UltraPse: A Universal and Extensible Software Platform for Representing Biological Sequences.

Science.gov (United States)

Du, Pu-Feng; Zhao, Wei; Miao, Yang-Yang; Wei, Le-Yi; Wang, Likun

2017-11-14

With the avalanche of biological sequences in public databases, one of the most challenging problems in computational biology is to predict their biological functions and cellular attributes. Most of the existing prediction algorithms can only handle fixed-length numerical vectors. Therefore, it is important to be able to represent biological sequences with various lengths using fixed-length numerical vectors. Although several algorithms, as well as software implementations, have been developed to address this problem, these existing programs can only provide a fixed number of representation modes. Every time a new sequence representation mode is developed, a new program will be needed. In this paper, we propose the UltraPse as a universal software platform for this problem. The function of the UltraPse is not only to generate various existing sequence representation modes, but also to simplify all future programming works in developing novel representation modes. The extensibility of UltraPse is particularly enhanced. It allows the users to define their own representation mode, their own physicochemical properties, or even their own types of biological sequences. Moreover, UltraPse is also the fastest software of its kind. The source code package, as well as the executables for both Linux and Windows platforms, can be downloaded from the GitHub repository.

Distinguishing between "function" and "effect" in genome biology.

Science.gov (United States)

Doolittle, W Ford; Brunet, Tyler D P; Linquist, Stefan; Gregory, T Ryan

2014-05-09

Much confusion in genome biology results from conflation of possible meanings of the word "function." We suggest that, in this connection, attention should be paid to evolutionary biologists and philosophers who have previously dealt with this problem. We need only decide that although all genomic structures have effects, only some of them should be said to have functions. Although it will very often be difficult or impossible to establish function (strictly defined), it should not automatically be assumed. We enjoin genomicists in particular to pay greater attention to parsing biological effects. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

A Unifying Theory of Biological Function

NARCIS (Netherlands)

van Hateren, J. H.

2017-01-01

A new theory that naturalizes biological function is explained and compared with earlier etiological and causal role theories. Etiological (or selected effects) theories explain functions from how they are caused over their evolutionary history. Causal role theories analyze how functional mechanisms

Coherent mode decomposition using mixed Wigner functions of Hermite-Gaussian beams.

Science.gov (United States)

Tanaka, Takashi

2017-04-15

A new method of coherent mode decomposition (CMD) is proposed that is based on a Wigner-function representation of Hermite-Gaussian beams. In contrast to the well-known method using the cross spectral density (CSD), it directly determines the mode functions and their weights without solving the eigenvalue problem. This facilitates the CMD of partially coherent light whose Wigner functions (and thus CSDs) are not separable, in which case the conventional CMD requires solving an eigenvalue problem with a large matrix and thus is numerically formidable. An example is shown regarding the CMD of synchrotron radiation, one of the most important applications of the proposed method.

A functional overview of conservation biological control

DEFF Research Database (Denmark)

Begg, Graham S; Cook, Samantha M; Dye, Richard

2017-01-01

Conservation biological control (CBC) is a sustainable approach to pest management that can contribute to a reduction in pesticide use as part of an Integrated Pest Management (IPM) strategy. CBC is based on the premise that countering habitat loss and environmental disturbance associated...... CBC prescriptions have proved elusive. To tackle this, we consolidate existing knowledge of CBC using a simple conceptual model that organises the functional elements of CBC into a common, unifying framework. We identify and integrate the key biological processes affecting natural enemies...... and their biological control function across local and regional scales, and consider the interactions, interdependencies and constraints that determine the outcome of CBC strategies. Conservation measures are often effective in supporting natural enemy populations but their success cannot be guaranteed; the greatest...

Uncovering Biological Network Function via Graphlet Degree Signatures

Directory of Open Access Journals (Sweden)

Nataša Pržulj

2008-01-01

Full Text Available Motivation: Proteins are essential macromolecules of life and thus understanding their function is of great importance. The number of functionally unclassified proteins is large even for simple and well studied organisms such as baker’s yeast. Methods for determining protein function have shifted their focus from targeting specific proteins based solely on sequence homology to analyses of the entire proteome based on protein-protein interaction (PPI networks. Since proteins interact to perform a certain function, analyzing structural properties of PPI networks may provide useful clues about the biological function of individual proteins, protein complexes they participate in, and even larger subcellular machines.Results: We design a sensitive graph theoretic method for comparing local structures of node neighborhoods that demonstrates that in PPI networks, biological function of a node and its local network structure are closely related. The method summarizes a protein’s local topology in a PPI network into the vector of graphlet degrees called the signature of the protein and computes the signature similarities between all protein pairs. We group topologically similar proteins under this measure in a PPI network and show that these protein groups belong to the same protein complexes, perform the same biological functions, are localized in the same subcellular compartments, and have the same tissue expressions. Moreover, we apply our technique on a proteome-scale network data and infer biological function of yet unclassified proteins demonstrating that our method can provide valuable guidelines for future experimental research such as disease protein prediction.Availability: Data is available upon request.

Dynamic simulation and modeling of the motion modes produced during the 3D controlled manipulation of biological micro/nanoparticles based on the AFM.

Science.gov (United States)

Saraee, Mahdieh B; Korayem, Moharam H

2015-08-07

Determining the motion modes and the exact position of a particle displaced during the manipulation process is of special importance. This issue becomes even more important when the studied particles are biological micro/nanoparticles and the goals of manipulation are the transfer of these particles within body cells, repair of cancerous cells and the delivery of medication to damaged cells. However, due to the delicate nature of biological nanoparticles and their higher vulnerability, by obtaining the necessary force of manipulation for the considered motion mode, we can prevent the sample from interlocking with or sticking to the substrate because of applying a weak force or avoid damaging the sample due to the exertion of excessive force. In this paper, the dynamic behaviors and the motion modes of biological micro/nanoparticles such as DNA, yeast, platelet and bacteria due to the 3D manipulation effect have been investigated. Since the above nanoparticles generally have a cylindrical shape, the cylindrical contact models have been employed in an attempt to more precisely model the forces exerted on the nanoparticle during the manipulation process. Also, this investigation has performed a comprehensive modeling and simulation of all the possible motion modes in 3D manipulation by taking into account the eccentricity of the applied load on the biological nanoparticle. The obtained results indicate that unlike the macroscopic scale, the sliding of nanoparticle on substrate in nano-scale takes place sooner than the other motion modes and that the spinning about the vertical and transverse axes and the rolling of nanoparticle occur later than the other motion modes. The simulation results also indicate that the applied force necessary for the onset of nanoparticle movement and the resulting motion mode depend on the size and aspect ratio of the nanoparticle. Copyright © 2015 Elsevier Ltd. All rights reserved.

Towards Integration of Biological and Physiological Functions at Multiple Levels

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Taishin eNomura

2010-12-01

Full Text Available An aim of systems physiology today can be stated as to establish logical and quantitative bridges between phenomenological attributes of physiological entities such as cells and organs and physical attributes of biological entities, i.e., biological molecules, allowing us to describe and better understand physiological functions in terms of underlying biological functions. This article illustrates possible schema that can be used for promoting systems physiology by integrating quantitative knowledge of biological and physiological functions at multiple levels of time and space with the use of information technology infrastructure. Emphasis will be made for systematic, modular, hierarchical, and standardized descriptions of mathematical models of the functions and advantages for the use of them.

``Green's function'' approach & low-mode asymmetries

Science.gov (United States)

Masse, Laurent; Clark, Dan; Salmonson, Jay; MacLaren, Steve; Ma, Tammy; Khan, Shahab; Pino, Jesse; Ralph, Jo; Czajka, C.; Tipton, Robert; Landen, Otto; Kyrala, Georges; 2 Team; 1 Team

2017-10-01

Long wavelength, low mode asymmetries are believed to play a leading role in limiting the performance of current ICF implosions on NIF. These long wavelength modes are initiated and driven by asymmetries in the x-ray flux from the hohlraum; however, the underlying hydrodynamics of the implosion also act to amplify these asymmetries. The work presented here aim to deepen our understanding of the interplay of the drive asymmetries and the underlying implosion hydrodynamics in determining the final imploded configuration. This is accomplished through a synthesis of numerical modeling, analytic theory, and experimental data. In detail, we use a Green's function approach to connect the drive asymmetry seen by the capsule to the measured inflight and hot spot symmetries. The approach has been validated against a suite of numerical simulations. Ultimately, we hope this work will identify additional measurements to further constrain the asymmetries and increase hohlraum illumination design flexibility on the NIF. The technique and derivation of associated error bars will be presented. LLC, (LLNS) Contract No. DE-AC52-07NA27344.

Complex mode indication function and its applications to spatial domain parameter estimation

Science.gov (United States)

Shih, C. Y.; Tsuei, Y. G.; Allemang, R. J.; Brown, D. L.

1988-10-01

This paper introduces the concept of the Complex Mode Indication Function (CMIF) and its application in spatial domain parameter estimation. The concept of CMIF is developed by performing singular value decomposition (SVD) of the Frequency Response Function (FRF) matrix at each spectral line. The CMIF is defined as the eigenvalues, which are the square of the singular values, solved from the normal matrix formed from the FRF matrix, [ H( jω)] H[ H( jω)], at each spectral line. The CMIF appears to be a simple and efficient method for identifying the modes of the complex system. The CMIF identifies modes by showing the physical magnitude of each mode and the damped natural frequency for each root. Since multiple reference data is applied in CMIF, repeated roots can be detected. The CMIF also gives global modal parameters, such as damped natural frequencies, mode shapes and modal participation vectors. Since CMIF works in the spatial domain, uneven frequency spacing data such as data from spatial sine testing can be used. A second-stage procedure for accurate damped natural frequency and damping estimation as well as mode shape scaling is also discussed in this paper.

Default-Mode Network Functional Connectivity in Aphasia: Therapy-Induced Neuroplasticity

Science.gov (United States)

Marcotte, Karine; Perlbarg, Vincent; Marrelec, Guillaume; Benali, Habib; Ansaldo, Ana Ines

2013-01-01

Previous research on participants with aphasia has mainly been based on standard functional neuroimaging analysis. Recent studies have shown that functional connectivity analysis can detect compensatory activity, not revealed by standard analysis. Little is known, however, about the default-mode network in aphasia. In the current study, we studied…

Partition functions in even dimensional AdS via quasinormal mode methods

International Nuclear Information System (INIS)

Keeler, Cynthia; Ng, Gim Seng

2014-01-01

In this note, we calculate the one-loop determinant for a massive scalar (with conformal dimension Δ) in even-dimensional AdS d+1 space, using the quasinormal mode method developed in http://dx.doi.org/10.1088/0264-9381/27/12/125001 by Denef, Hartnoll, and Sachdev. Working first in two dimensions on the related Euclidean hyperbolic plane H 2 , we find a series of zero modes for negative real values of Δ whose presence indicates a series of poles in the one-loop partition function Z(Δ) in the Δ complex plane; these poles contribute temperature-independent terms to the thermal AdS partition function computed in http://dx.doi.org/10.1088/0264-9381/27/12/125001. Our results match those in a series of papers by Camporesi and Higuchi, as well as Gopakumar et al. http://dx.doi.org/10.1007/JHEP11(2011)010 and Banerjee et al. http://dx.doi.org/10.1007/JHEP03(2011)147. We additionally examine the meaning of these zero modes, finding that they Wick-rotate to quasinormal modes of the AdS 2 black hole. They are also interpretable as matrix elements of the discrete series representations of SO(2,1) in the space of smooth functions on S 1 . We generalize our results to general even dimensional AdS 2n , again finding a series of zero modes which are related to discrete series representations of SO(2n,1), the motion group of H 2n .

Analysis of functional failure mode of commercial deep sub-micron SRAM induced by total dose irradiation

International Nuclear Information System (INIS)

Zheng Qi-Wen; Cui Jiang-Wei; Zhou Hang; Yu De-Zhao; Yu Xue-Feng; Lu Wu; Guo Qi; Ren Di-Yuan

2015-01-01

Functional failure mode of commercial deep sub-micron static random access memory (SRAM) induced by total dose irradiation is experimentally analyzed and verified by circuit simulation. We extensively characterize the functional failure mode of the device by testing its electrical parameters and function with test patterns covering different functional failure modes. Experimental results reveal that the functional failure mode of the device is a temporary function interruption caused by peripheral circuits being sensitive to the standby current rising. By including radiation-induced threshold shift and off-state leakage current in memory cell transistors, we simulate the influence of radiation on the functionality of the memory cell. Simulation results reveal that the memory cell is tolerant to irradiation due to its high stability, which agrees with our experimental result. (paper)

Function of dynamic models in systems biology: linking structure to behaviour.

Science.gov (United States)

Knüpfer, Christian; Beckstein, Clemens

2013-10-08

Dynamic models in Systems Biology are used in computational simulation experiments for addressing biological questions. The complexity of the modelled biological systems and the growing number and size of the models calls for computer support for modelling and simulation in Systems Biology. This computer support has to be based on formal representations of relevant knowledge fragments. In this paper we describe different functional aspects of dynamic models. This description is conceptually embedded in our "meaning facets" framework which systematises the interpretation of dynamic models in structural, functional and behavioural facets. Here we focus on how function links the structure and the behaviour of a model. Models play a specific role (teleological function) in the scientific process of finding explanations for dynamic phenomena. In order to fulfil this role a model has to be used in simulation experiments (pragmatical function). A simulation experiment always refers to a specific situation and a state of the model and the modelled system (conditional function). We claim that the function of dynamic models refers to both the simulation experiment executed by software (intrinsic function) and the biological experiment which produces the phenomena under investigation (extrinsic function). We use the presented conceptual framework for the function of dynamic models to review formal accounts for functional aspects of models in Systems Biology, such as checklists, ontologies, and formal languages. Furthermore, we identify missing formal accounts for some of the functional aspects. In order to fill one of these gaps we propose an ontology for the teleological function of models. We have thoroughly analysed the role and use of models in Systems Biology. The resulting conceptual framework for the function of models is an important first step towards a comprehensive formal representation of the functional knowledge involved in the modelling and simulation process

Time evolution of coupled-bunch modes from beta function variation in storage rings

Directory of Open Access Journals (Sweden)

Kai Meng Hock

2007-08-01

Full Text Available We present an analytical and numerical study of the equations of motion for bunches coupled by transverse wakefields. We base our study on a recent lattice design for the damping rings in the baseline configuration of the International Linear Collider. Using the macroparticle model, and assuming resistive wall wakefield coupling, we present numerical results on the time evolution of the multibunch modes. Decay modes display growth after initial decay, and mode amplitudes exhibit high-frequency oscillations. These phenomena are not expected if the beta function is assumed to have a constant, averaged value. We show analytically that they can come from coupling between modes caused by variation of the beta function in a real lattice. The effect is shown to be comparable to the effect of a nonuniform fill pattern and significantly larger than that of the higher-order mode wakefield localized in the rf cavities. Turning to the case of constant beta function, we develop a more complete treatment of the equations of motion. We derive general formulas for the bunch trajectories, and show that such formulas can only be valid in the limit of small wakefield coupling.

Fibroblast Growth Factors: Biology, Function, and Application for Tissue Regeneration

Directory of Open Access Journals (Sweden)

Ye-Rang Yun

2010-01-01

Full Text Available Fibroblast growth factors (FGFs that signal through FGF receptors (FGFRs regulate a broad spectrum of biological functions, including cellular proliferation, survival, migration, and differentiation. The FGF signal pathways are the RAS/MAP kinase pathway, PI3 kinase/AKT pathway, and PLCγ pathway, among which the RAS/MAP kinase pathway is known to be predominant. Several studies have recently implicated the in vitro biological functions of FGFs for tissue regeneration. However, to obtain optimal outcomes in vivo, it is important to enhance the half-life of FGFs and their biological stability. Future applications of FGFs are expected when the biological functions of FGFs are potentiated through the appropriate use of delivery systems and scaffolds. This review will introduce the biology and cellular functions of FGFs and deal with the biomaterials based delivery systems and their current applications for the regeneration of tissues, including skin, blood vessel, muscle, adipose, tendon/ligament, cartilage, bone, tooth, and nerve tissues.

Linking density functional and mode coupling models for supercooled liquids.

Science.gov (United States)

Premkumar, Leishangthem; Bidhoodi, Neeta; Das, Shankar P

2016-03-28

We compare predictions from two familiar models of the metastable supercooled liquid, respectively, constructed with thermodynamic and dynamic approaches. In the so called density functional theory the free energy F[ρ] of the liquid is a functional of the inhomogeneous density ρ(r). The metastable state is identified as a local minimum of F[ρ]. The sharp density profile characterizing ρ(r) is identified as a single particle oscillator, whose frequency is obtained from the parameters of the optimum density function. On the other hand, a dynamic approach to supercooled liquids is taken in the mode coupling theory (MCT) which predict a sharp ergodicity-non-ergodicity transition at a critical density. The single particle dynamics in the non-ergodic state, treated approximately, represents a propagating mode whose characteristic frequency is computed from the corresponding memory function of the MCT. The mass localization parameters in the above two models (treated in their simplest forms) are obtained, respectively, in terms of the corresponding natural frequencies depicted and are shown to have comparable magnitudes.

Linking density functional and mode coupling models for supercooled liquids

Energy Technology Data Exchange (ETDEWEB)

Premkumar, Leishangthem; Bidhoodi, Neeta; Das, Shankar P. [School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067 (India)

2016-03-28

We compare predictions from two familiar models of the metastable supercooled liquid, respectively, constructed with thermodynamic and dynamic approaches. In the so called density functional theory the free energy F[ρ] of the liquid is a functional of the inhomogeneous density ρ(r). The metastable state is identified as a local minimum of F[ρ]. The sharp density profile characterizing ρ(r) is identified as a single particle oscillator, whose frequency is obtained from the parameters of the optimum density function. On the other hand, a dynamic approach to supercooled liquids is taken in the mode coupling theory (MCT) which predict a sharp ergodicity-non-ergodicity transition at a critical density. The single particle dynamics in the non-ergodic state, treated approximately, represents a propagating mode whose characteristic frequency is computed from the corresponding memory function of the MCT. The mass localization parameters in the above two models (treated in their simplest forms) are obtained, respectively, in terms of the corresponding natural frequencies depicted and are shown to have comparable magnitudes.

Mode Shape Analysis of Multiple Cracked Functionally Graded Timoshenko Beams

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Tran Van Lien

Full Text Available Abstract The present paper addresses free vibration of multiple cracked Timoshenko beams made of Functionally Graded Material (FGM. Cracks are modeled by rotational spring of stiffness calculated from the crack depth and material properties vary according to the power law throughout the beam thickness. Governing equations for free vibration of the beam are formulated with taking into account actual position of the neutral plane. The obtained frequency equation and mode shapes are used for analysis of the beam mode shapes in dependence on the material and crack parameters. Numerical results validate usefulness of the proposed herein theory and show that mode shapes are good indication for detecting multiple cracks in Timoshenko FGM beams.

The biological function of consciousness

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Brian eEarl

2014-08-01

Full Text Available This research is an investigation of whether consciousness—one’s ongoing experience—influences one’s behavior and, if so, how. Analysis of the components, structure, properties, and temporal sequences of consciousness has established that, (1 contrary to one’s intuitive understanding, consciousness does not have an active, executive role in determining behavior; (2 consciousness does have a biological function; and (3 consciousness is solely information in various forms. Consciousness is associated with a flexible response mechanism (FRM for decision-making, planning, and generally responding in nonautomatic ways. The FRM generates responses by manipulating information and, to function effectively, its data input must be restricted to task-relevant information. The properties of consciousness correspond to the various input requirements of the FRM; and when important information is missing from consciousness, functions of the FRM are adversely affected; both of which indicate that consciousness is the input data to the FRM. Qualitative and quantitative information (shape, size, location, etc., is incorporated into the input data by a qualia array of colors, sounds, and so on, which makes the input conscious. This view of the biological function of consciousness provides an explanation why we have experiences; why we have emotional and other feelings, and why their loss is associated with poor decision-making; why blindsight patients do not spontaneously initiate responses to events in their blind field; why counter-habitual actions are only possible when the intended action is in mind; and the reason for inattentional blindness.

Noise Reduction for Nonlinear Nonstationary Time Series Data using Averaging Intrinsic Mode Function

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Christofer Toumazou

2013-07-01

Full Text Available A novel noise filtering algorithm based on averaging Intrinsic Mode Function (aIMF, which is a derivation of Empirical Mode Decomposition (EMD, is proposed to remove white-Gaussian noise of foreign currency exchange rates that are nonlinear nonstationary times series signals. Noise patterns with different amplitudes and frequencies were randomly mixed into the five exchange rates. A number of filters, namely; Extended Kalman Filter (EKF, Wavelet Transform (WT, Particle Filter (PF and the averaging Intrinsic Mode Function (aIMF algorithm were used to compare filtering and smoothing performance. The aIMF algorithm demonstrated high noise reduction among the performance of these filters.

Modified complementary ensemble empirical mode decomposition and intrinsic mode functions evaluation index for high-speed train gearbox fault diagnosis

Science.gov (United States)

Chen, Dongyue; Lin, Jianhui; Li, Yanping

2018-06-01

Complementary ensemble empirical mode decomposition (CEEMD) has been developed for the mode-mixing problem in Empirical Mode Decomposition (EMD) method. Compared to the ensemble empirical mode decomposition (EEMD), the CEEMD method reduces residue noise in the signal reconstruction. Both CEEMD and EEMD need enough ensemble number to reduce the residue noise, and hence it would be too much computation cost. Moreover, the selection of intrinsic mode functions (IMFs) for further analysis usually depends on experience. A modified CEEMD method and IMFs evaluation index are proposed with the aim of reducing the computational cost and select IMFs automatically. A simulated signal and in-service high-speed train gearbox vibration signals are employed to validate the proposed method in this paper. The results demonstrate that the modified CEEMD can decompose the signal efficiently with less computation cost, and the IMFs evaluation index can select the meaningful IMFs automatically.

Tailoring vibration mode shapes using topology optimization and functionally graded material concepts

International Nuclear Information System (INIS)

Rubio, Wilfredo Montealegre; Paulino, Glaucio H; Silva, Emilio Carlos Nelli

2011-01-01

Tailoring specified vibration modes is a requirement for designing piezoelectric devices aimed at dynamic-type applications. A technique for designing the shape of specified vibration modes is the topology optimization method (TOM) which finds an optimum material distribution inside a design domain to obtain a structure that vibrates according to specified eigenfrequencies and eigenmodes. Nevertheless, when the TOM is applied to dynamic problems, the well-known grayscale or intermediate material problem arises which can invalidate the post-processing of the optimal result. Thus, a more natural way for solving dynamic problems using TOM is to allow intermediate material values. This idea leads to the functionally graded material (FGM) concept. In fact, FGMs are materials whose properties and microstructure continuously change along a specific direction. Therefore, in this paper, an approach is presented for tailoring user-defined vibration modes, by applying the TOM and FGM concepts to design functionally graded piezoelectric transducers (FGPT) and non-piezoelectric structures (functionally graded structures—FGS) in order to achieve maximum and/or minimum vibration amplitudes at certain points of the structure, by simultaneously finding the topology and material gradation function. The optimization problem is solved by using sequential linear programming. Two-dimensional results are presented to illustrate the method

Mining Functional Modules in Heterogeneous Biological Networks Using Multiplex PageRank Approach.

Science.gov (United States)

Li, Jun; Zhao, Patrick X

2016-01-01

Identification of functional modules/sub-networks in large-scale biological networks is one of the important research challenges in current bioinformatics and systems biology. Approaches have been developed to identify functional modules in single-class biological networks; however, methods for systematically and interactively mining multiple classes of heterogeneous biological networks are lacking. In this paper, we present a novel algorithm (called mPageRank) that utilizes the Multiplex PageRank approach to mine functional modules from two classes of biological networks. We demonstrate the capabilities of our approach by successfully mining functional biological modules through integrating expression-based gene-gene association networks and protein-protein interaction networks. We first compared the performance of our method with that of other methods using simulated data. We then applied our method to identify the cell division cycle related functional module and plant signaling defense-related functional module in the model plant Arabidopsis thaliana. Our results demonstrated that the mPageRank method is effective for mining sub-networks in both expression-based gene-gene association networks and protein-protein interaction networks, and has the potential to be adapted for the discovery of functional modules/sub-networks in other heterogeneous biological networks. The mPageRank executable program, source code, the datasets and results of the presented two case studies are publicly and freely available at http://plantgrn.noble.org/MPageRank/.

Conditional mode regression: Application to functional time series prediction

OpenAIRE

Dabo-Niang, Sophie; Laksaci, Ali

2008-01-01

We consider $\\alpha$-mixing observations and deal with the estimation of the conditional mode of a scalar response variable $Y$ given a random variable $X$ taking values in a semi-metric space. We provide a convergence rate in $L^p$ norm of the estimator. A useful and typical application to functional times series prediction is given.

The Effect of Mode of Delivery on Postpartum Sexual Functioning in Primiparous Women

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Fatemeh Dabiri

2014-07-01

Full Text Available Objective: To evaluate the effect of mode of delivery on postpartum sexual functioning in primiparous women. Methods: In this cross-sectional descriptive study, 150 primiparous women in postpartum period, who attended the family planning or vaccination clinics, were enrolled for the study. Eighty-one had vaginal delivery with episiotomy and 69 had experienced cesarean section. Sexual function was evaluated by the Female Sexual Function Index within 3 and 6 months postpartum. Results: About 29% in vaginal delivery group and 37% in cesarean delivery group had resumed their sexual intercourses four weeks after delivery (p=0.280.There were no significant differences between mode of delivery and sexual functioning, including desire, arousal, lubrication, orgasm, satisfaction and pain. Conclusion: The present study showed that postpartum sexual functioning was not associated with the type of delivery.

Lipid polymorphism and the functional roles of lipids in biological membranes

NARCIS (Netherlands)

Cullis, P.R.; Kruijff, B. de

1979-01-01

The reasons for the great variety of lipids found in biological membranes, and the relations between lipid composition and membrane function pose major unsolved problems in membrane biology. Perhaps the only major functional role of lipids which may be regarded as firmly established involves the

Functional biology of sympatric krill species

DEFF Research Database (Denmark)

Agersted, Mette Dalgaard; Nielsen, Torkel Gissel

2016-01-01

Here we compare the functional biology of the sympatric krill species, Meganyctiphanes norvegica and Thysanoessa inermis. For M. norvegica, we investigated functional responses on diatoms and copepods, together with prey size spectra on plankton ,400 mm and copepods in the size range 500–3220 mm....... For T. inermis, only prey size spectrum on plankton ,400 mm were investigated. The prey size ranges of both species include organisms ,400 mm, and they consequently graze on several trophic levels. However, T. inermis feed on cells ,10 mm equivalent spherical diameter (ESD), whereas M. norvegica only...

Interactions between default mode and control networks as a function of increasing cognitive reasoning complexity.

Science.gov (United States)

Hearne, Luke; Cocchi, Luca; Zalesky, Andrew; Mattingley, Jason B

2015-07-01

Successful performance of challenging cognitive tasks depends on a consistent functional segregation of activity within the default-mode network, on the one hand, and control networks encompassing frontoparietal and cingulo-opercular areas on the other. Recent work, however, has suggested that in some cognitive control contexts nodes within the default-mode and control networks may actually cooperate to achieve optimal task performance. Here, we used functional magnetic resonance imaging to examine whether the ability to relate variables while solving a cognitive reasoning problem involves transient increases in connectivity between default-mode and control regions. Participants performed a modified version of the classic Wason selection task, in which the number of variables to be related is systematically varied across trials. As expected, areas within the default-mode network showed a parametric deactivation with increases in relational complexity, compared with neural activity in null trials. Critically, some of these areas also showed enhanced connectivity with task-positive control regions. Specifically, task-based connectivity between the striatum and the angular gyri, and between the thalamus and right temporal pole, increased as a function of relational complexity. These findings challenge the notion that functional segregation between regions within default-mode and control networks invariably support cognitive task performance, and reveal previously unknown roles for the striatum and thalamus in managing network dynamics during cognitive reasoning. © 2015 Wiley Periodicals, Inc.

The reflection of life functional entailment and imminence in relational biology

CERN Document Server

Louie, A H

2013-01-01

A. H. Louie’s The Reflection of Life: Functional Entailment and Imminence in Relational Biology is a continuation of the exploratory journey in relational biology which began with his 2009 monograph More Than Life Itself: A Synthetic Continuation in Relational Biology. The theme of his first book was ‘What is life?’; the theme of this sequel is “How do two life forms interact?” Biology is a subject concerned with organization of relations. Relational biology is the approach that advocates ‘function dictates structure”, rather than ‘structure implies function’. It is mathematics decoded into biological realizations. The book demonstrates some of the powers of the approach of relational biology, and illustrates how pertinent problems in biology can be better addressed this way. In the first volume the theory was developed by using partially ordered sets, lattices, simulations, models, Aristotle’s four causes, graphs, categories, simple and complex systems, anticipatory systems, and metabolis...

Normal mode-guided transition pathway generation in proteins.

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Byung Ho Lee

Full Text Available The biological function of proteins is closely related to its structural motion. For instance, structurally misfolded proteins do not function properly. Although we are able to experimentally obtain structural information on proteins, it is still challenging to capture their dynamics, such as transition processes. Therefore, we need a simulation method to predict the transition pathways of a protein in order to understand and study large functional deformations. Here, we present a new simulation method called normal mode-guided elastic network interpolation (NGENI that performs normal modes analysis iteratively to predict transition pathways of proteins. To be more specific, NGENI obtains displacement vectors that determine intermediate structures by interpolating the distance between two end-point conformations, similar to a morphing method called elastic network interpolation. However, the displacement vector is regarded as a linear combination of the normal mode vectors of each intermediate structure, in order to enhance the physical sense of the proposed pathways. As a result, we can generate more reasonable transition pathways geometrically and thermodynamically. By using not only all normal modes, but also in part using only the lowest normal modes, NGENI can still generate reasonable pathways for large deformations in proteins. This study shows that global protein transitions are dominated by collective motion, which means that a few lowest normal modes play an important role in this process. NGENI has considerable merit in terms of computational cost because it is possible to generate transition pathways by partial degrees of freedom, while conventional methods are not capable of this.

Moving mode shape function approach for spinning disk and asymmetric disc brake squeal

Science.gov (United States)

Kang, Jaeyoung

2018-06-01

The solution approach of an asymmetric spinning disk under stationary friction loads requires the mode shape function fixed in the disk in the assumed mode method when the equations of motion is described in the space-fixed frame. This model description will be termed the 'moving mode shape function approach' and it allows us to formulate the stationary contact load problem in both the axisymmetric and asymmetric disk cases. Numerical results show that the eigenvalues of the time-periodic axisymmetric disk system are time-invariant. When the axisymmetry of the disk is broken, the positive real parts of the eigenvalues highly vary with the rotation of the disk in the slow speeds in such application as disc brake squeal. By using the Floquet stability analysis, it is also shown that breaking the axisymmetry of the disc alters the stability boundaries of the system.

Single-mode biological distributed feedback laser

DEFF Research Database (Denmark)

Vannahme, Christoph; Maier-Flaig, Florian; Lemmer, Uli

2013-01-01

Single-mode second order distributed feedback (DFB) lasers of riboflavin (vitamin B2) doped gelatine films on nanostructured low refractive index material are demonstrated. Manufacturing is based on a simple UV nanoimprint and spin-coating. Emission wavelengths of 543 nm and 562 nm for two...

A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function.

Science.gov (United States)

Lai, Jason; Jin, Jing; Kubelka, Jan; Liberles, David A

2012-09-21

Since the dynamic nature of protein structures is essential for enzymatic function, it is expected that functional evolution can be inferred from the changes in protein dynamics. However, dynamics can also diverge neutrally with sequence substitution between enzymes without changes of function. In this study, a phylogenetic approach is implemented to explore the relationship between enzyme dynamics and function through evolutionary history. Protein dynamics are described by normal mode analysis based on a simplified harmonic potential force field applied to the reduced C(α) representation of the protein structure while enzymatic function is described by Enzyme Commission numbers. Similarity of the binding pocket dynamics at each branch of the protein family's phylogeny was analyzed in two ways: (1) explicitly by quantifying the normal mode overlap calculated for the reconstructed ancestral proteins at each end and (2) implicitly using a diffusion model to obtain the reconstructed lineage-specific changes in the normal modes. Both explicit and implicit ancestral reconstruction identified generally faster rates of change in dynamics compared with the expected change from neutral evolution at the branches of potential functional divergences for the α-amylase, D-isomer-specific 2-hydroxyacid dehydrogenase, and copper-containing amine oxidase protein families. Normal mode analysis added additional information over just comparing the RMSD of static structures. However, the branch-specific changes were not statistically significant compared to background function-independent neutral rates of change of dynamic properties and blind application of the analysis would not enable prediction of changes in enzyme specificity. Copyright © 2012 Elsevier Ltd. All rights reserved.

Milk protein tailoring to improve functional and biological properties

Directory of Open Access Journals (Sweden)

JEAN-MARC CHOBERT

2012-01-01

Full Text Available Proteins are involved in every aspects of life: structure, motion, catalysis, recognition and regulation. Today's highly sophisticated science of the modifications of proteins has ancient roots. The tailoring of proteins for food and medical uses precedes the beginning of what is called biochemistry. Chemical modification of proteins was pursued early in the twentieth century as an analytical procedure for side-chain amino acids. Later, methods were developed for specific inactivation of biologically active proteins and titration of their essential groups. Enzymatic modifications were mainly developed in the seventies when many more enzymes became economically available. Protein engineering has become a valuable tool for creating or improving proteins for practical use and has provided new insights into protein structure and function. The actual and potential use of milk proteins as food ingredients has been a popular topic for research over the past 40 years. With today's sophisticated analytical, biochemical and biological research tools, the presence of compounds with biological activity has been demonstrated. Improvements in separation techniques and enzyme technology have enabled efficient and economic isolation and modification of milk proteins, which has made possible their use as functional foods, dietary supplements, nutraceuticals and medical foods. In this review, some chemical and enzymatic modifications of milk proteins are described, with particular focus on their functional and biological properties.

Diurnal rhythmicity in biological processes involved in bioavailability of functional food factors.

Science.gov (United States)

Tsurusaki, Takashi; Sakakibara, Hiroyuki; Aoshima, Yoshiki; Yamazaki, Shunsuke; Sakono, Masanobu; Shimoi, Kayoko

2013-05-01

In the past few decades, many types of functional factors have been identified in dietary foods; for example, flavonoids are major groups widely distributed in the plant kingdom. However, the absorption rates of the functional food factors are usually low, and many of these are difficult to be absorbed in the intact forms because of metabolization by biological processes during absorption. To gain adequate beneficial effects, it is therefore mandatory to know whether functional food factors are absorbed in sufficient quantity, and then reach target organs while maintaining beneficial effects. These are the reasons why the bioavailability of functional food factors has been well investigated using rodent models. Recently, many of the biological processes have been reported to follow diurnal rhythms recurring every 24 h. Therefore, absorption and metabolism of functional food factors influenced by the biological processes may vary with time of day. Consequently, the evaluation of the bioavailability of functional food factors using rodent models should take into consideration the timing of consumption. In this review, we provide a perspective overview of the diurnal rhythm of biological processes involved in the bioavailability of functional food factors, particularly flavonoids.

Integrated Biological Control

International Nuclear Information System (INIS)

JOHNSON, A.R.

2002-01-01

Biological control is any activity taken to prevent, limit, clean up, or remediate potential environmental, health and safety, or workplace quality impacts from plants, animals, or microorganisms. At Hanford the principal emphasis of biological control is to prevent the transport of radioactive contamination by biological vectors (plants, animals, or microorganisms), and where necessary, control and clean up resulting contamination. Other aspects of biological control at Hanford include industrial weed control (e.g.; tumbleweeds), noxious weed control (invasive, non-native plant species), and pest control (undesirable animals such as rodents and stinging insects; and microorganisms such as molds that adversely affect the quality of the workplace environment). Biological control activities may be either preventive (apriori) or in response to existing contamination spread (aposteriori). Surveillance activities, including ground, vegetation, flying insect, and other surveys, and apriori control actions, such as herbicide spraying and placing biological barriers, are important in preventing radioactive contamination spread. If surveillance discovers that biological vectors have spread radioactive contamination, aposteriori control measures, such as fixing contamination, followed by cleanup and removal of the contamination to an approved disposal location are typical response functions. In some cases remediation following the contamination cleanup and removal is necessary. Biological control activities for industrial weeds, noxious weeds and pests have similar modes of prevention and response

Biological pathways and genetic mechanisms involved in social functioning.

Science.gov (United States)

Ordoñana, Juan R; Bartels, Meike; Boomsma, Dorret I; Cella, David; Mosing, Miriam; Oliveira, Joao R; Patrick, Donald L; Veenhoven, Ruut; Wagner, Gert G; Sprangers, Mirjam A G

2013-08-01

To describe the major findings in the literature regarding associations between biological and genetic factors and social functioning, paying special attention to: (1) heritability studies on social functioning and related concepts; (2) hypothesized biological pathways and genetic variants that could be involved in social functioning, and (3) the implications of these results for quality-of-life research. A search of Web of Science and PubMed databases was conducted using combinations of the following keywords: genetics, twins, heritability, social functioning, social adjustment, social interaction, and social dysfunction. Variability in the definitions and measures of social functioning was extensive. Moderate to high heritability was reported for social functioning and related concepts, including prosocial behavior, loneliness, and extraversion. Disorders characterized by impairments in social functioning also show substantial heritability. Genetic variants hypothesized to be involved in social functioning are related to the network of brain structures and processes that are known to affect social cognition and behavior. Better knowledge and understanding about the impact of genetic factors on social functioning is needed to help us to attain a more comprehensive view of health-related quality-of-life (HRQOL) and will ultimately enhance our ability to identify those patients who are vulnerable to poor social functioning.

THz time domain spectroscopy of biomolecular conformational modes

International Nuclear Information System (INIS)

Markelz, Andrea; Whitmire, Scott; Hillebrecht, Jay; Birge, Robert

2002-01-01

We discuss the use of terahertz time domain spectroscopy for studies of conformational flexibility and conformational change in biomolecules. Protein structural dynamics are vital to biological function with protein flexibility affecting enzymatic reaction rates and sensory transduction cycling times. Conformational mode dynamics occur on the picosecond timescale and with the collective vibrational modes associated with these large scale structural motions in the 1-100 cm -1 range. We have performed THz time domain spectroscopy (TTDS) of several biomolecular systems to explore the sensitivity of TTDS to distinguish different molecular species, different mutations within a single species and different conformations of a given biomolecule. We compare the measured absorbances to normal mode calculations and find that the TTDS absorbance reflects the density of normal modes determined by molecular mechanics calculations, and is sensitive to both conformation and mutation. These early studies demonstrate some of the advantages and limitations of using TTDS for the study of biomolecules

Biologic variability and correlation of platelet function testing in healthy dogs.

Science.gov (United States)

Blois, Shauna L; Lang, Sean T; Wood, R Darren; Monteith, Gabrielle

2015-12-01

Platelet function tests are influenced by biologic variability, including inter-individual (CVG ) and intra-individual (CVI ), as well as analytic (CVA ) variability. Variability in canine platelet function testing is unknown, but if excessive, would make it difficult to interpret serial results. Additionally, the correlation between platelet function tests is poor in people, but not well described in dogs. The aims were to: (1) identify the effect of variation in preanalytic factors (venipuncture, elapsed time until analysis) on platelet function tests; (2) calculate analytic and biologic variability of adenosine diphosphate (ADP) and arachidonic acid (AA)-induced thromboelastograph platelet mapping (TEG-PM), ADP-, AA-, and collagen-induced whole blood platelet aggregometry (WBA), and collagen/ADP and collagen/epinephrine platelet function analysis (PFA-CADP, PFA-CEPI); and (3) determine the correlation between these variables. In this prospective observational trial, platelet function was measured once every 7 days, for 4 consecutive weeks, in 9 healthy dogs. In addition, CBC, TEG-PM, WBA, and PFA were performed. Overall coefficients of variability ranged from 13.3% to 87.8% for the platelet function tests. Biologic variability was highest for AA-induced maximum amplitude generated during TEG-PM (MAAA; CVG = 95.3%, CVI = 60.8%). Use of population-based reference intervals (RI) was determined appropriate only for PFA-CADP (index of individuality = 10.7). There was poor correlation between most platelet function tests. Use of population-based RI appears inappropriate for most platelet function tests, and tests poorly correlate with one another. Future studies on biologic variability and correlation of platelet function tests should be performed in dogs with platelet dysfunction and those treated with antiplatelet therapy. © 2015 American Society for Veterinary Clinical Pathology.

Dynamic Biological Functioning Important for Simulating and Stabilizing Ocean Biogeochemistry

Science.gov (United States)

Buchanan, P. J.; Matear, R. J.; Chase, Z.; Phipps, S. J.; Bindoff, N. L.

2018-04-01

The biogeochemistry of the ocean exerts a strong influence on the climate by modulating atmospheric greenhouse gases. In turn, ocean biogeochemistry depends on numerous physical and biological processes that change over space and time. Accurately simulating these processes is fundamental for accurately simulating the ocean's role within the climate. However, our simulation of these processes is often simplistic, despite a growing understanding of underlying biological dynamics. Here we explore how new parameterizations of biological processes affect simulated biogeochemical properties in a global ocean model. We combine 6 different physical realizations with 6 different biogeochemical parameterizations (36 unique ocean states). The biogeochemical parameterizations, all previously published, aim to more accurately represent the response of ocean biology to changing physical conditions. We make three major findings. First, oxygen, carbon, alkalinity, and phosphate fields are more sensitive to changes in the ocean's physical state. Only nitrate is more sensitive to changes in biological processes, and we suggest that assessment protocols for ocean biogeochemical models formally include the marine nitrogen cycle to assess their performance. Second, we show that dynamic variations in the production, remineralization, and stoichiometry of organic matter in response to changing environmental conditions benefit the simulation of ocean biogeochemistry. Third, dynamic biological functioning reduces the sensitivity of biogeochemical properties to physical change. Carbon and nitrogen inventories were 50% and 20% less sensitive to physical changes, respectively, in simulations that incorporated dynamic biological functioning. These results highlight the importance of a dynamic biology for ocean properties and climate.

Composite Structural Motifs of Binding Sites for Delineating Biological Functions of Proteins

Science.gov (United States)

Kinjo, Akira R.; Nakamura, Haruki

2012-01-01

Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs that represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures. PMID:22347478

Linking structural features of protein complexes and biological function.

Science.gov (United States)

Sowmya, Gopichandran; Breen, Edmond J; Ranganathan, Shoba

2015-09-01

Protein-protein interaction (PPI) establishes the central basis for complex cellular networks in a biological cell. Association of proteins with other proteins occurs at varying affinities, yet with a high degree of specificity. PPIs lead to diverse functionality such as catalysis, regulation, signaling, immunity, and inhibition, playing a crucial role in functional genomics. The molecular principle of such interactions is often elusive in nature. Therefore, a comprehensive analysis of known protein complexes from the Protein Data Bank (PDB) is essential for the characterization of structural interface features to determine structure-function relationship. Thus, we analyzed a nonredundant dataset of 278 heterodimer protein complexes, categorized into major functional classes, for distinguishing features. Interestingly, our analysis has identified five key features (interface area, interface polar residue abundance, hydrogen bonds, solvation free energy gain from interface formation, and binding energy) that are discriminatory among the functional classes using Kruskal-Wallis rank sum test. Significant correlations between these PPI interface features amongst functional categories are also documented. Salt bridges correlate with interface area in regulator-inhibitors (r = 0.75). These representative features have implications for the prediction of potential function of novel protein complexes. The results provide molecular insights for better understanding of PPIs and their relation to biological functions. © 2015 The Protein Society.

Single-wavelength functional photoacoustic microscopy in biological tissue

OpenAIRE

Danielli, Amos; Favazza, Christopher P.; Maslov, Konstantin; Wang, Lihong V.

2011-01-01

Recently, we developed a reflection-mode relaxation photoacoustic microscope, based on saturation intensity, to measure picosecond relaxation times using a nanosecond laser. Here, using the different relaxation times of oxygenated and deoxygenated hemoglobin molecules, both possessing extremely low fluorescence quantum yields, the oxygen saturation was quantified in vivo with single-wavelength photoacoustic microscopy. All previous functional photoacoustic microscopy measurements required ima...

Modulation of steady state functional connectivity in the default mode and working memory networks by cognitive load.

Science.gov (United States)

Newton, Allen T; Morgan, Victoria L; Rogers, Baxter P; Gore, John C

2011-10-01

Interregional correlations between blood oxygen level dependent (BOLD) magnetic resonance imaging (fMRI) signals in the resting state have been interpreted as measures of connectivity across the brain. Here we investigate whether such connectivity in the working memory and default mode networks is modulated by changes in cognitive load. Functional connectivity was measured in a steady-state verbal identity N-back task for three different conditions (N = 1, 2, and 3) as well as in the resting state. We found that as cognitive load increases, the functional connectivity within both the working memory the default mode network increases. To test whether functional connectivity between the working memory and the default mode networks changed, we constructed maps of functional connectivity to the working memory network as a whole and found that increasingly negative correlations emerged in a dorsal region of the posterior cingulate cortex. These results provide further evidence that low frequency fluctuations in BOLD signals reflect variations in neural activity and suggests interaction between the default mode network and other cognitive networks. Copyright © 2010 Wiley-Liss, Inc.

Single-wavelength functional photoacoustic microscopy in biological tissue.

Science.gov (United States)

Danielli, Amos; Favazza, Christopher P; Maslov, Konstantin; Wang, Lihong V

2011-03-01

Recently, we developed a reflection-mode relaxation photoacoustic microscope, based on saturation intensity, to measure picosecond relaxation times using a nanosecond laser. Here, using the different relaxation times of oxygenated and deoxygenated hemoglobin molecules, both possessing extremely low fluorescence quantum yields, the oxygen saturation was quantified in vivo with single-wavelength photoacoustic microscopy. All previous functional photoacoustic microscopy measurements required imaging with multiple-laser-wavelength measurements to quantify oxygen saturation. Eliminating the need for multiwavelength measurements removes the influence of spectral properties on oxygenation calculations and improves the portability and cost-effectiveness of functional or molecular photoacoustic microscopy.

Two-mode PLC-based mode multi/demultiplexer for mode and wavelength division multiplexed transmission.

Science.gov (United States)

Hanzawa, Nobutomo; Saitoh, Kuimasa; Sakamoto, Taiji; Matsui, Takashi; Tsujikawa, Kyozo; Koshiba, Masanori; Yamamoto, Fumihiko

2013-11-04

We proposed a PLC-based mode multi/demultiplexer (MUX/DEMUX) with an asymmetric parallel waveguide for mode division multiplexed (MDM) transmission. The mode MUX/DEMUX including a mode conversion function with an asymmetric parallel waveguide can be realized by matching the effective indices of the LP(01) and LP(11) modes of two waveguides. We report the design of a mode MUX/DEMUX that can support C-band WDM-MDM transmission. The fabricated mode MUX/DEMUX realized a low insertion loss of less than 1.3 dB and high a mode extinction ratio that exceeded 15 dB. We used the fabricated mode MUX/DEMUX to achieve a successful 2 mode x 4 wavelength x 10 Gbps transmission over a 9 km two-mode fiber with a penalty of less than 1 dB.

Task Analytic Models to Guide Analysis and Design: Use of the Operator Function Model to Represent Pilot-Autoflight System Mode Problems

Science.gov (United States)

Degani, Asaf; Mitchell, Christine M.; Chappell, Alan R.; Shafto, Mike (Technical Monitor)

1995-01-01

Task-analytic models structure essential information about operator interaction with complex systems, in this case pilot interaction with the autoflight system. Such models serve two purposes: (1) they allow researchers and practitioners to understand pilots' actions; and (2) they provide a compact, computational representation needed to design 'intelligent' aids, e.g., displays, assistants, and training systems. This paper demonstrates the use of the operator function model to trace the process of mode engagements while a pilot is controlling an aircraft via the, autoflight system. The operator function model is a normative and nondeterministic model of how a well-trained, well-motivated operator manages multiple concurrent activities for effective real-time control. For each function, the model links the pilot's actions with the required information. Using the operator function model, this paper describes several mode engagement scenarios. These scenarios were observed and documented during a field study that focused on mode engagements and mode transitions during normal line operations. Data including time, ATC clearances, altitude, system states, and active modes and sub-modes, engagement of modes, were recorded during sixty-six flights. Using these data, seven prototypical mode engagement scenarios were extracted. One scenario details the decision of the crew to disengage a fully automatic mode in favor of a semi-automatic mode, and the consequences of this action. Another describes a mode error involving updating aircraft speed following the engagement of a speed submode. Other scenarios detail mode confusion at various phases of the flight. This analysis uses the operator function model to identify three aspects of mode engagement: (1) the progress of pilot-aircraft-autoflight system interaction; (2) control/display information required to perform mode management activities; and (3) the potential cause(s) of mode confusion. The goal of this paper is twofold

A strategy for minimizing common mode human error in executing critical functions and tasks

International Nuclear Information System (INIS)

Beltracchi, L.; Lindsay, R.W.

1992-01-01

Human error in execution of critical functions and tasks can be costly. The Three Mile Island and the Chernobyl Accidents are examples of results from human error in the nuclear industry. There are similar errors that could no doubt be cited from other industries. This paper discusses a strategy to minimize common mode human error in the execution of critical functions and tasks. The strategy consists of the use of human redundancy, and also diversity in human cognitive behavior: skill-, rule-, and knowledge-based behavior. The authors contend that the use of diversity in human cognitive behavior is possible, and it minimizes common mode error

SU-E-T-54: Benefits of Biological Cost Functions

International Nuclear Information System (INIS)

Demirag, N

2014-01-01

Purpose: To verify the benefits of the biological cost functions. Methods: TG166 patients were used for the test case scenarios. Patients were planned using Monaco V5.0 (CMS/Elekta, St.Louis, MO) Monaco has 3 biological and 8 physical CFs. In this study the plans were optimized using 3 different scenarios. 1- Biological CFs only 2-Physical CFs only 3- Combination of Physical and Biological CFsMonaco has 3 biological CFs. Target EUD used for the targets, derived from the poisson cell kill model, has an α value that controls the cold spots inside the target. α values used in the optimization were 0.5 and 0.8. if cold spots needs to be penalized α value increased. Serial CF: it's called serial to mimic the behaviour of the serial organs, if a high k value like 12 or 14 is used it controls the maximum dose. Serial CF has a k parameter that is used to shape the whole dvh curve. K value ranges between 1–20. k:1 is used to control the mean dose, lower k value controls the mean dose, higher k value controls the higher dose, using 2 serial CFs with different k values controls the whole DVH. Paralel CF controls the percentage of the volume that tolerates higher doses than the reference dose to mimic the behaviour of the paralel organs. Results: It was possible to achive clinically accepted plans in all 3 scenarios. The benefit of the biological cost functions were to control the mean dose for target and OAR, to shape the DVH curve using one EUD value and one k value simplifies the optimization process. Using the biological CFs alone, it was hard to control the dose at a point. Conclusion: Biological CFs in Monaco doesn't require the ntcp/tcp values from the labs and useful to shape the whole dvh curve. I work as an applications support specialist for Elekta and I am a Ph.D. Student in Istanbul University for radiation therapy physics

Preparative scale production of functional mouse aquaporin 4 using different cell-free expression modes.

Directory of Open Access Journals (Sweden)

Lei Kai

Full Text Available The continuous progress in the structural and functional characterization of aquaporins increasingly attracts attention to study their roles in certain mammalian diseases. Although several structures of aquaporins have already been solved by crystallization, the challenge of producing sufficient amounts of functional proteins still remains. CF (cell free expression has emerged in recent times as a promising alternative option in order to synthesize large quantities of membrane proteins, and the focus of this report was to evaluate the potential of this technique for the production of eukaryotic aquaporins. We have selected the mouse aquaporin 4 as a representative of mammalian aquaporins. The protein was synthesized in an E. coli extract based cell-free system with two different expression modes, and the efficiencies of two modes were compared. In both, the P-CF (cell-free membrane protein expression as precipitate mode generating initial aquaporin precipitates as well as in the D-CF (cell-free membrane protein expression in presence of detergent mode, generating directly detergent solubilized samples, we were able to obtain mg amounts of protein per ml of cell-free reaction. Purified aquaporin samples solubilized in different detergents were reconstituted into liposomes, and analyzed for the water channel activity. The calculated P(f value of proteoliposome samples isolated from the D-CF mode was 133 µm/s at 10°C, which was 5 times higher as that of the control. A reversible inhibitory effect of mercury chloride was observed, which is consistent with previous observations of in vitro reconstituted aquaporin 4. In this study, a fast and convenient protocol was established for functional expression of aquaporins, which could serve as basis for further applications such as water filtration.

Evolutionary cell biology: functional insight from "endless forms most beautiful".

Science.gov (United States)

Richardson, Elisabeth; Zerr, Kelly; Tsaousis, Anastasios; Dorrell, Richard G; Dacks, Joel B

2015-12-15

In animal and fungal model organisms, the complexities of cell biology have been analyzed in exquisite detail and much is known about how these organisms function at the cellular level. However, the model organisms cell biologists generally use include only a tiny fraction of the true diversity of eukaryotic cellular forms. The divergent cellular processes observed in these more distant lineages are still largely unknown in the general scientific community. Despite the relative obscurity of these organisms, comparative studies of them across eukaryotic diversity have had profound implications for our understanding of fundamental cell biology in all species and have revealed the evolution and origins of previously observed cellular processes. In this Perspective, we will discuss the complexity of cell biology found across the eukaryotic tree, and three specific examples of where studies of divergent cell biology have altered our understanding of key functional aspects of mitochondria, plastids, and membrane trafficking. © 2015 Richardson et al. 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).

Chemically-functionalized microcantilevers for detection of chemical, biological and explosive material

Science.gov (United States)

Pinnaduwage, Lal A [Knoxville, TN; Thundat, Thomas G [Knoxville, TN; Brown, Gilbert M [Knoxville, TN; Hawk, John Eric [Olive Branch, MS; Boiadjiev, Vassil I [Knoxville, TN

2007-04-24

A chemically functionalized cantilever system has a cantilever coated on one side thereof with a reagent or biological species which binds to an analyte. The system is of particular value when the analyte is a toxic chemical biological warfare agent or an explosive.

Heavy water effects on the structure, functions and behavior of biological systems

International Nuclear Information System (INIS)

Buzgariu, Wanda; Caloianu, Maria; Moldovan, Lucia; Titescu, G.

2003-01-01

The H 2 O substitution for D 2 O either in environment or in the culture medium of the living systems generates changes in their main functions and composition. In this paper some of the heavy water effects in biological systems such as structural and functional changes were reviewed: normal cell architecture alterations, cell division and membrane functions disturbance, muscular contractility and the perturbations of biological oscillators such as circadian rhythm, heart rate, respiratory cycle, tidal and ultradian rhythm. (authors)

Guaranteed performance in reaching mode of sliding mode ...

Indian Academy of Sciences (India)

R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

addresses the design of constant plus proportional rate reaching law-based SMC for second-order ... Reaching mode; sliding mode controlled systems; output tracking ... The uncertainty in the input distribution function g is expressed as.

Sharing Structure and Function in Biological Design with SBOL 2.0.

Science.gov (United States)

Roehner, Nicholas; Beal, Jacob; Clancy, Kevin; Bartley, Bryan; Misirli, Goksel; Grünberg, Raik; Oberortner, Ernst; Pocock, Matthew; Bissell, Michael; Madsen, Curtis; Nguyen, Tramy; Zhang, Michael; Zhang, Zhen; Zundel, Zach; Densmore, Douglas; Gennari, John H; Wipat, Anil; Sauro, Herbert M; Myers, Chris J

2016-06-17

The Synthetic Biology Open Language (SBOL) is a standard that enables collaborative engineering of biological systems across different institutions and tools. SBOL is developed through careful consideration of recent synthetic biology trends, real use cases, and consensus among leading researchers in the field and members of commercial biotechnology enterprises. We demonstrate and discuss how a set of SBOL-enabled software tools can form an integrated, cross-organizational workflow to recapitulate the design of one of the largest published genetic circuits to date, a 4-input AND sensor. This design encompasses the structural components of the system, such as its DNA, RNA, small molecules, and proteins, as well as the interactions between these components that determine the system's behavior/function. The demonstrated workflow and resulting circuit design illustrate the utility of SBOL 2.0 in automating the exchange of structural and functional specifications for genetic parts, devices, and the biological systems in which they operate.

Resting-state functional connectivity of the default mode network associated with happiness.

Science.gov (United States)

Luo, Yangmei; Kong, Feng; Qi, Senqing; You, Xuqun; Huang, Xiting

2016-03-01

Happiness refers to people's cognitive and affective evaluation of their life. Why are some people happier than others? One reason might be that unhappy people are prone to ruminate more than happy people. The default mode network (DMN) is normally active during rest and is implicated in rumination. We hypothesized that unhappiness may be associated with increased default-mode functional connectivity during rest, including the medial prefrontal cortex (MPFC), posterior cingulate cortex (PCC) and inferior parietal lobule (IPL). The hyperconnectivity of these areas may be associated with higher levels of rumination. One hundred forty-eight healthy participants underwent a resting-state fMRI scan. A group-independent component analysis identified the DMNs. Results indicated increased functional connectivity in the DMN was associated with lower levels of happiness. Specifically, relative to happy people, unhappy people exhibited greater functional connectivity in the anterior medial cortex (bilateral MPFC), posterior medial cortex regions (bilateral PCC) and posterior parietal cortex (left IPL). Moreover, the increased functional connectivity of the MPFC, PCC and IPL, correlated positively with the inclination to ruminate. These results highlight the important role of the DMN in the neural correlates of happiness, and suggest that rumination may play an important role in people's perceived happiness. © The Author (2015). Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Communication: Effect of accidental mode degeneracy on Raman intensity in 2D materials: Hybrid functional study of bilayer phosphorene

Energy Technology Data Exchange (ETDEWEB)

Sun, Yi-Yang; Zhang, Shengbai [Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, Troy, New York 12180 (United States)

2016-07-14

Bulk black phosphorus has two optical phonon modes labeled as A{sub g}{sup 2} and B{sub 2u}, respectively, that are nearly degenerate in frequency. However, density functional theory calculations using local or semi-local functionals cannot reproduce this degeneracy. Here, we propose a hybrid functional approach aided by van der Waals (vdW) force fields, which can accurately describe the lattice dynamic and electronic properties of both bulk and few-layer black phosphorus (phosphorene). Using this approach we show that in bilayer phosphorene, the two Raman modes derived from the B{sub 2u} and A{sub g}{sup 2} modes could exhibit strong resonance as a result of the accidental degeneracy so that both modes could be observed in Raman experiment. Without the mode degeneracy, however, the Raman intensity of the B{sub 2u}-derived mode would be too weak to be observed. We further show that the accidental degeneracy is correlated to the applied strain, which enables Raman spectroscopy to be a powerful tool for characterizing built-in strains in 2D materials, e.g., due to the interaction with substrates, which has emerged as an important issue in vdW epitaxy.

Construction of Biologically Functional Bacterial Plasmids In Vitro

Science.gov (United States)

Cohen, Stanley N.; Chang, Annie C. Y.; Boyer, Herbert W.; Helling, Robert B.

1973-01-01

The construction of new plasmid DNA species by in vitro joining of restriction endonuclease-generated fragments of separate plasmids is described. Newly constructed plasmids that are inserted into Escherichia coli by transformation are shown to be biologically functional replicons that possess genetic properties and nucleotide base sequences from both of the parent DNA molecules. Functional plasmids can be obtained by reassociation of endonuclease-generated fragments of larger replicons, as well as by joining of plasmid DNA molecules of entirely different origins. Images PMID:4594039

Evaluation of common mode failure of safety functions for limiting fault events

International Nuclear Information System (INIS)

Rezendes, J.P.; Hyde, A.W.

2004-01-01

The draft U.S. Nuclear Regulatory Commission (NRC) policy on digital protection system software requires all Advanced Light Water Reactors (ALWRs) to be evaluated assuming a hypothetical common mode failure (CMF) which incapacitates the normal automatic initiation of safety functions. The System 80 + ALWR has been evaluated for such hypothetical conditions. The results show that the diverse automatic and manual protective systems in System 80 + provide ample safety performance margins relative to core coolability, offsite radiological releases. Reactor Coolant System (RCS) pressurization and containment integrity. This deterministic evaluation served to quantify the significant inherent safety margins in the System 80 + Standard Plant design even in the event of this extremely low probability scenario of a common mode failure. (author)

Marine Carotenoids: Biological Functions and Commercial Applications

Science.gov (United States)

Vílchez, Carlos; Forján, Eduardo; Cuaresma, María; Bédmar, Francisco; Garbayo, Inés; Vega, José M.

2011-01-01

Carotenoids are the most common pigments in nature and are synthesized by all photosynthetic organisms and fungi. Carotenoids are considered key molecules for life. Light capture, photosynthesis photoprotection, excess light dissipation and quenching of singlet oxygen are among key biological functions of carotenoids relevant for life on earth. Biological properties of carotenoids allow for a wide range of commercial applications. Indeed, recent interest in the carotenoids has been mainly for their nutraceutical properties. A large number of scientific studies have confirmed the benefits of carotenoids to health and their use for this purpose is growing rapidly. In addition, carotenoids have traditionally been used in food and animal feed for their color properties. Carotenoids are also known to improve consumer perception of quality; an example is the addition of carotenoids to fish feed to impart color to farmed salmon. PMID:21556162

Modes of action for biological control of Botrytis cinerea by antagonistic bacteria

Directory of Open Access Journals (Sweden)

Rana HAIDAR

2017-01-01

Full Text Available The role of beneficial bacteria in biocontrol of plant diseases, particularly those caused by the necrotrophic fungus Botrytis cinerea, has been investigated by testing many bacteria under laboratory and field conditions. Bacteria may protect plants against B. cinerea by direct antagonistic interactions between biocontrol agents and this pathogen, as well as indirect effects through the induction of host resistance. This review focuses on various bacteria that act as biological control agents (BCAs of B. cinerea and their associated mechanisms. The modes of action (MoAs include: i synthesis of anti-fungal metabolites, such as antibiotics, cell wall-degrading enzymes and volatile organic compounds (VOCs; ii competition for nutrients and/or a niche; and iii induction of host resistance. The challenge for development of BCAs is to reduce the variability of efficiency and to prove persistence under a large range of conditions. We discuss the advantages and drawbacks of MoA for future applications of bacteria in the field and in post-harvest storage, as well as combination of different MoAs as a strategy to achieve a more regular efficacy.

Biological properties of extracellular vesicles and their physiological functions

Directory of Open Access Journals (Sweden)

María Yáñez-Mó

2015-05-01

Full Text Available In the past decade, extracellular vesicles (EVs have been recognized as potent vehicles of intercellular communication, both in prokaryotes and eukaryotes. This is due to their capacity to transfer proteins, lipids and nucleic acids, thereby influencing various physiological and pathological functions of both recipient and parent cells. While intensive investigation has targeted the role of EVs in different pathological processes, for example, in cancer and autoimmune diseases, the EV-mediated maintenance of homeostasis and the regulation of physiological functions have remained less explored. Here, we provide a comprehensive overview of the current understanding of the physiological roles of EVs, which has been written by crowd-sourcing, drawing on the unique EV expertise of academia-based scientists, clinicians and industry based in 27 European countries, the United States and Australia. This review is intended to be of relevance to both researchers already working on EV biology and to newcomers who will encounter this universal cell biological system. Therefore, here we address the molecular contents and functions of EVs in various tissues and body fluids from cell systems to organs. We also review the physiological mechanisms of EVs in bacteria, lower eukaryotes and plants to highlight the functional uniformity of this emerging communication system.

Biological properties of extracellular vesicles and their physiological functions

Science.gov (United States)

Yáñez-Mó, María; Siljander, Pia R.-M.; Andreu, Zoraida; Zavec, Apolonija Bedina; Borràs, Francesc E.; Buzas, Edit I.; Buzas, Krisztina; Casal, Enriqueta; Cappello, Francesco; Carvalho, Joana; Colás, Eva; Silva, Anabela Cordeiro-da; Fais, Stefano; Falcon-Perez, Juan M.; Ghobrial, Irene M.; Giebel, Bernd; Gimona, Mario; Graner, Michael; Gursel, Ihsan; Gursel, Mayda; Heegaard, Niels H. H.; Hendrix, An; Kierulf, Peter; Kokubun, Katsutoshi; Kosanovic, Maja; Kralj-Iglic, Veronika; Krämer-Albers, Eva-Maria; Laitinen, Saara; Lässer, Cecilia; Lener, Thomas; Ligeti, Erzsébet; Linē, Aija; Lipps, Georg; Llorente, Alicia; Lötvall, Jan; Manček-Keber, Mateja; Marcilla, Antonio; Mittelbrunn, Maria; Nazarenko, Irina; Hoen, Esther N.M. Nolte-‘t; Nyman, Tuula A.; O'Driscoll, Lorraine; Olivan, Mireia; Oliveira, Carla; Pállinger, Éva; del Portillo, Hernando A.; Reventós, Jaume; Rigau, Marina; Rohde, Eva; Sammar, Marei; Sánchez-Madrid, Francisco; Santarém, N.; Schallmoser, Katharina; Ostenfeld, Marie Stampe; Stoorvogel, Willem; Stukelj, Roman; Van der Grein, Susanne G.; Vasconcelos, M. Helena; Wauben, Marca H. M.; De Wever, Olivier

2015-01-01

In the past decade, extracellular vesicles (EVs) have been recognized as potent vehicles of intercellular communication, both in prokaryotes and eukaryotes. This is due to their capacity to transfer proteins, lipids and nucleic acids, thereby influencing various physiological and pathological functions of both recipient and parent cells. While intensive investigation has targeted the role of EVs in different pathological processes, for example, in cancer and autoimmune diseases, the EV-mediated maintenance of homeostasis and the regulation of physiological functions have remained less explored. Here, we provide a comprehensive overview of the current understanding of the physiological roles of EVs, which has been written by crowd-sourcing, drawing on the unique EV expertise of academia-based scientists, clinicians and industry based in 27 European countries, the United States and Australia. This review is intended to be of relevance to both researchers already working on EV biology and to newcomers who will encounter this universal cell biological system. Therefore, here we address the molecular contents and functions of EVs in various tissues and body fluids from cell systems to organs. We also review the physiological mechanisms of EVs in bacteria, lower eukaryotes and plants to highlight the functional uniformity of this emerging communication system. PMID:25979354

Relative biological efficiency of 592 MeV protons. Analysis of the biological effect of secondary radiation

International Nuclear Information System (INIS)

Legeay, G.; Baarli, J.

1968-01-01

The relative biological efficiency (RBE) of high energy protons is of importance because of their effects in the field of radioprotection around large accelerators and during space-flights. The nature of the interactions between 592 MeV protons and biological tissues makes it necessary to take into consideration the contribution of secondary radiation to the biological effect. Since it is not possible to obtain from a synchrotron a beam having a sufficiently large cross-section to irradiate large animals, one has to resort to certain devices concerning the mode of exposure when small laboratory animals are used. By irradiating rats individually and in groups, and by using the lethal test as a function of time, the authors show that the value of the RBE is different for animals of the same species having the same biological parameters. Thus there appears an increase in the biological effect due to secondary radiation produced in nuclear cascades which develop in a large volume, for example that of a human being. (author) [fr

The functioning and behaviour of biological parents of children ...

African Journals Online (AJOL)

Parenting a child with ADHD may intensify parental stress through functional impairment notwithstanding the diagnosis of ADHD. Methods: Eighty-one biological parents of children diagnosed with attention-deficit/ hyperactivity disorder were screened using self-reporting measurements. ADHD self-report scale (ASRS-V 1.1) ...

Reconstructed phase spaces of intrinsic mode functions. Application to postural stability analysis.

Science.gov (United States)

Snoussi, Hichem; Amoud, Hassan; Doussot, Michel; Hewson, David; Duchêne, Jacques

2006-01-01

In this contribution, we propose an efficient nonlinear analysis method characterizing postural steadiness. The analyzed signal is the displacement of the centre of pressure (COP) collected from a force plate used for measuring postural sway. The proposed method consists of analyzing the nonlinear dynamics of the intrinsic mode functions (IMF) of the COP signal. The nonlinear properties are assessed through the reconstructed phase spaces of the different IMFs. This study shows some specific geometries of the attractors of some intrinsic modes. Moreover, the volume spanned by the geometric attractors in the reconstructed phase space represents an efficient indicator of the postural stability of the subject. Experiments results corroborate the effectiveness of the method to blindly discriminate young subjects, elderly subjects and subjects presenting a risk of falling.

N-acylation of phosphatidylethanolamine and its biological functions in mammals

DEFF Research Database (Denmark)

Wellner, Niels; Diep, Thi Ai; Janfelt, Christian

2013-01-01

N-acylphosphatidylethanolamine (NAPE) and N-acylplasmenylethanolamine (pNAPE) are widely found phospholipids, and they are precursors for N-acylethanolamines, a group of compounds that has a variety of biological effects and encompasses the endocannabinoid anandamide. NAPE and pNAPE are synthesiz...... reviews the metabolism, occurrence and assay of NAPE and pNAPE, and discusses the putative biological functions in mammals of these phospholipids. This article is part of a Special Issue entitled Phospholipids and Phospholipid Metabolism....

JUSTIFICATION OF MODES THERMAL PROCESSING OF THE SEMIFINISHED THORNY SKATE TO PRODUCTION OF FISH CULINARY PRODUCTS OF FUNCTIONAL PURPOSE

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V. V. Shchetinskii

2014-01-01

Full Text Available Summary. Raja radiatd, the non-conventional object of commercial fishing in North-East Atlantic region which is not under fishing quota should be declared as a cost-effective full bio raw material for the broad line food production enriched with chondroitin sulfate (a valuable biological component with proved anti-inflammatory and anti-tumor acting. The main obstacle for the industrial food processing of the Raja radiatd is a high level of urea in the muscle tissue. The patented technical solution to this problem is being proposed. Justified modes of preliminary and final heat treatment for a wide range of fish culinary products of functional purpose of the Raja radiatd. Assessed by calculation of indicators of the biological value of the protein ready culinary products of the pitch with regard to experimentally established weight loss, protein and fat at all stages of the thermal treatment of the material. The high level of chondroitin sulfate in the culinary finished product is experimentally confirmed. The outcome of the research was the development of formulations and manufacturing fish culinary products functionality of a wide range based on the use of Raja radiatd meat. Complex physico-chemical analysis of raw materials, semi-finished and finished products allowed to develop standards of waste, loss, and output of finished products, to optimize the formulation of products and technological conditions of its production. Experimentally determine some parameters of the nutritional value of new products, comprehensive assessment of its quality, which confirmed its improved handling compared to the same fishery products provided to the consumer market in Murmansk.

Revealing complex function, process and pathway interactions with high-throughput expression and biological annotation data.

Science.gov (United States)

Singh, Nitesh Kumar; Ernst, Mathias; Liebscher, Volkmar; Fuellen, Georg; Taher, Leila

2016-10-20

The biological relationships both between and within the functions, processes and pathways that operate within complex biological systems are only poorly characterized, making the interpretation of large scale gene expression datasets extremely challenging. Here, we present an approach that integrates gene expression and biological annotation data to identify and describe the interactions between biological functions, processes and pathways that govern a phenotype of interest. The product is a global, interconnected network, not of genes but of functions, processes and pathways, that represents the biological relationships within the system. We validated our approach on two high-throughput expression datasets describing organismal and organ development. Our findings are well supported by the available literature, confirming that developmental processes and apoptosis play key roles in cell differentiation. Furthermore, our results suggest that processes related to pluripotency and lineage commitment, which are known to be critical for development, interact mainly indirectly, through genes implicated in more general biological processes. Moreover, we provide evidence that supports the relevance of cell spatial organization in the developing liver for proper liver function. Our strategy can be viewed as an abstraction that is useful to interpret high-throughput data and devise further experiments.

Tablet-Based Functional MRI of the Trail Making Test: Effect of Tablet Interaction Mode

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Mahta Karimpoor

2017-10-01

Full Text Available The Trail Making Test (TMT is widely used for assessing executive function, frontal lobe abilities, and visual motor skills. Part A of this pen-and-paper test (TMT-A involves linking numbers randomly distributed in space, in ascending order. Part B (TMT-B alternates between linking numbers and letters. TMT-B is more demanding than TMT-A, but the mental processing that supports the performance of this test remains incompletely understood. Functional MRI (fMRI may help to clarify the relationship between TMT performance and brain activity, but providing an environment that supports real-world pen-and-paper interactions during fMRI is challenging. Previously, an fMRI-compatible tablet system was developed for writing and drawing with two modes of interaction: the original cursor-based, proprioceptive approach, and a new mode involving augmented reality to provide visual feedback of hand position (VFHP for enhanced user interaction. This study characterizes the use of the tablet during fMRI of young healthy adults (n = 22, with half of the subjects performing TMT with VFHP and the other half performing TMT without VFHP. Activation maps for both TMT-A and TMT-B performance showed considerable overlap between the two tablet modes, and no statistically differences in brain activity were detected when contrasting TMT-B vs. TMT-A for the two tablet modes. Behavioral results also showed no statistically different interaction effects for TMT-B vs. TMT-A for the two tablet modes. Tablet-based TMT scores showed reasonable convergent validity with those obtained by administering the standard pen-and-paper TMT to the same subjects. Overall, the results suggest that despite the slightly different mechanisms involved for the two modes of tablet interaction, both are suitable for use in fMRI studies involving TMT performance. This study provides information for using tablet-based TMT methods appropriately in future fMRI studies involving patients and healthy

Sliding mode control-based linear functional observers for discrete-time stochastic systems

Science.gov (United States)

Singh, Satnesh; Janardhanan, Sivaramakrishnan

2017-11-01

Sliding mode control (SMC) is one of the most popular techniques to stabilise linear discrete-time stochastic systems. However, application of SMC becomes difficult when the system states are not available for feedback. This paper presents a new approach to design a SMC-based functional observer for discrete-time stochastic systems. The functional observer is based on the Kronecker product approach. Existence conditions and stability analysis of the proposed observer are given. The control input is estimated by a novel linear functional observer. This approach leads to a non-switching type of control, thereby eliminating the fundamental cause of chatter. Furthermore, the functional observer is designed in such a way that the effect of process and measurement noise is minimised. Simulation example is given to illustrate and validate the proposed design method.

Metabolomics for functional genomics, systems biology, and biotechnology.

Science.gov (United States)

Saito, Kazuki; Matsuda, Fumio

2010-01-01

Metabolomics now plays a significant role in fundamental plant biology and applied biotechnology. Plants collectively produce a huge array of chemicals, far more than are produced by most other organisms; hence, metabolomics is of great importance in plant biology. Although substantial improvements have been made in the field of metabolomics, the uniform annotation of metabolite signals in databases and informatics through international standardization efforts remains a challenge, as does the development of new fields such as fluxome analysis and single cell analysis. The principle of transcript and metabolite cooccurrence, particularly transcriptome coexpression network analysis, is a powerful tool for decoding the function of genes in Arabidopsis thaliana. This strategy can now be used for the identification of genes involved in specific pathways in crops and medicinal plants. Metabolomics has gained importance in biotechnology applications, as exemplified by quantitative loci analysis, prediction of food quality, and evaluation of genetically modified crops. Systems biology driven by metabolome data will aid in deciphering the secrets of plant cell systems and their application to biotechnology.

Thalamocortical functional connectivity in Lennox-Gastaut syndrome is abnormally enhanced in executive-control and default-mode networks.

Science.gov (United States)

Warren, Aaron E L; Abbott, David F; Jackson, Graeme D; Archer, John S

2017-12-01

To identify abnormal thalamocortical circuits in the severe epilepsy of Lennox-Gastaut syndrome (LGS) that may explain the shared electroclinical phenotype and provide potential treatment targets. Twenty patients with a diagnosis of LGS (mean age = 28.5 years) and 26 healthy controls (mean age = 27.6 years) were compared using task-free functional magnetic resonance imaging (MRI). The thalamus was parcellated according to functional connectivity with 10 cortical networks derived using group-level independent component analysis. For each cortical network, we assessed between-group differences in thalamic functional connectivity strength using nonparametric permutation-based tests. Anatomical locations were identified by quantifying spatial overlap with a histologically informed thalamic MRI atlas. In both groups, posterior thalamic regions showed functional connectivity with visual, auditory, and sensorimotor networks, whereas anterior, medial, and dorsal thalamic regions were connected with networks of distributed association cortex (including the default-mode, anterior-salience, and executive-control networks). Four cortical networks (left and right executive-control network; ventral and dorsal default-mode network) showed significantly enhanced thalamic functional connectivity strength in patients relative to controls. Abnormal connectivity was maximal in mediodorsal and ventrolateral thalamic nuclei. Specific thalamocortical circuits are affected in LGS. Functional connectivity is abnormally enhanced between the mediodorsal and ventrolateral thalamus and the default-mode and executive-control networks, thalamocortical circuits that normally support diverse cognitive processes. In contrast, thalamic regions connecting with primary and sensory cortical networks appear to be less affected. Our previous neuroimaging studies show that epileptic activity in LGS is expressed via the default-mode and executive-control networks. Results of the present study suggest that

Aberrant functional connectivity of default-mode network in type 2 diabetes patients

International Nuclear Information System (INIS)

Cui, Ying; Jiao, Yun; Chen, Hua-Jun; Ding, Jie; Luo, Bing; Peng, Cheng-Yu; Ju, Sheng-Hong; Teng, Gao-Jun

2015-01-01

Type 2 diabetes mellitus is associated with increased risk for dementia. Patients with impaired cognition often show default-mode network disruption. We aimed to investigate the integrity of a default-mode network in diabetic patients by using independent component analysis, and to explore the relationship between network abnormalities, neurocognitive performance and diabetic variables. Forty-two patients with type 2 diabetes and 42 well-matched healthy controls were included and underwent resting-state functional MRI in a 3 Tesla unit. Independent component analysis was adopted to extract the default-mode network, including its anterior and posterior components. Z-maps of both sub-networks were compared between the two groups and correlated with each clinical variable. Patients showed increased connectivity around the medial prefrontal cortex in the anterior sub-network, but decreased connectivity around the posterior cingulate cortex in the posterior sub-network. The decreased connectivity in the posterior part was significantly correlated with the score on Complex Figure Test-delay recall test (r = 0.359, p = 0.020), the time spent on Trail-Making Test-part B (r = -0.346, p = 0.025) and the insulin resistance level (r = -0.404, p = 0.024). Dissociation pattern in the default-mode network was found in diabetic patients, which might provide powerful new insights into the neural mechanisms that underlie the diabetes-related cognitive decline. (orig.)

Aberrant functional connectivity of default-mode network in type 2 diabetes patients

Energy Technology Data Exchange (ETDEWEB)

Cui, Ying; Jiao, Yun; Chen, Hua-Jun; Ding, Jie; Luo, Bing; Peng, Cheng-Yu; Ju, Sheng-Hong; Teng, Gao-Jun [Medical School of Southeast University, Jiangsu Key Laboratory of Molecular and Functional Imaging, Department of Radiology, Zhongda Hospital, Nanjing, Jiangsu (China)

2015-11-15

Type 2 diabetes mellitus is associated with increased risk for dementia. Patients with impaired cognition often show default-mode network disruption. We aimed to investigate the integrity of a default-mode network in diabetic patients by using independent component analysis, and to explore the relationship between network abnormalities, neurocognitive performance and diabetic variables. Forty-two patients with type 2 diabetes and 42 well-matched healthy controls were included and underwent resting-state functional MRI in a 3 Tesla unit. Independent component analysis was adopted to extract the default-mode network, including its anterior and posterior components. Z-maps of both sub-networks were compared between the two groups and correlated with each clinical variable. Patients showed increased connectivity around the medial prefrontal cortex in the anterior sub-network, but decreased connectivity around the posterior cingulate cortex in the posterior sub-network. The decreased connectivity in the posterior part was significantly correlated with the score on Complex Figure Test-delay recall test (r = 0.359, p = 0.020), the time spent on Trail-Making Test-part B (r = -0.346, p = 0.025) and the insulin resistance level (r = -0.404, p = 0.024). Dissociation pattern in the default-mode network was found in diabetic patients, which might provide powerful new insights into the neural mechanisms that underlie the diabetes-related cognitive decline. (orig.)

MicroRNA functional network in pancreatic cancer: From biology to ...

Indian Academy of Sciences (India)

[Wang J and Sen S 2011 MicroRNA functional network in pancreatic cancer: From biology to biomarkers of disease. ... growth factor type I receptor; INSR, insulin receptor; IPA, Ingenuity Pathway Analysis; IPMN, ..... Prostate cancer signalling.

Micro-buckling in the nanocomposite structure of biological materials

Science.gov (United States)

Su, Yewang; Ji, Baohua; Hwang, Keh-Chih; Huang, Yonggang

2012-10-01

Nanocomposite structure, consisting of hard mineral and soft protein, is the elementary building block of biological materials, where the mineral crystals are arranged in a staggered manner in protein matrix. This special alignment of mineral is supposed to be crucial to the structural stability of the biological materials under compressive load, but the underlying mechanism is not yet clear. In this study, we performed analytical analysis on the buckling strength of the nanocomposite structure by explicitly considering the staggered alignment of the mineral crystals, as well as the coordination among the minerals during the buckling deformation. Two local buckling modes of the nanostructure were identified, i.e., the symmetric mode and anti-symmetric mode. We showed that the symmetric mode often happens at large aspect ratio and large volume fraction of mineral, while the anti-symmetric happens at small aspect ratio and small volume fraction. In addition, we showed that because of the coordination of minerals with the help of their staggered alignment, the buckling strength of these two modes approached to that of the ideally continuous fiber reinforced composites at large aspect ratio given by Rosen's model, insensitive to the existing "gap"-like flaws between mineral tips. Furthermore, we identified a mechanism of buckling mode transition from local to global buckling with increase of aspect ratio, which was attributed to the biphasic dependence of the buckling strength on the aspect ratio. That is, for small aspect ratio, the local buckling strength is smaller than that of global buckling so that it dominates the buckling behavior of the nanocomposite; for comparatively larger aspect ratio, the local buckling strength is higher than that of global buckling so that the global buckling dominates the buckling behavior. We also found that the hierarchical structure can effectively enhance the buckling strength, particularly, this structural design enables

The bottom-up approach to defining life : deciphering the functional organization of biological cells via multi-objective representation of biological complexity from molecules to cells

Directory of Open Access Journals (Sweden)

Sathish ePeriyasamy

2013-12-01

Full Text Available In silico representation of cellular systems needs to represent the adaptive dynamics of biological cells, recognizing a cell’s multi-objective topology formed by spatially and temporally cohesive intracellular structures. The design of these models needs to address the hierarchical and concurrent nature of cellular functions and incorporate the ability to self-organise in response to transitions between healthy and pathological phases, and adapt accordingly. The functions of biological systems are constantly evolving, due to the ever changing demands of their environment. Biological systems meet these demands by pursuing objectives, aided by their constituents, giving rise to biological functions. A biological cell is organised into an objective/task hierarchy. These objective hierarchy corresponds to the nested nature of temporally cohesive structures and representing them will facilitate in studying pleiotropy and polygeny by modeling causalities propagating across multiple interconnected intracellular processes. Although biological adaptations occur in physiological, developmental and reproductive timescales, the paper is focused on adaptations that occur within physiological timescales, where the biomolecular activities contributing to functional organisation, play a key role in cellular physiology. The paper proposes a multi-scale and multi-objective modelling approach from the bottom-up by representing temporally cohesive structures for multi-tasking of intracellular processes. Further the paper characterises the properties and constraints that are consequential to the organisational and adaptive dynamics in biological cells.

7th Annual Systems Biology Symposium: Systems Biology and Engineering

Energy Technology Data Exchange (ETDEWEB)

Galitski, Timothy P.

2008-04-01

Systems biology recognizes the complex multi-scale organization of biological systems, from molecules to ecosystems. The International Symposium on Systems Biology has been hosted by the Institute for Systems Biology in Seattle, Washington, since 2002. The annual two-day event gathers the most influential researchers transforming biology into an integrative discipline investingating complex systems. Engineering and application of new technology is a central element of systems biology. Genome-scale, or very small-scale, biological questions drive the enigneering of new technologies, which enable new modes of experimentation and computational analysis, leading to new biological insights and questions. Concepts and analytical methods in engineering are now finding direct applications in biology. Therefore, the 2008 Symposium, funded in partnership with the Department of Energy, featured global leaders in "Systems Biology and Engineering."

Virtual Agonist-antagonist Mechanisms Produce Biological Muscle-like Functions: An Application for Robot Joint Control

DEFF Research Database (Denmark)

Xiong, Xiaofeng; Wörgötter, Florentin; Manoonpong, Poramate

2014-01-01

Purpose – Biological muscles of animals have a surprising variety of functions, i.e., struts, springs, and brakes. According to this, the purpose of this paper is to apply virtual agonist-antagonist mechanisms to robot joint control allowing for muscle-like functions and variably compliant joint......, variably compliant joint motions can be produced without mechanically bulky and complex mechanisms or complex force/toque sensing at each joint. Moreover, through tuning the damping coefficient of the VAAM, the functions of the VAAM are comparable to biological muscles. Originality/value – The model (i.......e., VAAM) provides a way forward to emulate muscle-like functions that are comparable to those found in physiological experiments of biological muscles. Based on these muscle-like functions, the robotic joints can easily achieve variable compliance that does not require complex physical components...

Scavenger Receptor CD163 and Its Biological Functions

Directory of Open Access Journals (Sweden)

Gabriela Onofre

2009-01-01

Full Text Available CD163 is a member of scavenger receptor super family class B of the first subgroup. It is mapped to the region p13 on chromosome 12. Five different isoforms of CD163 have been described, which differ in the structure of their cytoplasmic domains and putative phosporylation sites. This scavenger receptor is selectively expressed on cells of monocytes and macrophages lineage exclusively. CD163 immunological function is essentially homeostatic. It also has other functions because participates in adhesion to endothelial cells, in tolerance induction and tissues regeneration. Other very important function of CD163 is the clearance of hemoglobin in its cell-free form and participation in anti-inflammation in its soluble form, exhibiting cytokine-like functions. We review the biological functions of CD163 which have been discovered until now. It seems apparent from this review that CD163 scavenger receptor can be used as biomarker in different diseases and as a valuable diagnostic parameter for prognosis of many diseases especially inflammatory disorders and sepsis.

Carotenoids from Marine Organisms: Biological Functions and Industrial Applications

Directory of Open Access Journals (Sweden)

Christian Galasso

2017-11-01

Full Text Available As is the case for terrestrial organisms, carotenoids represent the most common group of pigments in marine environments. They are generally biosynthesized by all autotrophic marine organisms, such as bacteria and archaea, algae and fungi. Some heterotrophic organisms also contain carotenoids probably accumulated from food or partly modified through metabolic reactions. These natural pigments are divided into two chemical classes: carotenes (such as lycopene and α- and β-carotene that are composed of hydrogen and carbon; xanthophylls (such as astaxanthin, fucoxanthin and lutein, which are constituted by hydrogen, carbon and oxygen. Carotenoids, as antioxidant compounds, assume a key role in the protection of cells. In fact, quenching of singlet oxygen, light capture and photosynthesis protection are the most relevant biological functions of carotenoids. The present review aims at describing (i the biological functions of carotenoids and their benefits for human health, (ii the most common carotenoids from marine organisms and (iii carotenoids having large success in pharmaceutical, nutraceutical and cosmeceutical industries, highlighting the scientific progress in marine species cultivation for natural pigments production.

Neurotrophin Propeptides: Biological Functions and Molecular Mechanisms.

Science.gov (United States)

Rafieva, Lola M; Gasanov, Eugene V

2016-01-01

Neurotrophins constitute a family of growth factors that play a key role in the regulation of the development and function of the central and peripheral nervous systems. A common feature of all the neurotrophins is their synthesis in cells as long precursors (pre-pro-neurotrophins) that contain an N-terminal signal peptide, a following propeptide and the mature neurotrophin. Although the signal peptide functions have been well studied, the role of neurotrophin propeptides is not so clear. Here, we briefly summarize the biochemistry of neurotrophin propeptides, including their role as folding-assistants for the mature factor and their role in processing and in secretion of neurotrophins. In the main part of the review we summarize our current state of knowledge of the biological activity of neurotrophin propeptides, their possible mechanisms of action, and their potential influence on the activity of the mature neurotrophins.

[Cycloferon biological activity characteristics].

Science.gov (United States)

Utkina, T M; Potekhina, L P; Kartashova, O L; Vasilchenko, A S

2014-01-01

Study the effect of cycloferon in experimental and clinical conditions on persistence properties of aurococci as well as features of their morpho-functional reaction by atomic force microscopy. The study was carried out in 12 Staphylococcus aureus clones isolated from mucous membrane of nose anterior part of a resident carrier. The effect of cycloferon in vivo was evaluated in 26 resident staphylococci carriers under the control of anti-carnosine activity of staphylococci. Anti-carnosine activity was determined by O.V. Bukharin et al. (1999), biofilm formation -by G.A. O'Toole et al. (2000). Staphylococci treated with cycloferon were studied by atomic force microscopy in contact mode using scanning probe SMM-2000 microscope. The decrease of persistence properties of staphylococci under the effect of cycloferon in vitro and in vivo may be examined as one of the mechanisms of biological activity of the preparation. A significant increase of S. aureus surface roughness and changes in their morphology under the effect of cycloferon allow stating the disorder of barrier functions in the aurococci cell wall. The data obtained expand the understanding of cycloferon biological activity mechanisms.

Re-evaluating concepts of biological function in clinical medicine: towards a new naturalistic theory of disease.

Science.gov (United States)

Chin-Yee, Benjamin; Upshur, Ross E G

2017-08-01

Naturalistic theories of disease appeal to concepts of biological function, and use the notion of dysfunction as the basis of their definitions. Debates in the philosophy of biology demonstrate how attributing functions in organisms and establishing the function-dysfunction distinction is by no means straightforward. This problematization of functional ascription has undermined naturalistic theories and led some authors to abandon the concept of dysfunction, favoring instead definitions based in normative criteria or phenomenological approaches. Although this work has enhanced our understanding of disease and illness, we need not necessarily abandon naturalistic concepts of function and dysfunction in the disease debate. This article attempts to move towards a new naturalistic theory of disease that overcomes the limitations of previous definitions and offers advantages in the clinical setting. Our approach involves a re-evaluation of concepts of biological function employed by naturalistic theories. Drawing on recent insights from the philosophy of biology, we develop a contextual and evaluative account of function that is better suited to clinical medicine and remains consistent with contemporary naturalism. We also show how an updated naturalistic view shares important affinities with normativist and phenomenological positions, suggesting a possibility for consilience in the disease debate.

Active Interaction Mapping as a tool to elucidate hierarchical functions of biological processes.

Science.gov (United States)

Farré, Jean-Claude; Kramer, Michael; Ideker, Trey; Subramani, Suresh

2017-07-03

Increasingly, various 'omics data are contributing significantly to our understanding of novel biological processes, but it has not been possible to iteratively elucidate hierarchical functions in complex phenomena. We describe a general systems biology approach called Active Interaction Mapping (AI-MAP), which elucidates the hierarchy of functions for any biological process. Existing and new 'omics data sets can be iteratively added to create and improve hierarchical models which enhance our understanding of particular biological processes. The best datatypes to further improve an AI-MAP model are predicted computationally. We applied this approach to our understanding of general and selective autophagy, which are conserved in most eukaryotes, setting the stage for the broader application to other cellular processes of interest. In the particular application to autophagy-related processes, we uncovered and validated new autophagy and autophagy-related processes, expanded known autophagy processes with new components, integrated known non-autophagic processes with autophagy and predict other unexplored connections.

The relationship between oral health status and biological and psychosocial function in the bedridden elderly.

Science.gov (United States)

Hanada, N; Tada, A

2001-01-01

The present study was conducted in order to determine what item of biological and psychosocial function is related to oral health status in the bedridden elderly. The subjects were 94 elderly individuals (30 males, 64 females) who had been admitted to a nursing home in Chiba city, Japan. We assessed the number of remaining teeth and the number of functional teeth as oral health status variables. Biological and psychosocial function levels were determined using the functional independence measure method developed by the State University of New York at Buffalo. More than 70% of subjects had less than ten remaining teeth. Almost all subjects needed prosthesis treatment. More than 50% of subjects had 27 or less functional teeth. Mann-Whitney U-test and logistic regression models showed that 'expression' was concerned with the number of remaining teeth and 'bladder management', 'locomotion', 'transfers' were related to the number of functional teeth. These data suggest close relation between oral health status and biological and psychosocial function levels in the bedridden elderly.

Paul Langerhans: a prilgrim "traveling" from functional histology to marine biology.

Science.gov (United States)

Raica, Marius; Cimpean, Anca Maria

2017-06-01

The nineteenth century was the time of a real revolution in science and medicine. A lot of seminal discoveries in medicine and biology were done in this time, and many of them were coincident with the introduction of the compound microscope by Hermann van Deijl and the standard histological technique by Paul Ehrlich. The main tissue types and individual cells were characterized and originally classified more than hundred years ago, although less attention was paid to their basic functions. This was mainly due to the modality of tissue specimen processing that allowed particularly detailed descriptive studies. Even so, we can notice some attempts to correlate the structure with the function. The German scientist Paul Langerhans, well-known for the discovery of Langerhans islets of the pancreas and Langerhans cells from the epidermis, tried to change the conventional fate of morphological studies introducing in his works functional hypothesis based on traditional microscopic observations even from the beginning of his scientific career. Paul Langerhans was a complex personality of the second half of the nineteenth century, not only in medicine, but also in other fields of biology. In the present review, presented is the life and research activity of Paul Langerhans, not only because of the importance of his discoveries, but also for perspectives that were opened by these findings in unexpected fields of medicine and biology.

Fault tree and failure mode and effects analysis of a digital safety function

International Nuclear Information System (INIS)

Maskuniitty, M.; Pulkkinen, U.

1995-01-01

The principles of fault tree and failure mode and effects analysis (FMEA) for the analysis of digital safety functions of nuclear power plants are discussed. Based on experiences from a case study, a proposal for a full scale analysis is presented. The feasibility and applicability the above mentioned reliability engineering methods are discussed. (author). 13 refs, 1 fig., 2 tabs

Knowledge base and functionality of concepts of some Filipino biology teachers in five biology topics

Science.gov (United States)

Barquilla, Manuel B.

2018-01-01

This mixed research, is a snapshot of some Filipino Biology teachers' knowledge structure and how their concepts of the five topics in Biology (Photosynthesis, Cellular Respiration, human reproductive system, Mendelian genetics and NonMendelian genetics) functions and develops inside a biology classroom. The study focuses on the six biology teachers and a total of 222 students in their respective classes. Of the Six (6) teachers, three (3) are under the Science curriculum and the other three (3) are under regular curriculum in both public and private schools in Iligan city and Lanao del Norte, Philippines. The study utilized classroom discourses, concept maps, interpretative case-study method, bracketing method, and concept analysis for qualitative part; the quantitative part uses a nonparametric statistical tool, Kendall's tau Coefficient for determining relationship and congruency while measures of central tendencies and dispersion (mean, and standard deviation) for concept maps scores interpretation. Knowledge Base of Biology teachers were evaluated by experts in field of specialization having a doctorate program (e.g. PhD in Genetics) and PhD Biology candidates. The data collection entailed seven (7) months immersion: one (1) month for preliminary phase for the researcher to gain teachers' and students' confidence and the succeeding six (6) months for main observation and data collection. The evaluation of teachers' knowledge base by experts indicated that teachers' knowledge of (65%) is lower than the minimum (75%) recommended by ABD-el-Khalick and Boujaoude (1997). Thus, the experts believe that content knowledge of the teachers is hardly adequate for their teaching assignment. Moreover, the teachers in this study do not systematically use reallife situation to apply the concepts they teach. They can identify concepts too abstract for their student; however, they seldom use innovative ways to bring the discussion to their students' level of readiness and

Progress in the biological function of alpha-enolase

Directory of Open Access Journals (Sweden)

Hong Ji

2016-03-01

Full Text Available Alpha-enolase (ENO1, also known as 2-phospho-D-glycerate hydrolase, is a metalloenzyme that catalyzes the conversion of 2-phosphoglyceric acid to phosphoenolpyruvic acid in the glycolytic pathway. It is a multifunctional glycolytic enzyme involved in cellular stress, bacterial and fungal infections, autoantigen activities, the occurrence and metastasis of cancer, parasitic infections, and the growth, development and reproduction of organisms. This article mainly reviews the basic characteristics and biological functions of ENO1.

Biological markers for kidney injury and renal function in the intensive care unit

NARCIS (Netherlands)

Royakkers, A.A.N.M.

2014-01-01

The purpose of the investigations described in this thesis was to seek for answers to two relevant questions in ICUs in resource-rich settings, i.e., can new biological markers play a role in early recognition of AKI, and can new biological markers predict recovery of renal function in patients who

Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions.

Science.gov (United States)

Xie, Hongbo; Vucetic, Slobodan; Iakoucheva, Lilia M; Oldfield, Christopher J; Dunker, A Keith; Uversky, Vladimir N; Obradovic, Zoran

2007-05-01

Identifying relationships between function, amino acid sequence, and protein structure represents a major challenge. In this study, we propose a bioinformatics approach that identifies functional keywords in the Swiss-Prot database that correlate with intrinsic disorder. A statistical evaluation is employed to rank the significance of these correlations. Protein sequence data redundancy and the relationship between protein length and protein structure were taken into consideration to ensure the quality of the statistical inferences. Over 200,000 proteins from the Swiss-Prot database were analyzed using this approach. The predictions of intrinsic disorder were carried out using PONDR VL3E predictor of long disordered regions that achieves an accuracy of above 86%. Overall, out of the 710 Swiss-Prot functional keywords that were each associated with at least 20 proteins, 238 were found to be strongly positively correlated with predicted long intrinsically disordered regions, whereas 302 were strongly negatively correlated with such regions. The remaining 170 keywords were ambiguous without strong positive or negative correlation with the disorder predictions. These functions cover a large variety of biological activities and imply that disordered regions are characterized by a wide functional repertoire. Our results agree well with literature findings, as we were able to find at least one illustrative example of functional disorder or order shown experimentally for the vast majority of keywords showing the strongest positive or negative correlation with intrinsic disorder. This work opens a series of three papers, which enriches the current view of protein structure-function relationships, especially with regards to functionalities of intrinsically disordered proteins, and provides researchers with a novel tool that could be used to improve the understanding of the relationships between protein structure and function. The first paper of the series describes our

[Recent advances of synthetic biology for production of functional ingredients in Chinese materia medica].

Science.gov (United States)

Su, Xin-Yao; Xue, Jian-Ping; Wang, Cai-Xia

2016-11-01

The functional ingredients in Chinese materia medica are the main active substance for traditional Chinese medicine and most of them are secondary metabolites derivatives. Until now,the main method to obtain those functional ingredients is through direct extraction from the Chinese materia medica. However, the income is very low because of the high extraction costs and the decreased medicinal plants. Synthetic biology technology, as a new and microbial approach, can be able to carry out large-scale production of functional ingredients and greatly ease the shortage of traditional Chinese medicine ingredients. This review mainly focused on the recent advances in synthetic biology for the functional ingredients production. Copyright© by the Chinese Pharmaceutical Association.

Identifying the default mode network structure using dynamic causal modeling on resting-state functional magnetic resonance imaging.

Science.gov (United States)

Di, Xin; Biswal, Bharat B

2014-02-01

The default mode network is part of the brain structure that shows higher neural activity and energy consumption when one is at rest. The key regions in the default mode network are highly interconnected as conveyed by both the white matter fiber tracing and the synchrony of resting-state functional magnetic resonance imaging signals. However, the causal information flow within the default mode network is still poorly understood. The current study used the dynamic causal modeling on a resting-state fMRI data set to identify the network structure underlying the default mode network. The endogenous brain fluctuations were explicitly modeled by Fourier series at the low frequency band of 0.01-0.08Hz, and those Fourier series were set as driving inputs of the DCM models. Model comparison procedures favored a model wherein the MPFC sends information to the PCC and the bilateral inferior parietal lobule sends information to both the PCC and MPFC. Further analyses provide evidence that the endogenous connectivity might be higher in the right hemisphere than in the left hemisphere. These data provided insight into the functions of each node in the DMN, and also validate the usage of DCM on resting-state fMRI data. © 2013.

Anisotropy and phonon modes from analysis of the dielectric function tensor and the inverse dielectric function tensor of monoclinic yttrium orthosilicate

Science.gov (United States)

Mock, A.; Korlacki, R.; Knight, S.; Schubert, M.

2018-04-01

We determine the frequency dependence of the four independent Cartesian tensor elements of the dielectric function for monoclinic symmetry Y2SiO5 using generalized spectroscopic ellipsometry from 40-1200 cm-1. Three different crystal cuts, each perpendicular to a principle axis, are investigated. We apply our recently described augmentation of lattice anharmonicity onto the eigendielectric displacement vector summation approach [A. Mock et al., Phys. Rev. B 95, 165202 (2017), 10.1103/PhysRevB.95.165202], and we present and demonstrate the application of an eigendielectric displacement loss vector summation approach with anharmonic broadening. We obtain an excellent match between all measured and model-calculated dielectric function tensor elements and all dielectric loss function tensor elements. We obtain 23 Au and 22 Bu symmetry long-wavelength active transverse and longitudinal optical mode parameters including their eigenvector orientation within the monoclinic lattice. We perform density functional theory calculations and obtain 23 Au symmetry and 22 Bu transverse and longitudinal optical mode parameters and their orientation within the monoclinic lattice. We compare our results from ellipsometry and density functional theory and find excellent agreement. We also determine the static and above reststrahlen spectral range dielectric tensor values and find a recently derived generalization of the Lyddane-Sachs-Teller relation for polar phonons in monoclinic symmetry materials satisfied [M. Schubert, Phys Rev. Lett. 117, 215502 (2016), 10.1103/PhysRevLett.117.215502].

Six coordination compounds: mode of cytotoxic action and biological evaluation

Directory of Open Access Journals (Sweden)

ali aydin

2016-09-01

Full Text Available This study describes the biological and anticancer properties of followed coordination compounds. IR spectra, magnetic properties, thermal analyses and crystal structures of six cyanido-complexes derivatives with [MII(CN4]2- (MII= Ni and Pd and [Co(CN6]3- anions and N-bishydeten (N,N-bis(2-hydroxyethylethylenediamine as a capping ligand have been previously reported. Here, we investigated these complexes denoted as[Ni(N-bishydetenNi(CN4] (C1, [Zn2(N-bishydeten2Ni(CN4] (C2, [Ni(N-bishydetenPd(CN4] (C3, [Cd(N-bishydeten2][Pd(CN4] (C4, [Ni2(N-bishydeten2Co(CN6].3H2O (C5 and K[Cd(N-bishydetenCo(CN6].1.5H2O (C6, which were tested for their anti-proliferative activity against human cervical cancer (HeLa, human colon cancer (HT29, rat glioma (C6 and African green monkey kidney (Vero cell lines. The DNA/BSA binding affinities of these compounds were also elucidated by spectroscopic titrations, displacement experiments and electrophoresis measurements. Studies on cancerous cells revealed that C1, C2, C4 and C6 exhibited significant antitumor activity and inhibited tumor progression in testing cell lines and showed high solubility in the solvent. Absorbance and emission spectra data results revealed that the complexes interact with the DNA via groove binding mode of interaction. Overall, these compounds have been found to demonstrate effective anti-proliferative activity against the cancer cell lines, indicating that they are a potent candidate for preclinical or clinical study.

Mediating objects: scientific and public functions of models in nineteenth-century biology.

Science.gov (United States)

Ludwig, David

2013-01-01

The aim of this article is to examine the scientific and public functions of two- and three-dimensional models in the context of three episodes from nineteenth-century biology. I argue that these models incorporate both data and theory by presenting theoretical assumptions in the light of concrete data or organizing data through theoretical assumptions. Despite their diverse roles in scientific practice, they all can be characterized as mediators between data and theory. Furthermore, I argue that these different mediating functions often reflect their different audiences that included specialized scientists, students, and the general public. In this sense, models in nineteenth-century biology can be understood as mediators between theory, data, and their diverse audiences.

Preliminary findings of altered functional connectivity of the default mode network linked to functional outcomes one year after pediatric traumatic brain injury.

Science.gov (United States)

Stephens, Jaclyn A; Salorio, Cynthia F; Barber, Anita D; Risen, Sarah R; Mostofsky, Stewart H; Suskauer, Stacy J

2017-07-10

This study examined functional connectivity of the default mode network (DMN) and examined brain-behavior relationships in a pilot cohort of children with chronic mild to moderate traumatic brain injury (TBI). Compared to uninjured peers, children with TBI demonstrated less anti-correlated functional connectivity between DMN and right Brodmann Area 40 (BA 40). In children with TBI, more anomalous less anti-correlated) connectivity between DMN and right BA 40 was linked to poorer performance on response inhibition tasks. Collectively, these preliminary findings suggest that functional connectivity between DMN and BA 40 may relate to longterm functional outcomes in chronic pediatric TBI.

Biomarkers of Aging: From Function to Molecular Biology

Directory of Open Access Journals (Sweden)

Karl-Heinz Wagner

2016-06-01

Full Text Available Aging is a major risk factor for most chronic diseases and functional impairments. Within a homogeneous age sample there is a considerable variation in the extent of disease and functional impairment risk, revealing a need for valid biomarkers to aid in characterizing the complex aging processes. The identification of biomarkers is further complicated by the diversity of biological living situations, lifestyle activities and medical treatments. Thus, there has been no identification of a single biomarker or gold standard tool that can monitor successful or healthy aging. Within this short review the current knowledge of putative biomarkers is presented, focusing on their application to the major physiological mechanisms affected by the aging process including physical capability, nutritional status, body composition, endocrine and immune function. This review emphasizes molecular and DNA-based biomarkers, as well as recent advances in other biomarkers such as microRNAs, bilirubin or advanced glycation end products.

Offshoring and access to location-specific advantages - the impact of governance mode and function

DEFF Research Database (Denmark)

Mykhaylenko, Alona; Motika, Agnes; Wæhrens, Brian Vejrum

how access to particular offshoring advantages may provide this link. The results of a quantitative survey of more than 1000 Scandinavian firms show that certain offshoring factors (governance mode and type of offshored function) indeed impact the access a company acquires to certain offshoring...... advantages, which may explain the unpredictability of previous performance outcomes....

Examining the Delivery Modes of Metacognitive Awareness and Active Reading Lessons in a College Nonmajors Introductory Biology Course

Directory of Open Access Journals (Sweden)

Kendra M. Hill

2014-02-01

Full Text Available Current research supports the role of metacognitive strategies to enhance reading comprehension. This study measured the effectiveness of online versus face-to-face metacognitive and active reading skills lessons introduced by Biology faculty to college students in a non-majors introductory biology course. These lessons were delivered in two lectures either online (Group 1: N = 154 or face-to-face (Group 2: N = 152. Previously validated pre- and post-surveys were used to collect and compare data by paired and independent t-test analysis (α = 0.05. Pre- and post-survey data showed a statistically significant improvement in both groups in metacognitive awareness (p = 0.001, p = 0.003, respectively and reading comprehension (p < 0.001 for both groups. When comparing the delivery mode of these lessons, no difference was detected between the online and face-to-face instruction for metacognitive awareness (pre- p = 0.619, post- p = 0.885. For reading comprehension, no difference in gains was demonstrated between online and face-to-face (p = 0.381, however, differences in pre- and post- test scores was measured (pre- p = 0.005, post- p = 0.038. This study suggests that biology instructors can easily introduce effective metacognitive awareness and active reading lessons into their course, either through online or face-to-face instruction.

Automated quantitative assessment of proteins' biological function in protein knowledge bases.

Science.gov (United States)

Mayr, Gabriele; Lepperdinger, Günter; Lackner, Peter

2008-01-01

Primary protein sequence data are archived in databases together with information regarding corresponding biological functions. In this respect, UniProt/Swiss-Prot is currently the most comprehensive collection and it is routinely cross-examined when trying to unravel the biological role of hypothetical proteins. Bioscientists frequently extract single entries and further evaluate those on a subjective basis. In lieu of a standardized procedure for scoring the existing knowledge regarding individual proteins, we here report about a computer-assisted method, which we applied to score the present knowledge about any given Swiss-Prot entry. Applying this quantitative score allows the comparison of proteins with respect to their sequence yet highlights the comprehension of functional data. pfs analysis may be also applied for quality control of individual entries or for database management in order to rank entry listings.

Automated Quantitative Assessment of Proteins' Biological Function in Protein Knowledge Bases

Directory of Open Access Journals (Sweden)

Gabriele Mayr

2008-01-01

Full Text Available Primary protein sequence data are archived in databases together with information regarding corresponding biological functions. In this respect, UniProt/Swiss-Prot is currently the most comprehensive collection and it is routinely cross-examined when trying to unravel the biological role of hypothetical proteins. Bioscientists frequently extract single entries and further evaluate those on a subjective basis. In lieu of a standardized procedure for scoring the existing knowledge regarding individual proteins, we here report about a computer-assisted method, which we applied to score the present knowledge about any given Swiss-Prot entry. Applying this quantitative score allows the comparison of proteins with respect to their sequence yet highlights the comprehension of functional data. pfs analysis may be also applied for quality control of individual entries or for database management in order to rank entry listings.

Exploring candidate biological functions by Boolean Function Networks for Saccharomyces cerevisiae.

Directory of Open Access Journals (Sweden)

Maria Simak

Full Text Available The great amount of gene expression data has brought a big challenge for the discovery of Gene Regulatory Network (GRN. For network reconstruction and the investigation of regulatory relations, it is desirable to ensure directness of links between genes on a map, infer their directionality and explore candidate biological functions from high-throughput transcriptomic data. To address these problems, we introduce a Boolean Function Network (BFN model based on techniques of hidden Markov model (HMM, likelihood ratio test and Boolean logic functions. BFN consists of two consecutive tests to establish links between pairs of genes and check their directness. We evaluate the performance of BFN through the application to S. cerevisiae time course data. BFN produces regulatory relations which show consistency with succession of cell cycle phases. Furthermore, it also improves sensitivity and specificity when compared with alternative methods of genetic network reverse engineering. Moreover, we demonstrate that BFN can provide proper resolution for GO enrichment of gene sets. Finally, the Boolean functions discovered by BFN can provide useful insights for the identification of control mechanisms of regulatory processes, which is the special advantage of the proposed approach. In combination with low computational complexity, BFN can serve as an efficient screening tool to reconstruct genes relations on the whole genome level. In addition, the BFN approach is also feasible to a wide range of time course datasets.

Adaptive variational mode decomposition method for signal processing based on mode characteristic

Science.gov (United States)

Lian, Jijian; Liu, Zhuo; Wang, Haijun; Dong, Xiaofeng

2018-07-01

Variational mode decomposition is a completely non-recursive decomposition model, where all the modes are extracted concurrently. However, the model requires a preset mode number, which limits the adaptability of the method since a large deviation in the number of mode set will cause the discard or mixing of the mode. Hence, a method called Adaptive Variational Mode Decomposition (AVMD) was proposed to automatically determine the mode number based on the characteristic of intrinsic mode function. The method was used to analyze the simulation signals and the measured signals in the hydropower plant. Comparisons have also been conducted to evaluate the performance by using VMD, EMD and EWT. It is indicated that the proposed method has strong adaptability and is robust to noise. It can determine the mode number appropriately without modulation even when the signal frequencies are relatively close.

Near-roadway monitoring of vehicle emissions as a function of mode of operation for light-duty vehicles.

Science.gov (United States)

Wen, Dongqi; Zhai, Wenjuan; Xiang, Sheng; Hu, Zhice; Wei, Tongchuan; Noll, Kenneth E

2017-11-01

Determination of the effect of vehicle emissions on air quality near roadways is important because vehicles are a major source of air pollution. A near-roadway monitoring program was undertaken in Chicago between August 4 and October 30, 2014, to measure ultrafine particles, carbon dioxide, carbon monoxide, traffic volume and speed, and wind direction and speed. The objective of this study was to develop a method to relate short-term changes in traffic mode of operation to air quality near roadways using data averaged over 5-min intervals to provide a better understanding of the processes controlling air pollution concentrations near roadways. Three different types of data analysis are provided to demonstrate the type of results that can be obtained from a near-roadway sampling program based on 5-min measurements: (1) development of vehicle emission factors (EFs) for ultrafine particles as a function of vehicle mode of operation, (2) comparison of measured and modeled CO 2 concentrations, and (3) application of dispersion models to determine concentrations near roadways. EFs for ultrafine particles are developed that are a function of traffic volume and mode of operation (free flow and congestion) for light-duty vehicles (LDVs) under real-world conditions. Two air quality models-CALINE4 (California Line Source Dispersion Model, version 4) and AERMOD (American Meteorological Society/U.S. Environmental Protection Agency Regulatory Model)-are used to predict the ultrafine particulate concentrations near roadways for comparison with measured concentrations. When using CALINE4 to predict air quality levels in the mixing cell, changes in surface roughness and stability class have no effect on the predicted concentrations. However, when using AERMOD to predict air quality in the mixing cell, changes in surface roughness have a significant impact on the predicted concentrations. The paper provides emission factors (EFs) that are a function of traffic volume and mode of

Single amino acid substitution in important hemoglobinopathies does not disturb molecular function and biological process

Directory of Open Access Journals (Sweden)

Viroj Wiwanitkit

2008-06-01

Full Text Available Viroj WiwanitkitDepartment of Laboratory Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, ThailandAbstract: Hemoglobin is an important protein found in the red cells of many animals. In humans, the hemoglobin is mainly distributed in the red blood cell. Single amino acid substitution is the main pathogenesis of most hemoglobin disorders. Here, the author used a new gene ontology technology to predict the molecular function and biological process of four important hemoglobin disorders with single substitution. The four studied important abnormal hemoglobins (Hb with single substitution included Hb S, Hb E, Hb C, and Hb J-Baltimore. Using the GoFigure server, the molecular function and biological process in normal and abnormal hemoglobins was predicted. Compared with normal hemoglobin, all studied abnormal hemoglobins had the same function and biological process. This indicated that the overall function of oxygen transportation is not disturbed in the studied hemoglobin disorders. Clinical findings of oxygen depletion in abnormal hemoglobin should therefore be due to the other processes rather than genomics, proteomics, and expression levels.Keywords: hemoglobin, amino acid, substitution, function

Beta limits in H-modes and VH-modes in JET

Energy Technology Data Exchange (ETDEWEB)

Smeulders, P; Hender, T C; Huysmans, G; Marcus, F; Ali-Arshad, S; Alper, B; Balet, B; Bures, M; Deliyanakis, N; Esch, H de; Fshpool, G; Jarvis, O N; Jones, T T.C.; Ketner, W; Koenig, R; Lawson, K; Lomas, P; O` Brien, D; Sadler, G; Stok, D; Stubberfield, P; Thomas, P; Thomen, K; Wesson, J [Commission of the European Communities, Abingdon (United Kingdom). JET Joint Undertaking; Nave, M F [Universidade Tecnica, Lisbon (Portugal). Inst. Superior Tecnico

1994-07-01

In Hot-ion H- and VH-modes, the highest achieved beta was about 10% below the Troyon value in the best case of discharge 26087. The operational space of the high beta discharges obtained before March 1992 has been explored as function of the parameters H{sub ITER89P}, {beta}{sub n}, q{sub 95}, I{sub p}. Also, a limiting envelope on the fusion reactivity as a function of the average plasma pressure and beta has been observed with R{sub DD} related to {beta}{sub {phi}}{sup 2}.B{sub {phi}}{sup 4}. MHD stability analysis shows that the JET VH modes at the edge are in the second region for ballooning mode stability. The dependence of ballooning stability and the n=1 external kink on the edge current density is analyzed. (authors). 6 figs., 6 refs.

Form and function: Perspectives on structural biology and resources for the future

International Nuclear Information System (INIS)

Vaughan, D.

1990-12-01

The purpose of this study is largely to explore and expand on the thesis that biological structures and their functions are suited to. Form indeed follows function and if we are to understand the workings of a living system, with all that such an understanding promises, we must first seek to describe the structure of its parts. Descriptions of a few achievements of structural biology lay the groundwork, but the substance of this booklet is a discussion of important questions yet unanswered and opportunities just beyond our grasp. The concluding pages then outline a course of action in which the Department of Energy would exercise its responsibility to develop the major resources needed to extend our reach and to answer some of those unanswered questions. 22 figs

Form and function: Perspectives on structural biology and resources for the future

Energy Technology Data Exchange (ETDEWEB)

Vaughan, D. (ed.)

1990-12-01

The purpose of this study is largely to explore and expand on the thesis that biological structures and their functions are suited to. Form indeed follows function and if we are to understand the workings of a living system, with all that such an understanding promises, we must first seek to describe the structure of its parts. Descriptions of a few achievements of structural biology lay the groundwork, but the substance of this booklet is a discussion of important questions yet unanswered and opportunities just beyond our grasp. The concluding pages then outline a course of action in which the Department of Energy would exercise its responsibility to develop the major resources needed to extend our reach and to answer some of those unanswered questions. 22 figs.

Implementation of biological tissue Mueller matrix for polarization-sensitive optical coherence tomography based on LabVIEW

Science.gov (United States)

Lin, Yongping; Zhang, Xiyang; He, Youwu; Cai, Jianyong; Li, Hui

2018-02-01

The Jones matrix and the Mueller matrix are main tools to study polarization devices. The Mueller matrix can also be used for biological tissue research to get complete tissue properties, while the commercial optical coherence tomography system does not give relevant analysis function. Based on the LabVIEW, a near real time display method of Mueller matrix image of biological tissue is developed and it gives the corresponding phase retardant image simultaneously. A quarter-wave plate was placed at 45 in the sample arm. Experimental results of the two orthogonal channels show that the phase retardance based on incident light vector fixed mode and the Mueller matrix based on incident light vector dynamic mode can provide an effective analysis method of the existing system.

Reduced Functional Connectivity of Default Mode and Set-Maintenance Networks in Ornithine Transcarbamylase Deficiency.

Directory of Open Access Journals (Sweden)

Ileana Pacheco-Colón

Full Text Available Ornithine transcarbamylase deficiency (OTCD is an X-chromosome linked urea cycle disorder (UCD that causes hyperammonemic episodes leading to white matter injury and impairments in executive functioning, working memory, and motor planning. This study aims to investigate differences in functional connectivity of two resting-state networks--default mode and set-maintenance--between OTCD patients and healthy controls.Sixteen patients with partial OTCD and twenty-two control participants underwent a resting-state scan using 3T fMRI. Combining independent component analysis (ICA and region-of-interest (ROI analyses, we identified the nodes that comprised each network in each group, and assessed internodal connectivity.Group comparisons revealed reduced functional connectivity in the default mode network (DMN of OTCD patients, particularly between the anterior cingulate cortex/medial prefrontal cortex (ACC/mPFC node and bilateral inferior parietal lobule (IPL, as well as between the ACC/mPFC node and the posterior cingulate cortex (PCC node. Patients also showed reduced connectivity in the set-maintenance network, especially between right anterior insula/frontal operculum (aI/fO node and bilateral superior frontal gyrus (SFG, as well as between the right aI/fO and ACC and between the ACC and right SFG.Internodal functional connectivity in the DMN and set-maintenance network is reduced in patients with partial OTCD compared to controls, most likely due to hyperammonemia-related white matter damage. Because several of the affected areas are involved in executive functioning, it is postulated that this reduced connectivity is an underlying cause of the deficits OTCD patients display in this cognitive domain.

Event-based text mining for biology and functional genomics

Science.gov (United States)

Thompson, Paul; Nawaz, Raheel; McNaught, John; Kell, Douglas B.

2015-01-01

The assessment of genome function requires a mapping between genome-derived entities and biochemical reactions, and the biomedical literature represents a rich source of information about reactions between biological components. However, the increasingly rapid growth in the volume of literature provides both a challenge and an opportunity for researchers to isolate information about reactions of interest in a timely and efficient manner. In response, recent text mining research in the biology domain has been largely focused on the identification and extraction of ‘events’, i.e. categorised, structured representations of relationships between biochemical entities, from the literature. Functional genomics analyses necessarily encompass events as so defined. Automatic event extraction systems facilitate the development of sophisticated semantic search applications, allowing researchers to formulate structured queries over extracted events, so as to specify the exact types of reactions to be retrieved. This article provides an overview of recent research into event extraction. We cover annotated corpora on which systems are trained, systems that achieve state-of-the-art performance and details of the community shared tasks that have been instrumental in increasing the quality, coverage and scalability of recent systems. Finally, several concrete applications of event extraction are covered, together with emerging directions of research. PMID:24907365

Functional Anthology of Intrinsic Disorder. I. Biological Processes and Functions of Proteins with Long Disordered Regions

Science.gov (United States)

Xie, Hongbo; Vucetic, Slobodan; Iakoucheva, Lilia M.; Oldfield, Christopher J.; Dunker, A. Keith; Uversky, Vladimir N.; Obradovic, Zoran

2008-01-01

Identifying relationships between function, amino acid sequence and protein structure represents a major challenge. In this study we propose a bioinformatics approach that identifies functional keywords in the Swiss-Prot database that correlate with intrinsic disorder. A statistical evaluation is employed to rank the significance of these correlations. Protein sequence data redundancy and the relationship between protein length and protein structure were taken into consideration to ensure the quality of the statistical inferences. Over 200,000 proteins from Swiss-Prot database were analyzed using this approach. The predictions of intrinsic disorder were carried out using PONDR VL3E predictor of long disordered regions that achieves an accuracy of above 86%. Overall, out of the 710 Swiss-Prot functional keywords that were each associated with at least 20 proteins, 238 were found to be strongly positively correlated with predicted long intrinsically disordered regions, whereas 302 were strongly negatively correlated with such regions. The remaining 170 keywords were ambiguous without strong positive or negative correlation with the disorder predictions. These functions cover a large variety of biological activities and imply that disordered regions are characterized by a wide functional repertoire. Our results agree well with literature findings, as we were able to find at least one illustrative example of functional disorder or order shown experimentally for the vast majority of keywords showing the strongest positive or negative correlation with intrinsic disorder. This work opens a series of three papers, which enriches the current view of protein structure-function relationships, especially with regards to functionalities of intrinsically disordered proteins and provides researchers with a novel tool that could be used to improve the understanding of the relationships between protein structure and function. The first paper of the series describes our statistical

A mixed-mode traffic assignment model with new time-flow impedance function

Science.gov (United States)

Lin, Gui-Hua; Hu, Yu; Zou, Yuan-Yang

2018-01-01

Recently, with the wide adoption of electric vehicles, transportation network has shown different characteristics and been further developed. In this paper, we present a new time-flow impedance function, which may be more realistic than the existing time-flow impedance functions. Based on this new impedance function, we present an optimization model for a mixed-mode traffic network in which battery electric vehicles (BEVs) and gasoline vehicles (GVs) are chosen. We suggest two approaches to handle the model: One is to use the interior point (IP) algorithm and the other is to employ the sequential quadratic programming (SQP) algorithm. Three numerical examples are presented to illustrate the efficiency of these approaches. In particular, our numerical results show that more travelers prefer to choosing BEVs when the distance limit of BEVs is long enough and the unit operating cost of GVs is higher than that of BEVs, and the SQP algorithm is faster than the IP algorithm.

Parameters Designing of Slide Mode Variable Structure Controller of Bus Voltage of DC Microgrid Based on Proportion Switching Function

Directory of Open Access Journals (Sweden)

Sun Zhenchuan

2017-01-01

Full Text Available Constant value control of the DC-bus voltage is a essential problem of the control system of the DC microgrids. DC-DC converters are applied in parallel to realize the transform of energy from the distributed generations (DGs to the DC-bus. Droop control methods are applied to the DC-bus voltage while PI controllers are used in controlling the duty ratios of the converters. This method may bring out the slow response speed of the system accompanied by the large ripple of the voltage. The slide mode variable structure control can speed up the response and reduce the ripple of the voltage as well. In the traditional slide mode control based on the proportion switching function, the denominator of the transfer function of the controlled plant is a second-order characteristic polynomial without the constant term. The denominators of the transfer functions of the buck DC-DC converters contain the constant terms. The designing of the parameters of the slide mode control based on the proportion switching function is analyzed based on mathematics deductions. Simulation results show that the selected parameters can not only speed up the response of the system but also greatly reduce the ripple of the voltage.

Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease.

Science.gov (United States)

Torres, Matthew P; Dewhurst, Henry; Sundararaman, Niveda

2016-11-01

Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function - a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) - a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al., 2015). Here, we apply SAPH-ire to the set of eukaryotic protein families containing experimental PTM and 3D structure data - capturing 1,325 protein families with 50,839 unique PTM sites organized into 31,747 modified alignment positions (MAPs), of which 2010 (∼6%) possess known biological function. Here, we show that using an artificial neural network model (SAPH-ire NN) trained to identify MAP hotspots with biological function results in prediction outcomes that far surpass the use of single hotspot features, including nearest neighbor PTM clustering methods. We find the greatest enhancement in prediction for positions with PTM counts of five or less, which represent 98% of all MAPs in the eukaryotic proteome and 90% of all MAPs found to have biological function. Analysis of the top 1092 MAP hotspots revealed 267 of truly unknown function (containing 5443 distinct PTMs). Of these, 165 hotspots could be mapped to human KEGG pathways for normal and/or disease physiology. Many high-ranking hotspots were also found to be disease-associated pathogenic sites of amino acid substitution despite the lack of observable PTM in the human protein family member. Taken together, these experiments demonstrate that the functional relevance of a PTM can be predicted very effectively by neural network models, revealing a large but testable

A Research on Maximum Symbolic Entropy from Intrinsic Mode Function and Its Application in Fault Diagnosis

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Zhuofei Xu

2017-01-01

Full Text Available Empirical mode decomposition (EMD is a self-adaptive analysis method for nonlinear and nonstationary signals. It has been widely applied to machinery fault diagnosis and structural damage detection. A novel feature, maximum symbolic entropy of intrinsic mode function based on EMD, is proposed to enhance the ability of recognition of EMD in this paper. First, a signal is decomposed into a collection of intrinsic mode functions (IMFs based on the local characteristic time scale of the signal, and then IMFs are transformed into a serious of symbolic sequence with different parameters. Second, it can be found that the entropies of symbolic IMFs are quite different. However, there is always a maximum value for a certain symbolic IMF. Third, take the maximum symbolic entropy as features to describe IMFs from a signal. Finally, the proposed features are applied to evaluate the effect of maximum symbolic entropy in fault diagnosis of rolling bearing, and then the maximum symbolic entropy is compared with other standard time analysis features in a contrast experiment. Although maximum symbolic entropy is only a time domain feature, it can reveal the signal characteristic information accurately. It can also be used in other fields related to EMD method.

The Nuclear Scissors Mode by Two Approaches (Wigner Function Moments Versus RPA)

CERN Document Server

Balbutsev, E B

2004-01-01

Two complementary methods to describe the collective motion, RPA and Wigner Function Moments (WFM) method, are compared on an example of a simple model - harmonic oscillator with quadrupole-quadrupole residual interaction. It is shown that they give identical formulae for eigenfrequencies and transition probabilities of all collective excitations of the model including the scissors mode, which is a subject of our especial attention. The normalization factor of the "synthetic" scissors state and its overlap with physical states are calculated analytically. The orthogonality of the spurious state to all physical states is proved rigorously.

The functional biology of human milk oligosaccharides.

Science.gov (United States)

Bode, Lars

2015-11-01

Human milk oligosaccharides (HMOs) are a group of complex sugars that are highly abundant in human milk, but currently not present in infant formula. More than a hundred different HMOs have been identified so far. The amount and composition of HMOs are highly variable between women, and each structurally defined HMO might have a distinct functionality. HMOs are not digested by the infant and serve as metabolic substrates for select microbes, contributing to shape the infant gut microbiome. HMOs act as soluble decoy receptors that block the attachment of viral, bacterial or protozoan parasite pathogens to epithelial cell surface sugars, which may help prevent infectious diseases in the gut and also the respiratory and urinary tracts. HMOs are also antimicrobials that act as bacteriostatic or bacteriocidal agents. In addition, HMOs alter host epithelial and immune cell responses with potential benefits for the neonate. The article reviews current knowledge as well as future challenges and opportunities related to the functional biology of HMOs. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Completeness of non-normalizable modes

International Nuclear Information System (INIS)

Mannheim, Philip D; Simbotin, Ionel

2006-01-01

We establish the completeness of some characteristic sets of non-normalizable modes by constructing fully localized square steps out of them, with each such construction expressly displaying the Gibbs phenomenon associated with trying to use a complete basis of modes to fit functions with discontinuous edges. As well as being of interest in and of itself, our study is also of interest to the recently introduced large extra dimension brane-localized gravity program of Randall and Sundrum, since the particular non-normalizable mode bases that we consider (specifically the irregular Bessel functions and the associated Legendre functions of the second kind) are associated with the tensor gravitational fluctuations which occur in those specific brane worlds in which the embedding of a maximally four-symmetric brane in a five-dimensional anti-de Sitter bulk leads to a warp factor which is divergent. Since the brane-world massless four-dimensional graviton has a divergent wavefunction in these particular cases, its resulting lack of normalizability is thus not seen to be any impediment to its belonging to a complete basis of modes, and consequently its lack of normalizability should not be seen as a criterion for not including it in the spectrum of observable modes. Moreover, because the divergent modes we consider form complete bases, we can even construct propagators out of them in which these modes appear as poles with residues which are expressly finite. Thus, even though normalizable modes appear in propagators with residues which are given as their finite normalization constants, non-normalizable modes can just as equally appear in propagators with finite residues too-it is just that such residues will not be associated with bilinear integrals of the modes

Functional reorganization of the default mode network across chronic pain conditions.

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Marwan N Baliki

Full Text Available Chronic pain is associated with neuronal plasticity. Here we use resting-state functional magnetic resonance imaging to investigate functional changes in patients suffering from chronic back pain (CBP, complex regional pain syndrome (CRPS and knee osteoarthritis (OA. We isolated five meaningful resting-state networks across the groups, of which only the default mode network (DMN exhibited deviations from healthy controls. All patient groups showed decreased connectivity of medial prefrontal cortex (MPFC to the posterior constituents of the DMN, and increased connectivity to the insular cortex in proportion to the intensity of pain. Multiple DMN regions, especially the MPFC, exhibited increased high frequency oscillations, conjoined with decreased phase locking with parietal regions involved in processing attention. Both phase and frequency changes correlated to pain duration in OA and CBP patients. Thus chronic pain seems to reorganize the dynamics of the DMN and as such reflect the maladaptive physiology of different types of chronic pain.

Effects of Physical Exercise on Cognitive Functioning and Wellbeing: Biological and Psychological Benefits

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Laura Mandolesi

2018-04-01

Full Text Available Much evidence shows that physical exercise (PE is a strong gene modulator that induces structural and functional changes in the brain, determining enormous benefit on both cognitive functioning and wellbeing. PE is also a protective factor for neurodegeneration. However, it is unclear if such protection is granted through modifications to the biological mechanisms underlying neurodegeneration or through better compensation against attacks. This concise review addresses the biological and psychological positive effects of PE describing the results obtained on brain plasticity and epigenetic mechanisms in animal and human studies, in order to clarify how to maximize the positive effects of PE while avoiding negative consequences, as in the case of exercise addiction.

Applications of sliding mode control in science and engineering

CERN Document Server

Lien, Chang-Hua

2017-01-01

Gathering 20 chapters contributed by respected experts, this book reports on the latest advances in and applications of sliding mode control in science and engineering. The respective chapters address applications of sliding mode control in the broad areas of chaos theory, robotics, electrical engineering, physics, chemical engineering, memristors, mechanical engineering, environmental engineering, finance, and biology. Special emphasis has been given to papers that offer practical solutions, and which examine design and modeling involving new types of sliding mode control such as higher order sliding mode control, terminal sliding mode control, super-twisting sliding mode control, and integral sliding mode control. This book serves as a unique reference guide to sliding mode control and its recent applications for graduate students and researchers with a basic knowledge of electrical and control systems engineering.

Distinct ubiquitin binding modes exhibited by SH3 domains: molecular determinants and functional implications.

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Jose L Ortega Roldan

Full Text Available SH3 domains constitute a new type of ubiquitin-binding domains. We previously showed that the third SH3 domain (SH3-C of CD2AP binds ubiquitin in an alternative orientation. We have determined the structure of the complex between first CD2AP SH3 domain and ubiquitin and performed a structural and mutational analysis to decipher the determinants of the SH3-C binding mode to ubiquitin. We found that the Phe-to-Tyr mutation in CD2AP and in the homologous CIN85 SH3-C domain does not abrogate ubiquitin binding, in contrast to previous hypothesis and our findings for the first two CD2AP SH3 domains. The similar alternative binding mode of the SH3-C domains of these related adaptor proteins is characterised by a higher affinity to C-terminal extended ubiquitin molecules. We conclude that CD2AP/CIN85 SH3-C domain interaction with ubiquitin constitutes a new ubiquitin-binding mode involved in a different cellular function and thus changes the previously established mechanism of EGF-dependent CD2AP/CIN85 mono-ubiquitination.

Default Mode Network Connectivity in Stroke Patients.

Science.gov (United States)

Tuladhar, Anil Man; Snaphaan, Liselore; Shumskaya, Elena; Rijpkema, Mark; Fernandez, Guillén; Norris, David G; de Leeuw, Frank-Erik

2013-01-01

The pathophysiology of episodic memory dysfunction after infarction is not completely understood. It has been suggested that infarctions located anywhere in the brain can induce widespread effects causing disruption of functional networks of the cortical regions. The default mode network, which includes the medial temporal lobe, is a functional network that is associated with episodic memory processing. We investigated whether the default mode network activity is reduced in stroke patients compared to healthy control subjects in the resting state condition. We assessed the whole brain network properties during resting state functional MRI in 21 control subjects and 20 'first-ever' stroke patients. Patients were scanned 9-12 weeks after stroke onset. Stroke lesions were located in various parts of the brain. Independent component analyses were conducted to identify the default mode network and to compare the group differences of the default mode network. Furthermore, region-of-interest based analysis was performed to explore the functional connectivity between the regions of the default mode network. Stroke patients performed significantly worse than control subjects on the delayed recall score on California verbal learning test. We found decreased functional connectivity in the left medial temporal lobe, posterior cingulate and medial prefrontal cortical areas within the default mode network and reduced functional connectivity between these regions in stroke patients compared with controls. There were no significant volumetric differences between the groups. These results demonstrate that connectivity within the default mode network is reduced in 'first-ever' stroke patients compared to control subjects. This phenomenon might explain the occurrence of post-stroke cognitive dysfunction in stroke patients.

Direct assignment of molecular vibrations via normal mode analysis of the neutron dynamic pair distribution function technique

International Nuclear Information System (INIS)

Fry-Petit, A. M.; Sheckelton, J. P.; McQueen, T. M.; Rebola, A. F.; Fennie, C. J.; Mourigal, M.; Valentine, M.; Drichko, N.

2015-01-01

For over a century, vibrational spectroscopy has enhanced the study of materials. Yet, assignment of particular molecular motions to vibrational excitations has relied on indirect methods. Here, we demonstrate that applying group theoretical methods to the dynamic pair distribution function analysis of neutron scattering data provides direct access to the individual atomic displacements responsible for these excitations. Applied to the molecule-based frustrated magnet with a potential magnetic valence-bond state, LiZn 2 Mo 3 O 8 , this approach allows direct assignment of the constrained rotational mode of Mo 3 O 13 clusters and internal modes of MoO 6 polyhedra. We anticipate that coupling this well known data analysis technique with dynamic pair distribution function analysis will have broad application in connecting structural dynamics to physical properties in a wide range of molecular and solid state systems

A Synthetic Biology Framework for Programming Eukaryotic Transcription Functions

Science.gov (United States)

Khalil, Ahmad S.; Lu, Timothy K.; Bashor, Caleb J.; Ramirez, Cherie L.; Pyenson, Nora C.; Joung, J. Keith; Collins, James J.

2013-01-01

SUMMARY Eukaryotic transcription factors (TFs) perform complex and combinatorial functions within transcriptional networks. Here, we present a synthetic framework for systematically constructing eukaryotic transcription functions using artificial zinc fingers, modular DNA-binding domains found within many eukaryotic TFs. Utilizing this platform, we construct a library of orthogonal synthetic transcription factors (sTFs) and use these to wire synthetic transcriptional circuits in yeast. We engineer complex functions, such as tunable output strength and transcriptional cooperativity, by rationally adjusting a decomposed set of key component properties, e.g., DNA specificity, affinity, promoter design, protein-protein interactions. We show that subtle perturbations to these properties can transform an individual sTF between distinct roles (activator, cooperative factor, inhibitory factor) within a transcriptional complex, thus drastically altering the signal processing behavior of multi-input systems. This platform provides new genetic components for synthetic biology and enables bottom-up approaches to understanding the design principles of eukaryotic transcriptional complexes and networks. PMID:22863014

AFM imaging of functionalized carbon nanotubes on biological membranes

International Nuclear Information System (INIS)

Lamprecht, C; Danzberger, J; Rangl, M; Gruber, H J; Hinterdorfer, P; Kienberger, F; Ebner, A; Liashkovich, I; Neves, V; Heister, E; Coley, H M; McFadden, J; Flahaut, E

2009-01-01

Multifunctional carbon nanotubes are promising for biomedical applications as their nano-size, together with their physical stability, gives access into the cell and various cellular compartments including the nucleus. However, the direct and label-free detection of carbon nanotube uptake into cells is a challenging task. The atomic force microscope (AFM) is capable of resolving details of cellular surfaces at the nanometer scale and thus allows following of the docking of carbon nanotubes to biological membranes. Here we present topographical AFM images of non-covalently functionalized single walled (SWNT) and double walled carbon nanotubes (DWNT) immobilized on different biological membranes, such as plasma membranes and nuclear envelopes, as well as on a monolayer of avidin molecules. We were able to visualize DWNT on the nuclear membrane while at the same time resolving individual nuclear pore complexes. Furthermore, we succeeded in localizing individual SWNT at the border of incubated cells and in identifying bundles of DWNT on cell surfaces by AFM imaging.

Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease*

Science.gov (United States)

Dewhurst, Henry; Sundararaman, Niveda

2016-01-01

Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function - a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) - a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al., 2015). Here, we apply SAPH-ire to the set of eukaryotic protein families containing experimental PTM and 3D structure data - capturing 1,325 protein families with 50,839 unique PTM sites organized into 31,747 modified alignment positions (MAPs), of which 2010 (∼6%) possess known biological function. Here, we show that using an artificial neural network model (SAPH-ire NN) trained to identify MAP hotspots with biological function results in prediction outcomes that far surpass the use of single hotspot features, including nearest neighbor PTM clustering methods. We find the greatest enhancement in prediction for positions with PTM counts of five or less, which represent 98% of all MAPs in the eukaryotic proteome and 90% of all MAPs found to have biological function. Analysis of the top 1092 MAP hotspots revealed 267 of truly unknown function (containing 5443 distinct PTMs). Of these, 165 hotspots could be mapped to human KEGG pathways for normal and/or disease physiology. Many high-ranking hotspots were also found to be disease-associated pathogenic sites of amino acid substitution despite the lack of observable PTM in the human protein family member. Taken together, these experiments demonstrate that the functional relevance of a PTM can be predicted very effectively by neural network models, revealing a large but testable

Mode-locking via dissipative Faraday instability.

Science.gov (United States)

Tarasov, Nikita; Perego, Auro M; Churkin, Dmitry V; Staliunas, Kestutis; Turitsyn, Sergei K

2016-08-09

Emergence of coherent structures and patterns at the nonlinear stage of modulation instability of a uniform state is an inherent feature of many biological, physical and engineering systems. There are several well-studied classical modulation instabilities, such as Benjamin-Feir, Turing and Faraday instability, which play a critical role in the self-organization of energy and matter in non-equilibrium physical, chemical and biological systems. Here we experimentally demonstrate the dissipative Faraday instability induced by spatially periodic zig-zag modulation of a dissipative parameter of the system-spectrally dependent losses-achieving generation of temporal patterns and high-harmonic mode-locking in a fibre laser. We demonstrate features of this instability that distinguish it from both the Benjamin-Feir and the purely dispersive Faraday instability. Our results open the possibilities for new designs of mode-locked lasers and can be extended to other fields of physics and engineering.

Biological activity of lactoferrin-functionalized biomimetic hydroxyapatite nanocrystals

Directory of Open Access Journals (Sweden)

Nocerino N

2014-03-01

Full Text Available Nunzia Nocerino,1 Andrea Fulgione,1 Marco Iannaccone,1 Laura Tomasetta,1 Flora Ianniello,1 Francesca Martora,1 Marco Lelli,2 Norberto Roveri,2 Federico Capuano,3 Rosanna Capparelli1 1Department of Agriculture Special Biotechnology Center Federico II, CeBIOTEC Biotechnology, University of Naples Federico II, Naples, 2Department of Chemistry, G Ciamician, Alma Mater Studiorum, University of Bologna, Bologna, 3Department of Food Inspection IZS ME, Naples, Italy Abstract: The emergence of bacterial strains resistant to antibiotics is a general public health problem. Progress in developing new molecules with antimicrobial properties has been made. In this study, we evaluated the biological activity of a hybrid nanocomposite composed of synthetic biomimetic hydroxyapatite surface-functionalized by lactoferrin (LF-HA. We evaluated the antimicrobial, anti-inflammatory, and antioxidant properties of LF-HA and found that the composite was active against both Gram-positive and Gram-negative bacteria, and that it modulated proinflammatory and anti-inflammatory responses and enhanced antioxidant properties as compared with LF alone. These results indicate the possibility of using LF-HA as an antimicrobial system and biomimetic hydroxyapatite as a candidate for innovative biomedical applications. Keywords: lactoferrin, hydroxyapatite nanocrystals, biomimetism, biological activity, drug delivery

Structural Biology Guides Antibiotic Discovery

Science.gov (United States)

Polyak, Steven

2014-01-01

Modern drug discovery programs require the contribution of researchers in a number of specialist areas. One of these areas is structural biology. Using X-ray crystallography, the molecular basis of how a drug binds to its biological target and exerts its mode of action can be defined. For example, a drug that binds into the active site of an…

[Biology and culture: a dimension of collaboration between anthropology and epidemiology].

Science.gov (United States)

Song, Leiming; Wang, Ning

2016-01-01

Biology is the important basis of epidemiological study. Based on biology, psychology, social and cultural factors can influence human's health and disease incidence. The medical mode has changed from "biomedical mode" to "bio-psycho-social medical model" , but culture factor was neglected somewhat during this process, so paying attention to culture factor in anthropologic study and using it as biologic basis in epidemiologic study might be a dimension of collaboration between of anthropology and epidemiology.

Aberrant default-mode functional and structural connectivity in heroin-dependent individuals.

Directory of Open Access Journals (Sweden)

Xiaofen Ma

Full Text Available Little is known about connectivity within the default mode network (DMN in heroin-dependent individuals (HDIs. In the current study, diffusion-tensor imaging (DTI and resting-state functional MRI (rs-fMRI were combined to investigate both structural and functional connectivity within the DMN in HDIs.Fourteen HDIs and 14 controls participated in the study. Structural (path length, tracts count, (fractional anisotropy FA and (mean diffusivity MD derived from DTI tractographyand functional (temporal correlation coefficient derived from rs-fMRI DMN connectivity changes were examined in HDIs. Pearson correlation analysis was performed to compare the structural/functional indices and duration of heroin use/Iowa gambling task(IGT performance in HDIs.HDIs had lower FA and higher MD in the tract connecting the posterior cingulate cortex/precuneus (PCC/PCUN to right parahippocampal gyrus (PHG, compared to the controls. HDIs also had decreased FA and track count in the tract connecting the PCC/PCUN and medial prefrontal cortex (MPFC, as well as decreased functional connectivity between the PCC/PCUN and bilateral PHG and MPFC, compared to controls. FA values for the tract connecting PCC/PCUN to the right PHG and connecting PCC/PCUN to the MPFC were negatively correlated to the duration of heroin use. The temporal correlation coefficients between the PCC/PCUN and the MPFC, and the FA values for the tract connecting the PCC/PCUN to the MPFC were positively correlated to IGT performance in HDIs.Structural and functional connectivity within the DMN are both disturbed in HDIs. This disturbance progresses as duration of heroin use increases and is related to deficits in decision making in HDIs.

Partition functions with spin in AdS2 via quasinormal mode methods

International Nuclear Information System (INIS)

Keeler, Cynthia; Lisbão, Pedro; Ng, Gim Seng

2016-01-01

We extend the results of http://dx.doi.org/10.1007/JHEP06(2014)099, computing one loop partition functions for massive fields with spin half in AdS 2 using the quasinormal mode method proposed by Denef, Hartnoll, and Sachdev http://dx.doi.org/10.1088/0264-9381/27/12/125001. We find the finite representations of SO(2,1) for spin zero and spin half, consisting of a highest weight state |h〉 and descendants with non-unitary values of h. These finite representations capture the poles and zeroes of the one loop determinants. Together with the asymptotic behavior of the partition functions (which can be easily computed using a large mass heat kernel expansion), these are sufficient to determine the full answer for the one loop determinants. We also discuss extensions to higher dimensional AdS 2n and higher spins.

Clinical history and biologic age predicted falls better than objective functional tests.

Science.gov (United States)

Gerdhem, Paul; Ringsberg, Karin A M; Akesson, Kristina; Obrant, Karl J

2005-03-01

Fall risk assessment is important because the consequences, such as a fracture, may be devastating. The objective of this study was to find the test or tests that best predicted falls in a population-based sample of elderly women. The fall-predictive ability of a questionnaire, a subjective estimate of biologic age and objective functional tests (gait, balance [Romberg and sway test], thigh muscle strength, and visual acuity) were compared in 984 randomly selected women, all 75 years of age. A recalled fall was the most important predictor for future falls. Only recalled falls and intake of psycho-active drugs independently predicted future falls. Women with at least five of the most important fall predictors (previous falls, conditions affecting the balance, tendency to fall, intake of psychoactive medication, inability to stand on one leg, high biologic age) had an odds ratio of 11.27 (95% confidence interval 4.61-27.60) for a fall (sensitivity 70%, specificity 79%). The more time-consuming objective functional tests were of limited importance for fall prediction. A simple clinical history, the inability to stand on one leg, and a subjective estimate of biologic age were more important as part of the fall risk assessment.

Observation of the low frequency vibrational modes of bacteriophage M13 in water by Raman spectroscopy

Directory of Open Access Journals (Sweden)

Tsen Shaw-Wei D

2006-09-01

Full Text Available Abstract Background Recently, a technique which departs radically from conventional approaches has been proposed. This novel technique utilizes biological objects such as viruses as nano-templates for the fabrication of nanostructure elements. For example, rod-shaped viruses such as the M13 phage and tobacco mosaic virus have been successfully used as biological templates for the synthesis of semiconductor and metallic nanowires. Results and discussion Low wave number (≤ 20 cm-1 acoustic vibrations of the M13 phage have been studied using Raman spectroscopy. The experimental results are compared with theoretical calculations based on an elastic continuum model and appropriate Raman selection rules derived from a bond polarizability model. The observed Raman mode has been shown to belong to one of the Raman-active axial torsion modes of the M13 phage protein coat. Conclusion It is expected that the detection and characterization of this low frequency vibrational mode can be used for applications in nanotechnology such as for monitoring the process of virus functionalization and self-assembly. For example, the differences in Raman spectra can be used to monitor the coating of virus with some other materials and nano-assembly process, such as attaching a carbon nanotube or quantum dots.

The functional and biological properties of whey proteins: prospects for the development of functional foods

Directory of Open Access Journals (Sweden)

H. J. T. KORHONEN

2008-12-01

Full Text Available Advances in processing technologies and the accumulation of scientific data on the functional and biological properties of whey components have contributed to the growing commercial valuation of cheese whey over the last decade. New membrane separation and chromatographic techniques have made it possible to fractionate and enrich various components of whey more efficiently than before. The specific properties of these components can now be examined in greater detail and new applications developed accordingly. The utilisation of cheese whey is evolving into a new industry producing a multitude of purified ingredients for numerous purposes. The most significant areas of R&D related to whey proteins include functional foods, the rheological properties of foodstuffs, and biopharmaceuticals.

Robust Adaptive Sliding Mode Control for Generalized Function Projective Synchronization of Different Chaotic Systems with Unknown Parameters

Directory of Open Access Journals (Sweden)

Xiuchun Li

2013-01-01

Full Text Available When the parameters of both drive and response systems are all unknown, an adaptive sliding mode controller, strongly robust to exotic perturbations, is designed for realizing generalized function projective synchronization. Sliding mode surface is given and the controlled system is asymptotically stable on this surface with the passage of time. Based on the adaptation laws and Lyapunov stability theory, an adaptive sliding controller is designed to ensure the occurrence of the sliding motion. Finally, numerical simulations are presented to verify the effectiveness and robustness of the proposed method even when both drive and response systems are perturbed with external disturbances.

Force reconstruction from tapping mode force microscopy experiments

International Nuclear Information System (INIS)

Payam, Amir F; Martin-Jimenez, Daniel; Garcia, Ricardo

2015-01-01

Fast, accurate, and robust nanomechanical measurements are intensely studied in materials science, applied physics, and molecular biology. Amplitude modulation force microscopy (tapping mode) is the most established nanoscale characterization technique of surfaces for air and liquid environments. However, its quantitative capabilities lag behind its high spatial resolution and robustness. We develop a general method to transform the observables into quantitative force measurements. The force reconstruction algorithm has been deduced on the assumption that the observables (amplitude and phase shift) are slowly varying functions of the tip–surface separation. The accuracy and applicability of the method is validated by numerical simulations and experiments. The method is valid for liquid and air environments, small and large free amplitudes, compliant and rigid materials, and conservative and non-conservative forces. (paper)

Effect of biological factors during functional scintigraphy of the heart

Energy Technology Data Exchange (ETDEWEB)

Breuel, H P; Emrich, D; Luig, H [Goettingen Univ. (F.R. Germany). Abt. fuer Nuklearmedizin

1976-07-01

The parameters relating to functional scintigraphy of the heart (average circulation time, peak time) depend not only on the method (injection technique, radiopharmaceutical), but also on biological factors. Failure to take these into consideration may result in an erroneous interpretation of the findings. Circulation time in normal children aged 6 to 14 years, as determined by isotope methods is significantly shorter than in normal adults. Patients with compensated heart disease, as well trained athletes, show significant increase in all portions of the circulation time, when compared with normals of similar ages. This indicates that deviation in the haemodynamics of the circulation as shown by functional scintigraphy, can only be interpreted in the light of clinical findings.

Tongue and Taste Organ Biology and Function: Homeostasis Maintained by Hedgehog Signaling.

Science.gov (United States)

Mistretta, Charlotte M; Kumari, Archana

2017-02-10

The tongue is an elaborate complex of heterogeneous tissues with taste organs of diverse embryonic origins. The lingual taste organs are papillae, composed of an epithelium that includes specialized taste buds, the basal lamina, and a lamina propria core with matrix molecules, fibroblasts, nerves, and vessels. Because taste organs are dynamic in cell biology and sensory function, homeostasis requires tight regulation in specific compartments or niches. Recently, the Hedgehog (Hh) pathway has emerged as an essential regulator that maintains lingual taste papillae, taste bud and progenitor cell proliferation and differentiation, and neurophysiological function. Activating or suppressing Hh signaling, with genetic models or pharmacological agents used in cancer treatments, disrupts taste papilla and taste bud integrity and can eliminate responses from taste nerves to chemical stimuli but not to touch or temperature. Understanding Hh regulation of taste organ homeostasis contributes knowledge about the basic biology underlying taste disruptions in patients treated with Hh pathway inhibitors.

PMS2 endonuclease activity has distinct biological functions and is essential for genome maintenance.

Science.gov (United States)

van Oers, Johanna M M; Roa, Sergio; Werling, Uwe; Liu, Yiyong; Genschel, Jochen; Hou, Harry; Sellers, Rani S; Modrich, Paul; Scharff, Matthew D; Edelmann, Winfried

2010-07-27

The DNA mismatch repair protein PMS2 was recently found to encode a novel endonuclease activity. To determine the biological functions of this activity in mammals, we generated endonuclease-deficient Pms2E702K knock-in mice. Pms2EK/EK mice displayed increased genomic mutation rates and a strong cancer predisposition. In addition, class switch recombination, but not somatic hypermutation, was impaired in Pms2EK/EK B cells, indicating a specific role in Ig diversity. In contrast to Pms2-/- mice, Pms2EK/EK male mice were fertile, indicating that this activity is dispensable in spermatogenesis. Therefore, the PMS2 endonuclease activity has distinct biological functions and is essential for genome maintenance and tumor suppression.

Surface Loving and Surface Avoiding modes

OpenAIRE

Combe, Nicolas; Huntzinger, Jean Roch; Morillo, Joseph

2008-01-01

International audience; We theoretically study the propagation of sound waves in GaAs/AlAs superlattices focussing on periodic modes in the vicinity of the band gaps. Based on analytical and numerical calculations, we show that these modes are the product of a quickly oscillating function times a slowly varying envelope function. We carefully study the phase of the envelope function compared to the surface of a semi-infinite superlattice. Especially, the dephasing of the superlattice compared...

Functions of MicroRNAs in Cardiovascular Biology and Disease

Science.gov (United States)

Hata, Akiko

2015-01-01

In 1993, lin-4 was discovered as a critical modulator of temporal development in Caenorhabditis elegans and, most notably, as the first in the class of small, single-stranded noncoding RNAs now defined as microRNAs (miRNAs). Another eight years elapsed before miRNA expression was detected in mammalian cells. Since then, explosive advancements in the field of miRNA biology have elucidated the basic mechanism of miRNA biogenesis, regulation, and gene-regulatory function. The discovery of this new class of small RNAs has augmented the complexity of gene-regulatory programs as well as the understanding of developmental and pathological processes in the cardiovascular system. Indeed, the contributions of miRNAs in cardiovascular development and function have been widely explored, revealing the extensive role of these small regulatory RNAs in cardiovascular physiology. PMID:23157557

Biological dosimetry intercomparison exercise: an evaluation of Triage and routine mode results by robust methods

International Nuclear Information System (INIS)

Di Giorgio, M.; Vallerga, M.B.; Radl, A.; Taja, M.R.; Barquinero, J.F.; Seoane, A.; De Luca, J.; Guerrero Carvajal, Y.C.; Stuck Oliveira, M.S.; Valdivia, P.; García Lima, O.; Lamadrid, A.; González Mesa, J.; Romero Aguilera, I.; Mandina Cardoso, T.; Arceo Maldonado, C.; Espinoza, M.E.; Martínez López, W.; Lloyd, D.C.; Méndez Acuña, L.; Di Tomaso, M.V.; Roy, L.; Lindholm, C.; Romm, H.; Güçlü, I.

2011-01-01

Well-defined protocols and quality management standards are indispensable for biological dosimetry laboratories. Participation in periodic proficiency testing by interlaboratory comparisons is also required. This harmonization is essential if a cooperative network is used to respond to a mass casualty event. Here we present an international intercomparison based on dicentric chromosome analysis for dose assessment performed in the framework of the IAEA Regional Latin American RLA/9/054 Project. The exercise involved 14 laboratories, 8 from Latin America and 6 from Europe. The performance of each laboratory and the reproducibility of the exercise were evaluated using robust methods described in ISO standards. The study was based on the analysis of slides from samples irradiated with 0.75 (DI) and 2.5 Gy (DII). Laboratories were required to score the frequency of dicentrics and convert them to estimated doses, using their own dose-effect curves, after the analysis of 50 or 100 cells (triage mode) and after conventional scoring of 500 cells or 100 dicentrics. In the conventional scoring, at both doses, all reported frequencies were considered as satisfactory, and two reported doses were considered as questionable. The analysis of the data dispersion among the dicentric frequencies and among doses indicated a better reproducibility for estimated doses (15.6% for DI and 8.8% for DII) than for frequencies (24.4% for DI and 11.4% for DII), expressed by the coefficient of variation. In the two triage modes, although robust analysis classified some reported frequencies or doses as unsatisfactory or questionable, all estimated doses were in agreement with the accepted error of ±0.5 Gy. However, at the DI dose and for 50 scored cells, 5 out of the 14 reported confidence intervals that included zero dose and could be interpreted as false negatives. This improved with 100 cells, where only one confidence interval included zero dose. At the DII dose, all estimations fell within

Default mode network connectivity during task execution.

Science.gov (United States)

Vatansever, D; Menon, D K; Manktelow, A E; Sahakian, B J; Stamatakis, E A

2015-11-15

Initially described as task-induced deactivations during goal-directed paradigms of high attentional load, the unresolved functionality of default mode regions has long been assumed to interfere with task performance. However, recent evidence suggests a potential default mode network involvement in fulfilling cognitive demands. We tested this hypothesis in a finger opposition paradigm with task and fixation periods which we compared with an independent resting state scan using functional magnetic resonance imaging and a comprehensive analysis pipeline including activation, functional connectivity, behavioural and graph theoretical assessments. The results indicate task specific changes in the default mode network topography. Behaviourally, we show that increased connectivity of the posterior cingulate cortex with the left superior frontal gyrus predicts faster reaction times. Moreover, interactive and dynamic reconfiguration of the default mode network regions' functional connections illustrates their involvement with the task at hand with higher-level global parallel processing power, yet preserved small-world architecture in comparison with rest. These findings demonstrate that the default mode network does not disengage during this paradigm, but instead may be involved in task relevant processing. Copyright © 2015 Elsevier Inc. All rights reserved.

Towards automated human gait disease classification using phase space representation of intrinsic mode functions

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Pratiher, Sawon; Patra, Sayantani; Pratiher, Souvik

2017-06-01

A novel analytical methodology for segregating healthy and neurological disorders from gait patterns is proposed by employing a set of oscillating components called intrinsic mode functions (IMF's). These IMF's are generated by the Empirical Mode Decomposition of the gait time series and the Hilbert transformed analytic signal representation forms the complex plane trace of the elliptical shaped analytic IMFs. The area measure and the relative change in the centroid position of the polygon formed by the Convex Hull of these analytic IMF's are taken as the discriminative features. Classification accuracy of 79.31% with Ensemble learning based Adaboost classifier validates the adequacy of the proposed methodology for a computer aided diagnostic (CAD) system for gait pattern identification. Also, the efficacy of several potential biomarkers like Bandwidth of Amplitude Modulation and Frequency Modulation IMF's and it's Mean Frequency from the Fourier-Bessel expansion from each of these analytic IMF's has been discussed for its potency in diagnosis of gait pattern identification and classification.

High-frequency dual mode pulsed wave Doppler imaging for monitoring the functional regeneration of adult zebrafish hearts

Science.gov (United States)

Kang, Bong Jin; Park, Jinhyoung; Kim, Jieun; Kim, Hyung Ham; Lee, Changyang; Hwang, Jae Youn; Lien, Ching-Ling; Shung, K. Kirk

2015-01-01

Adult zebrafish is a well-known small animal model for studying heart regeneration. Although the regeneration of scars made by resecting the ventricular apex has been visualized with histological methods, there is no adequate imaging tool for tracking the functional recovery of the damaged heart. For this reason, high-frequency Doppler echocardiography using dual mode pulsed wave Doppler, which provides both tissue Doppler (TD) and Doppler flow in a same cardiac cycle, is developed with a 30 MHz high-frequency array ultrasound imaging system. Phantom studies show that the Doppler flow mode of the dual mode is capable of measuring the flow velocity from 0.1 to 15 cm s−1 with high accuracy (p-value = 0.974 > 0.05). In the in vivo study of zebrafish, both TD and Doppler flow signals were simultaneously obtained from the zebrafish heart for the first time, and the synchronized valve motions with the blood flow signals were identified. In the longitudinal study on the zebrafish heart regeneration, the parameters for diagnosing the diastolic dysfunction, for example, E/Em < 10, E/A < 0.14 for wild-type zebrafish, were measured, and the type of diastolic dysfunction caused by the amputation was found to be similar to the restrictive filling. The diastolic function was fully recovered within four weeks post-amputation. PMID:25505135

Policy learning in the Eurozone crisis: modes, power and functionality.

Science.gov (United States)

Dunlop, Claire A; Radaelli, Claudio M

In response to the attacks on the sovereign debt of some Eurozone countries, European Union (EU) leaders have created a set of preventive and corrective policy instruments to coordinate macro-economic policies and reforms. In this article, we deal with the European Semester, a cycle of information exchange, monitoring and surveillance. Countries that deviate from the targets are subjected to increasing monitoring and more severe 'corrective' interventions, in a pyramid of responsive exchanges between governments and EU institutions. This is supposed to generate coordination and convergence towards balanced economies via mechanisms of learning. But who is learning what? Can the EU learn in the 'wrong' mode? We contribute to the literature on theories of the policy process by showing how modes of learning can be operationalized and used in empirical analysis. We use policy learning as theoretical framework to establish empirically the prevalent mode of learning and its implications for both the power of the Commission and the normative question of whether the EU is learning in the 'correct' mode.

Pulmonary Capillary Hemorrhage Induced by Different Imaging Modes of Diagnostic Ultrasound.

Science.gov (United States)

Miller, Douglas L; Dong, Zhihong; Dou, Chunyan; Raghavendran, Krishnan

2018-05-01

The induction of pulmonary capillary hemorrhage (PCH) is a well-established non-thermal biological effect of pulsed ultrasound in animal models. Typically, research has been done using laboratory pulsed ultrasound systems with a fixed beam and, recently, by B-mode diagnostic ultrasound. In this study, a GE Vivid 7 Dimension ultrasound machine with 10 L linear array probe was used at 6.6 MHz to explore the relative PCH efficacy of B-mode imaging, M-mode (fixed beam), color angio mode Doppler imaging and pulsed Doppler mode (fixed beam). Anesthetized rats were scanned in a warmed water bath, and thresholds were determined by scanning at different power steps, 2 dB apart, in different groups of six rats. Exposures were performed for 5 min, except for a 15-s M-mode group. Peak rarefactional pressure amplitude thresholds were 1.5 MPa for B-mode and 1.1 MPa for angio Doppler mode. For the non-scanned modes, thresholds were 1.1 MPa for M-mode and 0.6 MPa for pulsed Doppler mode with its relatively high duty cycle (7.7 × 10 -3 vs. 0.27 × 10 -3 for M-mode). Reducing the duration of M-mode to 15 s (from 300 s) did not significantly reduce PCH (area, volume or depth) for some power settings, but the threshold was increased to 1.4 MPa. Pulmonary sonographers should be aware of this unique adverse bio-effect of diagnostic ultrasound and should consider reduced on-screen mechanical index settings for potentially vulnerable patients. Copyright © 2018 World Federation for Ultrasound in Medicine and Biology. Published by Elsevier Inc. All rights reserved.

Characteristics of microbial community functional structure of a biological coking wastewater treatment system.

Science.gov (United States)

Joshi, Dev Raj; Zhang, Yu; Zhang, Hong; Gao, Yingxin; Yang, Min

2018-01-01

Nitrogenous heterocyclic compounds are key pollutants in coking wastewater; however, the functional potential of microbial communities for biodegradation of such contaminants during biological treatment is still elusive. Herein, a high throughput functional gene array (GeoChip 5.0) in combination with Illumina HiSeq2500 sequencing was used to compare and characterize the microbial community functional structure in a long run (500days) bench scale bioreactor treating coking wastewater, with a control system treating synthetic wastewater. Despite the inhibitory toxic pollutants, GeoChip 5.0 detected almost all key functional gene (average 61,940 genes) categories in the coking wastewater sludge. With higher abundance, aromatic ring cleavage dioxygenase genes including multi ring1,2diox; one ring2,3diox; catechol represented significant functional potential for degradation of aromatic pollutants which was further confirmed by Illumina HiSeq2500 analysis results. Response ratio analysis revealed that three nitrogenous compound degrading genes- nbzA (nitro-aromatics), tdnB (aniline), and scnABC (thiocyanate) were unique for coking wastewater treatment, which might be strong cause to increase ammonia level during the aerobic process. Additionally, HiSeq2500 elucidated carbozole and isoquinoline degradation genes in the system. These findings expanded our understanding on functional potential of microbial communities to remove organic nitrogenous pollutants; hence it will be useful in optimization strategies for biological treatment of coking wastewater. Copyright © 2017. Published by Elsevier B.V.

Biologically inspired flexible quasi-single-mode random laser: An integration of Pieris canidia butterfly wing and semiconductors

Science.gov (United States)

Wang, Cih-Su; Chang, Tsung-Yuan; Lin, Tai-Yuan; Chen, Yang-Fang

2014-10-01

Quasi-periodic structures of natural biomaterial membranes have great potentials to serve as resonance cavities to generate ecological friendly optoelectronic devices with low cost. To achieve the first attempt for the illustration of the underlying principle, the Pieris canidia butterfly wing was embedded with ZnO nanoparticles. Quite interestingly, it is found that the bio-inspired quasi-single-mode random laser can be achieved by the assistance of the skeleton of the membrane, in which ZnO nanoparticles act as emitting gain media. Such unique characteristics can be interpreted well by the Fabry-Perot resonance existing in the window-like quasi-periodic structure of butterfly wing. Due to the inherently promising flexibility of butterfly wing membrane, the laser action can still be maintained during the bending process. Our demonstrated approach not only indicates that the natural biological structures can provide effective scattering feedbacks but also pave a new avenue towards designing bio-controlled photonic devices.

Biologically inspired flexible quasi-single-mode random laser: an integration of Pieris canidia butterfly wing and semiconductors.

Science.gov (United States)

Wang, Cih-Su; Chang, Tsung-Yuan; Lin, Tai-Yuan; Chen, Yang-Fang

2014-10-23

Quasi-periodic structures of natural biomaterial membranes have great potentials to serve as resonance cavities to generate ecological friendly optoelectronic devices with low cost. To achieve the first attempt for the illustration of the underlying principle, the Pieris canidia butterfly wing was embedded with ZnO nanoparticles. Quite interestingly, it is found that the bio-inspired quasi-single-mode random laser can be achieved by the assistance of the skeleton of the membrane, in which ZnO nanoparticles act as emitting gain media. Such unique characteristics can be interpreted well by the Fabry-Perot resonance existing in the window-like quasi-periodic structure of butterfly wing. Due to the inherently promising flexibility of butterfly wing membrane, the laser action can still be maintained during the bending process. Our demonstrated approach not only indicates that the natural biological structures can provide effective scattering feedbacks but also pave a new avenue towards designing bio-controlled photonic devices.

Distortional Modes of Thin-Walled Beams

DEFF Research Database (Denmark)

Jönsson, Jeppe; Andreassen, Michael Joachim

2009-01-01

The classic thin-walled beam theory for open and closed cross-sections can be generalized by including distortional displacement modes. The introduction of additional displacement modes leads to coupled differential equations, which seems to have prohibited the use of exact shape functions...... in the modelling of coupled torsion and distortion. However, if the distortional displacement modes are chosen as those which decouple the differential equations as in non proportionally damped modal dynamic analysis then it may be possible to use exact shape functions and perform analysis on a reduced problem....... In the recently developed generalized beam theory (GBT) the natural distortional displacement modes are determined on the basis of a quadratic eigenvalue problem. However, as in linear modal dynamic analysis of proportionally damped structures this problem has been solved approximately using linear eigenvalue...

The Integrated Mode Management Interface

Science.gov (United States)

Hutchins, Edwin

1996-01-01

Mode management is the processes of understanding the character and consequences of autoflight modes, planning and selecting the engagement, disengagement and transitions between modes, and anticipating automatic mode transitions made by the autoflight system itself. The state of the art is represented by the latest designs produced by each of the major airframe manufacturers, the Boeing 747-400, the Boeing 777, the McDonnell Douglas MD-11, and the Airbus A320/A340 family of airplanes. In these airplanes autoflight modes are selected by manipulating switches on the control panel. The state of the autoflight system is displayed on the flight mode annunciators. The integrated mode management interface (IMMI) is a graphical interface to autoflight mode management systems for aircraft equipped with flight management computer systems (FMCS). The interface consists of a vertical mode manager and a lateral mode manager. Autoflight modes are depicted by icons on a graphical display. Mode selection is accomplished by touching (or mousing) the appropriate icon. The IMMI provides flight crews with an integrated interface to autoflight systems for aircraft equipped with flight management computer systems (FMCS). The current version is modeled on the Boeing glass-cockpit airplanes (747-400, 757/767). It runs on the SGI Indigo workstation. A working prototype of this graphics-based crew interface to the autoflight mode management tasks of glass cockpit airplanes has been installed in the Advanced Concepts Flight Simulator of the CSSRF of NASA Ames Research Center. This IMMI replaces the devices in FMCS equipped airplanes currently known as mode control panel (Boeing), flight guidance control panel (McDonnell Douglas), and flight control unit (Airbus). It also augments the functions of the flight mode annunciators. All glass cockpit airplanes are sufficiently similar that the IMMI could be tailored to the mode management system of any modern cockpit. The IMMI does not replace the

A Gaussian mixture model based cost function for parameter estimation of chaotic biological systems

Science.gov (United States)

Shekofteh, Yasser; Jafari, Sajad; Sprott, Julien Clinton; Hashemi Golpayegani, S. Mohammad Reza; Almasganj, Farshad

2015-02-01

As we know, many biological systems such as neurons or the heart can exhibit chaotic behavior. Conventional methods for parameter estimation in models of these systems have some limitations caused by sensitivity to initial conditions. In this paper, a novel cost function is proposed to overcome those limitations by building a statistical model on the distribution of the real system attractor in state space. This cost function is defined by the use of a likelihood score in a Gaussian mixture model (GMM) which is fitted to the observed attractor generated by the real system. Using that learned GMM, a similarity score can be defined by the computed likelihood score of the model time series. We have applied the proposed method to the parameter estimation of two important biological systems, a neuron and a cardiac pacemaker, which show chaotic behavior. Some simulated experiments are given to verify the usefulness of the proposed approach in clean and noisy conditions. The results show the adequacy of the proposed cost function.

Frequency-Dependent Altered Functional Connections of Default Mode Network in Alzheimer’s Disease

Directory of Open Access Journals (Sweden)

Youjun Li

2017-08-01

Full Text Available Alzheimer’s disease (AD is a neurodegenerative disorder associated with the progressive dysfunction of cognitive ability. Previous research has indicated that the default mode network (DMN is closely related to cognition and is impaired in Alzheimer’s disease. Because recent studies have shown that different frequency bands represent specific physiological functions, DMN functional connectivity studies of the different frequency bands based on resting state fMRI (RS-fMRI data may provide new insight into AD pathophysiology. In this study, we explored the functional connectivity based on well-defined DMN regions of interest (ROIs from the five frequency bands: slow-5 (0.01–0.027 Hz, slow-4 (0.027–0.073 Hz, slow-3 (0.073–0.198 Hz, slow-2 (0.198–0.25 Hzs and standard low-frequency oscillations (LFO (0.01–0.08 Hz. We found that the altered functional connectivity patterns are mainly in the frequency band of slow-5 and slow-4 and that the decreased connections are long distance, but some relatively short connections are increased. In addition, the altered functional connections of the DMN in AD are frequency dependent and differ between the slow-5 and slow-4 bands. Mini-Mental State Examination scores were significantly correlated with the altered functional connectivity patterns in the slow-5 and slow-4 bands. These results indicate that frequency-dependent functional connectivity changes might provide potential biomarkers for AD pathophysiology.

Mode-field half-widths of Gaussian approximation for the fundamental mode of two kinds of optical waveguides

International Nuclear Information System (INIS)

Lian-Huang, Li; Fu-Yuan, Guo

2009-01-01

This paper analyzes the characteristic of matching efficiency between the fundamental mode of two kinds of optical waveguides and its Gaussian approximate field. Then, it presents a new method where the mode-field half-width of Gaussian approximation for the fundamental mode should be defined according to the maximal matching efficiency method. The relationship between the mode-field half-width of the Gaussian approximate field obtained from the maximal matching efficiency and normalized frequency is studied; furthermore, two formulas of mode-field half-widths as a function of normalized frequency are proposed

Click Chemistry Mediated Functionalization of Vertical Nanowires for Biological Applications.

Science.gov (United States)

Vutti, Surendra; Schoffelen, Sanne; Bolinsson, Jessica; Buch-Månson, Nina; Bovet, Nicolas; Nygård, Jesper; Martinez, Karen L; Meldal, Morten

2016-01-11

Semiconductor nanowires (NWs) are gaining significant importance in various biological applications, such as biosensing and drug delivery. Efficient and controlled immobilization of biomolecules on the NW surface is crucial for many of these applications. Here, we present for the first time the use of the Cu(I) -catalyzed alkyne-azide cycloaddition and its strain-promoted variant for the covalent functionalization of vertical NWs with peptides and proteins. The potential of the approach was demonstrated in two complementary applications of measuring enzyme activity and protein binding, which is of general interest for biological studies. The attachment of a peptide substrate provided NW arrays for the detection of protease activity. In addition, green fluorescent protein was immobilized in a site-specific manner and recognized by antibody binding to demonstrate the proof-of-concept for the use of covalently modified NWs for diagnostic purposes using minute amounts of material. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Default Mode Network as a Biomarker of Persistent Complaints after Mild Traumatic Brain Injury: A Longitudinal Functional Magnetic Resonance Imaging Study.

Science.gov (United States)

van der Horn, Harm J; Scheenen, Myrthe E; de Koning, Myrthe E; Liemburg, Edith J; Spikman, Jacoba M; van der Naalt, Joukje

2017-12-01

The objective of this study was to examine longitudinal functional connectivity of resting-state networks in patients with and without complaints after uncomplicated mild traumatic brain injury (mTBI). Second, we aimed to determine the value of network connectivity in predicting persistent complaints, anxiety, depression and long-term outcome. Thirty mTBI patients with three or more post-traumatic complaints at 2 weeks post-injury, 19 without complaints, and 20 matched healthy controls were selected for this study. Resting-state functional MRI (fMRI) was performed in patients at 1 month and 3 months post-injury, and once in healthy controls. Independent component analysis (ICA) was used to investigate the default mode, executive and salience networks. Persistent post-traumatic complaints, anxiety, and depression were measured at 3 months post-injury, and outcome was determined at 1 year post-injury. Within the group with complaints, higher functional connectivity between the anterior and posterior components of the default mode network at 1 month post-injury was associated with a greater number of complaints at 3 months post-injury (ρ = 0.59, p = 0.001). Minor longitudinal changes in functional connectivity were found for patients with and without complaints after mTBI, which were limited to connectivity within the precuneus component of the default mode network. No significant results were found for the executive and salience networks. Current results suggest that the default mode network may serve as a biomarker of persistent complaints in patients with uncomplicated mTBI.

Mental Task Classification Scheme Utilizing Correlation Coefficient Extracted from Interchannel Intrinsic Mode Function.

Science.gov (United States)

Rahman, Md Mostafizur; Fattah, Shaikh Anowarul

2017-01-01

In view of recent increase of brain computer interface (BCI) based applications, the importance of efficient classification of various mental tasks has increased prodigiously nowadays. In order to obtain effective classification, efficient feature extraction scheme is necessary, for which, in the proposed method, the interchannel relationship among electroencephalogram (EEG) data is utilized. It is expected that the correlation obtained from different combination of channels will be different for different mental tasks, which can be exploited to extract distinctive feature. The empirical mode decomposition (EMD) technique is employed on a test EEG signal obtained from a channel, which provides a number of intrinsic mode functions (IMFs), and correlation coefficient is extracted from interchannel IMF data. Simultaneously, different statistical features are also obtained from each IMF. Finally, the feature matrix is formed utilizing interchannel correlation features and intrachannel statistical features of the selected IMFs of EEG signal. Different kernels of the support vector machine (SVM) classifier are used to carry out the classification task. An EEG dataset containing ten different combinations of five different mental tasks is utilized to demonstrate the classification performance and a very high level of accuracy is achieved by the proposed scheme compared to existing methods.

Partition functions with spin in AdS{sub 2} via quasinormal mode methods

Energy Technology Data Exchange (ETDEWEB)

Keeler, Cynthia [Niels Bohr International Academy, Niels Bohr Institute,University of Copenhagen, Blegdamsvej 17, DK 2100, Copenhagen (Denmark); Lisbão, Pedro [Department of Physics, University of Michigan,Ann Arbor, MI-48109 (United States); Ng, Gim Seng [Department of Physics, McGill University,Montréal, QC H3A 2T8 (Canada)

2016-10-12

We extend the results of http://dx.doi.org/10.1007/JHEP06(2014)099, computing one loop partition functions for massive fields with spin half in AdS{sub 2} using the quasinormal mode method proposed by Denef, Hartnoll, and Sachdev http://dx.doi.org/10.1088/0264-9381/27/12/125001. We find the finite representations of SO(2,1) for spin zero and spin half, consisting of a highest weight state |h〉 and descendants with non-unitary values of h. These finite representations capture the poles and zeroes of the one loop determinants. Together with the asymptotic behavior of the partition functions (which can be easily computed using a large mass heat kernel expansion), these are sufficient to determine the full answer for the one loop determinants. We also discuss extensions to higher dimensional AdS{sub 2n} and higher spins.

New Method to Study the Vibrational Modes of Biomolecules in the Terahertz Range Based on a Single-Stage Raman Spectrometer.

Science.gov (United States)

Kalanoor, Basanth S; Ronen, Maria; Oren, Ziv; Gerber, Doron; Tischler, Yaakov R

2017-03-31

The low-frequency vibrational (LFV) modes of biomolecules reflect specific intramolecular and intermolecular thermally induced fluctuations that are driven by external perturbations, such as ligand binding, protein interaction, electron transfer, and enzymatic activity. Large efforts have been invested over the years to develop methods to access the LFV modes due to their importance in the studies of the mechanisms and biological functions of biomolecules. Here, we present a method to measure the LFV modes of biomolecules based on Raman spectroscopy that combines volume holographic filters with a single-stage spectrometer, to obtain high signal-to-noise-ratio spectra in short acquisition times. We show that this method enables LFV mode characterization of biomolecules even in a hydrated environment. The measured spectra exhibit distinct features originating from intra- and/or intermolecular collective motion and lattice modes. The observed modes are highly sensitive to the overall structure, size, long-range order, and configuration of the molecules, as well as to their environment. Thus, the LFV Raman spectrum acts as a fingerprint of the molecular structure and conformational state of a biomolecule. The comprehensive method we present here is widely applicable, thus enabling high-throughput study of LFV modes of biomolecules.

Polymeric electrochemical element for adaptive networks: Pulse mode

International Nuclear Information System (INIS)

Smerieri, Anteo; Berzina, Tatiana; Erokhin, Victor; Fontana, M. P.

2008-01-01

An electrochemically controlled polymeric heterojunction working as a memristor, i.e., having memory properties, was investigated in pulse mode, mimicking synaptic behavior of signal transmission in biological systems. Influence of parameters such as pulse duration, interval between pulses, and value of potential base level was analyzed. Learning capabilities were shown to be reversible and repeatable for both potentiation and inhibition of signal transmission. The adaptive behavior of the element was investigated and was shown to be more efficient than the dc mode

The Relationship between Mode of Delivery and Sexual Function in Nulliparous Women

Directory of Open Access Journals (Sweden)

Aytay Alesheikh

2016-07-01

Full Text Available Background & aim: Sexual activity is one of the most important aspects of a marital life. Childbirth is also a major event in the life of women, and the period of postpartum is a time of emotional upheaval. Since women believe that vaginal delivery could negatively affect their sexual function after childbirth, they tend to give birth through caesarean section. Therefore, this study aimed to evaluate the relationship between mode of delivery and sexual function in nulliparous women referred to healthcare centers in Mashhad, Iran. Methods: This correlational study was conducted on 450 nulliparous women, divided into two groups of vaginal delivery and cesarean section in 2014. Suubjects were selected via multistage sampling. Data collection tools included Female Sexual Function Index (FSFI, Depression, Anxiety and Stress scale (DASS-21, and Cassidy social support scale. Data was analyzed in SPSS version 16 using Spearman correlation coefficient and Mann-Whitney test, T-test, ANOVA, and Kruskal-Wallis. Moreover, general linear model was used to control confounding variables, and P-value of less than 0.05 was considered statistically significant. Results: Independent t-test results indicated that mean scores of sexual function in two groups of the study were 26.11±4.36 and 26.38±4.41, respectively, which revealed no statistically significant difference between the groups (P=0.509. Conclusion: No significant difference was observed between the vaginal delivery and caesarean section groups regarding sexual function. Therefore, it seems that cesarean section does not necessarily lead to pleasing sexual relationships in postpartum period compared to vaginal delivery.

A new integrative model of cerebral activation, deactivation and default mode function in Alzheimer's disease

International Nuclear Information System (INIS)

Wermke, Marc; Sorg, Christian; Wohlschlaeger, Afra M.; Drzezga, Alexander

2008-01-01

Functional imaging methods such as positron emission tomography (PET) and functional magnetic resonance imaging (fMRI) allow in vivo assessment of cerebral metabolism at rest and cerebral responses to cognitive stimuli. Activation studies with different cognitive tasks have deepened the understanding of underlying pathology leading to Alzheimer disease (AD) and how the brain reacts to and potentially compensates the imposed damage inflicted by this disease. The aim of this manuscript study was to summarize current findings of activation studies in healthy people at risk for AD, in people with mild cognitive impairment (MCI) as a possible progenitor of AD and finally in patients with manifest AD, adding recent results about impaired deactivation abilities and default mode function in AD. A new comprehensive model will be introduced integrating these heterogeneous findings and explaining their impact on cognitive performance. (orig.)

[The hyperiricosuria as an indicator of derangement of biologic functions of endoecology and adaptation, biologic reactions of excretion, inflammation and arterial tension].

Science.gov (United States)

Titov, V N; Oshchepkova, E V; Dmitriev, V A; Gushchina, O V; Shiriaeva, Iu K; Iashin, A Ia

2012-04-01

During millions years in all animals allantoine (oxidized by uricase uric acid) was catabolite of purines and ascorbic acid was an acceptor of active forms of oxygen. The proximal tubules of nephron reabsorbed the trace amounts of uric acid Then during phylogenesis the primates had a mutation of ascorbic acid gen minus. Later on occurred a second spontaneous mutation and uricase gen minus and uric acid became catabolites of purines. In absence of ascorbic acid synthesis ions of urates became a major capturers of active forms of oxygen and all uric acid as before underwent the reabsorption. Later the carriers were formed which began in epithelium of proximal tubules to secrete all uric acid into urine. At every incident of "littering" of intercellular medium with endogenic flogogens (impairment of biologic function of endoecology) under compensatory development of biologic reaction of inflammation the need in inactivation of active forms of oxygen increases. Hence later on in phylogenesis one more stage was formed--post secretory reabsorption of uric acid In the biologic reaction of inflammation epithelium of proximal tubules initiates retentional hyperiricosuria. The general antioxidant activity of human blood plasma in 60% is presented by urates' ions. The excretion of uric acid includes 4 stages: filtration, full reabsorption, secretion and post secretory reabsorption. In phylogenesis these stages formed in sequence. The mild hyperiricosuria is most frequently considered as a non-specific indicator of activation of biologic reaction of inflammation. The productive hyperiricosuria develops more infrequently under surplus of meat food and cytolysis syndrome (intensification of cell loss in vivo). Under concentration of uric acid more than 400 mkmol/l part of urates circulates in intercellular medium in the form of crystals. The microcrystals of uric acid (biologic "litter") initiate the syndrome of systemic inflammatory response as an endogenic flogogen

Modifications in resting state functional anticorrelation between default mode network and dorsal attention network: comparison among young adults, healthy elders and mild cognitive impairment patients.

Science.gov (United States)

Esposito, Roberto; Cieri, Filippo; Chiacchiaretta, Piero; Cera, Nicoletta; Lauriola, Mariella; Di Giannantonio, Massimo; Tartaro, Armando; Ferretti, Antonio

2018-02-01

Resting state brain activity incorporates different components, including the Default Mode Network and the Dorsal Attention Network, also known as task-negative network and task-positive network respectively. These two networks typically show an anticorrelated activity during both spontaneous oscillations and task execution. However modifications of this anticorrelated activity pattern with age and pathology are still unclear. The present study aimed to investigate differences in resting state Default Mode Network-Dorsal Attention Network functional anticorrelation among young adults, healthy elders and Mild Cognitive Impairment patients. We retrospectively enrolled in this study 27 healthy young adults (age range: 25-35 y.o.; mean age: 28,5), 26 healthy elders (age range: 61-72 y.o.; mean age: 65,1) and 17 MCI patients (age range 64-87 y.o.; mean age: 73,6). Mild Cognitive Impairment patients were selected following Petersen criteria. All participants underwent neuropsychological evaluation and resting state functional Magnetic Resonance Imaging. Spontaneous anticorrelated activity between Default Mode Network and Dorsal Attention Network was observed in each group. This anticorrelation was significantly decreased with age in most Default Mode Network-Dorsal Attention Network connections (p Default Mode Network and the right inferior parietal sulcus node of the Dorsal Attention Network was significantly decreased when comparing Mild Cognitive Impairment with normal elders (p Default Mode Network and Dorsal Attention Network is part of the normal aging process and that Mild Cognitive Impairment status is associated with more evident inter-networks functional connectivity changes.

FUNCTION IN BIOLOGY: ETIOLOGICAL AND ORGANIZATIONAL PERSPECTIVES

Directory of Open Access Journals (Sweden)

Charbel Niño El-Hani

2009-10-01

Full Text Available ABSTRACT. In this paper, we argue for a taxonomy of approaches to function based on different epistemological perspectives assumed with regard to the treatment of this central concept in the life sciences. We distinguish between etiological and organizational perspectives on function, analyzing two distinct theories related to each perspective: Wright’s selectionist etiological approach and Godfrey-Smith’s modern history theory of functions, in the case of the etiological perspective; and Cummins’ functional analysis and Collier’s interactivist approach to function, among organizational accounts. We explain differences and similarities between these theories and the broader perspectives on function, arguing for a particular way of understanding the consensus without unity in debates about function. While explaining the accounts of function, we also deal with the relationship between this concept and other important biological concepts, such as adaptation, selection, complexity, and autonomy. We also advance an argument for the limits and prospects of the explanatory role of function in evolution. By arguing that changes in functionality are always grounded on changes in systems’ organization, we show that function can never explain the origins of traits. Nevertheless, it can explain the spread of traits in populations, but only when we are dealing with functionally novel traits. Finally, we stress that organizational accounts of function are needed to understand how new functions appear by means of changes in systems’ organization. KEYWORDS: Function; Teleology; Explanation; Etiology; Organization.   RESUMEN. En este artículo, argumentamos a favor de una taxonomía de abordajes sobre función basada en diferentes perspectivas epistemológicas a cerca del tratamiento de este concepto central en las ciencias de la vida. Distinguimos entre perspectivas etiológicas y organizacionales sobre función, analizando dos teorías distintas

Wave Propagation of Coupled Modes in the DNA Double Helix

International Nuclear Information System (INIS)

Tabi, Conrad B.; Mohamadou, Alidou; Kofane, Timoleon C.

2010-06-01

The dynamics of waves propagating along the DNA molecule is described by the coupled nonlinear Schroedinger equations. We consider both the single and the coupled nonlinear excitation modes, and we discuss their biological implications. Furthermore, the characteristics of the coupled mode solution are discussed and we show that such a solution can describe the local opening observed within the transcription and the replication phenomena. (author)

Enzymes for ecdysteroid biosynthesis: their biological functions in insects and beyond.

Science.gov (United States)

Niwa, Ryusuke; Niwa, Yuko S

2014-01-01

Steroid hormones are responsible for the coordinated regulation of many aspects of biological processes in multicellular organisms. Since the last century, many studies have identified and characterized steroidogenic enzymes in vertebrates, including mammals. However, much less is known about invertebrate steroidogenic enzymes. In the last 15 years, a number of steroidogenic enzymes and their functions have been characterized in ecdysozoan animals, especially in the fruit fly Drosophila melanogaster. In this review, we summarize the latest knowledge of enzymes crucial for synthesizing ecdysteroids, the principal insect steroid hormones. We also discuss the functional conservation and diversity of ecdysteroidogenic enzymes in other insects and even non-insect species, such as nematodes, vertebrates, and lower eukaryotes.

Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysis

Directory of Open Access Journals (Sweden)

Kanehisa Minoru

2006-04-01

Full Text Available Abstract Background Elementary mode analysis of metabolic pathways has proven to be a valuable tool for assessing the properties and functions of biochemical systems. However, little comprehension of how individual elementary modes are used in real cellular states has been achieved so far. A quantitative measure of fluxes carried by individual elementary modes is of great help to identify dominant metabolic processes, and to understand how these processes are redistributed in biological cells in response to changes in environmental conditions, enzyme kinetics, or chemical concentrations. Results Selecting a valid decomposition of a flux distribution onto a set of elementary modes is not straightforward, since there is usually an infinite number of possible such decompositions. We first show that two recently introduced decompositions are very closely related and assign the same fluxes to reversible elementary modes. Then, we show how such decompositions can be used in combination with kinetic modelling to assess the effects of changes in enzyme kinetics on the usage of individual metabolic routes, and to analyse the range of attainable states in a metabolic system. This approach is illustrated by the example of yeast glycolysis. Our results indicate that only a small subset of the space of stoichiometrically feasible steady states is actually reached by the glycolysis system, even when large variation intervals are allowed for all kinetic parameters of the model. Among eight possible elementary modes, the standard glycolytic route remains dominant in all cases, and only one other elementary mode is able to gain significant flux values in steady state. Conclusion These results indicate that a combination of structural and kinetic modelling significantly constrains the range of possible behaviours of a metabolic system. All elementary modes are not equal contributors to physiological cellular states, and this approach may open a direction toward a

Piezoelectric microelectromechanical resonant sensors for chemical and biological detection.

Science.gov (United States)

Pang, Wei; Zhao, Hongyuan; Kim, Eun Sok; Zhang, Hao; Yu, Hongyu; Hu, Xiaotang

2012-01-07

Piezoelectric microelectromechanical systems (MEMS) resonant sensors, known for their excellent mass resolution, have been studied for many applications, including DNA hybridization, protein-ligand interactions, and immunosensor development. They have also been explored for detecting antigens, organic gas, toxic ions, and explosives. Most piezoelectric MEMS resonant sensors are acoustic sensors (with specific coating layers) that enable selective and label-free detection of biological events in real time. These label-free technologies have recently garnered significant attention for their sensitive and quantitative multi-parameter analysis of biological systems. Since piezoelectric MEMS resonant sensors do more than transform analyte mass or thickness into an electrical signal (e.g., frequency and impedance), special attention must be paid to their potential beyond microweighing, such as measuring elastic and viscous properties, and several types of sensors currently under development operate at different resonant modes (i.e., thickness extensional mode, thickness shear mode, lateral extensional mode, flexural mode, etc.). In this review, we provide an overview of recent developments in micromachined resonant sensors and activities relating to biochemical interfaces for acoustic sensors.

The functional biology and trophic role of krill (Thysanoessa raschii) in a Greenlandic fjord

DEFF Research Database (Denmark)

Agersted, Mette Dalgaard; Nielsen, Torkel Gissel; Munk, Peter

2011-01-01

Despite being a key zooplankton group, knowledge on krill biology from the Arctic is inadequate. The present study examine the functional biology and evaluate the trophic role of krill in the GodthAyenbsfjord (64 degrees N, 51 degrees W) SW Greenland, through a combination of fieldwork...... and laboratory experiments. Krill biomass was highest in the middle fjord and inner fjord, whereas no krill was found offshore. The dominating species Thysanoessa raschii revealed a type III functional response when fed with the diatom Thalassiosira weissflogii. At food saturation, T. raschii exhibited a daily...... ration of 1% body C d(-1). Furthermore, T. raschii was capable of exploiting plankton cells from 5 to 400 mu m, covering several trophic levels of the pelagic food web. The calculated grazing impact by T. raschii on the fjord plankton community was negligible. However, the schooling and migratory...

PreproVIP-derived peptides in the human female genital tract: expression and biological function

DEFF Research Database (Denmark)

Bredkjoer, H E; Palle, C; Ekblad, E

1997-01-01

The aim of the study was to elucidate the localization, distribution, colocalization and biological effect of preproVIP-derived peptides in the human female genital tract. Radioimmunoassays applying antisera against the five functional domains of the VIP precursor in combination with immunohistoc......The aim of the study was to elucidate the localization, distribution, colocalization and biological effect of preproVIP-derived peptides in the human female genital tract. Radioimmunoassays applying antisera against the five functional domains of the VIP precursor in combination...... with immunohistochemistry were used. The effect of preproVIP 22-79, preproVIP 111-122 and preproVIP 156-170 on genital smooth muscle activity in the Fallopian tube was investigated in vitro and compared to that of VIP. All the preproVIP-derived peptides were expressed throughout the genital tract in neuronal elements...

Linking biological soil crust diversity to ecological functions

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Glaser, Karin; Borchhardt, Nadine; Schulz, Karoline; Mikhailyuk, Tatiana; Baumann, Karen; Leinweber, Peter; Ulf, Karsten

2016-04-01

Biological soil crusts (BSCs) are an association of different microorganisms and soil particles in the top millimeters of the soil. They are formed by algae, cyanobacteria, microfungi, bacteria, bryophytes and lichens in various compositions. Our aim was to determine and compare the biodiversity of all occurring organisms in biogeographically different habitats, ranging from polar (both Arctic and Antarctic), subpolar (Scandinavia), temperate (Germany) to dry regions (Chile). The combination of microscopy and molecular techniques (next-generation sequencing) revealed highly diverse crust communities, whose composition clustered by region and correlates with habitat characteristics such as water content. The BSC biodiversity was then linked to the ecological function of the crusts. The functional role of the BSCs in the biogeochemical cycles of carbon, nitrogen and phosphorous is evaluated using an array of state of the art soil chemistry methods including Py-FIMS (pyrolysis field ionization mass spectrometry) and XANES (x-ray absorbance near edge structure). Total P as well as P fractions were quantified in all BSCs, adjacent soil underneath and comparable nearby soil of BSC-free areas revealing a remarkable accumulation of total phosphorous and a distinct pattern of P fractions in the crust. Further, we observed an indication of a different P-speciation composition in the crust compared with BSC-free soil. The data allow answering the question whether BSCs act as sink or source for these compounds, and how biodiversity controls the biogeochemical function of BSCs.

Coupled-mode theory and Fano resonances in guided-mode resonant gratings: the conical diffraction mounting.

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Bykov, Dmitry A; Doskolovich, Leonid L; Soifer, Victor A

2017-01-23

We study resonances of guided-mode resonant gratings in conical mounting. By developing 2D time-dependent coupled-mode theory we obtain simple approximations of the transmission and reflection coefficients. Being functions of the incident light's frequency and in-plane wave vector components, the obtained approximations can be considered as multi-variable generalizations of the Fano line shape. We show that the approximations are in good agreement with the rigorously calculated transmission and reflection spectra. We use the developed theory to investigate angular tolerances of the considered structures and to obtain mode excitation conditions. In particular, we obtain the cross-polarization mode excitation conditions in the case of conical mounting.

Decay Mode Solutions for Kadomtsev-Petviashvili Equation

International Nuclear Information System (INIS)

Fan Guohao; Deng Shufang; Zhang Meng

2012-01-01

The decay mode solutions for the Kadomtsev-Petviashvili (KP) equation are derived by Hirota method (direct method). The decay mode solution is a new set of analytical solutions with Airy function. (general)

A Bayesian spatial model for neuroimaging data based on biologically informed basis functions.

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Huertas, Ismael; Oldehinkel, Marianne; van Oort, Erik S B; Garcia-Solis, David; Mir, Pablo; Beckmann, Christian F; Marquand, Andre F

2017-11-01

The dominant approach to neuroimaging data analysis employs the voxel as the unit of computation. While convenient, voxels lack biological meaning and their size is arbitrarily determined by the resolution of the image. Here, we propose a multivariate spatial model in which neuroimaging data are characterised as a linearly weighted combination of multiscale basis functions which map onto underlying brain nuclei or networks or nuclei. In this model, the elementary building blocks are derived to reflect the functional anatomy of the brain during the resting state. This model is estimated using a Bayesian framework which accurately quantifies uncertainty and automatically finds the most accurate and parsimonious combination of basis functions describing the data. We demonstrate the utility of this framework by predicting quantitative SPECT images of striatal dopamine function and we compare a variety of basis sets including generic isotropic functions, anatomical representations of the striatum derived from structural MRI, and two different soft functional parcellations of the striatum derived from resting-state fMRI (rfMRI). We found that a combination of ∼50 multiscale functional basis functions accurately represented the striatal dopamine activity, and that functional basis functions derived from an advanced parcellation technique known as Instantaneous Connectivity Parcellation (ICP) provided the most parsimonious models of dopamine function. Importantly, functional basis functions derived from resting fMRI were more accurate than both structural and generic basis sets in representing dopamine function in the striatum for a fixed model order. We demonstrate the translational validity of our framework by constructing classification models for discriminating parkinsonian disorders and their subtypes. Here, we show that ICP approach is the only basis set that performs well across all comparisons and performs better overall than the classical voxel-based approach

Mode-mode coupling theory of itinerant electron antiferromagnetism in superconducting state

International Nuclear Information System (INIS)

Fujimoto, Yukinobu; Miyake, Kazumasa

2012-01-01

It has been considered since the first discovery of a high-T c cuprate that an antiferromagnetic (AF) state and a superconducting (SC) state are separated in it. However, it is very intriguing that the coexistence of the AF and SC states has recently been observed in HgBa 2 Ca 4 Cu 5 O 12+ (Hg-1245). Moreover, it is very novel that this coexistence of these two states appears if the SC-transition temperature T c is higher than the AF-transition temperature T N . The mode-mode coupling theory can provide a clear elucidation of this novel phenomenon. A key point of this theory is that the AF susceptibility consists of the random-phase-approximation (RPA) term and the mode-mode coupling one. The RPA term works to make a positive contribution to the emergence of the antiferromagnetic critical point (AF-CP). In contrast, the mode-mode coupling term works to make a negative contribution to the emergence of the AF-CP. However, the growth of the SC-gap function in the d x 2 -y 2 -wave SC state works to suppress the negative contribution of the mode-mode coupling term to the emergence of the AF-CP. Moreover, the effect of SC fluctuations near the SC-transition temperature T c suppresses the mode-mode coupling term of the AF susceptibility that works to hinder the AF ordering. For these two reasons, there is a possibility that the d x 2 -y 2 -wave SC state is likely to promote the emergence of the AF-CP. Namely, the appearance of the above-mentioned novel coexistence of the AF and SC states observed in Hg-1245 can be explained qualitatively on the basis of this idea.

Damage-free vibrational spectroscopy of biological materials in the electron microscope.

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Rez, Peter; Aoki, Toshihiro; March, Katia; Gur, Dvir; Krivanek, Ondrej L; Dellby, Niklas; Lovejoy, Tracy C; Wolf, Sharon G; Cohen, Hagai

2016-03-10

Vibrational spectroscopy in the electron microscope would be transformative in the study of biological samples, provided that radiation damage could be prevented. However, electron beams typically create high-energy excitations that severely accelerate sample degradation. Here this major difficulty is overcome using an 'aloof' electron beam, positioned tens of nanometres away from the sample: high-energy excitations are suppressed, while vibrational modes of energies electron energy loss spectra from biogenic guanine crystals in their native state, resolving their characteristic C-H, N-H and C=O vibrational signatures with no observable radiation damage. The technique opens up the possibility of non-damaging compositional analyses of organic functional groups, including non-crystalline biological materials, at a spatial resolution of ∼10 nm, simultaneously combined with imaging in the electron microscope.

Biological effects of simple changes in functionality on rhodium metalloinsertors

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Weidmann, Alyson G.; Komor, Alexis C.; Barton, Jacqueline K.

2013-01-01

DNA mismatch repair (MMR) is crucial to ensuring the fidelity of the genome. The inability to correct single base mismatches leads to elevated mutation rates and carcinogenesis. Using metalloinsertors–bulky metal complexes that bind with high specificity to mismatched sites in the DNA duplex–our laboratory has adopted a new chemotherapeutic strategy through the selective targeting of MMR-deficient cells, that is, those that have a propensity for cancerous transformation. Rhodium metalloinsertors display inhibitory effects selectively in cells that are deficient in the MMR machinery, consistent with this strategy. However, a highly sensitive structure–function relationship is emerging with the development of new complexes that highlights the importance of subcellular localization. We have found that small structural modifications, for example a hydroxyl versus a methyl functional group, can yield profound differences in biological function. Despite similar binding affinities and selectivities for DNA mismatches, only one metalloinsertor shows selective inhibition of cellular proliferation in MMR-deficient versus -proficient cells. Studies of whole-cell, nuclear and mitochondrial uptake reveal that this selectivity depends upon targeting DNA mismatches in the cell nucleus. PMID:23776288

Structure, function, and behaviour of computational models in systems biology.

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Knüpfer, Christian; Beckstein, Clemens; Dittrich, Peter; Le Novère, Nicolas

2013-05-31

Systems Biology develops computational models in order to understand biological phenomena. The increasing number and complexity of such "bio-models" necessitate computer support for the overall modelling task. Computer-aided modelling has to be based on a formal semantic description of bio-models. But, even if computational bio-models themselves are represented precisely in terms of mathematical expressions their full meaning is not yet formally specified and only described in natural language. We present a conceptual framework - the meaning facets - which can be used to rigorously specify the semantics of bio-models. A bio-model has a dual interpretation: On the one hand it is a mathematical expression which can be used in computational simulations (intrinsic meaning). On the other hand the model is related to the biological reality (extrinsic meaning). We show that in both cases this interpretation should be performed from three perspectives: the meaning of the model's components (structure), the meaning of the model's intended use (function), and the meaning of the model's dynamics (behaviour). In order to demonstrate the strengths of the meaning facets framework we apply it to two semantically related models of the cell cycle. Thereby, we make use of existing approaches for computer representation of bio-models as much as possible and sketch the missing pieces. The meaning facets framework provides a systematic in-depth approach to the semantics of bio-models. It can serve two important purposes: First, it specifies and structures the information which biologists have to take into account if they build, use and exchange models. Secondly, because it can be formalised, the framework is a solid foundation for any sort of computer support in bio-modelling. The proposed conceptual framework establishes a new methodology for modelling in Systems Biology and constitutes a basis for computer-aided collaborative research.

Correlation of Respiratory Signals and Electrocardiogram Signals via Empirical Mode Decomposition

KAUST Repository

El Fiky, Ahmed Osama

2011-05-24

Recently Electrocardiogram (ECG) signals are being broadly used as an essential diagnosing tool in different clinical applications as they carry a reliable representation not only for cardiac activities, but also for other associated biological processes, like respiration. However, the process of recording and collecting them has usually suffered from the presence of some undesired noises, which in turn affects the reliability of such representations.Therefore, de-noising ECG signals became a hot research field for signal processing experts to ensure better and clear representation of the different cardiac activities. Given the nonlinear and non-stationary properties of ECGs, it is not a simple task to cancel the undesired noise terms without affecting the biological physics of them. In this study, we are interested in correlating the ECG signals with respiratory parameters, specifically the lung volume and lung pressure. We have focused on the concept of de-noising ECG signals by means of signal decomposition using an algorithm called the Empirical Mode Decomposition (EMD) where the original ECG signals are being decomposed into a set of intrinsic mode functions (IMF). Then, we have provided criteria based on which some of these IMFs have been adapted to reconstruct de-noised ECG version. Finally, we have utilized de-noised ECGs as well as IMFs for to study the correlation with lung volume and lung pressure. These correlation studies have showed some clear resemblance especially between the oscillations of ECGs and lung pressures.

TCA Cycle and Mitochondrial Membrane Potential Are Necessary for Diverse Biological Functions.

Science.gov (United States)

Martínez-Reyes, Inmaculada; Diebold, Lauren P; Kong, Hyewon; Schieber, Michael; Huang, He; Hensley, Christopher T; Mehta, Manan M; Wang, Tianyuan; Santos, Janine H; Woychik, Richard; Dufour, Eric; Spelbrink, Johannes N; Weinberg, Samuel E; Zhao, Yingming; DeBerardinis, Ralph J; Chandel, Navdeep S

2016-01-21

Mitochondrial metabolism is necessary for the maintenance of oxidative TCA cycle function and mitochondrial membrane potential. Previous attempts to decipher whether mitochondria are necessary for biological outcomes have been hampered by genetic and pharmacologic methods that simultaneously disrupt multiple functions linked to mitochondrial metabolism. Here, we report that inducible depletion of mitochondrial DNA (ρ(ο) cells) diminished respiration, oxidative TCA cycle function, and the mitochondrial membrane potential, resulting in diminished cell proliferation, hypoxic activation of HIF-1, and specific histone acetylation marks. Genetic reconstitution only of the oxidative TCA cycle function specifically in these inducible ρ(ο) cells restored metabolites, resulting in re-establishment of histone acetylation. In contrast, genetic reconstitution of the mitochondrial membrane potential restored ROS, which were necessary for hypoxic activation of HIF-1 and cell proliferation. These results indicate that distinct mitochondrial functions associated with respiration are necessary for cell proliferation, epigenetics, and HIF-1 activation. Copyright © 2016 Elsevier Inc. All rights reserved.

The Escherichia coli modE gene: effect of modE mutations on molybdate dependent modA expression.

Science.gov (United States)

McNicholas, P M; Chiang, R C; Gunsalus, R P

1996-11-15

The Escherichia coli modABCD operon, which encodes a high-affinity molybdate uptake system, is transcriptionally regulated in response to molybdate availability by ModE. Here we describe a highly effective enrichment protocol, applicable to any gene with a repressor role, and establish its application in the isolation of transposon mutations in modE. In addition we show that disruption of the ModE C-terminus abolishes derepression in the absence of molybdate, implying this region of ModE controls the repressor activity. Finally, a mutational analysis of a proposed molybdate binding motif indicates that this motif does not function in regulating the repressor activity of ModE.

Binding modes and functional surface of anti-mammalian scorpion α-toxins to sodium channels.

Science.gov (United States)

Chen, Rong; Chung, Shin-Ho

2012-10-02

Scorpion α-toxins bind to the voltage-sensing domains of voltage-gated sodium (Na(V)) channels and interfere with the inactivation mechanisms. The functional surface of α-toxins has been shown to contain an NC-domain consisting of the five-residue turn (positions 8-12) and the C-terminus (positions 56-64) and a core-domain centered on the residue 18. The NC- and core-domains are interconnected by the linker-domain (positions 8-18). Here with atomistic molecular dynamics simulations, we examine the binding modes between two α-toxins, the anti-mammalian AahII and the anti-insect LqhαIT, and the voltage-sensing domain of rat Na(V)1.2, a subtype of Na(V) channels expressed in nerve cells. Both toxins are docked to the extracellular side of the voltage-sensing domain of Na(V)1.2 using molecular dynamics simulations, with the linker-domain assumed to wedge into the binding pocket. Several salt bridges and hydrophobic clusters are observed to form between the NC- and core-domains of the toxins and Na(V)1.2 and stabilize the toxin-channel complexes. The binding modes predicted are consistent with available mutagenesis data and can readily explain the relative affinities of AahII and LqhαIT for Na(V)1.2. The dissociation constants for the two toxin-channel complexes are derived, which compare favorably with experiment. Our models demonstrate that the functional surface of anti-mammalian scorpion α-toxins is centered on the linker-domain, similar to that of β-toxins.

Role of soil biology and soil functions in relation to land use intensity.

Science.gov (United States)

Bondi, Giulia; Wall, David; Bacher, Matthias; Emmet-Booth, Jeremy; Graça, Jessica; Marongiu, Irene; Creamer, Rachel

2017-04-01

The delivery of the ecosystem's functions is predominantly controlled by soil biology. The biology found in a gram of soil contains more than ten thousand individual species of bacteria and fungi (Torsvik et al., 1990). Understanding the role and the requirements of these organisms is essential for the protection and the sustainable use of soils. Soil biology represents the engine of all the processes occurring in the soil and it supports the ecosystem services such as: 1) nutrient mineralisation 2) plant production 3) water purification and regulation and 4) carbon cycling and storage. During the last years land management type and intensity have been identified as major drivers for microbial performance in soil. For this reason land management needs to be appropriately studied to understand the role of soil biology within this complex interplay of functions. We aimed to study whether and how land management drives soil biological processes and related functions. To reach this objective we built a land use intensity index (LUI) able to quantify the impact of the common farming practices carried out in Irish grassland soils. The LUI is derived from a detailed farmer questionnaire on grassland management practices at 38 farms distributed in the five major agro-climatic regions of Ireland defined by Holden and Brereton (2004). Soils were classified based on their drainage status according to the Irish Soil Information System by Creamer et al. (2014). This detailed questionnaire is then summarised into 3 management intensity components: (i) intensity of Fertilisation (Fi), (ii) frequency of Mowing (Mi) and (iii) intensity of Livestock Grazing (Gi). Sites were sampled to assess the impact of land management intensity on microbial community structure and enzyme behaviour in relation to nitrogen, phosphorus and carbon cycling. Preliminary results for enzymes linked to C and N cycles showed higher activity in relation to low grazing pressure (low Gi). Enzymes linked to P

Functional dependence of resonant harmonics on nanomechanical parameters in dynamic mode atomic force microscopy.

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Gramazio, Federico; Lorenzoni, Matteo; Pérez-Murano, Francesc; Rull Trinidad, Enrique; Staufer, Urs; Fraxedas, Jordi

2017-01-01

We present a combined theoretical and experimental study of the dependence of resonant higher harmonics of rectangular cantilevers of an atomic force microscope (AFM) as a function of relevant parameters such as the cantilever force constant, tip radius and free oscillation amplitude as well as the stiffness of the sample's surface. The simulations reveal a universal functional dependence of the amplitude of the 6th harmonic (in resonance with the 2nd flexural mode) on these parameters, which can be expressed in terms of a gun-shaped function. This analytical expression can be regarded as a practical tool for extracting qualitative information from AFM measurements and it can be extended to any resonant harmonics. The experiments confirm the predicted dependence in the explored 3-45 N/m force constant range and 2-345 GPa sample's stiffness range. For force constants around 25 N/m, the amplitude of the 6th harmonic exhibits the largest sensitivity for ultrasharp tips (tip radius below 10 nm) and polymers (Young's modulus below 20 GPa).

Microstructure, mechanical properties, and biological response to functionally graded HA coatings

International Nuclear Information System (INIS)

Rabiei, Afsaneh; Blalock, Travis; Thomas, Brent; Cuomo, Jerry; Yang, Y.; Ong, Joo

2007-01-01

Hydroxyapatite (HA) [Ca 10 (PO 4 ) 6 (OH) 2 ] is the primary mineral content, representing 43% by weight, of bone. Applying a thin layer of HA, to the surface of a metal implant, can promote osseointegration and increase the mechanical stability of the implant. In this study, a biocompatible coating comprising an HA film with functionally graded crystallinity is being deposited on a heated substrate in an Ion Beam Assisted Deposition (IBAD) system. The microstructure of the film was studied using Transmission Electron Microscopy techniques. Finally, initial cell adhesion and cell differentiation on the coating was evaluated using ATCC CRL 1486 human embryonic palatal mesenchymal cell, an osteoblast precursor cell line. The results have shown superior mechanical properties and biological response to the functionally graded HA film

The Widespread Prevalence and Functional Significance of Silk-Like Structural Proteins in Metazoan Biological Materials.

Directory of Open Access Journals (Sweden)

Carmel McDougall

Full Text Available In nature, numerous mechanisms have evolved by which organisms fabricate biological structures with an impressive array of physical characteristics. Some examples of metazoan biological materials include the highly elastic byssal threads by which bivalves attach themselves to rocks, biomineralized structures that form the skeletons of various animals, and spider silks that are renowned for their exceptional strength and elasticity. The remarkable properties of silks, which are perhaps the best studied biological materials, are the result of the highly repetitive, modular, and biased amino acid composition of the proteins that compose them. Interestingly, similar levels of modularity/repetitiveness and similar bias in amino acid compositions have been reported in proteins that are components of structural materials in other organisms, however the exact nature and extent of this similarity, and its functional and evolutionary relevance, is unknown. Here, we investigate this similarity and use sequence features common to silks and other known structural proteins to develop a bioinformatics-based method to identify similar proteins from large-scale transcriptome and whole-genome datasets. We show that a large number of proteins identified using this method have roles in biological material formation throughout the animal kingdom. Despite the similarity in sequence characteristics, most of the silk-like structural proteins (SLSPs identified in this study appear to have evolved independently and are restricted to a particular animal lineage. Although the exact function of many of these SLSPs is unknown, the apparent independent evolution of proteins with similar sequence characteristics in divergent lineages suggests that these features are important for the assembly of biological materials. The identification of these characteristics enable the generation of testable hypotheses regarding the mechanisms by which these proteins assemble and direct the

The Structure and Function of Biological Networks

Science.gov (United States)

Wu, Daniel Duanqing

2010-01-01

Biology has been revolutionized in recent years by an explosion in the availability of data. Transforming this new wealth of data into meaningful biological insights and clinical breakthroughs requires a complete overhaul both in the questions being asked and the methodologies used to answer them. A major challenge in organizing and understanding…

All-fiber optical mode switching based on cascaded mode selective couplers for short-reach MDM networks

Science.gov (United States)

Ren, Fang; Li, Juhao; Wu, Zhongying; Yu, Jinyi; Mo, Qi; Wang, Jianping; He, Yongqi; Chen, Zhangyuan; Li, Zhengbin

2017-04-01

We propose and experimentally demonstrate an all-fiber optical mode switching structure supporting independent switching, exchanging, adding, and dropping functionalities in which each mode can be switched individually. The mode switching structure consists of cascaded mode selective couplers (MSCs) capable of exciting and selecting specific higher order modes in few-mode fibers with high efficiency and one multiport optical switch routing the independent spatial modes to their destinations. The data carried on three different spatial modes can be switched, exchanged, added, and dropped through this all-fiber structure. For this experimental demonstration, optical on-off-keying (OOK) signals at 10-Gb/s carried on three spatial modes are successfully processed with open and clear eye diagrams. The mode switch exhibits power penalties of less than 3.1 dB after through operation, less than 2.7 dB after exchange operation, less than 2.8 dB after switching operation, and less than 1.6 dB after mode adding and dropping operations at the bit-error rate (BER) of 10-3, while all three channels carried on three spatial modes are simultaneously routed. The proposed structure, compatible with current optical switching networks based on single-mode fibers, can potentially be used to expand the switching scalability in advanced and flexible short-reach mode-division multiplexing-based networks.

Equilibrium radionuclide assessment of left ventricular ejection and filling. Comparison of list mode-and multigated frame-mode measurements

Energy Technology Data Exchange (ETDEWEB)

Sugrue, D.D.; McKenna, W.J.; Dickie, S.; Oakley, C.M.; Myers, M.J.; Lavender, J.P. (Royal Postgraduate Medical School, London (UK))

1983-10-01

The relationship as studied between radionuclide indices of left ventricular systolic and diastolic function acquired in conventional multigated frame-mode compared to list-mode in patients with sinus rhythm. The study showed that frame-mode and list-mode measurements of ejection and filling indices are not significantly different in these patients but that backward reformatting of data acquired in list-mode is necessary to measure the atrial contribution to LV stroke counts. It was concluded that valid measurements of left ventricular systolic ejection and diastolic filling can be made in patients in sinus rhythm using frame-mode acquisition with the exception of measurements of the contribution from atrial systole to stroke volume.

Pectin: cell biology and prospects for functional analysis.

Science.gov (United States)

Willats, W G; McCartney, L; Mackie, W; Knox, J P

2001-09-01

Pectin is a major component of primary cell walls of all land plants and encompasses a range of galacturonic acid-rich polysaccharides. Three major pectic polysaccharides (homogalacturonan, rhamnogalacturonan-I and rhamnogalacturonan-II) are thought to occur in all primary cell walls. This review surveys what is known about the structure and function of these pectin domains. The high degree of structural complexity and heterogeneity of the pectic matrix is produced both during biosynthesis in the endomembrane system and as a result of the action of an array of wall-based pectin-modifying enzymes. Recent developments in analytical techniques and in the generation of anti-pectin probes have begun to place the structural complexity of pectin in cell biological and developmental contexts. The in muro de-methyl-esterification of homogalacturonan by pectin methyl esterases is emerging as a key process for the local modulation of matrix properties. Rhamnogalacturonan-I comprises a highly diverse population of spatially and developmentally regulated polymers, whereas rhamnogalacturonan-II appears to be a highly conserved and stable pectic domain. Current knowledge of biosynthetic enzymes, plant and microbial pectinases and the interactions of pectin with other cell wall components and the impact of molecular genetic approaches are reviewed in terms of the functional analysis of pectic polysaccharides in plant growth and development.

Biological adaptations for functional features of language in the face of cultural evolution.

Science.gov (United States)

Christiansen, Morten H; Reali, Florencia; Chater, Nick

2011-04-01

Although there may be no true language universals, it is nonetheless possible to discern several family resemblance patterns across the languages of the world. Recent work on the cultural evolution of language indicates the source of these patterns is unlikely to be an innate universal grammar evolved through biological adaptations for arbitrary linguistic features. Instead, it has been suggested that the patterns of resemblance emerge because language has been shaped by the brain, with individual languages representing different but partially overlapping solutions to the same set of nonlinguistic constraints. Here, we use computational simulations to investigate whether biological adaptation for functional features of language, deriving from cognitive and communicative constraints, may nonetheless be possible alongside rapid cultural evolution. Specifically, we focus on the Baldwin effect as an evolutionary mechanism by which previously learned linguistic features might become innate through natural selection across many generations of language users. The results indicate that cultural evolution of language does not necessarily prevent functional features of language from becoming genetically fixed, thus potentially providing a particularly informative source of constraints on cross-linguistic resemblance patterns.

The Information Content of Discrete Functions and Their Application in Genetic Data Analysis.

Science.gov (United States)

Sakhanenko, Nikita A; Kunert-Graf, James; Galas, David J

2017-12-01

The complex of central problems in data analysis consists of three components: (1) detecting the dependence of variables using quantitative measures, (2) defining the significance of these dependence measures, and (3) inferring the functional relationships among dependent variables. We have argued previously that an information theory approach allows separation of the detection problem from the inference of functional form problem. We approach here the third component of inferring functional forms based on information encoded in the functions. We present here a direct method for classifying the functional forms of discrete functions of three variables represented in data sets. Discrete variables are frequently encountered in data analysis, both as the result of inherently categorical variables and from the binning of continuous numerical variables into discrete alphabets of values. The fundamental question of how much information is contained in a given function is answered for these discrete functions, and their surprisingly complex relationships are illustrated. The all-important effect of noise on the inference of function classes is found to be highly heterogeneous and reveals some unexpected patterns. We apply this classification approach to an important area of biological data analysis-that of inference of genetic interactions. Genetic analysis provides a rich source of real and complex biological data analysis problems, and our general methods provide an analytical basis and tools for characterizing genetic problems and for analyzing genetic data. We illustrate the functional description and the classes of a number of common genetic interaction modes and also show how different modes vary widely in their sensitivity to noise.

Functional MRI Assessment of Task-Induced Deactivation of the Default Mode Network in Alzheimer’s Disease and At-Risk Older Individuals

Directory of Open Access Journals (Sweden)

Maija Pihlajamäki

2009-01-01

Full Text Available Alzheimer’s disease (AD is the most common form of dementia in old age, and is characterized by prominent impairment of episodic memory. Recent functional imaging studies in AD have demonstrated alterations in a distributed network of brain regions supporting memory function, including regions of the default mode network. Previous positron emission tomography studies of older individuals at risk for AD have revealed hypometabolism of association cortical regions similar to the metabolic abnormalities seen in AD patients. In recent functional magnetic resonance imaging (fMRI studies of AD, corresponding brain default mode regions have also been found to demonstrate an abnormal fMRI task-induced deactivation response pattern. That is, the relative decreases in fMRI signal normally observed in the default mode regions in healthy subjects performing a cognitive task are not seen in AD patients, or may even be reversed to a paradoxical activation response. Our recent studies have revealed alterations in the pattern of deactivation also in elderly individuals at risk for AD by virtue of their APOE e4 genotype, or evidence of mild cognitive impairment (MCI. In agreement with recent reports from other groups, these studies demonstrate that the pattern of fMRI task-induced deactivation is progressively disrupted along the continuum from normal aging to MCI and to clinical AD and more impaired in e4 carriers compared to non-carriers. These findings will be discussed in the context of current literature regarding functional imaging of the default network in AD and at-risk populations.

Application of Compton suppression spectrometry in the improvement of nuclear analytical techniques for biological samples

International Nuclear Information System (INIS)

Ahmed, Y. A.; Ewa, I.O.B.; Funtua, I.I.; Jonah, S.A.; Landsberger, S.

2007-01-01

Compton Suppression Factors (SF) and Compton Reduction Factors (RF) of the UT Austin's Compton suppression spectrometer being parameters characterizing the system performance were measured using ''1''3''7Cs and ''6''0Co point sources. The system performance was evaluated as a function of energy and geometry. The (P/C), A(P/C), (P/T), Cp, and Ce were obtained for each of the parameters. The natural background reduction factor in the anticoincidence mode and that of normal mode was calculated and its effect on the detection limit of biological samples evaluated. Applicability of the spectrometer and the method for biological samples was tested in the measurement of twenty-four elements (Ba, Sr, I, Br, Cu, V, Mg, Na, Cl, Mn, Ca, Sn, In, K, Mo, Cd, Zn, As, Sb, Ni, Rb, Cs, Fe, and Co) commonly found in food, milk, tea and tobacco items. They were determined from seven National Institute for Standard and Technology (NIST) certified reference materials (rice flour, oyster tissue, non-fat powdered milk, peach leaves, tomato leaves, apple leaves, and citrus leaves). Our results shows good agreement with the NIST certified values, indicating that the method developed in the present study is suitable for the determination of aforementioned elements in biological samples without undue interference problems

Improved diagnostic accuracy of Alzheimer's disease by combining regional cortical thickness and default mode network functional connectivity: Validated in the Alzheimer's disease neuroimaging initiative set

International Nuclear Information System (INIS)

Park, Ji Eun; Park, Bum Woo; Kim, Sang Joon; Kim, Ho Sung; Choi, Choong Gon; Jung, Seung Jung; Oh, Joo Young; Shim, Woo Hyun; Lee, Jae Hong; Roh, Jee Hoon

2017-01-01

To identify potential imaging biomarkers of Alzheimer's disease by combining brain cortical thickness (CThk) and functional connectivity and to validate this model's diagnostic accuracy in a validation set. Data from 98 subjects was retrospectively reviewed, including a study set (n = 63) and a validation set from the Alzheimer's Disease Neuroimaging Initiative (n = 35). From each subject, data for CThk and functional connectivity of the default mode network was extracted from structural T1-weighted and resting-state functional magnetic resonance imaging. Cortical regions with significant differences between patients and healthy controls in the correlation of CThk and functional connectivity were identified in the study set. The diagnostic accuracy of functional connectivity measures combined with CThk in the identified regions was evaluated against that in the medial temporal lobes using the validation set and application of a support vector machine. Group-wise differences in the correlation of CThk and default mode network functional connectivity were identified in the superior temporal (p < 0.001) and supramarginal gyrus (p = 0.007) of the left cerebral hemisphere. Default mode network functional connectivity combined with the CThk of those two regions were more accurate than that combined with the CThk of both medial temporal lobes (91.7% vs. 75%). Combining functional information with CThk of the superior temporal and supramarginal gyri in the left cerebral hemisphere improves diagnostic accuracy, making it a potential imaging biomarker for Alzheimer's disease

Enhanced Sleep Mode MAC Control for EPON

DEFF Research Database (Denmark)

Yan, Ying; Dittmann, Lars

2011-01-01

This paper introduces sleep mode operations for EPON. New MAC control functions are proposed to schedule sleep periods. Traffic profiles are considered to optimize energy efficiency and network performances. Simulation results are analyzed in OPNET modeler.......This paper introduces sleep mode operations for EPON. New MAC control functions are proposed to schedule sleep periods. Traffic profiles are considered to optimize energy efficiency and network performances. Simulation results are analyzed in OPNET modeler....

Importance of N-Glycosylation on CD147 for Its Biological Functions

Science.gov (United States)

Bai, Yang; Huang, Wan; Ma, Li-Tian; Jiang, Jian-Li; Chen, Zhi-Nan

2014-01-01

Glycosylation of glycoproteins is one of many molecular changes that accompany malignant transformation. Post-translational modifications of proteins are closely associated with the adhesion, invasion, and metastasis of tumor cells. CD147, a tumor-associated antigen that is highly expressed on the cell surface of various tumors, is a potential target for cancer diagnosis and therapy. A significant biochemical property of CD147 is its high level of glycosylation. Studies on the structure and function of CD147 glycosylation provide valuable clues to the development of targeted therapies for cancer. Here, we review current understanding of the glycosylation characteristics of CD147 and the glycosyltransferases involved in the biosynthesis of CD147 N-glycans. Finally, we discuss proteins regulating CD147 glycosylation and the biological functions of CD147 glycosylation. PMID:24739808

Importance of N-Glycosylation on CD147 for Its Biological Functions

Directory of Open Access Journals (Sweden)

Yang Bai

2014-04-01

Full Text Available Glycosylation of glycoproteins is one of many molecular changes that accompany malignant transformation. Post-translational modifications of proteins are closely associated with the adhesion, invasion, and metastasis of tumor cells. CD147, a tumor-associated antigen that is highly expressed on the cell surface of various tumors, is a potential target for cancer diagnosis and therapy. A significant biochemical property of CD147 is its high level of glycosylation. Studies on the structure and function of CD147 glycosylation provide valuable clues to the development of targeted therapies for cancer. Here, we review current understanding of the glycosylation characteristics of CD147 and the glycosyltransferases involved in the biosynthesis of CD147 N-glycans. Finally, we discuss proteins regulating CD147 glycosylation and the biological functions of CD147 glycosylation.

Functionalized gold nanoparticle supported sensory mechanisms applied in detection of chemical and biological threat agents: A review

International Nuclear Information System (INIS)

Upadhyayula, Venkata K.K.

2012-01-01

Highlights: ► Smart sensors are needed for detection of chemical and biological threat agents. ► Smart sensors detect analytes with rapid speed, high sensitivity and selectivity. ► Functionalized gold nanoparticles (GNPs) can potentially smart sense threat agents. ► Functionalized GNPs support multiple analytical methods for sensing threat agents. ► Threat agents of all types can be detected using functionalized GNPs. - Abstract: There is a great necessity for development of novel sensory concepts supportive of smart sensing capabilities in defense and homeland security applications for detection of chemical and biological threat agents. A smart sensor is a detection device that can exhibit important features such as speed, sensitivity, selectivity, portability, and more importantly, simplicity in identifying a target analyte. Emerging nanomaterial based sensors, particularly those developed by utilizing functionalized gold nanoparticles (GNPs) as a sensing component potentially offer many desirable features needed for threat agent detection. The sensitiveness of physical properties expressed by GNPs, e.g. color, surface plasmon resonance, electrical conductivity and binding affinity are significantly enhanced when they are subjected to functionalization with an appropriate metal, organic or biomolecular functional groups. This sensitive nature of functionalized GNPs can be potentially exploited in the design of threat agent detection devices with smart sensing capabilities. In the presence of a target analyte (i.e., a chemical or biological threat agent) a change proportional to concentration of the analyte is observed, which can be measured either by colorimetric, fluorimetric, electrochemical or spectroscopic means. This article provides a review of how functionally modified gold colloids are applied in the detection of a broad range of threat agents, including radioactive substances, explosive compounds, chemical warfare agents, biotoxins, and

Functionalized gold nanoparticle supported sensory mechanisms applied in detection of chemical and biological threat agents: A review

Energy Technology Data Exchange (ETDEWEB)

Upadhyayula, Venkata K.K., E-mail: Upadhyayula.Venkata@epa.gov [Oak Ridge Institute of Science and Education (ORISE), MC-100-44, PO Box 117, Oak Ridge, TN 37831 (United States)

2012-02-17

Highlights: Black-Right-Pointing-Pointer Smart sensors are needed for detection of chemical and biological threat agents. Black-Right-Pointing-Pointer Smart sensors detect analytes with rapid speed, high sensitivity and selectivity. Black-Right-Pointing-Pointer Functionalized gold nanoparticles (GNPs) can potentially smart sense threat agents. Black-Right-Pointing-Pointer Functionalized GNPs support multiple analytical methods for sensing threat agents. Black-Right-Pointing-Pointer Threat agents of all types can be detected using functionalized GNPs. - Abstract: There is a great necessity for development of novel sensory concepts supportive of smart sensing capabilities in defense and homeland security applications for detection of chemical and biological threat agents. A smart sensor is a detection device that can exhibit important features such as speed, sensitivity, selectivity, portability, and more importantly, simplicity in identifying a target analyte. Emerging nanomaterial based sensors, particularly those developed by utilizing functionalized gold nanoparticles (GNPs) as a sensing component potentially offer many desirable features needed for threat agent detection. The sensitiveness of physical properties expressed by GNPs, e.g. color, surface plasmon resonance, electrical conductivity and binding affinity are significantly enhanced when they are subjected to functionalization with an appropriate metal, organic or biomolecular functional groups. This sensitive nature of functionalized GNPs can be potentially exploited in the design of threat agent detection devices with smart sensing capabilities. In the presence of a target analyte (i.e., a chemical or biological threat agent) a change proportional to concentration of the analyte is observed, which can be measured either by colorimetric, fluorimetric, electrochemical or spectroscopic means. This article provides a review of how functionally modified gold colloids are applied in the detection of a broad

Biological response to purification and acid functionalization of carbon nanotubes

Science.gov (United States)

Figarol, Agathe; Pourchez, Jérémie; Boudard, Delphine; Forest, Valérie; Tulliani, Jean-Marc; Lecompte, Jean-Pierre; Cottier, Michèle; Bernache-Assollant, Didier; Grosseau, Philippe

2014-07-01

Acid functionalization has been considered as an easy way to enhance the dispersion and biodegradation of carbon nanotubes (CNT). However, inconsistencies between toxicity studies of acid functionalized CNT remain unexplained. This could be due to a joint effect of the main physicochemical modifications resulting from an acid functionalization: addition of surface acid groups and purification from catalytic metallic impurities. In this study, the impact on CNT biotoxicity of these two physiochemical features was assessed separately. The in vitro biological response of RAW 264.7 macrophages was evaluated after exposure to 15-240 µg mL-1 of two types of multi-walled CNT. For each type of CNT (small: 20 nm diameter, and big: 90 nm diameter), three different surface chemical properties were studied (total of six CNT samples): pristine, acid functionalized and desorbed. Desorbed CNT were purified by the acid functionalization but presented a very low amount of surface acid groups due to a thermal treatment under vacuum. A Janus effect of acid functionalization with two opposite impacts is highlighted. The CNT purification decreased the overall toxicity, while the surface acid groups intensified it when present at a specific threshold. These acid groups especially amplified the pro-inflammatory response. The threshold mechanism which seemed to regulate the impact of acid groups should be further studied to determine its value and potential link to the other physicochemical state of the CNT. The results suggest that, for a safer-design approach, the benefit-risk balance of an acid functionalization has to be considered, depending on the CNT primary state of purification. Further research should be conducted in this direction.

STAT6: its role in interleukin 4-mediated biological functions.

Science.gov (United States)

Takeda, K; Kishimoto, T; Akira, S

1997-05-01

Interleukin (IL) 4 is known to be a cytokine which plays a central role in the regulation of immune response. Studies on cytokine signal transduction have clarified the mechanism by which IL4 exerts its functions. Two cytoplasmic proteins, signal transducer and activator of transcription (STAT) 6 and IL4-induced phosphotyrosine substrate/insulin receptor substrate 2 (4PS/IRS2), are activated in IL4 signal transduction. Recent studies from STAT6-deficient mice have revealed the essential role of STAT6 in IL4-mediated biological actions. In addition, STAT6 has also been demonstrated to be important for the functions mediated by IL13, which is related to IL4. IL4 and IL13 have been shown to induce the production of IgE, which is a major mediator in an allergic response. These findings indicate that STAT6 activation is involved in IL4- and IL13-mediated disorders such as allergy.

Covalent Organic Framework Functionalized with 8-Hydroxyquinoline as a Dual-Mode Fluorescent and Colorimetric pH Sensor.

Science.gov (United States)

Chen, Long; He, Linwei; Ma, Fuyin; Liu, Wei; Wang, Yaxing; Silver, Mark A; Chen, Lanhua; Zhu, Lin; Gui, Daxiang; Diwu, Juan; Chai, Zhifang; Wang, Shuao

2018-05-09

Real-time and accurate detection of pH in aqueous solution is of great significance in chemical, environmental, and engineering-related fields. We report here the use of 8-hydroxyquinoline-functionalized covalent organic framework (COF-HQ) for dual-mode pH sensing. In the fluorescent mode, the emission intensity of COF-HQ weakened as the pH decreased, and also displayed a good linear relationship against pH in the range from 1 to 5. In addition, COF-HQ showed discernible color changes from yellow to black as the acidity increased and can be therefore used as a colorimetric pH sensor. All these changes are reversible and COF-HQ can be recycled for multiple detection runs owing to its high hydrolytical stability. It can be further assembled into a mixed matrix membrane for practical applications.

On Mode Correlation of Solar Acoustic Oscillations

Directory of Open Access Journals (Sweden)

Heon-Young Chang

2009-09-01

Full Text Available In helioseismology it is normally assumed that p-mode oscillations are excited in a statistically independent fashion. Unfortunately, however, this issue is not clearly settled down in that two experiments exist, which apparently look in discrepancy. That is, Appourchaux et al.~(2000 looked at bin-to-bin correlation and found no evidence that the assumption is invalid. On the other hand, Roth (2001 reported that p-mode pairs with nearby frequencies tend to be anti-correlated, possibly by a mode-coupling effect. This work is motivated by an idea that one may test if there exists an excess of anticorrelated power variations of pairs of solar p-modes. We have analyzed a 72-day MDI spherical-harmonic time series to examine temporal variations of p-mode power and their correlation. The power variation is computed by a running-window method after the previous study by Roth (2001, and then distribution function of power correlation between mode pairs is produced. We have confirmed Roth's result that there is an excess of anti-correlated p-mode pairs with nearby frequencies. On the other hand, the amount of excess was somewhat smaller than the previous study. Moreover, the distribution function does not exhibit significant change when we paired modes with non-nearby frequencies, implying that the excess is not due to mode coupling. We conclude that the origin of this excess of anticorrelations may not be a solar physical process, by pointing out the possibility of statistical bias playing the central role in producing the excess.

The functionality of biological knowledge in the workplace. Integrating school and workplace learning about reproduction

NARCIS (Netherlands)

Mazereeuw, M.

2013-01-01

This thesis reports on a design research project about a learning, supervising and teaching strategy to enable students in agricultural preparatory vocational secondary education (VMBO) to recognize the functionality of biological knowledge of reproduction in work placement sites. Although

Expanding Pseudorandom Functions

DEFF Research Database (Denmark)

Damgård, Ivan Bjerre; Nielsen, Jesper Buus

2002-01-01

Given any weak pseudorandom function, we present a general and efficient technique transforming such a function to a new weak pseudorandom function with an arbitrary length output. This implies, among other things, an encryption mode for block ciphers. The mode is as efficient as known (and widely...... used) encryption modes as CBC mode and counter (CTR) mode, but is provably secure against chosen-plaintext attack (CPA) already if the underlying symmetric cipher is secure against known-plaintext attack (KPA). We prove that CBC, CTR and Jutla’s integrity aware modes do not have this property....... In particular, we prove that when using a KPA secure block cipher, then: CBC mode is KPA secure, but need not be CPA secure, Jutla’s modes need not be CPA secure, and CTR mode need not be even KPA secure. The analysis is done in a concrete security framework....

Modelling life trajectories and mode choice using Bayesian belief networks

NARCIS (Netherlands)

Verhoeven, M.

2010-01-01

Traditionally, transport mode choice was primarily examined as a stand alone problem. Given a purpose and destination, the choice of transport mode was modelled as a function of the various attributes of the transport mode alternatives. Later, transport mode choice decisions were modelled as part of

Analysis of Unsteady Propagation of Mode Ⅲ Crack in Arbitrary Direction in Functionally Graded Materials

Energy Technology Data Exchange (ETDEWEB)

Lee, Kwang Ho [Kyungpook National University, Daegu (Korea, Republic of); Cho, Sang Bong [Kyungnam University, Changwon (Korea, Republic of); Hawong, Jai Sug [Yeungnam University, Gyungsan (Korea, Republic of)

2015-02-15

The stress and displacement fields at the crack tip were studied during the unsteady propagation of a mode Ⅲ crack in a direction that was different from the property graduation direction in functionally graded materials (FGMs). The property graduation in FGMs was assumed based on the linearly varying shear modulus under a constant density and the exponentially varying shear modulus and density. To obtain the solution of the harmonic function, the general partial differential equation of the dynamic equilibrium equation was transformed into a Laplace equation. Based on the Laplace equation, the stress and displacement fields, which depended on the time rates of change in the crack tip speed and stress intensity factor, were obtained through an asymptotic analysis. Using the stress and displacement fields, the effects of the angled property variation on the stresses, displacements, and stress intensity factors are discussed.

Fused-fiber-based 3-dB mode insensitive power splitters for few-mode optical fiber networks

Science.gov (United States)

Ren, Fang; Huang, Xiaoshan; Wang, Jianping

2017-11-01

We propose a 3-dB mode insensitive power splitter (MIPS) capable of broadcasting and combining optical signals. It is fabricated with two identical few-mode fibers (FMFs) by a heating and pulling technique. The mode-dependent power transfer characteristic as a function of pulling length is investigated. For exploiting its application, we experimentally demonstrate both FMF-based transmissive and reflective star couplers consisting of multiple 3-dB mode insensitive power splitters, which perform broadcasting and routing signals in few-mode optical fiber networks such as mode-division multiplexing (MDM) local area networks using star topology. For experimental demonstration, optical on-off keying signals at 10 Gb/s carried on three spatial modes are successfully processed with open and clear eye diagrams. Measured bit error ratio results show reasonable power penalties. It is found that a reflective star coupler in MDM networks can reduce half of the total amount of required fibers comparing to that of a transmissive star coupler. This MIPS is more efficient, more reliable, more flexible, and more cost-effective for future expansion and application in few-mode optical fiber networks.

On the functional significance of retrieval mode: Task switching disrupts the recollection of conceptual stimulus information from episodic memory.

Science.gov (United States)

Küper, Kristina

2018-01-01

Episodic memory retrieval is assumed to be associated with the tonic cognitive state of retrieval mode. Despite extensive research into the neurophysiological correlates of retrieval mode, as of yet, relatively little is known about its functional significance. The present event-related potential (ERP) study was aimed at examining the impact of retrieval mode on the specificity of memory content retrieved in the course of familiarity and recollection processes. In two experiments, participants performed a recognition memory inclusion task in which they had to distinguish identically repeated and re-colored versions of study items from new items. In Experiment 1, participants had to alternate between the episodic memory task and a semantic task requiring a natural/artificial decision. In Experiment 2, the two tasks were instead performed in separate blocks. ERPs locked to the preparatory cues in the test phases indicated that participants did not establish retrieval mode on switch trials in Experiment 1. In the absence of retrieval mode, neither type of studied item elicited ERP correlates of familiarity-based retrieval (FN400). Recollection-related late positive complex (LPC) old/new effects emerged only for identically repeated but not for conceptually identical but perceptually changed versions of study items. With blocked retrieval in Experiment 2, both types of old items instead elicited equivalent FN400 and LPC old/new effects. The LPC data indicate that retrieval mode may play an important role in the successful recollection of conceptual stimulus information. The FN400 results additionally suggest that task switching may have a detrimental effect on familiarity-based memory retrieval. Copyright © 2017 Elsevier B.V. All rights reserved.

Examining the Modes Malware Suppliers Use to Provide Goods and Services

Directory of Open Access Journals (Sweden)

Tony Bailetti

2016-02-01

Full Text Available Malware suppliers use various modes to provide goods and services to customers. By mode, we mean “the way” the malware supplier chooses to function. These modes increase monetization opportunities and enable many security breaches worldwide. A theoretically sound framework that can be used to examine the various modes that malware suppliers use to produce and sell malware is needed. We apply a general model specified recently by Hagiu and Wright to study five modes that malware suppliers use to deliver goods and services to their customers. The framework presented in this article can be used to predict the mode in which a malware supplier will function; to study which types of malware suppliers, agents, and customers are attracted to each mode; to discover new modes; and to better understand the threat a malware supplier presents.

PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways

OpenAIRE

Mi, Huaiyu; Guo, Nan; Kejariwal, Anish; Thomas, Paul D.

2006-01-01

PANTHER is a freely available, comprehensive software system for relating protein sequence evolution to the evolution of specific protein functions and biological roles. Since 2005, there have been three main improvements to PANTHER. First, the sequences used to create evolutionary trees are carefully selected to provide coverage of phylogenetic as well as functional information. Second, PANTHER is now a member of the InterPro Consortium, and the PANTHER hidden markov Models (HMMs) are distri...

Socio-sexuality and episodic memory function in women: further evidence of an adaptive "mating mode".

Science.gov (United States)

Smith, David S; Jones, Benedict C; Allan, Kevin

2013-08-01

The functionalist memory perspective predicts that information of adaptive value may trigger specific processing modes. It was recently demonstrated that women's memory is sensitive to cues of male sexual dimorphism (i.e., masculinity) that convey information of adaptive value for mate choice because they signal health and genetic quality, as well as personality traits important in relationship contexts. Here, we show that individual differences in women's mating strategies predict the effect of facial masculinity cues upon memory, strengthening the case for functional design within memory. Using the revised socio-sexual orientation inventory, Experiment 1 demonstrates that women pursuing a short-term, uncommitted mating strategy have enhanced source memory for men with exaggerated versus reduced masculine facial features, an effect that reverses in women who favor long-term committed relationships. The reversal in the direction of the effect indicates that it does not reflect the sex typicality of male faces per se. The same pattern occurred within women's source memory for women's faces, implying that the memory bias does not reflect the perceived attractiveness of faces per se. In Experiment 2, we reran the experiment using men's faces to establish the reliability of the core finding and replicated Experiment 1's results. Masculinity cues may therefore trigger a specific mode within women's episodic memory. We discuss why this mode may be triggered by female faces and its possible role in mate choice. In so doing, we draw upon the encoding specificity principle and the idea that episodic memory limits the scope of stereotypical inferences about male behavior.

A dual-mode nanosensor based on carbon quantum dots and gold nanoparticles for discriminative detection of glutathione in human plasma.

Science.gov (United States)

Shi, Yupeng; Pan, Yi; Zhang, Heng; Zhang, Zhaomin; Li, Mei-Jin; Yi, Changqing; Yang, Mengsu

2014-06-15

Glutathione (GSH) plays key roles in biological systems and serves many cellular functions. Since biothiols all incorporate thiol, carboxylic and amino groups, discriminative detection of GSH over cysteine (Cys) and homocysteine (Hcy) is still challenging. We herein report a dual-mode nanosensor with both colorimetric and fluorometric readout based on carbon quantum dots and gold nanoparticles for discriminative detection of GSH over Cys/Hcy. The proposed sensing system consists of AuNPs and fluorescent carbon quantum dots (CQDs), where CQDs function as fluorometric reporter, and AuNPs serve a dual function as colorimetric reporter and fluorescence quencher. The mechanism of the nanosensor is based on two distance-dependent phenomenons, color change of AuNPs and FRET. Through controlling the surface properties of as-prepared nanoparticles, the addition of CQDs into AuNPs colloid solution might induce the aggregation of AuNPs and CQDs, leading to AuNPs color changing from red to blue and CQDs fluorescence quench. However, the presence of GSH can protect AuNPs from being aggregated and enlarge the inter-particle distance, which subsequently produces color change and fluorescent signal recovery. The nanosensor described in this report reflects on its simplicity and flexibility, where no further surface functionalization is required for the as-prepared nanoparticles, leading to less laborious and more cost-effective synthesis. The proposed dual-mode nanosensor demonstrated highly selectivity toward GSH, and allows the detection of GSH as low as 50 nM. More importantly, the nanosensor could not only function in aqueous solution for GSH detection with high sensitivity but also exhibit sensitive responses toward GSH in complicated biological environments, demonstrating its potential in bioanalysis and biodection, which might be significant in disease diagnosis in the future. Copyright © 2014 Elsevier B.V. All rights reserved.

Nonlinear mode coupling in rotating stars and the r-mode instability in neutron stars

International Nuclear Information System (INIS)

Schenk, A.K.; Arras, P.; Flanagan, E.E.; Teukolsky, S.A.; Wasserman, I.

2002-01-01

We develop the formalism required to study the nonlinear interaction of modes in rotating Newtonian stars, assuming that the mode amplitudes are only mildly nonlinear. The formalism is simpler than previous treatments of mode-mode interactions for spherical stars, and simplifies and corrects previous treatments for rotating stars. At linear order, we elucidate and extend slightly a formalism due to Schutz, show how to decompose a general motion of a rotating star into a sum over modes, and obtain uncoupled equations of motion for the mode amplitudes under the influence of an external force. Nonlinear effects are added perturbatively via three-mode couplings, which suffices for moderate amplitude modal excitations; the formalism is easy to extend to higher order couplings. We describe a new, efficient way to compute the modal coupling coefficients, to zeroth order in the stellar rotation rate, using spin-weighted spherical harmonics. The formalism is general enough to allow computation of the initial trends in the evolution of the spin frequency and differential rotation of the background star. We apply this formalism to derive some properties of the coupling coefficients relevant to the nonlinear interactions of unstable r modes in neutron stars, postponing numerical integrations of the coupled equations of motion to a later paper. First, we clarify some aspects of the expansion in stellar rotation frequency Ω that is often used to compute approximate mode functions. We show that, in zero-buoyancy stars, the rotational modes (those modes whose frequencies vanish as Ω→0) are orthogonal to zeroth order in Ω. From an astrophysical viewpoint, the most interesting result of this paper is that many couplings of r modes to other rotational modes are small: either they vanish altogether because of various selection rules, or they vanish to lowest order in Ω or in compressibility. In particular, in zero-buoyancy stars, the coupling of three r modes is forbidden

Structure and function in biology

International Nuclear Information System (INIS)

Hirs, C.H.W.

1976-01-01

A summary is given of the history of the developments of structural chemistry in biology beginning with the work of the bacteriologist Ehrlich leading to a comprehensive examination of the influence of size and configuration on the interaction between specific antibodies and side-chain determinants. Recent developments include the recognition of a higher order of specificity in the interaction of proteins with one another

Real-Time Detection of Staphylococcus Aureus Using Whispering Gallery Mode Optical Microdisks

Directory of Open Access Journals (Sweden)

Hala Ghali

2016-05-01

Full Text Available Whispering Gallery Mode (WGM microresonators have recently been studied as a means to achieve real-time label-free detection of biological targets such as virus particles, specific DNA sequences, or proteins. Due to their high quality (Q factors, WGM resonators can be highly sensitive. A biosensor also needs to be selective, requiring proper functionalization of its surface with the appropriate ligand that will attach the biomolecule of interest. In this paper, WGM microdisks are used as biosensors for detection of Staphylococcus aureus. The microdisks are functionalized with LysK, a phage protein specific for staphylococci at the genus level. A binding event on the surface shifts the resonance peak of the microdisk resonator towards longer wavelengths. This reactive shift can be used to estimate the surface density of bacteria that bind to the surface of the resonator. The limit of detection of a microdisk with a Q-factor around 104 is on the order of 5 pg/mL, corresponding to 20 cells. No binding of Escherichia coli to the resonators is seen, supporting the specificity of the functionalization scheme.

A new integrative model of cerebral activation, deactivation and default mode function in Alzheimer's disease

Energy Technology Data Exchange (ETDEWEB)

Wermke, Marc [Technische Universitaet, Department of Nuclear Medicine, Munich (Germany); Technische Universitaet Muenchen, Nuklearmedizinische Klinik u. Poliklinik, Klinikum rechts der Isar, Muenchen (Germany); Sorg, Christian [Technische Universitaet, Department of Psychiatry and Psychotherapy, Munich (Germany); Wohlschlaeger, Afra M. [Technische Universitaet, Departments of Neuroradiology and Neurology, Munich (Germany); Drzezga, Alexander [Technische Universitaet, Department of Nuclear Medicine, Munich (Germany)

2008-03-15

Functional imaging methods such as positron emission tomography (PET) and functional magnetic resonance imaging (fMRI) allow in vivo assessment of cerebral metabolism at rest and cerebral responses to cognitive stimuli. Activation studies with different cognitive tasks have deepened the understanding of underlying pathology leading to Alzheimer disease (AD) and how the brain reacts to and potentially compensates the imposed damage inflicted by this disease. The aim of this manuscript study was to summarize current findings of activation studies in healthy people at risk for AD, in people with mild cognitive impairment (MCI) as a possible progenitor of AD and finally in patients with manifest AD, adding recent results about impaired deactivation abilities and default mode function in AD. A new comprehensive model will be introduced integrating these heterogeneous findings and explaining their impact on cognitive performance. (orig.)

Modeling Operating Modes for the Monju Nuclear Power Plant

DEFF Research Database (Denmark)

Lind, Morten; Yoshikawa, H.; Jørgensen, Sten Bay

2012-01-01

of the process plant, its function and its structural elements. The paper explains how the means-end concepts of MFM can be used to provide formalized definitions of plant operation modes. The paper will introduce the mode types defined by MFM and show how selected operation modes can be represented...

Biological assessment of aquaculture effects on effluent-receiving streams in Ghana using structural and functional composition of fish and macroinvertebrate assemblages.

Science.gov (United States)

Ansah, Yaw Boamah; Frimpong, Emmanuel A; Amisah, Stephen

2012-07-01

Biological assessment of aquatic ecosystems is widely employed as an alternative or complement to chemical and toxicity testing due to numerous advantages of using biota to determine ecosystem condition. These advantages, especially to developing countries, include the relatively low cost and technical requirements. This study was conducted to determine the biological impacts of aquaculture operations on effluent-receiving streams in the Ashanti Region of Ghana. We collected water, fish and benthic macroinvertebrate samples from 12 aquaculture effluent-receiving streams upstream and downstream of fish farms and 12 reference streams between May and August of 2009, and then calculated structural and functional metrics for biotic assemblages. Fish species with non-guarding mode of reproduction were more abundant in reference streams than downstream (P = 0.0214) and upstream (P = 0.0251), and sand-detritus spawning fish were less predominant in reference stream than upstream (P = 0.0222) and marginally less in downstream locations (P = 0.0539). A possible subsidy-stress response of macroinvertebrate family richness and abundance was also observed, with nutrient (nitrogen) augmentation from aquaculture and other farming activities likely. Generally, there were no, or only marginal differences among locations downstream and upstream of fish farms and in reference streams in terms of several other biotic metrics considered. Therefore, the scale of impact in the future will depend not only on the management of nutrient augmentation from pond effluents, but also on the consideration of nutrient discharges from other industries like fruit and vegetable farming within the study area.

Biological radiation effects and radioprotection standards

International Nuclear Information System (INIS)

Clerc, H.

1991-03-01

In this report, after recalling the mode of action of ionizing radiations, the notions of dose, dose equivalents and the values of natural irradiation, the author describes the biological radiation effects. Then he presents the ICRP recommendations and their applications to the french radioprotection system

Preserved functional connectivity in the default mode and salience networks is associated with youthful memory in superaging

OpenAIRE

Barrett, Lisa; Zhang, Jiahe; Andreano, Joseph; Dickerson, Bradford; Touroutoglou, Alexandra

2018-01-01

'Superagers' are older adults who, despite their advanced age, maintain youthful memory. Previous morphometry studies revealed multiple default mode network (DMN) and salience network (SN) regions whose cortical thickness is preserved in superagers and correlates with memory performance. In this study, we examined the intrinsic functional connectivity within DMN and SN in 41 young (24.5 ± 3.6 years old) and 40 elderly adults (66.9 ± 5.5 years old). As in prior studies, superaging was defined ...

High-frequency dual mode pulsed wave Doppler imaging for monitoring the functional regeneration of adult zebrafish hearts

OpenAIRE

Kang, Bong Jin; Park, Jinhyoung; Kim, Jieun; Kim, Hyung Ham; Lee, Changyang; Hwang, Jae Youn; Lien, Ching-Ling; Shung, K. Kirk

2015-01-01

Adult zebrafish is a well-known small animal model for studying heart regeneration. Although the regeneration of scars made by resecting the ventricular apex has been visualized with histological methods, there is no adequate imaging tool for tracking the functional recovery of the damaged heart. For this reason, high-frequency Doppler echocardiography using dual mode pulsed wave Doppler, which provides both tissue Doppler (TD) and Doppler flow in a same cardiac cycle, is developed with a 30 ...

Large scale fusion of gray matter and resting-state functional MRI reveals common and shared biological markers across the psychosis spectrum in the B-SNIP cohort

Directory of Open Access Journals (Sweden)

Zheng eWang

2015-12-01

Full Text Available To investigate whether aberrant interactions between brain structure and function present similarly or differently across probands with psychotic illnesses (schizophrenia (SZ, schizoaffective disorder (SAD, and bipolar I disorder with psychosis (BP and whether these deficits are shared with their first-degree non-psychotic relatives. A total of 1199 subjects were assessed, including 220 SZ, 147 SAD, 180 psychotic BP, 150 first-degree relatives of SZ, 126 SAD relatives, 134 BP relatives and 242 healthy controls. All subjects underwent structural MRI (sMRI and resting-state functional MRI (rs-fMRI scanning. Joint independent analysis (jICA was used to fuse sMRI gray matter (GM and rs-fMRI amplitude of low frequency fluctuations (ALFF data to identify the relationship between the two modalities. Joint ICA revealed two significantly fused components. The association between functional brain alteration in a prefrontal-striatal-thalamic-cerebellar network and structural abnormalities in the default mode network (DMN was found to be common across psychotic diagnoses and correlated with cognitive function, social function and Schizo-Bipolar Scale (SBS scores. The fused alteration in the temporal lobe was unique to SZ and SAD. The above effects were not seen in any relative group (including those with cluster-A personality. Using a multivariate fused approach involving two widely used imaging markers we demonstrate both shared and distinct biological traits across the psychosis spectrum. Further, our results suggest that the above traits are psychosis biomarkers rather than endophenotypes.

Late-stage diversification of biologically active pyridazinones via a direct C-H functionalization strategy.

Science.gov (United States)

Li, Wei; Fan, Zhoulong; Geng, Kaijun; Xu, Youjun; Zhang, Ao

2015-01-14

Divergent C-H functionalization reactions (arylation, carboxylation, olefination, thiolation, acetoxylation, halogenation, naphthylation) using a pyridazinone moiety as an internal directing group were successfully established. This approach offers a late-stage, ortho-selective diversification of a biologically active pyridazinone scaffold. Seven series of novel pyridazinone analogues were synthesized conveniently as the synthetic precursors of potential sortase A (SrtA) inhibitors.

Reconfigurable Mixed Mode Universal Filter

Directory of Open Access Journals (Sweden)

Neelofer Afzal

2014-01-01

Full Text Available This paper presents a novel mixed mode universal filter configuration capable of working in voltage and transimpedance mode. The proposed single filter configuration can be reconfigured digitally to realize all the five second order filter functions (types at single output port. Other salient features of proposed configuration include independently programmable filter parameters, full cascadability, and low sensitivity figure. However, all these features are provided at the cost of quite large number of active elements. It needs three digitally programmable current feedback amplifiers and three digitally programmable current conveyors. Use of six active elements is justified by introducing three additional reduced hardware mixed mode universal filter configurations and its comparison with reported filters.

Biological warfare agents

Directory of Open Access Journals (Sweden)

Duraipandian Thavaselvam

2010-01-01

Full Text Available The recent bioterrorist attacks using anthrax spores have emphasized the need to detect and decontaminate critical facilities in the shortest possible time. There has been a remarkable progress in the detection, protection and decontamination of biological warfare agents as many instrumentation platforms and detection methodologies are developed and commissioned. Even then the threat of biological warfare agents and their use in bioterrorist attacks still remain a leading cause of global concern. Furthermore in the past decade there have been threats due to the emerging new diseases and also the re-emergence of old diseases and development of antimicrobial resistance and spread to new geographical regions. The preparedness against these agents need complete knowledge about the disease, better research and training facilities, diagnostic facilities and improved public health system. This review on the biological warfare agents will provide information on the biological warfare agents, their mode of transmission and spread and also the detection systems available to detect them. In addition the current information on the availability of commercially available and developing technologies against biological warfare agents has also been discussed. The risk that arise due to the use of these agents in warfare or bioterrorism related scenario can be mitigated with the availability of improved detection technologies.

Biological warfare agents

Science.gov (United States)

Thavaselvam, Duraipandian; Vijayaraghavan, Rajagopalan

2010-01-01

The recent bioterrorist attacks using anthrax spores have emphasized the need to detect and decontaminate critical facilities in the shortest possible time. There has been a remarkable progress in the detection, protection and decontamination of biological warfare agents as many instrumentation platforms and detection methodologies are developed and commissioned. Even then the threat of biological warfare agents and their use in bioterrorist attacks still remain a leading cause of global concern. Furthermore in the past decade there have been threats due to the emerging new diseases and also the re-emergence of old diseases and development of antimicrobial resistance and spread to new geographical regions. The preparedness against these agents need complete knowledge about the disease, better research and training facilities, diagnostic facilities and improved public health system. This review on the biological warfare agents will provide information on the biological warfare agents, their mode of transmission and spread and also the detection systems available to detect them. In addition the current information on the availability of commercially available and developing technologies against biological warfare agents has also been discussed. The risk that arise due to the use of these agents in warfare or bioterrorism related scenario can be mitigated with the availability of improved detection technologies. PMID:21829313

Geometric phase due to orbit-orbit interaction: rotating LP11 modes in a two-mode fiber

Science.gov (United States)

Pradeep Chakravarthy, T.; Naik, Dinesh N.; Viswanathan, Nirmal K.

2017-10-01

Accumulation of geometric phase due to non-coplanar propagation of higher-order modes in an optical fiber is experimentally demonstrated. Vertically-polarized LP11 fiber mode, excited in a horizontally-held, torsion-free, step-index, two-mode optical fiber, rotates due to asymmetry in the propagating k-vectors, arising due to off-centered beam location at the fiber input. Perceiving the process as due to rotation of the fiber about the off-axis launch position, the orbital Berry phase accumulation upon scanning the launch position in a closed-loop around the fiber axis manifests as rotational Doppler effect, a consequence of orbit-orbit interaction. The anticipated phase accumulation as a function of the input launch position, observed through interferometry is connected to the mode rotation angle, quantified using the autocorrelation method.

Functional MRI Assessment of Task-Induced Deactivation of the Default Mode Network in Alzheimer?s Disease and At-Risk Older Individuals

OpenAIRE

Pihlajam?ki, Maija; Sperling, Reisa A.

2009-01-01

Alzheimer’s disease (AD) is the most common form of dementia in old age, and is characterized by prominent impairment of episodic memory. Recent functional imaging studies in AD have demonstrated alterations in a distributed network of brain regions supporting memory function, including regions of the default mode network. Previous positron emission tomography studies of older individuals at risk for AD have revealed hypometabolism of association cortical regions similar to the metabolic abno...

Renormalized modes in cuprate superconductors

Science.gov (United States)

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

2018-04-01

The renormalized mode frequencies are obtained with the help of quantum dynamical approach of many body phonon Green's function technique via a general Hamiltonian (excluding BCS Hamiltonian) including the effects of phonons and electrons, anharmonicities and electron-phonon interactions. The numerical estimates have been carried out to study the renormalized mode frequency of high temperature cuprate superconductor (HTS) YBa2Cu3O7-δ using modified Born-Mayer-Huggins interaction potential (MBMHP) best applicable to study the dynamical properties of all HTS.

Trapped Mode Study in the LHC Rotatable Collimator

CERN Document Server

Xiao, L; Smith, J C; Caspers, F

2010-01-01

A rotatable collimator is proposed for the LHC phase II collimation upgrade. When the beam crosses the collimator, trapped modes will be excited that result in beam energy loss and collimator power dissipation. Some of the trapped modes can also generate transverse kick on the beam and affect the beam operation. In this paper the parallel eigensolver code Omega3P is used to search for all the trapped modes below 2GHz in the collimator, including longitudinal modes and transverse modes. The loss factors and kick factors of the trapped modes are calculated as function of the jaw positions. The amplitude ratio between transverse and longitudinal trapped mode intensity can be used as a direct measure of the position of the beam. We present simulation results and discuss the results.

Impurity modes in the one-dimensional XXZ Heisenberg model

International Nuclear Information System (INIS)

Sousa, J.M.; Leite, R.V.; Landim, R.R.; Costa Filho, R.N.

2014-01-01

A Green's function formalism is used to calculate the energy of impurity modes associated with one and/or two magnetic impurities in the one-dimensional Heisenberg XXZ magnetic chain. The system can be tuned from the Heisenberg to the Ising model varying a parameter λ. A numerical study is performed showing two types of localized modes (s and p). The modes depend on λ and the degeneracy of the acoustic modes is broken.

Assessment of intraoperative oxygenation function and trauma degree of PCV-VG and VCV mode for elderly patients with laparoscopic abdominal surgery

Directory of Open Access Journals (Sweden)

Jun Pu

2017-03-01

Full Text Available Objective: To study the intraoperative oxygenation function and trauma degree of pressurecontrolled ventilation-volume guaranteed (PCV-VG and volume-controlled ventilation (VCV mode for elderly patients with laparoscopic abdominal surgery. Methods: 60 elderly patients with laparoscopic abdominal surgery were selected for study and randomly divided into two groups (n=30, group A received ventilation in accordance with sequential VCV-PCV-VG mode, group B received ventilation in accordance with the sequential PCV-VG-VCV mode, and the respiratory function parameters and arterial blood gas parameters and serum damage indexes were determined before the start of pneumoperitoneum (T0, 1 h after the start of the first ventilation mode after the start of pneumoperitoneum (T1, 1 h after the switch of ventilation mode (T2 and after the end of pneumoperitoneum (T3. Results: At T1, Ppeak, mean airway pressure (Pmean and plateau airway pressure (Pplant of group A were significantly higher than those of group B (P<0.05, partial pressure of oxygen (PaO2 was significantly lower than that of group B (P<0.05, and pulse oxygen saturation (SpO2 and partial pressure of carbon dioxide (PaCO2 were not significantly different from those of group B; at T2 and T3, Ppeak, Pmean and Pplant of group A were significantly lower than those of group B (P<0.05, PaO2 were significantly lower than those of group B (P<0.05, and SpO2 and PaCO2 were not significantly different from those of group B. At T1, serum soluble receptor for advanced glycation endproduct (sRAGE, KL-6 (krebs. von den Iungen-6, tumor necrosis factor-α (TNF-α and malondialdehyde (MDA content of group A were significantly higher than those of group B (P<0.05; at T3, serum sRAGE, KL-6, TNF-α and MDA content of group A were significantly lower than those of group B (P<0.05. Conclusions: PCV-VG mode for elderly patients with laparoscopic abdominal surgery can reduce airway pressure, improve lung compliance and

Functional soil microbial diversity across Europe estimated by EEA, MicroResp and BIOLOG

DEFF Research Database (Denmark)

Winding, Anne; Rutgers, Michiel; Creamer, Rachel

consisting of 81 soil samples covering five Biogeograhical Zones and three land-uses in order to test the sensitivity, ease and cost of performance and biological significance of the data output. The techniques vary in how close they are to in situ functions; dependency on growth during incubation......Soil microorganisms are abundant and essential for the bio-geochemical processes of soil, soil quality and soil ecosystem services. All this is dependent on the actual functions the microbial communities are performing in the soil. Measuring soil respiration has for many years been the basis...... of estimating soil microbial activity. However, today several techniques are in use for determining microbial functional diversity and assessing soil biodiversity: Methods based on CO2 development by the microbes such as substrate induced respiration (SIR) on specific substrates have lead to the development...

Altered functional connectivity of the default mode network in Williams syndrome: a multimodal approach.

Science.gov (United States)

Sampaio, Adriana; Moreira, Pedro Silva; Osório, Ana; Magalhães, Ricardo; Vasconcelos, Cristiana; Férnandez, Montse; Carracedo, Angel; Alegria, Joana; Gonçalves, Óscar F; Soares, José Miguel

2016-07-01

Resting state brain networks are implicated in a variety of relevant brain functions. Importantly, abnormal patterns of functional connectivity (FC) have been reported in several neurodevelopmental disorders. In particular, the Default Mode Network (DMN) has been found to be associated with social cognition. We hypothesize that the DMN may be altered in Williams syndrome (WS), a neurodevelopmental genetic disorder characterized by an unique cognitive and behavioral phenotype. In this study, we assessed the architecture of the DMN using fMRI in WS patients and typically developing matched controls (sex and age) in terms of FC and volumetry of the DMN. Moreover, we complemented the analysis with a functional connectome approach. After excluding participants due to movement artifacts (n = 3), seven participants with WS and their respective matched controls were included in the analyses. A decreased FC between the DMN regions was observed in the WS group when compared with the typically developing group. Specifically, we found a decreased FC in a posterior hub of the DMN including the precuneus, calcarine and the posterior cingulate of the left hemisphere. The functional connectome approach showed a focalized and global increased FC connectome in the WS group. The reduced FC of the posterior hub of the DMN in the WS group is consistent with immaturity of the brain FC patterns and may be associated with the singularity of their visual spatial phenotype. © 2016 John Wiley & Sons Ltd.

Cognition from life: the two modes of cognition that underlie moral behavior

Directory of Open Access Journals (Sweden)

Tjeerd C Andringa

2015-04-01

Full Text Available We argue that the capacity to live life to the benefit of self and others originates in the defining properties of life. These lead to two modes of cognition; the coping mode that is preoccupied with the satisfaction of pressing needs and the co-creation mode that aims at the realization of a world where pressing needs occur less frequently. We have used the Rule of Conservative Changes – stating that new functions can only scaffold on evolutionary older, yet highly stable functions – to predict that the interplay of these two modes define a number of core functions in psychology associated with moral behavior. We explore this prediction with five examples reflecting different theoretical approaches to human cognition and action selection. We conclude the paper with the observation that science is currently dominated by the coping mode and that the benefits of the co-creation mode may be necessary to generate realistic prospects for a modern synthesis in the sciences of the mind.

Cognition from life: the two modes of cognition that underlie moral behavior.

Science.gov (United States)

Andringa, Tjeerd C; Bosch, Kirsten A Van Den; Wijermans, Nanda

2015-01-01

We argue that the capacity to live life to the benefit of self and others originates in the defining properties of life. These lead to two modes of cognition; the coping mode that is preoccupied with the satisfaction of pressing needs and the co-creation mode that aims at the realization of a world where pressing needs occur less frequently. We have used the Rule of Conservative Changes - stating that new functions can only scaffold on evolutionary older, yet highly stable functions - to predict that the interplay of these two modes define a number of core functions in psychology associated with moral behavior. We explore this prediction with five examples reflecting different theoretical approaches to human cognition and action selection. We conclude the paper with the observation that science is currently dominated by the coping mode and that the benefits of the co-creation mode may be necessary to generate realistic prospects for a modern synthesis in the sciences of the mind.

New modes of assisted mechanical ventilation.

Science.gov (United States)

Suarez-Sipmann, F

2014-05-01

Recent major advances in mechanical ventilation have resulted in new exciting modes of assisted ventilation. Compared to traditional ventilation modes such as assisted-controlled ventilation or pressure support ventilation, these new modes offer a number of physiological advantages derived from the improved patient control over the ventilator. By implementing advanced closed-loop control systems and using information on lung mechanics, respiratory muscle function and respiratory drive, these modes are specifically designed to improve patient-ventilator synchrony and reduce the work of breathing. Depending on their specific operational characteristics, these modes can assist spontaneous breathing efforts synchronically in time and magnitude, adapt to changing patient demands, implement automated weaning protocols, and introduce a more physiological variability in the breathing pattern. Clinicians have now the possibility to individualize and optimize ventilatory assistance during the complex transition from fully controlled to spontaneous assisted ventilation. The growing evidence of the physiological and clinical benefits of these new modes is favoring their progressive introduction into clinical practice. Future clinical trials should improve our understanding of these modes and help determine whether the claimed benefits result in better outcomes. Copyright © 2013 Elsevier España, S.L. and SEMICYUC. All rights reserved.

TALE factors use two distinct functional modes to control an essential zebrafish gene expression program.

Science.gov (United States)

Ladam, Franck; Stanney, William; Donaldson, Ian J; Yildiz, Ozge; Bobola, Nicoletta; Sagerström, Charles G

2018-06-18

TALE factors are broadly expressed embryonically and known to function in complexes with transcription factors (TFs) like Hox proteins at gastrula/segmentation stages, but it is unclear if such generally expressed factors act by the same mechanism throughout embryogenesis. We identify a TALE-dependent gene regulatory network (GRN) required for anterior development and detect TALE occupancy associated with this GRN throughout embryogenesis. At blastula stages, we uncover a novel functional mode for TALE factors, where they occupy genomic DECA motifs with nearby NF-Y sites. We demonstrate that TALE and NF-Y form complexes and regulate chromatin state at genes of this GRN. At segmentation stages, GRN-associated TALE occupancy expands to include HEXA motifs near PBX:HOX sites. Hence, TALE factors control a key GRN, but utilize distinct DNA motifs and protein partners at different stages - a strategy that may also explain their oncogenic potential and may be employed by other broadly expressed TFs. © 2018, Ladam et al.

Modeling Operating Modes during Plant Life Cycle

DEFF Research Database (Denmark)

Jørgensen, Sten Bay; Lind, Morten

2012-01-01

Modelling process plants during normal operation requires a set a basic assumptions to define the desired functionalities which lead to fullfillment of the operational goal(-s) for the plant. However during during start-up and shut down as well as during batch operation an ensemble of interrelated...... modes are required to cover the whole operational window of a processs plant including intermediary operating modes. Development of such an model ensemble for a plant would constitute a systematic way of defining the possible plant operating modes and thus provide a platform for also defining a set...... of candidate control structures. The present contribution focuses on development of a model ensemble for a plant with an illustartive example for a bioreactor. Starting from a functional model a process plant may be conceptually designed and qualitative operating models may be developed to cover the different...

The emerging molecular biology toolbox for the study of long noncoding RNA biology.

Science.gov (United States)

Fok, Ezio T; Scholefield, Janine; Fanucchi, Stephanie; Mhlanga, Musa M

2017-10-01

Long noncoding RNAs (lncRNAs) have been implicated in many biological processes. However, due to the unique nature of lncRNAs and the consequential difficulties associated with their characterization, there is a growing disparity between the rate at which lncRNAs are being discovered and the assignment of biological function to these transcripts. Here we present a molecular biology toolbox equipped to help dissect aspects of lncRNA biology and reveal functionality. We outline an approach that begins with a broad survey of genome-wide, high-throughput datasets to identify potential lncRNA candidates and then narrow the focus on specific methods that are well suited to interrogate the transcripts of interest more closely. This involves the use of imaging-based strategies to validate these candidates and observe the behaviors of these transcripts at single molecule resolution in individual cells. We also describe the use of gene editing tools and interactome capture techniques to interrogate functionality and infer mechanism, respectively. With the emergence of lncRNAs as important molecules in healthy and diseased cellular function, it remains crucial to deepen our understanding of their biology.

A Tricky Trait: Applying the Fruits of the "Function Debate" in the Philosophy of Biology to the "Venom Debate" in the Science of Toxinology.

Science.gov (United States)

Jackson, Timothy N W; Fry, Bryan G

2016-09-07

The "function debate" in the philosophy of biology and the "venom debate" in the science of toxinology are conceptually related. Venom systems are complex multifunctional traits that have evolved independently numerous times throughout the animal kingdom. No single concept of function, amongst those popularly defended, appears adequate to describe these systems in all their evolutionary contexts and extant variations. As such, a pluralistic view of function, previously defended by some philosophers of biology, is most appropriate. Venom systems, like many other functional traits, exist in nature as points on a continuum and the boundaries between "venomous" and "non-venomous" species may not always be clearly defined. This paper includes a brief overview of the concept of function, followed by in-depth discussion of its application to venom systems. A sound understanding of function may aid in moving the venom debate forward. Similarly, consideration of a complex functional trait such as venom may be of interest to philosophers of biology.

Perchlorate exposure and association with iron homeostasis and other biological functions among NHANES 2005-2008 subjects

Science.gov (United States)

Perchlorate exposure and association with iron homeostasis and other biological functions among NHANES 2005-2008 subjects Schreinemachers DM, Ghio AJ, Cascio WE, Sobus JR. U.S. EPA, RTP, NC, USA Perchlorate (ClO4-), an environmental pollutant, is a known thyroid toxicant and...

Different functional modes of BAR domain proteins in formation and plasticity of mammalian postsynapses.

Science.gov (United States)

Kessels, Michael M; Qualmann, Britta

2015-09-01

A plethora of cell biological processes involve modulations of cellular membranes. By using extended lipid-binding interfaces, some proteins have the power to shape membranes by attaching to them. Among such membrane shapers, the superfamily of Bin-Amphiphysin-Rvs (BAR) domain proteins has recently taken center stage. Extensive structural work on BAR domains has revealed a common curved fold that can serve as an extended membrane-binding interface to modulate membrane topologies and has allowed the grouping of the BAR domain superfamily into subfamilies with structurally slightly distinct BAR domain subtypes (N-BAR, BAR, F-BAR and I-BAR). Most BAR superfamily members are expressed in the mammalian nervous system. Neurons are elaborately shaped and highly compartmentalized cells. Therefore, analyses of synapse formation and of postsynaptic reorganization processes (synaptic plasticity) - a basis for learning and memory formation - has unveiled important physiological functions of BAR domain superfamily members. These recent advances, furthermore, have revealed that the functions of BAR domain proteins include different aspects. These functions are influenced by the often complex domain organization of BAR domain proteins. In this Commentary, we review these recent insights and propose to classify BAR domain protein functions into (1) membrane shaping, (2) physical integration, (3) action through signaling components, and (4) suppression of other BAR domain functions. © 2015. Published by The Company of Biologists Ltd.

Preparation of polymer monolithic column functionalized by arsonic acid groups for mixed-mode capillary liquid chromatography.

Science.gov (United States)

Qin, Zhang-Na; Yu, Qiong-Wei; Wang, Ren-Qi; Feng, Yu-Qi

2018-04-27

A mixed-mode polymer monolithic column functionalized by arsonic acid groups was prepared by single-step in situ copolymerization of monomers p-methacryloylaminophenylarsonic acid (p-MAPHA) and pentaerythritol triacrylate (PETA). The prepared poly(p-MAPHA-co-PETA) monolithic column has a homogeneous monolithic structure with good permeability and mechanical stability. Zeta potential measurements reveal that the monolithic stationary phase holds a negative surface charge when the mobile phase resides in the pH range of 3.0-8.0. The retention mechanisms of prepared monolithic column are explored by the separation of selected polycyclic aromatic hydrocarbons (PAHs), nucleosides, and three basic compounds. The results indicate that the column functions in three different separation modes associated with reversed-phase chromatography based on hydrophobic interaction, hydrophilic interaction chromatography, and cation-exchange chromatography. The column efficiency of prepared monolithic column is estimated to be 70,000 and 76,000 theoretical plates/m for thiourea and naphthalene, respectively, at a linear flow velocity of 0.85 mm/s using acetonitrile/H 2 O (85/15, v/v) as the mobile phase. Furthermore, an analysis of the retention factors obtained for the PAHs indicates that the prepared monolithic column exhibits good reproducibility with relative standard deviations of 2.9%, 4.0%, and 4.7% based on run-to-run injections, column-to-column preparation, and batch-to-batch preparation, respectively. Finally, we investigate the separation performance of the proposed monolithic column for select phenols, sulfonamides, nucleobases and nucleosides. Copyright © 2018 Elsevier B.V. All rights reserved.

Vibrational lifetimes of protein amide modes

International Nuclear Information System (INIS)

Peterson, K.A.; Rella, C.A.

1995-01-01

Measurement of the lifetimes of vibrational modes in proteins has been achieved with a single frequency infrared pump-probe technique using the Stanford Picosecond Free-electron Laser, These are the first direct measurements of vibrational dynamics in the polyamide structure of proteins. In this study, modes associated with the protein backbone are investigated. Results for the amide I band, which consists mainly of the stretching motion of the carbonyl unit of the amide linkage, show that relaxation from the first vibrational excited level (v=1) to the vibrational ground state (v=0) occurs within 1.5 picoseconds with apparent first order kinetics. Comparison of lifetimes for myoglobin and azurin, which have differing secondary structures, show a small but significant difference. The lifetime for the amide I band of myoglobin is 300 femtoseconds shorter than for azurin. Further measurements are in progress on other backbone vibrational modes and on the temperature dependence of the lifetimes. Comparison of vibrational dynamics for proteins with differing secondary structure and for different vibrational modes within a protein will lead to a greater understanding of energy transfer and dissipation in biological systems. In addition, these results have relevance to tissue ablation studies which have been conducted with pulsed infrared lasers. Vibrational lifetimes are necessary for calculating the rate at which the energy from absorbed infrared photons is converted to equilibrium thermal energy within the irradiated volume. The very fast vibrational lifetimes measured here indicate that mechanisms which involve direct vibrational up-pumping of the amide modes with consecutive laser pulses, leading to bond breakage or weakening, are not valid

6d Dirac fermion on a rectangle; scrutinizing boundary conditions, mode functions and spectrum

Directory of Open Access Journals (Sweden)

Yukihiro Fujimoto

2017-09-01

Full Text Available We classify possible boundary conditions of a 6d Dirac fermion Ψ on a rectangle under the requirement that the 4d Lorentz structure is maintained, and derive the profiles and spectrum of the zero modes and nonzero KK modes under the two specific boundary conditions, (i 4d-chirality positive components being zero at the boundaries and (ii internal chirality positive components being zero at the boundaries. In the case of (i, twofold degenerated chiral zero modes appear which are localized towards specific directions of the rectangle pointed by an angle parameter θ. This leads to an implication for a new direction of pursuing the origin of three generations in the matter fields of the standard model, even though triple-degenerated zero modes are not realized in the six dimensions. When such 6d fermions couple with a 6d scalar with a vacuum expectation value, θ contributes to a mass matrix of zero-mode fermions consisting of Yukawa interactions. The emergence of the angle parameter θ originates from a rotational symmetry in the degenerated chiral zero modes on the rectangle extra dimensions since they do not feel the boundaries. In the case of (ii, this rotational symmetry is promoted to the two-dimensional conformal symmetry though no chiral massless zero mode appears. We also discuss the correspondence between our model on a rectangle and orbifold models in some details.

Biology of bone and how it orchestrates the form and function of the skeleton

Science.gov (United States)

Sommerfeldt, D. W.; Rubin, C. T.

2001-01-01

The principal role of the skeleton is to provide structural support for the body. While the skeleton also serves as the body's mineral reservoir, the mineralized structure is the very basis of posture, opposes muscular contraction resulting in motion, withstands functional load bearing, and protects internal organs. Although the mass and morphology of the skeleton is defined, to some extent, by genetic determinants, it is the tissue's ability to remodel--the local resorption and formation of bone--which is responsible for achieving this intricate balance between competing responsibilities. The aim of this review is to address bone's form-function relationship, beginning with extensive research in the musculoskeletal disciplines, and focusing on several recent cellular and molecular discoveries which help understand the complex interdependence of bone cells, growth factors, physical stimuli, metabolic demands, and structural responsibilities. With a clinical and spine-oriented audience in mind, the principles of bone cell and molecular biology and physiology are presented, and an attempt has been made to incorporate epidemiologic data and therapeutic implications. Bone research remains interdisciplinary by nature, and a deeper understanding of bone biology will ultimately lead to advances in the treatment of diseases and injuries to bone itself.

Radioactive probe studies of coordination modes of heavy metal ions from natural waters to functionalized magnetic nanoparticles

CERN Document Server

Carvalho Soares, J; Lopes, C; Araujo, J

We propose to use PAC, Perturbed Angular Correlations, to study the local environment of ionic species (Hg$^{2+}$, Cd$^{2+}$) coordinated on functionalized magnetic nanoparticles. Studies include the analysis of different nanoparticle sizes (30-100nm), and the monitoring of time/steps dependence of the coordination of those cations at the nanoparticle surfaces. Combined with theoretical calculations, the obtained data will support the understanding of local coordination modes, which is essential to help to improve methods of magnetically assisted separation of such hazardous contaminants from water.

Detection of biologically active diterpenoic acids by Raman Spectroscopy

DEFF Research Database (Denmark)

Talian, Ivan; Orinak, Andrej; Efremov, Evtim V.

2010-01-01

Three poorly detectable, biologically active diterpenoic acids, kaurenoic, abietic, and gibberellic acid, were studied by using different modes of Raman spectroscopy. Because of their structural similarities, in the absence of strongly polarizable groups, conventional Raman spectroscopy is not su......Three poorly detectable, biologically active diterpenoic acids, kaurenoic, abietic, and gibberellic acid, were studied by using different modes of Raman spectroscopy. Because of their structural similarities, in the absence of strongly polarizable groups, conventional Raman spectroscopy...... few enhanced Raman lines. SERS spectra with 514-nm excitation with Ag colloids were also relatively weak. The best SERS spectrawere obtained with 785-nm excitation on a novel nanostructured substrate, 'black silicon' coated with a 400-nm gold layer. The spectra showed clear differences...

Default mode network connectivity as a function of familial and environmental risk for psychotic disorder.

Science.gov (United States)

Peeters, Sanne C T; van de Ven, Vincent; Gronenschild, Ed H B M; Patel, Ameera X; Habets, Petra; Goebel, Rainer; van Os, Jim; Marcelis, Machteld

2015-01-01

Research suggests that altered interregional connectivity in specific networks, such as the default mode network (DMN), is associated with cognitive and psychotic symptoms in schizophrenia. In addition, frontal and limbic connectivity alterations have been associated with trauma, drug use and urban upbringing, though these environmental exposures have never been examined in relation to DMN functional connectivity in psychotic disorder. Resting-state functional MRI scans were obtained from 73 patients with psychotic disorder, 83 non-psychotic siblings of patients with psychotic disorder and 72 healthy controls. Posterior cingulate cortex (PCC) seed-based correlation analysis was used to estimate functional connectivity within the DMN. DMN functional connectivity was examined in relation to group (familial risk), group × environmental exposure (to cannabis, developmental trauma and urbanicity) and symptomatology. There was a significant association between group and PCC connectivity with the inferior parietal lobule (IPL), the precuneus (PCu) and the medial prefrontal cortex (MPFC). Compared to controls, patients and siblings had increased PCC connectivity with the IPL, PCu and MPFC. In the IPL and PCu, the functional connectivity of siblings was intermediate to that of controls and patients. No significant associations were found between DMN connectivity and (subclinical) psychotic/cognitive symptoms. In addition, there were no significant interactions between group and environmental exposures in the model of PCC functional connectivity. Increased functional connectivity in individuals with (increased risk for) psychotic disorder may reflect trait-related network alterations. The within-network "connectivity at rest" intermediate phenotype was not associated with (subclinical) psychotic or cognitive symptoms. The association between familial risk and DMN connectivity was not conditional on environmental exposure.

Multilevel functional genomics data integration as a tool for understanding physiology: a network biology perspective.

Science.gov (United States)

Davidsen, Peter K; Turan, Nil; Egginton, Stuart; Falciani, Francesco

2016-02-01

The overall aim of physiological research is to understand how living systems function in an integrative manner. Consequently, the discipline of physiology has since its infancy attempted to link multiple levels of biological organization. Increasingly this has involved mathematical and computational approaches, typically to model a small number of components spanning several levels of biological organization. With the advent of "omics" technologies, which can characterize the molecular state of a cell or tissue (intended as the level of expression and/or activity of its molecular components), the number of molecular components we can quantify has increased exponentially. Paradoxically, the unprecedented amount of experimental data has made it more difficult to derive conceptual models underlying essential mechanisms regulating mammalian physiology. We present an overview of state-of-the-art methods currently used to identifying biological networks underlying genomewide responses. These are based on a data-driven approach that relies on advanced computational methods designed to "learn" biology from observational data. In this review, we illustrate an application of these computational methodologies using a case study integrating an in vivo model representing the transcriptional state of hypoxic skeletal muscle with a clinical study representing muscle wasting in chronic obstructive pulmonary disease patients. The broader application of these approaches to modeling multiple levels of biological data in the context of modern physiology is discussed. Copyright © 2016 the American Physiological Society.

From transcriptome to biological function: environmental stress in an ectothermic vertebrate, the coral reef fish Pomacentrus moluccensis

Directory of Open Access Journals (Sweden)

Ward Alister C

2007-10-01

Full Text Available Abstract Background Our understanding of the importance of transcriptional regulation for biological function is continuously improving. We still know, however, comparatively little about how environmentally induced stress affects gene expression in vertebrates, and the consistency of transcriptional stress responses to different types of environmental stress. In this study, we used a multi-stressor approach to identify components of a common stress response as well as components unique to different types of environmental stress. We exposed individuals of the coral reef fish Pomacentrus moluccensis to hypoxic, hyposmotic, cold and heat shock and measured the responses of approximately 16,000 genes in liver. We also compared winter and summer responses to heat shock to examine the capacity for such responses to vary with acclimation to different ambient temperatures. Results We identified a series of gene functions that were involved in all stress responses examined here, suggesting some common effects of stress on biological function. These common responses were achieved by the regulation of largely independent sets of genes; the responses of individual genes varied greatly across different stress types. In response to heat exposure over five days, a total of 324 gene loci were differentially expressed. Many heat-responsive genes had functions associated with protein turnover, metabolism, and the response to oxidative stress. We were also able to identify groups of co-regulated genes, the genes within which shared similar functions. Conclusion This is the first environmental genomic study to measure gene regulation in response to different environmental stressors in a natural population of a warm-adapted ectothermic vertebrate. We have shown that different types of environmental stress induce expression changes in genes with similar gene functions, but that the responses of individual genes vary between stress types. The functions of heat

Biological control of the cucurbit powdery mildew pathogen Podosphaera xanthii by means of the epiphytic fungus Pseudozyma aphidis and parasitism as a mode of action

Directory of Open Access Journals (Sweden)

Aviva eGafni

2015-03-01

Full Text Available Epiphytic yeasts, which colonize plant surfaces, may possess activity that can be harnessed to help plants defend themselves against various pathogens. Due to their unique characteristics, epiphytic yeasts belonging to the genus Pseudozyma hold great potential for use as biocontrol agents. We identified a unique, biologically active isolate of the epiphytic yeast Pseudozyma aphidis that is capable of inhibiting Botrytis cinerea via a dual mode of action, namely induced resistance and antibiosis. Here, we show that strain L12 of P. aphidis can reduce the severity of powdery mildew caused by Podosphaera xanthii on cucumber plants with an efficacy of 75%. Confocal and scanning electron microscopy analyses demonstrated P. aphidis proliferation on infected tissue and its production of long hyphae that parasitize the powdery mildew hyphae and spores as an ectoparasite. We also show that crude extract of P. aphidis metabolites can inhibit P. xanthii spore germination in planta. Our results suggest that in addition to its antibiosis mode of action, P. aphidis may also act as an ectoparasite on P. xanthii. These results indicate that P. aphidis strain L12 has the potential to control powdery mildew.

Biological control of the cucurbit powdery mildew pathogen Podosphaera xanthii by means of the epiphytic fungus Pseudozyma aphidis and parasitism as a mode of action.

Science.gov (United States)

Gafni, Aviva; Calderon, Claudia E; Harris, Raviv; Buxdorf, Kobi; Dafa-Berger, Avis; Zeilinger-Reichert, Einat; Levy, Maggie

2015-01-01

Epiphytic yeasts, which colonize plant surfaces, may possess activity that can be harnessed to help plants defend themselves against various pathogens. Due to their unique characteristics, epiphytic yeasts belonging to the genus Pseudozyma hold great potential for use as biocontrol agents. We identified a unique, biologically active isolate of the epiphytic yeast Pseudozyma aphidis that is capable of inhibiting Botrytis cinerea via a dual mode of action, namely induced resistance and antibiosis. Here, we show that strain L12 of P. aphidis can reduce the severity of powdery mildew caused by Podosphaera xanthii on cucumber plants with an efficacy of 75%. Confocal and scanning electron microscopy analyses demonstrated P. aphidis proliferation on infected tissue and its production of long hyphae that parasitize the powdery mildew hyphae and spores as an ectoparasite. We also show that crude extract of P. aphidis metabolites can inhibit P. xanthii spore germination in planta. Our results suggest that in addition to its antibiosis as mode of action, P. aphidis may also act as an ectoparasite on P. xanthii. These results indicate that P. aphidis strain L12 has the potential to control powdery mildew.

Functional profiles reveal unique ecological roles of various biological soil crust organisms

Science.gov (United States)

Bowker, M.A.; Mau, R.L.; Maestre, F.T.; Escolar, C.; Castillo-Monroy, A. P.

2011-01-01

1. At the heart of the body of research on biodiversity effects on ecosystem function is the debate over whether different species tend to be functionally singular or redundant. When we consider ecosystem multi-function, the provision of multiple ecosystem functions simultaneously, we may find that seemingly redundant species may in fact play unique roles in ecosystems. 2. Over the last few decades, the significance of biological soil crusts (BSCs) as ecological boundaries and ecosystem engineers, and their multi-functional nature, has become increasingly well documented. We compiled 'functional profiles' of the organisms in this understudied community, to determine whether functional singularity emerges when multiple ecosystem functions are considered. 3. In two data sets, one representing multiple sites around the semi-arid regions of Spain (regional scale), and another from a single site in central Spain (local scale), we examined correlations between the abundance or frequency of BSC species in a community, and multiple surrogates of ecosystem functioning. There was a wide array of apparent effects of species on specific functions. 4. Notably, in gypsiferous soils and at regional scale, we found that indicators of carbon (C) and phosphorus cycling were apparently suppressed and promoted by the lichens Diploschistes diacapsis and Squamarina lentigera, respectively. The moss Pleurochaete squarrosa appears to promote C cycling in calcareous soils at this spatial scale. At the local scale in gypsiferous soils, D. diacapsis positively correlated with carbon cycling, but negatively with nitrogen cycling, whereas numerous lichens exhibited the opposite profile. 5. We found a high degree of functional singularity, i.e. that species were highly individualistic in their effects on multiple functions. Many functional attributes were not easily predictable from existing functional grouping systems based primarily on morphology. 6. Our results suggest that maintaining

Function-Based Algorithms for Biological Sequences

Science.gov (United States)

Mohanty, Pragyan Sheela P.

2015-01-01

Two problems at two different abstraction levels of computational biology are studied. At the molecular level, efficient pattern matching algorithms in DNA sequences are presented. For gene order data, an efficient data structure is presented capable of storing all gene re-orderings in a systematic manner. A common characteristic of presented…

Laser Covariance Vibrometry for Unsymmetrical Mode Detection

Science.gov (United States)

2006-09-01

2 CMIF Complex Modal Indicator Function . . . . . . . . . . . . . 2 FDAC Frequency Domain Acceptance Criterion . . . . . . . . . . 2 OEM’s Original...complex modal indicator function ( CMIF ) [23] a set of singular value decomposition response functions and the frequency domain acceptance criterion...AFITGEENP03-02. 59. Phillips, Allyn W., Randall J. Allemang, and William A. Fladung. “The Complex Mode Indicator Function ( CMIF ) as a Parameter

Determining the impacts of trawling on benthic function in European waters : a biological traits approach

DEFF Research Database (Denmark)

Bolam, Stefan; Kenny, Andrew; Garcia, Clement

characteristics, have allowed us to better understand the interactions between the benthic fauna and their environment at a functional level. We present the initial findings of work conducted under the auspices of the EU-funded project ‘BENTHIS’ which aims to improve our understanding of the impacts of trawling...... on benthic ecosystem functioning over much larger spatial scales than previously undertaken. Biological traits information from 887 stations across European waters (Norwegian, UK, Belgian, Dutch, Danish waters, the Mediterranean and Black Sea) were analysed to: i) quantify the relationships between infaunal...

Path-integral quantization of solitons using the zero-mode Feynman rule

International Nuclear Information System (INIS)

Sung Sheng Chang

1978-01-01

We propose a direct expansion treatment to quantize solitons without collective coordinates. Feynman's path integral for a free particle subject to an external force is directly used as the generating functional for the zero-frequency mode. The generating functional has no infrared singularity and defines a zero-mode Feynman rule which also gives a correct perturbative expansion for the harmonic-oscillator Green's function by treating the quadratic potential as a perturbation. We use the zero-mode Feynman rule to calculate the energy shift due to the second-order quantum corrections for solitons. Our result agrees with previous predictions using the collective-coordinate method or the method of Goldstone and Jackiw

Guided mode cutoff in rare-earth doped rod-type PCFs

DEFF Research Database (Denmark)

Poli, F.; Cucinotta, A.; Passaro, D.

2008-01-01

Guided mode properties of rare-earth doped photonic crystal fibers are investigated as a function of the core refractive index, showing the possibility to obtain cutoff at low normalized wavelength.......Guided mode properties of rare-earth doped photonic crystal fibers are investigated as a function of the core refractive index, showing the possibility to obtain cutoff at low normalized wavelength....

A promising future for integrative biodiversity research: an increased role of scale-dependency and functional biology

Science.gov (United States)

Schmitz, L.

2016-01-01

Studies into the complex interaction between an organism and changes to its biotic and abiotic environment are fundamental to understanding what regulates biodiversity. These investigations occur at many phylogenetic, temporal and spatial scales and within a variety of biological and geological disciplines but often in relative isolation. This issue focuses on what can be achieved when ecological mechanisms are integrated into analyses of deep-time biodiversity patterns through the union of fossil and extant data and methods. We expand upon this perspective to argue that, given its direct relevance to the current biodiversity crisis, greater integration is needed across biodiversity research. We focus on the need to understand scaling effects, how lower-level ecological and evolutionary processes scale up and vice versa, and the importance of incorporating functional biology. Placing function at the core of biodiversity research is fundamental, as it establishes how an organism interacts with its abiotic and biotic environment and it is functional diversity that ultimately determines important ecosystem processes. To achieve full integration, concerted and ongoing efforts are needed to build a united and interactive community of biodiversity researchers, with education and interdisciplinary training at its heart. PMID:26977068

A promising future for integrative biodiversity research: an increased role of scale-dependency and functional biology.

Science.gov (United States)

Price, S A; Schmitz, L

2016-04-05

Studies into the complex interaction between an organism and changes to its biotic and abiotic environment are fundamental to understanding what regulates biodiversity. These investigations occur at many phylogenetic, temporal and spatial scales and within a variety of biological and geological disciplines but often in relative isolation. This issue focuses on what can be achieved when ecological mechanisms are integrated into analyses of deep-time biodiversity patterns through the union of fossil and extant data and methods. We expand upon this perspective to argue that, given its direct relevance to the current biodiversity crisis, greater integration is needed across biodiversity research. We focus on the need to understand scaling effects, how lower-level ecological and evolutionary processes scale up and vice versa, and the importance of incorporating functional biology. Placing function at the core of biodiversity research is fundamental, as it establishes how an organism interacts with its abiotic and biotic environment and it is functional diversity that ultimately determines important ecosystem processes. To achieve full integration, concerted and ongoing efforts are needed to build a united and interactive community of biodiversity researchers, with education and interdisciplinary training at its heart. © 2016 The Author(s).

Mode of production of monomolecular structuring water in liquid crystalline form

International Nuclear Information System (INIS)

Hasanov, A.M.

2011-01-01

Full text : Mode to protect living organisms from the biological effects of electromagnetic radiation of mobile phones and personal computers, including the determination of the energy absorbed by the body over time, depending on the biological factors of the body, characterized in that a biological factor using the total amount of water contained in the body, with time corresponding to the absorbed energy is equated to the maximum allowable rate, determined by the formula dt=dEBBNH/EodEeksp. Here K is the coefficient of the percentage of water in biological tissues, dEeksp. - Experimentally established energy flux density of the mobile phone or personal computer, dEBBNH ∼10mkVt/si 2 - maximum permissible rate of absorbed energy.

The role of ontologies in biological and biomedical research: a functional perspective

KAUST Repository

Hoehndorf, Robert

2015-04-10

Ontologies are widely used in biological and biomedical research. Their success lies in their combination of four main features present in almost all ontologies: provision of standard identifiers for classes and relations that represent the phenomena within a domain; provision of a vocabulary for a domain; provision of metadata that describes the intended meaning of the classes and relations in ontologies; and the provision of machine-readable axioms and definitions that enable computational access to some aspects of the meaning of classes and relations. While each of these features enables applications that facilitate data integration, data access and analysis, a great potential lies in the possibility of combining these four features to support integrative analysis and interpretation of multimodal data. Here, we provide a functional perspective on ontologies in biology and biomedicine, focusing on what ontologies can do and describing how they can be used in support of integrative research. We also outline perspectives for using ontologies in data-driven science, in particular their application in structured data mining and machine learning applications.

The role of ontologies in biological and biomedical research: a functional perspective

KAUST Repository

Hoehndorf, Robert; Schofield, P. N.; Gkoutos, G. V.

2015-01-01

Ontologies are widely used in biological and biomedical research. Their success lies in their combination of four main features present in almost all ontologies: provision of standard identifiers for classes and relations that represent the phenomena within a domain; provision of a vocabulary for a domain; provision of metadata that describes the intended meaning of the classes and relations in ontologies; and the provision of machine-readable axioms and definitions that enable computational access to some aspects of the meaning of classes and relations. While each of these features enables applications that facilitate data integration, data access and analysis, a great potential lies in the possibility of combining these four features to support integrative analysis and interpretation of multimodal data. Here, we provide a functional perspective on ontologies in biology and biomedicine, focusing on what ontologies can do and describing how they can be used in support of integrative research. We also outline perspectives for using ontologies in data-driven science, in particular their application in structured data mining and machine learning applications.

Omega-mode perturbation theory and reactor kinetics for analyzing accelerator-driven subcritical systems

International Nuclear Information System (INIS)

Ren-Tai, Chiang

2003-01-01

An ω-mode first-order perturbation theory is developed for analyzing the time- and space-dependent neutron behavior in Accelerator-Driven Subcritical Systems (ADSS). The generalized point-kinetics equations are systematically derived using the ω-mode first-order perturbation theory and Fredholm Alternative Theorem. Seven sets of the ω-mode eigenvalues exist with using six groups of delayed neutrons and all ω eigenvalues are negative in ADSS. Seven ω-mode adjoint and forward eigenfunctions are employed to form the point-kinetic parameters. The neutron flux is expressed as a linear combination of the products of seven ω-eigenvalue-mode shape functions and their corresponding time functions up to the first order terms, and the lowest negative ω-eigenvalue mode is the dominant mode. (author)

Bio-templated CdSe quantum dots green synthesis in the functional protein, lysozyme, and biological activity investigation

International Nuclear Information System (INIS)

Wang, Qisui; Li, Song; Liu, Peng; Min, Xinmin

2012-01-01

Bifunctional fluorescence (CdSe Quantum Dots) – protein (Lysozyme) nanocomposites were synthesized at room temperature by a protein-directed, solution-phase, green-synthetic method. Fluorescence (FL) and absorption spectra showed that CdSe QDs were prepared successfully with Lyz. The average particle size and crystalline structure of QDs were investigated by high-resolution transmission electron microscopy (HRTEM) and X-ray diffraction (XRD), respectively. With attenuated total reflection-fourier transform infrared (ATR-FTIR) spectra and thermogravimetric (TG) analysis, it was confirmed that there is interaction between QDs and amide I, amide II groups in Lyz. FL polarization was measured and FL imaging was done to monitor whether QDs could be responsible for possible changes in the conformation and activity of Lyz. Interestingly, the results showed Lyz still retain the biological activity after formation of QDs, but the secondary structure of the Lyz was changed. And the advantage of this synthesis method is producing excellent fluorescent QDs with specifically biological function. -- Highlights: ► Lysozyme-directed green synthesis of CdSe quantum dots. ► Lysozyme still retain the biological activity after formation of CdSe. ► The method is the production of fluorescent QDs with highly specific and functions.

Default mode network segregation and social deficits in autism spectrum disorder: Evidence from non-medicated children.

Science.gov (United States)

Yerys, Benjamin E; Gordon, Evan M; Abrams, Danielle N; Satterthwaite, Theodore D; Weinblatt, Rachel; Jankowski, Kathryn F; Strang, John; Kenworthy, Lauren; Gaillard, William D; Vaidya, Chandan J

2015-01-01

Functional pathology of the default mode network is posited to be central to social-cognitive impairment in autism spectrum disorders (ASD). Altered functional connectivity of the default mode network's midline core may be a potential endophenotype for social deficits in ASD. Generalizability from prior studies is limited by inclusion of medicated participants and by methods favoring restricted examination of network function. This study measured resting-state functional connectivity in 22 8-13 year-old non-medicated children with ASD and 22 typically developing controls using seed-based and network segregation functional connectivity methods. Relative to controls the ASD group showed both under- and over-functional connectivity within default mode and non-default mode regions, respectively. ASD symptoms correlated negatively with the connection strength of the default mode midline core-medial prefrontal cortex-posterior cingulate cortex. Network segregation analysis with the participation coefficient showed a higher area under the curve for the ASD group. Our findings demonstrate that the default mode network in ASD shows a pattern of poor segregation with both functional connectivity metrics. This study confirms the potential for the functional connection of the midline core as an endophenotype for social deficits. Poor segregation of the default mode network is consistent with an excitation/inhibition imbalance model of ASD.

Embryonic stem cell interactomics: the beginning of a long road to biological function.

Science.gov (United States)

Yousefi, Maram; Hajihoseini, Vahid; Jung, Woojin; Hosseinpour, Batol; Rassouli, Hassan; Lee, Bonghee; Baharvand, Hossein; Lee, KiYoung; Salekdeh, Ghasem Hosseini

2012-12-01

Embryonic stem cells (ESCs) are capable of unlimited self-renewal while maintaining pluripotency. They are of great interest in regenerative medicine due to their ability to differentiate into all cell types of the three embryonic germ layers. Recently, induced pluripotent stem cells (iPSCs) have shown similarities to ESCs and thus promise great therapeutic potential in regenerative medicine. Despite progress in stem cell biology, our understanding of the exact mechanisms by which pluripotency and self-renewal are established and maintained is largely unknown. A better understanding of these processes may lead to discovery of alternative ways for reprogramming, differentiation and more reliable applications of stem cells in therapies. It has become evident that proteins generally function as members of large complexes that are part of a more complex network. Therefore, the identification of protein-protein interactions (PPI) is an efficient strategy for understanding protein function and regulation. Systematic genome-wide and pathway-specific PPI analysis of ESCs has generated a network of ESC proteins, including major transcription factors. These PPI networks of ESCs may contribute to a mechanistic understanding of self-renewal and pluripotency. In this review we describe different experimental approaches for the identification of PPIs along with various databases. We discuss biological findings and technical challenges encountered with interactome studies of pluripotent stem cells, and provide insight into how interactomics is likely to develop.

Geometric transformations of optical orbital angular momentum spatial modes

Science.gov (United States)

He, Rui; An, Xin

2018-02-01

With the aid of the bosonic mode conversions in two different coordinate frames, we show that (1) the coordinate eigenstate is exactly the EPR entangled state representation, and (2) the Laguerre-Gaussian (LG) mode is exactly the wave function of the common eigenvector of the orbital angular momentum and the total photon number operator. Moreover, by using the conversion of the bosonic modes, theWigner representation of the LG mode can be obtained directly. It provides an alternative to the method of Simon and Agarwal.

Minimal information: an urgent need to assess the functional reliability of recombinant proteins used in biological experiments

Directory of Open Access Journals (Sweden)

de Marco Ario

2008-07-01

Full Text Available Abstract Structural characterization of proteins used in biological experiments is largely neglected. In most publications, the information available is totally insufficient to judge the functionality of the proteins used and, therefore, the significance of identified protein-protein interactions (was the interaction specific or due to unspecific binding of misfolded protein regions? or reliability of kinetic and thermodynamic data (how much protein was in its native form?. As a consequence, the results of single experiments might not only become questionable, but the whole reliability of systems biology, built on these fundaments, would be weakened. The introduction of Minimal Information concerning purified proteins to add as metadata to the main body of a manuscript would render straightforward the assessment of their functional and structural qualities and, consequently, of results obtained using these proteins. Furthermore, accepted standards for protein annotation would simplify data comparison and exchange. This article has been envisaged as a proposal for aggregating scientists who share the opinion that the scientific community needs a platform for Minimum Information for Protein Functionality Evaluation (MIPFE.

PLC-based mode multi/demultiplexers for mode division multiplexing

Science.gov (United States)

Saitoh, Kunimasa; Hanzawa, Nobutomo; Sakamoto, Taiji; Fujisawa, Takeshi; Yamashita, Yoko; Matsui, Takashi; Tsujikawa, Kyozo; Nakajima, Kazuhide

2017-02-01

Recently developed PLC-based mode multi/demultiplexers (MUX/DEMUXs) for mode division multiplexing (MDM) transmission are reviewed. We firstly show the operation principle and basic characteristics of PLC-based MUX/DEMUXs with an asymmetric directional coupler (ADC). We then demonstrate the 3-mode (2LP-mode) multiplexing of the LP01, LP11a, and LP11b modes by using fabricated PLC-based mode MUX/DEMUX on one chip. In order to excite LP11b mode in the same plane, a PLC-based LP11 mode rotator is introduced. Finally, we show the PLC-based 6-mode (4LP-mode) MUX/DEMUX with a uniform height by using ADCs, LP11 mode rotators, and tapered waveguides. It is shown that the LP21a mode can be excited from the LP11b mode by using ADC, and the two nearly degenerated LP21b and LP02 modes can be (de)multiplexed separately by using tapered mode converter from E13 (E31) mode to LP21b (LP02) mode.

Delivery Mode and the Transition of Pioneering Gut-Microbiota Structure, Composition and Predicted Metabolic Function

Directory of Open Access Journals (Sweden)

Noel T. Mueller

2017-12-01

Full Text Available Cesarean (C-section delivery, recently shown to cause excess weight gain in mice, perturbs human neonatal gut microbiota development due to the lack of natural mother-to-newborn transfer of microbes. Neonates excrete first the in-utero intestinal content (referred to as meconium hours after birth, followed by intestinal contents reflective of extra-uterine exposure (referred to as transition stool 2 to 3 days after birth. It is not clear when the effect of C-section on the neonatal gut microbiota emerges. We examined bacterial DNA in carefully-collected meconium, and the subsequent transitional stool, from 59 neonates [13 born by scheduled C-section and 46 born by vaginal delivery] in a private hospital in Brazil. Bacterial DNA was extracted, and the V4 region of the 16S rRNA gene was sequenced using the Illumina MiSeq (San Diego, CA, USA platform. We found evidence of bacterial DNA in the majority of meconium samples in our study. The bacterial DNA structure (i.e., beta diversity of meconium differed significantly from that of the transitional stool microbiota. There was a significant reduction in bacterial alpha diversity (e.g., number of observed bacterial species and change in bacterial composition (e.g., reduced Proteobacteria in the transition from meconium to stool. However, changes in predicted microbiota metabolic function from meconium to transitional stool were only observed in vaginally-delivered neonates. Within sample comparisons showed that delivery mode was significantly associated with bacterial structure, composition and predicted microbiota metabolic function in transitional-stool samples, but not in meconium samples. Specifically, compared to vaginally delivered neonates, the transitional stool of C-section delivered neonates had lower proportions of the genera Bacteroides, Parabacteroides and Clostridium. These differences led to C-section neonates having lower predicted abundance of microbial genes related to metabolism of

Synthetic Biology: Putting Synthesis into Biology

Science.gov (United States)

Liang, Jing; Luo, Yunzi; Zhao, Huimin

2010-01-01

The ability to manipulate living organisms is at the heart of a range of emerging technologies that serve to address important and current problems in environment, energy, and health. However, with all its complexity and interconnectivity, biology has for many years been recalcitrant to engineering manipulations. The recent advances in synthesis, analysis, and modeling methods have finally provided the tools necessary to manipulate living systems in meaningful ways, and have led to the coining of a field named synthetic biology. The scope of synthetic biology is as complicated as life itself – encompassing many branches of science, and across many scales of application. New DNA synthesis and assembly techniques have made routine the customization of very large DNA molecules. This in turn has allowed the incorporation of multiple genes and pathways. By coupling these with techniques that allow for the modeling and design of protein functions, scientists have now gained the tools to create completely novel biological machineries. Even the ultimate biological machinery – a self-replicating organism – is being pursued at this moment. It is the purpose of this review to dissect and organize these various components of synthetic biology into a coherent picture. PMID:21064036

Experimental status of the nuclear spin scissors mode

Science.gov (United States)

Balbutsev, E. B.; Molodtsova, I. V.; Schuck, P.

2018-04-01

With the Wigner function moments (WFM) method the scissors mode of the actinides and rare earth nuclei are investigated. The unexplained experimental fact that in 232Th a double hump structure is found finds a natural explanation within WFM. It is predicted that the lower peak corresponds to an isovector spin scissors mode whereas the higher-lying states corresponds to the conventional isovector orbital scissors mode. The experimental situation is scrutinized in this respect concerning practically all results of M 1 excitations.

Functional properties and differential mode of regulation of the nitrate transporter from a plant symbiotic ascomycete

Science.gov (United States)

Montanini, Barbara; Viscomi, Arturo R.; Bolchi, Angelo; Martin, Yusé; Siverio, José M.; Balestrini, Raffaella; Bonfante, Paola; Ottonello, Simone

2005-01-01

Nitrogen assimilation by plant symbiotic fungi plays a central role in the mutualistic interaction established by these organisms, as well as in nitrogen flux in a variety of soils. In the present study, we report on the functional properties, structural organization and distinctive mode of regulation of TbNrt2 (Tuber borchii NRT2 family transporter), the nitrate transporter of the mycorrhizal ascomycete T. borchii. As revealed by experiments conducted in a nitrate-uptake-defective mutant of the yeast Hansenula polymorpha, TbNrt2 is a high-affinity transporter (Km=4.7 μM nitrate) that is bispecific for nitrate and nitrite. It is expressed in free-living mycelia and in mycorrhizae, where it preferentially accumulates in the plasma membrane of root-contacting hyphae. The TbNrt2 mRNA, which is transcribed from a single-copy gene clustered with the nitrate reductase gene in the T. borchii genome, was specifically up-regulated following transfer of mycelia to nitrate- (or nitrite)-containing medium. However, at variance with the strict nitrate-dependent induction commonly observed in other organisms, TbNrt2 was also up-regulated (at both the mRNA and the protein level) following transfer to a nitrogen-free medium. This unusual mode of regulation differs from that of the adjacent nitrate reductase gene, which was expressed at basal levels under nitrogen deprivation conditions and required nitrate for induction. The functional and expression properties, described in the present study, delineate TbNrt2 as a versatile transporter that may be especially suited to cope with the fluctuating (and often low) mineral nitrogen concentrations found in most natural, especially forest, soils. PMID:16201972

Default-mode network and deep gray-matter analysis in neuromyelitis optica patients.

Science.gov (United States)

Rueda-Lopes, Fernanda C; Pessôa, Fernanda M C; Tukamoto, Gustavo; Malfetano, Fabíola Rachid; Scherpenhuijzen, Simone Batista; Alves-Leon, Soniza; Gasparetto, Emerson L

2018-02-20

The aim of our study was to detect functional changes in default-mode network of neuromyelitis optica (NMO) patients using resting-state functional magnetic resonance images and the evaluation of subcortical gray-matter structures volumes. NMO patients (n=28) and controls patients (n=19) were enrolled. We used the integrated registration and segmentation tool, part of FMRIB's Software Library (FSL) to segment subcortical structures including the thalamus, caudate nucleus, putamen, hippocampus and amygdalae. Resting-state functional magnetic resonance images were post-processed using the Multivariate Exploratory Linear Optimized Decomposition into Independent Components, also part of FSL. Average Z-values extracted from the default-mode network were compared between patients and controls using t-tests (P values default-mode network of patients compared to controls, notably in the precuneus and right hippocampus (corrected Pdefault-mode network. The hyperactivity of certain default-mode network areas may reflect cortical compensation for subtle structural damage in NMO patients. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

Variations in the Biological Functions of HIV-1 Clade C Envelope in a SHIV-Infected Rhesus Macaque during Disease Progression.

Directory of Open Access Journals (Sweden)

For Yue Tso

Full Text Available A better understanding of how the biological functions of the HIV-1 envelope (Env changes during disease progression may aid the design of an efficacious anti-HIV-1 vaccine. Although studies from patient had provided some insights on this issue, the differences in the study cohorts and methodology had make it difficult to reach a consensus of the variations in the HIV-1 Env functions during disease progression. To this end, an animal model that can be infected under controlled environment and reflect the disease course of HIV-1 infection in human will be beneficial. Such an animal model was previously demonstrated by the infection of macaque with SHIV, expressing HIV-1 clade C Env V1-V5 region. By using this model, we examined the changes in biological functions of Env in the infected animal over the entire disease course. Our data showed an increase in the neutralization resistance phenotype over time and coincided with the decrease in the net charges of the V1-V5 region. Infection of PBMC with provirus expressing various Env clones, isolated from the infected animal over time, showed a surprisingly better replicative fitness for viruses expressing the Env from early time point. Biotinylation and ELISA data also indicated a decrease of cell-surface-associated Env and virion-associated gp120 content with disease progression. This decrease did not affect the CD4-binding capability of Env, but were positively correlated with the decrease of Env fusion ability. Interestingly, some of these changes in biological functions reverted to the pre-AIDS level during advance AIDS. These data suggested a dynamic relationship between the Env V1-V5 region with the host immune pressure. The observed changes of biological functions in this setting might reflect and predict those occurring during natural disease progression in human.

An infinite set of Ward identities for adiabatic modes in cosmology

International Nuclear Information System (INIS)

Hinterbichler, Kurt; Hui, Lam; Khoury, Justin

2014-01-01

We show that the correlation functions of any single-field cosmological model with constant growing-modes are constrained by an infinite number of novel consistency relations, which relate N+1-point correlation functions with a soft-momentum scalar or tensor mode to a symmetry transformation on N-point correlation functions of hard-momentum modes. We derive these consistency relations from Ward identities for an infinite tower of non-linearly realized global symmetries governing scalar and tensor perturbations. These symmetries can be labeled by an integer n. At each order n, the consistency relations constrain — completely for n = 0,1, and partially for n ≥ 2 — the q n behavior of the soft limits. The identities at n = 0 recover Maldacena's original consistency relations for a soft scalar and tensor mode, n = 1 gives the recently-discovered conformal consistency relations, and the identities for n ≥ 2 are new. As a check, we verify directly that the n = 2 identity is satisfied by known correlation functions in slow-roll inflation

The development of peptide-based interfacial biomaterials for generating biological functionality on the surface of bioinert materials.

Science.gov (United States)

Meyers, Steven R; Khoo, Xiaojuan; Huang, Xin; Walsh, Elisabeth B; Grinstaff, Mark W; Kenan, Daniel J

2009-01-01

Biomaterials used in implants have traditionally been selected based on their mechanical properties, chemical stability, and biocompatibility. However, the durability and clinical efficacy of implantable biomedical devices remain limited in part due to the absence of appropriate biological interactions at the implant interface and the lack of integration into adjacent tissues. Herein, we describe a robust peptide-based coating technology capable of modifying the surface of existing biomaterials and medical devices through the non-covalent binding of modular biofunctional peptides. These peptides contain at least one material binding sequence and at least one biologically active sequence and thus are termed, "Interfacial Biomaterials" (IFBMs). IFBMs can simultaneously bind the biomaterial surface while endowing it with desired biological functionalities at the interface between the material and biological realms. We demonstrate the capabilities of model IFBMs to convert native polystyrene, a bioinert surface, into a bioactive surface that can support a range of cell activities. We further distinguish between simple cell attachment with insufficient integrin interactions, which in some cases can adversely impact downstream biology, versus biologically appropriate adhesion, cell spreading, and cell survival mediated by IFBMs. Moreover, we show that we can use the coating technology to create spatially resolved patterns of fluorophores and cells on substrates and that these patterns retain their borders in culture.

On the limitations of standard statistical modeling in biological systems: a full Bayesian approach for biology.

Science.gov (United States)

Gomez-Ramirez, Jaime; Sanz, Ricardo

2013-09-01

One of the most important scientific challenges today is the quantitative and predictive understanding of biological function. Classical mathematical and computational approaches have been enormously successful in modeling inert matter, but they may be inadequate to address inherent features of biological systems. We address the conceptual and methodological obstacles that lie in the inverse problem in biological systems modeling. We introduce a full Bayesian approach (FBA), a theoretical framework to study biological function, in which probability distributions are conditional on biophysical information that physically resides in the biological system that is studied by the scientist. Copyright © 2013 Elsevier Ltd. All rights reserved.

Nonlinear Mirror and Weibel modes: peculiarities of quasi-linear dynamics

Directory of Open Access Journals (Sweden)

O. A. Pokhotelov

2010-12-01

Full Text Available A theory for nonlinear evolution of the mirror modes near the instability threshold is developed. It is shown that during initial stage the major instability saturation is provided by the flattening of the velocity distribution function in the vicinity of small parallel ion velocities. The relaxation scenario in this case is accompanied by rapid attenuation of resonant particle interaction which is replaced by a weaker adiabatic interaction with mirror modes. The saturated plasma state can be considered as a magnetic counterpart to electrostatic BGK modes. After quasi-linear saturation a further nonlinear scenario is controlled by the mode coupling effects and nonlinear variation of the ion Larmor radius. Our analytical model is verified by relevant numerical simulations. Test particle and PIC simulations indeed show that it is a modification of distribution function at small parallel velocities that results in fading away of free energy driving the mirror mode. The similarity with resonant Weibel instability is discussed.

Gyrokinetic Stability Studies of the Microtearing Mode in the National Spherical Torus Experiment H-mode

International Nuclear Information System (INIS)

Baumgaertel J.A., Redi M.H., Budny R.V., Rewoldt G., Dorland W.

2005-01-01

Insight into plasma microturbulence and transport is being sought using linear simulations of drift waves on the National Spherical Torus Experiment (NSTX), following a study of drift wave modes on the Alcator C-Mod Tokamak. Microturbulence is likely generated by instabilities of drift waves, which cause transport of heat and particles. Understanding this transport is important because the containment of heat and particles is required for the achievement of practical nuclear fusion. Microtearing modes may cause high heat transport through high electron thermal conductivity. It is hoped that microtearing will be stable along with good electron transport in the proposed low collisionality International Thermonuclear Experimental Reactor (ITER). Stability of the microtearing mode is investigated for conditions at mid-radius in a high density NSTX high performance (H-mode) plasma, which is compared to the proposed ITER plasmas. The microtearing mode is driven by the electron temperature gradient, and believed to be mediated by ion collisions and magnetic shear. Calculations are based on input files produced by TRXPL following TRANSP (a time-dependent transport analysis code) analysis. The variability of unstable mode growth rates is examined as a function of ion and electron collisionalities using the parallel gyrokinetic computational code GS2. Results show the microtearing mode stability dependence for a range of plasma collisionalities. Computation verifies analytic predictions that higher collisionalities than in the NSTX experiment increase microtearing instability growth rates, but that the modes are stabilized at the highest values. There is a transition of the dominant mode in the collisionality scan to ion temperature gradient character at both high and low collisionalities. The calculations suggest that plasma electron thermal confinement may be greatly improved in the low-collisionality ITER

Improved diagnostic accuracy of Alzheimer's disease by combining regional cortical thickness and default mode network functional connectivity: Validated in the Alzheimer's disease neuroimaging initiative set

Energy Technology Data Exchange (ETDEWEB)

Park, Ji Eun; Park, Bum Woo; Kim, Sang Joon; Kim, Ho Sung; Choi, Choong Gon; Jung, Seung Jung; Oh, Joo Young; Shim, Woo Hyun [Dept. of Radiology and Research Institute of Radiology, University of Ulsan College of Medicine, Asan Medical Center, Seoul (Korea, Republic of); Lee, Jae Hong; Roh, Jee Hoon [University of Ulsan College of Medicine, Asan Medical Center, Seoul (Korea, Republic of)

2017-11-15

To identify potential imaging biomarkers of Alzheimer's disease by combining brain cortical thickness (CThk) and functional connectivity and to validate this model's diagnostic accuracy in a validation set. Data from 98 subjects was retrospectively reviewed, including a study set (n = 63) and a validation set from the Alzheimer's Disease Neuroimaging Initiative (n = 35). From each subject, data for CThk and functional connectivity of the default mode network was extracted from structural T1-weighted and resting-state functional magnetic resonance imaging. Cortical regions with significant differences between patients and healthy controls in the correlation of CThk and functional connectivity were identified in the study set. The diagnostic accuracy of functional connectivity measures combined with CThk in the identified regions was evaluated against that in the medial temporal lobes using the validation set and application of a support vector machine. Group-wise differences in the correlation of CThk and default mode network functional connectivity were identified in the superior temporal (p < 0.001) and supramarginal gyrus (p = 0.007) of the left cerebral hemisphere. Default mode network functional connectivity combined with the CThk of those two regions were more accurate than that combined with the CThk of both medial temporal lobes (91.7% vs. 75%). Combining functional information with CThk of the superior temporal and supramarginal gyri in the left cerebral hemisphere improves diagnostic accuracy, making it a potential imaging biomarker for Alzheimer's disease.

Synthetic biological networks

International Nuclear Information System (INIS)

Archer, Eric; Süel, Gürol M

2013-01-01

Despite their obvious relationship and overlap, the field of physics is blessed with many insightful laws, while such laws are sadly absent in biology. Here we aim to discuss how the rise of a more recent field known as synthetic biology may allow us to more directly test hypotheses regarding the possible design principles of natural biological networks and systems. In particular, this review focuses on synthetic gene regulatory networks engineered to perform specific functions or exhibit particular dynamic behaviors. Advances in synthetic biology may set the stage to uncover the relationship of potential biological principles to those developed in physics. (review article)

Mammalian Synthetic Biology: Engineering Biological Systems.

Science.gov (United States)

Black, Joshua B; Perez-Pinera, Pablo; Gersbach, Charles A

2017-06-21

The programming of new functions into mammalian cells has tremendous application in research and medicine. Continued improvements in the capacity to sequence and synthesize DNA have rapidly increased our understanding of mechanisms of gene function and regulation on a genome-wide scale and have expanded the set of genetic components available for programming cell biology. The invention of new research tools, including targetable DNA-binding systems such as CRISPR/Cas9 and sensor-actuator devices that can recognize and respond to diverse chemical, mechanical, and optical inputs, has enabled precise control of complex cellular behaviors at unprecedented spatial and temporal resolution. These tools have been critical for the expansion of synthetic biology techniques from prokaryotic and lower eukaryotic hosts to mammalian systems. Recent progress in the development of genome and epigenome editing tools and in the engineering of designer cells with programmable genetic circuits is expanding approaches to prevent, diagnose, and treat disease and to establish personalized theranostic strategies for next-generation medicines. This review summarizes the development of these enabling technologies and their application to transforming mammalian synthetic biology into a distinct field in research and medicine.

Permeating disciplines: Overcoming barriers between molecular simulations and classical structure-function approaches in biological ion transport.

Science.gov (United States)

Howard, Rebecca J; Carnevale, Vincenzo; Delemotte, Lucie; Hellmich, Ute A; Rothberg, Brad S

2018-04-01

Ion translocation across biological barriers is a fundamental requirement for life. In many cases, controlling this process-for example with neuroactive drugs-demands an understanding of rapid and reversible structural changes in membrane-embedded proteins, including ion channels and transporters. Classical approaches to electrophysiology and structural biology have provided valuable insights into several such proteins over macroscopic, often discontinuous scales of space and time. Integrating these observations into meaningful mechanistic models now relies increasingly on computational methods, particularly molecular dynamics simulations, while surfacing important challenges in data management and conceptual alignment. Here, we seek to provide contemporary context, concrete examples, and a look to the future for bridging disciplinary gaps in biological ion transport. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain. Copyright © 2017 Elsevier B.V. All rights reserved.

Mode-by-mode summation for the zero point electromagnetic energy of an infinite cylinder

International Nuclear Information System (INIS)

Milton, K.A.; Nesterenko, A.V.; Nesterenko, V.V.

1999-01-01

Using the mode-by-mode summation technique the zero point energy of the electromagnetic field is calculated for the boundary conditions given on the surface of an infinite solid cylinder. It is assumed that the dielectric and magnetic characteristics of the material which makes up the cylinder (var-epsilon 1 ,μ 1 ) and of that which makes up the surroundings (var-epsilon 2 ,μ 2 ) obey the relation var-epsilon 1 μ 1 =var-epsilon 2 μ 2 . With this assumption all the divergences cancel. The divergences are regulated by making use of zeta function techniques. Numerical calculations are carried out for a dilute dielectric-diamagnetic cylinder and for a perfectly conducting cylindrical shell. The Casimir energy in the first case vanishes, and in the second is in a complete agreement with that obtained by DeRaad and Milton who employed a Green close-quote s function technique with an ultraviolet regulator. copyright 1999 The American Physical Society

Hot Spots in a Network of Functional Sites

Science.gov (United States)

Ozbek, Pemra; Soner, Seren; Haliloglu, Turkan

2013-01-01

It is of significant interest to understand how proteins interact, which holds the key phenomenon in biological functions. Using dynamic fluctuations in high frequency modes, we show that the Gaussian Network Model (GNM) predicts hot spot residues with success rates ranging between S 8–58%, C 84–95%, P 5–19% and A 81–92% on unbound structures and S 8–51%, C 97–99%, P 14–50%, A 94–97% on complex structures for sensitivity, specificity, precision and accuracy, respectively. High specificity and accuracy rates with a single property on unbound protein structures suggest that hot spots are predefined in the dynamics of unbound structures and forming the binding core of interfaces, whereas the prediction of other functional residues with similar dynamic behavior explains the lower precision values. The latter is demonstrated with the case studies; ubiquitin, hen egg-white lysozyme and M2 proton channel. The dynamic fluctuations suggest a pseudo network of residues with high frequency fluctuations, which could be plausible for the mechanism of biological interactions and allosteric regulation. PMID:24023934

On normal modes in classical Hamiltonian systems

NARCIS (Netherlands)

van Groesen, Embrecht W.C.

1983-01-01

Normal modes of Hamittonian systems that are even and of classical type are characterized as the critical points of a normalized kinetic energy functional on level sets of the potential energy functional. With the aid of this constrained variational formulation the existence of at least one family

Jet behaviors and ejection mode recognition of electrohydrodynamic direct-write

Science.gov (United States)

Zheng, Jianyi; Zhang, Kai; Jiang, Jiaxin; Wang, Xiang; Li, Wenwang; Liu, Yifang; Liu, Juan; Zheng, Gaofeng

2018-01-01

By introducing image recognition and micro-current testing, jet behavior research was conducted, in which the real-time recognition of ejection mode was realized. To study the factors influencing ejection modes and the current variation trends under different modes, an Electrohydrodynamic Direct-Write (EDW) system with functions of current detection and ejection mode recognition was firstly built. Then a program was developed to recognize the jet modes. As the voltage applied to the metal tip increased, four jet ejection modes in EDW occurred: droplet ejection mode, Taylor cone ejection mode, retractive ejection mode and forked ejection mode. In this work, the corresponding relationship between the ejection modes and the effect on fiber deposition as well as current was studied. The real-time identification of ejection mode and detection of electrospinning current was realized. The results in this paper are contributed to enhancing the ejection stability, providing a good technical basis to produce continuous uniform nanofibers controllably.

Amplification of magnetic modes in laser-created plasmas

International Nuclear Information System (INIS)

Matte, J.P.; Bendib, A.; Luciani, J.F.

1987-01-01

The amplification of magnetic (Weibel) modes in laser-plasma interaction is investigated by use of unperturbed distribution functions given by Fokker-Planck simulations and a dispersion relation valid for all collisionality regimes. In the five cases studied, a strongly growing mode is found in the underdense plasma, where v-bar/sub x/ 2 2 , and the usual slowly growing one in the overdense plasma. The first mode grows convectively outwards by more than 10 4 . The convection velocities are found to be very different from Nernst values

Ovary and fimbrial stem cells: biology, niche and cancer origins.

Science.gov (United States)

Ng, Annie; Barker, Nick

2015-10-01

The mammalian ovary is covered by a single-layered epithelium that undergoes rupture and remodelling following each ovulation. Although resident stem cells are presumed to be crucial for this cyclic regeneration, their identity and mode of action have been elusive. Surrogate stemness assays and in vivo fate-mapping studies using recently discovered stem cell markers have identified stem cell pools in the ovary and fimbria that ensure epithelial homeostasis. Recent findings provide insights into intrinsic mechanisms and local extrinsic cues that govern the function of ovarian and fimbrial stem cells. These discoveries have advanced our understanding of stem cell biology in the ovary and fimbria, and lay the foundations for evaluating the contribution of resident stem cells to the initiation and progression of human epithelial ovarian cancer.

Spatial-mode switchable ring fiber laser based on low mode-crosstalk all-fiber mode MUX/DEMUX

Science.gov (United States)

Ren, Fang; Yu, Jinyi; Wang, Jianping

2018-05-01

We report an all-fiber ring laser that emits linearly polarized (LP) modes based on the intracavity all-fiber mode multiplexer/demultiplexer (MUX/DEMUX). Multiple LP modes in ring fiber laser are generated by taking advantage of mode MUX/DEMUX. The all-fiber mode MUX/DEMUX are composed of cascaded mode-selective couplers (MSCs). The output lasing mode of the ring fiber laser can be switched among the three lowest-order LP modes by employing combination of a mode MUX and a simple N × 1 optical switch. The slope efficiencies, optical spectra and mode profiles are measured.

Surface functionalization of bioactive glasses with natural molecules of biological significance, Part I: Gallic acid as model molecule

Science.gov (United States)

Zhang, Xin; Ferraris, Sara; Prenesti, Enrico; Verné, Enrica

2013-12-01

Gallic acid (3,4,5-trihydroxybenzoic acid, GA) and its derivatives are a group of biomolecules (polyphenols) obtained from plants. They have effects which are potentially beneficial to heath, for example they are antioxidant, anticarcinogenic and antibacterial, as recently investigated in many fields such as medicine, food and plant sciences. The main drawbacks of these molecules are both low stability and bioavailability. In this research work the opportunity to graft GA to bioactive glasses is investigated, in order to deliver the undamaged biological molecule into the body, using the biomaterial surfaces as a localized carrier. GA was considered for functionalization since it is a good model molecule for polyphenols and presents several interesting biological activities, like antibacterial, antioxidant and anticarcinogenic properties. Two different silica based bioactive glasses (SCNA and CEL2), with different reactivity, were employed as substrates. UV photometry combined with the Folin&Ciocalteu reagent was adopted to test the concentration of GA in uptake solution after functionalization. This test verified how much GA consumption occurred with surface modification and it was also used on solid samples to test the presence of GA on functionalized glasses. XPS and SEM-EDS techniques were employed to characterize the modification of material surface properties and functional group composition before and after functionalization.

Celiac disease biodetection using lossy-mode resonances generated in tapered single-mode optical fibers

Science.gov (United States)

Socorro, A. B.; Corres, J. M.; Del Villar, I.; Matias, I. R.; Arregui, F. J.

2014-05-01

This work presents the development and test of an anti-gliadin antibodies biosensor based on lossy mode resonances (LMRs) to detect celiac disease. Several polyelectrolites were used to perform layer-by-layer assembly processes in order to generate the LMR and to fabricate a gliadin-embedded thin-film. The LMR shifted 20 nm when immersed in a 5 ppm anti-gliadin antibodies-PBS solution, what makes this bioprobe suitable for detecting celiac disease. This is the first time, to our knowledge, that LMRs are used to detect celiac disease and these results suppose promising prospects on the use of such phenomena as biological detectors.

FUSE: a profit maximization approach for functional summarization of biological networks.

Science.gov (United States)

Seah, Boon-Siew; Bhowmick, Sourav S; Dewey, C Forbes; Yu, Hanry

2012-03-21

The availability of large-scale curated protein interaction datasets has given rise to the opportunity to investigate higher level organization and modularity within the protein interaction network (PPI) using graph theoretic analysis. Despite the recent progress, systems level analysis of PPIS remains a daunting task as it is challenging to make sense out of the deluge of high-dimensional interaction data. Specifically, techniques that automatically abstract and summarize PPIS at multiple resolutions to provide high level views of its functional landscape are still lacking. We present a novel data-driven and generic algorithm called FUSE (Functional Summary Generator) that generates functional maps of a PPI at different levels of organization, from broad process-process level interactions to in-depth complex-complex level interactions, through a pro t maximization approach that exploits Minimum Description Length (MDL) principle to maximize information gain of the summary graph while satisfying the level of detail constraint. We evaluate the performance of FUSE on several real-world PPIS. We also compare FUSE to state-of-the-art graph clustering methods with GO term enrichment by constructing the biological process landscape of the PPIS. Using AD network as our case study, we further demonstrate the ability of FUSE to quickly summarize the network and identify many different processes and complexes that regulate it. Finally, we study the higher-order connectivity of the human PPI. By simultaneously evaluating interaction and annotation data, FUSE abstracts higher-order interaction maps by reducing the details of the underlying PPI to form a functional summary graph of interconnected functional clusters. Our results demonstrate its effectiveness and superiority over state-of-the-art graph clustering methods with GO term enrichment.

Understanding the Biological Roles of Pectins in Plants through Physiological and Functional Characterizations of Plant and Fungal Mutants

DEFF Research Database (Denmark)

Stranne, Maria

The plant cell wall is a dynamic structure and it is involved in regulating a number of physiological features of plants such as physical strength, growth, cell differentiation, intercellular communication, water movement and defense responses. Pectins constitute a major class of plant cell wall...... polysaccharides and consist of backbones rich in galacturonic acids, which are decorated with a range of functional groups including acetyl esters and arabinan sidechains. Although much effort has been made to uncover biological functions of pectins in plants and remarkable progresses have taken place, many...... aspects remain elusive. Studies described in this thesis aimed at gaining new insights into the biological roles of pectin acetylation and arabinosylation in the model plant Arabidopsis thaliana. The thesis consists of four chapters: physiological characterization of cell wall mutants affected in cell...

Effect of step function-like perturbation on intermittent contact mode sensors: a response analysis

International Nuclear Information System (INIS)

Kokavecz, Janos; Heszler, Peter; Toth, Zsolt; Mechler, Adam

2003-01-01

The dynamics of the intermittent contact mode (ICM) probe was investigated. In the experimental study we applied a step function signal to the Z piezo drive and recorded the amplitude signal of the probe while the probe was engaged with the surface. Transient overshoots appear at the edges of the steps. These transients are absent from the control contact force measurements, that is, they are proper to the ICM operation. The phenomenon was investigated by numerical calculations, focused on the effect of change of the drive frequency and the quality factor. We concluded, that the low value of the quality factor results in small transients and short settling time, which are necessary for fast atomic force microscopic operation. Simultaneously, the interaction force increases. Our calculations indicate that the tip-sample force can be lowered by setting the drive frequency slightly below the resonance

Concepts for space nuclear multi-mode reactors

International Nuclear Information System (INIS)

Myrabo, L.; Botts, T.E.; Powell, J.R.

1983-01-01

A number of nuclear multi-mode reactor power plants are conceptualized for use with solid core, fixed particle bed and rotating particle bed reactors. Multi-mode systems generate high peak electrical power in the open cycle mode, with MHD generator or turbogenerator converters and cryogenically stored coolants. Low level stationkeeping power and auxiliary reactor cooling (i.e., for the removal of reactor afterheat) are provided in a closed cycle mode. Depending on reactor design, heat transfer to the low power converters can be accomplished by heat pipes, liquid metal coolants or high pressure gas coolants. Candidate low power conversion cycles include Brayton turbogenerator, Rankine turbogenerator, thermoelectric and thermionic approaches. A methodology is suggested for estimating the system mass of multi-mode nuclear power plants as a function of peak electric power level and required mission run time. The masses of closed cycle nuclear and open cycle chemical power systems are briefly examined to identify the regime of superiority for nuclear multi-mode systems. Key research and technology issues for such power plants are also identified

Measurement of specimen-induced aberrations of biological samples using phase stepping interferometry.

Science.gov (United States)

Schwertner, M; Booth, M J; Neil, M A A; Wilson, T

2004-01-01

Confocal or multiphoton microscopes, which deliver optical sections and three-dimensional (3D) images of thick specimens, are widely used in biology. These techniques, however, are sensitive to aberrations that may originate from the refractive index structure of the specimen itself. The aberrations cause reduced signal intensity and the 3D resolution of the instrument is compromised. It has been suggested to correct for aberrations in confocal microscopes using adaptive optics. In order to define the design specifications for such adaptive optics systems, one has to know the amount of aberrations present for typical applications such as with biological samples. We have built a phase stepping interferometer microscope that directly measures the aberration of the wavefront. The modal content of the wavefront is extracted by employing Zernike mode decomposition. Results for typical biological specimens are presented. It was found for all samples investigated that higher order Zernike modes give only a small contribution to the overall aberration. Therefore, these higher order modes can be neglected in future adaptive optics sensing and correction schemes implemented into confocal or multiphoton microscopes, leading to more efficient designs.

Nuclear scissors modes and hidden angular momenta

Energy Technology Data Exchange (ETDEWEB)

Balbutsev, E. B., E-mail: balbuts@theor.jinr.ru; Molodtsova, I. V. [Joint Institute for Nuclear Research (Russian Federation); Schuck, P. [Université Paris-Sud, Institut de Physique Nucléaire, IN2P3–CNRS (France)

2017-01-15

The coupled dynamics of low-lying modes and various giant resonances are studied with the help of the Wigner Function Moments method generalized to take into account spin degrees of freedom and pair correlations simultaneously. The method is based on Time-Dependent Hartree–Fock–Bogoliubov equations. The model of the harmonic oscillator including spin–orbit potential plus quadrupole–quadrupole and spin–spin interactions is considered. New low-lying spin-dependent modes are analyzed. Special attention is paid to the scissors modes. A new source of nuclear magnetism, connected with counter-rotation of spins up and down around the symmetry axis (hidden angular momenta), is discovered. Its inclusion into the theory allows one to improve substantially the agreement with experimental data in the description of energies and transition probabilities of scissors modes.

Strategies for the chemical and biological functionalization of scaffolds for cardiac tissue engineering: a review.

Science.gov (United States)

Tallawi, Marwa; Rosellini, Elisabetta; Barbani, Niccoletta; Cascone, Maria Grazia; Rai, Ranjana; Saint-Pierre, Guillaume; Boccaccini, Aldo R

2015-07-06

The development of biomaterials for cardiac tissue engineering (CTE) is challenging, primarily owing to the requirement of achieving a surface with favourable characteristics that enhances cell attachment and maturation. The biomaterial surface plays a crucial role as it forms the interface between the scaffold (or cardiac patch) and the cells. In the field of CTE, synthetic polymers (polyglycerol sebacate, polyethylene glycol, polyglycolic acid, poly-l-lactide, polyvinyl alcohol, polycaprolactone, polyurethanes and poly(N-isopropylacrylamide)) have been proven to exhibit suitable biodegradable and mechanical properties. Despite the fact that they show the required biocompatible behaviour, most synthetic polymers exhibit poor cell attachment capability. These synthetic polymers are mostly hydrophobic and lack cell recognition sites, limiting their application. Therefore, biofunctionalization of these biomaterials to enhance cell attachment and cell material interaction is being widely investigated. There are numerous approaches for functionalizing a material, which can be classified as mechanical, physical, chemical and biological. In this review, recent studies reported in the literature to functionalize scaffolds in the context of CTE, are discussed. Surface, morphological, chemical and biological modifications are introduced and the results of novel promising strategies and techniques are discussed.

Meet-in-the-Middle Preimage Attacks on Hash Modes of Generalized Feistel and Misty Schemes with SP Round Function

Science.gov (United States)

Moon, Dukjae; Hong, Deukjo; Kwon, Daesung; Hong, Seokhie

We assume that the domain extender is the Merkle-Damgård (MD) scheme and he message is padded by a ‘1’, and minimum number of ‘0’s, followed by a fixed size length information so that the length of padded message is multiple of block length. Under this assumption, we analyze securities of the hash mode when the compression function follows the Davies-Meyer (DM) scheme and the underlying block cipher is one of the plain Feistel or Misty scheme or the generalized Feistel or Misty schemes with Substitution-Permutation (SP) round function. We do this work based on Meet-in-the-Middle (MitM) preimage attack techniques, and develop several useful initial structures.

How biological soil crusts became recognized as a functional unit: a selective history

Science.gov (United States)

Lange, Otto L.; Belnap, Jayne

2016-01-01

It is surprising that despite the world-wide distribution and general importance of biological soil crusts (biocrusts), scientific recognition and functional analysis of these communities is a relatively young field of science. In this chapter, we sketch the historical lines that led to the recognition of biocrusts as a community with important ecosystem functions. The idea of biocrusts as a functional ecological community has come from two main scientific branches: botany and soil science. For centuries, botanists have long recognized that multiple organisms colonize the soil surface in the open and often dry areas occurring between vascular plants. Much later, after the initial taxonomic and phyto-sociological descriptions were made, soil scientists and agronomists observed that these surface organisms interacted with soils in ways that changed the soil structure. In the 1970’s, research on these communities as ecological units that played an important functional role in drylands began in earnest, and these studies have continued to this day. Here, we trace the history of these studies from the distant past until 1990, when biocrusts became well-known to scientists and the public.

Spatial Disassociation of Disrupted Functional Connectivity for the Default Mode Network in Patients with End-Stage Renal Disease.

Directory of Open Access Journals (Sweden)

Xiaofen Ma

Full Text Available To investigate the aberrant functional connectivity of the default mode network (DMN in patients with end-stage renal disease (ESRD and their clinical relevance.Resting-state functional MRI data were collected from 31 patients with ESRD (24 men, 24-61 years and 31 age- and gender-matched healthy controls (HCs, 21 men, 26-61years. A whole-brain seed-based functional connectivity analysis of these collected R-fMRI data was performed by locating the seeds in the posterior cingulate cortex (PCC and ventromedial prefrontal cortex (vmPFC to investigate the functional connectivity of the posterior and anterior DMN over the whole brain, respectively.Compared to the HCs, the patients exhibited significantly decreased functional connectivity with the PCC in the left middle temporal gyrus, the right anterior cingulate gyrus, and the bilateral medial superior frontal gyrus. For the vmPFC seed, only the right thalamus showed significantly decreased functional connectivity in the patients with ESRD compared to HCs. Interestingly, functional connectivity between the PCC and right medial superior frontal gyrus exhibited a significantly positive correlation with the hemoglobin level in the patients.Our findings suggest a spatially specific disruption of functional connectivity in the DMN in patients with ESRD, thereby providing novel insights into our understanding of the neurophysiology mechanism that underlies the disease.

Optimization of polysaccharides extraction from watermelon rinds: Structure, functional and biological activities.

Science.gov (United States)

Romdhane, Molka Ben; Haddar, Anissa; Ghazala, Imen; Jeddou, Khawla Ben; Helbert, Claire Boisset; Ellouz-Chaabouni, Semia

2017-02-01

In the present work, optimization of hot water extraction, structural characteristics, functional properties, and biological activities of polysaccharides extracted from watermelon rinds (WMRP) were investigated. The physicochemical characteristics and the monosaccharide composition of these polysaccharides were then determined using chemical composition analysis, Fourier transform infrared (FT-IR) spectroscopy, scanning electron microscopy (SEM) and gas chromatography-flame ionization detection (GC-FID). SEM images showed that extracted polysaccharides had a rough surface with many cavities. GC-FID results proved that galactose was the dominant sugar in the extracted polysaccharides, followed by arabinose, glucose, galacturonic acid, rhamnose, mannose, xylose and traces of glucuronic acid. The findings revealed that WMRP displayed excellent antihypertensive and antioxidant activities. Those polysaccharides had also a protection effect against hydroxyl radical-induced DNA damage. Functional properties of extracted polysaccharides were also evaluated. WMRP showed good interfacial dose-dependent proprieties. Overall, the results suggested that WMRP presents a promising natural source of antioxidants and antihypertensive agents. Copyright © 2016 Elsevier Ltd. All rights reserved.

Microtearing modes

International Nuclear Information System (INIS)

Garbet, X.; Mourgues, F.; Samain, A.; Zou, X.

1990-01-01

A serious degradation of confinement with additional heating is commonly observed on most tokamaks. The microtearing modes could provide an explanation for this experimental fact. They are driven linearly unstable by diamagnetism in collisional regimes, but it may be shown that the collisions in non linear regimes provide a small diffusion coefficient which can be only significant at the plasme edge. In the bulk of the plasma, the microtearing turbulence could play a basic role if it is unstable in the collisionless regime. While it is linearly stable without collisions, it could be driven unstable in realistic regimes by the radial diffusion it induces. To study this effect, we have used a model where the non linear action of the modes on a given helicity component is represented by a diffusion operator. They are found unstable for reasonable β p =2μ o nT/B 2 p , with a special radial profile of the potential vector A. The problem arises the validity of this model where non linearities in the trajectories behaviour are replaced by the diffusion which broadens resonances. To test this procedure, we calculate the actual electron distribution function when it is determined by the ergodicity of the field lines. We compute the correlations of the distribution function with the magnetic perturbation and compare them with the analytical expressions derived from the resonance broadening model. (author) 3 refs., 2 figs

Connecting Structure-Property and Structure-Function Relationships across the Disciplines of Chemistry and Biology: Exploring Student Perceptions

Science.gov (United States)

Kohn, Kathryn P.; Underwood, Sonia M.; Cooper, Melanie M.

2018-01-01

While many university students take science courses in multiple disciplines, little is known about how they perceive common concepts from different disciplinary perspectives. Structure-property and structure-function relationships have long been considered important explanatory concepts in the disciplines of chemistry and biology, respectively.…

Carcinogenesis: alterations in reciprocal interactions of normal functional structure of biologic systems.

Science.gov (United States)

Davydyan, Garri

2015-12-01

The evolution of biologic systems (BS) includes functional mechanisms that in some conditions may lead to the development of cancer. Using mathematical group theory and matrix analysis, previously, it was shown that normally functioning BS are steady functional structures regulated by three basis regulatory components: reciprocal links (RL), negative feedback (NFB) and positive feedback (PFB). Together, they form an integrative unit maintaining system's autonomy and functional stability. It is proposed that phylogenetic development of different species is implemented by the splitting of "rudimentary" characters into two relatively independent functional parts that become encoded in chromosomes. The functional correlate of splitting mechanisms is RL. Inversion of phylogenetic mechanisms during ontogenetic development leads cell differentiation until cells reach mature states. Deterioration of reciprocal structure in the genome during ontogenesis gives rise of pathological conditions characterized by unsteadiness of the system. Uncontrollable cell proliferation and invasive cell growth are the leading features of the functional outcomes of malfunctioning systems. The regulatory element responsible for these changes is RL. In matrix language, pathological regulation is represented by matrices having positive values of diagonal elements ( TrA  > 0) and also positive values of matrix determinant ( detA  > 0). Regulatory structures of that kind can be obtained if the negative entry of the matrix corresponding to RL is replaced with the positive one. To describe not only normal but also pathological states of BS, a unit matrix should be added to the basis matrices representing RL, NFB and PFB. A mathematical structure corresponding to the set of these four basis functional patterns (matrices) is a split quaternion (coquaternion). The structure and specific role of basis elements comprising four-dimensional linear space of split quaternions help to understand what

Biological Petri Nets

CERN Document Server

Wingender, E

2011-01-01

It was suggested some years ago that Petri nets might be well suited to modeling metabolic networks, overcoming some of the limitations encountered by the use of systems employing ODEs (ordinary differential equations). Much work has been done since then which confirms this and demonstrates the usefulness of this concept for systems biology. Petri net technology is not only intuitively understood by scientists trained in the life sciences, it also has a robust mathematical foundation and provides the required degree of flexibility. As a result it appears to be a very promising approach to mode

Dynamic feedback for multi-mode plasma instabilities

International Nuclear Information System (INIS)

Sen, A.K.

1978-01-01

Constant feedback, which has been used exclusively, fails to stabilize more than one mode of a plasma instability. It is shown that a suitable dynamic or frequency-dependent feedback can stabilize all modes. Methods are developed in which such a feedback structure can be chosen in terms of its poles and zeros in relation to those of the plasma transfer function in the complex frequency plane. The synthesis procedure for such a feedback structure, in the form of an integrated electronic circuit is also discussed. As an example, a dynamic feedback for multi-mode stabilization of a collisional drift wave instability is developed in detail. (author)

Cognitive and behavioral comorbidities in Rolandic epilepsy and their relation with default mode network's functional connectivity and organization.

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Ofer, Isabell; Jacobs, Julia; Jaiser, Nathalie; Akin, Burak; Hennig, Jürgen; Schulze-Bonhage, Andreas; LeVan, Pierre

2018-01-01

Rolandic epilepsy (RE) is characterized by typical interictal-electroencephalogram (EEG) patterns mainly localized in centrotemporal and parietooccipital areas. An aberrant intrinsic organization of the default mode network (DMN) due to repeated disturbances from spike-generating areas may be able to account for specific cognitive deficits and behavioral problems in RE. The aim of the present study was to investigate cognitive development (CD) and socioemotional development (SED) in patients with RE during active disease in relation to DMN connectivity and network topology. In 10 children with RE and active EEG, CD was assessed using the Wechsler Intelligence Scale for Children-IV (WISC-IV); SED was assessed using the Fünf-Faktoren-Fragebogen für Kinder (FFFK), a Big-Five inventory for the assessment of personality traits in children. Functional connectivity (FC) in the DMN was determined from a 15-minute resting state functional magnetic resonance imaging (fMRI), and network properties were calculated using standard graph-theoretical measures. More severe deficits of verbal abilities tended to be associated with an earlier age at epilepsy onset, but were not directly related to the number of seizures and disease duration. Nonetheless, at the network level, disease duration was associated with alterations of the efficiency and centrality of parietal network nodes and midline structures. Particularly, centrality of the left inferior parietal lobe (IPL) was found to be linked with CD. Reduced centrality of the left IPL and alterations supporting a rather segregated processing within DMN's subsystems was associated with a more favorable CD. A more complicated SED was associated with high seizure frequency and long disease duration, and revealed links with a less favorable CD. An impaired CD and - because of their interrelation - SED might be mediated by a common pathomechanism reflected in an aberrant organization, and thus, a potential functional deficit of the DMN

A Tricky Trait: Applying the Fruits of the “Function Debate” in the Philosophy of Biology to the “Venom Debate” in the Science of Toxinology

Science.gov (United States)

Jackson, Timothy N. W.; Fry, Bryan G.

2016-01-01

The “function debate” in the philosophy of biology and the “venom debate” in the science of toxinology are conceptually related. Venom systems are complex multifunctional traits that have evolved independently numerous times throughout the animal kingdom. No single concept of function, amongst those popularly defended, appears adequate to describe these systems in all their evolutionary contexts and extant variations. As such, a pluralistic view of function, previously defended by some philosophers of biology, is most appropriate. Venom systems, like many other functional traits, exist in nature as points on a continuum and the boundaries between “venomous” and “non-venomous” species may not always be clearly defined. This paper includes a brief overview of the concept of function, followed by in-depth discussion of its application to venom systems. A sound understanding of function may aid in moving the venom debate forward. Similarly, consideration of a complex functional trait such as venom may be of interest to philosophers of biology. PMID:27618098

A Tricky Trait: Applying the Fruits of the “Function Debate” in the Philosophy of Biology to the “Venom Debate” in the Science of Toxinology

Directory of Open Access Journals (Sweden)

Timothy N. W. Jackson

2016-09-01

Full Text Available The “function debate” in the philosophy of biology and the “venom debate” in the science of toxinology are conceptually related. Venom systems are complex multifunctional traits that have evolved independently numerous times throughout the animal kingdom. No single concept of function, amongst those popularly defended, appears adequate to describe these systems in all their evolutionary contexts and extant variations. As such, a pluralistic view of function, previously defended by some philosophers of biology, is most appropriate. Venom systems, like many other functional traits, exist in nature as points on a continuum and the boundaries between “venomous” and “non-venomous” species may not always be clearly defined. This paper includes a brief overview of the concept of function, followed by in-depth discussion of its application to venom systems. A sound understanding of function may aid in moving the venom debate forward. Similarly, consideration of a complex functional trait such as venom may be of interest to philosophers of biology.

Radiogas chromatography mass spectrometry in the selected ion monitoring mode

International Nuclear Information System (INIS)

Doerfler, D.L.; Rosenblum, E.R.; Malloy, J.M.; Naworal, J.D.; McManus, I.R.; Campbell, I.M.

1980-01-01

The value of selected ion monitoring in analyzing biological radio isotope incorporation experiments by radiogas chromatography mass spectrometry is illustrated with reference to the biosynthesis of the mycotoxin mycophenolic acid in Penicillium brevicompactum and the mode of action of the anticholesterolemic drug 20,25-diazacholesterol. Both examples used 1-[ 14 C]acetate precursors. It is shown that the increased sensitivity and specificity of the selected ion monitoring mode detector permits straightforward detection and identification of the relatively small cellular pools associated with metabolic intermediates. The computer program RADSIM is described. Problems that still exist in using radiogas gas chromatography mass spectrometry technology to analyse isotope incorporation experiments are discussed. (author)

Application of surface plasmons to biological and chemical sensors

International Nuclear Information System (INIS)

Kajikawa, Kotaro

2015-01-01

Surface plasmons (SPs) are a collective normal mode of electrons localized at a metallic surface. It has been used for biological sensors since 1990s. This is because it has the following specific characters: (a) The resonance condition is sensitive to the surrounding dielectric constants (refractive indexes) and (b) Highly enhanced optical-electric-fields are produced adjacent to SPs. A brief introduction is given on the principle of the biological and chemical sensors based on SPs for the readers working in the fields other than SPs, followed by a review on the recent developments of the biological and chemical sensors. (author)

Green leaf volatiles: biosynthesis, biological functions and their applications in biotechnology.

Science.gov (United States)

ul Hassan, Muhammad Naeem; Zainal, Zamri; Ismail, Ismanizan

2015-08-01

Plants have evolved numerous constitutive and inducible defence mechanisms to cope with biotic and abiotic stresses. These stresses induce the expression of various genes to activate defence-related pathways that result in the release of defence chemicals. One of these defence mechanisms is the oxylipin pathway, which produces jasmonates, divinylethers and green leaf volatiles (GLVs) through the peroxidation of polyunsaturated fatty acids (PUFAs). GLVs have recently emerged as key players in plant defence, plant-plant interactions and plant-insect interactions. Some GLVs inhibit the growth and propagation of plant pathogens, including bacteria, viruses and fungi. In certain cases, GLVs released from plants under herbivore attack can serve as aerial messengers to neighbouring plants and to attract parasitic or parasitoid enemies of the herbivores. The plants that perceive these volatile signals are primed and can then adapt in preparation for the upcoming challenges. Due to their 'green note' odour, GLVs impart aromas and flavours to many natural foods, such as vegetables and fruits, and therefore, they can be exploited in industrial biotechnology. The aim of this study was to review the progress and recent developments in research on the oxylipin pathway, with a specific focus on the biosynthesis and biological functions of GLVs and their applications in industrial biotechnology. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Quasinormal modes of Kerr-de Sitter black holes

International Nuclear Information System (INIS)

Yoshida, Shijun; Uchikata, Nami; Futamase, Toshifumi

2010-01-01

We calculate the fundamental quasinormal modes of the Kerr-de Sitter black hole for the first time. In order to calculate the quasinormal modes, we employ the master equations derived by Suzuki, Takasugi, and Umetsu, who transform the Teukolsky equations for the Kerr-de Sitter black hole into the standard form of the Heun's equation. The transformed functions are expanded around the outer horizon of the black hole or the symmetric axis in the Froebenius series whose coefficients satisfy a three-term recurrence relation. These three-term recurrence relations allow us to use Leaver's continued fraction method to calculate the angular separation constant and the quasinormal mode frequency. Any unstable fundamental quasinormal mode is not found in this paper. It is also observed that for some black holes characterized by a large mass parameter, some retrograde modes in the slow rotation limit become prograde as the black hole spin increases. This phenomenon does not occur for the fundamental modes of the Kerr black hole.

Marine Carotenoids: Biological Functions and Commercial Applications

NARCIS (Netherlands)

Vilchez, C.; Forján, E.; Cuaresma, M.; Bédmar, F.; Garbayo, I.; Vega, J.M.

2011-01-01

Carotenoids are the most common pigments in nature and are synthesized by all photosynthetic organisms and fungi. Carotenoids are considered key molecules for life. Light capture, photosynthesis photoprotection, excess light dissipation and quenching of singlet oxygen are among key biological

Physical characterization of diesel exhaust nucleation mode particles

Energy Technology Data Exchange (ETDEWEB)

Lahde, T.

2013-11-01

An increasing concern of the adverse health effects of aerosol particles is forcing the combustion engine industry to develop engines with lower particle emissions. The industry has put most of their efforts into soot control and has achieved a significant reduction in diesel exhaust particle mass. Nevertheless, it is not clear that the large particles, dominating the mass, cause the harmfulness of the exhaust particles in the biological interaction. Nowadays, the harmful potential of diesel exhaust particles often connects with the particle surface area, and the view has turned to particle number below 100 nm size range. Unfortunately, the achieved low exhaust particle mass does not necessarily imply a low particle number. This text focuses on the physical characteristics of diesel exhaust nucleation model particles. The volatility characteristics and the electrical charge state of the particles are studied first. Second, the relation between the nonvolatile nucleation mode emissions and the soot, the nitrogen oxide (NO{sub x}) emissions and the engine parameters are covered. The nucleation mode particles had distinctively different physical characteristics with different after-treatment systems. The nucleation mode was volatile and electrically neutral with a diesel particle filter after-treatment system. Without an after-treatment system or with an after-treatment system with low particle removal efficiency, the nucleation mode was partly nonvolatile and included an electrical charge. The difference suggests different formation routes for the nucleation particles with different after-treatment systems. The existence of the nonvolatile nucleation mode particles also affected the soot mode charge state. The soot charge state was positively biased when the nonvolatile nucleation mode was detected but slightly negatively biased when the nonvolatile nucleation mode was absent. The nonvolatile nucleation mode was always negatively biased. This electrical charge

Coral Reef Health Indices versus the Biological, Ecological and Functional Diversity of Fish and Coral Assemblages in the Caribbean Sea.

Science.gov (United States)

Díaz-Pérez, Leopoldo; Rodríguez-Zaragoza, Fabián Alejandro; Ortiz, Marco; Cupul-Magaña, Amílcar Leví; Carriquiry, Jose D; Ríos-Jara, Eduardo; Rodríguez-Troncoso, Alma Paola; García-Rivas, María Del Carmen

2016-01-01

This study evaluated the relationship between the indices known as the Reef Health Index (RHI) and two-dimensional Coral Health Index (2D-CHI) and different representative metrics of biological, ecological and functional diversity of fish and corals in 101 reef sites located across seven zones in the western Caribbean Sea. Species richness and average taxonomic distinctness were used to asses biological estimation; while ecological diversity was evaluated with the indices of Shannon diversity and Pielou´s evenness, as well as by taxonomic diversity and distinctness. Functional diversity considered the number of functional groups, the Shannon diversity and the functional Pielou´s evenness. According to the RHI, 57.15% of the zones were classified as presenting a "poor" health grade, while 42.85% were in "critical" grade. Based on the 2D-CHI, 28.5% of the zones were in "degraded" condition and 71.5% were "very degraded". Differences in fish and coral diversity among sites and zones were demonstrated using permutational ANOVAs. Differences between the two health indices (RHI and 2D-CHI) and some indices of biological, ecological and functional diversity of fish and corals were observed; however, only the RHI showed a correlation between the health grades and the species and functional group richness of fish at the scale of sites, and with the species and functional group richness and Shannon diversity of the fish assemblages at the scale of zones. None of the health indices were related to the metrics analyzed for the coral diversity. In general, our study suggests that the estimation of health indices should be complemented with classic community indices, or should at least include diversity indices of fish and corals, in order to improve the accuracy of the estimated health status of coral reefs in the western Caribbean Sea.

Pair distribution functions of amorphous organic thin films from synchrotron X-ray scattering in transmission mode

Directory of Open Access Journals (Sweden)

Chenyang Shi

2017-09-01

Full Text Available Using high-brilliance high-energy synchrotron X-ray radiation, for the first time the total scattering of a thin organic glass film deposited on a strongly scattering inorganic substrate has been measured in transmission mode. The organic thin film was composed of the weakly scattering pharmaceutical substance indomethacin in the amorphous state. The film was 130 µm thick atop a borosilicate glass substrate of equal thickness. The atomic pair distribution function derived from the thin-film measurement is in excellent agreement with that from bulk measurements. This ability to measure the total scattering of amorphous organic thin films in transmission will enable accurate in situ structural studies for a wide range of materials.

High degree modes and instrumental effects

Energy Technology Data Exchange (ETDEWEB)

Korzennik, S G [Harvard-Smithsonian Center for Astrophysics, Cambridge, MA (United States); Rabello-Soares, M C; Schou, J [Stanford University, Stanford, CA (United States)], E-mail: skorzennik@cfa.harvard.edu

2008-10-15

frequencies resulting from solar activity over most of solar cycle 23. We present the correlation of medium and high degree modes with different solar indices. Our results confirm that the frequency shift scaled by the relative mode inertia is a function of frequency alone and follows a simple power law.

Emotional faces and the default mode network.

Science.gov (United States)

Sreenivas, S; Boehm, S G; Linden, D E J

2012-01-11

The default-mode network (DMN) of the human brain has become a central topic of cognitive neuroscience research. Although alterations in its resting state activity and in its recruitment during tasks have been reported for several mental and neurodegenerative disorders, its role in emotion processing has received relatively little attention. We investigated brain responses to different categories of emotional faces with functional magnetic resonance imaging (fMRI) and found deactivation in ventromedial prefrontal cortex (VMPFC), posterior cingulate gyrus (PC) and cuneus. This deactivation was modulated by emotional category and was less prominent for happy than for sad faces. These deactivated areas along the midline conformed to areas of the DMN. We also observed emotion-dependent deactivation of the left middle frontal gyrus, which is not a classical component of the DMN. Conversely, several areas in a fronto-parietal network commonly linked with attention were differentially activated by emotion categories. Functional connectivity patterns, as obtained by correlation of activation levels, also varied between emotions. VMPFC, PC or cuneus served as hubs between the DMN-type areas and the fronto-parietal network. These data support recent suggestions that the DMN is not a unitary system but differentiates according to task and even type of stimulus. The emotion-specific differential pattern of DMN deactivation may be explored further in patients with mood disorder, where the quest for biological markers of emotional biases is still ongoing. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

FUSE: a profit maximization approach for functional summarization of biological networks

Directory of Open Access Journals (Sweden)

Seah Boon-Siew

2012-03-01

Full Text Available Abstract Background The availability of large-scale curated protein interaction datasets has given rise to the opportunity to investigate higher level organization and modularity within the protein interaction network (PPI using graph theoretic analysis. Despite the recent progress, systems level analysis of PPIS remains a daunting task as it is challenging to make sense out of the deluge of high-dimensional interaction data. Specifically, techniques that automatically abstract and summarize PPIS at multiple resolutions to provide high level views of its functional landscape are still lacking. We present a novel data-driven and generic algorithm called FUSE (Functional Summary Generator that generates functional maps of a PPI at different levels of organization, from broad process-process level interactions to in-depth complex-complex level interactions, through a pro t maximization approach that exploits Minimum Description Length (MDL principle to maximize information gain of the summary graph while satisfying the level of detail constraint. Results We evaluate the performance of FUSE on several real-world PPIS. We also compare FUSE to state-of-the-art graph clustering methods with GO term enrichment by constructing the biological process landscape of the PPIS. Using AD network as our case study, we further demonstrate the ability of FUSE to quickly summarize the network and identify many different processes and complexes that regulate it. Finally, we study the higher-order connectivity of the human PPI. Conclusion By simultaneously evaluating interaction and annotation data, FUSE abstracts higher-order interaction maps by reducing the details of the underlying PPI to form a functional summary graph of interconnected functional clusters. Our results demonstrate its effectiveness and superiority over state-of-the-art graph clustering methods with GO term enrichment.

Excited-state lifetimes of far-infrared collective modes in proteins

NARCIS (Netherlands)

Xie, A.; van der Meer, L.; Austin, R. H.

2002-01-01

Vibrational excitations of low frequency collective modes are essential for functionally important conformational transitions in proteins. Here we report the first direct measurement on the lifetime of vibrational excitations of the collective modes at 87 pm (115 cm(-1)) in bacteriorhodopsin, a

Fostering synergy between cell biology and systems biology.

Science.gov (United States)

Eddy, James A; Funk, Cory C; Price, Nathan D

2015-08-01

In the shared pursuit of elucidating detailed mechanisms of cell function, systems biology presents a natural complement to ongoing efforts in cell biology. Systems biology aims to characterize biological systems through integrated and quantitative modeling of cellular information. The process of model building and analysis provides value through synthesizing and cataloging information about cells and molecules, predicting mechanisms and identifying generalizable themes, generating hypotheses and guiding experimental design, and highlighting knowledge gaps and refining understanding. In turn, incorporating domain expertise and experimental data is crucial for building towards whole cell models. An iterative cycle of interaction between cell and systems biologists advances the goals of both fields and establishes a framework for mechanistic understanding of the genome-to-phenome relationship. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Non-Markovian reduced dynamics based upon a hierarchical effective-mode representation

Energy Technology Data Exchange (ETDEWEB)

Burghardt, Irene [Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt (Germany); Martinazzo, Rocco [Dipartimento di Chimica, Universita degli Studi di Milano, v. Golgi 19, 20133 Milano (Italy); Hughes, Keith H. [School of Chemistry, Bangor University, Bangor, Gwynedd LL57 2UW (United Kingdom)

2012-10-14

A reduced dynamics representation is introduced which is tailored to a hierarchical, Mori-chain type representation of a bath of harmonic oscillators which are linearly coupled to a subsystem. We consider a spin-boson system where a single effective mode is constructed so as to absorb all system-environment interactions, while the residual bath modes are coupled bilinearly to the primary mode and among each other. Using a cumulant expansion of the memory kernel, correlation functions for the primary mode are obtained, which can be suitably approximated by truncated chains representing the primary-residual mode interactions. A series of reduced-dimensional bath correlation functions is thus obtained, which can be expressed as Fourier-Laplace transforms of spectral densities that are given in truncated continued-fraction form. For a master equation which is second order in the system-bath coupling, the memory kernel is re-expressed in terms of local-in-time equations involving auxiliary densities and auxiliary operators.

Michael Levitt and Computational Biology

Science.gov (United States)

dropdown arrow Site Map A-Z Index Menu Synopsis Michael Levitt and Computational Biology Resources with Michael Levitt, PhD, professor of structural biology at the Stanford University School of Medicine, has function. ... Levitt's early work pioneered computational structural biology, which helped to predict

Academic Beliefs and Behaviors in On-Campus and Online General Education Biology Classes

Science.gov (United States)

Noll, Christopher B.

2015-01-01

This study examined the effect of course delivery mode on academic help-seeking beliefs and behaviors, academic self-efficacy, and the levels of individual interest in biology of students in an entry-level General Education biology course. This intersection of online education, science courses, and academic success factors merits attention because…

Multipolar modes in dielectric disk resonator for wireless power transfer

Science.gov (United States)

Song, Mingzhao; Belov, Pavel; Kapitanova, Polina

2017-09-01

We demonstrate a magnetic resonant WPT system based on dielectric disk resonators and investigated the WPT efficiency as a function of separation. It has been demonstrated that the power transfer can be achieved at different multipolar modes. The numerical study shows that the highest WPT efficiency of 99% can be obtained for the MQ mode in an ideal case. However, the efficiency of MQ mode decays much faster than the MD mode which suggests that a trade-off has to be made in the practical WPT system design.

Simple immunoglobulin G sensor based on thin core single-mode fiber

Science.gov (United States)

Zheng, Yingfang; Lang, Tingting; Shen, Tingting; Shen, Changyu

2018-03-01

In this paper, a simple fiber biosensor (FOB) for immunoglobulin G (IgG) detection is designed and experimentally verified. The FOB is constructed by a 20 mm long thin core single-mode fiber (TCSMF) sandwiched between two single-mode optical fibers (SMFs). First, the refractive index (RI) sensitivity of the fiber structures is calculated by the beam propagation method. The refractive index sensing experiment is performed using different concentrations of glycerol solutions, and the experimental results are mostly consistent with the simulation predictions. The experimental RI sensitivity increases with the surrounding RI and reaches 82.7 nm/RIU. Then the surface of the FOB is functionalized by APTES for covalent bonding. The human IgG and goat anti-human IgG are chosen as a bioconjugated pair to examine the bio-sensing effectiveness of this FOB. The sensitivity of IgG detection is determined to be 10.4 nm/(mg/ml). And the serum IgG concentration in normal adults lies within the range of 6-16 mg/ml (Worsfold et al., 1985), so the sensor is applicable to human IgG monitoring. The specificity of the FOB is also verified by a contrast experiment conducted using rabbit immunoglobulin G. The proposed FOB is simple, low loss, cost-effective, and can be used for various biological and chemical applications.

Modes of winter precipitation variability in the North Atlantic

Energy Technology Data Exchange (ETDEWEB)

Zorita, E. [GKSS-Forschungszentrum Geesthacht GmbH (Germany). Inst. fuer Hydrophysik; Saenz, J.; Fernandez, J.; Zubillaga, J. [Bilbao Univ. (Spain)

2001-07-01

The modes of variability of winter precipitation in the North Atlantic sector are identified by Empirical Orthogonal Functions Analysis in the NCEP/NCAR global reanalysis data sets. These modes are also present in a gridded precipitation data set over the Western Europe. The large-scale fields of atmospheric seasonal mean circulation, baroclinic activity, evaporation and humidity transport that are connected to the rainfall modes have been also analyzed in order to investigate the physical mechanisms that are causally linked to the rainfall modes. The results indicate that the leading rainfall mode is associated to the North Atlantic oscillation and represents a meridional redistribution of precipitation in the North Atlantic through displacements of the storm tracks. The second mode is related to evaporation anomalies in the Eastern Atlantic that precipitate almost entirely in the Western Atlantic. The third mode seems to be associated to meridional transport of water vapor from the Tropical Atlantic. (orig.)

Characterization of the stability and bio-functionality of tethered proteins on bioengineered scaffolds: implications for stem cell biology and tissue repair.

Science.gov (United States)

Wang, Ting-Yi; Bruggeman, Kiara A F; Sheean, Rebecca K; Turner, Bradley J; Nisbet, David R; Parish, Clare L

2014-05-23

Various engineering applications have been utilized to deliver molecules and compounds in both innate and biological settings. In the context of biological applications, the timely delivery of molecules can be critical for cellular and organ function. As such, previous studies have demonstrated the superiority of long-term protein delivery, by way of protein tethering onto bioengineered scaffolds, compared with conventional delivery of soluble protein in vitro and in vivo. Despite such benefits little knowledge exists regarding the stability, release kinetics, longevity, activation of intracellular pathway, and functionality of these proteins over time. By way of example, here we examined the stability, degradation and functionality of a protein, glial-derived neurotrophic factor (GDNF), which is known to influence neuronal survival, differentiation, and neurite morphogenesis. Enzyme-linked immunosorbent assays (ELISA) revealed that GDNF, covalently tethered onto polycaprolactone (PCL) electrospun nanofibrous scaffolds, remained present on the scaffold surface for 120 days, with no evidence of protein leaching or degradation. The tethered GDNF protein remained functional and capable of activating downstream signaling cascades, as revealed by its capacity to phosphorylate intracellular Erk in a neural cell line. Furthermore, immobilization of GDNF protein promoted cell survival and differentiation in culture at both 3 and 7 days, further validating prolonged functionality of the protein, well beyond the minutes to hours timeframe observed for soluble proteins under the same culture conditions. This study provides important evidence of the stability and functionality kinetics of tethered molecules. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Biological functioning of PAH-polluted and thermal desorption-treated soils assessed by fauna and microbial bioindicators.

Science.gov (United States)

Cébron, Aurélie; Cortet, Jérôme; Criquet, Stéven; Biaz, Asmaa; Calvert, Virgile; Caupert, Cécile; Pernin, Céline; Leyval, Corinne

2011-11-01

A large number of soil bioindicators were used to assess biological diversity and activity in soil polluted with polycyclic aromatic hydrocarbons (PAHs) and the same soil after thermal desorption (TD) treatment. Abundance and biodiversity of bacteria, fungi, protozoa, nematodes and microarthropods, as well as functional parameters such as enzymatic activities and soil respiration, were assessed during a two year period of in situ monitoring. We investigated the influence of vegetation (spontaneous vegetation and Medicago sativa) and TD treatment on biological functioning. Multivariate analysis was performed to analyze the whole data set. A principal response curve (PRC) technique was used to evaluate the different treatments (various vegetation and contaminated vs. TD soil) contrasted with control (bare) soil over time. Our results indicated the value of using a number of complementary bioindicators, describing both diversity and functions, to assess the influence of vegetation on soil and discriminate polluted from thermal desorption (TD)-treated soil. Plants had an influence on the abundance and activity of all organisms examined in our study, favoring the whole trophic chain development. However, although TD-treated soil had a high abundance and diversity of microorganisms and fauna, enzymatic activities were weak because of the strong physical and chemical modifications of this soil. Copyright © 2011 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Functional knowledge transfer for high-accuracy prediction of under-studied biological processes.

Directory of Open Access Journals (Sweden)

Christopher Y Park

Full Text Available A key challenge in genetics is identifying the functional roles of genes in pathways. Numerous functional genomics techniques (e.g. machine learning that predict protein function have been developed to address this question. These methods generally build from existing annotations of genes to pathways and thus are often unable to identify additional genes participating in processes that are not already well studied. Many of these processes are well studied in some organism, but not necessarily in an investigator's organism of interest. Sequence-based search methods (e.g. BLAST have been used to transfer such annotation information between organisms. We demonstrate that functional genomics can complement traditional sequence similarity to improve the transfer of gene annotations between organisms. Our method transfers annotations only when functionally appropriate as determined by genomic data and can be used with any prediction algorithm to combine transferred gene function knowledge with organism-specific high-throughput data to enable accurate function prediction. We show that diverse state-of-art machine learning algorithms leveraging functional knowledge transfer (FKT dramatically improve their accuracy in predicting gene-pathway membership, particularly for processes with little experimental knowledge in an organism. We also show that our method compares favorably to annotation transfer by sequence similarity. Next, we deploy FKT with state-of-the-art SVM classifier to predict novel genes to 11,000 biological processes across six diverse organisms and expand the coverage of accurate function predictions to processes that are often ignored because of a dearth of annotated genes in an organism. Finally, we perform in vivo experimental investigation in Danio rerio and confirm the regulatory role of our top predicted novel gene, wnt5b, in leftward cell migration during heart development. FKT is immediately applicable to many bioinformatics

BiologicalNetworks 2.0 - an integrative view of genome biology data

Directory of Open Access Journals (Sweden)

Ponomarenko Julia

2010-12-01

Full Text Available Abstract Background A significant problem in the study of mechanisms of an organism's development is the elucidation of interrelated factors which are making an impact on the different levels of the organism, such as genes, biological molecules, cells, and cell systems. Numerous sources of heterogeneous data which exist for these subsystems are still not integrated sufficiently enough to give researchers a straightforward opportunity to analyze them together in the same frame of study. Systematic application of data integration methods is also hampered by a multitude of such factors as the orthogonal nature of the integrated data and naming problems. Results Here we report on a new version of BiologicalNetworks, a research environment for the integral visualization and analysis of heterogeneous biological data. BiologicalNetworks can be queried for properties of thousands of different types of biological entities (genes/proteins, promoters, COGs, pathways, binding sites, and other and their relations (interactions, co-expression, co-citations, and other. The system includes the build-pathways infrastructure for molecular interactions/relations and module discovery in high-throughput experiments. Also implemented in BiologicalNetworks are the Integrated Genome Viewer and Comparative Genomics Browser applications, which allow for the search and analysis of gene regulatory regions and their conservation in multiple species in conjunction with molecular pathways/networks, experimental data and functional annotations. Conclusions The new release of BiologicalNetworks together with its back-end database introduces extensive functionality for a more efficient integrated multi-level analysis of microarray, sequence, regulatory, and other data. BiologicalNetworks is freely available at http://www.biologicalnetworks.org.

Functional biology and ecological role of krill in Northern marine ecosystems

DEFF Research Database (Denmark)

Agersted, Mette Dalgaard

Krill is an understudied key group of zooplankton, which transfers energy through the food web by linking lower and higher trophic levels. Furthermore, krill play an important role in the biological pump by transporting carbon out of the euphotic zone to depth by diel vertical migration (DVM...... to be the key factor determining the trophic position of a species, where the largest species had the highest trophic position. The species were feeding on the same food items, which could lead to competition for food. However, there is a difference between the two functional groups, represented by M. norvegica...... for the two dominating species within the fjord, T. inermis and T. raschii. The krill grazed community at this time of year. Yet, the grazing impact was similar to the copepods’, which are normally...

Mode-coupling theory and bunch lengthening in SPEAR II

International Nuclear Information System (INIS)

Suzuki, T.; Chin, Y.; Satoh, K.

1983-01-01

A mode-coupling theory of bunched-beam instabilities is developed for a Gaussian bunch. The theory converts Sacherer's integral equation with mode coupling into a matrix eigenvalue problem. The present theory assumes well-defined azimuthal modes and takes into account radial modes which are expressed as superpositions of orthogonal functions. The theory is applied to bunch lengthening observed at SPEAR II. The theory explains qualitative features of the experimental results fairly well, but quantitative agreement is not too good. This is ascribed to insufficient knowledge of the coupling impedance of SPEAR II or to the possibility that such effects as radiation damping and quantum excitation should be included. (author)

A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language.

Science.gov (United States)

Nguyen, Tramy; Roehner, Nicholas; Zundel, Zach; Myers, Chris J

2016-06-17

Standards are important to synthetic biology because they enable exchange and reproducibility of genetic designs. This paper describes a procedure for converting between two standards: the Systems Biology Markup Language (SBML) and the Synthetic Biology Open Language (SBOL). SBML is a standard for behavioral models of biological systems at the molecular level. SBOL describes structural and basic qualitative behavioral aspects of a biological design. Converting SBML to SBOL enables a consistent connection between behavioral and structural information for a biological design. The conversion process described in this paper leverages Systems Biology Ontology (SBO) annotations to enable inference of a designs qualitative function.

Bottom-up synthetic biology: modular design for making artificial platelets

Science.gov (United States)

Majumder, Sagardip; Liu, Allen P.

2018-01-01

Engineering artificial cells to mimic one or multiple fundamental cell biological functions is an emerging area of synthetic biology. Reconstituting functional modules from biological components in vitro is a challenging yet an important essence of bottom-up synthetic biology. Here we describe the concept of building artificial platelets using bottom-up synthetic biology and the four functional modules that together could enable such an ambitious effort.

Plasmon-polariton modes of dense Au nanowire arrays

Energy Technology Data Exchange (ETDEWEB)

Yan, Hongdan; Lemmens, Peter; Wulferding, Dirk; Cetin, Mehmet Fatih [IPKM, TU-BS, Braunschweig (Germany); Tornow, Sabine; Zwicknagl, Gertrud [IMP, TU-BS, Braunschweig (Germany); Krieg, Ulrich; Pfnuer, Herbert [IFP, LU Hannover (Germany); Daum, Winfried; Lilienkamp, Gerhard [IEPT, TU Clausthal (Germany); Schilling, Meinhard [EMG, TU-BS, Braunschweig (Germany)

2011-07-01

Using optical absorption and other techniques we study plasmon-polariton modes of dense Au nanowire arrays as function of geometrical parameters and coupling to molecular degrees of freedom. For this instance we electrochemically deposit Au nanowires in porous alumina with well controlled morphology and defect concentration. Transverse and longitudinal modes are observed in the absorption spectra resulting from the anisotropic plasmonic structure. The longitudinal mode shows a blue shift of energy with increasing length of the wires due to the more collective nature of this response. We compare our observations with model calculations and corresponding results on 2D Ag nanowire lattices.

Teleology then and now: the question of Kant's relevance for contemporary controversies over function in biology.

Science.gov (United States)

Zammito, John

2006-12-01

'Naturalism' is the aspiration of contemporary philosophy of biology, and Kant simply cannot be refashioned into a naturalist. Instead, epistemological 'deflation' was the decisive feature of Kant's treatment of the 'biomedical' science in his day, so it is not surprising that this might attract some philosophers of science to him today. A certain sense of impasse in the contemporary 'function talk' seems to motivate renewed interest in Kant. Kant--drawing on his eighteenth-century predecessors-provided a discerning and powerful characterization of what biologists had to explain in organic form. His difference from the rest is that he opined that it was impossible to explain it. Its 'inscrutability' was intrinsic. The third Critique essentially proposed the reduction of biology to a kind of pre-scientific descriptivism, doomed never to attain authentic scientificity, to have its 'Newton of the blade of grass'. By contrast, for Locke, and a fortiori for Buffon and his followers, 'intrinsic purposiveness' was a fact of the matter about concrete biological phenomena; the features of internal self-regulation were hypotheses arising out of actual research practice. The difference comes most vividly to light once we recognize Kant's distinction of the concept of organism from the concept of life. If biology must conceptualize self-organization as actual in the world, Kant's regulative/constitutive distinction is pointless in practice and the (naturalist) philosophy of biology has urgent work to undertake for which Kant turns out not to be very helpful.

Plasmon Modes of Vertically Aligned Superlattices

DEFF Research Database (Denmark)

Filonenko, Konstantin; Duggen, Lars; Willatzen, Morten

2017-01-01

By using the Finite Element Method we visualize the modes of vertically aligned superlattice composed of gold and dielectric nanocylinders and investigate the emitter-plasmon interaction in approximation of weak coupling. We find that truncated vertically aligned superlattice can function...

Effects of mode profile on tunneling and traversal of ultracold atoms through vacuum-induced potentials

Science.gov (United States)

Badshah, Fazal; Irfan, Muhammad; Qamar, Sajid; Qamar, Shahid

2016-04-01

We consider the resonant interaction of an ultracold two-level atom with an electromagnetic field inside a high-Q micromaser cavity. In particular, we study the tunneling and traversal of ultracold atoms through vacuum-induced potentials for secant hyperbolic square and sinusoidal cavity mode functions. The phase time which may be considered as an appropriate measure of the time required for the atoms to cross the cavity, significantly modifies with the change of cavity mode profile. For example, switching between the sub and superclassical behaviors in phase time can occur due to the mode function. Similarly, negative phase time appears for the transmission of the two-level atoms in both excited and ground states for secant hyperbolic square mode function which is in contrast to the mesa mode case.

Dual-cavity mode converter for a fundamental mode output in an over-moded relativistic backward-wave oscillator

Energy Technology Data Exchange (ETDEWEB)

Li, Jiawei; Huang, Wenhua [Department of Electronic Engineering and Information Science, University of Science and Technology of China, Hefei 230027 (China); Science and Technology on High Power Microwave Laboratory, Northwest Institute of Nuclear Technology, Xi' an 710024 (China); Xiao, Renzhen; Bai, Xianchen; Zhang, Yuchuan; Zhang, Xiaowei; Shao, Hao; Chen, Changhua [Science and Technology on High Power Microwave Laboratory, Northwest Institute of Nuclear Technology, Xi' an 710024 (China); Zhu, Qi [Department of Electronic Engineering and Information Science, University of Science and Technology of China, Hefei 230027 (China)

2015-03-16

A dual-cavity TM{sub 02}–TM{sub 01} mode converter is designed for a dual-mode operation over-moded relativistic backward-wave oscillator. With the converter, the fundamental mode output is achieved. Particle-in-cell simulation shows that the efficiency of beam-wave conversion was over 46% and a pureTM{sub 01} mode output was obtained. Effects of end reflection provided by the mode converter were studied. Adequate TM{sub 01} mode feedback provided by the converter enhances conversion efficiency. The distance between the mode converter and extraction cavity critically affect the generation of microwaves depending on the reflection phase of TM{sub 01} mode feedback.

Dual-cavity mode converter for a fundamental mode output in an over-moded relativistic backward-wave oscillator

International Nuclear Information System (INIS)

Li, Jiawei; Huang, Wenhua; Xiao, Renzhen; Bai, Xianchen; Zhang, Yuchuan; Zhang, Xiaowei; Shao, Hao; Chen, Changhua; Zhu, Qi

2015-01-01

A dual-cavity TM 02 –TM 01 mode converter is designed for a dual-mode operation over-moded relativistic backward-wave oscillator. With the converter, the fundamental mode output is achieved. Particle-in-cell simulation shows that the efficiency of beam-wave conversion was over 46% and a pureTM 01 mode output was obtained. Effects of end reflection provided by the mode converter were studied. Adequate TM 01 mode feedback provided by the converter enhances conversion efficiency. The distance between the mode converter and extraction cavity critically affect the generation of microwaves depending on the reflection phase of TM 01 mode feedback

Post - SM4 Flux Calibration of the STIS Echelle Modes

Science.gov (United States)

Bostroem, Azalee; Aloisi, A.; Bohlin, R. C.; Proffitt, C. R.; Osten, R. A.; Lennon, D.

2010-07-01

Like all STIS spectroscopic modes, STIS echelle modes show a wavelength dependent decline in detector sensitivity with time. The echelle sensitivity is further affected by a time-dependent shift in the blaze function. To better correct the effects of the echelle sensitivity loss and the blaze function changes, we derive new baselines for echelle sensitivities from post-HST Servicing Mission 4 observations of the standard star G191-B2B. We present how these baseline sensitivities compare to pre-failure trends.

Structural and Conformational Chemistry from Electrochemical Molecular Machines. Replicating Biological Functions. A Review.

Science.gov (United States)

Otero, Toribio F

2017-12-14

Each constitutive chain of a conducting polymer electrode acts as a reversible multi-step electrochemical molecular motor: reversible reactions drive reversible conformational movements of the chain. The reaction-driven cooperative actuation of those molecular machines generates, or destroys, inside the film the free volume required to lodge/expel balancing counterions and solvent: reactions drive reversible film volume variations, which basic structural components are here identified and quantified from electrochemical responses. The content of the reactive dense gel (chemical molecular machines, ions and water) mimics that of the intracellular matrix in living functional cells. Reaction-driven properties (composition-dependent properties) and devices replicate biological functions and organs. An emerging technological world of soft, wet, reaction-driven, multifunctional and biomimetic devices and the concomitant zoomorphic or anthropomorphic robots is presented. © 2017 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mode conversion in magneto photonic crystal fibre

International Nuclear Information System (INIS)

Otmani, Hamza; Bouchemat, Mohamed; Hocini, Abdesselam; Boumaza, Touraya; Benmerkhi, Ahlem

2017-01-01

The first concept of an integrated isolator was based on nonreciprocal TE–TM mode conversion, the nonreciprocal coupling between these modes is caused by the Faraday rotation if the magnetization is aligned along the z–axis, parallel to mode propagation. We propose to study this magneto-optical phenomenon, by the simulation of magneto photonic crystal fibre (MPCF), it consists of a periodic triangular lattice of air-holes filled with magnetic fluid which consists of magnetic nanoparticles into a BIG (Bismuth Iron Garnet) fibre. We simulated the influence of gyrotropy and the wavelength, and calculated Faraday rotation and modal birefringence. In this fibre the light is guided by internal total reflection, like classical fibres. However it was shown that they could function on a mode conversion much stronger than conventional fibres. - Highlights: • We propose to study mode conversion TE–TM, by the simulation of magneto photonic crystal fibre (MPCF). • We simulated the influence of gyrotropy. • We simulated the wavelength. • We calculated Faraday rotation. • We calculated modal birefringence.

Lumped Mass Modeling for Local-Mode-Suppressed Element Connectivity

DEFF Research Database (Denmark)

Joung, Young Soo; Yoon, Gil Ho; Kim, Yoon Young

2005-01-01

connectivity parameterization (ECP) is employed. On the way to the ultimate crashworthy structure optimization, we are now developing a local mode-free topology optimization formulation that can be implemented in the ECP method. In fact, the local mode-freeing strategy developed here can be also used directly...... experiencing large structural changes, appears to be still poor. In ECP, the nodes of the domain-discretizing elements are connected by zero-length one-dimensional elastic links having varying stiffness. For computational efficiency, every elastic link is now assumed to have two lumped masses at its ends....... Choosing appropriate penalization functions for lumped mass and link stiffness is important for local mode-free results. However, unless the objective and constraint functions are carefully selected, it is difficult to obtain clear black-and-white results. It is shown that the present formulation is also...

Single-mode fiber laser based on core-cladding mode conversion.

Science.gov (United States)

Suzuki, Shigeru; Schülzgen, Axel; Peyghambarian, N

2008-02-15

A single-mode fiber laser based on an intracavity core-cladding mode conversion is demonstrated. The fiber laser consists of an Er-doped active fiber and two fiber Bragg gratings. One Bragg grating is a core-cladding mode converter, and the other Bragg grating is a narrowband high reflector that selects the lasing wavelength. Coupling a single core mode and a single cladding mode by the grating mode converter, the laser operates as a hybrid single-mode laser. This approach for designing a laser cavity provides a much larger mode area than conventional large-mode-area step-index fibers.

Effect of modes interaction on the resistive wall mode stability

International Nuclear Information System (INIS)

Chen Longxi; Wu Bin

2013-01-01

Effects of modes interaction on the resistive wall mode (RWM) stability are studied. When considering the modes interaction effects, the linear growth rate of the most unstable (3, 1) mode decreases. After linear evolution, the RWM saturates at the nonlinear phase. The saturation can be attributed to flux piling up on the resistive wall. When some modes exist, the (3, 1) mode saturates at lower level compared with single mode evolution. Meanwhile, the magnetic energy of the (5, 2) mode increases correspondingly, but the magnetic energy saturation level of the (2, 1) mode changes weakly. (authors)

Scaling Fiber Lasers to Large Mode Area: An Investigation of Passive Mode-Locking Using a Multi-Mode Fiber.

Science.gov (United States)

Ding, Edwin; Lefrancois, Simon; Kutz, Jose Nathan; Wise, Frank W

2011-01-01

The mode-locking of dissipative soliton fiber lasers using large mode area fiber supporting multiple transverse modes is studied experimentally and theoretically. The averaged mode-locking dynamics in a multi-mode fiber are studied using a distributed model. The co-propagation of multiple transverse modes is governed by a system of coupled Ginzburg-Landau equations. Simulations show that stable and robust mode-locked pulses can be produced. However, the mode-locking can be destabilized by excessive higher-order mode content. Experiments using large core step-index fiber, photonic crystal fiber, and chirally-coupled core fiber show that mode-locking can be significantly disturbed in the presence of higher-order modes, resulting in lower maximum single-pulse energies. In practice, spatial mode content must be carefully controlled to achieve full pulse energy scaling. This paper demonstrates that mode-locking performance is very sensitive to the presence of multiple waveguide modes when compared to systems such as amplifiers and continuous-wave lasers.

Activities in biological radiation research at the AGF

International Nuclear Information System (INIS)

1984-01-01

The AGF is working on a wide spectrum of biological radiation research, with the different scientific disciplines contributing different methodologies to long-term research projects. The following fields are studied: 1. Molecular and cellular modes of action of radiation. 2. Detection and characterisation of biological radiation damage, especially in humans. 3. Medical applications of radiation effects. 4. Concepts and methods of radiation protection. The studies will lead to suggestions for radiation protection and improved radiotherapy. They may also contribute to the development of environmental protection strategies. (orig./MG) [de

The CB1 Neutral Antagonist Tetrahydrocannabivarin Reduces Default Mode Network and Increases Executive Control Network Resting State Functional Connectivity in Healthy Volunteers.

Science.gov (United States)

Rzepa, Ewelina; Tudge, Luke; McCabe, Ciara

2015-09-10

The cannabinoid cannabinoid type 1 (CB1) neutral antagonist tetrahydrocannabivarin (THCv) has been suggested as a possible treatment for obesity, but without the depressogenic side-effects of inverse antagonists such as Rimonabant. However, how THCv might affect the resting state functional connectivity of the human brain is as yet unknown. We examined the effects of a single 10mg oral dose of THCv and placebo in 20 healthy volunteers in a randomized, within-subject, double-blind design. Using resting state functional magnetic resonance imaging and seed-based connectivity analyses, we selected the amygdala, insula, orbitofrontal cortex, and dorsal medial prefrontal cortex (dmPFC) as regions of interest. Mood and subjective experience were also measured before and after drug administration using self-report scales. Our results revealed, as expected, no significant differences in the subjective experience with a single dose of THCv. However, we found reduced resting state functional connectivity between the amygdala seed region and the default mode network and increased resting state functional connectivity between the amygdala seed region and the dorsal anterior cingulate cortex and between the dmPFC seed region and the inferior frontal gyrus/medial frontal gyrus. We also found a positive correlation under placebo for the amygdala-precuneus connectivity with the body mass index, although this correlation was not apparent under THCv. Our findings are the first to show that treatment with the CB1 neutral antagonist THCv decreases resting state functional connectivity in the default mode network and increases connectivity in the cognitive control network and dorsal visual stream network. This effect profile suggests possible therapeutic activity of THCv for obesity, where functional connectivity has been found to be altered in these regions. © The Author 2015. Published by Oxford University Press on behalf of CINP.

Linear mode conversion in a toroidal plasma

International Nuclear Information System (INIS)

Hellsten, T.

1980-05-01

Linear mode conversion at the perpendicular ion cyclotron resonance has been treated for an axially symmetric toroidal plasma. The mode conversion appears between a fast electromagnetic wave and a slow-quasi electrostatic wave, due to finite electron inertia. The problem reduces to the Orr-Sommerfeld equation where the coefficients determining the reflectron, transmission and conversion are functions of the arc length along a poloidal intersection of the resonance surface. These coefficients can be determined from eigenfunctions of an ordinary differential equation. (author)

Sliding-Mode Observer for Speed and Position Sensorless Control of Linear-PMSM

Directory of Open Access Journals (Sweden)

Kazraji Saeed Masoumi

2014-05-01

Full Text Available The paper presents a sliding-mode observer that utilizes sigmoid function for speed and position sensorless control of permanent-magnet linear synchronous motor (PMLSM. In conventional sliding mode observer method there are the chattering phenomenon and the phase lag. Thus, in order to avoid the usage of the low pass filter and the phase compensator based on back EMF, in this paper a sliding mode observer with sigmoid function for detecting the back EMF in a PMLSM is designed to estimate the speed and the position of the rotor. Most of conventional sliding mode observers use sign or saturation functions which need low pass filter in order to detect back electromotive force (back EMF. In this paper a sigmoid function is used instead of discontinuous sign function to decrease undesirable chattering phenomenon. By reducing the chattering, detecting of the back EMF can be made directly from switching signal without any low pass filter. Thus the delay time in the proposed observer is eliminated because of the low pass filter. Furthermore, there is no need to compensate phase fault in position and speed estimating of linear-PMSM. Advantages of the proposed observer have been shown by simulation with MATLAB software.

Triazole nucleoside derivatives bearing aryl functionalities on the nucleobases show antiviral and anticancer activity.

Science.gov (United States)

Xia, Yi; Qu, Fanqi; Peng, Ling

2010-08-01

Synthetic nucleoside mimics are important candidates in the searing for antiviral and anticancer drugs. Ribavirin, the first antiviral nucleoside drug, is unique in its antiviral activity with mutilple modes of action, which are mainly due to its special triazole heterocycle as nucleobase. Additionally, introducing aromatic functionalities to the nucleobase is able to confer novel mechanisms of action for nucleoside mimics. With the aim to combine the special characteristics of unnatural triazole heterocycles with those of the appended aromatic groups on the nucleobases, novel 1,2,4-triazole nucleoside analogs bearing aromatic moieties were designed and developed. The present short review summarizes the molecular design, chemical synthesis and biological activity of these triazole nucleoside analogs. Indeed, the discovery of antiviral and anticancer activities shown by these triazole nucleosides as well as the new mechanism underlying the biological activity by one of the anticancer leads has validated the rationale for molecular design and impacted us to further explore the concept with the aim of developing structurally novel nucleoside drug candidates with new modes of action.

Synthesis and Characterization of Rhodamine B-ethylenediamine-hyaluronan Acid as Potential Biological Functional Materials

Science.gov (United States)

Li, Y. L.; Wang, W. X.; Wang, Y.; Zhang, W. B.; Gong, H. M.; Liu, M. X.

2018-05-01

The purpose of this study is to synthesize and characterize fluorescent polymers, rhodamine B-ethylenediamine-hyaluronan acid (RhB-EA-HA). RhB-EA-HA was successfully synthesized by ester ammonolysis reaction and amidation reaction. Moreover, the structural properties of RhB-EA-HA were characterized by 1H-NMR spectra, UV-vis spectrometry and Fourier transform infrared spectroscopy (FT-IR). RhB-EA-HA can be grafted on the surface of silica nanomaterials, which may be potential biological functional materials for drug delivery system.

Analysis of a large-break LOCA at lower operational modes

Energy Technology Data Exchange (ETDEWEB)

Jeong, H.Y.; Jun, H.Y.; Lee, K. [Korea Electric Power Corporation, Taejon (Korea)

2000-10-01

To improve Technical Specifications and Emergency Operating Guidelines (EOGs) applicable at lower operational modes it is required to perform the safety analysis reflecting the operational characteristics in those modes. Because the component availability and system configurations at lower modes are different from those of power mode, the plant safety at lower modes should be confirmed through independent analyses. In the present study, a large-break loss-of-coolant accident is analyzed to evaluate the containment pressure and temperature control function for the preparation of EOGs applicable at lower modes. To reach the required shutdown condition, the plant cool-down is controlled by the secondary steam flow and auxiliary feedwater. The mass and energy releases from primary system are obtained from RELAP5/MOD3.1 calculation and the containment pressure and temperature are evaluated with CONTEMPT-LT code. The reference plant is Korean Next Generation Reactor having 4,000 MW thermal power. Two cases of cold leg LOCA initiated at Mode 3 with and without SIT operation are calculated. At the given plant conditions, all safety injection pumps are still available. The calculation at the condition of maximum mass and energy release shows that the containment pressure and temperature can be controlled within acceptable criteria, which means the operations of 2 or 4 fan coolers are the possible success paths to achieve the containment P/T control safety function. The peak cladding temperature with minimum safety injection flow does not show remarkable excursion, which implies the lower mode LOCA at Mode 3 can be bounded by the results obtained at full power from the viewpoint of ECCS performance. (author)

Mode analysis of heuristic behavior of searching for multimodal optimum point

Energy Technology Data Exchange (ETDEWEB)

Kamei, K; Araki, Y; Inoue, K

1982-01-01

Describes an experimental study of a heuristic behavior of searching for the global optimum (maximum) point of a two-dimensional, multimodal, nonlinear and unknown function. First, the authors define three modes dealing with the trial purposes, called the purpose modes and show the heuristic search behaviors expressed by the purpose modes which the human subjects select in the search experiments. Second, the authors classify the heuristic search behaviors into three types according to the mode transitions and extracts eight states of searches which cause the mode transitions. Third, a model of the heuristic search behavior is composed of the eight mode transitions. The analysis of the heuristic search behaviors by use of the purpose modes plays an important role in the heuristic search techniques. 6 references.

Biomechanical justification of the choice of optimum mode for passing the individual pursuit race

Directory of Open Access Journals (Sweden)

A.N. Kolumbet

2018-04-01

Full Text Available Purpose : biomechanical justification of the choice of optimum mode of passing competitive distance of 4 km individual pursuit on track. Material : The qualified cyclists (n=14 participated in researches. The modified stationary cycle Monark was used. Cyclists performed work in two modes - A and B. Results : The mode B is physiologically more favorable. The mode B should be considered as a model of passing a distance in preliminary races of individual pursuit. Work in the mode A demands terminal mobilization of organism functions. Work in the mode A is more effective in the achievement of sports result. It can be used only once in the final race of competitions. Conclusions : The received data should be considered as a demonstration of specific features of passing a distance in the competitive modes. The tactical variant of competitive program creation is defined by the individual functional state.

Evaluation of phrenic nerve and diaphragm function with peripheral nerve stimulation and M-mode ultrasonography in potential pediatric phrenic nerve or diaphragm pacing candidates.

Science.gov (United States)

Skalsky, Andrew J; Lesser, Daniel J; McDonald, Craig M

2015-02-01

Assessing phrenic nerve function in the setting of diaphragmatic paralysis in diaphragm pacing candidates can be challenging. Traditional imaging modalities and electrodiagnostic evaluations are technically difficult. Either modality alone is not a direct measure of the function of the phrenic nerve and diaphragm unit. In this article, the authors present their method for evaluating phrenic nerve function and the resulting diaphragm function. Stimulating the phrenic nerve with transcutaneous stimulation and directly observing the resulting movement of the hemidiaphragm with M-mode ultrasonography provides quantitative data for predicting the success of advancing technologies such as phrenic nerve pacing and diaphragm pacing. Copyright © 2015 Elsevier Inc. All rights reserved.

A Critical Perspective on Synthetic Biology

OpenAIRE

Michel Morange

2009-01-01

Synthetic biology emerged around 2000 as a new biological discipline. It shares with systems biology the same modular vision of organisms, but is more concerned with applications than with a better understanding of the functioning of organisms. A herald of this new discipline is Craig Venter who aims to create an artificial microorganism with the minimal genome compatible with life and to implement into it different 'functional modules' to generate new micro-organisms adapted to specific task...

Nuclear scissors mode with pairing

International Nuclear Information System (INIS)

Balbutsev, E. B.; Malov, L. A.; Schuck, P.; Urban, M.; Vinas, X.

2008-01-01

The coupled dynamics of the scissors mode and the isovector giant quadrupole resonance are studied using a generalized Wigner function moments method, taking into account pair correlations. Equations of motion for angular momentum, quadrupole moment, and other relevant collective variables are derived on the basis of the time-dependent Hartree-Fock-Bogolyubov equations. Analytical expressions for energy centroids and transition probabilities are found for the harmonic-oscillator model with the quadrupole-quadrupole residual interaction and monopole pairing force. Deformation dependences of energies and B(M1) values are correctly reproduced. The inclusion of pair correlations leads to a drastic improvement in the description of qualitative and quantitative characteristics of the scissors mode.

Computational structural biology: methods and applications

National Research Council Canada - National Science Library

Schwede, Torsten; Peitsch, Manuel Claude

2008-01-01

... sequencing reinforced the observation that structural information is needed to understand the detailed function and mechanism of biological molecules such as enzyme reactions and molecular recognition events. Furthermore, structures are obviously key to the design of molecules with new or improved functions. In this context, computational structural biology...

GPSR: A Resource for Genomics Proteomics and Systems Biology

Indian Academy of Sciences (India)

First page Back Continue Last page Overview Graphics. GPSR: A Resource for Genomics Proteomics and Systems Biology. A journey from simple computer programs to drug/vaccine informatics. Limitations of existing web services. History repeats (Web to Standalone); Graphics vs command mode. General purpose ...

Molecular Imaging in Synthetic Biology, and Synthetic Biology in Molecular Imaging.

Science.gov (United States)

Gilad, Assaf A; Shapiro, Mikhail G

2017-06-01

Biomedical synthetic biology is an emerging field in which cells are engineered at the genetic level to carry out novel functions with relevance to biomedical and industrial applications. This approach promises new treatments, imaging tools, and diagnostics for diseases ranging from gastrointestinal inflammatory syndromes to cancer, diabetes, and neurodegeneration. As these cellular technologies undergo pre-clinical and clinical development, it is becoming essential to monitor their location and function in vivo, necessitating appropriate molecular imaging strategies, and therefore, we have created an interest group within the World Molecular Imaging Society focusing on synthetic biology and reporter gene technologies. Here, we highlight recent advances in biomedical synthetic biology, including bacterial therapy, immunotherapy, and regenerative medicine. We then discuss emerging molecular imaging approaches to facilitate in vivo applications, focusing on reporter genes for noninvasive modalities such as magnetic resonance, ultrasound, photoacoustic imaging, bioluminescence, and radionuclear imaging. Because reporter genes can be incorporated directly into engineered genetic circuits, they are particularly well suited to imaging synthetic biological constructs, and developing them provides opportunities for creative molecular and genetic engineering.

Localized transversal-rotational modes in linear chains of equal masses.

Science.gov (United States)

Pichard, H; Duclos, A; Groby, J-P; Tournat, V; Gusev, V E

2014-01-01

The propagation and localization of transversal-rotational waves in a two-dimensional granular chain of equal masses are analyzed in this study. The masses are infinitely long cylinders possessing one translational and one rotational degree of freedom. Two dispersive propagating modes are predicted in this granular crystal. By considering the semi-infinite chain with a boundary condition applied at its beginning, the analytical study demonstrates the existence of localized modes, each mode composed of two evanescent modes. Their existence, position (either in the gap between the propagating modes or in the gap above the upper propagating mode), and structure of spatial localization are analyzed as a function of the relative strength of the shear and bending interparticle interactions and for different boundary conditions. This demonstrates the existence of a localized mode in a semi-infinite monatomic chain when transversal-rotational waves are considered, while it is well known that these types of modes do not exist when longitudinal waves are considered.

Isoscalar compression modes in relativistic random phase approximation

International Nuclear Information System (INIS)

Ma, Zhong-yu; Van Giai, Nguyen.; Wandelt, A.; Vretenar, D.; Ring, P.

2001-01-01

Monopole and dipole compression modes in nuclei are analyzed in the framework of a fully consistent relativistic random phase approximation (RRPA), based on effective mean-field Lagrangians with nonlinear meson self-interaction terms. The large effect of Dirac sea states on isoscalar strength distribution functions is illustrated for the monopole mode. The main contribution of Fermi and Dirac sea pair states arises through the exchange of the scalar meson. The effect of vector meson exchange is much smaller. For the monopole mode, RRPA results are compared with constrained relativistic mean-field calculations. A comparison between experimental and calculated energies of isoscalar giant monopole resonances points to a value of 250-270 MeV for the nuclear matter incompressibility. A large discrepancy remains between theoretical predictions and experimental data for the dipole compression mode

Ordinary mode instability associated with thermal ring distribution

Science.gov (United States)

Hadi, F.; Yoon, P. H.; Qamar, A.

2015-02-01

The purely growing ordinary (O) mode instability driven by excessive parallel temperature anisotropy has recently received renewed attention owing to its potential applicability to the solar wind plasma. Previous studies of O mode instability have assumed either bi-Maxwellian or counter-streaming velocity distributions. For solar wind plasma trapped in magnetic mirror-like geometry such as magnetic clouds or in the vicinity of the Earth's collisionless bow shock environment, however, the velocity distribution function may possess a loss-cone feature. The O-mode instability in such a case may be excited for cyclotron harmonics as well as the purely growing branch. The present paper investigates the O-mode instability for plasmas characterized by the parallel Maxwellian distribution and perpendicular thermal ring velocity distribution in order to understand the general stability characteristics.

Ordinary mode instability associated with thermal ring distribution

Energy Technology Data Exchange (ETDEWEB)

Hadi, F.; Qamar, A. [Institute of Physics and Electronics, University of Peshawar, Peshawar 25000 (Pakistan); Yoon, P. H. [Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742 (United States); School of Space Research, Kyung Hee University, Yongin-Si, Gyeonggi-Do 446-701 (Korea, Republic of)

2015-02-15

The purely growing ordinary (O) mode instability driven by excessive parallel temperature anisotropy has recently received renewed attention owing to its potential applicability to the solar wind plasma. Previous studies of O mode instability have assumed either bi-Maxwellian or counter-streaming velocity distributions. For solar wind plasma trapped in magnetic mirror-like geometry such as magnetic clouds or in the vicinity of the Earth's collisionless bow shock environment, however, the velocity distribution function may possess a loss-cone feature. The O-mode instability in such a case may be excited for cyclotron harmonics as well as the purely growing branch. The present paper investigates the O-mode instability for plasmas characterized by the parallel Maxwellian distribution and perpendicular thermal ring velocity distribution in order to understand the general stability characteristics.

Distinct Neural-Functional Effects of Treatments With Selective Serotonin Reuptake Inhibitors, Electroconvulsive Therapy, and Transcranial Magnetic Stimulation and Their Relations to Regional Brain Function in Major Depression: A Meta-analysis.

Science.gov (United States)

Chau, David T; Fogelman, Phoebe; Nordanskog, Pia; Drevets, Wayne C; Hamilton, J Paul

2017-05-01

Functional neuroimaging studies have examined the neural substrates of treatments for major depressive disorder (MDD). Low sample size and methodological heterogeneity, however, undermine the generalizability of findings from individual studies. We conducted a meta-analysis to identify reliable neural changes resulting from different modes of treatment for MDD and compared them with each other and with reliable neural functional abnormalities observed in depressed versus control samples. We conducted a meta-analysis of studies reporting changes in brain activity (e.g., as indexed by positron emission tomography) following treatments with selective serotonin reuptake inhibitors (SSRIs), electroconvulsive therapy (ECT), or transcranial magnetic stimulation. Additionally, we examined the statistical reliability of overlap among thresholded meta-analytic SSRI, ECT, and transcranial magnetic stimulation maps as well as a map of abnormal neural function in MDD. Our meta-analysis revealed that 1) SSRIs decrease activity in the anterior insula, 2) ECT decreases activity in central nodes of the default mode network, 3) transcranial magnetic stimulation does not result in reliable neural changes, and 4) regional effects of these modes of treatment do not significantly overlap with each other or with regions showing reliable functional abnormality in MDD. SSRIs and ECT produce neurally distinct effects relative to each other and to the functional abnormalities implicated in depression. These treatments therefore may exert antidepressant effects by diminishing neural functions not implicated in depression but that nonetheless impact mood. We discuss how the distinct neural changes resulting from SSRIs and ECT can account for both treatment effects and side effects from these therapies as well as how to individualize these treatments. Copyright © 2017 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

Redox Biology in Neurological Function, Dysfunction, and Aging.

Science.gov (United States)

Franco, Rodrigo; Vargas, Marcelo R

2018-04-23

Reduction oxidation (redox) reactions are central to life and when altered, they can promote disease progression. In the brain, redox homeostasis is recognized to be involved in all aspects of central nervous system (CNS) development, function, aging, and disease. Recent studies have uncovered the diverse nature by which redox reactions and homeostasis contribute to brain physiology, and when dysregulated to pathological consequences. Redox reactions go beyond what is commonly described as oxidative stress and involve redox mechanisms linked to signaling and metabolism. In contrast to the nonspecific nature of oxidative damage, redox signaling involves specific oxidation/reduction reactions that regulate a myriad of neurological processes such as neurotransmission, homeostasis, and degeneration. This Forum is focused on the role of redox metabolism and signaling in the brain. Six review articles from leading scientists in the field that appraise the role of redox metabolism and signaling in different aspects of brain biology including neurodevelopment, neurotransmission, aging, neuroinflammation, neurodegeneration, and neurotoxicity are included. An original research article exemplifying these concepts uncovers a novel link between oxidative modifications, redox signaling, and neurodegeneration. This Forum highlights the recent advances in the field and we hope it encourages future research aimed to understand the mechanisms by which redox metabolism and signaling regulate CNS physiology and pathophysiology. Antioxid. Redox Signal. 00, 000-000.

Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function.

Science.gov (United States)

Chasman, Daniel I; Fuchsberger, Christian; Pattaro, Cristian; Teumer, Alexander; Böger, Carsten A; Endlich, Karlhans; Olden, Matthias; Chen, Ming-Huei; Tin, Adrienne; Taliun, Daniel; Li, Man; Gao, Xiaoyi; Gorski, Mathias; Yang, Qiong; Hundertmark, Claudia; Foster, Meredith C; O'Seaghdha, Conall M; Glazer, Nicole; Isaacs, Aaron; Liu, Ching-Ti; Smith, Albert V; O'Connell, Jeffrey R; Struchalin, Maksim; Tanaka, Toshiko; Li, Guo; Johnson, Andrew D; Gierman, Hinco J; Feitosa, Mary F; Hwang, Shih-Jen; Atkinson, Elizabeth J; Lohman, Kurt; Cornelis, Marilyn C; Johansson, Asa; Tönjes, Anke; Dehghan, Abbas; Lambert, Jean-Charles; Holliday, Elizabeth G; Sorice, Rossella; Kutalik, Zoltan; Lehtimäki, Terho; Esko, Tõnu; Deshmukh, Harshal; Ulivi, Sheila; Chu, Audrey Y; Murgia, Federico; Trompet, Stella; Imboden, Medea; Coassin, Stefan; Pistis, Giorgio; Harris, Tamara B; Launer, Lenore J; Aspelund, Thor; Eiriksdottir, Gudny; Mitchell, Braxton D; Boerwinkle, Eric; Schmidt, Helena; Cavalieri, Margherita; Rao, Madhumathi; Hu, Frank; Demirkan, Ayse; Oostra, Ben A; de Andrade, Mariza; Turner, Stephen T; Ding, Jingzhong; Andrews, Jeanette S; Freedman, Barry I; Giulianini, Franco; Koenig, Wolfgang; Illig, Thomas; Meisinger, Christa; Gieger, Christian; Zgaga, Lina; Zemunik, Tatijana; Boban, Mladen; Minelli, Cosetta; Wheeler, Heather E; Igl, Wilmar; Zaboli, Ghazal; Wild, Sarah H; Wright, Alan F; Campbell, Harry; Ellinghaus, David; Nöthlings, Ute; Jacobs, Gunnar; Biffar, Reiner; Ernst, Florian; Homuth, Georg; Kroemer, Heyo K; Nauck, Matthias; Stracke, Sylvia; Völker, Uwe; Völzke, Henry; Kovacs, Peter; Stumvoll, Michael; Mägi, Reedik; Hofman, Albert; Uitterlinden, Andre G; Rivadeneira, Fernando; Aulchenko, Yurii S; Polasek, Ozren; Hastie, Nick; Vitart, Veronique; Helmer, Catherine; Wang, Jie Jin; Stengel, Bénédicte; Ruggiero, Daniela; Bergmann, Sven; Kähönen, Mika; Viikari, Jorma; Nikopensius, Tiit; Province, Michael; Ketkar, Shamika; Colhoun, Helen; Doney, Alex; Robino, Antonietta; Krämer, Bernhard K; Portas, Laura; Ford, Ian; Buckley, Brendan M; Adam, Martin; Thun, Gian-Andri; Paulweber, Bernhard; Haun, Margot; Sala, Cinzia; Mitchell, Paul; Ciullo, Marina; Kim, Stuart K; Vollenweider, Peter; Raitakari, Olli; Metspalu, Andres; Palmer, Colin; Gasparini, Paolo; Pirastu, Mario; Jukema, J Wouter; Probst-Hensch, Nicole M; Kronenberg, Florian; Toniolo, Daniela; Gudnason, Vilmundur; Shuldiner, Alan R; Coresh, Josef; Schmidt, Reinhold; Ferrucci, Luigi; Siscovick, David S; van Duijn, Cornelia M; Borecki, Ingrid B; Kardia, Sharon L R; Liu, Yongmei; Curhan, Gary C; Rudan, Igor; Gyllensten, Ulf; Wilson, James F; Franke, Andre; Pramstaller, Peter P; Rettig, Rainer; Prokopenko, Inga; Witteman, Jacqueline; Hayward, Caroline; Ridker, Paul M; Parsa, Afshin; Bochud, Murielle; Heid, Iris M; Kao, W H Linda; Fox, Caroline S; Köttgen, Anna

2012-12-15

In conducting genome-wide association studies (GWAS), analytical approaches leveraging biological information may further understanding of the pathophysiology of clinical traits. To discover novel associations with estimated glomerular filtration rate (eGFR), a measure of kidney function, we developed a strategy for integrating prior biological knowledge into the existing GWAS data for eGFR from the CKDGen Consortium. Our strategy focuses on single nucleotide polymorphism (SNPs) in genes that are connected by functional evidence, determined by literature mining and gene ontology (GO) hierarchies, to genes near previously validated eGFR associations. It then requires association thresholds consistent with multiple testing, and finally evaluates novel candidates by independent replication. Among the samples of European ancestry, we identified a genome-wide significant SNP in FBXL20 (P = 5.6 × 10(-9)) in meta-analysis of all available data, and additional SNPs at the INHBC, LRP2, PLEKHA1, SLC3A2 and SLC7A6 genes meeting multiple-testing corrected significance for replication and overall P-values of 4.5 × 10(-4)-2.2 × 10(-7). Neither the novel PLEKHA1 nor FBXL20 associations, both further supported by association with eGFR among African Americans and with transcript abundance, would have been implicated by eGFR candidate gene approaches. LRP2, encoding the megalin receptor, was identified through connection with the previously known eGFR gene DAB2 and extends understanding of the megalin system in kidney function. These findings highlight integration of existing genome-wide association data with independent biological knowledge to uncover novel candidate eGFR associations, including candidates lacking known connections to kidney-specific pathways. The strategy may also be applicable to other clinical phenotypes, although more testing will be needed to assess its potential for discovery in general.

Modes in light wave propagating in semiconductor laser

Science.gov (United States)

Manko, Margarita A.

1994-01-01

The study of semiconductor laser based on an analogy of the Schrodinger equation and an equation describing light wave propagation in nonhomogeneous medium is developed. The active region of semiconductor laser is considered as optical waveguide confining the electromagnetic field in the cross-section (x,y) and allowing waveguide propagation along the laser resonator (z). The mode structure is investigated taking into account the transversal and what is the important part of the suggested consideration longitudinal nonhomogeneity of the optical waveguide. It is shown that the Gaussian modes in the case correspond to spatial squeezing and correlation. Spatially squeezed two-mode structure of nonhomogeneous optical waveguide is given explicitly. Distribution of light among the laser discrete modes is presented. Properties of the spatially squeezed two-mode field are described. The analog of Franck-Condon principle for finding the maxima of the distribution function and the analog of Ramsauer effect for control of spatial distribution of laser emission are discussed.

Different shades of default mode disturbance in schizophrenia: Subnodal covariance estimation in structure and function.

Science.gov (United States)

Lefort-Besnard, Jérémy; Bassett, Danielle S; Smallwood, Jonathan; Margulies, Daniel S; Derntl, Birgit; Gruber, Oliver; Aleman, Andre; Jardri, Renaud; Varoquaux, Gaël; Thirion, Bertrand; Eickhoff, Simon B; Bzdok, Danilo

2018-02-01

Schizophrenia is a devastating mental disease with an apparent disruption in the highly associative default mode network (DMN). Interplay between this canonical network and others probably contributes to goal-directed behavior so its disturbance is a candidate neural fingerprint underlying schizophrenia psychopathology. Previous research has reported both hyperconnectivity and hypoconnectivity within the DMN, and both increased and decreased DMN coupling with the multimodal saliency network (SN) and dorsal attention network (DAN). This study systematically revisited network disruption in patients with schizophrenia using data-derived network atlases and multivariate pattern-learning algorithms in a multisite dataset (n = 325). Resting-state fluctuations in unconstrained brain states were used to estimate functional connectivity, and local volume differences between individuals were used to estimate structural co-occurrence within and between the DMN, SN, and DAN. In brain structure and function, sparse inverse covariance estimates of network coupling were used to characterize healthy participants and patients with schizophrenia, and to identify statistically significant group differences. Evidence did not confirm that the backbone of the DMN was the primary driver of brain dysfunction in schizophrenia. Instead, functional and structural aberrations were frequently located outside of the DMN core, such as in the anterior temporoparietal junction and precuneus. Additionally, functional covariation analyses highlighted dysfunctional DMN-DAN coupling, while structural covariation results highlighted aberrant DMN-SN coupling. Our findings reframe the role of the DMN core and its relation to canonical networks in schizophrenia. We thus underline the importance of large-scale neural interactions as effective biomarkers and indicators of how to tailor psychiatric care to single patients. © 2017 Wiley Periodicals, Inc.

Integration of multiscale dendritic spine structure and function data into systems biology models

Directory of Open Access Journals (Sweden)

James J Mancuso

2014-11-01

Full Text Available Comprising 1011 neurons with 1014 synaptic connections the human brain is the ultimate systems biology puzzle. An increasing body of evidence highlights the observation that changes in brain function, both normal and pathological, consistently correlate with dynamic changes in neuronal anatomy. Anatomical changes occur on a full range of scales from the trafficking of individual proteins, to alterations in synaptic morphology both individually and on a systems level, to reductions in long distance connectivity and brain volume. The major sites of contact for synapsing neurons are dendritic spines, which provide an excellent metric for the number and strength of signaling connections between elements of functional neuronal circuits. A comprehensive model of anatomical changes and their functional consequences would be a holy grail for the field of systems neuroscience but its realization appears far on the horizon. Various imaging technologies have advanced to allow for multi-scale visualization of brain plasticity and pathology, but computational analysis of the massive big data sets involved forms the bottleneck toward the creation of multiscale models of brain structure and function. While a full accounting of techniques and progress toward a comprehensive model of brain anatomy and function is beyond the scope of this or any other single paper, this review serves to highlight the opportunities for analysis of neuronal spine anatomy and function provided by new imaging technologies and the high-throughput application of older technologies while surveying the strengths and weaknesses of currently available computational analytical tools and room for future improvement.

Tunable deformation modes shape contractility in active biopolymer networks

Science.gov (United States)

Stam, Samantha; Banerjee, Shiladitya; Weirich, Kim; Freedman, Simon; Dinner, Aaron; Gardel, Margaret

Biological polymer-based materials remodel under active, molecular motor-driven forces to perform diverse physiological roles, such as force transmission and spatial self-organization. Critical to understanding these biomaterials is elucidating the role of microscopic polymer deformations, such as stretching, bending, buckling, and relative sliding, on material remodeling. Here, we report that the shape of motor-driven deformations can be used to identify microscopic deformation modes and determine how they propagate to longer length scales. In cross-linked actin networks with sufficiently low densities of the motor protein myosin II, microscopic network deformations are predominantly uniaxial, or dominated by sliding. However, longer-wavelength modes are mostly biaxial, or dominated by bending and buckling, indicating that deformations with uniaxial shapes do not propagate across length scales significantly larger than that of individual polymers. As the density of myosin II is increased, biaxial modes dominate on all length scales we examine due to buildup of sufficient stress to produce smaller-wavelength buckling. In contrast, when we construct networks from unipolar, rigid actin bundles, we observe uniaxial, sliding-based contractions on 1 to 100 μm length scales. Our results demonstrate the biopolymer mechanics can be used to tune deformation modes which, in turn, control shape changes in active materials.

Deciphering death: a commentary on Gompertz (1825) 'On the nature of the function expressive of the law of human mortality, and on a new mode of determining the value of life contingencies'.

Science.gov (United States)

Kirkwood, Thomas B L

2015-04-19

In 1825, the actuary Benjamin Gompertz read a paper, 'On the nature of the function expressive of the law of human mortality, and on a new mode of determining the value of life contingencies', to the Royal Society in which he showed that over much of the adult human lifespan, age-specific mortality rates increased in an exponential manner. Gompertz's work played an important role in shaping the emerging statistical science that underpins the pricing of life insurance and annuities. Latterly, as the subject of ageing itself became the focus of scientific study, the Gompertz model provided a powerful stimulus to examine the patterns of death across the life course not only in humans but also in a wide range of other organisms. The idea that the Gompertz model might constitute a fundamental 'law of mortality' has given way to the recognition that other patterns exist, not only across the species range but also in advanced old age. Nevertheless, Gompertz's way of representing the function expressive of the pattern of much of adult mortality retains considerable relevance for studying the factors that influence the intrinsic biology of ageing. This commentary was written to celebrate the 350th anniversary of the journal Philosophical Transactions of the Royal Society.

Effective representation of amide III, II, I, and A modes on local vibrational modes: Analysis of ab initio quantum calculation results.

Science.gov (United States)

Hahn, Seungsoo

2016-10-28

The Hamiltonian matrix for the first excited vibrational states of a protein can be effectively represented by local vibrational modes constituting amide III, II, I, and A modes to simulate various vibrational spectra. Methods for obtaining the Hamiltonian matrix from ab initio quantum calculation results are discussed, where the methods consist of three steps: selection of local vibrational mode coordinates, calculation of a reduced Hessian matrix, and extraction of the Hamiltonian matrix from the Hessian matrix. We introduce several methods for each step. The methods were assessed based on the density functional theory calculation results of 24 oligopeptides with four different peptide lengths and six different secondary structures. The completeness of a Hamiltonian matrix represented in the reduced local mode space is improved by adopting a specific atom group for each amide mode and reducing the effect of ignored local modes. The calculation results are also compared to previous models using C=O stretching vibration and transition dipole couplings. We found that local electric transition dipole moments of the amide modes are mainly bound on the local peptide planes. Their direction and magnitude are well conserved except amide A modes, which show large variation. Contrary to amide I modes, the vibrational coupling constants of amide III, II, and A modes obtained by analysis of a dipeptide are not transferable to oligopeptides with the same secondary conformation because coupling constants are affected by the surrounding atomic environment.

Collective oscillations and coupled modes in confined microfluidic droplet arrays

Science.gov (United States)

Schiller, Ulf D.; Fleury, Jean-Baptiste; Seemann, Ralf; Gompper, Gerhard

Microfluidic droplets have a wide range of applications ranging from analytic assays in cellular biology to controlled mixing in chemical engineering. Ensembles of microfluidic droplets are interesting model systems for non-equilibrium many-body phenomena. When flowing in a microchannel, trains of droplets can form microfluidic crystals whose dynamics are governed by long-range hydrodynamic interactions and boundary effects. In this contribution, excitation mechanisms for collective waves in dense and confined microfluidic droplet arrays are investigated by experiments and computer simulations. We demonstrate that distinct modes can be excited by creating specific `defect' patterns in flowing droplet trains. While longitudinal modes exhibit a short-lived cascade of pairs of laterally displacing droplets, transversely excited modes form propagating waves that behave like microfluidic phonons. We show that the confinement induces a coupling between longitudinal and transverse modes. We also investigate the life time of the collective oscillations and discuss possible mechanisms for the onset of instabilities. Our results demonstrate that microfluidic phonons can exhibit effects beyond the linear theory, which can be studied particularly well in dense and confined systems. This work was supported by Deutsche Forschungsgemeinschaft under Grant No. SE 1118/4.

A new class of g-modes in neutron stars

Science.gov (United States)

Reisenegger, Andreas; Goldreich, Peter

1992-01-01

Because a neutron star is born hot, its internal composition is close to chemical equilibrium. In the fluid core, this implies that the ratio of the number densities of charged particles (protons and electrons) to neutrons is an increasing function of the mass density. This composition gradient stably stratifies the matter giving rise to a Brunt-Vaisala frequency N of about 500/s. Consequently, a neutron star core provides a cavity that supports gravity modes (g-modes). These g-modes are distinct from those previously identified with the thermal stratification of the surface layers and the chemical stratification of the crust. We compute the lowest-order, quadrupolar, g-modes for cold, Newtonian, neutron star models with M/solar M = 0.581 and M/solar M = 1.405, and show that the crustal and core g-modes have similar periods. We also discuss damping mechanisms and estimate damping rates for the core g-modes. Particular attention is paid to damping due to the emission of gravitational radiation.

Evaluation of mode equivalence of the MSKCC Bowel Function Instrument, LASA Quality of Life, and Subjective Significance Questionnaire items administered by Web, interactive voice response system (IVRS), and paper.

Science.gov (United States)

Bennett, Antonia V; Keenoy, Kathleen; Shouery, Marwan; Basch, Ethan; Temple, Larissa K

2016-05-01

To assess the equivalence of patient-reported outcome (PRO) survey responses across Web, interactive voice response system (IVRS), and paper modes of administration. Postoperative colorectal cancer patients with home Web/e-mail and phone were randomly assigned to one of the eight study groups: Groups 1-6 completed the survey via Web, IVRS, and paper, in one of the six possible orders; Groups 7-8 completed the survey twice, either by Web or by IVRS. The 20-item survey, including the MSKCC Bowel Function Instrument (BFI), the LASA Quality of Life (QOL) scale, and the Subjective Significance Questionnaire (SSQ) adapted to bowel function, was completed from home on consecutive days. Mode equivalence was assessed by comparison of mean scores across modes and intraclass correlation coefficients (ICCs) and was compared to the test-retest reliability of Web and IVRS. Of 170 patients, 157 completed at least one survey and were included in analysis. Patients had mean age 56 (SD = 11), 53% were male, 81% white, 53% colon, and 47% rectal cancer; 78% completed all assigned surveys. Mean scores for BFI total score, BFI subscale scores, LASA QOL, and adapted SSQ varied by mode by less than one-third of a score point. ICCs across mode were: BFI total score (Web-paper = 0.96, Web-IVRS = 0.97, paper-IVRS = 0.97); BFI subscales (range = 0.88-0.98); LASA QOL (Web-paper = 0.98, Web-IVRS = 0.78, paper-IVRS = 0.80); and SSQ (Web-paper = 0.92, Web-IVRS = 0.86, paper-IVRS = 0.79). Mode equivalence was demonstrated for the BFI total score, BFI subscales, LASA QOL, and adapted SSQ, supporting the use of multiple modes of PRO data capture in clinical trials.

Detection of Metabolism Function of Microbial Community of Corpses by Biolog-Eco Method.

Science.gov (United States)

Jiang, X Y; Wang, J F; Zhu, G H; Ma, M Y; Lai, Y; Zhou, H

2016-06-01

To detect the changes of microbial community functional diversity of corpses with different postmortem interval （PMI） and to evaluate forensic application value for estimating PMI. The cultivation of microbial community from the anal swabs of a Sus scrofa and a human corpse placed in field environment from 0 to 240 h after death was performed using the Biolog-Eco Microplate and the variations of the absorbance values were also monitored. Combined with the technology of forensic pathology and flies succession, the metabolic characteristics and changes of microbial community on the decomposed corpse under natural environment were also observed. The diversity of microbial metabolism function was found to be negatively correlated with the number of maggots in the corpses. The freezing processing had the greatest impact on average well color development value at 0 h and the impact almost disappeared after 48 h. The diversity of microbial metabolism of the samples became relatively unstable after 192 h. The principal component analysis showed that 31 carbon sources could be consolidated for 5 principal components （accumulative contribution ratio >90%）.The carbon source tsquare-analysis showed that N -acetyl- D -glucosamine and L -serine were the dominant carbon sources for estimating the PMI （0=240 h） of the Sus scrofa and human corpse. The Biolog-Eco method can be used to reveal the metabolic differences of the carbon resources utilization of the microbial community on the corpses during 0-240 h after death, which could provide a new basis for estimating the PMI. Copyright© by the Editorial Department of Journal of Forensic Medicine

Reciprocity relations and the mode conversion-absorption equation with an inhomogeneous source term

International Nuclear Information System (INIS)

Cho, S.; Swanson, D.G.

1990-01-01

The fourth-order mode conversion equation is solved completely via the Green's function to include an inhomogeneous source term. This Green's function itself contains all the plasma responsive effects such as mode conversion and absorption, and can be used to describe the spontaneous emission. In the course of the analysis, the reciprocity relations between coupling parameters are proved

Modeling and simulation of viscoelastic biological particles' 3D manipulation using atomic force microscopy

Science.gov (United States)

Korayem, M. H.; Habibi Sooha, Y.; Rastegar, Z.

2018-05-01

Manipulation of the biological particles by atomic force microscopy is used to transfer these particles inside body's cells, diagnosis and destruction of the cancer cells and drug delivery to damaged cells. According to the impossibility of simultaneous observation of this process, the importance of modeling and simulation can be realized. The contact of the tip with biological particle is important during manipulation, therefore, the first step of the modeling is choosing appropriate contact model. Most of the studies about contact between atomic force microscopy and biological particles, consider the biological particle as an elastic material. This is not an appropriate assumption because biological cells are basically soft and this assumption ignores loading history. In this paper, elastic and viscoelastic JKR theories were used in modeling and simulation of the 3D manipulation for three modes of tip-particle sliding, particle-substrate sliding and particle-substrate rolling. Results showed that critical force and time in motion modes (sliding and rolling) for two elastic and viscoelastic states are very close but these magnitudes were lower in the viscoelastic state. Then, three friction models, Coulomb, LuGre and HK, were used for tip-particle sliding mode in the first phase of manipulation to make results closer to reality. In both Coulomb and LuGre models, critical force and time are very close for elastic and viscoelastic states but in general critical force and time prediction of HK model was higher than LuGre and the LuGre model itself had higher prediction than Coulomb.

Review of Biological Network Data and Its Applications

Directory of Open Access Journals (Sweden)

Donghyeon Yu

2013-12-01

Full Text Available Studying biological networks, such as protein-protein interactions, is key to understanding complex biological activities. Various types of large-scale biological datasets have been collected and analyzed with high-throughput technologies, including DNA microarray, next-generation sequencing, and the two-hybrid screening system, for this purpose. In this review, we focus on network-based approaches that help in understanding biological systems and identifying biological functions. Accordingly, this paper covers two major topics in network biology: reconstruction of gene regulatory networks and network-based applications, including protein function prediction, disease gene prioritization, and network-based genome-wide association study.

Mechanical and biological properties of the micro-/nano-grain functionally graded hydroxyapatite bioceramics for bone tissue engineering.

Science.gov (United States)

Zhou, Changchun; Deng, Congying; Chen, Xuening; Zhao, Xiufen; Chen, Ying; Fan, Yujiang; Zhang, Xingdong

2015-08-01

Functionally graded materials (FGM) open the promising approach for bone tissue repair. In this study, a novel functionally graded hydroxyapatite (HA) bioceramic with micrograin and nanograin structure was fabricated. Its mechanical properties were tailored by composition of micrograin and nanograin. The dynamic mechanical analysis (DMA) indicated that the graded HA ceramics had similar mechanical property compared to natural bones. Their cytocompatibility was evaluated via fluorescent microscopy and MTT colorimetric assay. The viability and proliferation of rabbit bone marrow mesenchymal stem cells (BMSCs) on ceramics indicated that this functionally graded HA ceramic had better cytocompatibility than conventional HA ceramic. This study demonstrated that functionally graded HA ceramics create suitable structures to satisfy both the mechanical and biological requirements of bone tissues. Copyright © 2015 Elsevier Ltd. All rights reserved.

Biology, behaviour and functional response of Cydnocoris gilvus Brum. (Heteroptera: Reduviidae: Harpactorinae a predator of Tea Mosquito Bug (Helopeltis antonii Sign. on cashew in India

Directory of Open Access Journals (Sweden)

K.K. Srikumar

2014-06-01

Full Text Available Helopeltis spp. (Hemiptera: Miridae are major sucking pests of cashew (Anacardium occidentale L. in India. Cydnocoris gilvus Brum. (Heteroptera: Reduviidae: Harpactorinae is recorded as a potential predator of Helopeltis spp. Biology, mating behaviour and functional response of C. gilvus were studied by rearing in the laboratory (temperature 26-28 0C; relative humidity 89-94 % with wax moth, Galleria mellonella, larvae. Based on laboratory rearing, the fecundity was 56.33 eggs in 8.67 batches per female. The average stadial period was 37.3 days, with a maximum of 11 days for V instar and a minimum of 4.5 days for III instars. C. gilvus took 45.5 days to complete a generation. The innate capacity of natural increase was 0.07 with a gross reproduction of 67.8 females per female. The adult exhibited a pin and jab mode of predation in a sequence of actions. The sequential action of mating comprised arousal (1.32 min, approach (12.30 min, riding over (140.48 min and copulation (85.40 min. The predator responded to increasing prey density by killing more prey than at lower prey densities

Heterogeneous Silicon III-V Mode-Locked Lasers

Science.gov (United States)

Davenport, Michael Loehrlein

Mode-locked lasers are useful for a variety of applications, such as sensing, telecommunication, and surgical instruments. This work focuses on integrated-circuit mode-locked lasers: those that combine multiple optical and electronic functions and are manufactured together on a single chip. While this allows production at high volume and lower cost, the true potential of integration is to open applications for mode-locked laser diodes where solid state lasers cannot fit, either due to size and power consumption constraints, or where small optical or electrical paths are needed for high bandwidth. Unfortunately, most high power and highly stable mode-locked laser diode demonstrations in scientific literature are based on the Fabry-Perot resonator design, with cleaved mirrors, and are unsuitable for use in integrated circuits because of the difficulty of producing integrated Fabry-Perot cavities. We use silicon photonics and heterogeneous integration with III-V gain material to produce the most powerful and lowest noise fully integrated mode-locked laser diode in the 20 GHz frequency range. If low noise and high peak power are required, it is arguably the best performing fully integrated mode-locked laser ever demonstrated. We present the design methodology and experimental pathway to realize a fully integrated mode-locked laser diode. The construction of the device, beginning with the selection of an integration platform, and proceeding through the fabrication process to final optimization, is presented in detail. The dependence of mode-locked laser performance on a wide variety of design parameters is presented. Applications for integrated circuit mode-locked lasers are also discussed, as well as proposed methods for using integration to improve mode-locking performance to beyond the current state of the art.

Biological-based and physical-based optimization for biological evaluation of prostate patient's plans