performed at the B3LYP/6-311++G(2d,p) and aug-cc-pVTZ levels of theory with D3BJ dispersion correction. It is particularly satisfying to note that the clusters-in-a-liquid approach has captured all main experimental features in IR, VCD, Raman and ROA spectra of methyl glycidate in water. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Utility of CRISPR/Cas9 systems in hematology research.

PubMed

Lucas, Daniel; O'Leary, Heather A; Ebert, Benjamin L; Cowan, Chad A; Tremblay, Cedric S

2017-10-01

Since the end of the 20th century, novel approaches have emerged to manipulate experimental models of hematological disorders so that they more accurately mirror what is observed in the clinical setting. Despite these technological advances, the characterization of crucial genes for benign or malignant hematological disorders remains challenging, given the dynamic nature of the hematopoietic system and the genetic heterogeneity of these disorders. To overcome this limitation, genome-editing technologies have been developed to manipulate the genome specifically via deletion, insertion, or modification of targeted loci. These technologies have progressed swiftly, allowing their common use to investigate genetic function in experimental hematology. Among them, homologous-recombination-mediated targeting technologies have facilitated the manipulation of specific loci by generating knock-out and knock-in models. Despite promoting significant advances in our understanding of the molecular mechanisms involved in hematology, these inefficient, time-consuming, and labor-intensive approaches did not permit the development of cellular or animal models, recapitulating the complexity of hematological disorders. On October 26, 2016, Drs. Ben Ebert and Chad Cowan shared their knowledge of and experience with the utilization of CRISPR for models of myeloid malignancy, disease, and novel therapeutics in an International Society for Experimental Hematology webinar titled "Utility of CRISPR/Cas9 Systems in Hematology Research." Here, we provide an overview of the topics they covered, including their insights into the novel applications of the technique and its strengths and limitations. Copyright © 2017 ISEH – Society for Hematology and Stem Cells. Published by Elsevier Inc. All rights reserved.

Direct measurement of nuclear cross-section of astrophysical interest: Results and perspectives

NASA Astrophysics Data System (ADS)

Cavanna, Francesca; Prati, Paolo

2018-03-01

Stellar evolution and nucleosynthesis are interconnected by a wide network of nuclear reactions: the study of such connection is usually known as nuclear astrophysics. The main task of this discipline is the determination of nuclear cross-section and hence of the reaction rate in different scenarios, i.e. from the synthesis of a few very light isotopes just after the Big Bang to the heavy element production in the violent explosive end of massive stars. The experimental determination of reaction cross-section at the astrophysical relevant energies is extremely difficult, sometime impossible, due to the Coulomb repulsion between the interacting nuclei which turns out in cross-section values down to the fbar level. To overcome these obstacles, several experimental approaches have been developed and the adopted techniques can be roughly divided into two categories, i.e. direct and indirect methods. In this review paper, the general problem of nuclear astrophysics is introduced and discussed from the point of view of experimental approach. We focus on direct methods and in particular on the features of low-background experiments performed at underground laboratory facilities. The present knowledge of reactions involved in the Big Bang and stellar hydrogen-burning scenarios is discussed as well as the ongoing projects aiming to investigate mainly the helium- and carbon-burning phases. Worldwide, a new generation of experiment in the MeV range is in the design phase or at the very first steps and decisive progresses are expected to come in the next years.

Modeling cell adhesion and proliferation: a cellular-automata based approach.

PubMed

Vivas, J; Garzón-Alvarado, D; Cerrolaza, M

Cell adhesion is a process that involves the interaction between the cell membrane and another surface, either a cell or a substrate. Unlike experimental tests, computer models can simulate processes and study the result of experiments in a shorter time and lower costs. One of the tools used to simulate biological processes is the cellular automata, which is a dynamic system that is discrete both in space and time. This work describes a computer model based on cellular automata for the adhesion process and cell proliferation to predict the behavior of a cell population in suspension and adhered to a substrate. The values of the simulated system were obtained through experimental tests on fibroblast monolayer cultures. The results allow us to estimate the cells settling time in culture as well as the adhesion and proliferation time. The change in the cells morphology as the adhesion over the contact surface progress was also observed. The formation of the initial link between cell and the substrate of the adhesion was observed after 100 min where the cell on the substrate retains its spherical morphology during the simulation. The cellular automata model developed is, however, a simplified representation of the steps in the adhesion process and the subsequent proliferation. A combined framework of experimental and computational simulation based on cellular automata was proposed to represent the fibroblast adhesion on substrates and changes in a macro-scale observed in the cell during the adhesion process. The approach showed to be simple and efficient.

Assessing the Accuracy of Generalized Inferences From Comparison Group Studies Using a Within-Study Comparison Approach: The Methodology.

PubMed

Jaciw, Andrew P

2016-06-01

Various studies have examined bias in impact estimates from comparison group studies (CGSs) of job training programs, and in education, where results are benchmarked against experimental results. Such within-study comparison (WSC) approaches investigate levels of bias in CGS-based impact estimates, as well as the success of various design and analytic strategies for reducing bias. This article reviews past literature and summarizes conditions under which CGSs replicate experimental benchmark results. It extends the framework to, and develops the methodology for, situations where results from CGSs are generalized to untreated inference populations. Past research is summarized; methods are developed to examine bias in program impact estimates based on cross-site comparisons in a multisite trial that are evaluated against site-specific experimental benchmarks. Students in Grades K-3 in 79 schools in Tennessee; students in Grades 4-8 in 82 schools in Alabama. Grades K-3 Stanford Achievement Test (SAT) in reading and math scores; Grades 4-8 SAT10 reading scores. Past studies show that bias in CGS-based estimates can be limited through strong design, with local matching, and appropriate analysis involving pretest covariates and variables that represent selection processes. Extension of the methodology to investigate accuracy of generalized estimates from CGSs shows bias from confounders and effect moderators. CGS results, when extrapolated to untreated inference populations, may be biased due to variation in outcomes and impact. Accounting for effects of confounders or moderators may reduce bias. © The Author(s) 2016.

Kβ Mainline X-ray Emission Spectroscopy as an Experimental Probe of Metal–Ligand Covalency

PubMed Central

2015-01-01

The mainline feature in metal Kβ X-ray emission spectroscopy (XES) has long been recognized as an experimental marker for the spin state of the metal center. However, even within a series of metal compounds with the same nominal oxidation and spin state, significant changes are observed that cannot be explained on the basis of overall spin. In this work, the origin of these effects is explored, both experimentally and theoretically, in order to develop the chemical information content of Kβ mainline XES. Ligand field expressions are derived that describe the behavior of Kβ mainlines for first row transition metals with any dn count, allowing for a detailed analysis of the factors governing mainline shape. Further, due to limitations associated with existing computational approaches, we have developed a new methodology for calculating Kβ mainlines using restricted active space configuration interaction (RAS–CI) calculations. This approach eliminates the need for empirical parameters and provides a powerful tool for investigating the effects that chemical environment exerts on the mainline spectra. On the basis of a detailed analysis of the intermediate and final states involved in these transitions, we confirm the known sensitivity of Kβ mainlines to metal spin state via the 3p–3d exchange coupling. Further, a quantitative relationship between the splitting of the Kβ mainline features and the metal–ligand covalency is established. Thus, this study furthers the quantitative electronic structural information that can be extracted from Kβ mainline spectroscopy. PMID:24914450

Learning with older people--Outcomes of a quasi-experimental study.

PubMed

Koskinen, Sanna; Salminen, Leena; Puukka, Pauli; Leino-Kilpi, Helena

2016-02-01

Nursing students' interest in older people nursing needs to be enhanced, as there is a demand for competent nurses who prefer to work in older people nursing. Educational approaches involving older people are encouraging; they increase positive learning outcomes. The aim of this study was to evaluate the outcomes of the Learning with Older People Programme (LOPP) in terms of nursing students' interest in older people nursing, their attitudes towards older people and their knowledge level about ageing. A quasi-experimental, pre-post-test design with non-equivalent comparison group was used. Two different Finnish nursing schools geographically apart from each other. A nonprobability, convenience sample of nursing students (n=87; n=46 in the intervention group, n=41 in the comparison group) in the middle of their 3.5 year bachelor degree studies and enrolled in compulsory theoretical older people nursing courses participated in the study. Data were collected in 2014 using a structured questionnaire that included background questions, students' interest in older people nursing as a primary outcome measure and their attitudes towards older people and knowledge level about ageing as secondary outcome measures. The data were analysed statistically. In the intervention group, students' interest in older people nursing was significantly higher and their attitudes towards older people were more positive than those of students in the comparison group. There were no significant differences between the groups in terms of the students' knowledge level about ageing. An educational approach involving older people resulted in encouraging outcomes. It is worth considering whether or not older people could be a valuable resource for nursing education. Copyright © 2015 Elsevier Ltd. All rights reserved.

A functional selectivity mechanism at the serotonin-2A GPCR involves ligand-dependent conformations of intracellular loop 2

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

Perez-Aguilar, Jose Manuel; Shan, Jufang; LeVine, Michael V.

With recent progress in determination of G protein-coupled receptor (GPCR) structure with crystallography, a variety of other experimental approaches (e.g., NMR spectroscopy, fluorescent-based assays, mass spectrometry techniques) are also being used to characterize state-specific and ligand-specific conformational states. MD simulations offer a powerful complementary approach to elucidate the dynamic features associated with ligand-specific GPCR conformations. To shed light on the conformational elements and dynamics of the important aspect of GPCR functional selectivity, we carried out unbiased microsecond-length MD simulations of the human serotonin 2A receptor (5-HT 2AR) in the absence of ligand and bound to four distinct serotonergic agonists. Themore » 5-HT 2AR is a suitable system to study the structural features involved in the ligand-dependent conformational heterogeneity of GPCRs because it is well-characterized experimentally and exhibits a strong agonist-specific phenotype in that some 5-HT 2AR agonists induce LSD-like hallucinations, while others lack this psychoactive property entirely. Here we report evidence for structural and dynamic differences in 5-HT 2AR interacting with such pharmacologically distinct ligands, hallucinogens, and nonhallucinogens obtained from all-atom MD simulations. Differential ligand binding contacts were identified for structurally similar hallucinogens and nonhallucinogens and found to correspond to different conformations in the intracellular loop 2 (ICL2). From the different ICL2 conformations, functional selective phenotypes are suggested through effects on dimerization and/or distinct direct interaction with effector proteins. Lastly, the findings are presented in the context of currently proposed hallucinogenesis mechanisms, and ICL2 is proposed as a fine-tuning selective switch that can differentiates modes of 5-HT 2AR activation.« less

A functional selectivity mechanism at the serotonin-2A GPCR involves ligand-dependent conformations of intracellular loop 2

DOE PAGES

Perez-Aguilar, Jose Manuel; Shan, Jufang; LeVine, Michael V.; ...

2014-10-14

With recent progress in determination of G protein-coupled receptor (GPCR) structure with crystallography, a variety of other experimental approaches (e.g., NMR spectroscopy, fluorescent-based assays, mass spectrometry techniques) are also being used to characterize state-specific and ligand-specific conformational states. MD simulations offer a powerful complementary approach to elucidate the dynamic features associated with ligand-specific GPCR conformations. To shed light on the conformational elements and dynamics of the important aspect of GPCR functional selectivity, we carried out unbiased microsecond-length MD simulations of the human serotonin 2A receptor (5-HT 2AR) in the absence of ligand and bound to four distinct serotonergic agonists. Themore » 5-HT 2AR is a suitable system to study the structural features involved in the ligand-dependent conformational heterogeneity of GPCRs because it is well-characterized experimentally and exhibits a strong agonist-specific phenotype in that some 5-HT 2AR agonists induce LSD-like hallucinations, while others lack this psychoactive property entirely. Here we report evidence for structural and dynamic differences in 5-HT 2AR interacting with such pharmacologically distinct ligands, hallucinogens, and nonhallucinogens obtained from all-atom MD simulations. Differential ligand binding contacts were identified for structurally similar hallucinogens and nonhallucinogens and found to correspond to different conformations in the intracellular loop 2 (ICL2). From the different ICL2 conformations, functional selective phenotypes are suggested through effects on dimerization and/or distinct direct interaction with effector proteins. Lastly, the findings are presented in the context of currently proposed hallucinogenesis mechanisms, and ICL2 is proposed as a fine-tuning selective switch that can differentiates modes of 5-HT 2AR activation.« less