WorldWideScience

Sample records for dependent biological functions

  1. The relativity of biological function.

    Science.gov (United States)

    Laubichler, Manfred D; Stadler, Peter F; Prohaska, Sonja J; Nowick, Katja

    2015-12-01

    Function is a central concept in biological theories and explanations. Yet discussions about function are often based on a narrow understanding of biological systems and processes, such as idealized molecular systems or simple evolutionary, i.e., selective, dynamics. Conflicting conceptions of function continue to be used in the scientific literature to support certain claims, for instance about the fraction of "functional DNA" in the human genome. Here we argue that all biologically meaningful interpretations of function are necessarily context dependent. This implies that they derive their meaning as well as their range of applicability only within a specific theoretical and measurement context. We use this framework to shed light on the current debate about functional DNA and argue that without considering explicitly the theoretical and measurement contexts all attempts to integrate biological theories are prone to fail.

  2. A Unifying Theory of Biological Function.

    Science.gov (United States)

    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 serve the current capacities of their containing system. The new proposal unifies the key notions of both kinds of theories, but goes beyond them by explaining how functions in an organism can exist as factors with autonomous causal efficacy. The goal-directedness and normativity of functions exist in this strict sense as well. The theory depends on an internal physiological or neural process that mimics an organism's fitness, and modulates the organism's variability accordingly. The structure of the internal process can be subdivided into subprocesses that monitor specific functions in an organism. The theory matches well with each intuition on a previously published list of intuited ideas about biological functions, including intuitions that have posed difficulties for other theories.

  3. Extracting Various Classes of Data From Biological Text Using the Concept of Existence Dependency.

    Science.gov (United States)

    Taha, Kamal

    2015-11-01

    One of the key goals of biological natural language processing (NLP) is the automatic information extraction from biomedical publications. Most current constituency and dependency parsers overlook the semantic relationships between the constituents comprising a sentence and may not be well suited for capturing complex long-distance dependences. We propose in this paper a hybrid constituency-dependency parser for biological NLP information extraction called EDCC. EDCC aims at enhancing the state of the art of biological text mining by applying novel linguistic computational techniques that overcome the limitations of current constituency and dependency parsers outlined earlier, as follows: 1) it determines the semantic relationship between each pair of constituents in a sentence using novel semantic rules; and 2) it applies a semantic relationship extraction model that extracts information from different structural forms of constituents in sentences. EDCC can be used to extract different types of data from biological texts for purposes such as protein function prediction, genetic network construction, and protein-protein interaction detection. We evaluated the quality of EDCC by comparing it experimentally with six systems. Results showed marked improvement.

  4. Functions in Biological Kind Classification

    Science.gov (United States)

    Lombrozo, Tania; Rehder, Bob

    2012-01-01

    Biological traits that serve functions, such as a zebra's coloration (for camouflage) or a kangaroo's tail (for balance), seem to have a special role in conceptual representations for biological kinds. In five experiments, we investigate whether and why functional features are privileged in biological kind classification. Experiment 1…

  5. Emergence of ratio-dependent and predator-dependent functional responses for pollination mutualism and seed parasitism

    Science.gov (United States)

    DeAngelis, Donald L.; Holland, J. Nathaniel

    2006-01-01

    Prey (N) dependence [g(N)], predator (P) dependence [g(P) or g(N,P)], and ratio dependence [f(P/N)] are often seen as contrasting forms of the predator's functional response describing predator consumption rates on prey resources in predator–prey and parasitoid–host interactions. Analogously, prey-, predator-, and ratio-dependent functional responses are apparently alternative functional responses for other types of consumer–resource interactions. These include, for example, the fraction of flowers pollinated or seeds parasitized in pollination (pre-dispersal) seed-parasitism mutualisms, such as those between fig wasps and fig trees or yucca moths and yucca plants. Here we examine the appropriate functional responses for how the fraction of flowers pollinated and seeds parasitized vary with the density of pollinators (predator dependence) or the ratio of pollinator and flower densities (ratio dependence). We show that both types of functional responses can emerge from minor, but biologically important variations on a single model. An individual-based model was first used to describe plant–pollinator interactions. Conditional upon on whether the number of flowers visited by the pollinator was limited by factors other than search time (e.g., by the number of eggs it had to lay, if it was also a seed parasite), and on whether the pollinator could directly find flowers on a plant, or had to search, the simulation results lead to either a predator-dependent or a ratio-dependent functional response. An analytic model was then used to show mathematically how these two cases can arise.

  6. IMRT optimization with pseudo-biologic objective function

    International Nuclear Information System (INIS)

    Yi, B. Y.; Ahn, S. D.; Kim, J. H.; Lee, S. W.; Choi, E. K.

    2002-01-01

    The pseudo-biologic objective function has been proposed for the IMRT optimization. It is similar to the biological objective function in mathematical shape, but uses physical parameters. The pseudo-biologic objective function concept is consisted of the target coverage index (TCI) and the organ score index (OSI), was introduced. The TCI was expressed as the sum of all of the weighted bins of target dose volume histogram (DVH). The weights were given as the normal distribution of which the average is 100 % and the standard deviation is ±. The OSI was expressed as similar way. The average of the normal distribution was 0% of the dose and that of standard deviation was selected as a function of limiting dose and its importance. The objective function could be calculated as the product of the TCI and OSI's. The RTP Tool Box (RTB) was used for this study. The constraints applied in the optimization was intuitively clinical experience based numbers, while the physical objective function asks just numbers which are not necessarily based on the clinic, and the parameters for the biologic objective functions are uncertain. The OSI's from the pseudo-biological function showed better results than from the physical functions, while TCI's showed similar tendency. We could show that the pseudo-biologic function can be used for an IMRT objective function on behalf of the biological objective function

  7. Perspective: Fundamental aspects of time-dependent density functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Maitra, Neepa T. [Department of Physics and Astronomy, Hunter College and the Physics Program at the Graduate Center of the City University of New York, 695 Park Avenue, New York, New York 10065 (United States)

    2016-06-14

    In the thirty-two years since the birth of the foundational theorems, time-dependent density functional theory has had a tremendous impact on calculations of electronic spectra and dynamics in chemistry, biology, solid-state physics, and materials science. Alongside the wide-ranging applications, there has been much progress in understanding fundamental aspects of the functionals and the theory itself. This Perspective looks back to some of these developments, reports on some recent progress and current challenges for functionals, and speculates on future directions to improve the accuracy of approximations used in this relatively young theory.

  8. 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

  9. 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.

  10. Feedback dynamics and cell function: Why systems biology is called Systems Biology.

    Science.gov (United States)

    Wolkenhauer, Olaf; Mesarovic, Mihajlo

    2005-05-01

    A new paradigm, like Systems Biology, should challenge the way research has been conducted previously. This Opinion article aims to present Systems Biology, not as the application of engineering principles to biology but as a merger of systems- and control theory with molecular- and cell biology. In our view, the central dogma of Systems Biology is that it is system dynamics that gives rise to the functioning and function of cells. The concepts of feedback regulation and control of pathways and the coordination of cell function are emphasized as an important area of Systems Biology research. The hurdles and risks for this area are discussed from the perspective of dynamic pathway modelling. Most of all, the aim of this article is to promote mathematical modelling and simulation as a part of molecular- and cell biology. Systems Biology is a success if it is widely accepted that there is nothing more practical than a good theory.

  11. Functional model of biological neural networks.

    Science.gov (United States)

    Lo, James Ting-Ho

    2010-12-01

    A functional model of biological neural networks, called temporal hierarchical probabilistic associative memory (THPAM), is proposed in this paper. THPAM comprises functional models of dendritic trees for encoding inputs to neurons, a first type of neuron for generating spike trains, a second type of neuron for generating graded signals to modulate neurons of the first type, supervised and unsupervised Hebbian learning mechanisms for easy learning and retrieving, an arrangement of dendritic trees for maximizing generalization, hardwiring for rotation-translation-scaling invariance, and feedback connections with different delay durations for neurons to make full use of present and past informations generated by neurons in the same and higher layers. These functional models and their processing operations have many functions of biological neural networks that have not been achieved by other models in the open literature and provide logically coherent answers to many long-standing neuroscientific questions. However, biological justifications of these functional models and their processing operations are required for THPAM to qualify as a macroscopic model (or low-order approximate) of biological neural networks.

  12. Understanding Biological Rates and their Temperature Dependence, from Enzymes to Ecosystems

    Science.gov (United States)

    Prentice, E.; Arcus, V. L.

    2017-12-01

    Temperature responses over various scales in biological systems follow a similar pattern; negative curvature results in an optimum temperature (Topt) for activity/growth/turnover, with decreases in rates on either side of Topt. Previously this downturn in rates at high temperatures has been attributed to enzyme denaturation, where a failing of the basic driving units of metabolism was used to describe curvature at the enzyme and organism level. However, recent developments in our understanding of the factors governing enzyme rates at different temperatures have guided a new understanding of the responses of biological systems. Enzymes catalyse reactions by driving the substrate through a high energy species, which is tightly bound to the enzyme. Macromolecular rate theory (MMRT) has recently been developed to account for the changes in the system brought about by this tight binding, specifically the change in the physical parameter heat capacity (ΔCǂp), and the effect this has on the temperature dependence of enzyme reactions. A negative ΔCǂp imparts the signature negative curvature to rates in the absence of denaturation, and finds that Topt, ΔCǂp and curvature are all correlated, placing constraints on biological systems. The simplest of cells comprise thousands of enzymatically catalysed reactions, functioning in series and in parallel in metabolic pathways to determine the overall growth rate of an organism. Intuitively, the temperature effects of enzymes play a role in determining the overall temperature dependence of an organism, in tandem with cellular level regulatory responses. However, the effect of individual Topt values and curvature on overall pathway behaviour is less apparent. Here, this is investigated in the context of MMRT through the in vitro characterisation of a six-step metabolic pathway to understand the steps in isolation and functioning in series. Pathway behaviour is found to be approximately an average of the properties of the

  13. 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

  14. 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).

  15. Biological repair with time-dependent irradiation

    International Nuclear Information System (INIS)

    Broyles, A.A.; Shapiro, C.S.

    1985-01-01

    Recent experiments have provided new data that explore the effectiveness of biological repair in assessing damage due to exposures from ionizing radiation. These data are mainly from experiments conducted at constant dose rates, to study the effectiveness per unit dose of different dose rates. Here, we develop new formulae to estimate the effectiveness of an arbitrary time-dependent dose rate exposure

  16. Wind dependence of ambient noise in a biologically rich coastal area.

    Science.gov (United States)

    Mathias, Delphine; Gervaise, Cédric; Di Iorio, Lucia

    2016-02-01

    The wind dependence of acoustic spectrum between 100 Hz and 16 kHz is investigated for coastal biologically rich areas. The analysis of 5 months of continuous measurements run in a 10 m deep shallow water environment off Brittany (France) showed that wind dependence of spectral levels is subject to masking by biological sounds. When dealing with raw data, the wind dependence of spectral levels was not significant for frequencies where biological sounds were present (2 to 10 kHz). An algorithm developed by Kinda, Simard, Gervaise, Mars, and Fortier [J. Acoust. Soc. Am. 134(1), 77-87 (2013)] was used to automatically filter out the loud distinctive biological contribution and estimated the ambient noise spectrum. The wind dependence of ambient noise spectrum was always significant after application of this filter. A mixture model for ambient noise spectrum which accounts for the richness of the soundscape is proposed. This model revealed that wind dependence holds once the wind speed was strong enough to produce sounds higher in amplitude than the biological chorus (9 kn at 3 kHz, 11 kn at 8 kHz). For these higher wind speeds, a logarithmic affine law was adequate and its estimated parameters were compatible with previous studies (average slope 27.1 dB per decade of wind speed increase).

  17. Path-dependent functions

    International Nuclear Information System (INIS)

    Khrapko, R.I.

    1985-01-01

    A uniform description of various path-dependent functions is presented with the help of expansion of the type of the Taylor series. So called ''path-integrals'' and ''path-tensor'' are introduced which are systems of many-component quantities whose values are defined for arbitrary paths in coordinated region of space in such a way that they contain a complete information on the path. These constructions are considered as elementary path-dependent functions and are used instead of power monomials in the usual Taylor series. Coefficients of such an expansion are interpreted as partial derivatives dependent on the order of the differentiations or else as nonstandard cavariant derivatives called two-point derivatives. Some examples of pathdependent functions are presented.Space curvature tensor is considered whose geometrica properties are determined by the (non-transitive) translator of parallel transport of a general type. Covariant operation leading to the ''extension'' of tensor fiels is pointed out

  18. 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.

  19. 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.

  20. 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...

  1. 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

  2. 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...

  3. 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.

  4. Towards Integration of Biological and Physiological Functions at Multiple Levels

    Directory of Open Access Journals (Sweden)

    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.

  5. Discovery of functional and approximate functional dependencies in relational databases

    Directory of Open Access Journals (Sweden)

    Ronald S. King

    2003-01-01

    Full Text Available This study develops the foundation for a simple, yet efficient method for uncovering functional and approximate functional dependencies in relational databases. The technique is based upon the mathematical theory of partitions defined over a relation's row identifiers. Using a levelwise algorithm the minimal non-trivial functional dependencies can be found using computations conducted on integers. Therefore, the required operations on partitions are both simple and fast. Additionally, the row identifiers provide the added advantage of nominally identifying the exceptions to approximate functional dependencies, which can be used effectively in practical data mining applications.

  6. 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

  7. 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.

  8. Time-dependent potential-functional embedding theory

    International Nuclear Information System (INIS)

    Huang, Chen; Libisch, Florian; Peng, Qing; Carter, Emily A.

    2014-01-01

    We introduce a time-dependent potential-functional embedding theory (TD-PFET), in which atoms are grouped into subsystems. In TD-PFET, subsystems can be propagated by different suitable time-dependent quantum mechanical methods and their interactions can be treated in a seamless, first-principles manner. TD-PFET is formulated based on the time-dependent quantum mechanics variational principle. The action of the total quantum system is written as a functional of the time-dependent embedding potential, i.e., a potential-functional formulation. By exploiting the Runge-Gross theorem, we prove the uniqueness of the time-dependent embedding potential under the constraint that all subsystems share a common embedding potential. We derive the integral equation that such an embedding potential needs to satisfy. As proof-of-principle, we demonstrate TD-PFET for a Na 4 cluster, in which each Na atom is treated as one subsystem and propagated by time-dependent Kohn-Sham density functional theory (TDDFT) using the adiabatic local density approximation (ALDA). Our results agree well with a direct TDDFT calculation on the whole Na 4 cluster using ALDA. We envision that TD-PFET will ultimately be useful for studying ultrafast quantum dynamics in condensed matter, where key regions are solved by highly accurate time-dependent quantum mechanics methods, and unimportant regions are solved by faster, less accurate methods

  9. The biological function of consciousness

    Directory of Open Access Journals (Sweden)

    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.

  10. Chewing Maintains Hippocampus-Dependent Cognitive Function.

    Science.gov (United States)

    Chen, Huayue; Iinuma, Mitsuo; Onozuka, Minoru; Kubo, Kin-Ya

    2015-01-01

    Mastication (chewing) is important not only for food intake, but also for preserving and promoting the general health. Recent studies have showed that mastication helps to maintain cognitive functions in the hippocampus, a central nervous system region vital for spatial memory and learning. The purpose of this paper is to review the recent progress of the association between mastication and the hippocampus-dependent cognitive function. There are multiple neural circuits connecting the masticatory organs and the hippocampus. Both animal and human studies indicated that cognitive functioning is influenced by mastication. Masticatory dysfunction is associated with the hippocampal morphological impairments and the hippocampus-dependent spatial memory deficits, especially in elderly. Mastication is an effective behavior for maintaining the hippocampus-dependent cognitive performance, which deteriorates with aging. Therefore, chewing may represent a useful approach in preserving and promoting the hippocampus-dependent cognitive function in older people. We also discussed several possible mechanisms involved in the interaction between mastication and the hippocampal neurogenesis and the future directions for this unique fascinating research.

  11. Specifying Functional Requirements Dependency in the REWiki

    OpenAIRE

    ZHANG, ZHANG

    2013-01-01

    Most of the individual requirements cannot be treated in isolation. Requirements may affect each other in various ways. The dependency between requirements impacts a number of software development aspects and activities. How to classify and specify requirements dependency remains a classic research topic. This research aims at providing an approach of specifying functional requirements dependency. In this thesis we generalize a classification of functional requirements dependency. We also pro...

  12. Biological effects of simple changes in functionality on rhodium metalloinsertors

    Science.gov (United States)

    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

  13. 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/.

  14. Mediator-dependent Nuclear Receptor Functions

    Science.gov (United States)

    Chen, Wei; Roeder, Robert

    2011-01-01

    As gene-specific transcription factors, nuclear hormone receptors are broadly involved in many important biological processes. Their function on target genes requires the stepwise assembly of different coactivator complexes that facilitate chromatin remodeling and subsequent preinitiation complex (PIC) formation and function. Mediator has proved to be a crucial, and general, nuclear receptor-interacting coactivator, with demonstrated functions in transcription steps ranging from chromatin remodeling to subsequent PIC formation and function. Here we discuss (i) our current understanding of pathways that nuclear receptors and other interacting cofactors employ to recruit Mediator to target gene enhancers and promoters, including conditional requirements for the strong NR-Mediator interactions mediated by the NR AF2 domain and the MED1 LXXLLL motifs and (ii) mechanisms by which Mediator acts to transmit signals from enhancer-bound nuclear receptors to the general transcription machinery at core promoters to effect PIC formation and function. PMID:21854863

  15. Knowledge-fused differential dependency network models for detecting significant rewiring in biological networks.

    Science.gov (United States)

    Tian, Ye; Zhang, Bai; Hoffman, Eric P; Clarke, Robert; Zhang, Zhen; Shih, Ie-Ming; Xuan, Jianhua; Herrington, David M; Wang, Yue

    2014-07-24

    Modeling biological networks serves as both a major goal and an effective tool of systems biology in studying mechanisms that orchestrate the activities of gene products in cells. Biological networks are context-specific and dynamic in nature. To systematically characterize the selectively activated regulatory components and mechanisms, modeling tools must be able to effectively distinguish significant rewiring from random background fluctuations. While differential networks cannot be constructed by existing knowledge alone, novel incorporation of prior knowledge into data-driven approaches can improve the robustness and biological relevance of network inference. However, the major unresolved roadblocks include: big solution space but a small sample size; highly complex networks; imperfect prior knowledge; missing significance assessment; and heuristic structural parameter learning. To address these challenges, we formulated the inference of differential dependency networks that incorporate both conditional data and prior knowledge as a convex optimization problem, and developed an efficient learning algorithm to jointly infer the conserved biological network and the significant rewiring across different conditions. We used a novel sampling scheme to estimate the expected error rate due to "random" knowledge. Based on that scheme, we developed a strategy that fully exploits the benefit of this data-knowledge integrated approach. We demonstrated and validated the principle and performance of our method using synthetic datasets. We then applied our method to yeast cell line and breast cancer microarray data and obtained biologically plausible results. The open-source R software package and the experimental data are freely available at http://www.cbil.ece.vt.edu/software.htm. Experiments on both synthetic and real data demonstrate the effectiveness of the knowledge-fused differential dependency network in revealing the statistically significant rewiring in biological

  16. Predictors of functional dependency after stroke in Nigeria.

    Science.gov (United States)

    Ojagbemi, Akin; Owolabi, Mayowa

    2013-11-01

    The factors impacting poststroke functional dependency have not been adequately explored in sub-Saharan Africa. This study examined the risk factors for functional dependency in a group of Nigerian African stroke survivors. One hundred twenty-eight stroke survivors attending a tertiary general hospital in southwestern Nigeria were consecutively recruited and assessed for functional dependency using the modified Rankin Scale (mRS). Stroke was diagnosed according to the World Health Organization criteria. Candidate independent variables assessed included the demographic and clinical characteristics of survivors, cognitive dysfunction, and a diagnosis of major depressive disorder. Variables with significant relationship to functional dependency were entered into a logistic regression model to identify factors that were predictive of functional dependency among the stroke survivors. In all, 60.9% of the stroke survivors were functionally dependent (mRS scores≥3), with mean±SD mRS scores of 2.71±1.01. Female sex (P=.003; odds ratio [OR] 3.08; 95% confidence interval [CI] 1.47-6.44), global cognitive dysfunction (P=.002; OR 5.04; 95% CI 1.79-14.16), and major depressive disorder (Pdependency in univariate analysis. Major depressive disorder was an independent predictor of functional dependency in multivariate analysis (P<.0001; OR 6.89; 95% CI 2.55-18.6; R2=0.19). Depression, female sex, and cognitive dysfunction were strongly associated with poorer functioning after stroke. Interventions aimed at depression and cognitive dysfunction after stroke may improve functional independence in stroke survivors. Copyright © 2013 National Stroke Association. Published by Elsevier Inc. All rights reserved.

  17. Wave function for time-dependent harmonically confined electrons in a time-dependent electric field.

    Science.gov (United States)

    Li, Yu-Qi; Pan, Xiao-Yin; Sahni, Viraht

    2013-09-21

    The many-body wave function of a system of interacting particles confined by a time-dependent harmonic potential and perturbed by a time-dependent spatially homogeneous electric field is derived via the Feynman path-integral method. The wave function is comprised of a phase factor times the solution to the unperturbed time-dependent Schrödinger equation with the latter being translated by a time-dependent value that satisfies the classical driven equation of motion. The wave function reduces to that of the Harmonic Potential Theorem wave function for the case of the time-independent harmonic confining potential.

  18. Cytosol-dependent membrane fusion in ER, nuclear envelope and nuclear pore assembly: biological implications.

    Science.gov (United States)

    Rafikova, Elvira R; Melikov, Kamran; Chernomordik, Leonid V

    2010-01-01

    Endoplasmic reticulum and nuclear envelope rearrangements after mitosis are often studied in the reconstitution system based on Xenopus egg extract. In our recent work we partially replaced the membrane vesicles in the reconstitution mix with protein-free liposomes to explore the relative contributions of cytosolic and transmembrane proteins. Here we discuss our finding that cytosolic proteins mediate fusion between membranes lacking functional transmembrane proteins and the role of membrane fusion in endoplasmic reticulum and nuclear envelope reorganization. Cytosol-dependent liposome fusion has allowed us to restore, without adding transmembrane nucleoporins, functionality of nuclear pores, their spatial distribution and chromatin decondensation in nuclei formed at insufficient amounts of membrane material and characterized by only partial decondensation of chromatin and lack of nuclear transport. Both the mechanisms and the biological implications of the discovered coupling between spatial distribution of nuclear pores, chromatin decondensation and nuclear transport are discussed.

  19. 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

  20. 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...

  1. 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...

  2. Spin dependent photon structure functions

    International Nuclear Information System (INIS)

    Manohar, A.V.; Massachusetts Inst. of Tech., Cambridge

    1989-01-01

    Spin dependent structure functions of the photon are studied using the operator product expansion. There are new twist-two photon and gluon operators which contribute. The structure functions g 1 and F 3 are calculable in QCD, but differ from their free quark values. The corrections to F 3 are suppressed by 1/log Q 2 . The calculation is an extension of the analysis of Witten for the spin averaged structure functions F 1 and F 2 . (orig.)

  3. 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.

  4. 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.

  5. 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.

  6. The cell biology of T-dependent B cell activation

    DEFF Research Database (Denmark)

    Owens, T; Zeine, R

    1989-01-01

    The requirement that CD4+ helper T cells recognize antigen in association with class II Major Histocompatibility Complex (MHC) encoded molecules constrains T cells to activation through intercellular interaction. The cell biology of the interactions between CD4+ T cells and antigen-presenting cells...... includes multipoint intermolecular interactions that probably involve aggregation of both polymorphic and monomorphic T cell surface molecules. Such aggregations have been shown in vitro to markedly enhance and, in some cases, induce T cell activation. The production of T-derived lymphokines that have been...... implicated in B cell activation is dependent on the T cell receptor for antigen and its associated CD3 signalling complex. T-dependent help for B cell activation is therefore similarly MHC-restricted and involves T-B intercellular interaction. Recent reports that describe antigen-independent B cell...

  7. 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.

  8. Analyses in zebrafish embryos reveal that nanotoxicity profiles are dependent on surface-functionalization controlled penetrance of biological membranes.

    Science.gov (United States)

    Paatero, Ilkka; Casals, Eudald; Niemi, Rasmus; Özliseli, Ezgi; Rosenholm, Jessica M; Sahlgren, Cecilia

    2017-08-21

    Mesoporous silica nanoparticles (MSNs) are extensively explored as drug delivery systems, but in depth understanding of design-toxicity relationships is still scarce. We used zebrafish (Danio rerio) embryos to study toxicity profiles of differently surface functionalized MSNs. Embryos with the chorion membrane intact, or dechoroniated embryos, were incubated or microinjected with amino (NH 2 -MSNs), polyethyleneimine (PEI-MSNs), succinic acid (SUCC-MSNs) or polyethyleneglycol (PEG-MSNs) functionalized MSNs. Toxicity was assessed by viability and cardiovascular function. NH 2 -MSNs, SUCC-MSNs and PEG-MSNs were well tolerated, 50 µg/ml PEI-MSNs induced 100% lethality 48 hours post fertilization (hpf). Dechoroniated embryos were more sensitive and 10 µg/ml PEI-MSNs reduced viability to 5% at 96hpf. Sensitivity to PEG- and SUCC-, but not NH 2 -MSNs, was also enhanced. Typically cardiovascular toxicity was evident prior to lethality. Confocal microscopy revealed that PEI-MSNs penetrated into the embryos whereas PEG-, NH2- and SUCC-MSNs remained aggregated on the skin surface. Direct exposure of inner organs by microinjecting NH 2 -MSNs and PEI-MSNs demonstrated that the particles displayed similar toxicity indicating that functionalization affects the toxicity profile by influencing penetrance through biological barriers. The data emphasize the need for careful analyses of toxicity mechanisms in relevant models and constitute an important knowledge step towards the development of safer and sustainable nanotherapies.

  9. 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.

  10. Evidence that two ATP-dependent (Lon proteases in Borrelia burgdorferi serve different functions.

    Directory of Open Access Journals (Sweden)

    James L Coleman

    2009-11-01

    Full Text Available The canonical ATP-dependent protease Lon participates in an assortment of biological processes in bacteria, including the catalysis of damaged or senescent proteins and short-lived regulatory proteins. Borrelia spirochetes are unusual in that they code for two putative ATP-dependent Lon homologs, Lon-1 and Lon-2. Borrelia burgdorferi, the etiologic agent of Lyme disease, is transmitted through the blood feeding of Ixodes ticks. Previous work in our laboratory reported that B. burgdorferi lon-1 is upregulated transcriptionally by exposure to blood in vitro, while lon-2 is not. Because blood induction of Lon-1 may be of importance in the regulation of virulence factors critical for spirochete transmission, the clarification of functional roles for these two proteases in B. burgdorferi was the object of this study. On the chromosome, lon-2 is immediately downstream of ATP-dependent proteases clpP and clpX, an arrangement identical to that of lon of Escherichia coli. Phylogenetic analysis revealed that Lon-1 and Lon-2 cluster separately due to differences in the NH(2-terminal substrate binding domains that may reflect differences in substrate specificity. Recombinant Lon-1 manifested properties of an ATP-dependent chaperone-protease in vitro but did not complement an E. coli Lon mutant, while Lon-2 corrected two characteristic Lon-mutant phenotypes. We conclude that B. burgdorferi Lons -1 and -2 have distinct functional roles. Lon-2 functions in a manner consistent with canonical Lon, engaged in cellular homeostasis. Lon-1, by virtue of its blood induction, and as a unique feature of the Borreliae, may be important in host adaptation from the arthropod to a warm-blooded host.

  11. 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.

  12. Functional-dependent and size-dependent uptake of nanoparticles in PC12

    International Nuclear Information System (INIS)

    Sakai, N; Matsui, Y; Nakayama, A; Yoneda, M; Tsuda, A

    2011-01-01

    It is suggested that the uptake of nanoparticles is changed by the particle size or the surface modification. In this study, we quantified the uptake of nanoparticles in PC12 cells exposed Quantum Dots with different surface modification or fluorescent polystyrene particles with different particle size. The PC12 cells were exposed three types of the Quantum Dots (carboxyl base-functionalized, amino base-functionalized or non-base-functionalized) or three types of the fluorescent particles (22 nm, 100 nm or 1000 nm) for 3 hours. The uptake of the nanoparticles was quantified with a spectrofluorophotometer. The carboxyl base-functionalized Quantum Dots were considerably taken up by the cells than the non-base-functionalized Quantum Dots. Conversely, the amino base-functionalized Quantum Dots were taken up by the cells less frequently than the non-base-functionalized Quantum Dots. The particle number of the 22 nm-nanoparticles taken up by the cells was about 53 times higher than the 100 nm-particles. However, the particle weight of the 100 nm-particles taken up by the cells was higher than that of the 22 nm-nanoparticles. The 1000 nm-particles were adhered to the cell membrane, but they were little taken up by the cells. We concluded that nanoparticles can be taken up nerve cells in functional-dependent and size-dependent manners.

  13. 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.

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

    Science.gov (United States)

    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

  15. 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

  16. Context dependence of students' views about the role of equations in understanding biology.

    Science.gov (United States)

    Watkins, Jessica; Elby, Andrew

    2013-06-01

    Students' epistemological views about biology--their ideas about what "counts" as learning and understanding biology--play a role in how they approach their courses and respond to reforms. As introductory biology courses incorporate more physics and quantitative reasoning, student attitudes about the role of equations in biology become especially relevant. However, as documented in research in physics education, students' epistemologies are not always stable and fixed entities; they can be dynamic and context-dependent. In this paper, we examine an interview with an introductory student in which she discusses the use of equations in her reformed biology course. In one part of the interview, she expresses what sounds like an entrenched negative stance toward the role equations can play in understanding biology. However, later in the interview, when discussing a different biology topic, she takes a more positive stance toward the value of equations. These results highlight how a given student can have diverse ways of thinking about the value of bringing physics and math into biology. By highlighting how attitudes can shift in response to different tasks, instructional environments, and contextual cues, we emphasize the need to attend to these factors, rather than treating students' beliefs as fixed and stable.

  17. 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).

  18. Age-Dependent Pleiotropy Between General Cognitive Function and Major Psychiatric Disorders.

    Science.gov (United States)

    Hill, W David; Davies, Gail; Liewald, David C; McIntosh, Andrew M; Deary, Ian J

    2016-08-15

    General cognitive function predicts psychiatric illness across the life course. This study examines the role of pleiotropy in explaining the link between cognitive function and psychiatric disorder. We used two large genome-wide association study data sets on cognitive function-one from older age, n = 53,949, and one from childhood, n = 12,441. We also used genome-wide association study data on educational attainment, n = 95,427, to examine the validity of its use as a proxy phenotype for cognitive function. Using a new method, linkage disequilibrium regression, we derived genetic correlations, free from the confounding of clinical state between psychiatric illness and cognitive function. We found a genetic correlation of .711 (p = 2.26e-12) across the life course for general cognitive function. We also showed a positive genetic correlation between autism spectrum disorder and cognitive function in childhood (rg = .360, p = .0009) and for educational attainment (rg = .322, p = 1.37e-5) but not in older age. In schizophrenia, we found a negative genetic correlation between older age cognitive function (rg = -.231, p = 3.81e-12) but not in childhood or for educational attainment. For Alzheimer's disease, we found negative genetic correlations with childhood cognitive function (rg = -.341, p = .001), educational attainment (rg = -.324, p = 1.15e-5), and with older age cognitive function (rg = -.324, p = 1.78e-5). The pleiotropy exhibited between cognitive function and psychiatric disorders changed across the life course. These age-dependent associations might explain why negative selection has not removed variants causally associated with autism spectrum disorder or schizophrenia. Copyright © 2016 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

  19. 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.

  20. 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.

  1. 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)

  2. Substrates of neuropsychological functioning in stimulant dependence: a review of functional neuroimaging research

    NARCIS (Netherlands)

    Crunelle, C.L.; Veltman, D.J.; Booij, J.; van Emmerik-van Oortmerssen, K.; van den Brink, W.

    2012-01-01

    Stimulant dependence is associated with neuropsychological impairments. Here, we summarize and integrate the existing neuroimaging literature on the neural substrates of neuropsychological (dys)function in stimulant dependence, including cocaine, (meth-)amphetamine, ecstasy and nicotine dependence,

  3. Functionalized Nanodiamonds for Biological and Medical Applications.

    Science.gov (United States)

    Lai, Lin; Barnard, Amanda S

    2015-02-01

    Nanodiamond is a promising material for biological and medical applications, owning to its relatively inexpensive and large-scale synthesis, unique structure, and superior optical properties. However, most biomedical applications, such as drug delivery and bio-imaging, are dependent upon the precise control of the surfaces, and can be significantly affected by the type, distribution and stability of chemical funtionalisations of the nanodiamond surface. In this paper, recent studies on nanodiamonds and their biomedical applications by conjugating with different chemicals are reviewed, while highlighting the critical importance of surface chemical states for various applications.

  4. 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.

  5. Angle-dependent strong-field molecular ionization rates with tuned range-separated time-dependent density functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Sissay, Adonay [Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803 (United States); Abanador, Paul; Mauger, François; Gaarde, Mette; Schafer, Kenneth J. [Department of Physics and Astronomy, Louisiana State University, Baton Rouge, Louisiana 70803 (United States); Lopata, Kenneth, E-mail: klopata@lsu.edu [Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803 (United States); Center for Computation and Technology, Louisiana State University, Baton Rouge, Louisiana 70803 (United States)

    2016-09-07

    Strong-field ionization and the resulting electronic dynamics are important for a range of processes such as high harmonic generation, photodamage, charge resonance enhanced ionization, and ionization-triggered charge migration. Modeling ionization dynamics in molecular systems from first-principles can be challenging due to the large spatial extent of the wavefunction which stresses the accuracy of basis sets, and the intense fields which require non-perturbative time-dependent electronic structure methods. In this paper, we develop a time-dependent density functional theory approach which uses a Gaussian-type orbital (GTO) basis set to capture strong-field ionization rates and dynamics in atoms and small molecules. This involves propagating the electronic density matrix in time with a time-dependent laser potential and a spatial non-Hermitian complex absorbing potential which is projected onto an atom-centered basis set to remove ionized charge from the simulation. For the density functional theory (DFT) functional we use a tuned range-separated functional LC-PBE*, which has the correct asymptotic 1/r form of the potential and a reduced delocalization error compared to traditional DFT functionals. Ionization rates are computed for hydrogen, molecular nitrogen, and iodoacetylene under various field frequencies, intensities, and polarizations (angle-dependent ionization), and the results are shown to quantitatively agree with time-dependent Schrödinger equation and strong-field approximation calculations. This tuned DFT with GTO method opens the door to predictive all-electron time-dependent density functional theory simulations of ionization and ionization-triggered dynamics in molecular systems using tuned range-separated hybrid functionals.

  6. Angle-dependent strong-field molecular ionization rates with tuned range-separated time-dependent density functional theory

    International Nuclear Information System (INIS)

    Sissay, Adonay; Abanador, Paul; Mauger, François; Gaarde, Mette; Schafer, Kenneth J.; Lopata, Kenneth

    2016-01-01

    Strong-field ionization and the resulting electronic dynamics are important for a range of processes such as high harmonic generation, photodamage, charge resonance enhanced ionization, and ionization-triggered charge migration. Modeling ionization dynamics in molecular systems from first-principles can be challenging due to the large spatial extent of the wavefunction which stresses the accuracy of basis sets, and the intense fields which require non-perturbative time-dependent electronic structure methods. In this paper, we develop a time-dependent density functional theory approach which uses a Gaussian-type orbital (GTO) basis set to capture strong-field ionization rates and dynamics in atoms and small molecules. This involves propagating the electronic density matrix in time with a time-dependent laser potential and a spatial non-Hermitian complex absorbing potential which is projected onto an atom-centered basis set to remove ionized charge from the simulation. For the density functional theory (DFT) functional we use a tuned range-separated functional LC-PBE*, which has the correct asymptotic 1/r form of the potential and a reduced delocalization error compared to traditional DFT functionals. Ionization rates are computed for hydrogen, molecular nitrogen, and iodoacetylene under various field frequencies, intensities, and polarizations (angle-dependent ionization), and the results are shown to quantitatively agree with time-dependent Schrödinger equation and strong-field approximation calculations. This tuned DFT with GTO method opens the door to predictive all-electron time-dependent density functional theory simulations of ionization and ionization-triggered dynamics in molecular systems using tuned range-separated hybrid functionals.

  7. 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

  8. A rapid Q-PCR titration protocol for adenovirus and helper-dependent adenovirus vectors that produces biologically relevant results

    Science.gov (United States)

    Gallaher, Sean D.; Berk, Arnold J.

    2013-01-01

    Adenoviruses are employed in the study of cellular processes and as expression vectors used in gene therapy. The success and reproducibility of these studies is dependent in part on having accurate and meaningful titers of replication competent and helper-dependent adenovirus stocks, which is problematic due to the use of varied and divergent titration protocols. Physical titration methods, which quantify the total number of viral particles, are used by many, but are poor at estimating activity. Biological titration methods, such as plaque assays, are more biologically relevant, but are time consuming and not applicable to helper-dependent gene therapy vectors. To address this, a protocol was developed called “infectious genome titration” in which viral DNA is isolated from the nuclei of cells ~3 h post-infection, and then quantified by Q-PCR. This approach ensures that only biologically active virions are counted as part of the titer determination. This approach is rapid, robust, sensitive, reproducible, and applicable to all forms of adenovirus. Unlike other Q-PCR-based methods, titers determined by this protocol are well correlated with biological activity. PMID:23624118

  9. 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

  10. 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.

  11. 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

  12. Modelling the dependability in Network Function Virtualisation

    OpenAIRE

    Lin, Wenqi

    2017-01-01

    Network Function Virtualization has been brought up to allow the TSPs to have more possibilities and flexibilities to provision services with better load optimizing, energy utilizing and dynamic scaling. Network functions will be decoupled from the underlying dedicated hardware into software instances that run on commercial off-the-shelf servers. However, the development is still at an early stage and the dependability concerns raise by the virtualization of the network functions are touched ...

  13. Substrates of neuropsychological functioning in stimulant dependence: a review of functional neuroimaging research

    NARCIS (Netherlands)

    Crunelle, Cleo L.; Veltman, Dick J.; Booij, Jan; Emmerik-van Oortmerssen, Katelijne; den Brink, Wim

    2012-01-01

    Stimulant dependence is associated with neuropsychological impairments. Here, we summarize and integrate the existing neuroimaging literature on the neural substrates of neuropsychological (dys) function in stimulant dependence, including cocaine, (meth-) amphetamine, ecstasy and nicotine

  14. Selective functional activity measurement of a PEGylated protein with a modification-dependent activity assay.

    Science.gov (United States)

    Weber, Alfred; Engelmaier, Andrea; Mohr, Gabriele; Haindl, Sonja; Schwarz, Hans Peter; Turecek, Peter L

    2017-01-05

    BAX 855 (ADYNOVATE) is a PEGylated recombinant factor VIII (rFVIII) that showed prolonged circulatory half-life compared to unmodified rFVIII in hemophilic patients. Here, the development and validation of a novel assay is described that selectively measures the activity of BAX 855 as cofactor for the serine protease factor IX, which actives factor X. This method type, termed modification-dependent activity assay, is based on PEG-specific capture of BAX 855 by an anti-PEG IgG preparation, followed by a chromogenic FVIII activity assay. The assay principle enabled sensitive measurement of the FVIII cofactor activity of BAX 855 down to the pM-range without interference by non-PEGylated FVIII. The selectivity of the capture step, shown by competition studies to primarily target the terminal methoxy group of PEG, also allowed assessment of the intactness of the attached PEG chains. Altogether, the modification-dependent activity not only enriches, but complements the group of methods to selectively, accurately, and precisely measure a PEGylated drug in complex biological matrices. In contrast to all other methods described so far, it allows measurement of the biological activity of the PEGylated protein. Data obtained demonstrate that this new method principle can be extended to protein modifications other than PEGylation and to a variety of functional activity assays. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Manipulation of the membrane binding site of vitamin K-dependent proteins: Enhanced biological function of human factor VII

    OpenAIRE

    Shah, Amit M.; Kisiel, Walter; Foster, Donald C.; Nelsestuen, Gary L.

    1998-01-01

    Recent studies suggested that modification of the membrane contact site of vitamin K-dependent proteins may enhance the membrane affinity and function of members of this protein family. The properties of a factor VII mutant, factor VII-Q10E32, relative to wild-type factor VII (VII, containing P10K32), have been compared. Membrane affinity of VII-Q10E32 was about 20-fold higher than that of wild-type factor VII. The rate of autoactivation VII-Q10E32 with soluble tissue factor was 100-fold fast...

  16. Fungal NRPS-dependent siderophores: From function to prediction

    DEFF Research Database (Denmark)

    Sørensen, Jens Laurids; Knudsen, Michael; Hansen, Frederik Teilfeldt

    2014-01-01

    discuss the function of siderophores in relation to fungal iron uptake mechanisms and their importance for coexistence with host organisms. The chemical nature of the major groups of siderophores and their regulation is described along with the function and architecture of the large multi-domain enzymes...... responsible for siderophore synthesis, namely the non-ribosomal peptide synthetases (NRPSs). Finally, we present the most recent advances in our understanding of the structural biology of fungal NRPSs and discuss opportunities for the development of a fungal NRPS prediction server...

  17. 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) ...

  18. 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....

  19. 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.

  20. Wavelength dependence of biological damage induced by UV radiation on bacteria.

    Science.gov (United States)

    Santos, Ana L; Oliveira, Vanessa; Baptista, Inês; Henriques, Isabel; Gomes, Newton C M; Almeida, Adelaide; Correia, António; Cunha, Ângela

    2013-01-01

    The biological effects of UV radiation of different wavelengths (UVA, UVB and UVC) were assessed in nine bacterial isolates displaying different UV sensitivities. Biological effects (survival and activity) and molecular markers of oxidative stress [DNA strand breakage (DSB), generation of reactive oxygen species (ROS), oxidative damage to proteins and lipids, and the activity of antioxidant enzymes catalase and superoxide dismutase] were quantified and statistically analyzed in order to identify the major determinants of cell inactivation under the different spectral regions. Survival and activity followed a clear wavelength dependence, being highest under UVA and lowest under UVC. The generation of ROS, as well as protein and lipid oxidation, followed the same pattern. DNA damage (DSB) showed the inverse trend. Multiple stepwise regression analysis revealed that survival under UVA, UVB and UVC wavelengths was best explained by DSB, oxidative damage to lipids, and intracellular ROS levels, respectively.

  1. Ins and outs of systems biology vis-à-vis molecular biology: continuation or clear cut?

    Science.gov (United States)

    De Backer, Philippe; De Waele, Danny; Van Speybroeck, Linda

    2010-03-01

    The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology 'revolutionizes' molecular biology and 'transcends' its assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology's use of modelling and bioinformatics, and by its scale enlargement.

  2. 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.

  3. Differential surface phenotype and context-dependent reactivity of functionally diverse NKT cells.

    Science.gov (United States)

    Cameron, Garth; Godfrey, Dale I

    2018-03-05

    Natural Killer T (NKT) cells are a functionally diverse population that recognizes lipid-based antigens in association with the antigen-presenting molecule CD1d. Here, we define a technique to separate the functionally distinct thymic NKT1, NKT2 and NKT17 cell subsets by their surface expression of CD278 (ICOS) and the activation-associated glycoform of CD43, enabling the investigation of subset-specific effector-functions. We report that all three subsets express the transcription factor GATA-3 and the potential to produce IL-4 and IL-10 following activation. This questions the notion that NKT2 cells are the predominant source of IL-4 within the NKT cell pool, and suggests that IL-10-production may be more indicative of NKT cell plasticity than the existence of a distinct regulatory lineage or subset. We also show that many NKT17 cells are CD4 + and are biased toward Vβ8.3 TCR gene usage. Lastly, we demonstrate that the toll-like receptor (TLR) ligand lipopolysaccharide (LPS) can induce a NKT17 cell-biased response, even in the absence of exogenous antigen, and that combining LPS with α-GalCer resulted in enhanced IL-17A-production, and reduced levels of the immunosuppressive cytokine IL-10. This study provides a novel means to examine the context-dependent reactivity of the functionally heterogeneous NKT cell population and provides important new insight into the functional biology of these subsets. © 2018 Australasian Society for Immunology Inc.

  4. Determination of scattering coefficient considering wavelength and absorption dependence of anisotropy factor measured by polarized beam for biological tissues

    Science.gov (United States)

    Fukutomi, D.; Ishii, K.; Awazu, K.

    2015-12-01

    Anisotropy factor g, one of the optical properties of biological tissues, is the most important parameter to accurately determine scattering coefficient μs in the inverse Monte Carlo (iMC) simulation. It has been reported that g has wavelength and absorption dependence, however, there are few attempts in order to calculate μs of biological tissue considering the wavelength and absorption dependence of g. In this study, the scattering angular distributions of biological tissue phantoms were measured in order to determine g by using goniometric measurements with three polarization conditions at strongly and weakly absorbing wavelengths of hemoglobin. Then, optical properties, especially, μs were measured by integrating sphere measurements and iMC simulation in order to confirm the influence of measured g on optical properties in comparison of with general value of g (0.9) for soft biological tissue. Consequently, it was found that μs was overestimated at strongly absorbing wavelength, however, μs was underestimated at weakly absorbing wavelength if the g was not considered its wavelength and absorption dependence.

  5. 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.

  6. Significance tests for functional data with complex dependence structure

    KAUST Repository

    Staicu, Ana-Maria; Lahiri, Soumen N.; Carroll, Raymond J.

    2015-01-01

    We propose an L (2)-norm based global testing procedure for the null hypothesis that multiple group mean functions are equal, for functional data with complex dependence structure. Specifically, we consider the setting of functional data with a

  7. Time-dependent density functional theory for multi-component systems

    International Nuclear Information System (INIS)

    Tiecheng Li; Peiqing Tong

    1985-10-01

    The Runge-Gross version of Hohenberg-Kohn-Sham's density functional theory is generalized to multi-component systems, both for arbitrary time-dependent pure states and for arbitrary time-dependent ensembles. (author)

  8. Natural excitation orbitals from linear response theories : Time-dependent density functional theory, time-dependent Hartree-Fock, and time-dependent natural orbital functional theory

    NARCIS (Netherlands)

    Van Meer, R.; Gritsenko, O. V.; Baerends, E. J.

    2017-01-01

    Straightforward interpretation of excitations is possible if they can be described as simple single orbital-to-orbital (or double, etc.) transitions. In linear response time-dependent density functional theory (LR-TDDFT), the (ground state) Kohn-Sham orbitals prove to be such an orbital basis. In

  9. Which visual functions depend on intermediate visual regions? Insights from a case of developmental visual form agnosia.

    Science.gov (United States)

    Gilaie-Dotan, Sharon

    2016-03-01

    A key question in visual neuroscience is the causal link between specific brain areas and perceptual functions; which regions are necessary for which visual functions? While the contribution of primary visual cortex and high-level visual regions to visual perception has been extensively investigated, the contribution of intermediate visual areas (e.g. V2/V3) to visual processes remains unclear. Here I review more than 20 visual functions (early, mid, and high-level) of LG, a developmental visual agnosic and prosopagnosic young adult, whose intermediate visual regions function in a significantly abnormal fashion as revealed through extensive fMRI and ERP investigations. While expectedly, some of LG's visual functions are significantly impaired, some of his visual functions are surprisingly normal (e.g. stereopsis, color, reading, biological motion). During the period of eight-year testing described here, LG trained on a perceptual learning paradigm that was successful in improving some but not all of his visual functions. Following LG's visual performance and taking into account additional findings in the field, I propose a framework for how different visual areas contribute to different visual functions, with an emphasis on intermediate visual regions. Thus, although rewiring and plasticity in the brain can occur during development to overcome and compensate for hindering developmental factors, LG's case seems to indicate that some visual functions are much less dependent on strict hierarchical flow than others, and can develop normally in spite of abnormal mid-level visual areas, thereby probably less dependent on intermediate visual regions. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. Maitra-Burke example of initial-state dependence in time-dependent density-functional theory

    International Nuclear Information System (INIS)

    Holas, A.; Balawender, R.

    2002-01-01

    In a recent paper, Maitra and Burke [Phys. Rev. A 63, 042501 (2001); 64, 039901(E) (2001)] have given an interesting and instructive example that illustrates a specific feature of the time-dependent density-functional theory--the dependence of the reconstructed time-dependent potential not only on the electron density, but also on the initial state of the system. However, a concise form of its presentation by these authors is insufficient to reveal all its peculiarities. Our paper represents a very detailed study of this valuable example, intended to facilitate a better understanding and appreciation

  11. The dimer interface of the membrane type 1 matrix metalloproteinase hemopexin domain: crystal structure and biological functions.

    Science.gov (United States)

    Tochowicz, Anna; Goettig, Peter; Evans, Richard; Visse, Robert; Shitomi, Yasuyuki; Palmisano, Ralf; Ito, Noriko; Richter, Klaus; Maskos, Klaus; Franke, Daniel; Svergun, Dmitri; Nagase, Hideaki; Bode, Wolfram; Itoh, Yoshifumi

    2011-03-04

    Homodimerization is an essential step for membrane type 1 matrix metalloproteinase (MT1-MMP) to activate proMMP-2 and to degrade collagen on the cell surface. To uncover the molecular basis of the hemopexin (Hpx) domain-driven dimerization of MT1-MMP, a crystal structure of the Hpx domain was solved at 1.7 Å resolution. Two interactions were identified as potential biological dimer interfaces in the crystal structure, and mutagenesis studies revealed that the biological dimer possesses a symmetrical interaction where blades II and III of molecule A interact with blades III and II of molecule B. The mutations of amino acids involved in the interaction weakened the dimer interaction of Hpx domains in solution, and incorporation of these mutations into the full-length enzyme significantly inhibited dimer-dependent functions on the cell surface, including proMMP-2 activation, collagen degradation, and invasion into the three-dimensional collagen matrix, whereas dimer-independent functions, including gelatin film degradation and two-dimensional cell migration, were not affected. These results shed light on the structural basis of MT1-MMP dimerization that is crucial to promote cellular invasion.

  12. Elucidation of time-dependent systems biology cell response patterns with time course network enrichment

    DEFF Research Database (Denmark)

    Wiwie, Christian; Rauch, Alexander; Haakonsson, Anders

    2018-01-01

    , no methods exist to integrate time series data with networks, thus preventing the identification of time-dependent systems biology responses. We close this gap with Time Course Network Enrichment (TiCoNE). It combines a new kind of human-augmented clustering with a novel approach to network enrichment...

  13. 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.

  14. Discovering context-aware conditional functional dependencies

    Institute of Scientific and Technical Information of China (English)

    Yuefeng DU; Derong SHEN; Tiezheng NIE; Yue KOU; Ge YU

    2017-01-01

    Conditional functional dependencies(CFDs) are important techniques for data consistency.However,CFDs are limited to 1) provide the reasonable values for consistency repairing and 2) detect potential errors.This paper presents context-aware conditional functional dependencies(CCFDs) which contribute to provide reasonable values and detect potential errors.Especially,we focus on automatically discovering minimal CCFDs.In this paper,we present context relativity to measure the relationship of CFDs.The overlap of the related CFDs can provide reasonable values which result in more accuracy consistency repairing,and some related CFDs are combined into CCFDs.Moreover,we prove that discovering minimal CCFDs is NP-complete and we design the precise method and the heuristic method.We also present the dominating value to facilitate the process in both the precise method and the heuristic method.Additionally,the context relativity of the CFDs affects the cleaning results.We will give an approximate threshold of context relativity according to data distribution for suggestion.The repairing results are approved more accuracy,even evidenced by our empirical evaluation.

  15. Time-domain representation of frequency-dependent foundation impedance functions

    Science.gov (United States)

    Safak, E.

    2006-01-01

    Foundation impedance functions provide a simple means to account for soil-structure interaction (SSI) when studying seismic response of structures. Impedance functions represent the dynamic stiffness of the soil media surrounding the foundation. The fact that impedance functions are frequency dependent makes it difficult to incorporate SSI in standard time-history analysis software. This paper introduces a simple method to convert frequency-dependent impedance functions into time-domain filters. The method is based on the least-squares approximation of impedance functions by ratios of two complex polynomials. Such ratios are equivalent, in the time-domain, to discrete-time recursive filters, which are simple finite-difference equations giving the relationship between foundation forces and displacements. These filters can easily be incorporated into standard time-history analysis programs. Three examples are presented to show the applications of the method.

  16. 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...

  17. 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.

  18. 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.

  19. 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.

  20. Dependence of a class of non-integer power functions

    Directory of Open Access Journals (Sweden)

    Ming Li

    2016-10-01

    Full Text Available This short article exhibits that there exists critical point of the power for the generalized function t-a for a > 0. The present results show that it is long-range dependent if 0  1. My motivation of studying that dependence issue comes from the power-law type functions in fractal time series. The present results may yet be useful to investigate fractal behavior of fractal time series from a new point of view.

  1. 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.

  2. The World Federation of Societies of Biological Psychiatry (WFSBP) Guidelines for the Biological Treatment of Substance Use and Related Disorders. Part 2: Opioid dependence

    NARCIS (Netherlands)

    Soyka, Michael; Kranzler, Henry R.; van den Brink, Wim; Krystal, John; Möller, Hans-Jürgen; Kasper, Siegfried

    2011-01-01

    Objectives. To develop evidence-based practice guidelines for the pharmacological treatment of opioid abuse and dependence. Methods. An international task force of the World Federation of Societies of Biological Psychiatry (WFSBP) developed these practice guidelines after a systematic review of the

  3. 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.

  4. 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.

  5. Exact Time-Dependent Wave Functions of a Confined Time-Dependent Harmonic Oscillator with Two Moving Boundaries

    International Nuclear Information System (INIS)

    Lo, C.F.

    2009-01-01

    By applying the standard analytical techniques of solving partial differential equations, we have obtained the exact solution in terms of the Fourier sine series to the time-dependent Schroedinger equation describing a quantum one-dimensional harmonic oscillator of time-dependent frequency confined in an infinite square well with the two walls moving along some parametric trajectories. Based upon the orthonormal basis of quasi-stationary wave functions, the exact propagator of the system has also been analytically derived. Special cases like (i) a confined free particle, (ii) a confined time-independent harmonic oscillator, and (iii) an aging oscillator are examined, and the corresponding time-dependent wave functions are explicitly determined. Besides, the approach has been extended to solve the case of a confined generalized time-dependent harmonic oscillator for some parametric moving boundaries as well. (general)

  6. 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.

  7. Existence of time-dependent density-functional theory for open electronic systems: time-dependent holographic electron density theorem.

    Science.gov (United States)

    Zheng, Xiao; Yam, ChiYung; Wang, Fan; Chen, GuanHua

    2011-08-28

    We present the time-dependent holographic electron density theorem (TD-HEDT), which lays the foundation of time-dependent density-functional theory (TDDFT) for open electronic systems. For any finite electronic system, the TD-HEDT formally establishes a one-to-one correspondence between the electron density inside any finite subsystem and the time-dependent external potential. As a result, any electronic property of an open system in principle can be determined uniquely by the electron density function inside the open region. Implications of the TD-HEDT on the practicality of TDDFT are also discussed.

  8. 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

  9. Review of the functional morphology, biology and perturbation impacts on the boreal, habitat-forming horse mussel Modiolus modiolus (Bivalvia: Mytilidae: Modiolinae)

    DEFF Research Database (Denmark)

    Dinesen, Grete E.; Morton, Brian

    2014-01-01

    The boreal bivalve Modiolus modiolus is common subtidally where it aggregates to form extensive, long-lived, biogenic habitats with a diverse associated flora and, especially, fauna. Despite this ecological importance, M. modiolus has not been described in terms of its functional morphology and o...... several M. modiolus habitats with deleterious impacts on ecosystem functioning. Post-impact recovery times are slow and dependent on both local and mega-population distributions...... and overall biology. Modiolus modiolus is a typical epibenthic, suspension-feeding mytilid, albeit with anatomical modifications adapting it to a partially buried, gregarious lifestyle in a stable environment experiencing medium–high energy levels. The juvenile shell is covered partly in byssal setae secreted...... and locality. With age (≥ 20–45 years), shells often become deformed, particularly posteriorly and around the byssal gape, thereby increasing reproductive capacity (gonadal volume) without increasing somatic growth. Information on the biology, reproductive strategy and life history traits of M. modiolus...

  10. 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.

  11. 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

  12. 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

  13. [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.

  14. Linezolid-Dependent Function and Structure Adaptation of Ribosomes in a Staphylococcus epidermidis Strain Exhibiting Linezolid Dependence

    Science.gov (United States)

    Kokkori, Sofia; Apostolidi, Maria; Tsakris, Athanassios; Pournaras, Spyros

    2014-01-01

    Linezolid-dependent growth was recently reported in Staphylococcus epidermidis clinical strains carrying mutations associated with linezolid resistance. To investigate this unexpected behavior at the molecular level, we isolated active ribosomes from one of the linezolid-dependent strains and we compared them with ribosomes isolated from a wild-type strain. Both strains were grown in the absence and presence of linezolid. Detailed biochemical and structural analyses revealed essential differences in the function and structure of isolated ribosomes which were assembled in the presence of linezolid. The catalytic activity of peptidyltransferase was found to be significantly higher in the ribosomes derived from the linezolid-dependent strain. Interestingly, the same ribosomes exhibited an abnormal ribosomal subunit dissociation profile on a sucrose gradient in the absence of linezolid, but the profile was restored after treatment of the ribosomes with an excess of the antibiotic. Our study suggests that linezolid most likely modified the ribosomal assembly procedure, leading to a new functional ribosomal population active only in the presence of linezolid. Therefore, the higher growth rate of the partially linezolid-dependent strains could be attributed to the functional and structural adaptations of ribosomes to linezolid. PMID:24890589

  15. Classical Solutions of Path-Dependent PDEs and Functional Forward-Backward Stochastic Systems

    Directory of Open Access Journals (Sweden)

    Shaolin Ji

    2013-01-01

    Full Text Available In this paper we study the relationship between functional forward-backward stochastic systems and path-dependent PDEs. In the framework of functional Itô calculus, we introduce a path-dependent PDE and prove that its solution is uniquely determined by a functional forward-backward stochastic system.

  16. Naltrexone ameliorates functional network abnormalities in alcohol‐dependent individuals

    Science.gov (United States)

    Baek, Kwangyeol; Tait, Roger; Elliott, Rebecca; Ersche, Karen D.; Flechais, Remy; McGonigle, John; Murphy, Anna; Nestor, Liam J.; Orban, Csaba; Passetti, Filippo; Paterson, Louise M.; Rabiner, Ilan; Reed, Laurence; Smith, Dana; Suckling, John; Taylor, Eleanor M.; Bullmore, Edward T.; Lingford‐Hughes, Anne R.; Deakin, Bill; Nutt, David J.; Sahakian, Barbara J.; Robbins, Trevor W.; Voon, Valerie

    2017-01-01

    Abstract Naltrexone, an opioid receptor antagonist, is commonly used as a relapse prevention medication in alcohol and opiate addiction, but its efficacy and the mechanisms underpinning its clinical usefulness are not well characterized. In the current study, we examined the effects of 50‐mg naltrexone compared with placebo on neural network changes associated with substance dependence in 21 alcohol and 36 poly‐drug‐dependent individuals compared with 36 healthy volunteers. Graph theoretic and network‐based statistical analysis of resting‐state functional magnetic resonance imaging (MRI) data revealed that alcohol‐dependent subjects had reduced functional connectivity of a dispersed network compared with both poly‐drug‐dependent and healthy subjects. Higher local efficiency was observed in both patient groups, indicating clustered and segregated network topology and information processing. Naltrexone normalized heightened local efficiency of the neural network in alcohol‐dependent individuals, to the same levels as healthy volunteers. Naltrexone failed to have an effect on the local efficiency in abstinent poly‐substance‐dependent individuals. Across groups, local efficiency was associated with substance, but no alcohol exposure implicating local efficiency as a potential premorbid risk factor in alcohol use disorders that can be ameliorated by naltrexone. These findings suggest one possible mechanism for the clinical effects of naltrexone, namely, the amelioration of disrupted network topology. PMID:28247526

  17. Association between insulin and executive functioning in alcohol dependence: a pilot study.

    Science.gov (United States)

    Han, Changwoo; Bae, Hwallip; Won, Sung-Doo; Lim, Jaeyoung; Kim, Dai-Jin

    2015-01-01

    Alcohol dependence is a disorder ascribable to multiple factors and leads to cognitive impairment. Given that insulin dysregulation can cause cognitive impairment, patients with alcohol dependence are likely to develop insulin dysregulation such as that in diabetes. The purposes of this study are to identify an association between cognitive functioning and insulin and to investigate insulin as the biomarker of cognitive functioning in alcohol-dependent patients. Serum insulin levels were measured and cognitive functions were assessed in 45 patients with chronic alcoholism. The Korean version of the Consortium to Establish a Registry for Alzheimer's Disease (CERAD-K), a battery of cognitive function tests, was used to assess cognitive functioning. Serum insulin levels were not significantly correlated with most CERAD-K scores, but there was a significant negative correlation with scores on the Trail Making Test B, which is designed to measure executive functioning. Lower serum insulin levels were associated with slower executive functioning responses on the Trail Making Test B, suggesting that executive functioning may be in proportion to serum insulin levels. Thus, in patients with alcohol dependence, insulin level is associated with cognitive functioning. In addition, the present findings suggest that insulin level is a potential biomarker for determining cognitive functioning.

  18. 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.

  19. Time-dependent friction and solvation time correlation function

    International Nuclear Information System (INIS)

    Samanta, Alok; Ali, Sk Musharaf; Ghosh, Swapan K

    2005-01-01

    We have derived a new relation between the time-dependent friction and solvation time correlation function (STCF) for non-polar fluids. The friction values calculated using this relation and simulation results on STCF for a Lennard-Jones fluid are shown to have excellent agreement with the same obtained through mode-coupling theory. Also derived is a relation between the time-dependent dielectric friction and STCF for polar fluids. Routes are thus provided to obtain the time-dependent friction (non-polar as well as dielectric) from an experimentally measured quantity like STCF, even if the interparticle interaction potential is not known

  20. Precision measurement of the neutron spin dependent structure functions

    International Nuclear Information System (INIS)

    Kolomensky, Y.G.

    1997-02-01

    In experiment E154 at the Stanford Linear Accelerator Center the spin dependent structure function g 1 n (x, Q 2 ) of the neutron was measured by scattering longitudinally polarized 48.3 GeV electrons off a longitudinally polarized 3 He target. The high beam energy allowed the author to extend the kinematic coverage compared to the previous SLAC experiments to 0.014 ≤ x ≤ 0.7 with an average Q 2 of 5 GeV 2 . The author reports the integral of the spin dependent structure function in the measured range to be ∫ 0.014 0.7 dx g 1 n (x, 5 GeV 2 ) = -0.036 ± 0.004(stat.) ± 0.005(syst.). The author observes relatively large values of g 1 n at low x that call into question the reliability of data extrapolation to x → 0. Such divergent behavior disagrees with predictions of the conventional Regge theory, but is qualitatively explained by perturbative QCD. The author performs a Next-to-Leading Order perturbative QCD analysis of the world data on the nucleon spin dependent structure functions g 1 p and g 1 n paying careful attention to the experimental and theoretical uncertainties. Using the parameterizations of the helicity-dependent parton distributions obtained in the analysis, the author evolves the data to Q 2 = 5 GeV 2 , determines the first moments of the polarized structure functions of the proton and neutron, and finds agreement with the Bjorken sum rule

  1. 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.

  2. Measuring spin-dependent structure functions at CEBAF

    International Nuclear Information System (INIS)

    Schaefer, A.

    1994-01-01

    The author analyses whether CEBAF with a 10 GeV beam could contribute significantly to the understanding of spin-dependent deep-inelastic scattering as well as semi-inclusive reactions. The main advantage of CEBAF is the much better attainable statistics, its great disadvantage its comparably low energy, which limits the accessible x-range to about 0.15 to 0.7. Within these constraints CEBAF could provide (1) high precision data which would be very valuable to understand the Q 2 dependence of the spin-dependent structure functions g 1 (x) and G 2 (x) and (2) the by far most precise determination of the third moments of g 1 (x) and g 2 (x) the latter of which the author argues to be related to a fundamental property of the nucleon

  3. Wave Functions for Time-Dependent Dirac Equation under GUP

    Science.gov (United States)

    Zhang, Meng-Yao; Long, Chao-Yun; Long, Zheng-Wen

    2018-04-01

    In this work, the time-dependent Dirac equation is investigated under generalized uncertainty principle (GUP) framework. It is possible to construct the exact solutions of Dirac equation when the time-dependent potentials satisfied the proper conditions. In (1+1) dimensions, the analytical wave functions of the Dirac equation under GUP have been obtained for the two kinds time-dependent potentials. Supported by the National Natural Science Foundation of China under Grant No. 11565009

  4. Nontarget effects of chemical pesticides and biological pesticide on rhizospheric microbial community structure and function in Vigna radiata.

    Science.gov (United States)

    Singh, Sunil; Gupta, Rashi; Kumari, Madhu; Sharma, Shilpi

    2015-08-01

    Intensive agriculture has resulted in an indiscriminate use of pesticides, which demands in-depth analysis of their impact on indigenous rhizospheric microbial community structure and function. Hence, the objective of the present work was to study the impact of two chemical pesticides (chlorpyrifos and cypermethrin) and one biological pesticide (azadirachtin) at two dosages on the microbial community structure using cultivation-dependent approach and on rhizospheric bacterial communities involved in nitrogen cycle in Vigna radiata rhizosphere through cultivation-independent technique of real-time PCR. Cultivation-dependent study highlighted the adverse effects of both chemical pesticide and biopesticide on rhizospheric bacterial and fungal communities at different plant growth stages. Also, an adverse effect on number of genes and transcripts of nifH (nitrogen fixation); amoA (nitrification); and narG, nirK, and nirS (denitrification) was observed. The results from the present study highlighted two points, firstly that nontarget effects of pesticides are significantly detrimental to soil microflora, and despite being of biological origin, azadirachtin exerted negative impact on rhizospheric microbial community of V. radiata behaving similar to chemical pesticides. Hence, such nontarget effects of chemical pesticide and biopesticide in plants' rhizosphere, which bring out the larger picture in terms of their ecotoxicological effect, demand a proper risk assessment before application of pesticides as agricultural amendments.

  5. 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.

  6. 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.

  7. 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.

  8. Ecological aspects od electromagnetic irradiation effects of biological objects

    International Nuclear Information System (INIS)

    Volobuev, A.P.; Donnik, I.M.; Alekseenko, N.N.

    2005-01-01

    General description of electromagnetic field effects on biological objects depending on its frequency properties is stated in the paper. Basic principles of low frequency field effect (10 -1 -0 2 Hz) are detailed. General and specific regularities of biological objects response to a low frequency field on subcell, cell, and system levels were considered taking into account their functional state. (author)

  9. Altered Brain Functional Connectivity in Betel Quid-Dependent Chewers.

    Science.gov (United States)

    Huang, Xiaojun; Pu, Weidan; Liu, Haihong; Li, Xinmin; Greenshaw, Andrew J; Dursun, Serdar M; Xue, Zhimin; Liu, Zhening

    2017-01-01

    Betel quid (BQ) is a common psychoactive substance worldwide with particularly high usage in many Asian countries. This study aimed to explore the effect of BQ use on functional connectivity by comparing global functional brain networks and their subset between BQ chewers and healthy controls (HCs). Resting-state functional magnetic resonance imaging (fMRI) was obtained from 24 betel quid-dependent (BQD) male chewers and 27 healthy male individuals on a 3.0T scanner. We used independent component analysis (ICA) to determine components that represent the brain's functional networks and their spatial aspects of functional connectivity. Two sample t -tests were used to identify the functional connectivity differences in each network between these two groups. Seventeen networks were identified by ICA. Nine of them showed connectivity differences between BQD and HCs (two sample t -tests, p  betel quid dependence scale scores were positively related to the increased functional connectivity in the orbitofrontal ( r  = 0.39, p  = 0.03) while negatively related to the decreased functional connectivity in medial frontal/anterior cingulate networks ( r  = -0.35, p  = 0.02). Our findings provide further evidence that BQ chewing may lead to brain functional connectivity changes, which may play a key role in the psychological and physiological effects of BQ.

  10. 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

  11. [Principles of management in biological infections].

    Science.gov (United States)

    Płusa, Tadeusz

    2012-11-01

    The effectiveness of the management in respiratory infection is depending on the nature of the biological pathogen and the immune status of the patient. For this reason, providing assistance to victims the organ function support, similarly as defining the pathogen and targeted antibiotic therapy should be applied. Available diagnostic tests provide rapid ability to identify the pathogen and antibiotics are able to control infection. Lack of efficacy of treatment may indicate the diversity of the pathogen than previously known and raises suspicion of biological warfare pathogen.

  12. Executive functions and risky decision-making in patients with opiate dependence.

    Science.gov (United States)

    Brand, Matthias; Roth-Bauer, Martina; Driessen, Martin; Markowitsch, Hans J

    2008-09-01

    Recent evidence suggests that individuals with opiate dependence may have cognitive dysfunctions particularly within the spectrum of executive functioning and emotional processing. Such dysfunctions can also compromise daily decisions associated with risk-taking behaviors. However, it remains unclear whether patients addicted to opiates show impaired decision-making on gambling tasks that specify explicit rules for rewards and punishments and provide information about probabilities associated with different long-term outcomes. In this study, we examined 18 individuals with opiate dependence and 18 healthy comparison subjects, matched for age, gender, and education with the Game of Dice Task (GDT). The GDT is a gambling task with explicit rules for gains and losses and fix winning probabilities. In addition, all subjects completed a neuropsychological test battery that primarily focused on executive functions and a personality questionnaire. On the GDT, patients chose the risky alternatives more frequently than the control group. Patients' GDT performance was related to executive functioning but not to other neuropsychological constructs, personality or dependence specific variables with one exception that is the number of days of abstinence. Thus, patients with opiate dependence demonstrate abnormalities in decision-making that might be neuropsychologically associated with dysfunctional behavior in patients' daily lives. Decision-making and other neuropsychological functioning should be considered in the treatment of opiate dependence.

  13. Measuring spin-dependent structure functions at CEBAF

    Energy Technology Data Exchange (ETDEWEB)

    Schaefer, A. [Universitaet Frankfurt (Germany)

    1994-04-01

    The author analyses whether CEBAF with a 10 GeV beam could contribute significantly to the understanding of spin-dependent deep-inelastic scattering as well as semi-inclusive reactions. The main advantage of CEBAF is the much better attainable statistics, its great disadvantage its comparably low energy, which limits the accessible x-range to about 0.15 to 0.7. Within these constraints CEBAF could provide (1) high precision data which would be very valuable to understand the Q{sup 2} dependence of the spin-dependent structure functions g{sub 1}(x) and G{sub 2}(x) and (2) the by far most precise determination of the third moments of g{sub 1}(x) and g{sub 2}(x) the latter of which the author argues to be related to a fundamental property of the nucleon.

  14. 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

  15. 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.

  16. Structural and functional characteristics of cGMP-dependent methionine oxidation in Arabidopsis thaliana proteins

    KAUST Repository

    Marondedze, Claudius

    2013-01-05

    Background: Increasing structural and biochemical evidence suggests that post-translational methionine oxidation of proteins is not just a result of cellular damage but may provide the cell with information on the cellular oxidative status. In addition, oxidation of methionine residues in key regulatory proteins, such as calmodulin, does influence cellular homeostasis. Previous findings also indicate that oxidation of methionine residues in signaling molecules may have a role in stress responses since these specific structural modifications can in turn change biological activities of proteins. Findings. Here we use tandem mass spectrometry-based proteomics to show that treatment of Arabidopsis thaliana cells with a non-oxidative signaling molecule, the cell-permeant second messenger analogue, 8-bromo-3,5-cyclic guanosine monophosphate (8-Br-cGMP), results in a time-dependent increase in the content of oxidised methionine residues. Interestingly, the group of proteins affected by cGMP-dependent methionine oxidation is functionally enriched for stress response proteins. Furthermore, we also noted distinct signatures in the frequency of amino acids flanking oxidised and un-oxidised methionine residues on both the C- and N-terminus. Conclusions: Given both a structural and functional bias in methionine oxidation events in response to a signaling molecule, we propose that these are indicative of a specific role of such post-translational modifications in the direct or indirect regulation of cellular responses. The mechanisms that determine the specificity of the modifications remain to be elucidated. 2013 Marondedze et al.; licensee BioMed Central Ltd.

  17. Nitrate-dependent shoot sodium accumulation and osmotic functions of sodium in Arabidopsis under saline conditions.

    Science.gov (United States)

    Álvarez-Aragón, Rocío; Rodríguez-Navarro, Alonso

    2017-07-01

    Improving crop plants to be productive in saline soils or under irrigation with saline water would be an important technological advance in overcoming the food and freshwater crises that threaten the world population. However, even if the transformation of a glycophyte into a plant that thrives under seawater irrigation was biologically feasible, current knowledge about Na + effects would be insufficient to support this technical advance. Intriguingly, crucial details about Na + uptake and its function in the plant have not yet been well established. We here propose that under saline conditions two nitrate-dependent transport systems in series that take up and load Na + into the xylem constitute the major pathway for the accumulation of Na + in Arabidopsis shoots; this pathway can also function with chloride at high concentrations. In nrt1.1 nitrate transport mutants, plant Na + accumulation was partially defective, which suggests that NRT1.1 either partially mediates or modulates the nitrate-dependent Na + transport. Arabidopsis plants exposed to an osmotic potential of -1.0 MPa (400 mOsm) for 24 h showed high water loss and wilting in sorbitol or Na/MES, where Na + could not be accumulated. In contrast, in NaCl the plants that accumulated Na + lost a low amount of water, and only suffered transitory wilting. We discuss that in Arabidopsis plants exposed to high NaCl concentrations, root Na + uptake and tissue accumulation fulfil the primary function of osmotic adjustment, even if these processes lead to long-term toxicity. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

  18. Orbital-dependent exchange-correlation functionals in density-functional theory realized by the FLAPW method

    Energy Technology Data Exchange (ETDEWEB)

    Betzinger, Markus

    2011-12-14

    In this thesis, we extended the applicability of the full-potential linearized augmented-plane-wave (FLAPW) method, one of the most precise, versatile and generally applicable electronic structure methods for solids working within the framework of density-functional theory (DFT), to orbital-dependent functionals for the exchange-correlation (xc) energy. Two different schemes that deal with orbital-dependent functionals, the Kohn-Sham (KS) and the generalized Kohn-Sham (gKS) formalism, have been realized. Hybrid functionals, combining some amount of the orbital-dependent exact exchange energy with local or semi-local functionals of the density, are implemented within the gKS scheme. We work in particular with the PBE0 hybrid of Perdew, Burke, and Ernzerhof. Our implementation relies on a representation of the non-local exact exchange potential - its calculation constitutes the most time consuming step in a practical calculation - by an auxiliary mixed product basis (MPB). In this way, the matrix elements of the Hamiltonian corresponding to the non-local potential become a Brillouin-zone (BZ) sum over vector-matrix-vector products. Several techniques are developed and explored to further accelerate our numerical scheme. We show PBE0 results for a variety of semiconductors and insulators. In comparison with experiment, the PBE0 functional leads to improved band gaps and an improved description of localized states. Even for the ferromagnetic semiconductor EuO with localized 4f electrons, the electronic and magnetic properties are correctly described by the PBE0 functional. Subsequently, we discuss the construction of the local, multiplicative exact exchange (EXX) potential from the non-local, orbital-dependent exact exchange energy. For this purpose we employ the optimized effective potential (OEP) method. Central ingredients of the OEP equation are the KS wave-function response and the single-particle density response function. We show that a balance between the LAPW

  19. Orbital-dependent exchange-correlation functionals in density-functional theory realized by the FLAPW method

    International Nuclear Information System (INIS)

    Betzinger, Markus

    2011-01-01

    In this thesis, we extended the applicability of the full-potential linearized augmented-plane-wave (FLAPW) method, one of the most precise, versatile and generally applicable electronic structure methods for solids working within the framework of density-functional theory (DFT), to orbital-dependent functionals for the exchange-correlation (xc) energy. Two different schemes that deal with orbital-dependent functionals, the Kohn-Sham (KS) and the generalized Kohn-Sham (gKS) formalism, have been realized. Hybrid functionals, combining some amount of the orbital-dependent exact exchange energy with local or semi-local functionals of the density, are implemented within the gKS scheme. We work in particular with the PBE0 hybrid of Perdew, Burke, and Ernzerhof. Our implementation relies on a representation of the non-local exact exchange potential - its calculation constitutes the most time consuming step in a practical calculation - by an auxiliary mixed product basis (MPB). In this way, the matrix elements of the Hamiltonian corresponding to the non-local potential become a Brillouin-zone (BZ) sum over vector-matrix-vector products. Several techniques are developed and explored to further accelerate our numerical scheme. We show PBE0 results for a variety of semiconductors and insulators. In comparison with experiment, the PBE0 functional leads to improved band gaps and an improved description of localized states. Even for the ferromagnetic semiconductor EuO with localized 4f electrons, the electronic and magnetic properties are correctly described by the PBE0 functional. Subsequently, we discuss the construction of the local, multiplicative exact exchange (EXX) potential from the non-local, orbital-dependent exact exchange energy. For this purpose we employ the optimized effective potential (OEP) method. Central ingredients of the OEP equation are the KS wave-function response and the single-particle density response function. We show that a balance between the LAPW

  20. 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

  1. Lipid Cell Biology: A Focus on Lipids in Cell Division.

    Science.gov (United States)

    Storck, Elisabeth M; Özbalci, Cagakan; Eggert, Ulrike S

    2018-06-20

    Cells depend on hugely diverse lipidomes for many functions. The actions and structural integrity of the plasma membrane and most organelles also critically depend on membranes and their lipid components. Despite the biological importance of lipids, our understanding of lipid engagement, especially the roles of lipid hydrophobic alkyl side chains, in key cellular processes is still developing. Emerging research has begun to dissect the importance of lipids in intricate events such as cell division. This review discusses how these structurally diverse biomolecules are spatially and temporally regulated during cell division, with a focus on cytokinesis. We analyze how lipids facilitate changes in cellular morphology during division and how they participate in key signaling events. We identify which cytokinesis proteins are associated with membranes, suggesting lipid interactions. More broadly, we highlight key unaddressed questions in lipid cell biology and techniques, including mass spectrometry, advanced imaging, and chemical biology, which will help us gain insights into the functional roles of lipids.

  2. Towards biologically conformal radiation therapy (BCRT): Selective IMRT dose escalation under the guidance of spatial biology distribution

    International Nuclear Information System (INIS)

    Yang Yong; Xing Lei

    2005-01-01

    It is well known that the spatial biology distribution (e.g., clonogen density, radiosensitivity, tumor proliferation rate, functional importance) in most tumors and sensitive structures is heterogeneous. Recent progress in biological imaging is making the mapping of this distribution increasingly possible. The purpose of this work is to establish a theoretical framework to quantitatively incorporate the spatial biology data into intensity modulated radiation therapy (IMRT) inverse planning. In order to implement this, we first derive a general formula for determining the desired dose to each tumor voxel for a known biology distribution of the tumor based on a linear-quadratic model. The desired target dose distribution is then used as the prescription for inverse planning. An objective function with the voxel-dependent prescription is constructed with incorporation of the nonuniform dose prescription. The functional unit density distribution in a sensitive structure is also considered phenomenologically when constructing the objective function. Two cases with different hypothetical biology distributions are used to illustrate the new inverse planning formalism. For comparison, treatments with a few uniform dose prescriptions and a simultaneous integrated boost are also planned. The biological indices, tumor control probability (TCP) and normal tissue complication probability (NTCP), are calculated for both types of plans and the superiority of the proposed technique over the conventional dose escalation scheme is demonstrated. Our calculations revealed that it is technically feasible to produce deliberately nonuniform dose distributions with consideration of biological information. Compared with the conventional dose escalation schemes, the new technique is capable of generating biologically conformal IMRT plans that significantly improve the TCP while reducing or keeping the NTCPs at their current levels. Biologically conformal radiation therapy (BCRT

  3. 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

  4. 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

  5. FAK dimerization controls its kinase-dependent functions at focal adhesions

    KAUST Repository

    Brami-Cherrier, Karen; Gervasi, Nicolas; Arsenieva, Diana A.; Walkiewicz, Katarzyna; Boutterin, Marie Claude; Ortega, Á lvaro Darí o; Leonard, Paul G.; Seantier, Bastien; Gasmi, Laï la; Bouceba, Tahar; Kadaré , Gress; Girault -, Jean Antoine; Arold, Stefan T.

    2014-01-01

    Focal adhesion kinase (FAK) controls adhesion-dependent cell motility, survival, and proliferation. FAK has kinase-dependent and kinase-independent functions, both of which play major roles in embryogenesis and tumor invasiveness. The precise mechanisms of FAK activation are not known. Using x-ray crystallography, small angle x-ray scattering, and biochemical and functional analyses, we show that the key step for activation of FAK's kinase-dependent functions-autophosphorylation of tyrosine-397-requires site-specific dimerization of FAK. The dimers form via the association of the N-terminal FERM domain of FAK and are stabilized by an interaction between FERM and the C-terminal FAT domain. FAT binds to a basic motif on FERM that regulates co-activation and nuclear localization. FAK dimerization requires local enrichment, which occurs specifically at focal adhesions. Paxillin plays a dual role, by recruiting FAK to focal adhesions and by reinforcing the FAT:FERM interaction. Our results provide a structural and mechanistic framework to explain how FAK combines multiple stimuli into a site-specific function. The dimer interfaces we describe are promising targets for blocking FAK activation. © 2014 The Authors.

  6. FAK dimerization controls its kinase-dependent functions at focal adhesions

    KAUST Repository

    Brami-Cherrier, Karen

    2014-01-30

    Focal adhesion kinase (FAK) controls adhesion-dependent cell motility, survival, and proliferation. FAK has kinase-dependent and kinase-independent functions, both of which play major roles in embryogenesis and tumor invasiveness. The precise mechanisms of FAK activation are not known. Using x-ray crystallography, small angle x-ray scattering, and biochemical and functional analyses, we show that the key step for activation of FAK\\'s kinase-dependent functions-autophosphorylation of tyrosine-397-requires site-specific dimerization of FAK. The dimers form via the association of the N-terminal FERM domain of FAK and are stabilized by an interaction between FERM and the C-terminal FAT domain. FAT binds to a basic motif on FERM that regulates co-activation and nuclear localization. FAK dimerization requires local enrichment, which occurs specifically at focal adhesions. Paxillin plays a dual role, by recruiting FAK to focal adhesions and by reinforcing the FAT:FERM interaction. Our results provide a structural and mechanistic framework to explain how FAK combines multiple stimuli into a site-specific function. The dimer interfaces we describe are promising targets for blocking FAK activation. © 2014 The Authors.

  7. Brain functional connectivity in stimulant drug dependence and obsessive-compulsive disorder.

    Science.gov (United States)

    Meunier, David; Ersche, Karen D; Craig, Kevin J; Fornito, Alex; Merlo-Pich, Emilio; Fineberg, Naomi A; Shabbir, Shaila S; Robbins, Trevor W; Bullmore, Edward T

    2012-01-16

    There are reasons for thinking that obsessive-compulsive disorder (OCD) and drug dependence, although conventionally distinct diagnostic categories, might share important cognitive and neurobiological substrates. We tested this hypothesis directly by comparing brain functional connectivity measures between patients with OCD, stimulant dependent individuals (SDIs; many of whom were non-dependent users of other recreational drugs) and healthy volunteers. We measured functional connectivity between each possible pair of 506 brain regional functional MRI time series representing low frequency (0.03-0.06 Hz) spontaneous brain hemodynamics in healthy volunteers (N=18), patients with OCD (N=18) and SDIs (N=18). We used permutation tests to identify i) brain regions where strength of connectivity was significantly different in both patient groups compared to healthy volunteers; and ii) brain regions and connections which had significantly different functional connectivity between patient groups. We found that functional connectivity of right inferior and superior orbitofrontal cortex (OFC) was abnormally reduced in both disorders. Whether diagnosed as OCD or SDI, patients with higher scores on measures of compulsive symptom severity showed greater reductions of right orbitofrontal connectivity. Functional connections specifically between OFC and dorsal medial pre-motor and cingulate cortex were attenuated in both patient groups. However, patients with OCD demonstrated more severe and extensive reductions of functional connectivity compared to SDIs. OCD and stimulant dependence are not identical at the level of brain functional systems but they have some important abnormalities in common compared with healthy volunteers. Orbitofrontal connectivity may serve as a human brain systems biomarker for compulsivity across diagnostic categories. Copyright © 2011 Elsevier Inc. All rights reserved.

  8. Nonperturbative renormalization-group approach preserving the momentum dependence of correlation functions

    Science.gov (United States)

    Rose, F.; Dupuis, N.

    2018-05-01

    We present an approximation scheme of the nonperturbative renormalization group that preserves the momentum dependence of correlation functions. This approximation scheme can be seen as a simple improvement of the local potential approximation (LPA) where the derivative terms in the effective action are promoted to arbitrary momentum-dependent functions. As in the LPA, the only field dependence comes from the effective potential, which allows us to solve the renormalization-group equations at a relatively modest numerical cost (as compared, e.g., to the Blaizot-Mendéz-Galain-Wschebor approximation scheme). As an application we consider the two-dimensional quantum O(N ) model at zero temperature. We discuss not only the two-point correlation function but also higher-order correlation functions such as the scalar susceptibility (which allows for an investigation of the "Higgs" amplitude mode) and the conductivity. In particular, we show how, using Padé approximants to perform the analytic continuation i ωn→ω +i 0+ of imaginary frequency correlation functions χ (i ωn) computed numerically from the renormalization-group equations, one can obtain spectral functions in the real-frequency domain.

  9. Range-separated time-dependent density-functional theory with a frequency-dependent second-order Bethe-Salpeter correlation kernel

    Energy Technology Data Exchange (ETDEWEB)

    Rebolini, Elisa, E-mail: elisa.rebolini@kjemi.uio.no; Toulouse, Julien, E-mail: julien.toulouse@upmc.fr [Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Univ Paris 06, CNRS, 4 place Jussieu, F-75005 Paris (France)

    2016-03-07

    We present a range-separated linear-response time-dependent density-functional theory (TDDFT) which combines a density-functional approximation for the short-range response kernel and a frequency-dependent second-order Bethe-Salpeter approximation for the long-range response kernel. This approach goes beyond the adiabatic approximation usually used in linear-response TDDFT and aims at improving the accuracy of calculations of electronic excitation energies of molecular systems. A detailed derivation of the frequency-dependent second-order Bethe-Salpeter correlation kernel is given using many-body Green-function theory. Preliminary tests of this range-separated TDDFT method are presented for the calculation of excitation energies of the He and Be atoms and small molecules (H{sub 2}, N{sub 2}, CO{sub 2}, H{sub 2}CO, and C{sub 2}H{sub 4}). The results suggest that the addition of the long-range second-order Bethe-Salpeter correlation kernel overall slightly improves the excitation energies.

  10. 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.

  11. A comparison of dependence function estimators in multivariate extremes

    KAUST Repository

    Vettori, Sabrina; Huser, Raphaë l; Genton, Marc G.

    2017-01-01

    Various nonparametric and parametric estimators of extremal dependence have been proposed in the literature. Nonparametric methods commonly suffer from the curse of dimensionality and have been mostly implemented in extreme-value studies up to three dimensions, whereas parametric models can tackle higher-dimensional settings. In this paper, we assess, through a vast and systematic simulation study, the performance of classical and recently proposed estimators in multivariate settings. In particular, we first investigate the performance of nonparametric methods and then compare them with classical parametric approaches under symmetric and asymmetric dependence structures within the commonly used logistic family. We also explore two different ways to make nonparametric estimators satisfy the necessary dependence function shape constraints, finding a general improvement in estimator performance either (i) by substituting the estimator with its greatest convex minorant, developing a computational tool to implement this method for dimensions $$D\\ge 2$$D≥2 or (ii) by projecting the estimator onto a subspace of dependence functions satisfying such constraints and taking advantage of Bernstein–Bézier polynomials. Implementing the convex minorant method leads to better estimator performance as the dimensionality increases.

  12. A comparison of dependence function estimators in multivariate extremes

    KAUST Repository

    Vettori, Sabrina

    2017-05-11

    Various nonparametric and parametric estimators of extremal dependence have been proposed in the literature. Nonparametric methods commonly suffer from the curse of dimensionality and have been mostly implemented in extreme-value studies up to three dimensions, whereas parametric models can tackle higher-dimensional settings. In this paper, we assess, through a vast and systematic simulation study, the performance of classical and recently proposed estimators in multivariate settings. In particular, we first investigate the performance of nonparametric methods and then compare them with classical parametric approaches under symmetric and asymmetric dependence structures within the commonly used logistic family. We also explore two different ways to make nonparametric estimators satisfy the necessary dependence function shape constraints, finding a general improvement in estimator performance either (i) by substituting the estimator with its greatest convex minorant, developing a computational tool to implement this method for dimensions $$D\\\\ge 2$$D≥2 or (ii) by projecting the estimator onto a subspace of dependence functions satisfying such constraints and taking advantage of Bernstein–Bézier polynomials. Implementing the convex minorant method leads to better estimator performance as the dimensionality increases.

  13. Intake and time dependence of blueberry flavonoid-induced improvements in vascular function: a randomized, controlled, double-blind, crossover intervention study with mechanistic insights into biological activity.

    Science.gov (United States)

    Rodriguez-Mateos, Ana; Rendeiro, Catarina; Bergillos-Meca, Triana; Tabatabaee, Setareh; George, Trevor W; Heiss, Christian; Spencer, Jeremy Pe

    2013-11-01

    There are very limited data regarding the effects of blueberry flavonoid intake on vascular function in healthy humans. We investigated the impact of blueberry flavonoid intake on endothelial function in healthy men and assessed potential mechanisms of action by the assessment of circulating metabolites and neutrophil NADPH oxidase activity. Two randomized, controlled, double-blind, crossover human-intervention trials were conducted with 21 healthy men. Initially, the impact of blueberry flavonoid intake on flow-mediated dilation (FMD) and polyphenol absorption and metabolism was assessed at baseline and 1, 2, 4, and 6 h after consumption of blueberry containing 766, 1278, and 1791 mg total blueberry polyphenols or a macronutrient- and micronutrient-matched control drink (0 mg total blueberry polyphenols). Second, an intake-dependence study was conducted (from baseline to 1 h) with 319, 637, 766, 1278, and 1791 mg total blueberry polyphenols and a control. We observed a biphasic time-dependent increase in FMD, with significant increases at 1-2 and 6 h after consumption of blueberry polyphenols. No significant intake-dependence was observed between 766 and 1791 mg. However, at 1 h after consumption, FMD increased dose dependently to ≤766 mg total blueberry polyphenol intake, after which FMD plateaued. Increases in FMD were closely linked to increases in circulating metabolites and by decreases in neutrophil NADPH oxidase activity at 1-2 and 6 h. Blueberry intake acutely improves vascular function in healthy men in a time- and intake-dependent manner. These benefits may be mechanistically linked to the actions of circulating phenolic metabolites on neutrophil NADPH oxidase activity. This trial was registered at clinicaltrials.gov as NCT01292954 and NCT01829542.

  14. Bias-corrected estimation of stable tail dependence function

    DEFF Research Database (Denmark)

    Beirlant, Jan; Escobar-Bach, Mikael; Goegebeur, Yuri

    2016-01-01

    We consider the estimation of the stable tail dependence function. We propose a bias-corrected estimator and we establish its asymptotic behaviour under suitable assumptions. The finite sample performance of the proposed estimator is evaluated by means of an extensive simulation study where...

  15. IL-21 May Promote Granzyme B-Dependent NK/Plasmacytoid Dendritic Cell Functional Interaction in Cutaneous Lupus Erythematosus.

    Science.gov (United States)

    Salvi, Valentina; Vermi, William; Cavani, Andrea; Lonardi, Silvia; Carbone, Teresa; Facchetti, Fabio; Bosisio, Daniela; Sozzani, Silvano

    2017-07-01

    Autoimmune skin lesions are characterized by a complex cytokine milieu and by the accumulation of plasmacytoid dendritic cells (pDCs). Granzyme B (GrB) transcript is abundant in activated pDCs, though its mechanisms of regulation and biological role are largely unknown. Here we report that IL-21 was the only T helper 1/T helper 17 cytokine able to induce the expression and secretion of GrB by pDCs and that this action was counteracted by the autocrine production of type I IFNs. In lupus erythematosus skin lesions, the percentage of GrB + pDCs directly correlated with the IL-21/MxA ratio, indicating that the interplay between these two cytokines finely tunes the levels of pDC-dependent GrB also in vivo. In lupus erythematosus, pDCs colocalized with professional cytotoxic cells at sites of epithelial damage, suggesting a role in keratinocyte killing. Accordingly, we demonstrate that supernatants of IL-21-activated pDCs promoted autologous keratinocyte killing by natural killer cells and this action was dependent on GrB. These results propose a GrB-dependent functional interaction between pDCs and natural killer cells and highlight a negative feedback regulation by type I IFNs in vitro and in vivo that may function to limit excessive tissue damage. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  16. Investigating Lebanese Grade Seven Biology Teachers Mathematical Knowledge and Skills: A Case Study

    Science.gov (United States)

    Raad, Nawal Abou; Chatila, Hanadi

    2016-01-01

    This paper investigates Lebanese grade 7 biology teachers' mathematical knowledge and skills, by exploring how they explain a visual representation in an activity depending on the mathematical concept "Function". Twenty Lebanese in-service biology teachers participated in the study, and were interviewed about their explanation for the…

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

    Directory of Open Access Journals (Sweden)

    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.

  18. Altered Brain Functional Connectivity in Betel Quid-Dependent Chewers

    Directory of Open Access Journals (Sweden)

    Xiaojun Huang

    2017-11-01

    Full Text Available BackgroundBetel quid (BQ is a common psychoactive substance worldwide with particularly high usage in many Asian countries. This study aimed to explore the effect of BQ use on functional connectivity by comparing global functional brain networks and their subset between BQ chewers and healthy controls (HCs.MethodsResting-state functional magnetic resonance imaging (fMRI was obtained from 24 betel quid-dependent (BQD male chewers and 27 healthy male individuals on a 3.0T scanner. We used independent component analysis (ICA to determine components that represent the brain’s functional networks and their spatial aspects of functional connectivity. Two sample t-tests were used to identify the functional connectivity differences in each network between these two groups.ResultsSeventeen networks were identified by ICA. Nine of them showed connectivity differences between BQD and HCs (two sample t-tests, p < 0.001 uncorrected. We found increased functional connectivity in the orbitofrontal, bilateral frontoparietal, frontotemporal, occipital/parietal, frontotemporal/cerebellum, and temporal/limbic networks, and decreased connectivity in the parietal and medial frontal/anterior cingulate networks in the BQD compared to the HCs. The betel quid dependence scale scores were positively related to the increased functional connectivity in the orbitofrontal (r = 0.39, p = 0.03 while negatively related to the decreased functional connectivity in medial frontal/anterior cingulate networks (r = −0.35, p = 0.02.DiscussionOur findings provide further evidence that BQ chewing may lead to brain functional connectivity changes, which may play a key role in the psychological and physiological effects of BQ.

  19. Gauge-fixing parameter dependence of two-point gauge-variant correlation functions

    International Nuclear Information System (INIS)

    Zhai, C.

    1996-01-01

    The gauge-fixing parameter ξ dependence of two-point gauge-variant correlation functions is studied for QED and QCD. We show that, in three Euclidean dimensions, or for four-dimensional thermal gauge theories, the usual procedure of getting a general covariant gauge-fixing term by averaging over a class of covariant gauge-fixing conditions leads to a nontrivial gauge-fixing parameter dependence in gauge-variant two-point correlation functions (e.g., fermion propagators). This nontrivial gauge-fixing parameter dependence modifies the large-distance behavior of the two-point correlation functions by introducing additional exponentially decaying factors. These factors are the origin of the gauge dependence encountered in some perturbative evaluations of the damping rates and the static chromoelectric screening length in a general covariant gauge. To avoid this modification of the long-distance behavior introduced by performing the average over a class of covariant gauge-fixing conditions, one can either choose a vanishing gauge-fixing parameter or apply an unphysical infrared cutoff. copyright 1996 The American Physical Society

  20. Multicomponent density-functional theory for time-dependent systems

    NARCIS (Netherlands)

    Butriy, O.; Ebadi, H.; de Boeij, P. L.; van Leeuwen, R.; Gross, E. K. U.

    2007-01-01

    We derive the basic formalism of density functional theory for time-dependent electron-nuclear systems. The basic variables of this theory are the electron density in body-fixed frame coordinates and the diagonal of the nuclear N-body density matrix. The body-fixed frame transformation is carried

  1. Optical Absorption in Molecular Crystals from Time-Dependent Density Functional Theory

    Science.gov (United States)

    2017-04-23

    Our approach represents a full solid-state calculation, allowing for polarization ef- fects while still capable of capturing inter-molecular dis...AFRL-AFOSR-UK-TR-2017-0030 Optical absorption in molecular crystals from time-dependent density functional theory Leeor Kronik WEIZMANN INSTITUTE OF...from time-dependent density functional theory 5a.  CONTRACT NUMBER 5b.  GRANT NUMBER FA9550-15-1-0290 5c.  PROGRAM ELEMENT NUMBER 61102F 6. AUTHOR(S

  2. Renormalization, Wilson lines, and transverse-momentum-dependent parton-distribution functions

    International Nuclear Information System (INIS)

    Cherednikov, I. O.; Stefanis, N. G.

    2008-01-01

    We perform an analysis of transverse-momentum dependent parton-distribution functions, making use of their renormalization properties in terms of their leading-order anomalous dimensions. We show that the appropriate Wilson line in the light cone gauge, associated with such quantities, is a cusped one at light cone infinity. To cancel the ensuing cusp anomalous dimension, we include in the definition of the transverse-momentum dependent parton-distribution functions an additional soft counter term (gauge link) along that cusped transverse contour. We demonstrate that this is tantamount to an 'intrinsic (Coulomb) phase', which accumulates the full gauge history of the color-charged particle.

  3. 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

  4. 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.

  5. 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

  6. A postprocessing method in the HMC framework for predicting gene function based on biological instrumental data

    Science.gov (United States)

    Feng, Shou; Fu, Ping; Zheng, Wenbin

    2018-03-01

    Predicting gene function based on biological instrumental data is a complicated and challenging hierarchical multi-label classification (HMC) problem. When using local approach methods to solve this problem, a preliminary results processing method is usually needed. This paper proposed a novel preliminary results processing method called the nodes interaction method. The nodes interaction method revises the preliminary results and guarantees that the predictions are consistent with the hierarchy constraint. This method exploits the label dependency and considers the hierarchical interaction between nodes when making decisions based on the Bayesian network in its first phase. In the second phase, this method further adjusts the results according to the hierarchy constraint. Implementing the nodes interaction method in the HMC framework also enhances the HMC performance for solving the gene function prediction problem based on the Gene Ontology (GO), the hierarchy of which is a directed acyclic graph that is more difficult to tackle. The experimental results validate the promising performance of the proposed method compared to state-of-the-art methods on eight benchmark yeast data sets annotated by the GO.

  7. Density dependence of the nuclear energy-density functional

    Science.gov (United States)

    Papakonstantinou, Panagiota; Park, Tae-Sun; Lim, Yeunhwan; Hyun, Chang Ho

    2018-01-01

    Background: The explicit density dependence in the coupling coefficients entering the nonrelativistic nuclear energy-density functional (EDF) is understood to encode effects of three-nucleon forces and dynamical correlations. The necessity for the density-dependent coupling coefficients to assume the form of a preferably small fractional power of the density ρ is empirical and the power is often chosen arbitrarily. Consequently, precision-oriented parametrizations risk overfitting in the regime of saturation and extrapolations in dilute or dense matter may lose predictive power. Purpose: Beginning with the observation that the Fermi momentum kF, i.e., the cubic root of the density, is a key variable in the description of Fermi systems, we first wish to examine if a power hierarchy in a kF expansion can be inferred from the properties of homogeneous matter in a domain of densities, which is relevant for nuclear structure and neutron stars. For subsequent applications we want to determine a functional that is of good quality but not overtrained. Method: For the EDF, we fit systematically polynomial and other functions of ρ1 /3 to existing microscopic, variational calculations of the energy of symmetric and pure neutron matter (pseudodata) and analyze the behavior of the fits. We select a form and a set of parameters, which we found robust, and examine the parameters' naturalness and the quality of resulting extrapolations. Results: A statistical analysis confirms that low-order terms such as ρ1 /3 and ρ2 /3 are the most relevant ones in the nuclear EDF beyond lowest order. It also hints at a different power hierarchy for symmetric vs. pure neutron matter, supporting the need for more than one density-dependent term in nonrelativistic EDFs. The functional we propose easily accommodates known or adopted properties of nuclear matter near saturation. More importantly, upon extrapolation to dilute or asymmetric matter, it reproduces a range of existing microscopic

  8. A Magnetic Sensor System for Biological Detection

    KAUST Repository

    Li, Fuquan

    2015-05-01

    Magnetic biosensors detect biological targets through sensing the stray field of magnetic beads which label the targets. Commonly, magnetic biosensors employ the “sandwich” method to immobilize biological targets, i.e., the targets are sandwiched between a bio-functionalized sensor surface and bio-functionalized magnetic beads. This method has been used very successfully in different application, but its execution requires a rather elaborate procedure including several washing and incubation steps. This dissertation investigates a new magnetic biosensor concept, which enables a simple and effective detection of biological targets. The biosensor takes advantage of the size difference between bare magnetic beads and compounds of magnetic beads and biological targets. First, the detection of super-paramagnetic beads via magnetic tunnel junction (MTJ) sensors is implemented. Frequency modulation is used to enhance the signal-to-noise ratio, enabling the detection of a single magnetic bead. Second, the concept of the magnetic biosensor is investigated theoretically. The biosensor consists of an MTJ sensor, which detects the stray field of magnetic beads inside of a trap on top of the MTJ. A microwire between the trap and the MTJ is used to attract magnetic beads to the trapping well by applying a current to it. The MTJ sensor’s output depends on the number of beads inside the trap. If biological targets are in the sample solution, the beads will form bead compounds consisting of beads linked to the biological targets. Since bead compounds are larger than bare beads, the number of beads inside the trapping well will depend on the presence of biological targets. Hence, the output of the MTJ sensor will depend on the biological targets. The dependences of sensor signals on the sizes of the MTJ sensor, magnetic beads and biological targets are studied to find the optimum constellations for the detection of specific biological targets. The optimization is demonstrated

  9. 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

  10. Decay of autoionizing states in time-dependent density functional and reduced density matrix functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Kapoor, Varun; Brics, Martins; Bauer, Dieter [Institut fuer Physik, Universitaet Rostock, 18051 Rostock (Germany)

    2013-07-01

    Autoionizing states are inaccessible to time-dependent density functional theory (TDDFT) using known, adiabatic Kohn-Sham (KS) potentials. We determine the exact KS potential for a numerically exactly solvable model Helium atom interacting with a laser field that is populating an autoionizing state. The exact single-particle density of the population in the autoionizing state corresponds to that of the energetically lowest quasi-stationary state in the exact KS potential. We describe how this exact potential controls the decay by a barrier whose height and width allows for the density to tunnel out and decay with the same rate as in the ab initio time-dependent Schroedinger calculation. However, devising a useful exchange-correlation potential that is capable of governing such a scenario in general and in more complex systems is hopeless. As an improvement over TDDFT, time-dependent reduced density matrix functional theory has been proposed. We are able to obtain for the above described autoionization process the exact time-dependent natural orbitals (i.e., the eigenfunctions of the exact, time-dependent one-body reduced density matrix) and study the potentials that appear in the equations of motion for the natural orbitals and the structure of the two-body density matrix expanded in them.

  11. Time-dependent density-functional theory concepts and applications

    CERN Document Server

    Ullrich, Carsten A

    2011-01-01

    Time-dependent density-functional theory (TDDFT) describes the quantum dynamics of interacting electronic many-body systems formally exactly and in a practical and efficient manner. TDDFT has become the leading method for calculating excitation energies and optical properties of large molecules, with accuracies that rival traditional wave-function based methods, but at a fraction of the computational cost.This book is the first graduate-level text on the concepts and applications of TDDFT, including many examples and exercises, and extensive coverage of the literature. The book begins with a s

  12. The biological effects of low doses of radiation: medical, biological and ecological aspects

    International Nuclear Information System (INIS)

    Gun-Aajav, T.; Ajnai, L.; Manlaijav, G.

    2007-01-01

    Full text: The results of recent studies show that low doses of radiation make many different structural and functional changes in a cell and these changes are preserved for a long time. This phenomenon is called as effects of low doses of radiation in biophysics, radiation biology and radiation medicine. The structural and functional changes depend on doses and this dependence has non-linear and bimodal behaviour. More detail, the radiation effect goes up and reaches its maximum (Low doses maximum) in low doses region, then it goes down and takes its stationary means (there is a negative effect in a few cases). With increases in doses and with further increases it goes up. It is established that low dose's maximum depends on physiological state of a biological object, radiation quality and dose rate. During the experiments another special date was established. This specialty is that many different physical and chemical factors are mutually connected and have synergetic behaviour. At present, researches are concentrating their attention on the following three directions: 1. Direct and indirect interaction of radiation's low doses: 2. Interpretation of its molecular mechanism, regulation of the positive effects and elaboration of ways o removing negative effects: 3. Application of the objective research results into practice. In conclusion the authors mention the current concepts on interpretation of low doses effect mechanism, forward their own views and emphasize the importance of considering low doses effects in researches of environmental radiation pollution, radiation medicine and radiation protection. (author)

  13. 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.

  14. A critical review of the use and performance of different function types for modeling temperature-dependent development of arthropod larvae.

    Science.gov (United States)

    Quinn, Brady K

    2017-01-01

    Temperature-dependent development influences production rates of arthropods, including crustaceans important to fisheries and agricultural pests. Numerous candidate equation types (development functions) exist to describe the effect of temperature on development time, yet most studies use only a single type of equation and there is no consensus as to which, if any model predicts development rates better than the others, nor what the consequences of selecting a potentially incorrect model equation are on predicted development times. In this study, a literature search was performed of studies fitting development functions to development data of arthropod larvae (99 species). The published data of most (79) of these species were then fit with 33 commonly-used development functions. Overall performance of each function type and consequences of using a function other than the best one to model data were assessed. Performance was also related to taxonomy and the range of temperatures examined. The majority (91.1%) of studies were found to not use the best function out of those tested. Using the incorrect model lead to significantly less accurate (e.g., mean difference±SE 85.9±27.4%, range: -1.7 to 1725.5%) predictions of development times than the best function. Overall, more complex functions performed poorly relative to simpler ones. However, performance of some complex functions improved when wide temperature ranges were tested, which tended to be confined to studies of insects or arachnids compared with those of crustaceans. Results indicate the biological significance of choosing the best-fitting model to describe temperature-dependent development time data. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Measurement of the spin dependent structure functions of proton and neutron

    International Nuclear Information System (INIS)

    Rith, K.

    1989-01-01

    Recent results from the EMC experiment on the spin dependent structure function g 1 p (x) of the proton are discussed. They suggest that the nucleon spin does not originate from quark spins but rather from angular orbital momentum and gluon contributions. A proposed experiment at HERA is presented which will allow a very accurate measurement of the spin dependent structure functions and their integrals of both proton and neutron and a precise test of the Bjorken sum rule. (orig.)

  16. Balance functions: Multiplicity and transverse momentum dependence of the charge dependent correlations in ALICE

    CERN Document Server

    AUTHOR|(CDS)2078856; Snellings, Raimond; Christakoglou, Panos

    The measurement of charge-dependent correlations between positively and negatively charged particles as a function of pseudorapidity and azimuthal angle, known as the balance functions, provide insight to the properties of matter created in high-energy collisions. The balance functions are argued to probe the creation time of the particles and are also sensitive to the collective motion of the system. In this thesis, I present the results of the measured balance functions in p--Pb collisions at √sNN = 5.02~TeV obtained with the ALICE detector at the LHC. The results are compared with balance functions measured in pp and Pb--Pb collisions at √s=7~TeV and √sNN = 2.76~TeV$, respectively. The width of the balance functions in both pseudorapidity and azimuthal angle for non-identified charged particles decreases with increasing multiplicity in all three systems, for particles with low transverse momentum value pT < 2~GeV/c. For higher values of transverse momentum the balance functions become narrower and...

  17. Vascular risk factor burden, atherosclerosis, and functional dependence in old age: a population-based study.

    Science.gov (United States)

    Welmer, Anna-Karin; Liang, Yajun; Angleman, Sara; Santoni, Giola; Yan, Zhongrui; Cai, Chuanzhu; Qiu, Chengxuan

    2014-08-01

    Vascular risk factors such as hypertension and obesity have been associated with physical limitations among older adults. The purpose of this study is to examine whether individual and aggregated vascular risk factors (VRFs) are associated with functional dependence and to what extent carotid atherosclerosis (CAS) or peripheral artery disease (PAD) may mediate the possible associations of aggregated VRFs with functional dependence. This cross-sectional study included 1,451 community-living participants aged ≥60 years in the Confucius Hometown Aging Project of China. Data on demographic features, hypertension, high total cholesterol, obesity, smoking, physical inactivity, diabetes, CAS, PAD, and cardiovascular diseases (CVDs) were collected through an interview, a clinical examination, and laboratory tests. Functional dependence was defined as being dependent in at least one activity in the personal or instrumental activities of daily living. Data were analyzed using multiple logistic models controlling for potential confounders. We used the mediation model to explore the potential mediating effect of CAS and PAD on the associations of aggregated VRFs with functional dependence. Of the 1,451 participants, 222 (15.3%) had functional dependence. The likelihood of functional dependence increased linearly with increasing number of VRFs (hypertension, high total cholesterol, abdominal obesity, and physical inactivity) (p for trend dependence with clustering VRFs was mediated by CAS and PAD. Aggregation of multiple VRFs is associated with an increased likelihood of functional dependence among Chinese older adults; the association is partially mediated by carotid and peripheral artery atherosclerosis independently of CVDs.

  18. 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.

  19. Cranial computed tomography associated with development of functional dependence in a community-based elderly population

    International Nuclear Information System (INIS)

    Tsukishima, Eri; Shido, Koichi

    2002-01-01

    The purpose of this study was to investigate whether changes at computed tomography (CT) imaging in the ageing brain are associated with future risks for functional dependence. One hundred sixty residents aged 69 years and older at the cranial CT and were independently living in a rural community in Hokkaido, Japan. Cranial CT was performed between 1991 and 1993, graded for ventricular enlargement, sulcal enlargement, white matter change, and small infarction. Functional status was reassessed in 1998 in each participant. Multiple logistic regression analysis was performed to estimate the association of CT changes in the ageing brain with development of functional dependence over six years. Functional dependence was found in 19 residents at the second survey. After adjusting for age, sex, medical conditions, and cognitive functioning, small infarction and ventricular enlargement were significantly associated with development of functional dependence (adjusted odds ratio=9.27 and 4.62). After controlling for age, the age-related changes on cranial CT have significant association on development of functional dependence. (author)

  20. Nalmefene Reduces Reward Anticipation in Alcohol Dependence: An Experimental Functional Magnetic Resonance Imaging Study.

    Science.gov (United States)

    Quelch, Darren R; Mick, Inge; McGonigle, John; Ramos, Anna C; Flechais, Remy S A; Bolstridge, Mark; Rabiner, Eugenii; Wall, Matthew B; Newbould, Rexford D; Steiniger-Brach, Björn; van den Berg, Franz; Boyce, Malcolm; Østergaard Nilausen, Dorrit; Breuning Sluth, Lasse; Meulien, Didier; von der Goltz, Christoph; Nutt, David; Lingford-Hughes, Anne

    2017-06-01

    Nalmefene is a µ and δ opioid receptor antagonist, κ opioid receptor partial agonist that has recently been approved in Europe for treating alcohol dependence. It offers a treatment approach for alcohol-dependent individuals with "high-risk drinking levels" to reduce their alcohol consumption. However, the neurobiological mechanism underpinning its effects on alcohol consumption remains to be determined. Using a randomized, double-blind, placebo-controlled, within-subject crossover design we aimed to determine the effect of a single dose of nalmefene on striatal blood oxygen level-dependent (BOLD) signal change during anticipation of monetary reward using the monetary incentive delay task following alcohol challenge. Twenty-two currently heavy-drinking, non-treatment-seeking alcohol-dependent males were recruited. The effect of single dose nalmefene (18 mg) on changes in a priori defined striatal region of interest BOLD signal change during reward anticipation compared with placebo was investigated using functional magnetic resonance imaging. Both conditions were performed under intravenous alcohol administration (6% vol/vol infusion to achieve a target level of 80 mg/dL). Datasets from 18 participants were available and showed that in the presence of the alcohol infusion, nalmefene significantly reduced the BOLD response in the striatal region of interest compared with placebo. Nalmefene did not alter brain perfusion. Nalmefene blunts BOLD response in the mesolimbic system during anticipation of monetary reward and an alcohol infusion. This is consistent with nalmefene's actions on opioid receptors, which modulate the mesolimbic dopaminergic system, and provides a neurobiological basis for its efficacy. Copyright © 2017 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

  1. Computational complexity of time-dependent density functional theory

    International Nuclear Information System (INIS)

    Whitfield, J D; Yung, M-H; Tempel, D G; Aspuru-Guzik, A; Boixo, S

    2014-01-01

    Time-dependent density functional theory (TDDFT) is rapidly emerging as a premier method for solving dynamical many-body problems in physics and chemistry. The mathematical foundations of TDDFT are established through the formal existence of a fictitious non-interacting system (known as the Kohn–Sham system), which can reproduce the one-electron reduced probability density of the actual system. We build upon these works and show that on the interior of the domain of existence, the Kohn–Sham system can be efficiently obtained given the time-dependent density. We introduce a V-representability parameter which diverges at the boundary of the existence domain and serves to quantify the numerical difficulty of constructing the Kohn-Sham potential. For bounded values of V-representability, we present a polynomial time quantum algorithm to generate the time-dependent Kohn–Sham potential with controllable error bounds. (paper)

  2. ON PARTIAL DIFFERENTIAL AND DIFFERENCE EQUATIONS WITH SYMMETRIES DEPENDING ON ARBITRARY FUNCTIONS

    Directory of Open Access Journals (Sweden)

    Giorgio Gubbiotti

    2016-06-01

    Full Text Available In this note we present some ideas on when Lie symmetries, both point and generalized, can depend on arbitrary functions. We show a few examples, both in partial differential and partial difference equations where this happens. Moreover we show that the infinitesimal generators of generalized symmetries depending on arbitrary functions, both for continuous and discrete equations, effectively play the role of master symmetries.

  3. Range dependent characteristics in the head-related transfer functions of a bat-head cast: part 1. Monaural characteristics

    International Nuclear Information System (INIS)

    Kim, S; Allen, R; Rowan, D

    2012-01-01

    Knowledge of biological sonar systems has revolutionized many aspects of sonar engineering and further advances will benefit from more detailed understanding of their underlying acoustical processes. The anatomically diverse, complex and dynamic heads and ears of bats are known to be important for echolocation although their range-dependent properties are not well understood, particularly across the wide frequency range of some bats' vocalizations. The aim of this and a companion paper Kim et al (2012 Bioinspir. Biomim.) is to investigate bat-head acoustics as a function of bat-target distance, based on measurements up to 100 kHz and more robust examination of hardware characteristics in measurements than previously reported, using a cast of a bat head. In this first paper, we consider the spectral features at either ear (i.e. monaural head-related transfer functions). The results show, for example, that there is both higher magnitude and a stronger effect of distance at close range at relatively low frequencies. This might explain, at least in part, why bats adopt a strategy of changing the frequency range of their vocalizations while approaching a target. There is also potential advantage in the design of bio-inspired receivers of using range-dependent HRTFs and utilizing their distinguished frequency characteristics over the distance. (paper)

  4. 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.

  5. 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.

  6. Functional brain networks associated with cognitive control, cocaine dependence, and treatment outcome.

    Science.gov (United States)

    Worhunsky, Patrick D; Stevens, Michael C; Carroll, Kathleen M; Rounsaville, Bruce J; Calhoun, Vince D; Pearlson, Godfrey D; Potenza, Marc N

    2013-06-01

    Individuals with cocaine dependence often evidence poor cognitive control. The purpose of this exploratory study was to investigate networks of functional connectivity underlying cognitive control in cocaine dependence and examine the relationship of the networks to the disorder and its treatment. Independent component analysis (ICA) was applied to fMRI data to investigate if regional activations underlying cognitive control processes operate in functional networks, and whether these networks relate to performance and treatment outcome measures in cocaine dependence. Twenty patients completed a Stroop task during fMRI prior to entering outpatient treatment and were compared to 20 control participants. ICA identified five distinct functional networks related to cognitive control interference events. Cocaine-dependent patients displayed differences in performance-related recruitment of three networks. Reduced involvement of a "top-down" fronto-cingular network contributing to conflict monitoring correlated with better treatment retention. Greater engagement of two "bottom-up" subcortical and ventral prefrontal networks related to cue-elicited motivational processing correlated with abstinence during treatment. The identification of subcortical networks linked to cocaine abstinence and cortical networks to treatment retention suggests that specific circuits may represent important, complementary targets in treatment development for cocaine dependence. 2013 APA, all rights reserved

  7. 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

  8. Temperature dependence of the work function of ruthenium-based gate electrodes

    International Nuclear Information System (INIS)

    Alshareef, H.N.; Wen, H.C.; Luan, H.F.; Choi, K.; Harris, H.R.; Senzaki, Y.; Majhi, P.; Lee, B.H.; Foran, B.; Lian, G.

    2006-01-01

    The effect of device fabrication temperature on the work function of ruthenium (Ru) metal gate and its bilayers was investigated. The work function shows strong temperature dependence when Ru electrodes are deposited on silicon oxide, SiO 2 , but not on hafnium silicates (HfSiO x ). Specifically, the work function of Ru on SiO 2 increased from 4.5 eV at 500 deg. C to 5.0 eV at 700 deg. C. On further annealing to 900 deg. C or higher, the work function dropped to about 4.4 eV. In the case of HfSiO x , the work function of Ru changed by less than 100 mV over the same temperature range. Identical temperature dependence was observed using hafnium (Hf)/Ru and tantalum (Ta)/Ru bilayers. However, the peak values of the work function decreased with increasing Hf/Ru and Ta/Ru thickness ratios. Materials analysis suggests that these trends are driven by interactions at the Ru metal gate-dielectric interface

  9. Functional Brain Networks Associated with Cognitive Control, Cocaine Dependence and Treatment Outcome

    OpenAIRE

    Worhunsky, Patrick D.; Stevens, Michael C.; Carroll, Kathleen M.; Rounsaville, Bruce J.; Calhoun, Vince D.; Pearlson, Godfrey D.; Potenza, Marc N.

    2012-01-01

    Individuals with cocaine dependence often evidence poor cognitive control. The purpose of this exploratory study was to investigate networks of functional connectivity underlying cognitive control in cocaine dependence and examine the relationship of the networks to the disorder and its treatment. Independent component analysis (ICA) was applied to fMRI data to investigate if regional activations underlying cognitive control processes operate in functional networks, and whether these networks...

  10. Fitting a function to time-dependent ensemble averaged data

    DEFF Research Database (Denmark)

    Fogelmark, Karl; Lomholt, Michael A.; Irbäck, Anders

    2018-01-01

    Time-dependent ensemble averages, i.e., trajectory-based averages of some observable, are of importance in many fields of science. A crucial objective when interpreting such data is to fit these averages (for instance, squared displacements) with a function and extract parameters (such as diffusion...... method, weighted least squares including correlation in error estimation (WLS-ICE), to particle tracking data. The WLS-ICE method is applicable to arbitrary fit functions, and we provide a publically available WLS-ICE software....

  11. Systems Biology of the Fluxome

    Directory of Open Access Journals (Sweden)

    Miguel A. Aon

    2015-07-01

    Full Text Available The advent of high throughput -omics has made the accumulation of comprehensive data sets possible, consisting of changes in genes, transcripts, proteins and metabolites. Systems biology-inspired computational methods for translating metabolomics data into fluxomics provide a direct functional, dynamic readout of metabolic networks. When combined with appropriate experimental design, these methods deliver insightful knowledge about cellular function under diverse conditions. The use of computational models accounting for detailed kinetics and regulatory mechanisms allow us to unravel the control and regulatory properties of the fluxome under steady and time-dependent behaviors. This approach extends the analysis of complex systems from description to prediction, including control of complex dynamic behavior ranging from biological rhythms to catastrophic lethal arrhythmias. The powerful quantitative metabolomics-fluxomics approach will help our ability to engineer unicellular and multicellular organisms evolve from trial-and-error to a more predictable process, and from cells to organ and organisms.

  12. Decreased serum level of NGF in alcohol-dependent patients with declined executive function

    Directory of Open Access Journals (Sweden)

    Bae H

    2014-11-01

    Full Text Available Hwallip Bae,1 Youngsun Ra,1 Changwoo Han,2 Dai-Jin Kim3 1Department of Psychiatry, Myongji Hospital, Goyang, 2Department of Psychiatry, Keyo Hospital, Uiwang, 3Department of Psychiatry, Seoul St Mary’s Hospital, College of Medicine, Catholic University of Korea, Seoul, South Korea Abstract: The role of neurotrophic factors has been highlighted as a cause of decline in the cognitive function of alcohol-dependent patients. It is known that nerve-growth factor (NGF, one of the neurotrophins, is related to the growth and differentiation of nerve cells, as well as to a decline in cognitive function. The purpose of this study was to investigate the relationship between decreased NGF levels and cognitive decline in alcohol-dependent patients. The serum concentration of NGF was measured in 38 patients with chronic alcohol dependence, and several neuropsychological tests were also performed for cognitive function assessment. The results indicated a significant correlation between serum NGF level and the trail-making test part B, which evaluates executive function, but did not show a significant correlation with other cognitive function tests. An increased serum level of NGF was associated with a decreased completion time in the trail-making test B, and this finding indicates that a high serum level of NGF is related to greater executive function. This finding may imply a protective role of NGF in preventing neuron damage among patients with alcohol dependence. Larger controlled studies will be necessary in the future to investigate this issue further. Keywords: nerve-growth factor, alcohol dependence, executive function, trail-making test

  13. Detecting positive quadrant dependence and positive function dependence

    NARCIS (Netherlands)

    Janic-Wróblewska, A.; Kallenberg, W.C.M.; Ledwina, T.

    2004-01-01

    There is a lot of interest in positive dependence going beyond linear correlation. In this paper three new rank tests for testing independence against positive dependence are introduced. The first one is directed on positive quadrant dependence, the second and third one concentrate on positive

  14. Detecting positive quadrant dependence and positive function dependence

    NARCIS (Netherlands)

    Janic-Wróblewska, A.; Kallenberg, W.C.M.; Ledwina, T.

    2003-01-01

    There is a lot of interest in positive dependence going beyond linear correlation. In this paper three new rank tests for testing independence against positive dependence are introduced. The first one is directed on positive quadrant dependence, the second and third one concentrate on positive

  15. The Role of Soil Biological Function in Regulating Agroecosystem Services and Sustainability in the Quesungual Agroforestry System

    Science.gov (United States)

    Fonte, S.; Pauli, N.; Rousseau, L.; SIX, J. W. U. A.; Barrios, E.

    2014-12-01

    The Quesungual agroforestry system from western Honduras has been increasingly promoted as a promising alternative to traditional slash-and-burn agriculture in tropical dry forest regions of the Americas. Improved residue management and the lack of burning in this system can greatly impact soil biological functioning and a number of key soil-based ecosystem services, yet our understanding of these processes has not been thoroughly integrated to understand system functionality as a whole that can guide improved management. To address this gap, we present a synthesis of various field studies conducted in Central America aimed at: 1) quantifying the influence of the Quesungual agroforestry practices on soil macrofauna abundance and diversity, and 2) understanding how these organisms influence key soil-based ecosystem services that ultimately drive the success of this system. A first set of studies examined the impact of agroecosystem management on soil macrofauna populations, soil fertility and key soil processes. Results suggest that residue inputs (derived from tree biomass pruning), a lack of burning, and high tree densities, lead to conditions that support abundant, diverse soil macrofauna communities under agroforestry, with soil organic carbon content comparable to adjacent forest. Additionally, there is great potential in working with farmers to develop refined soil quality indicators for improved land management. A second line of research explored interactions between residue management and earthworms in the regulation of soil-based ecosystem services. Earthworms are the most prominent ecosystem engineers in these soils. We found that earthworms are key drivers of soil structure maintenance and the stabilization of soil organic matter within soil aggregates, and also had notable impacts on soil nutrient dynamics. However, the impact of earthworms appears to depend on residue management practices, thus indicating the need for an integrated approach for

  16. Unpolarised transverse momentum dependent distribution and fragmentation functions from SIDIS multiplicities

    International Nuclear Information System (INIS)

    Anselmino, M.; Boglione, M.; Gonzalez, H. J.O.; Melis, S.; Prokudin, A.

    2014-01-01

    In this study, the unpolarised transverse momentum dependent distribution and fragmentation functions are extracted from HERMES and COMPASS experimental measurements of SIDIS multiplicities for charged hadron production. The data are grouped into independent bins of the kinematical variables, in which the TMD factorisation is expected to hold. A simple factorised functional form of the TMDs is adopted, with a Gaussian dependence on the intrinsic transverse momentum, which turns out to be quite adequate in shape. HERMES data do not need any normalisation correction, while fits of the COMPASS data much improve with a y-dependent overall normalisation factor. A comparison of the extracted TMDs with previous EMC and JLab data confirms the adequacy of the simple gaussian distributions. The possible role of the TMD evolution is briefly considered

  17. 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.

  18. Analytical approaches to the determination of spin-dependent parton distribution functions at NNLO approximation

    Science.gov (United States)

    Salajegheh, Maral; Nejad, S. Mohammad Moosavi; Khanpour, Hamzeh; Tehrani, S. Atashbar

    2018-05-01

    In this paper, we present SMKA18 analysis, which is a first attempt to extract the set of next-to-next-leading-order (NNLO) spin-dependent parton distribution functions (spin-dependent PDFs) and their uncertainties determined through the Laplace transform technique and Jacobi polynomial approach. Using the Laplace transformations, we present an analytical solution for the spin-dependent Dokshitzer-Gribov-Lipatov-Altarelli-Parisi evolution equations at NNLO approximation. The results are extracted using a wide range of proton g1p(x ,Q2) , neutron g1n(x ,Q2) , and deuteron g1d(x ,Q2) spin-dependent structure functions data set including the most recent high-precision measurements from COMPASS16 experiments at CERN, which are playing an increasingly important role in global spin-dependent fits. The careful estimations of uncertainties have been done using the standard Hessian error propagation. We will compare our results with the available spin-dependent inclusive deep inelastic scattering data set and other results for the spin-dependent PDFs in literature. The results obtained for the spin-dependent PDFs as well as spin-dependent structure functions are clearly explained both in the small and large values of x .

  19. Sex matters: The effects of biological sex on adipose tissue biology and energy metabolism

    Directory of Open Access Journals (Sweden)

    Teresa G. Valencak

    2017-08-01

    Full Text Available Adipose tissue is a complex and multi-faceted organ. It responds dynamically to internal and external stimuli, depending on the developmental stage and activity of the organism. The most common functional subunits of adipose tissue, white and brown adipocytes, regulate and respond to endocrine processes, which then determine metabolic rate as well as adipose tissue functions. While the molecular aspects of white and brown adipose biology have become clearer in the recent past, much less is known about sex-specific differences in regulation and deposition of adipose tissue, and the specific role of the so-called pink adipocytes during lactation in females. This review summarises the current understanding of adipose tissue dynamics with a focus on sex-specific differences in adipose tissue energy metabolism and endocrine functions, focussing on mammalian model organisms as well as human-derived data. In females, pink adipocytes trans-differentiate during pregnancy from subcutaneous white adipocytes and are responsible for milk-secretion in mammary glands. Overlooking biological sex variation may ultimately hamper clinical treatments of many aspects of metabolic disorders. Keywords: Body fatness, Adipose tissue, Sex-specific differences, Adipokines, Adipocytes, Obesity, Energy metabolism

  20. Functional approach to a time-dependent self-consistent field theory

    International Nuclear Information System (INIS)

    Reinhardt, H.

    1979-01-01

    The time-dependent Hartree-Fock approximation is formulated within the path integral approach. It is shown that by a suitable choice of the collective field the classical equation of motion of the collective field coincides with the time-dependent Hartree (TDH) equation. The consideration is restricted to the TDH equation, since the exchange terms do not appear in the functional approach on the same footing as the direct terms

  1. 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.

  2. Textbooks for biology applied in schools in Russia

    Directory of Open Access Journals (Sweden)

    Sergey Vitalevich Sumatokhin

    2018-04-01

    Full Text Available This article describes textbooks that are used in the teaching of biology in schools in Russia. The characteristics of designing biological programme content are presented. The school textbook, as a book, consists of a system of texts, illustrations, apparatus for acquiring knowledge (methodical apparatus and elements for orientation in the presented contents. In the textbook of biology, different types of texts are distinguished: basic, additional, explanatory. In Russia, biology textbooks for the school public more than ten publishers. A set of biology textbooks, ensuring the continuity of the study of biology in grades 5-9 (10-11 is called the subject line. Authors of different subject lines of textbooks differently select and structure the content of biological education. Depending on the approach to the structuring of the educational material, all subject lines of textbooks can be divided into two groups (system-structural approach and functional approach. These approaches can have a linear or concentric content structure. Each teacher has the right to choose from the variety of subject lines of biology textbooks those that most satisfy his needs.

  3. Effects of alcohol intake on brain structure and function in non-alcohol-dependent drinkers

    NARCIS (Netherlands)

    Bruin, Eveline Astrid de

    2005-01-01

    About 85% of the adult population in the Netherlands regularly drinks alcohol. Chronic excessive alcohol intake in alcohol-dependent individuals is known to have damaging effects on brain structure and function. Relatives of alcohol-dependent individuals display differences in brain function that

  4. Mining approximate temporal functional dependencies with pure temporal grouping in clinical databases.

    Science.gov (United States)

    Combi, Carlo; Mantovani, Matteo; Sabaini, Alberto; Sala, Pietro; Amaddeo, Francesco; Moretti, Ugo; Pozzi, Giuseppe

    2015-07-01

    Functional dependencies (FDs) typically represent associations over facts stored by a database, such as "patients with the same symptom get the same therapy." In more recent years, some extensions have been introduced to represent both temporal constraints (temporal functional dependencies - TFDs), as "for any given month, patients with the same symptom must have the same therapy, but their therapy may change from one month to the next one," and approximate properties (approximate functional dependencies - AFDs), as "patients with the same symptomgenerallyhave the same therapy." An AFD holds most of the facts stored by the database, enabling some data to deviate from the defined property: the percentage of data which violate the given property is user-defined. According to this scenario, in this paper we introduce approximate temporal functional dependencies (ATFDs) and use them to mine clinical data. Specifically, we considered the need for deriving new knowledge from psychiatric and pharmacovigilance data. ATFDs may be defined and measured either on temporal granules (e.g.grouping data by day, week, month, year) or on sliding windows (e.g.a fixed-length time interval which moves over the time axis): in this regard, we propose and discuss some specific and efficient data mining techniques for ATFDs. We also developed two running prototypes and showed the feasibility of our proposal by mining two real-world clinical data sets. The clinical interest of the dependencies derived considering the psychiatry and pharmacovigilance domains confirms the soundness and the usefulness of the proposed techniques. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. 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.

  6. Significance tests for functional data with complex dependence structure.

    Science.gov (United States)

    Staicu, Ana-Maria; Lahiri, Soumen N; Carroll, Raymond J

    2015-01-01

    We propose an L 2 -norm based global testing procedure for the null hypothesis that multiple group mean functions are equal, for functional data with complex dependence structure. Specifically, we consider the setting of functional data with a multilevel structure of the form groups-clusters or subjects-units, where the unit-level profiles are spatially correlated within the cluster, and the cluster-level data are independent. Orthogonal series expansions are used to approximate the group mean functions and the test statistic is estimated using the basis coefficients. The asymptotic null distribution of the test statistic is developed, under mild regularity conditions. To our knowledge this is the first work that studies hypothesis testing, when data have such complex multilevel functional and spatial structure. Two small-sample alternatives, including a novel block bootstrap for functional data, are proposed, and their performance is examined in simulation studies. The paper concludes with an illustration of a motivating experiment.

  7. Significance tests for functional data with complex dependence structure

    KAUST Repository

    Staicu, Ana-Maria

    2015-01-01

    We propose an L (2)-norm based global testing procedure for the null hypothesis that multiple group mean functions are equal, for functional data with complex dependence structure. Specifically, we consider the setting of functional data with a multilevel structure of the form groups-clusters or subjects-units, where the unit-level profiles are spatially correlated within the cluster, and the cluster-level data are independent. Orthogonal series expansions are used to approximate the group mean functions and the test statistic is estimated using the basis coefficients. The asymptotic null distribution of the test statistic is developed, under mild regularity conditions. To our knowledge this is the first work that studies hypothesis testing, when data have such complex multilevel functional and spatial structure. Two small-sample alternatives, including a novel block bootstrap for functional data, are proposed, and their performance is examined in simulation studies. The paper concludes with an illustration of a motivating experiment.

  8. Predicting Translation Initiation Rates for Designing Synthetic Biology

    International Nuclear Information System (INIS)

    Reeve, Benjamin; Hargest, Thomas; Gilbert, Charlie; Ellis, Tom

    2014-01-01

    In synthetic biology, precise control over protein expression is required in order to construct functional biological systems. A core principle of the synthetic biology approach is a model-guided design and based on the biological understanding of the process, models of prokaryotic protein production have been described. Translation initiation rate is a rate-limiting step in protein production from mRNA and is dependent on the sequence of the 5′-untranslated region and the start of the coding sequence. Translation rate calculators are programs that estimate protein translation rates based on the sequence of these regions of an mRNA, and as protein expression is proportional to the rate of translation initiation, such calculators have been shown to give good approximations of protein expression levels. In this review, three currently available translation rate calculators developed for synthetic biology are considered, with limitations and possible future progress discussed.

  9. Time-dependent quantum fluid density functional theory of hydrogen ...

    Indian Academy of Sciences (India)

    A time-dependent generalized non-linear Schrödinger equation (GNLSE) of motion was earlier derived in our laboratory by combining density functional theory and quantum fluid dynamics in threedimensional space. In continuation of the work reported previously, the GNLSE is applied to provide additional knowledge on ...

  10. Culture, Urbanism and Changing Human Biology.

    Science.gov (United States)

    Schell, L M

    2014-04-03

    Anthropologists have long known that human activity driven by culture changes the environment. This is apparent in the archaeological record and through the study of the modern environment. Perhaps the largest change since the paleolithic era is the organization of human populations in cities. New environments can reshape human biology through evolution as shown by the evolution of the hominid lineage. Evolution is not the only process capable of reshaping our biology. Some changes in our human biology are adaptive and evolutionary while others are pathological. What changes in human biology may be wrought by the modern urban environment? One significant new change in the environment is the introduction of pollutants largely through urbanization. Pollutants can affect human biology in myriad ways. Evidence shows that human growth, reproduction, and cognitive functioning can be altered by some pollutants, and altered in different ways depending on the pollutant. Thus, pollutants have significance for human biologists and anthropologists generally. Further, they illustrate the bio-cultural interaction characterizing human change. Humans adapt by changing the environment, a cultural process, and then change biologically to adjust to that new environment. This ongoing, interactive process is a fundamental characteristic of human change over the millennia.

  11. A dependent stress-strength interference model based on mixed copula function

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Jian Xiong; An, Zong Wen; Liu, Bo [School of Mechatronics Engineering, Lanzhou University of Technology, Lanzhou (China)

    2016-10-15

    In the traditional Stress-strength interference (SSI) model, stress and strength must satisfy the basic assumption of mutual independence. However, a complex dependence between stress and strength exists in practical engineering. To evaluate structural reliability under the case that stress and strength are dependent, a mixed copula function is introduced to a new dependent SSI model. This model can fully characterize the dependence between stress and strength. The residual square sum method and genetic algorithm are also used to estimate the unknown parameters of the model. Finally, the validity of the proposed model is demonstrated via a practical case. Results show that traditional SSI model ignoring the dependence between stress and strength more easily overestimates product reliability than the new dependent SSI model.

  12. Functional interactions of HIV-infection and methamphetamine dependence during motor programming.

    Science.gov (United States)

    Archibald, Sarah L; Jacobson, Mark W; Fennema-Notestine, Christine; Ogasawara, Miki; Woods, Steven P; Letendre, Scott; Grant, Igor; Jernigan, Terry L

    2012-04-30

    Methamphetamine (METH) dependence is frequently comorbid with HIV infection and both have been linked to alterations of brain structure and function. In a previous study, we showed that the brain volume loss characteristic of HIV infection contrasts with METH-related volume increases in striatum and parietal cortex, suggesting distinct neurobiological responses to HIV and METH (Jernigan et al., 2005). Functional magnetic resonance imaging (fMRI) has the potential to reveal functional interactions between the effects of HIV and METH. In the present study, 50 participants were studied in four groups: an HIV+ group, a recently METH-dependent group, a dually affected group, and a group of unaffected community comparison subjects. An fMRI paradigm consisting of motor sequencing tasks of varying levels of complexity was administered to examine blood oxygenation level dependent (BOLD) changes. Within all groups, activity increased significantly with increasing task complexity in large clusters within sensorimotor and parietal cortex, basal ganglia, cerebellum, and cingulate. The task complexity effect was regressed on HIV status, METH status, and the HIV×METH interaction term in a simultaneous multiple regression. HIV was associated with less complexity-related activation in striatum, whereas METH was associated with less complexity-related activation in parietal regions. Significant interaction effects were observed in both cortical and subcortical regions; and, contrary to expectations, the complexity-related activation was less aberrant in dually affected than in single risk participants, in spite of comparable levels of neurocognitive impairment among the clinical groups. Thus, HIV and METH dependence, perhaps through their effects on dopaminergic systems, may have opposing functional effects on neural circuits involved in motor programming. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  13. A study of energy and effective atomic number dependence of the exposure build-up factors in biological samples

    International Nuclear Information System (INIS)

    Sidhu, G.S.; Singh, P.S.; Mudahar, G.S.

    2000-01-01

    A theoretical method is presented to determine the gamma-radiation build-up factors in various biological materials. The gamma energy range is 0.015-15.0 MeV, with penetration depths up to 40 mean free paths considered. The dependence of the exposure build-up factor on incident photon energy and the effective atomic number (Z eff ) has also been assessed. In a practical analysis of dose burden to gamma-irradiated biological materials, the sophistication of Monte Carlo computer techniques would be applied, with associated detailed modelling. However, a feature of the theoretical method presented is its ability to make the consequences of the physics of the scattering process in biological materials more transparent. In addition, it can be quickly employed to give a first-pass dose estimate prior to a more detailed computer study. (author)

  14. Effects of alcohol intake on brain structure and function in non-alcohol-dependent drinkers

    OpenAIRE

    Bruin, Eveline Astrid de

    2005-01-01

    About 85% of the adult population in the Netherlands regularly drinks alcohol. Chronic excessive alcohol intake in alcohol-dependent individuals is known to have damaging effects on brain structure and function. Relatives of alcohol-dependent individuals display differences in brain function that are similar to those found in alcoholics, even if they have never been drinking alcohol. This suggests that brain damage in alcohol-dependent individuals is at least partly related to genetic factors...

  15. Neuropsychological Impairment in Detoxified Alcohol-Dependent Subjects with Preserved Psychosocial Functioning

    Directory of Open Access Journals (Sweden)

    Catherine Martelli

    2017-09-01

    Full Text Available BackgroundChronic alcoholism and its related cognitive impairments are associated with increased social, relational, and professional deficits which have a variable overall impact on social integration. These impairments are known to have varying severities and have rarely been studied among healthy alcohol-dependent subjects with preserved psychosocial functioning. Thus, the objective of this study is to describe neuropsychological performance in this particular population.MethodTwenty-nine socially adjusted alcohol-dependent men, hospitalized for a first or second withdrawal and abstinent for 3 weeks minimum, were compared to 29 healthy non-alcoholic controls. All subjects underwent clinical and psychiatric examination, neuropsychological tests of memory (M, working memory (WM, and executive functions (EF. Comparisons were performed using Student’s t-tests or Mann–Whitney U tests.ResultsNo group differences were found on the Self-Reported Social Adjustment Scale (SAS-SR or in the Mini-Mental State Examination. Compared to controls, patients had greater episodic, spatial, and WM deficits as well as slightly altered executive functions. In contrast, their executive functions (spontaneous flexibility, criteria generation, rule maintenance, and inhibitory control were relatively preserved.ConclusionOur sample of socially and professionally integrated alcoholic patients shows fewer cognitive deficits than described in previous studies. Our results suggest that early on, alcohol-dependent subjects develop compensatory adaptation processes to preserve social function and adaptation. Minor cognitive impairments should be screened early in the disease to integrate cognitive interventions into the health-care plan to thus eventually prevent further socio-professional marginalization.

  16. Temperature-dependent phase transitions in zeptoliter volumes of a complex biological membrane

    International Nuclear Information System (INIS)

    Nikiforov, Maxim P; Jesse, Stephen; Kalinin, Sergei V; Hohlbauch, Sophia; Proksch, Roger; King, William P; Voitchovsky, Kislon; Contera, Sonia Antoranz

    2011-01-01

    Phase transitions in purple membrane have been a topic of debate for the past two decades. In this work we present studies of a reversible transition of purple membrane in the 50-60 deg. C range in zeptoliter volumes under different heating regimes (global heating and local heating). The temperature of the reversible phase transition is 52 ± 5 deg. C for both local and global heating, supporting the hypothesis that this transition is mainly due to a structural rearrangement of bR molecules and trimers. To achieve high resolution measurements of temperature-dependent phase transitions, a new scanning probe microscopy-based method was developed. We believe that our new technique can be extended to other biological systems and can contribute to the understanding of inhomogeneous phase transitions in complex systems.

  17. Distinct roles of autophagy-dependent and -independent functions of FIP200 revealed by generation and analysis of a mutant knock-in mouse model

    Science.gov (United States)

    Chen, Song; Wang, Chenran; Yeo, Syn; Liang, Chun-Chi; Okamoto, Takako; Sun, Shaogang; Wen, Jian; Guan, Jun-Lin

    2016-01-01

    Autophagy is an evolutionarily conserved cellular process controlled through a set of essential autophagy genes (Atgs). However, there is increasing evidence that most, if not all, Atgs also possess functions independent of their requirement in canonical autophagy, making it difficult to distinguish the contributions of autophagy-dependent or -independent functions of a particular Atg to various biological processes. To distinguish these functions for FIP200 (FAK family-interacting protein of 200 kDa), an Atg in autophagy induction, we examined FIP200 interaction with its autophagy partner, Atg13. We found that residues 582–585 (LQFL) in FIP200 are required for interaction with Atg13, and mutation of these residues to AAAA (designated the FIP200-4A mutant) abolished its canonical autophagy function in vitro. Furthermore, we created a FIP200-4A mutant knock-in mouse model and found that specifically blocking FIP200 interaction with Atg13 abolishes autophagy in vivo, providing direct support for the essential role of the ULK1/Atg13/FIP200/Atg101 complex in the process beyond previous studies relying on the complete knockout of individual components. Analysis of the new mouse model showed that nonautophagic functions of FIP200 are sufficient to fully support embryogenesis by maintaining a protective role in TNFα-induced apoptosis. However, FIP200-mediated canonical autophagy is required to support neonatal survival and tumor cell growth. These studies provide the first genetic evidence linking an Atg's autophagy and nonautophagic functions to different biological processes in vivo. PMID:27013233

  18. Transverse momentum dependent fragmentation function at next-to-next-to-leading order

    NARCIS (Netherlands)

    Garcia, M.; Scimemi, I.; Vladimirov, A.

    2016-01-01

    We calculate the unpolarized transverse momentum dependent fragmentation function at next-to-next-to-leading order, evaluating separately the transverse momentum dependent (TMD) soft factor and the TMD collinear correlator. For the first time, the cancellation of spurious rapidity divergences in a

  19. Dependence of biologically active UV radiation on the atmospheric ozone in 2000 - 2001 over Stara Zagora, Bulgaria

    International Nuclear Information System (INIS)

    Gogosheva, Tz.; Petkov, B.; Mendeva, B.; Krastev, D.

    2003-01-01

    This study investigates how the changes in simultaneously measured ozone columns influence the biologically active UV irradiance. Spectral ground-based measurements of direct solar ultraviolet radiation performed at Stara Zagora (42 o N, 25 o E), Bulgaria in 2000 - 2001 are used in conjunction with the total ozone content to investigate the relation to the biologically active UV radiation, depending on the solar zenith angle (SZA) and the ozone. The device measures the direct solar radiation in the range 290 - 360 nm at 1 nm resolution. The direct sun UV doses for some specific biological effects (erythema and eyes) are obtained as the integral in the wavelength interval between 290 and 330 nm of the UV solar spectrum weighted with an action spectrum, typical of each effect. For estimation of the sensitivity of biological doses to the atmospheric ozone we calculate the radiation amplification factor (RAF) defined as the percentage increase in the column amount of the atmospheric ozone. The biological doses increase significantly with the decrease of the SZA. The doses of SZA=20 o are about three times larger than doses at SZA=50 o . The RAF derived from our spectral measurements shows an increase of RAF along with the decreasing ozone. For example, the ozone reduction by 1% increases the erythemal dose by about 2%. (authors)

  20. [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

  1. 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

  2. A class of covariate-dependent spatiotemporal covariance functions

    Science.gov (United States)

    Reich, Brian J; Eidsvik, Jo; Guindani, Michele; Nail, Amy J; Schmidt, Alexandra M.

    2014-01-01

    In geostatistics, it is common to model spatially distributed phenomena through an underlying stationary and isotropic spatial process. However, these assumptions are often untenable in practice because of the influence of local effects in the correlation structure. Therefore, it has been of prolonged interest in the literature to provide flexible and effective ways to model non-stationarity in the spatial effects. Arguably, due to the local nature of the problem, we might envision that the correlation structure would be highly dependent on local characteristics of the domain of study, namely the latitude, longitude and altitude of the observation sites, as well as other locally defined covariate information. In this work, we provide a flexible and computationally feasible way for allowing the correlation structure of the underlying processes to depend on local covariate information. We discuss the properties of the induced covariance functions and discuss methods to assess its dependence on local covariate information by means of a simulation study and the analysis of data observed at ozone-monitoring stations in the Southeast United States. PMID:24772199

  3. Functional loss of two ceramide synthases elicits autophagy-dependent lifespan extension in C. elegans.

    Directory of Open Access Journals (Sweden)

    Mai-Britt Mosbech

    Full Text Available Ceramide and its metabolites constitute a diverse group of lipids, which play important roles as structural entities of biological membranes as well as regulators of cellular growth, differentiation, and development. The C. elegans genome comprises three ceramide synthase genes; hyl-1, hyl-2, and lagr-1. HYL-1 function is required for synthesis of ceramides and sphingolipids containing very long acyl-chains (≥C24, while HYL-2 is required for synthesis of ceramides and sphingolipids containing shorter acyl-chains (≤C22. Here we show that functional loss of HYL-2 decreases lifespan, while loss of HYL-1 or LAGR-1 does not affect lifespan. We show that loss of HYL-1 and LAGR-1 functions extend lifespan in an autophagy-dependent manner, as knock down of the autophagy-associated gene ATG-12 abolishes hyl-1;lagr-1 longevity. The transcription factors PHA-4/FOXA, DAF-16/FOXO, and SKN-1 are also required for the observed lifespan extension, as well as the increased number of autophagosomes in hyl-1;lagr-1 animals. Both autophagic events and the transcription factors PHA-4/FOXA, DAF-16, and SKN-1 have previously been associated with dietary restriction-induced longevity. Accordingly, we find that hyl-1;lagr-1 animals display reduced feeding, increased resistance to heat, and reduced reproduction. Collectively, our data suggest that specific sphingolipids produced by different ceramide synthases have opposing roles in determination of C. elegans lifespan. We propose that loss of HYL-1 and LAGR-1 result in dietary restriction-induced autophagy and consequently prolonged longevity.

  4. 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.

  5. Cell Elasticity Determines Macrophage Function

    Science.gov (United States)

    Patel, Naimish R.; Bole, Medhavi; Chen, Cheng; Hardin, Charles C.; Kho, Alvin T.; Mih, Justin; Deng, Linhong; Butler, James; Tschumperlin, Daniel; Fredberg, Jeffrey J.; Krishnan, Ramaswamy; Koziel, Henry

    2012-01-01

    Macrophages serve to maintain organ homeostasis in response to challenges from injury, inflammation, malignancy, particulate exposure, or infection. Until now, receptor ligation has been understood as being the central mechanism that regulates macrophage function. Using macrophages of different origins and species, we report that macrophage elasticity is a major determinant of innate macrophage function. Macrophage elasticity is modulated not only by classical biologic activators such as LPS and IFN-γ, but to an equal extent by substrate rigidity and substrate stretch. Macrophage elasticity is dependent upon actin polymerization and small rhoGTPase activation, but functional effects of elasticity are not predicted by examination of gene expression profiles alone. Taken together, these data demonstrate an unanticipated role for cell elasticity as a common pathway by which mechanical and biologic factors determine macrophage function. PMID:23028423

  6. Cell elasticity determines macrophage function.

    Directory of Open Access Journals (Sweden)

    Naimish R Patel

    Full Text Available Macrophages serve to maintain organ homeostasis in response to challenges from injury, inflammation, malignancy, particulate exposure, or infection. Until now, receptor ligation has been understood as being the central mechanism that regulates macrophage function. Using macrophages of different origins and species, we report that macrophage elasticity is a major determinant of innate macrophage function. Macrophage elasticity is modulated not only by classical biologic activators such as LPS and IFN-γ, but to an equal extent by substrate rigidity and substrate stretch. Macrophage elasticity is dependent upon actin polymerization and small rhoGTPase activation, but functional effects of elasticity are not predicted by examination of gene expression profiles alone. Taken together, these data demonstrate an unanticipated role for cell elasticity as a common pathway by which mechanical and biologic factors determine macrophage function.

  7. Functional diversification of hsp40: distinct j-protein functional requirements for two prions allow for chaperone-dependent prion selection.

    Science.gov (United States)

    Harris, Julia M; Nguyen, Phil P; Patel, Milan J; Sporn, Zachary A; Hines, Justin K

    2014-07-01

    Yeast prions are heritable amyloid aggregates of functional yeast proteins; their propagation to subsequent cell generations is dependent upon fragmentation of prion protein aggregates by molecular chaperone proteins. Mounting evidence indicates the J-protein Sis1 may act as an amyloid specificity factor, recognizing prion and other amyloid aggregates and enabling Ssa and Hsp104 to act in prion fragmentation. Chaperone interactions with prions, however, can be affected by variations in amyloid-core structure resulting in distinct prion variants or 'strains'. Our genetic analysis revealed that Sis1 domain requirements by distinct variants of [PSI+] are strongly dependent upon overall variant stability. Notably, multiple strong [PSI+] variants can be maintained by a minimal construct of Sis1 consisting of only the J-domain and glycine/phenylalanine-rich (G/F) region that was previously shown to be sufficient for cell viability and [RNQ+] prion propagation. In contrast, weak [PSI+] variants are lost under the same conditions but maintained by the expression of an Sis1 construct that lacks only the G/F region and cannot support [RNQ+] propagation, revealing mutually exclusive requirements for Sis1 function between these two prions. Prion loss is not due to [PSI+]-dependent toxicity or dependent upon a particular yeast genetic background. These observations necessitate that Sis1 must have at least two distinct functional roles that individual prions differentially require for propagation and which are localized to the glycine-rich domains of the Sis1. Based on these distinctions, Sis1 plasmid-shuffling in a [PSI+]/[RNQ+] strain permitted J-protein-dependent prion selection for either prion. We also found that, despite an initial report to the contrary, the human homolog of Sis1, Hdj1, is capable of [PSI+] prion propagation in place of Sis1. This conservation of function is also prion-variant dependent, indicating that only one of the two Sis1-prion functions may have

  8. Sustaining biological welfare for our future through consistent science

    Directory of Open Access Journals (Sweden)

    Shimomura Yoshihiro

    2013-01-01

    Full Text Available Abstract Physiological anthropology presently covers a very broad range of human knowledge and engineering technologies. This study reviews scientific inconsistencies within a variety of areas: sitting posture; negative air ions; oxygen inhalation; alpha brain waves induced by music and ultrasound; 1/f fluctuations; the evaluation of feelings using surface electroencephalography; Kansei; universal design; and anti-stress issues. We found that the inconsistencies within these areas indicate the importance of integrative thinking and the need to maintain the perspective on the biological benefit to humanity. Analytical science divides human physiological functions into discrete details, although individuals comprise a unified collection of whole-body functions. Such disparate considerations contribute to the misunderstanding of physiological functions and the misevaluation of positive and negative values for humankind. Research related to human health will, in future, depend on the concept of maintaining physiological functions based on consistent science and on sustaining human health to maintain biological welfare in future generations.

  9. Exact-exchange time-dependent density-functional theory for static and dynamic polarizabilities

    International Nuclear Information System (INIS)

    Hirata, So; Ivanov, Stanislav; Bartlett, Rodney J.; Grabowski, Ireneusz

    2005-01-01

    Time-dependent density-functional theory (TDDFT) employing the exact-exchange functional has been formulated on the basis of the optimized-effective-potential (OEP) method of Talman and Shadwick for second-order molecular properties and implemented into a Gaussian-basis-set, trial-vector algorithm. The only approximation involved, apart from the lack of correlation effects and the use of Gaussian-type basis functions, was the consistent use of the adiabatic approximation in the exchange kernel and in the linear response function. The static and dynamic polarizabilities and their anisotropy predicted by the TDDFT with exact exchange (TDOEP) agree accurately with the corresponding values from time-dependent Hartree-Fock theory, the exact-exchange counterpart in the wave function theory. The TDOEP is free from the nonphysical asymptotic decay of the exchange potential of most conventional density functionals or from any other manifestations of the incomplete cancellation of the self-interaction energy. The systematic overestimation of the absolute values and dispersion of polarizabilities that plagues most conventional TDDFT cannot be seen in the TDOEP

  10. Time-dependent density functional theory for many-electron systems interacting with cavity photons.

    Science.gov (United States)

    Tokatly, I V

    2013-06-07

    Time-dependent (current) density functional theory for many-electron systems strongly coupled to quantized electromagnetic modes of a microcavity is proposed. It is shown that the electron-photon wave function is a unique functional of the electronic (current) density and the expectation values of photonic coordinates. The Kohn-Sham system is constructed, which allows us to calculate the above basic variables by solving self-consistent equations for noninteracting particles. We suggest possible approximations for the exchange-correlation potentials and discuss implications of this approach for the theory of open quantum systems. In particular we show that it naturally leads to time-dependent density functional theory for systems coupled to the Caldeira-Leggett bath.

  11. Determination of the scattering coefficient of biological tissue considering the wavelength and absorption dependence of the anisotropy factor

    Science.gov (United States)

    Fukutomi, Daichi; Ishii, Katsunori; Awazu, Kunio

    2016-04-01

    The anisotropy factor g, one of the optical properties of biological tissues, has a strong influence on the calculation of the scattering coefficient μ s in inverse Monte Carlo (iMC) simulations. It has been reported that g has the wavelength and absorption dependence; however, few attempts have been made to calculate μ s using g values by taking the wavelength and absorption dependence into account. In this study, the angular distributions of scattered light for biological tissue phantoms containing hemoglobin as a light absorber were measured by a goniometric optical setup at strongly (405 nm) and weakly (664 nm) absorbing wavelengths to obtain g. Subsequently, the optical properties were calculated with the measured values of g by integrating sphere measurements and an iMC simulation, and compared with the results obtained with a conventional g value of 0.9. The μ s values with measured g were overestimated at the strongly absorbing wavelength, but underestimated at the weakly absorbing wavelength if 0.9 was used in the iMC simulation.

  12. Transverse momentum dependent (TMD) parton distribution functions : status and prospects

    NARCIS (Netherlands)

    Angeles-Martinez, R.; Bacchetta, A.; Balitsky, I.I.; Boer, D.; Boglione, M.; Boussarie, R.; Ceccopieri, F.A.; Cherednikov, I.O.; Connor, P.; Echevarria, M. G.; Ferrera, G.; Luyando, J. Grados; Hautmann, F.; Jung, H.; Kasemets, T.; Kutak, K.; Lansberg, J.P.; Lelek, A.; Lykasov, G.; Martinez, J. D. Madrigal; Mulders, P. J.; Nocera, Emanuele R.; Petreska, E.; Pisano, C.; Placakyte, R.; Radescu, V.; Radici, M.; Schnell, G.; Scimemi, I.; Signori, A.; Szymanowski, L.; Monfared, S. Taheri; van der Veken, F.F.; van Haevermaet, H.J.; van Mechelen, P.; Vladimirov, A.; Wallon, S.

    2015-01-01

    We review transverse momentum dependent (TMD) parton distribution functions, their application to topical issues in high-energy physics phenomenology, and their theoretical connections with QCD resummation, evolution and factorization theorems. We illustrate the use of TMDs via examples of

  13. 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...

  14. 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...

  15. Fundamentals of time-dependent density functional theory

    International Nuclear Information System (INIS)

    Marques, Miguel A.L.; Rubio, Angel

    2012-01-01

    There have been many significant advances in time-dependent density functional theory over recent years, both in enlightening the fundamental theoretical basis of the theory, as well as in computational algorithms and applications. This book, as successor to the highly successful volume Time-Dependent Density Functional Theory (Lect. Notes Phys. 706, 2006) brings together for the first time all recent developments in a systematic and coherent way. First, a thorough pedagogical presentation of the fundamental theory is given, clarifying aspects of the original proofs and theorems, as well as presenting fresh developments that extend the theory into new realms such as alternative proofs of the original Runge-Gross theorem, open quantum systems, and dispersion forces to name but a few. Next, all of the basic concepts are introduced sequentially and building in complexity, eventually reaching the level of open problems of interest. Contemporary applications of the theory are discussed, from real-time coupled-electron-ion dynamics, to excited-state dynamics and molecular transport. Last but not least, the authors introduce and review recent advances in computational implementation, including massively parallel architectures and graphical processing units. Special care has been taken in editing this volume as a multi-author textbook, following a coherent line of thought, and making all the relevant connections between chapters and concepts consistent throughout. As such it will prove to be the text of reference in this field, both for beginners as well as expert researchers and lecturers teaching advanced quantum mechanical methods to model complex physical systems, from molecules to nanostructures, from biocomplexes to surfaces, solids and liquids. (orig.)

  16. Linking biological soil crust diversity to ecological functions

    Science.gov (United States)

    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.

  17. Sub-populations of alcohol-dependent patients: differences in psychological functioning between high- and low-frequency alcohol consumers.

    Science.gov (United States)

    Hiltunen, A J; Koechling, U M; Voltaire-Carlsson, A; Borg, S

    1996-07-01

    The purpose of the present study was to examine the processes underlying relapse to drinking using objective biological validation of self-reported recent alcohol consumption, using the ratio of 5-hydroxytryptophol to 5-hydroxyindol-3-ylacetic acid (5-HTOL/5-HIAA), a new biological marker to detect single episodes of drinking, in a sample of 38 male alcohol-dependent patients (DSM-III-R) who were assessed prospectively in terms of their clinical symptomatology over a 6-month treatment period. Results showed that nearly all patients obtained positive 5-HTOL/5-HIAA samples during the course of treatment. However, upon closer inspection, results revealed a bimodal distribution for alcohol intake with high and low frequency of consumption episodes. Results showed that high frequency consumers obtained higher ratings of clinical symptoms as measured by the Comprehensive Psychopathological Rating Scale (CPRS) and by the St Göran's Semi-structured Interview (SGSI) compared to low frequency alcohol consumers on symptoms of inner tension, lack of initiative, risk of relapse (as rated by therapists and as rated by patients themselves), dysphoria, negative craving for alcohol, and positive craving for alcohol. The present results provided evidence for the existence of two sub-populations of alcoholics, those who have frequent lapses and those who have low frequency of sporadic lapses. Further, these two sub-populations were shown to differ with respect to overall psychological functioning, and craving for alcohol. In conclusion, the present findings have important treatment implications in that reliable identification of patients' consumption patterns using biological markers would allow for the design of individually tailored treatment needs.

  18. Layer-dependent band alignment and work function of few-layer phosphorene.

    Science.gov (United States)

    Cai, Yongqing; Zhang, Gang; Zhang, Yong-Wei

    2014-10-20

    Using first-principles calculations, we study the electronic properties of few-layer phosphorene focusing on layer-dependent behavior of band gap, work function band alignment and carrier effective mass. It is found that few-layer phosphorene shows a robust direct band gap character, and its band gap decreases with the number of layers following a power law. The work function decreases rapidly from monolayer (5.16 eV) to trilayer (4.56 eV), and then slowly upon further increasing the layer number. Compared to monolayer phosphorene, there is a drastic decrease of hole effective mass along the ridge (zigzag) direction for bilayer phosphorene, indicating a strong interlayer coupling and screening effect. Our study suggests that 1). Few-layer phosphorene with a layer-dependent band gap and a robust direct band gap character is promising for efficient solar energy harvest. 2). Few-layer phosphorene outperforms monolayer counterpart in terms of a lighter carrier effective mass, a higher carrier density and a weaker scattering due to enhanced screening. 3). The layer-dependent band edges and work functions of few-layer phosphorene allow for modification of Schottky barrier with enhanced carrier injection efficiency. It is expected that few-layer phosphorene will present abundant opportunities for a plethora of new electronic applications.

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

    Science.gov (United States)

    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.

  20. Social network types and functional dependency in older adults in Mexico

    Directory of Open Access Journals (Sweden)

    Espinosa-Alarcón Patricia

    2010-02-01

    Full Text Available Abstract Background Social networks play a key role in caring for older adults. A better understanding of the characteristics of different social networks types (TSNs in a given community provides useful information for designing policies to care for this age group. Therefore this study has three objectives: 1 To derive the TSNs among older adults affiliated with the Mexican Institute of Social Security; 2 To describe the main characteristics of the older adults in each TSN, including the instrumental and economic support they receive and their satisfaction with the network; 3 To determine the association between functional dependency and the type of social network. Methods Secondary data analysis of the 2006 Survey of Autonomy and Dependency (N = 3,348. The TSNs were identified using the structural approach and cluster analysis. The association between functional dependency and the TSNs was evaluated with Poisson regression with robust variance analysis in which socio-demographic characteristics, lifestyle and medical history covariates were included. Results We identified five TSNs: diverse with community participation (12.1%, diverse without community participation (44.3%; widowed (32.0%; nonfriends-restricted (7.6%; nonfamily-restricted (4.0%. Older adults belonging to widowed and restricted networks showed a higher proportion of dependency, negative self-rated health and depression. Older adults with functional dependency more likely belonged to a widowed network (adjusted prevalence ratio 1.5; 95%CI: 1.1-2.1. Conclusion The derived TSNs were similar to those described in developed countries. However, we identified the existence of a diverse network without community participation and a widowed network that have not been previously described. These TSNs and restricted networks represent a potential unmet need of social security affiliates.

  1. Temperature-dependent dielectric function of germanium in the UV–vis spectral range: A first-principles study

    International Nuclear Information System (INIS)

    Yang, J.Y.; Liu, L.H.; Tan, J.Y.

    2014-01-01

    The study of temperature dependence of thermophysical parameter dielectric function is key to understanding thermal radiative transfer in high-temperature environments. Limited by self-radiation and thermal oxidation, however, it is difficult to directly measure the high-temperature dielectric function of solids with present experimental technologies. In this work, we implement two first-principles methods, the ab initio molecular dynamics (AIMD) and density functional perturbation theory (DFPT), to study the temperature dependence of dielectric function of germanium (Ge) in the UV–vis spectral range in order to provide data of high-temperature dielectric function for radiative transfer study in high-temperature environments. Both the two methods successfully predict the temperature dependence of dielectric function of Ge. Moreover, the good agreement between the calculated results of the AIMD approach and experimental data at 825 K enables us to predict the high-temperature dielectric function of Ge with the AIMD method in the UV–vis spectral range. - Highlights: • The temperature dependence of dielectric function of germanium (Ge) is investigated with two first-principles methods. • The temperature effect on dielectric function of Ge is discussed. • The high-temperature dielectric function of Ge is predicted

  2. 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.

  3. Biological Fate of Fe3O4 Core-Shell Mesoporous Silica Nanoparticles Depending on Particle Surface Chemistry

    Science.gov (United States)

    Rascol, Estelle; Daurat, Morgane; Da Silva, Afitz; Maynadier, Marie; Dorandeu, Christophe; Charnay, Clarence; Garcia, Marcel; Lai-Kee-Him, Joséphine; Bron, Patrick; Auffan, Mélanie; Angeletti, Bernard; Devoisselle, Jean-Marie; Guari, Yannick; Gary-Bobo, Magali; Chopineau, Joël

    2017-01-01

    The biological fate of nanoparticles (NPs) for biomedical applications is highly dependent of their size and charge, their aggregation state and their surface chemistry. The chemical composition of the NPs surface influences their stability in biological fluids, their interaction with proteins, and their attraction to the cell membranes. In this work, core-shell magnetic mesoporous silica nanoparticles (Fe3O4@MSN), that are considered as potential theranostic candidates, are coated with polyethylene glycol (PEG) or 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipid bilayer. Their biological fate is studied in comparison to the native NPs. The physicochemical properties of these three types of NPs and their suspension behavior in different media are investigated. The attraction to a membrane model is also evaluated using a supported lipid bilayer. The surface composition of NPs strongly influences their dispersion in biological fluids mimics, protein binding and their interaction with cell membrane. While none of these types of NPs is found to be toxic on mice four days after intravenous injection of a dose of 40 mg kg−1 of NPs, their surface coating nature influences the in vivo biodistribution. Importantly, NP coated with DMPC exhibit a strong accumulation in liver and a very low accumulation in lung in comparison with nude or PEG ones. PMID:28665317

  4. [Influence of functional dependence on the case mix in a geriatric unit].

    Science.gov (United States)

    González-Guerrero, José Luis; Alonso-Fernández, Teresa; Gálvez, Noemí; García-Mayolín, Nieves

    2008-01-01

    To determine the influence of pre-admission functional status on the case mix in a geriatric unit, after adjustment by the diagnosis-related groups (DRG) patient classification system. We performed a retrospective observational study in patients admitted to the geriatric unit of a general hospital over a 2-year period. Patients with a length of stay of less than 2 days and transfers from other medical services and hospitals were excluded. The following data were obtained from the minimum data set and from chart review: age, sex, place of residence before admission, Charlson comorbidity index, pre-admission functional status and mobility, cognitive status, length of hospital stay, rate of in-hospital mortality, and the DRG (and DRG weight) for each patient. A total of 1065 patients were included in this study. The mean age was 84 years (64-102), and 64% were women. Patients with lower functional status were more often female (67.1 vs 55.8%; PDRG weight (P=.03). Once the more frequent DRG were reviewed, patients who were dependent had a greater number of respiratory infections and renal problems and had fewer cerebrovascular diseases. Some clinical characteristics differ in patients with functional dependence. This finding could influence the clinical management of medical services that treat more dependent patients.

  5. METHODS OF ASSESSMENT OF THE RELATIVE BIOLOGICAL EFFECTIVENESS OF NEUTRONS IN NEUTRON THERAPY

    Directory of Open Access Journals (Sweden)

    V. A. Lisin

    2017-01-01

    Full Text Available The relative biological effectiveness (RBE of fast neutrons is an important factor influencing the quality of neutron therapy therefore, the assessment of RBE is of great importance. Experimental and clinical studies as well as different mathematical and radiobiological models are used for assessing RBE. Research is conducted for neutron sources differing in the method of producing particles, energy and energy spectrum. Purpose: to find and analyze the dose-dependence of fast neutron RBE in neutron therapy using the U-120 cyclotron and NG-12I generator. Material and methods: The optimal method for assessing the relative biological effectiveness of neutrons for neutron therapy was described. To analyze the dependence of the RBE on neutron dose, the multi-target model of cell survival was applied. Results: The dependence of the RBE of neutrons produced from the U-120 cyclotron and NG-120 generator on the dose level was found for a single irradiation of biological objects. It was shown that the function of neutron dose was consistent with similar dependencies found by other authors in the experimental and clinical studies.

  6. Abnormal intrinsic functional hubs in alcohol dependence: evidence from a voxelwise degree centrality analysis

    Directory of Open Access Journals (Sweden)

    Luo X

    2017-07-01

    Full Text Available Xiaoping Luo,1,2 Linghong Guo,1 Xi-Jian Dai,3 Qinglai Wang,2 Wenzhong Zhu,2 Xinjun Miao,2 Honghan Gong1 1Department of Radiology, The First Affiliated Hospital of Nanchang University, Nangchang, Jiangxi, People’s Republic of China; 2Department of Radiology, Wenzhou Chinese Medicine Hospital, Wenzhou, Zhejiang, People’s Republic of China; 3Department of Medical Imaging, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, People’s Republic of China Objective: To explore the abnormal intrinsic functional hubs in alcohol dependence using voxelwise degree centrality analysis approach, and their relationships with clinical features.Materials and methods: Twenty-four male alcohol dependence subjects free of medicine (mean age, 50.21±9.62 years and 24 age- and education-matched male healthy controls (mean age, 50.29±8.92 years were recruited. The alcohol use disorders identification test and the severity of alcohol dependence questionnaire (SADQ were administered to assess the severity of alcohol craving. Voxelwise degree centrality approach was used to assess the abnormal intrinsic functional hubs features in alcohol dependence. Simple linear regression analysis was performed to investigate the relationships between the clinical features and abnormal intrinsic functional hubs.Results: Compared with healthy controls, alcohol dependence subjects exhibited significantly different degree centrality values in widespread left lateralization brain areas, including higher degree centrality values in the left precentral gyrus (BA 6, right hippocampus (BA 35, 36, and left orbitofrontal cortex (BA 11 and lower degree centrality values in the left cerebellum posterior lobe, bilateral secondary visual network (BA 18, and left precuneus (BA 7, 19. SADQ revealed a negative linear correlation with the degree centrality value in the left precentral gyrus (R2=0.296, P=0.006.Conclusion: The specific abnormal intrinsic functional hubs appear

  7. Predicting kidney graft failure using time-dependent renal function covariates

    NARCIS (Netherlands)

    de Bruijne, Mattheus H. J.; Sijpkens, Yvo W. J.; Paul, Leendert C.; Westendorp, Rudi G. J.; van Houwelingen, Hans C.; Zwinderman, Aeilko H.

    2003-01-01

    Chronic rejection and recurrent disease are the major causes of late graft failure in renal transplantation. To assess outcome, most researchers use Cox proportional hazard analysis with time-fixed covariates. We developed a model adding time-dependent renal function covariates to improve the

  8. Predator-dependent functional response in wolves: from food limitation to surplus killing.

    Science.gov (United States)

    Zimmermann, Barbara; Sand, Håkan; Wabakken, Petter; Liberg, Olof; Andreassen, Harry Peter

    2015-01-01

    The functional response of a predator describes the change in per capita kill rate to changes in prey density. This response can be influenced by predator densities, giving a predator-dependent functional response. In social carnivores which defend a territory, kill rates also depend on the individual energetic requirements of group members and their contribution to the kill rate. This study aims to provide empirical data for the functional response of wolves Canis lupus to the highly managed moose Alces alces population in Scandinavia. We explored prey and predator dependence, and how the functional response relates to the energetic requirements of wolf packs. Winter kill rates of GPS-collared wolves and densities of cervids were estimated for a total of 22 study periods in 15 wolf territories. The adult wolves were identified as the individuals responsible for providing kills to the wolf pack, while pups could be described as inept hunters. The predator-dependent, asymptotic functional response models (i.e. Hassell-Varley type II and Crowley-Martin) performed best among a set of 23 competing linear, asymptotic and sigmoid models. Small wolf packs acquired >3 times as much moose biomass as required to sustain their field metabolic rate (FMR), even at relatively low moose abundances. Large packs (6-9 wolves) acquired less biomass than required in territories with low moose abundance. We suggest the surplus killing by small packs is a result of an optimal foraging strategy to consume only the most nutritious parts of easy accessible prey while avoiding the risk of being detected by humans. Food limitation may have a stabilizing effect on pack size in wolves, as supported by the observed negative relationship between body weight of pups and pack size. © 2014 The Authors. Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society.

  9. 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

  10. 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

  11. 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

  12. 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…

  13. 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.

  14. 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.

  15. Functional near infrared spectroscopy as a potential biological assessment of addiction recovery: preliminary findings.

    Science.gov (United States)

    Dempsey, Jared P; Harris, Kitty S; Shumway, Sterling T; Kimball, Thomas G; Herrera, J Caleb; Dsauza, Cynthia M; Bradshaw, Spencer D

    2015-03-01

    Addiction science has primarily utilized self-report, continued substance use, and relapse factors to explore the process of recovery. However, the entry into successful abstinence substantially reduces our assessment abilities. Advances in neuroscience may be the key to objective understanding, treating, and monitoring long-term success in addiction recovery. To explore functional near infrared spectroscopy (fNIR) as a viable technique in the assessment of addiction-cue reactivity. Specifically, prefrontal cortex (PFC) activation to alcohol cues was explored among formally alcohol-dependent individuals, across varying levels of successful abstinence. The aim of the investigation was to identify patterns of PFC activation change consistent with duration of abstinence. A total of 15 formally alcohol-dependent individuals, with abstinence durations ranging from 1 month to 10 years, viewed alcohol images during fNIR PFC assessment. Participants also subjectively rated the same images for affect and arousal level. Subjective ratings of alcohol cues did not significantly correlate with duration of abstinence. As expected, days of abstinence did not significantly correlate with neutral cue fNIR reactivity. However, for alcohol cues, fNIR results showed increased days of abstinence was associated with decreased activation within the dorsolateral and dorsomedial prefrontal cortex regions. The present results suggest that fNIR may be a viable tool in the assessment of addiction-cue reactivity. RESULTS also support previous findings on the importance of dorsolateral and dorsomedial PFC in alcohol-cue activation. The findings build upon these past results suggesting that fNIR-assessed activation may represent a robust biological marker of successful addiction recovery.

  16. New parametrization for the scale dependent growth function in general relativity

    International Nuclear Information System (INIS)

    Dent, James B.; Dutta, Sourish; Perivolaropoulos, Leandros

    2009-01-01

    We study the scale-dependent evolution of the growth function δ(a,k) of cosmological perturbations in dark energy models based on general relativity. This scale dependence is more prominent on cosmological scales of 100h -1 Mpc or larger. We derive a new scale-dependent parametrization which generalizes the well-known Newtonian approximation result f 0 (a)≡(dlnδ 0 /dlna)=Ω(a) γ (γ=(6/11) for ΛCDM) which is a good approximation on scales less than 50h -1 Mpc. Our generalized parametrization is of the form f(a)=(f 0 (a)/1+ξ(a,k)), where ξ(a,k)=(3H 0 2 Ω 0m )/(ak 2 ). We demonstrate that this parametrization fits the exact result of a full general relativistic evaluation of the growth function up to horizon scales for both ΛCDM and dynamical dark energy. In contrast, the scale independent parametrization does not provide a good fit on scales beyond 5% of the horizon scale (k≅0.01h -1 Mpc).

  17. Molecular mechanisms of temperature-dependent sex determination in the context of ecological developmental biology.

    Science.gov (United States)

    Matsumoto, Yuiko; Crews, David

    2012-05-06

    Temperature-dependent sex determination (TSD) is a prime example of phenotypic plasticity in that gonadal sex is determined by the temperature of the incubating egg. In the red-eared slider turtle (Trachemys scripta), the effect of temperature can be overridden by exogenous ligands, i.e., sex steroid hormones and steroid metabolism enzyme inhibitors, during the temperature-sensitive period (TSP) of development. Precisely how the physical signal of temperature is transduced into a biological signal that ultimately results in sex determination remains unknown. In this review, we discuss the sex determining pathway underlying TSD by focusing on two candidate sex determining genes, Forkhead box protein L2 (FoxL2) and Doublesex mab3- related transcription factor 1 (Dmrt1). They appear to be involved in transducing the environmental temperature signal into a biological signal that subsequently determines gonadal sex. FoxL2 and Dmrt1 exhibit gonad-typical patterns of expression in response to temperature during the TSP in the red-eared slider turtle. Further, the biologically active ligands regulate the expression of FoxL2 and Dmrt1 during development to modify gonad trajectory. The precise regulatory mechanisms of expression of these genes by temperature or exogenous ligands are not clear. However, the environment often influences developmental gene expression by altering the epigenetic status in regulatory regions. Here, we will discuss if the regulation of FoxL2 and Dmrt1 expression by environment is mediated through epigenetic mechanisms during development in species with TSD. Published by Elsevier Ireland Ltd.

  18. Optical properties of Al nanostructures from time dependent density functional theory

    KAUST Repository

    Mokkath, Junais Habeeb; Schwingenschlö gl, Udo

    2016-01-01

    The optical properties of Al nanostructures are investigated by means of time dependent density functional theory, considering chains of varying length and ladders/stripes of varying aspect ratio. The absorption spectra show redshifting

  19. Transverse Momentum Dependent Parton Distribution Functions through SIDIS and Drell-Yan at COMPASS

    CERN Document Server

    AUTHOR|(CDS)2079419; Ramos, Sérgio; Quintans, Catarina

    The spin structure of the nucleon has been studied at the COMPASS experiment at CERN. The Semi-Inclusive Deep Inelastic Scattering (SIDIS) measurements are a powerful tool to access the Parton Distribution Functions (PDFs) and the Transverse Momentum Dependent Parton Distribution Functions (TMD PDFs). The COMPASS polarised target gives the opportunity to measure the azimuthal modulations depending on the spin orientation and the extraction of the transverse spin asymmetries, which are convolutions of TMD PDFs of the nucleon and Fragmentation Functions (FF). The analysis of these data is done in several kinematic bins, which provides a vast input for the theoreticians to extract the TMDs and the FFs and their kinematic dependence. The TMD PDFs are also accessible through the measurement of the Drell-Yan process, in this case the transverse spin asymmetries are convolutions of two TMD PDFs, one corresponding to the annihilating quark from the beam hadron and the other to the annihilating quark from the target h...

  20. Aberrant regional brain activities in alcohol dependence: a functional magnetic resonance imaging study

    Directory of Open Access Journals (Sweden)

    Tu XZ

    2018-03-01

    Full Text Available Xianzhu Tu,1 Juanjuan Wang,2 Xuming Liu,3 Jiyong Zheng4 1Department of Psychiatry, Seventh People’s Hospital of Wenzhou City, Wenzhou, Zhejiang, People’s Republic of China; 2Department of Neurology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People’s Republic of China; 3Department of Radiology, The Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou, Zhejiang, People’s Republic of China; 4Department of Medical Imaging, The Affiliated Huai’an No 1 People’s Hospital of Nanjing Medical University, Huai’an, Jiangsu, People’s Republic of China Objective: Whether moderate alcohol consumption has health benefits remains controversial, but the harmful effects of excessive alcohol consumption on behavior and brain function are well recognized. The aim of this study was to investigate alcohol-induced regional brain activities and their relationships with behavioral factors. Subjects and methods: A total of 29 alcohol-dependent subjects (9 females and 20 males and 29 status-matched healthy controls (11 females and 18 males were recruited. Severity of alcohol dependence questionnaire (SADQ and alcohol use disorders identification test (AUDIT were used to evaluate the severity of alcohol craving. Regional homogeneity (ReHo analysis was used to explore the alcohol-induced regional brain changes. Receiver operating characteristic (ROC curve was used to investigate the ability of regional brain activities to distinguish alcohol-dependent subjects from healthy controls. Pearson correlations were used to investigate the relationships between alcohol-induced ReHo differences and behavioral factors. Results: Alcohol-dependent subjects related to healthy controls showed higher ReHo areas in the right superior frontal gyrus (SFG, bilateral medial frontal gyrus (MFG, left precentral gyrus (PG, bilateral middle temporal gyrus (MTG, and right inferior temporal gyrus (ITG and lower ReHo areas in

  1. Nonlinear signaling on biological networks: The role of stochasticity and spectral clustering

    Science.gov (United States)

    Hernandez-Hernandez, Gonzalo; Myers, Jesse; Alvarez-Lacalle, Enrique; Shiferaw, Yohannes

    2017-03-01

    Signal transduction within biological cells is governed by networks of interacting proteins. Communication between these proteins is mediated by signaling molecules which bind to receptors and induce stochastic transitions between different conformational states. Signaling is typically a cooperative process which requires the occurrence of multiple binding events so that reaction rates have a nonlinear dependence on the amount of signaling molecule. It is this nonlinearity that endows biological signaling networks with robust switchlike properties which are critical to their biological function. In this study we investigate how the properties of these signaling systems depend on the network architecture. Our main result is that these nonlinear networks exhibit bistability where the network activity can switch between states that correspond to a low and high activity level. We show that this bistable regime emerges at a critical coupling strength that is determined by the spectral structure of the network. In particular, the set of nodes that correspond to large components of the leading eigenvector of the adjacency matrix determines the onset of bistability. Above this transition the eigenvectors of the adjacency matrix determine a hierarchy of clusters, defined by its spectral properties, which are activated sequentially with increasing network activity. We argue further that the onset of bistability occurs either continuously or discontinuously depending upon whether the leading eigenvector is localized or delocalized. Finally, we show that at low network coupling stochastic transitions to the active branch are also driven by the set of nodes that contribute more strongly to the leading eigenvector. However, at high coupling, transitions are insensitive to network structure since the network can be activated by stochastic transitions of a few nodes. Thus this work identifies important features of biological signaling networks that may underlie their biological

  2. Probabilistic biological network alignment.

    Science.gov (United States)

    Todor, Andrei; Dobra, Alin; Kahveci, Tamer

    2013-01-01

    Interactions between molecules are probabilistic events. An interaction may or may not happen with some probability, depending on a variety of factors such as the size, abundance, or proximity of the interacting molecules. In this paper, we consider the problem of aligning two biological networks. Unlike existing methods, we allow one of the two networks to contain probabilistic interactions. Allowing interaction probabilities makes the alignment more biologically relevant at the expense of explosive growth in the number of alternative topologies that may arise from different subsets of interactions that take place. We develop a novel method that efficiently and precisely characterizes this massive search space. We represent the topological similarity between pairs of aligned molecules (i.e., proteins) with the help of random variables and compute their expected values. We validate our method showing that, without sacrificing the running time performance, it can produce novel alignments. Our results also demonstrate that our method identifies biologically meaningful mappings under a comprehensive set of criteria used in the literature as well as the statistical coherence measure that we developed to analyze the statistical significance of the similarity of the functions of the aligned protein pairs.

  3. Cardiac structure and function and dependency in the oldest old.

    Science.gov (United States)

    Leibowitz, David; Jacobs, Jeremy M; Stessman-Lande, Irit; Cohen, Aharon; Gilon, Dan; Ein-Mor, Eliana; Stessman, Jochanan

    2011-08-01

    To examine the association between cardiac function and activities of daily living (ADLs) in an age-homogenous, community-dwelling population born in 1920 and 1921. Cross-sectional analysis of a prospective cohort study. Community-dwelling elderly population. Participants were recruited from the Jerusalem Longitudinal Cohort Study, which has followed an age-homogenous cohort of Jerusalem residents born in 1920 and 1921. Four hundred eighty-nine of the participants (228 male, 261 female) from the most recent set of data collection in 2005 and 2006 underwent echocardiography at their place of residence in addition to structured interviews and physical examination. A home-based comprehensive assessment was performed to assess health and functional status, including performance of ADLs. Dependence was defined as needing assistance with one or more basic ADLs. Standard echocardiographic assessment of cardiac structure and function, including ejection fraction (EF) and diastolic function as assessed using early diastolic mitral annular tissue velocity measurements obtained using tissue Doppler, was performed. Of the participants with limitation in at least one ADL, significantly more had low EF (dependence in ADL had higher left ventricular mass index (LVMI) (129.3 vs 119.7 g/m²) and left atrial volume index (LAVI) (41.3 vs 36.7 mL/m²). There were no differences between the groups in percentage of participants with impaired diastolic function or average ratio of early diastolic transmitral flow velocity to early diastolic mitral annular tissue velocity (11.5 vs 11.8; P=.64). In this age-homogenous cohort of the oldest old, high LVMI and LAVI and indices of systolic but not diastolic function as assessed according to Doppler were associated with limitations in ADLs. © 2011, Copyright the Authors. Journal compilation © 2011, The American Geriatrics Society.

  4. Time-dependent effects of ultraviolet and nonthermal atmospheric pressure plasma on the biological activity of titanium

    Science.gov (United States)

    Choi, Sung-Hwan; Jeong, Won-Seok; Cha, Jung-Yul; Lee, Jae-Hoon; Yu, Hyung-Seog; Choi, Eun-Ha; Kim, Kwang-Mahn; Hwang, Chung-Ju

    2016-09-01

    Here, we evaluated time-dependent changes in the effects of ultraviolet (UV) and nonthermal atmospheric pressure plasma (NTAPPJ) on the biological activity of titanium compared with that of untreated titanium. Grade IV machined surface titanium discs (12-mm diameter) were used immediately and stored up to 28 days after 15-min UV or 10-min NTAPPJ treatment. Changes of surface characteristics over time were evaluated using scanning electron microscopy, surface profiling, contact angle analysis, X-ray photoelectron spectroscopy, and surface zeta-potential. Changes in biological activity over time were as determined by analysing bovine serum albumin adsorption, MC3T3-E1 early adhesion and morphometry, and alkaline phosphatase (ALP) activity between groups. We found no differences in the effects of treatment on titanium between UV or NTAPPJ over time; both treatments resulted in changes from negatively charged hydrophobic (bioinert) to positively charged hydrophilic (bioactive) surfaces, allowing enhancement of albumin adsorption, osteoblastic cell attachment, and cytoskeleton development. Although this effect may not be prolonged for promotion of cell adhesion until 4 weeks, the effects were sufficient to maintain ALP activity after 7 days of incubation. This positive effect of UV and NTAPPJ treatment can enhance the biological activity of titanium over time.

  5. 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

  6. 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.

  7. 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

  8. 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

  9. Orientation-dependent backbone-only residue pair scoring functions for fixed backbone protein design

    Directory of Open Access Journals (Sweden)

    Bordner Andrew J

    2010-04-01

    Full Text Available Abstract Background Empirical scoring functions have proven useful in protein structure modeling. Most such scoring functions depend on protein side chain conformations. However, backbone-only scoring functions do not require computationally intensive structure optimization and so are well suited to protein design, which requires fast score evaluation. Furthermore, scoring functions that account for the distinctive relative position and orientation preferences of residue pairs are expected to be more accurate than those that depend only on the separation distance. Results Residue pair scoring functions for fixed backbone protein design were derived using only backbone geometry. Unlike previous studies that used spherical harmonics to fit 2D angular distributions, Gaussian Mixture Models were used to fit the full 3D (position only and 6D (position and orientation distributions of residue pairs. The performance of the 1D (residue separation only, 3D, and 6D scoring functions were compared by their ability to identify correct threading solutions for a non-redundant benchmark set of protein backbone structures. The threading accuracy was found to steadily increase with increasing dimension, with the 6D scoring function achieving the highest accuracy. Furthermore, the 3D and 6D scoring functions were shown to outperform side chain-dependent empirical potentials from three other studies. Next, two computational methods that take advantage of the speed and pairwise form of these new backbone-only scoring functions were investigated. The first is a procedure that exploits available sequence data by averaging scores over threading solutions for homologs. This was evaluated by applying it to the challenging problem of identifying interacting transmembrane alpha-helices and found to further improve prediction accuracy. The second is a protein design method for determining the optimal sequence for a backbone structure by applying Belief Propagation

  10. Cognitive dysfunction and anxious-impulsive personality traits are endophenotypes for drug dependence.

    Science.gov (United States)

    Ersche, Karen D; Turton, Abigail J; Chamberlain, Samuel R; Müller, Ulrich; Bullmore, Edward T; Robbins, Trevor W

    2012-09-01

    Not everyone who takes drugs becomes addicted, but the likelihood of developing drug addiction is greater in people with a family history of drug or alcohol dependence. Relatively little is known about how genetic risk mediates the development of drug dependence. By comparing the phenotypic profile of individuals with and without a family history of addiction, the authors sought to clarify the extent to which cognitive dysfunction and personality traits are shared by family members--and therefore likely to have predated drug dependence--and which aspects are specific to drug-dependent individuals. The authors assessed cognitive function and personality traits associated with drug dependence in stimulant-dependent individuals (N=50), their biological siblings without a history of drug dependence (N=50), and unrelated healthy volunteers (N=50). Cognitive function was significantly impaired in the stimulant-dependent individuals across a range of domains. Deficits in executive function and response control were identified in both the stimulant-dependent individuals and in their non-drug-dependent siblings. Drug-dependent individuals and their siblings also exhibited elevated anxious-impulsive personality traits relative to healthy comparison volunteers. Deficits in executive function and response regulation as well as anxious-impulsive personality traits may represent endophenotypes associated with the risk of developing cocaine or amphetamine dependence. The identification of addiction endophenotypes may be useful in facilitating the rational development of therapeutic and preventive strategies.

  11. A-dependence of structure functions and multiquark clusters in nuclei

    International Nuclear Information System (INIS)

    Kondratyuk, L.; Shmatikov, M.

    1984-01-01

    Assuming existence of 12q-clusters (bags) in nuclei the structure functions of deep inelastic scattering of leptons on nuclei are discussed. Universal momentum distribution of quarks in a multiquark cluster is used with high-momentum component falling exponentially PHIsub(q)sup(2)(k) approximately esup(-k/ksub(0)) with k 0 approximately equal to 50-60 MeV/c. The admixture of 12q-cluster W required for the description of SLAG data increases from 10% for 4 He to 30% for Au. The A-dependence of W agrees well with the A-dependence of cumulative particle spectra

  12. 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.

  13. Dynamics of Gaussian Wigner functions derived from a time-dependent variational principle

    Directory of Open Access Journals (Sweden)

    Jens Aage Poulsen

    2017-11-01

    Full Text Available By using a time-dependent variational principle formulated for Wigner phase-space functions, we obtain the optimal time-evolution for two classes of Gaussian Wigner functions, namely those of either thawed real-valued or frozen but complex Gaussians. It is shown that tunneling effects are approximately included in both schemes.

  14. Communication: Orbital instabilities and triplet states from time-dependent density functional theory and long-range corrected functionals

    Science.gov (United States)

    Sears, John S.; Koerzdoerfer, Thomas; Zhang, Cai-Rong; Brédas, Jean-Luc

    2011-10-01

    Long-range corrected hybrids represent an increasingly popular class of functionals for density functional theory (DFT) that have proven to be very successful for a wide range of chemical applications. In this Communication, we examine the performance of these functionals for time-dependent (TD)DFT descriptions of triplet excited states. Our results reveal that the triplet energies are particularly sensitive to the range-separation parameter; this sensitivity can be traced back to triplet instabilities in the ground state coming from the large effective amounts of Hartree-Fock exchange included in these functionals. As such, the use of standard long-range corrected functionals for the description of triplet states at the TDDFT level is not recommended.

  15. Dependence of the giant dipole strength function on excitation energy

    International Nuclear Information System (INIS)

    Draper, J.E.; Newton, J.O.; Sobotka, L.G.; Lindenberger, H.; Wozniak, G.J.; Moretto, L.G.; Stephens, F.S.; Diamond, R.M.; McDonald, R.J.

    1982-01-01

    Spectra of γ rays associated with deep-inelastic products from the 1150-MeV 136 Xe+ 181 Ta reaction have been measured. The yield of 10--20-MeV γ rays initially increases rapidly with the excitation energy of the products and then more slowly for excitation energies in excess of 120 MeV. Statistical-model calculations with ground-state values of the giant dipole strength function fail to reproduce the shape of the measured γ-ray spectra. This suggests a dependence of the giant dipole strength function on excitation energy

  16. 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

  17. Etymology of transition metal biomolecules as a learning aid in Biological Chemistry

    International Nuclear Information System (INIS)

    Silva, Jose A.L. da

    2013-01-01

    Numerous functional biomolecules are associated with metals, i.e. the metallobiomolecules; more specifically, some are dependent on transition metals required for several crucial biological roles. Nevertheless, their names can lead to ambiguous interpretations concerning the properties and performances of this group of biological molecules. Their etymology may be useful by providing a more perceptive insight into their features. However, etymology can lead to incongruous conclusions, requiring an especially careful approach to prevent errors. Examples illustrating these subjects shall be examined (author)

  18. The spin-dependent structure function g1 of the deuteron

    International Nuclear Information System (INIS)

    Bueltmann, S.

    1996-01-01

    Results on the spin-dependent structure function g 1 d of the deuteron measured by the Spin Muon Collaboration at CERN are presented. They are based on deep-inelastic scattering of 190 GeV polarized muons off a polarized deuteron target in the kinematic range of 0.003 ≤ x Bj ≤ 0.7 and 1 GeV 2 ≤ Q 2 ≤ 60 GeV 2 . The structure function is found to be negative for small values of x Bj , while the proton structure function g 1 p measured earlier by the SMC is positive over the whole x Bj -range. The Bjorken sum rule is in good agreement with the first moments of the structure functions, while the Ellis-Jaffe sum rule is violated by more than three standard deviations for the deuteron measurement. (author)

  19. Synthesis, characterization and functionalization of silicon nanoparticle based hybrid nanomaterials for photovoltaic and biological applications

    Science.gov (United States)

    Xu, Zejing

    Silicon nanoparticles are attractive candidates for biological, photovoltaic and energy storage applications due to their size dependent optoelectronic properties. These include tunable light emission, high brightness, and stability against photo-bleaching relative to organic dyes (see Chapter 1). The preparation and characterization of silicon nanoparticle based hybrid nanomaterials and their relevance to photovoltaic and biological applications are described. The surface-passivated silicon nanoparticles were produced in one step from the reactive high-energy ball milling (RHEBM) of silicon wafers with various organic ligands. The surface structure and optical properties of the passivated silicon nanoparticles were systematically characterized. Fast approaches for purifying and at the same time size separating the silicon nanoparticles using a gravity GPC column were developed. The hydrodynamic diameter and size distribution of these size-separated silicon nanoparticles were determined using GPC and Diffusion Ordered NMR Spectroscopy (DOSY) as fast, reliable alternative approaches to TEM. Water soluble silicon nanoparticles were synthesized by grafting PEG polymers onto functionalized silicon nanoparticles with distal alkyne or azide moieties. The surface-functionalized silicon nanoparticles were produced from the reactive high-energy ball milling (RHEBM) of silicon wafers with a mixture of either 5-chloro-1-pentyne in 1-pentyne or 1,7 octadiyne in 1-hexyne to afford air and water stable chloroalkyl or alkynyl terminated nanoparticles, respectively. Nanoparticles with the ω-chloroalkyl substituents were easily converted to ω-azidoalkyl groups through the reaction of the silicon nanoparticles with sodium azide in DMF. The azido terminated nanoparticles were then grafted with monoalkynyl-PEG polymers using a copper catalyzed alkyne-azide cycloaddition (CuAAC) reaction to afford core-shell silicon nanoparticles with a covalently attached PEG shell. Covalently

  20. An efficient and accurate method to obtain the energy-dependent Green function for general potentials

    International Nuclear Information System (INIS)

    Kramer, T; Heller, E J; Parrott, R E

    2008-01-01

    Time-dependent quantum mechanics provides an intuitive picture of particle propagation in external fields. Semiclassical methods link the classical trajectories of particles with their quantum mechanical propagation. Many analytical results and a variety of numerical methods have been developed to solve the time-dependent Schroedinger equation. The time-dependent methods work for nearly arbitrarily shaped potentials, including sources and sinks via complex-valued potentials. Many quantities are measured at fixed energy, which is seemingly not well suited for a time-dependent formulation. Very few methods exist to obtain the energy-dependent Green function for complicated potentials without resorting to ensemble averages or using certain lead-in arrangements. Here, we demonstrate in detail a time-dependent approach, which can accurately and effectively construct the energy-dependent Green function for very general potentials. The applications of the method are numerous, including chemical, mesoscopic, and atomic physics

  1. Q2 dependence of the spin structure function in the resonance region

    International Nuclear Information System (INIS)

    Li, Z.; Li, Z.

    1994-01-01

    In this paper, we show what we can learn from the CEBAF experiments on spin-structure functions, and the transition from the Drell-Hearn-Gerasimov sum rule in the real photon limit to the spin-dependent sum rules in deep inelastic scattering, and how the asymmetry A 1 (x,Q 2 ) approaches the scaling limit in the resonance region. The spin structure function in the resonance region alone cannot determine the spin-dependent sum rule due to the kinematic restriction of the resonance region. The integral ∫ 0 1 {A 1 (x,Q 2 )F 2 (x,Q 2 )/2x[1+R(x,Q 2 )]}dx is estimated from Q 2 =0--2.5 GeV 2 . The result shows that there is a region where both contributions from the baryon resonances and the deep inelastic scattering are important; thus it provides important information on the high twist effects on the spin-dependent sum rule

  2. Wavelength dependence of the bidirectional reflectance distribution function (BRDF) of beach sands.

    Science.gov (United States)

    Doctor, Katarina Z; Bachmann, Charles M; Gray, Deric J; Montes, Marcos J; Fusina, Robert A

    2015-11-01

    The wavelength dependence of the dominant directional reflective properties of beach sands was demonstrated using principal component analysis and the related correlation matrix. In general, we found that the hyperspectral bidirectional reflectance distribution function (BRDF) of beach sands has weak wavelength dependence. Its BRDF varies slightly in three broad wavelength regions. The variations are more evident in surfaces of greater visual roughness than in smooth surfaces. The weak wavelength dependence of the BRDF of beach sand can be captured using three broad wavelength regions instead of hundreds of individual wavelengths.

  3. The implications of non-linear biological oscillations on human electrophysiology for electrohypersensitivity (EHS) and multiple chemical sensitivity (MCS).

    Science.gov (United States)

    Sage, Cindy

    2015-01-01

    The 'informational content' of Earth's electromagnetic signaling is like a set of operating instructions for human life. These environmental cues are dynamic and involve exquisitely low inputs (intensities) of critical frequencies with which all life on Earth evolved. Circadian and other temporal biological rhythms depend on these fluctuating electromagnetic inputs to direct gene expression, cell communication and metabolism, neural development, brainwave activity, neural synchrony, a diversity of immune functions, sleep and wake cycles, behavior and cognition. Oscillation is also a universal phenomenon, and biological systems of the heart, brain and gut are dependent on the cooperative actions of cells that function according to principles of non-linear, coupled biological oscillations for their synchrony. They are dependent on exquisitely timed cues from the environment at vanishingly small levels. Altered 'informational content' of environmental cues can swamp natural electromagnetic cues and result in dysregulation of normal biological rhythms that direct growth, development, metabolism and repair mechanisms. Pulsed electromagnetic fields (PEMF) and radiofrequency radiation (RFR) can have the devastating biological effects of disrupting homeostasis and desynchronizing normal biological rhythms that maintain health. Non-linear, weak field biological oscillations govern body electrophysiology, organize cell and tissue functions and maintain organ systems. Artificial bioelectrical interference can give false information (disruptive signaling) sufficient to affect critical pacemaker cells (of the heart, gut and brain) and desynchronize functions of these important cells that orchestrate function and maintain health. Chronic physiological stress undermines homeostasis whether it is chemically induced or electromagnetically induced (or both exposures are simultaneous contributors). This can eventually break down adaptive biological responses critical to health

  4. Fluorination of some highly functionalized cycloalkanes: chemoselectivity and substrate dependence.

    Science.gov (United States)

    Remete, Attila Márió; Nonn, Melinda; Fustero, Santos; Haukka, Matti; Fülöp, Ferenc; Kiss, Loránd

    2017-01-01

    A study exploring the chemical behavior of some dihydroxylated β-amino ester stereo- and regioisomers, derived from unsaturated cyclic β-amino acids is described. The nucleophilic fluorinations involving hydroxy-fluorine exchange of some highly functionalized alicyclic diol derivatives have been carried out in view of selective fluorination, investigating substrate dependence, neighboring group assistance and chemodifferentiation.

  5. On the Q2-dependence of quark and diquark fragmentation functions

    International Nuclear Information System (INIS)

    Bartl, A.

    1988-01-01

    The Q 2 -dependence of quark and diquark fragmentation functions is studied by means of evolution equations and compared with the experimental data. Some comments on the evolution of charm quark fragmentation are also presented. 20 refs., 4 figs. (Author)

  6. 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...

  7. Competing failure analysis in phased-mission systems with multiple functional dependence groups

    International Nuclear Information System (INIS)

    Wang, Chaonan; Xing, Liudong; Peng, Rui; Pan, Zhusheng

    2017-01-01

    A phased-mission system (PMS) involves multiple, consecutive, non-overlapping phases of operation. The system structure function and component failure behavior in a PMS can change from phase to phase, posing big challenges to the system reliability analysis. Further complicating the problem is the functional dependence (FDEP) behavior where the failure of certain component(s) causes other component(s) to become unusable or inaccessible or isolated. Previous studies have shown that FDEP can cause competitions between failure propagation and failure isolation in the time domain. While such competing failure effects have been well addressed in single-phase systems, only little work has focused on PMSs with a restrictive assumption that a single FDEP group exists in one phase of the mission. Many practical systems (e.g., computer systems and networks), however may involve multiple FDEP groups during the mission. Moreover, different FDEP groups can be dependent due to sharing some common components; they may appear in a single phase or multiple phases. This paper makes new contributions by modeling and analyzing reliability of PMSs subject to multiple FDEP groups through a Markov chain-based methodology. Propagated failures with both global and selective effects are considered. Four case studies are presented to demonstrate application of the proposed method. - Highlights: • Reliability of phased-mission systems subject to competing failure propagation and isolation effects is modeled. • Multiple independent or dependent functional dependence groups are considered. • Propagated failures with global effects and selective effects are studied. • Four case studies demonstrate generality and application of the proposed Markov-based method.

  8. Fluorination of some highly functionalized cycloalkanes: chemoselectivity and substrate dependence

    Directory of Open Access Journals (Sweden)

    Attila Márió Remete

    2017-11-01

    Full Text Available A study exploring the chemical behavior of some dihydroxylated β-amino ester stereo- and regioisomers, derived from unsaturated cyclic β-amino acids is described. The nucleophilic fluorinations involving hydroxy–fluorine exchange of some highly functionalized alicyclic diol derivatives have been carried out in view of selective fluorination, investigating substrate dependence, neighboring group assistance and chemodifferentiation.

  9. 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

  10. Decay of hollow states in time-dependent density functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Kapoor, Varun; Bauer, Dieter [Institut fuer Physik, Wismarsche Str. 43-45, Universitaet Rostock, Rostock-18051 (Germany)

    2012-07-01

    Hollow or multiply excited states are inaccessible in time dependent density functional theory (TDDFT) using adiabatic Kohn-Sham potentials. We determine the exact Kohn Sham (KS) potential for doubly excited states in an exactly solvable model Helium atom. The exact single-particle density corresponds to the energetically lowest quasi-stationary state in the exact KS potential. We describe how this exact potential controls the decay by a barrier whose origin is traced back to phase of the exact KS orbital. The potential controls the barrier height and width in order for the density to tunnel out and decay with the same rate as the doubly excited state in the ab initio time-dependent Schroedinger calculation. Instead, adiabatic KS potentials only show direct photoionization but no autoionization. A frequency-dependent linear response kernel would be necessary in order to capture the decay of autoionizing states.

  11. A multiwell platform for studying stiffness-dependent cell biology.

    Science.gov (United States)

    Mih, Justin D; Sharif, Asma S; Liu, Fei; Marinkovic, Aleksandar; Symer, Matthew M; Tschumperlin, Daniel J

    2011-01-01

    Adherent cells are typically cultured on rigid substrates that are orders of magnitude stiffer than their tissue of origin. Here, we describe a method to rapidly fabricate 96 and 384 well platforms for routine screening of cells in tissue-relevant stiffness contexts. Briefly, polyacrylamide (PA) hydrogels are cast in glass-bottom plates, functionalized with collagen, and sterilized for cell culture. The Young's modulus of each substrate can be specified from 0.3 to 55 kPa, with collagen surface density held constant over the stiffness range. Using automated fluorescence microscopy, we captured the morphological variations of 7 cell types cultured across a physiological range of stiffness within a 384 well plate. We performed assays of cell number, proliferation, and apoptosis in 96 wells and resolved distinct profiles of cell growth as a function of stiffness among primary and immortalized cell lines. We found that the stiffness-dependent growth of normal human lung fibroblasts is largely invariant with collagen density, and that differences in their accumulation are amplified by increasing serum concentration. Further, we performed a screen of 18 bioactive small molecules and identified compounds with enhanced or reduced effects on soft versus rigid substrates, including blebbistatin, which abolished the suppression of lung fibroblast growth at 1 kPa. The ability to deploy PA gels in multiwell plates for high throughput analysis of cells in tissue-relevant environments opens new opportunities for the discovery of cellular responses that operate in specific stiffness regimes.

  12. A multiwell platform for studying stiffness-dependent cell biology.

    Directory of Open Access Journals (Sweden)

    Justin D Mih

    Full Text Available Adherent cells are typically cultured on rigid substrates that are orders of magnitude stiffer than their tissue of origin. Here, we describe a method to rapidly fabricate 96 and 384 well platforms for routine screening of cells in tissue-relevant stiffness contexts. Briefly, polyacrylamide (PA hydrogels are cast in glass-bottom plates, functionalized with collagen, and sterilized for cell culture. The Young's modulus of each substrate can be specified from 0.3 to 55 kPa, with collagen surface density held constant over the stiffness range. Using automated fluorescence microscopy, we captured the morphological variations of 7 cell types cultured across a physiological range of stiffness within a 384 well plate. We performed assays of cell number, proliferation, and apoptosis in 96 wells and resolved distinct profiles of cell growth as a function of stiffness among primary and immortalized cell lines. We found that the stiffness-dependent growth of normal human lung fibroblasts is largely invariant with collagen density, and that differences in their accumulation are amplified by increasing serum concentration. Further, we performed a screen of 18 bioactive small molecules and identified compounds with enhanced or reduced effects on soft versus rigid substrates, including blebbistatin, which abolished the suppression of lung fibroblast growth at 1 kPa. The ability to deploy PA gels in multiwell plates for high throughput analysis of cells in tissue-relevant environments opens new opportunities for the discovery of cellular responses that operate in specific stiffness regimes.

  13. Radial dependence of biological response of spores of Bacillus subtilis around tracks of heavy ions

    International Nuclear Information System (INIS)

    Facius, R.; Buecker, H.; Reitz, G.; Schaefer, M.

    1978-01-01

    Results on the biological action of heavy cosmic particles from the Biostack I and II experiments had been reported at the two preceeding symposia on microdosimetry. Analysis of these results with respect to spores of Bacillus subtilis indicated that the range of inactivation by a single heavy ion extended to larger impact parameters than to be expected from delta-ray dose only. Improved experimental techniques, as described at the last symposium, were successfully applied for the evaluation of the latest Biostack III experiment during the Apollo-Soyuz Test Project (ASTP). These techniques allowed the determination of the impact parameters with an accuracy of down to +-0.2 μm, which is well below the size of a spore. Results of the ASTP experiment will be presented concerning the physical composition of the radiation field and the biological response of the spores in dependence on the impact parameter. These results confirm the previous findings insofar as inactivation of spores reaches out to about 4-5 μm. This finding will be discussed together with results from other Biostack test objects. Comparative accelerator experiments with Bacillus subtilis spores are presented in an additional paper

  14. Time-dependent density-functional theory in the projector augmented-wave method

    DEFF Research Database (Denmark)

    Walter, Michael; Häkkinen, Hannu; Lehtovaara, Lauri

    2008-01-01

    We present the implementation of the time-dependent density-functional theory both in linear-response and in time-propagation formalisms using the projector augmented-wave method in real-space grids. The two technically very different methods are compared in the linear-response regime where we...

  15. Pulse frequency dependency of photobiomodulation on the bioenergetic functions of human dental pulp stem cells.

    Science.gov (United States)

    Kim, Hong Bae; Baik, Ku Youn; Choung, Pill-Hoon; Chung, Jong Hoon

    2017-11-21

    Photobiomodulation (PBM) therapy contributes to pain relief, wound healing, and tissue regeneration. The pulsed wave (PW) mode has been reported to be more effective than the continuous wave (CW) mode when applying PBM to many biological systems. However, the reason for the higher effectiveness of PW-PBM is poorly understood. Herein, we suggest using delayed luminescence (DL) as a reporter of mitochondrial activity after PBM treatment. DL originates mainly from mitochondrial electron transport chain systems, which produce reactive oxygen species (ROS) and adenosine triphosphate (ATP). The decay time of DL depends on the pulse frequencies of applied light, which correlate with the biological responses of human dental pulp stem cells (hDPSCs). Using a low-power light whose wavelength is 810 nm and energy density is 38 mJ/cm 2 , we find that a 300-Hz pulse frequency prolonged the DL pattern and enhanced alkaline phosphatase activity. In addition, we analyze mitochondrial morphological changes and their volume density and find evidence supporting mitochondrial physiological changes from PBM treatment. Our data suggest a new methodology for determining the effectiveness of PBM and the specific pulse frequency dependency of PBM in the differentiation of hDPSCs.

  16. MLH1 function is context dependent in colorectal cancers.

    Science.gov (United States)

    Jackson, Thomas; Ahmed, Mohamed A H; Seth, Rashmi; Jackson, Darryl; Ilyas, Mohammad

    2011-02-01

    Loss of mismatch repair (MMR) function in sporadic colorectal cancer occurs most commonly because of inactivation of MLH1, and it causes an increase in mutation rate. However, it is uncertain whether loss of MMR alters any other cellular function. The aim of this study was to investigate the role of MMR in regulating cell numbers and apoptosis. MLH1 protein levels were manipulated by (a) cloning and forcibly expressing MLH1 in HCT116 (a cell line with MLH1 mutation) and RKO (a cell line with MLH1 silencing), and (b) knockdown of MLH1 in SW480 (a cell line with normal MMR function). Cell number and apoptotic bodies were measured in standard and 'high stress' (ie, after staurosporine exposure) conditions. Restoration of MLH1 function in HCT116 and RKO resulted in increased cell number (pculture conditions. However, on induction of apoptotic stress, restoration of MLH1 resulted in reduced cell numbers (pcontext dependent: in 'low stress' conditions it may act to inhibit apoptosis, while in 'high stress' conditions it may induce apoptosis. However, within the context of chromosomal instability, the effect of MLH1 on cell numbers is limited.

  17. Multiscale time-dependent density functional theory: Demonstration for plasmons.

    Science.gov (United States)

    Jiang, Jiajian; Abi Mansour, Andrew; Ortoleva, Peter J

    2017-08-07

    Plasmon properties are of significant interest in pure and applied nanoscience. While time-dependent density functional theory (TDDFT) can be used to study plasmons, it becomes impractical for elucidating the effect of size, geometric arrangement, and dimensionality in complex nanosystems. In this study, a new multiscale formalism that addresses this challenge is proposed. This formalism is based on Trotter factorization and the explicit introduction of a coarse-grained (CG) structure function constructed as the Weierstrass transform of the electron wavefunction. This CG structure function is shown to vary on a time scale much longer than that of the latter. A multiscale propagator that coevolves both the CG structure function and the electron wavefunction is shown to bring substantial efficiency over classical propagators used in TDDFT. This efficiency follows from the enhanced numerical stability of the multiscale method and the consequence of larger time steps that can be used in a discrete time evolution. The multiscale algorithm is demonstrated for plasmons in a group of interacting sodium nanoparticles (15-240 atoms), and it achieves improved efficiency over TDDFT without significant loss of accuracy or space-time resolution.

  18. Wave function for harmonically confined electrons in time-dependent electric and magnetostatic fields.

    Science.gov (United States)

    Zhu, Hong-Ming; Chen, Jin-Wang; Pan, Xiao-Yin; Sahni, Viraht

    2014-01-14

    We derive via the interaction "representation" the many-body wave function for harmonically confined electrons in the presence of a magnetostatic field and perturbed by a spatially homogeneous time-dependent electric field-the Generalized Kohn Theorem (GKT) wave function. In the absence of the harmonic confinement - the uniform electron gas - the GKT wave function reduces to the Kohn Theorem wave function. Without the magnetostatic field, the GKT wave function is the Harmonic Potential Theorem wave function. We further prove the validity of the connection between the GKT wave function derived and the system in an accelerated frame of reference. Finally, we provide examples of the application of the GKT wave function.

  19. 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.

  20. Response functions for infinite fermion systems with velocity dependent interactions

    International Nuclear Information System (INIS)

    Garcia-Recio, C.; Salcedo, L.L.; Navarro, J.; Nguyen Van Giai

    1991-01-01

    Response functions of infinite Fermi systems are studied in the framework of the self-consistent Random Phase Approximation. Starting from an effective interaction with velocity and density dependence, or equivalently from a local energy density functional, algebraic expressions for the RPA response function are derived. Simple formulae for the energy-weighted and polarizability sum rules are obtained. The method is illustrated by applications to nuclear matter and liquid 3 He. In nuclear matter, it is shown that existing Skyrme interactions give spin-isospin response functions close to those calculated with finite range interactions. The different renormalization of longitudinal and transverse Coulomb sum rules in nuclear matter is discussed. In 3 He, the low-lying collective spin oscillation can be well described in a wide range of momenta with a Skyrme-type interaction if the relevant Landau parameters are fitted. For the high-lying density oscillation, the introduction of a finite range term in the energy functional improves considerably the agreement with the data. (author) 54 refs., 19 figs., 4 tabs

  1. Inhibitory Synaptic Plasticity - Spike timing dependence and putative network function.

    Directory of Open Access Journals (Sweden)

    Tim P Vogels

    2013-07-01

    Full Text Available While the plasticity of excitatory synaptic connections in the brain has been widely studied, the plasticity of inhibitory connections is much less understood. Here, we present recent experimental and theoretical □ndings concerning the rules of spike timing-dependent inhibitory plasticity and their putative network function. This is a summary of a workshop at the COSYNE conference 2012.

  2. Brain State-dependent Functional Hemispheric Specialization in Men but not in Women

    OpenAIRE

    Mohr, Christine; Michel, Christoph M.; Lantz, Goran; Ortigue, Stephanie; Viaud-Delmon, Isabelle; Landis, Theodor

    2017-01-01

    Hemispheric specialization is reliably demonstrated in patients with unilateral lesions or disconnected hemispheres, but is inconsistent in healthy populations. The reason for this paradox is unclear. We propose that functional hemispheric specialization in healthy participants depends upon functional brain states at stimulus arrival (FBS). Brain activity was recorded from 123 surface electrodes while 22 participants (11 women) performed lateralized lexical decisions (left hemisphere processi...

  3. Empathy, and its relationship with cognitive and emotional functions in alcohol dependency.

    Science.gov (United States)

    Erol, Almila; Akyalcin Kirdok, Asusinem; Zorlu, Nabi; Polat, Serap; Mete, Levent

    2017-04-01

    Empathy can be defined as the ability to understand the other's thoughts and feelings. It contains both cognitive and emotional components. The aim of this study was to investigate the empathy ability of patients with alcohol dependency in association with cognitive and emotional functions, after acute detoxification and during long-term abstinence. Thirty-three alcohol dependent inpatients that completed a detoxification process and stayed abstinent throughout the study, and 33 healthy comparison subjects that matched the patients for age, gender, and education level were included in the study. All the participants were administered the Facial Emotion Identification Test (FEIT), Facial Emotion Discrimination Test (FEDT), Trail Making Test (TMT), Digit Span Test (DST), Auditory Consonant Trigram Test (ACT), and Empathy Quotient Scale (EQS). All the tests were repeated after 3 months of abstinence. At the first evaluation conducted after detoxification, patients performed significantly worse than healthy comparisons in almost all tests. At the second evaluation, which was conducted after 3 months of abstinence, the patients improved significantly in all measures, and no significant differences were detected between the patient and comparison groups. There were significant correlations between the test scores and EQS score. Alcohol dependency has deleterious effects on empathy ability, and cognitive and emotional functions. Those impairments can improve with abstinence. Empathy ability has strong relationships with cognitive and emotional functions.

  4. Hydrodynamic perspective on memory in time-dependent density-functional theory

    International Nuclear Information System (INIS)

    Thiele, M.; Kuemmel, S.

    2009-01-01

    The adiabatic approximation of time-dependent density-functional theory is studied in the context of nonlinear excitations of two-electron singlet systems. We compare the exact time evolution of these systems to the adiabatically exact one obtained from time-dependent Kohn-Sham calculations relying on the exact ground-state exchange-correlation potential. Thus, we can show under which conditions the adiabatic approximation breaks down and memory effects become important. The hydrodynamic formulation of quantum mechanics allows us to interpret these results and relate them to dissipative effects in the Kohn-Sham system. We show how the breakdown of the adiabatic approximation can be inferred from the rate of change of the ground-state noninteracting kinetic energy.

  5. Time-dependent internal density functional theory formalism and Kohn-Sham scheme for self-bound systems

    International Nuclear Information System (INIS)

    Messud, Jeremie

    2009-01-01

    The stationary internal density functional theory (DFT) formalism and Kohn-Sham scheme are generalized to the time-dependent case. It is proven that, in the time-dependent case, the internal properties of a self-bound system (such as an atomic nuclei or a helium droplet) are all defined by the internal one-body density and the initial state. A time-dependent internal Kohn-Sham scheme is set up as a practical way to compute the internal density. The main difference from the traditional DFT formalism and Kohn-Sham scheme is the inclusion of the center-of-mass correlations in the functional.

  6. Time-dependent importance sampling in semiclassical initial value representation calculations for time correlation functions.

    Science.gov (United States)

    Tao, Guohua; Miller, William H

    2011-07-14

    An efficient time-dependent importance sampling method is developed for the Monte Carlo calculation of time correlation functions via the initial value representation (IVR) of semiclassical (SC) theory. A prefactor-free time-dependent sampling function weights the importance of a trajectory based on the magnitude of its contribution to the time correlation function, and global trial moves are used to facilitate the efficient sampling the phase space of initial conditions. The method can be generally applied to sampling rare events efficiently while avoiding being trapped in a local region of the phase space. Results presented in the paper for two system-bath models demonstrate the efficiency of this new importance sampling method for full SC-IVR calculations.

  7. [Functional dependency and falls in elderly living in poverty in Mexico].

    Science.gov (United States)

    Manrique-Espinoza, Betty; Salinas-Rodríguez, Aarón; Moreno-Tamayo, Karla; Téllez-Rojo, Martha M

    2011-01-01

    To determine the prevalence of functional dependency (FD) on Mexican elderly living in extreme poverty conditions and to estimate the association between falls and FD. A survey was conducted with three stages for selection, stratified by type of locality (rural or urban) and nationally representative of the 2006 Oportunidades Program. The target population was composed of individuals 70 years of age and older who were beneficiaries of the Oportunidades Program. A total of 30.9% of the elderly presented FD. The gender stratified logistic regression model resulted in an odds ratio (OR) for women of 1.25 (I.C:1.13-1.39) for the association between the increase in the number of falls and FD and OR=1.12 (I.C:0.97-1.29) for men. Given the vulnerable conditions in which these older adults live, specific interventions need to be implemented to prevent falls in order to reduce the risk of functional dependency.

  8. Regarding the use and misuse of retinal protonated Schiff base photochemistry as a test case for time-dependent density-functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Valsson, Omar [Department of Chemistry and Applied Biosciences, ETH Zurich and Facoltà di Informatica, Instituto di Scienze Computationali, Università della Svizzera italiana, Via Giuseppe Buffi 13, CH-6900 Lugano (Switzerland); Filippi, Claudia, E-mail: c.filippi@utwente.nl [MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands); Casida, Mark E., E-mail: mark.casida@ujf-grenoble.fr [Laboratoire de Chimie Théorique, Département de Chimie Moléculaire (DCM), Institut de Chimie Moléculaire de Grenoble (ICMG), Université Joseph Fourier, Grenoble I, F-3801 Grenoble (France)

    2015-04-14

    The excited-state relaxation of retinal protonated Schiff bases (PSBs) is an important test case for biological applications of time-dependent (TD) density-functional theory (DFT). While well-known shortcomings of approximate TD-DFT might seem discouraging for application to PSB relaxation, progress continues to be made in the development of new functionals and of criteria allowing problematic excitations to be identified within the framework of TD-DFT itself. Furthermore, experimental and theoretical ab initio advances have recently lead to a revised understanding of retinal PSB photochemistry, calling for a reappraisal of the performance of TD-DFT in describing this prototypical photoactive system. Here, we re-investigate the performance of functionals in (TD-)DFT calculations in light of these new benchmark results, which we extend to larger PSB models. We focus on the ability of the functionals to describe primarily the early skeletal relaxation of the chromophore and investigate how far along the out-of-plane pathways these functionals are able to describe the subsequent rotation around formal single and double bonds. Conventional global hybrid and range-separated hybrid functionals are investigated as the presence of Hartree-Fock exchange reduces problems with charge-transfer excitations as determined by the Peach-Benfield-Helgaker-Tozer Λ criterion and by comparison with multi-reference perturbation theory results. While we confirm that most functionals cannot render the complex photobehavior of the retinal PSB, do we also observe that LC-BLYP gives the best description of the initial part of the photoreaction.

  9. RNA and RNP as Building Blocks for Nanotechnology and Synthetic Biology.

    Science.gov (United States)

    Ohno, Hirohisa; Saito, Hirohide

    2016-01-01

    Recent technologies that aimed to elucidate cellular function have revealed essential roles for RNA molecules in living systems. Our knowledge concerning functional and structural information of naturally occurring RNA and RNA-protein (RNP) complexes is increasing rapidly. RNA and RNP interaction motifs are structural units that function as building blocks to constitute variety of complex structures. RNA-central synthetic biology and nanotechnology are constructive approaches that employ the accumulated information and build synthetic RNA (RNP)-based circuits and nanostructures. Here, we describe how to design and construct synthetic RNA (RNP)-based devices and structures at the nanometer-scale for biological and future therapeutic applications. RNA/RNP nanostructures can also be utilized as the molecular scaffold to control the localization or interactions of target molecule(s). Moreover, RNA motifs recognized by RNA-binding proteins can be applied to make protein-responsive translational "switches" that can turn gene expression "on" or "off" depending on the intracellular environment. This "synthetic RNA and RNP world" will expand tools for nanotechnology and synthetic biology. In addition, these reconstructive approaches would lead to a greater understanding of building principle in naturally occurring RNA/RNP molecules and systems. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. The Biology of Neisseria Adhesins

    Directory of Open Access Journals (Sweden)

    Miao-Chiu Hung

    2013-07-01

    Full Text Available Members of the genus Neisseria include pathogens causing important human diseases such as meningitis, septicaemia, gonorrhoea and pelvic inflammatory disease syndrome. Neisseriae are found on the exposed epithelia of the upper respiratory tract and the urogenital tract. Colonisation of these exposed epithelia is dependent on a repertoire of diverse bacterial molecules, extending not only from the surface of the bacteria but also found within the outer membrane. During invasive disease, pathogenic Neisseriae also interact with immune effector cells, vascular endothelia and the meninges. Neisseria adhesion involves the interplay of these multiple surface factors and in this review we discuss the structure and function of these important molecules and the nature of the host cell receptors and mechanisms involved in their recognition. We also describe the current status for recently identified Neisseria adhesins. Understanding the biology of Neisseria adhesins has an impact not only on the development of new vaccines but also in revealing fundamental knowledge about human biology.

  11. An Fc engineering approach that modulates antibody-dependent cytokine release without altering cell-killing functions.

    Science.gov (United States)

    Kinder, Michelle; Greenplate, Allison R; Strohl, William R; Jordan, Robert E; Brezski, Randall J

    2015-01-01

    Cytotoxic therapeutic monoclonal antibodies (mAbs) often mediate target cell-killing by eliciting immune effector functions via Fc region interactions with cellular and humoral components of the immune system. Key functions include antibody-dependent cell-mediated cytotoxicity (ADCC), antibody-dependent cellular phagocytosis (ADCP), and complement-dependent cytotoxicity (CDC). However, there has been increased appreciation that along with cell-killing functions, the induction of antibody-dependent cytokine release (ADCR) can also influence disease microenvironments and therapeutic outcomes. Historically, most Fc engineering approaches have been aimed toward modulating ADCC, ADCP, or CDC. In the present study, we describe an Fc engineering approach that, while not resulting in impaired ADCC or ADCP, profoundly affects ADCR. As such, when peripheral blood mononuclear cells are used as effector cells against mAb-opsonized tumor cells, the described mAb variants elicit a similar profile and quantity of cytokines as IgG1. In contrast, although the variants elicit similar levels of tumor cell-killing as IgG1 with macrophage effector cells, the variants do not elicit macrophage-mediated ADCR against mAb-opsonized tumor cells. This study demonstrates that Fc engineering approaches can be employed to uncouple macrophage-mediated phagocytic and subsequent cell-killing functions from cytokine release.

  12. Protein-polymer nano-machines. Towards synthetic control of biological processes

    Directory of Open Access Journals (Sweden)

    Alexander Cameron

    2004-09-01

    Full Text Available Abstract The exploitation of nature's machinery at length scales below the dimensions of a cell is an exciting challenge for biologists, chemists and physicists, while advances in our understanding of these biological motifs are now providing an opportunity to develop real single molecule devices for technological applications. Single molecule studies are already well advanced and biological molecular motors are being used to guide the design of nano-scale machines. However, controlling the specific functions of these devices in biological systems under changing conditions is difficult. In this review we describe the principles underlying the development of a molecular motor with numerous potential applications in nanotechnology and the use of specific synthetic polymers as prototypic molecular switches for control of the motor function. The molecular motor is a derivative of a TypeI Restriction-Modification (R-M enzyme and the synthetic polymer is drawn from the class of materials that exhibit a temperature-dependent phase transition. The potential exploitation of single molecules as functional devices has been heralded as the dawn of new era in biotechnology and medicine. It is not surprising, therefore, that the efforts of numerous multidisciplinary teams 12. have been focused in attempts to develop these systems. as machines capable of functioning at the low sub-micron and nanometre length-scales 3. However, one of the obstacles for the practical application of single molecule devices is the lack of functional control methods in biological media, under changing conditions. In this review we describe the conceptual basis for a molecular motor (a derivative of a TypeI Restriction-Modification enzyme with numerous potential applications in nanotechnology and the use of specific synthetic polymers as prototypic molecular switches for controlling the motor function 4.

  13. Altered Long- and Short-Range Functional Connectivity in Patients with Betel Quid Dependence: A Resting-State Functional MRI Study

    Directory of Open Access Journals (Sweden)

    Tao Liu

    2016-12-01

    Full Text Available Objective: Addiction is a chronic relapsing brain disease. Brain structural abnormalities may constitute an abnormal neural network that underlies the risk of drug dependence. We hypothesized that individuals with Betel Quid Dependence (BQD have functional connectivity alterations that can be described by long- and short-range functional connectivity density(FCD maps. Methods: We tested this hypothesis using functional magnetic resonance imaging (fMRI data from subjects of the Han ethnic group in Hainan, China. Here, we examined BQD individuals (n = 33 and age-, sex-, and education-matched healthy controls (HCs (n = 32 in a rs-fMRI study to observe FCD alterations associated with the severity of BQD. Results: Compared with HCs, long-range FCD was decreased in the right anterior cingulate cortex (ACC and increased in the left cerebellum posterior lobe (CPL and bilateral inferior parietal lobule (IPL in the BQD group. Short-range FCD was reduced in the right ACC and left dorsolateral prefrontal cortex (dlPFC, and increased in the left CPL. The short-range FCD alteration in the right ACC displayed a negative correlation with the Betel Quid Dependence Scale (BQDS (r=-0.432, P=0.012, and the long-range FCD alteration of left IPL showed a positive correlation with the duration of BQD(r=0.519, P=0.002 in BQD individuals. Conclusions: fMRI revealed differences in long- and short- range FCD in BQD individuals, and these alterations might be due to BQ chewing, BQ dependency, or risk factors for developing BQD.

  14. Multi-configuration time-dependent density-functional theory based on range separation

    DEFF Research Database (Denmark)

    Fromager, E.; Knecht, S.; Jensen, Hans Jørgen Aagaard

    2013-01-01

    Multi-configuration range-separated density-functional theory is extended to the time-dependent regime. An exact variational formulation is derived. The approximation, which consists in combining a long-range Multi-Configuration- Self-Consistent Field (MCSCF) treatment with an adiabatic short...... (srGGA) approximations. As expected, when modeling long-range interactions with the MCSCF model instead of the adiabatic Buijse-Baerends density-matrix functional as recently proposed by Pernal [J. Chem. Phys. 136, 184105 (2012)10.1063/1.4712019], the description of both the 1D doubly-excited state...

  15. Functional p53 in cells contributes to the anticancer effect of the cyclin-dependent kinase inhibitor roscovitine

    Czech Academy of Sciences Publication Activity Database

    Paprskářová, Martina; Kryštof, Vladimír; Jorda, Radek; Džubák, P.; Hajdúch, M.; Wesierska-Gadek, J.; Strnad, Miroslav

    2009-01-01

    Roč. 107, č. 3 (2009), s. 428-437 ISSN 0730-2312 R&D Projects: GA ČR GA204/08/0511 Institutional research plan: CEZ:AV0Z50380511 Keywords : APOPTOSIS * CYCLIN-DEPENDENT KINASE * OLOMOUCINE II * p53 Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.935, year: 2009

  16. Gene coexpression network analysis as a source of functional annotation for rice genes.

    Directory of Open Access Journals (Sweden)

    Kevin L Childs

    Full Text Available With the existence of large publicly available plant gene expression data sets, many groups have undertaken data analyses to construct gene coexpression networks and functionally annotate genes. Often, a large compendium of unrelated or condition-independent expression data is used to construct gene networks. Condition-dependent expression experiments consisting of well-defined conditions/treatments have also been used to create coexpression networks to help examine particular biological processes. Gene networks derived from either condition-dependent or condition-independent data can be difficult to interpret if a large number of genes and connections are present. However, algorithms exist to identify modules of highly connected and biologically relevant genes within coexpression networks. In this study, we have used publicly available rice (Oryza sativa gene expression data to create gene coexpression networks using both condition-dependent and condition-independent data and have identified gene modules within these networks using the Weighted Gene Coexpression Network Analysis method. We compared the number of genes assigned to modules and the biological interpretability of gene coexpression modules to assess the utility of condition-dependent and condition-independent gene coexpression networks. For the purpose of providing functional annotation to rice genes, we found that gene modules identified by coexpression analysis of condition-dependent gene expression experiments to be more useful than gene modules identified by analysis of a condition-independent data set. We have incorporated our results into the MSU Rice Genome Annotation Project database as additional expression-based annotation for 13,537 genes, 2,980 of which lack a functional annotation description. These results provide two new types of functional annotation for our database. Genes in modules are now associated with groups of genes that constitute a collective functional

  17. Fitting a function to time-dependent ensemble averaged data.

    Science.gov (United States)

    Fogelmark, Karl; Lomholt, Michael A; Irbäck, Anders; Ambjörnsson, Tobias

    2018-05-03

    Time-dependent ensemble averages, i.e., trajectory-based averages of some observable, are of importance in many fields of science. A crucial objective when interpreting such data is to fit these averages (for instance, squared displacements) with a function and extract parameters (such as diffusion constants). A commonly overlooked challenge in such function fitting procedures is that fluctuations around mean values, by construction, exhibit temporal correlations. We show that the only available general purpose function fitting methods, correlated chi-square method and the weighted least squares method (which neglects correlation), fail at either robust parameter estimation or accurate error estimation. We remedy this by deriving a new closed-form error estimation formula for weighted least square fitting. The new formula uses the full covariance matrix, i.e., rigorously includes temporal correlations, but is free of the robustness issues, inherent to the correlated chi-square method. We demonstrate its accuracy in four examples of importance in many fields: Brownian motion, damped harmonic oscillation, fractional Brownian motion and continuous time random walks. We also successfully apply our method, weighted least squares including correlation in error estimation (WLS-ICE), to particle tracking data. The WLS-ICE method is applicable to arbitrary fit functions, and we provide a publically available WLS-ICE software.

  18. Sensitivity and uncertainty analysis for functionals of the time-dependent nuclide density field

    International Nuclear Information System (INIS)

    Williams, M.L.; Weisbin, C.R.

    1978-04-01

    An approach to extend the present ORNL sensitivity program to include functionals of the time-dependent nuclide density field is developed. An adjoint equation for the nuclide field was derived previously by using generalized perturbation theory; the present derivation makes use of a variational principle and results in the same equation. The physical significance of this equation is discussed and compared to that of the time-dependent neutron adjoint equation. Computational requirements for determining sensitivity profiles and uncertainties for functionals of the time-dependent nuclide density vector are developed within the framework of the existing FORSS system; in this way the current capability is significantly extended. The development, testing, and use of an adjoint version of the ORIGEN isotope generation and depletion code are documented. Finally, a sample calculation is given which estimates the uncertainty in the plutonium inventory at shutdown of a PWR due to assumed uncertainties in uranium and plutonium cross sections. 8 figures, 4 tables

  19. 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.

  20. Benchmarks for electronically excited states: Time-dependent density functional theory and density functional theory based multireference configuration interaction

    DEFF Research Database (Denmark)

    Silva-Junior, Mario R.; Schreiber, Marko; Sauer, Stephan P. A.

    2008-01-01

    Time-dependent density functional theory (TD-DFT) and DFT-based multireference configuration interaction (DFT/MRCI) calculations are reported for a recently proposed benchmark set of 28 medium-sized organic molecules. Vertical excitation energies, oscillator strengths, and excited-state dipole...

  1. 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.

  2. 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...

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

    Science.gov (United States)

    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).

  4. 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.

  5. Trial function method and exact solutions to the generalized nonlinear Schrödinger equation with time-dependent coefficient

    International Nuclear Information System (INIS)

    Cao Rui; Zhang Jian

    2013-01-01

    In this paper, the trial function method is extended to study the generalized nonlinear Schrödinger equation with time-dependent coefficients. On the basis of a generalized traveling wave transformation and a trial function, we investigate the exact envelope traveling wave solutions of the generalized nonlinear Schrödinger equation with time-dependent coefficients. Taking advantage of solutions to trial function, we successfully obtain exact solutions for the generalized nonlinear Schrödinger equation with time-dependent coefficients under constraint conditions. (general)

  6. Time dependent-density functional theory (TD-DFT) and experimental studies of UV-Visible spectra and cyclic voltammetry for Cu(II) complex with Et2DTC

    Science.gov (United States)

    Valle, Eliana Maira A.; Maltarollo, Vinicius Gonçalves; Almeida, Michell O.; Honorio, Kathia Maria; dos Santos, Mauro Coelho; Cerchiaro, Giselle

    2018-04-01

    In this work, we studied the complexation mode between copper(II) ion and the specific ligand investigated as carriers of metals though biological membranes, diethyldithiocarbamate (Et2DTC). It is important to understand how this occurs because it is an important intracellular chelator with potential therapeutic applications. Theoretical and experimental UV visible studies were performed to investigate the complexation mode between copper and the ligand. Electrochemical studies were also performed to complement the spectroscopic analyses. According to the theoretical calculations, using TD-DFT (Time dependent density functional theory), with B3LYP functional and DGDVZP basis set, implemented in Gaussian 03 package, it was observed that the formation of the complex [Cu(Et2DTC)2] is favorable with higher electron density over the sulfur atoms of the ligand. UV/Vis spectra have a charge transfer band at 450 nm, with the DMSO-d6 band shift from 800 to 650 nm. The electrochemical experiments showed the formation of a new redox process, referring to the complex, where the reduction peak potential of copper is displaced to less positive region. Therefore, the results obtained from this study give important insights on possible mechanisms involved in several biological processes related to the studied system.

  7. Tolerance induction to a thymus-dependent antigen in vitro: treatment of nonadherent cells with tolerogen biologically filtered in vitro

    International Nuclear Information System (INIS)

    Geyer, J.W.; Kong, Y.M.

    1974-01-01

    Highly tolerogenic bovine gamma globulin (BGG), a thymus-dependent antigen, was prepared by biologic filtration in vitro. It readily induced tolerance in vivo in BALB/c mice and also rendered their nonadherent lymph node cells tolerant after in vitro incubation. Biologic filtration in vitro was carried out by incubating 2.5 x 10 7 lymph node cells with 10 mg of nontolerogenic BGG in 10 ml of Eagle's medium containing 2 percent normal mouse serum at 37 0 C for 6 hr. The BGG-containing medium was clarified by centrifugation and was used without further dilution. For tolerance induction in vitro, lymph node cells were separated into adherent and nonadherent populations on Falcon plastic. These cells were incubated for 0 to 18 hr at 37 0 C with biologically filtered BGG (bBGG). After incubation, the cells were washed three times and (2 to 2.5) x 10 7 nonadherent or 4 x 10 6 adherent cells were injected iv with their untreated counterpart into lethally irradiated mice which had received 10 6 bone marrow cells. The recipients were then challenged with 300 μg of aggregated BGG, and tolerance was assayed by the elimination of labeled BGG, rosette formation, and passive hemagglutination. Spleen cells were similarly treated for comparison. Our findings show that tolerance was not induced in vitro in adherent lymph node cells. However, in the nonadherent populations, those from the lymph node but not the spleen were rendered tolerant. The acquisition of tolerance in vitro was gradual. It was dependent upon the length of exposure to bBGG and required at least 6 hr

  8. DPP4 inhibitors promote biological functions of human endothelial progenitor cells by targeting the SDF-1/CXCR4 signaling pathway

    Directory of Open Access Journals (Sweden)

    Liu Feng

    2016-01-01

    Full Text Available Dipeptidyl peptidase 4 (DPP4 inhibitors(oral hypoglycemic agentshave beneficial effects during the early stages of diabetes. In this study, we evaluated the role of DPP4inhibitorsonthe biological functions of cultured human endothelial progenitor cells (EPCs. After treating EPCs with the DPP4 inhibitors sitagliptin and vildagliptin, we examined the mRNA expression of DPP4, vascular endothelial growth factor (VEGF,VEGF receptor 2 (VEGFR-2,endothelial nitric oxide synthase (eNOS, caspase-3,stromal cell-derived factor-1 (SDF-1, chemokine (C-X-C motif receptor 4 (CXCR4 were measured by RT-PCR. The protein expression of SDF-1 and CXCR4 was determined by Western blot; cell proliferation was tested by the MTT method, and DPP4 activity was determined by a DPP4 assay. Our results revealed that DPP4 expression and activity were inhibited following the treatment with various doses of DPP4 inhibitors. Cell proliferation and the expression of VEGF, VEGFR-2andeNOS were up regulated, while cell apoptosis was inhibited by DPP4 inhibitors in a dose-dependent manner. DPP4 inhibitors activated the SDF-1/CXCR4 signaling pathway, shown by the elevated expression of SDF-1/CXCR4. This further proved that after the SDF-1/CXCR4 signaling pathway was blocked by its inhibitor ADM3100, the effects of DPP4 inhibitors on the proliferation and apoptosis, and the expression of VEGF, VEGFR-2and eNOS of EPCs were significantly reduced. These findings suggest that DPP4 inhibitors promote the biological functions of human EPCs by up regulating the SDF-1/CXCR4 signaling pathway.

  9. Time-dependent density functional theory for open quantum systems with unitary propagation.

    Science.gov (United States)

    Yuen-Zhou, Joel; Tempel, David G; Rodríguez-Rosario, César A; Aspuru-Guzik, Alán

    2010-01-29

    We extend the Runge-Gross theorem for a very general class of open quantum systems under weak assumptions about the nature of the bath and its coupling to the system. We show that for Kohn-Sham (KS) time-dependent density functional theory, it is possible to rigorously include the effects of the environment within a bath functional in the KS potential. A Markovian bath functional inspired by the theory of nonlinear Schrödinger equations is suggested, which can be readily implemented in currently existing real-time codes. Finally, calculations on a helium model system are presented.

  10. Nanomechanical strength mechanisms of hierarchical biological materials and tissues.

    Science.gov (United States)

    Buehler, Markus J; Ackbarow, Theodor

    2008-12-01

    Biological protein materials (BPMs), intriguing hierarchical structures formed by assembly of chemical building blocks, are crucial for critical functions of life. The structural details of BPMs are fascinating: They represent a combination of universally found motifs such as alpha-helices or beta-sheets with highly adapted protein structures such as cytoskeletal networks or spider silk nanocomposites. BPMs combine properties like strength and robustness, self-healing ability, adaptability, changeability, evolvability and others into multi-functional materials at a level unmatched in synthetic materials. The ability to achieve these properties depends critically on the particular traits of these materials, first and foremost their hierarchical architecture and seamless integration of material and structure, from nano to macro. Here, we provide a brief review of this field and outline new research directions, along with a review of recent research results in the development of structure-property relationships of biological protein materials exemplified in a study of vimentin intermediate filaments.

  11. 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.

  12. 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

  13. Non-dipolar gauge links for transverse-momentum-dependent pion wave functions

    International Nuclear Information System (INIS)

    Wang, Y.M.

    2016-01-01

    I discuss the factorization-compatible definitions of transverse-momentum-dependent (TMD) pion wave functions which are fundamental theory inputs entering QCD factorization formulae for many hard exclusive processes. I will first demonstrate that the soft subtraction factor introduced to remove both rapidity and pinch singularities can be greatly reduced by making the maximal use of the freedom to construct the Wilson-line paths when defining the TMD wave functions. I will then turn to show that the newly proposed TMD definition with non-dipolar Wilson lines is equivalent to the one with dipolar gauge links and with a complicated soft function, to all orders of the perturbative expansion in the strong coupling, as far as the infrared behavior is concerned. (author)

  14. Trait-Dependent Biogeography: (Re)Integrating Biology into Probabilistic Historical Biogeographical Models.

    Science.gov (United States)

    Sukumaran, Jeet; Knowles, L Lacey

    2018-04-20

    The development of process-based probabilistic models for historical biogeography has transformed the field by grounding it in modern statistical hypothesis testing. However, most of these models abstract away biological differences, reducing species to interchangeable lineages. We present here the case for reintegration of biology into probabilistic historical biogeographical models, allowing a broader range of questions about biogeographical processes beyond ancestral range estimation or simple correlation between a trait and a distribution pattern, as well as allowing us to assess how inferences about ancestral ranges themselves might be impacted by differential biological traits. We show how new approaches to inference might cope with the computational challenges resulting from the increased complexity of these trait-based historical biogeographical models. Copyright © 2018 Elsevier Ltd. All rights reserved.

  15. 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

  16. [Biological function of trophology and the pathogenesis of metabolic syndrome--syndrome of overeating. Phylogenetically theory of general pathology, role of leptin and adiponectin].

    Science.gov (United States)

    Titov, V N

    2014-01-01

    Metabolic syndrome (overeating) is a phylogenetically-determined succession of symptoms with the same pathogenesis. There is only one etiological factor, namely, increased consumption of physiologically optimal food. Enterocytes and omental fat cells are a phylogenetically early paracrine-regulated cell community that realizes the biological reactions of exo- and endotrophy. Visceral obesity, high levels of unesterified fatty acids (FA), formation of a pool of micellar FA in the blood, integration of these FA into endothelial cell plasma membrane and enlargement of adipocytes are the causes of hydrodynamic pressure elevation. Toll-like receptors recognize the associates between albumin and greater than physiological number of FA as "foreing" and initiate inflammatory response. "Endoplasm stress" develops in lipid-overloaded cells, protein synthesis (folding) in them is impaired and apoptosis-like cell death is activated. Visceral fat is a phylogenetically early depot of FA to fulfill the biological function of homeostasis, trophology, endoecology and adaptation; it is regulated at the level of paracrine communities and is anatomically limited. The subcutaneous fat depot fulfills the phylogenetically late function of locomotion; the depot size is not anatomically limited. Visceral fat cells have no receptors for phylogenetically late insulin (INS); specialized adipocyes bearing INS and GLUT4 receptors are cells that form the subcutaneous depot. These cells are regulated by phylogenetically late humoral factors at the entire body level. Leptin is an initiator of humoral hypothalamic regulation of in vivo number of ontogenetically programmed number of visceral INS-insensitive fat cells. It prevents "endoplasm stress" and apoptosis, being designed to regulate the amount of consumed food. Leptin initiates storage of FA from visceral pool into subcutaneous pool. Adiponectin is a phylogenetically late humoral hypothalamic regulatory factor that controls optimal number of

  17. 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…

  18. 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...

  19. 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.

  20. [The contributing risk factors, prevention and treatment of functional dependence among the oldest-old and elderly subjects].

    Science.gov (United States)

    Liu, Dianrong; Tan, Jiping; Guo, Yuhe; Ye, Guanghua; Zhu, Linqi; Zhang, Jun; Li, Yinghao; Deng, Yucheng; Wang, Guichen; Wang, Luning

    2014-10-01

    To compare the risk factors on the functional dependence between the oldest-old and elderly veterans. A cross-sectional survey was conducted among veterans ( ≥ 60 years of age) lived in 44 veterans' communities in Beijing. The socio-demographic information and history of non-communicable chronic diseases were collected via face-to-face interviews, and the functional status was assessed by the 20-item version of the Activities of Daily Living Scale. The risk factors associated with increased hazard of the functional dependence in the oldest-old ( ≥ 80 years old) were cognitive impairment, extrapyramidal diseases, cerebral infarction, transient ischemic attack, sleep disorders, hypnotics, osteoarthrosis, hypertension and fall with the odds ratio (OR) of 1.241-2.962 (all P fall, cardiovascular diseases, osteoarthrosis and hearing loss were the risk factors for that in the elderly subjects (aged 60-79 years). The OR was 1.232-5.790 (all P risk of functional dependence in both the oldest-old and elderly people. Neuropsychiatric disorders are the leading causes contributed to the functional dependence among oldest-old and elderly population. Neurodegenerative diseases in the oldest-old, stroke and depression in elderly people should be the priorities in ameliorating disability. Healthy lifestyle and avocational activities could improve the functional status of the oldest-old and elderly population.

  1. 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.

  2. 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.

  3. 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.

  4. Green's function method with consideration of temperature dependent material properties for fatigue monitoring of nuclear power plants

    International Nuclear Information System (INIS)

    Koo, Gyeong-Hoi; Kwon, Jong-Jooh; Kim, Wanjae

    2009-01-01

    In this paper, a method to consider temperature dependent material properties when using the Green's function method is proposed by using a numerical weight function approach. This is verified by using detailed finite element analyses for a pressurizer spray nozzle with various assumed thermal transient load cases. From the results, it is found that the temperature dependent material properties can significantly affect the maximum peak stresses and the proposed method can resolve this problem with the weight function approach. Finally, it is concluded that the temperature dependency of the material properties affects the maximum stress ranges for a fatigue evaluation. Therefore, it is necessary to consider this effect to monitor fatigue damage when using a Green's function method for the real operating conditions in a nuclear power plant

  5. Relationship Between Functional Mobility and Balance and Dependency in Activity of Daily Living in Elderly After “Hip Arthroplasty”

    Directory of Open Access Journals (Sweden)

    Gholam Hassan Mirzaie

    2013-01-01

    Full Text Available Objectives: The purpose of this study was to investigate correlation between functional mobility with balance and dependency in activity of daily living in elderly after “hip arthroplasty” (HA and its comparison with healthy subjects. Methods & Materials: The current cross-sectional study was done on 15 patients with age mean and standard deviation (72±9.6 with hip osteoarthritis 6 months after “hip arthroplasty” (HA and 15 healthy subjects with age mean and standard deviation (72.7±1.4 as control group. Patient group was assigned with non- probability convenient sampling and control group selected with matched assignment. Functional mobility measured with Timed Up & Go Test (TUG, functional balance with Functional Reach (FR and Berg Balance Scale (BBS and dependency in activity of daily living measured with Modified Barthel Index (MBI. Pearsons correlation coefficient used for stastistical analysis. Results: Results of this study indicated significantly and stronge correlation between functional mobility and balance and dependency in activity of daily living in patient group (r>0.50. Also medium correlation existed between functional mobility and balance with dependency in activity of daily living in control group (r>0.30. Conclusion: Functional mobility and balance and dependency in activity of daily living in the elderly who had HA showed significant positive correlation. In addition correlation between functional mobility and balance and dependency in activity of daily living in patient group is better and higher than healthy group.

  6. 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.

  7. Edaphic macrofauna as biological indicator of the conservation/disturbance status of soil. Results obtained in Cuba

    International Nuclear Information System (INIS)

    Cabrera, Grisel

    2012-01-01

    In order to predict the degradation status of a soil, a group of variables comprising its physical, chemical and/or biological properties is used. Macrofauna, which includes soil invertebrates higher than 2 mm of diameter, is a biological component that can be used for such purpose. Its taxonomic richness as well as its density, biomass and functional composition change depending on the effect of diverse land uses and managements. This review reaffirms that the macrofauna characteristics and the results obtained, mainly in Cuba, about its variation in ecosystems with different anthropization levels, support the potential use of this fauna as biological indicator of the soil's conservation status. Future studies should consider a lower taxonomic level in the identification of macrofauna, and relate its taxonomic and functional composition to the climate and pedological factors. (author)

  8. Calculation and applications of the frequency dependent neutron detector response functions

    International Nuclear Information System (INIS)

    Van Dam, H.; Van Hagen, T.H.J.J. der; Hoogenboom, J.E.; Keijzer, J.

    1994-01-01

    The theoretical basis is presented for the evaluation of the frequency dependent function that enables to calculate the response of a neutron detector to parametric fluctuations ('noise') or oscillations in reactor core. This function describes the 'field view' of a detector and can be calculated with a static transport code under certain conditions which are discussed. Two applications are presented: the response of an ex-core detector to void fraction fluctuations in a BWR and of both in and ex-core detectors to a rotating neutron absorber near or inside a research reactor core. (authors). 7 refs., 4 figs

  9. Alterations in Brain Structure and Functional Connectivity in Alcohol Dependent Patients and Possible Association with Impulsivity.

    Science.gov (United States)

    Wang, Junkai; Fan, Yunli; Dong, Yue; Ma, Mengying; Ma, Yi; Dong, Yuru; Niu, Yajuan; Jiang, Yin; Wang, Hong; Wang, Zhiyan; Wu, Liuzhen; Sun, Hongqiang; Cui, Cailian

    2016-01-01

    Previous studies have documented that heightened impulsivity likely contributes to the development and maintenance of alcohol use disorders. However, there is still a lack of studies that comprehensively detected the brain changes associated with abnormal impulsivity in alcohol addicts. This study was designed to investigate the alterations in brain structure and functional connectivity associated with abnormal impulsivity in alcohol dependent patients. Brain structural and functional magnetic resonance imaging data as well as impulsive behavior data were collected from 20 alcohol dependent patients and 20 age- and sex-matched healthy controls respectively. Voxel-based morphometry was used to investigate the differences of grey matter volume, and tract-based spatial statistics was used to detect abnormal white matter regions between alcohol dependent patients and healthy controls. The alterations in resting-state functional connectivity in alcohol dependent patients were examined using selected brain areas with gray matter deficits as seed regions. Compared with healthy controls, alcohol dependent patients had significantly reduced gray matter volume in the mesocorticolimbic system including the dorsal posterior cingulate cortex, the dorsal anterior cingulate cortex, the medial prefrontal cortex, the orbitofrontal cortex and the putamen, decreased fractional anisotropy in the regions connecting the damaged grey matter areas driven by higher radial diffusivity value in the same areas and decreased resting-state functional connectivity within the reward network. Moreover, the gray matter volume of the left medial prefrontal cortex exhibited negative correlations with various impulse indices. These findings suggest that chronic alcohol dependence could cause a complex neural changes linked to abnormal impulsivity.

  10. WE-H-BRA-05: Investigation of LET Spectral Dependence of the Biological Effects of Therapeutic Protons

    Energy Technology Data Exchange (ETDEWEB)

    Guan, F; Bronk, L; Kerr, M; Wang, X; Li, Y; Peeler, C; Sahoo, N; Patel, D; Mirkovic, D; Titt, U; Grosshans, D; Mohan, R [UT MD Anderson Cancer Center, Houston, TX (United States)

    2016-06-15

    Purpose: To investigate the dependence of biologic effect (BE) of therapeutic protons on LET spectra by comparing BEs with equal dose-averaged LET (LETd) derived from different LET spectra using high-throughput in vitro clonogenic survival assays. Methods: We used Geant4 to design the relevant experimental setups and perform the dose, LETd, and LET spectra calculations for spot-scanning protons. The clonogenic assay was performed using the H460 lung cancer cell line cultured in 96-well plates. In the first experimental setup (S1), cells were irradiated using 127.4 MeV protons with a 93.22 mm Lucite buildup resulting in a LETd value of 3.4 keV/µm in the cell layer. In the second experimental setup (S2), cells were irradiated by a combination of 127.4 MeV and 136.4 MeV protons with a 96.61 mm Lucite buildup. The LETd values in the cell layer were 11.4 keV/µm and 1.5 keV/µm respectively, but an average LETd of 3.4 keV/µm was obtained by adjusting the relative fluence of each beam. Ten discrete dose levels with 0.5 Gy increments were delivered. Results: In the two setups, the energies or LET spectra were different but resulted in identical LETd values. We quantified the dose contributions from high-LET (≥10 keV/µm, threshold determined by previous experiments) events in the LET spectra separately for these two setups as 3.2% and 10.5%. The biologic effects at each identical dose level yielded statistically significant different survival curves (extra sum-of-squares F-test, P<0.0001). The second setup with a higher contribution from high-LET events exhibited the higher biologic effect with a dose enhancement factor of 1.17±0.03 at 0.10 surviving fraction. Conclusion: The dose-averaged LET may not be an accurate indicator of the biological effects of protons. Detailed LET spectra may need to be considered explicitly to accurately quantify the biologic effects of protons. Funding Support: U19 CA021239-35, R21 CA187484-01 and MDACC-IRG.

  11. Biological intercomparison using gut crypt survivals for proton and carbon ions

    International Nuclear Information System (INIS)

    Uzawa, Akiko; Ando, Koichi; Furusawa, Yoshiya

    2006-01-01

    Charged particle therapy depends on biological information for the dose prescription. Relative biological effectiveness or relative biological effectiveness (RBE) for this requirement could basically be provided by experimental data. As RBE values of protons and carbon ions depend on several factors such as cell/tissue type, endpoint, dose and fractionation schedule, a single RBE value could not function as a master key to open all rooms filled with guests of different radiosensitivities. However, any biological model with accurate reproducibility is useful for comparing biological effectiveness between different facilities. We used mouse gut crypt survivals as endpoint, and compared the cell killing efficiency of proton beams at three Japanese facilities. Three Linac X-ray machines with 4 and 6 MeV were used as reference beams, and there was only a small variation (coefficient of variance <2%) in biological effectiveness among them. The RBE values of protons relative to Linac X-rays ranged from 1.0 to 1.11 at the middle of a 6-cm SOBP (spread-out Bragg peak) and from 0.96 to 1.01 at the entrance plateau. The coefficient of variance for protons ranged between 4.0 and 5.1%. The biological comparison of carbon ions showed fairly good agreement in that the difference in biological effectiveness between National Institute of Radiological Sciences (NIRS)/Heavy Ion Medical Accelerator in Chiba (HIMAC) and Gesellschaft fur Schwerionenforschung (GSI)/Heavy Ion Synchrotron (SIS) was 1% for three positions within the 6-cm SOBP. The coefficient of variance was <1.7, <0.6 and <1.6% for proximal, middle and distal SOBP, respectively. We conclude that the inter-institutional variation of biological effectiveness is smaller for carbon ions than protons, and that beam-spreading methods of carbon ions do not critically influence gut crypt survival. (author)

  12. 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.

  13. Signals for transversity and transverse-momentum-dependent quark distribution functions studied at the HERMES experiment

    Energy Technology Data Exchange (ETDEWEB)

    Diefenthaler, Markus

    2010-08-15

    Intention of the present thesis was the study of transverse-momentum dependent quark distribution functions. In the focus stood the Fourier analysis of azimutal single-spin asymmetries of pions and charged kaons performed within the HERMES experiment. These asymmetries were reconstructed from deep-inelastic scattering events on a transversely polarized proton target and decomposed in Fourier components. In the framework of quantum chromodynamics such components can be interpreted as folding of quark distribution and fragmentation functions. By the analysis of the transverse-momentum dependent quark distribution functions the study of spin-orbit correlations in the internal of the nucleon was made possible. By this conclusions on the orbital angular momentum of the quarks can be drawn. The extracted Fourier components extend the hitherto available informations on the transverse-momentum dependent quark distribution functions remarkably. The presented Fourier analysis made not only a detection of the Collins and Sivers effects possible, but beyond the extraction of the signals of the pretzelosity and worm-gear distributions. The so obtained results will conclusively contribute to the understanding of future measurements in this field and furthermore make possible a test of fundamental predictions of quantum chromodynamics.

  14. 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

  15. First-Principles Momentum-Dependent Local Ansatz Wavefunction and Momentum Distribution Function Bands of Iron

    Science.gov (United States)

    Kakehashi, Yoshiro; Chandra, Sumal

    2016-04-01

    We have developed a first-principles local ansatz wavefunction approach with momentum-dependent variational parameters on the basis of the tight-binding LDA+U Hamiltonian. The theory goes beyond the first-principles Gutzwiller approach and quantitatively describes correlated electron systems. Using the theory, we find that the momentum distribution function (MDF) bands of paramagnetic bcc Fe along high-symmetry lines show a large deviation from the Fermi-Dirac function for the d electrons with eg symmetry and yield the momentum-dependent mass enhancement factors. The calculated average mass enhancement m*/m = 1.65 is consistent with low-temperature specific heat data as well as recent angle-resolved photoemission spectroscopy (ARPES) data.

  16. 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.

  17. Profile of Executive and Memory Function Associated with Amphetamine and Opiate Dependence

    Science.gov (United States)

    Ersche, Karen D; Clark, Luke; London, Mervyn; Robbins, Trevor W; Sahakian, Barbara J

    2007-01-01

    Cognitive function was assessed in chronic drug users on neurocognitive measures of executive and memory function. Current amphetamine users were contrasted with current opiate users, and these two groups were compared with former users of these substances (abstinent for at least one year). Four groups of participants were recruited: amphetamine-dependent individuals, opiate-dependent individuals, former users of amphetamines, and/or opiates and healthy non-drug taking controls. Participants were administered the Tower of London (TOL) planning task and the 3D-IDED attentional set-shifting task to assess executive function, and Paired Associates Learning and Delayed Pattern Recognition Memory tasks to assess visual memory function. The three groups of substance users showed significant impairments on TOL planning, Pattern Recognition Memory and Paired Associates Learning. Current amphetamine users displayed a greater degree of impairment than current opiate users. Consistent with previous research showing that healthy men are performing better on visuo-spatial tests than women, our male controls remembered significantly more paired associates than their female counterparts. This relationship was reversed in drug users. While performance of female drug users was normal, male drug users showed significant impairment compared to both their female counterparts and male controls. There was no difference in performance between current and former drug users. Neither years of drug abuse nor years of drug abstinence were associated with performance. Chronic drug users display pronounced neuropsychological impairment in the domains of executive and memory function. Impairment persists after several years of drug abstinence and may reflect neuropathology in frontal and temporal cortices. PMID:16160707

  18. 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.

  19. 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.

  20. Sex Dependence of Cognitive Functions in Bipolar Disorder

    Directory of Open Access Journals (Sweden)

    Aleksandra Suwalska

    2014-01-01

    Full Text Available The objective of the present study was to assess the performance of lithium treated euthymic bipolar patients in tests measuring spatial working memory (SWM, planning, and verbal fluency and to delineate the influence of gender on cognitive functioning. Fifty-nine euthymic bipolar patients, treated with lithium carbonate for at least 5 yr, were studied. Patients and controls underwent a neuropsychological assessment. Bipolar patients had significantly worse results than the healthy controls in the spatial memory and planning as well as verbal fluency tests. We detected a gender-related imbalance in the SWM results. Deficits in SWM were observed in male-only comparisons but not in female-only comparisons. The SWM scores were significantly poorer in male patients than in male controls. In female-only comparisons, female patients did not have significantly poorer SWM results in any category than their controls. Bipolar women scored worse in some other tests. The present study points to the different patterns of neuropsychological disturbances in female and male patients and suggests that sex-dependent differences should be taken into account in order to tailor the therapeutic intervention aimed at the improvement of cognitive functions.

  1. Reproductive function and biological dosimetry prospective study of young thyroid differentiated cancer patients treated with I-131

    International Nuclear Information System (INIS)

    Di Giorgio, M.; Vallerga, M.B.; Taja, M.R.; Radl, A.; Chebel, Graciela; Fadel, Ana Maria; Gutierrez, Silvia; Normandi, Eduardo; Levalle, Oscar; Kundt, Miriam

    2011-01-01

    The administration of I-131 in the management of differentiated thyroid cancer (DTC) is a well established practice. As the spermatogonia is highly sensitive to radiation, large doses of internal radiation could result in adverse effects on reproductive function such as oligo/azoospermia and infertility. During spermiogenesis, mammalian chromatin undergoes replacement of nuclear histones by protamines, which yields a DNA sixfold more highly condensed in spermatozoa than in mitotic chromosomes. The structure of this highly packaged chromatin shows a low binding capacity for several fluorochromes and dyes such as chromomycin A3 (CMA3). The aim of this study is to assess the correlation between reproductive function (endocrine and exocrine testicular function, and levels of CMA3 stainability) and biological dosimetry in a prospective study of 4 young DTC patients treated with I-131. In this context, a background level of CMA3 binding in mature human sperm was established. It revealed a variable accessibility of CMA3 to the DNA that is dependant on packaging quality and thus, indicative of protamine deficiency. The identification of altered stainability suggests DNA damage as well as epigenetic effects, which may be indicators of male infertility. Transient impairment of spermatogenesis associated with an increase in FSH, an altered spermiogram and even azoospermia was observed after the administration of cumulative activities. Overall, testosterone levels were preserved, except in one case, which presented a drastically diminished value associated with an increase in LH level. As peripheral blood lymphocytes and spermatogonia have equivalent radiosensitivity (interphase death) we hypothesize that the knowledge of DNA damage recovery in peripheral lymphocytes could correlate with spermatogonia recovery and with FSH evolution. (authors)

  2. Coherent states for the time dependent harmonic oscillator: the step function

    International Nuclear Information System (INIS)

    Moya-Cessa, Hector; Fernandez Guasti, Manuel

    2003-01-01

    We study the time evolution for the quantum harmonic oscillator subjected to a sudden change of frequency. It is based on an approximate analytic solution to the time dependent Ermakov equation for a step function. This approach allows for a continuous treatment that differs from former studies that involve the matching of two time independent solutions at the time when the step occurs

  3. 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)

  4. Radiation physics, biophysics, and radiation biology

    International Nuclear Information System (INIS)

    Hall, E.J.

    1992-05-01

    The following research programs from the Center for Radiological Research of Columbia University are described: Design and development of a new wall-less ultra miniature proportional counter for nanodosimetry; some recent measurements of ionization distributions for heavy ions at nanometer site sizes with a wall-less proportional counter; a calculation of exciton energies in periodic systems with helical symmetry: application to a hydrogen fluoride chain; electron energy-loss function in polynucleotide and the question of plasmon excitation; a non-parametric, microdosimetric-based approach to the evaluation of the biological effects of low doses of ionizing radiation; high-LET radiation risk assessment at medium doses; high-LET radiobiological effects: increased lesion severity or increased lesion proximity; photoneutrons generated by high energy medical linacs; the biological effectiveness of neutrons; implications for radiation protection; molecular characterization of oncogenes induced by neutrons; and the inverse dose-rate effect for oncogenic transformation by charged particles is LET dependent

  5. Cingulate cortex functional connectivity predicts future relapse in alcohol dependent individuals

    Directory of Open Access Journals (Sweden)

    Yasmin Zakiniaeiz

    2017-01-01

    Full Text Available Alcohol dependence is a chronic relapsing illness. Alcohol and stress cues have consistently been shown to increase craving and relapse risk in recovering alcohol dependent (AUD patients. However, differences in functional connectivity in response to these cues have not been studied using data-driven approaches. Here, voxel-wise connectivity is used in a whole-brain investigation of functional connectivity differences associated with alcohol and stress cues and to examine whether these differences are related to subsequent relapse. In Study 1, 45, 4- to 8-week abstinent, recovering AUD patients underwent functional magnetic resonance imaging during individualized imagery of alcohol, stress, and neutral cues. Relapse measures were collected prospectively for 90 days post-discharge from inpatient treatment. AUD patients showed blunted anterior (ACC, mid (MCC and posterior cingulate cortex (PCC, voxel-wise connectivity responses to stress compared to neutral cues and blunted PCC response to alcohol compared to neutral cues. Using Cox proportional hazard regression, weaker connectivity in ACC and MCC during neutral exposure was associated with longer time to relapse (better recovery outcome. Similarly, greater connectivity in PCC during alcohol-cue compared to stress cue was associated with longer time to relapse. In Study 2, a sub-group of 30 AUD patients were demographically-matched to 30 healthy control (HC participants for group comparisons. AUD compared to HC participants showed reduced cingulate connectivity during alcohol and stress cues. Using novel data-driven approaches, the cingulate cortex emerged as a key region in the disruption of functional connectivity during alcohol and stress-cue processing in AUD patients and as a marker of subsequent alcohol relapse.

  6. Functional capacity and dependency in transfer and dressing are associated with depressive symptoms in older people.

    Science.gov (United States)

    Boström, Gustaf; Conradsson, Mia; Rosendahl, Erik; Nordström, Peter; Gustafson, Yngve; Littbrand, Håkan

    2014-01-01

    This study examined associations between depressive symptoms and functional capacity, overall dependency in personal activities of daily living (ADLs), and dependency in individual ADL tasks, respectively, in people with a high mean age, large range of functional capacity, and wide spectrum of dependency in ADLs. Cross-sectional data from three studies were used. A total of 392 individuals living in community and residential care facilities were included. Mean age was 86.2 years, 72% were women, 75% were dependent in ADLs, 42% had depression, and 39% had dementia. Depressive symptoms were assessed with the 15-item Geriatric Depression Scale (GDS-15), functional capacity with the Berg Balance Scale (BBS), and ADLs with the Barthel ADL Index. Multiple linear regression analyses with comprehensive adjustments were performed between GDS-15 and BBS, GDS-15 and Barthel ADL Index, and GDS-15 and each individual ADL task, separately. GDS-15 score was associated with BBS score (unstandardized b =-0.03, P=0.008), but not with Barthel ADL Index score (unstandardized b =-0.07, P=0.068). No significant interaction effects of sex, dementia, or living conditions were found in these associations. Among individual ADL tasks, dependency in transfer (unstandardized b =-1.03, P=0.007) and dressing (unstandardized b =-0.70, P=0.035) were associated with depressive symptoms. Functional capacity seems to be independently associated with depressive symptoms in older people living in community and residential care facilities, whereas overall ADL performance may not be associated. Dependency in the individual ADL tasks of transfer and dressing appear to be independently associated with depressive symptoms and may be an important focus of future interdisciplinary multifactorial intervention studies.

  7. Spatially heterogeneous dynamics investigated via a time-dependent four-point density correlation function

    DEFF Research Database (Denmark)

    Lacevic, N.; Starr, F. W.; Schrøder, Thomas

    2003-01-01

    correlation function g4(r,t) and corresponding "structure factor" S4(q,t) which measure the spatial correlations between the local liquid density at two points in space, each at two different times, and so are sensitive to dynamical heterogeneity. We study g4(r,t) and S4(q,t) via molecular dynamics......Relaxation in supercooled liquids above their glass transition and below the onset temperature of "slow" dynamics involves the correlated motion of neighboring particles. This correlated motion results in the appearance of spatially heterogeneous dynamics or "dynamical heterogeneity." Traditional...... two-point time-dependent density correlation functions, while providing information about the transient "caging" of particles on cooling, are unable to provide sufficiently detailed information about correlated motion and dynamical heterogeneity. Here, we study a four-point, time-dependent density...

  8. 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.

  9. 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.

  10. Equilibration in the time-dependent Hartree-Fock approach probed with the Wigner distribution function

    International Nuclear Information System (INIS)

    Loebl, N.; Maruhn, J. A.; Reinhard, P.-G.

    2011-01-01

    By calculating the Wigner distribution function in the reaction plane, we are able to probe the phase-space behavior in the time-dependent Hartree-Fock scheme during a heavy-ion collision in a consistent framework. Various expectation values of operators are calculated by evaluating the corresponding integrals over the Wigner function. In this approach, it is straightforward to define and analyze quantities even locally. We compare the Wigner distribution function with the smoothed Husimi distribution function. Different reaction scenarios are presented by analyzing central and noncentral 16 O + 16 O and 96 Zr + 132 Sn collisions. Although we observe strong dissipation in the time evolution of global observables, there is no evidence for complete equilibration in the local analysis of the Wigner function. Because the initial phase-space volumes of the fragments barely merge and mean values of the observables are conserved in fusion reactions over thousands of fm/c, we conclude that the time-dependent Hartree-Fock method provides a good description of the early stage of a heavy-ion collision but does not provide a mechanism to change the phase-space structure in a dramatic way necessary to obtain complete equilibration.

  11. Critique of the foundations of time-dependent density-functional theory

    International Nuclear Information System (INIS)

    Schirmer, J.; Dreuw, A.

    2007-01-01

    The general expectation that, in principle, the time-dependent density-functional theory (TDDFT) is an exact formulation of the time evolution of an interacting N-electron system is critically reexamined. It is demonstrated that the previous TDDFT foundation, resting on four theorems by Runge and Gross (RG) [Phys. Rev. Lett. 52, 997 (1984)], is invalid because undefined phase factors corrupt the RG action integral functionals. Our finding confirms much of a previous analysis by van Leeuwen [Int. J. Mod. Phys. B 15, 1969 (2001)]. To analyze the RG theorems and other aspects of TDDFT, an utmost simplification of the Kohn-Sham (KS) concept has been introduced, in which the ground-state density is obtained from a single KS equation for one spatial (spinless) orbital. The time-dependent (TD) form of this radical Kohn-Sham (rKS) scheme, which has the same validity status as the ordinary KS version, has proved to be a valuable tool for analysis. The rKS concept is used to clarify also the alternative nonvariational formulation of TD KS theory. We argue that it is just a formal theory, allowing one to reproduce but not predict the time development of the exact density of the interacting N-electron system. Besides the issue of the formal exactness of TDDFT, it is shown that both the static and time-dependent KS linear response equations neglect the particle-particle (p-p) and hole-hole (h-h) matrix elements of the perturbing operator. For a local (multiplicative) operator this does not lead to a loss of information due to a remarkable general property of local operators. Accordingly, no logical inconsistency arises with respect to DFT, because DFT requires any external potential to be local. For a general nonlocal operator the error resulting from the neglected matrix elements is of second order in the electronic repulsion

  12. The Effect of Group Therapy With Transactional Analysis Approach on Emotional Intelligence, Executive Functions and Drug Dependency.

    Science.gov (United States)

    Forghani, Masoomeh; Ghanbari Hashem Abadi, Bahram Ali

    2016-06-01

    The aim of the present study was to evaluate the effect of group psychotherapy with transactional analysis (TA) approach on emotional intelligence (EI), executive functions and substance dependency among drug-addicts at rehabilitation centers in Mashhad city, Iran, in 2013. In this quasi-experimental study with pretest, posttest, case- control stages, 30 patients were selected from a rehabilitation center and randomly divided into two groups. The case group received 12 sessions of group psychotherapy with transactional analysis approach. Then the effects of independent variable (group psychotherapy with TA approach) on EI, executive function and drug dependency were assessed. The Bar-on test was used for EI, Stroop test for measuring executive function and morphine test, meth-amphetamines and B2 test for evaluating drug dependency. Data were analyzed using multifactorial covariance analysis, Levenes' analysis, MANCOVA, t-student and Pearson correlation coefficient tests t with SPSS software. Our results showed that group psychotherapy with the TA approach was effective in improving EI, executive functions and decreasing drug dependency (P addicts and prevents addiction recurrence by improving the coping capabilities and some mental functions of the subjects. However, there are some limitations regarding this study including follow-up duration and sample size.

  13. 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.

  14. Existence results for impulsive neutral functional differential equations with state-dependent delay

    Directory of Open Access Journals (Sweden)

    Mani Mallika Arjunan

    2009-04-01

    Full Text Available In this article, we study the existence of mild solutions for a class of impulsive abstract partial neutral functional differential equations with state-dependent delay. The results are obtained by using Leray-Schauder Alternative fixed point theorem. Example is provided to illustrate the main result.

  15. 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.

  16. 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...

  17. ‘Developmental Delay’ Reconsidered: The Critical Role of Age-Dependent, Co-variant Development

    Directory of Open Access Journals (Sweden)

    Yonata Levy

    2018-04-01

    Full Text Available In memory of Annette Karmiloff-Smith.This paper reviews recent neurobiological research reporting structural co-variance and temporal dependencies in age-dependent gene expression, parameters of cortical maturation, long range connectivity and interaction of the biological network with the environment. This research suggests that age by size trajectories of brain structures relate to functional properties more than absolute sizes. In line with these findings, recent behavioral studies of typically developing children whose language development was delayed reported long term consequences of such delays. As for neurodevelopmental disorders, disrupted developmental timing and slow acquisitional pace are hallmarks of these populations. It is argued that these behavioral and neuro-biological results highlight the need to commit to a developmental model which will reflect the fact that temporal dependencies overseeing structural co-variance among developmental components are major regulatory factors of typical development of the brain/mind network. Consequently, the concept of ‘developmental delay’ in developmental theorizing needs to be reconsidered.

  18. Chemical Variability and Biological Activities of Brassica rapa var. rapifera Parts Essential Oils Depending on Geographic Variation and Extraction Technique.

    Science.gov (United States)

    Saka, Boualem; Djouahri, Abderrahmane; Djerrad, Zineb; Terfi, Souhila; Aberrane, Sihem; Sabaou, Nasserdine; Baaliouamer, Aoumeur; Boudarene, Lynda

    2017-06-01

    In the present work, the Brassica rapa var. rapifera parts essential oils and their antioxidant and antimicrobial activities were investigated for the first time depending on geographic origin and extraction technique. Gas-chromatography (GC) and GC/mass spectrometry (MS) analyses showed several constituents, including alcohols, aldehydes, esters, ketones, norisoprenoids, terpenic, nitrogen and sulphur compounds, totalizing 38 and 41 compounds in leaves and root essential oils, respectively. Nitrogen compounds were the main volatiles in leaves essential oils and sulphur compounds were the main volatiles in root essential oils. Qualitative and quantitative differences were found among B. rapa var. rapifera parts essential oils collected from different locations and extracted by hydrodistillation and microwave-assisted hydrodistillation techniques. Furthermore, our findings showed a high variability for both antioxidant and antimicrobial activities. The highlighted variability reflects the high impact of plant part, geographic variation and extraction technique on chemical composition and biological activities, which led to conclude that we should select essential oils to be investigated carefully depending on these factors, in order to isolate the bioactive components or to have the best quality of essential oil in terms of biological activities and preventive effects in food. © 2017 Wiley-VHCA AG, Zurich, Switzerland.

  19. Hemodynamics, functional state of endothelium and renal function, platelets depending on the body mass index in patients with chronic heart failure and preserved systolic function

    Directory of Open Access Journals (Sweden)

    Kushnir Yu.

    2014-03-01

    Full Text Available The aim of the study was to evaluate hemodynamics, endothelium function of kidneys and platelets depending on the body mass index (BMI in patients with chronic heart failure (CHF and preserved systolic function. 42 patients (mean age - 76,690,83 years with CHF II-III FC NYHA with preserved systolic function (LVEF>45% were enrolled. Echocardiography was performed, endothelial function, serum creatinine levels and microalbuminuria were determined in patients. BMI and glomerulation filtration rate were calculated by formulas. The morphological and functional status of platelets was estimated by electronic microscopy. It was defined that increased BMI in patients with CHF and preserved systolic function determines the structural and functional changes of the myocardium and leads to the endothelial and renal functional changes. An increased risk of thrombogenesis was established in patients with overweight and obesity.

  20. Are there approximate relations among transverse momentum dependent distribution functions?

    Energy Technology Data Exchange (ETDEWEB)

    Harutyun AVAKIAN; Anatoli Efremov; Klaus Goeke; Andreas Metz; Peter Schweitzer; Tobias Teckentrup

    2007-10-11

    Certain {\\sl exact} relations among transverse momentum dependent parton distribution functions due to QCD equations of motion turn into {\\sl approximate} ones upon the neglect of pure twist-3 terms. On the basis of available data from HERMES we test the practical usefulness of one such ``Wandzura-Wilczek-type approximation'', namely of that connecting $h_{1L}^{\\perp(1)a}(x)$ to $h_L^a(x)$, and discuss how it can be further tested by future CLAS and COMPASS data.

  1. A novel biological function of soluble biglycan: Induction of erythropoietin production and polycythemia.

    Science.gov (United States)

    Frey, Helena; Moreth, Kristin; Hsieh, Louise Tzung-Harn; Zeng-Brouwers, Jinyang; Rathkolb, Birgit; Fuchs, Helmut; Gailus-Durner, Valérie; Iozzo, Renato V; de Angelis, Martin Hrabě; Schaefer, Liliana

    2017-06-01

    Secondary polycythemia, a disease characterized by a selective increase in circulating mature erythrocytes, is caused by enhanced erythropoietin (Epo) concentrations triggered by hypoxia-inducible factor-2α (HIF-2α). While mechanisms of hypoxia-dependent stabilization of HIF-2α protein are well established, data regarding oxygen-independent regulation of HIF-2α are sparse. In this study, we generated a novel transgenic mouse model, in which biglycan was constitutively overexpressed and secreted by hepatocytes (BGN Tg ), thereby providing a constant source of biglycan released into the blood stream. We discovered that although the mice were apparently normal, they harbored an increase in mature circulating erythrocytes. In addition to erythrocytosis, the BGN Tg mice showed elevated hemoglobin concentrations, hematocrit values and enhanced total iron binding capacity, revealing a clinical picture of polycythemia. In BGN Tg mice markedly enhanced Epo mRNA expression was observed in the liver and kidney, while elevated Epo protein levels were found in liver, kidney and blood. Mechanistically, we showed that the transgenic animals had an abundance of HIF-2α protein in the liver and kidney. Finally, by transiently overexpressing circulating biglycan in mice deficient in various Toll-like receptors (TLRs), we determined that this novel function of biglycan to promote Epo synthesis was specifically mediated by a selective interaction with TLR2. Thus, we discovered a novel biological pathway of soluble biglycan inducing HIF-2α protein stabilization and Epo production presumably in an oxygen-independent manner, ultimately giving rise to secondary polycythemia.

  2. First-principles momentum-dependent local ansatz wavefunction and momentum distribution function bands of iron

    International Nuclear Information System (INIS)

    Kakehashi, Yoshiro; Chandra, Sumal

    2016-01-01

    We have developed a first-principles local ansatz wavefunction approach with momentum-dependent variational parameters on the basis of the tight-binding LDA+U Hamiltonian. The theory goes beyond the first-principles Gutzwiller approach and quantitatively describes correlated electron systems. Using the theory, we find that the momentum distribution function (MDF) bands of paramagnetic bcc Fe along high-symmetry lines show a large deviation from the Fermi–Dirac function for the d electrons with e g symmetry and yield the momentum-dependent mass enhancement factors. The calculated average mass enhancement m*/m = 1.65 is consistent with low-temperature specific heat data as well as recent angle-resolved photoemission spectroscopy (ARPES) data. (author)

  3. 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.

  4. Optical properties of Al nanostructures from time dependent density functional theory

    KAUST Repository

    Mokkath, Junais Habeeb

    2016-04-05

    The optical properties of Al nanostructures are investigated by means of time dependent density functional theory, considering chains of varying length and ladders/stripes of varying aspect ratio. The absorption spectra show redshifting for increasing length and aspect ratio. For the chains the absorption is dominated by HOMO → LUMO transitions, whereas ladders and stripes reveal more complex spectra of plasmonic nature above a specific aspect ratio.

  5. Apoptosis-Inducing-Factor-Dependent Mitochondrial Function Is Required for T Cell but Not B Cell Function.

    Science.gov (United States)

    Milasta, Sandra; Dillon, Christopher P; Sturm, Oliver E; Verbist, Katherine C; Brewer, Taylor L; Quarato, Giovanni; Brown, Scott A; Frase, Sharon; Janke, Laura J; Perry, S Scott; Thomas, Paul G; Green, Douglas R

    2016-01-19

    The role of apoptosis inducing factor (AIF) in promoting cell death versus survival remains controversial. We report that the loss of AIF in fibroblasts led to mitochondrial electron transport chain defects and loss of proliferation that could be restored by ectopic expression of the yeast NADH dehydrogenase Ndi1. Aif-deficiency in T cells led to decreased peripheral T cell numbers and defective homeostatic proliferation, but thymic T cell development was unaffected. In contrast, Aif-deficient B cells developed and functioned normally. The difference in the dependency of T cells versus B cells on AIF for function and survival correlated with their metabolic requirements. Ectopic Ndi1 expression rescued homeostatic proliferation of Aif-deficient T cells. Despite its reported roles in cell death, fibroblasts, thymocytes and B cells lacking AIF underwent normal death. These studies suggest that the primary role of AIF relates to complex I function, with differential effects on T and B cells. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. 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.

  7. 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.…

  8. 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

  9. Temperature and air-fuel ratio dependent specific heat ratio functions for lean burned and unburned mixture

    International Nuclear Information System (INIS)

    Ceviz, M.A.; Kaymaz, I.

    2005-01-01

    The most important thermodynamic property used in heat release calculations for engines is the specific heat ratio. The functions proposed in the literature for the specific heat ratio are temperature dependent and apply at or near stoichiometric air-fuel ratios. However, the specific heat ratio is also influenced by the gas composition in the engine cylinder and especially becomes important for lean combustion engines. In this study, temperature and air-fuel ratio dependent specific heat ratio functions were derived to minimize the error by using an equilibrium combustion model for burned and unburned mixtures separately. After the error analysis between the equilibrium combustion model and the derived functions is presented, the results of the global specific heat ratio function, as varying with mass fraction burned, were compared with the proposed functions in the literature. The results of the study showed that the derived functions are more feasible at lean operating conditions of a spark ignition engine

  10. Growth-rate-dependent dynamics of a bacterial genetic oscillator

    Science.gov (United States)

    Osella, Matteo; Lagomarsino, Marco Cosentino

    2013-01-01

    Gene networks exhibiting oscillatory dynamics are widespread in biology. The minimal regulatory designs giving rise to oscillations have been implemented synthetically and studied by mathematical modeling. However, most of the available analyses generally neglect the coupling of regulatory circuits with the cellular “chassis” in which the circuits are embedded. For example, the intracellular macromolecular composition of fast-growing bacteria changes with growth rate. As a consequence, important parameters of gene expression, such as ribosome concentration or cell volume, are growth-rate dependent, ultimately coupling the dynamics of genetic circuits with cell physiology. This work addresses the effects of growth rate on the dynamics of a paradigmatic example of genetic oscillator, the repressilator. Making use of empirical growth-rate dependencies of parameters in bacteria, we show that the repressilator dynamics can switch between oscillations and convergence to a fixed point depending on the cellular state of growth, and thus on the nutrients it is fed. The physical support of the circuit (type of plasmid or gene positions on the chromosome) also plays an important role in determining the oscillation stability and the growth-rate dependence of period and amplitude. This analysis has potential application in the field of synthetic biology, and suggests that the coupling between endogenous genetic oscillators and cell physiology can have substantial consequences for their functionality.

  11. A (time-dependent) density functional theory study of the optoelectronic properties of bis-triisopropylsilylethynyl-functionalized acenes

    International Nuclear Information System (INIS)

    Malloci, G.; Cappellini, G.; Mulas, G.; Mattoni, A.

    2013-01-01

    We report a comparative study of the optoelectronic properties of small acenes (benzene, anthracene, and pentacene) and their bis-triisopropylsilylethynyl (TIPS) functionalized counterparts. We computed the fundamental gap using density functional theory (DFT) in the framework of the ΔSCF scheme, and the optical absorption spectra by means of time-dependent DFT. Upon TIPS functionalization we observed a lowering of the ionization energy and a rise of the electron affinity; we consequently predict a systematic reduction of the fundamental electronic gap which decreases from ∼ 40% for benzene to ∼ 16% for pentacene. This trend is reflected in the computed optical absorption spectra: for all TIPS-molecules the onset of absorption is red-shifted as compared to their plain precursors. In the case of TIPS-pentacene, in particular, the computed spectrum agrees with the available experimental data. - Highlights: • We evaluate the effect of triisopropylsilylethynyl (TIPS)-substitution on acenes. • We compared the fundamental gap and the optical absorption as a function of size. • We found a general gap reduction following TIPS functionalization. • The gap reduction decreases at increasing size, from 40% for n = 1 to 16% for n = 5. • The onset of absorption is red-shifted as compared to TIPS precursors

  12. A (time-dependent) density functional theory study of the optoelectronic properties of bis-triisopropylsilylethynyl-functionalized acenes

    Energy Technology Data Exchange (ETDEWEB)

    Malloci, G., E-mail: giuliano.malloci@dsf.unica.it [Istituto Officina dei Materiali (CNR-IOM), Unità di Cagliari, Cittadella Universitaria, I-09042 Monserrato (Italy); Cappellini, G. [Istituto Officina dei Materiali (CNR-IOM), Unità di Cagliari, Cittadella Universitaria, I-09042 Monserrato (Italy); Dipartimento di Fisica, Università degli Studi di Cagliari, Cittadella Universitaria, I-09042 Monserrato (Italy); Mulas, G. [INAF-Osservatorio Astronomico di Cagliari, Strada 54, Località Poggio dei Pini, I-09012 Capoterra (Italy); Mattoni, A. [Istituto Officina dei Materiali (CNR-IOM), Unità di Cagliari, Cittadella Universitaria, I-09042 Monserrato (Italy)

    2013-09-30

    We report a comparative study of the optoelectronic properties of small acenes (benzene, anthracene, and pentacene) and their bis-triisopropylsilylethynyl (TIPS) functionalized counterparts. We computed the fundamental gap using density functional theory (DFT) in the framework of the ΔSCF scheme, and the optical absorption spectra by means of time-dependent DFT. Upon TIPS functionalization we observed a lowering of the ionization energy and a rise of the electron affinity; we consequently predict a systematic reduction of the fundamental electronic gap which decreases from ∼ 40% for benzene to ∼ 16% for pentacene. This trend is reflected in the computed optical absorption spectra: for all TIPS-molecules the onset of absorption is red-shifted as compared to their plain precursors. In the case of TIPS-pentacene, in particular, the computed spectrum agrees with the available experimental data. - Highlights: • We evaluate the effect of triisopropylsilylethynyl (TIPS)-substitution on acenes. • We compared the fundamental gap and the optical absorption as a function of size. • We found a general gap reduction following TIPS functionalization. • The gap reduction decreases at increasing size, from 40% for n = 1 to 16% for n = 5. • The onset of absorption is red-shifted as compared to TIPS precursors.

  13. 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

  14. 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.

  15. The necessity of a theory of biology for tissue engineering: metabolism-repair systems.

    Science.gov (United States)

    Ganguli, Suman; Hunt, C Anthony

    2004-01-01

    Since there is no widely accepted global theory of biology, tissue engineering and bioengineering lack a theoretical understanding of the systems being engineered. By default, tissue engineering operates with a "reductionist" theoretical approach, inherited from traditional engineering of non-living materials. Long term, that approach is inadequate, since it ignores essential aspects of biology. Metabolism-repair systems are a theoretical framework which explicitly represents two "functional" aspects of living organisms: self-repair and self-replication. Since repair and replication are central to tissue engineering, we advance metabolism-repair systems as a potential theoretical framework for tissue engineering. We present an overview of the framework, and indicate directions to pursue for extending it to the context of tissue engineering. We focus on biological networks, both metabolic and cellular, as one such direction. The construction of these networks, in turn, depends on biological protocols. Together these concepts may help point the way to a global theory of biology appropriate for tissue engineering.

  16. 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.

  17. Condition dependence of male and female genital structures in the seed beetle Callosobruchus maculatus (Coleoptera: Bruchidae).

    Science.gov (United States)

    Cayetano, L; Bonduriansky, R

    2015-07-01

    Theory predicts that costly secondary sexual traits will evolve heightened condition dependence, and many studies have reported strong condition dependence of signal and weapon traits in a variety of species. However, although genital structures often play key roles in intersexual interactions and appear to be subject to sexual or sexually antagonistic selection, few studies have examined the condition dependence of genital structures, especially in both sexes simultaneously. We investigated the responses of male and female genital structures to manipulation of larval diet quality (new versus once-used mung beans) in the bruchid seed beetle Callosobruchus maculatus. We quantified effects on mean relative size and static allometry of the male aedeagus, aedeagal spines, flap and paramere and the female reproductive tract and bursal spines. None of the male traits showed a significant effect of diet quality. In females, we found that longer bursal spines (relative to body size) were expressed on low-quality diet. Although the function of bursal spines is poorly understood, we suggest that greater bursal spine length in low-condition females may represent a sexually antagonistic adaptation. Overall, we found no evidence that genital traits in C. maculatus are expressed to a greater extent when nutrients are more abundant. This suggests that, even though some genital traits appear to function as secondary sexual traits, genital traits do not exhibit heightened condition dependence in this species. We discuss possible reasons for this finding. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

  18. Density functional and theoretical study of the temperature and pressure dependency of the plasmon energy of solids

    International Nuclear Information System (INIS)

    Attarian Shandiz, M.; Gauvin, R.

    2014-01-01

    The temperature and pressure dependency of the volume plasmon energy of solids was investigated by density functional theory calculations. The volume change of crystal is the major factor responsible for the variation of valence electron density and plasmon energy in the free electron model. Hence, to introduce the effect of temperature and pressure for the density functional theory calculations of plasmon energy, the temperature and pressure dependency of lattice parameter was used. Also, by combination of the free electron model and the equation of state based on the pseudo-spinodal approach, the temperature and pressure dependency of the plasmon energy was modeled. The suggested model is in good agreement with the results of density functional theory calculations and available experimental data for elements with the free electron behavior.

  19. Chapter 5:Biological Properties of Wood

    Science.gov (United States)

    Rebecca E. Ibach

    2013-01-01

    There are numerous biological degradations that wood is exposed to in various environments. Biological damage occurs when a log, sawn product, or final product is not stored, handled, or designed properly. Biological organisms such as bacteria, mold, stain, decay fungi, insects, and marine borers depend heavily on temperature and moisture conditions to grow. Figure 5.1...

  20. 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

  1. From Biology to Quality (BQ)

    DEFF Research Database (Denmark)

    Nielsen, Michael Engelbrecht; Ingerslev, Hans-Christian

    2011-01-01

    “Quality is never an accident; it is always the result of high intention, sincere effort, intelligent direction and skilful execution; it represents the wise choice of many alternatives.” (William A. Foster) The quality of fish meat is dependent upon a wide range of biological and non-biological ...

  2. 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.

  3. Age by Disease Biological Interactions: Implications for Late-Life Depression

    Directory of Open Access Journals (Sweden)

    Brandon eMcKinney

    2012-11-01

    Full Text Available Onset of depressive symptoms after the age of 65, or late-life depression (LLD, is common and poses a significant burden on affected individuals, caretakers and society. Evidence suggests a unique biological basis for LLD, but current hypotheses do not account for its pathophysiological complexity. Here we propose a novel etiological framework for LLD, the age-by-disease biological interaction hypothesis, based on the observations that the subset of genes that undergoes lifelong progressive changes in expression is restricted to a specific set of biological processes, and that a disproportionate number of these age-dependent genes have been previously and similarly implicated in neurodegenerative and neuropsychiatric disorders, including depression. The age-by-disease biological interaction hypothesis posits that age-dependent biological processes (i are pushed in LLD-promoting directions by changes in gene expression naturally occurring during brain aging, which (ii directly contribute to pathophysiological mechanisms of LLD, and (iii that individual variability in rates of age-dependent changes determines risk or resiliency to develop age-related disorders, including LLD. We review observations supporting this hypothesis, including consistent and specific age-dependent changes in brain gene expression, and their overlap with neuropsychiatric and neurodegenerative disease pathways. We then review preliminary reports supporting the genetic component of this hypothesis. Other potential biological mediators of age-dependent gene changes are proposed. We speculate that studies examining the relative contribution of these mechanisms to age-dependent changes and related disease mechanisms will not only provide critical information on the biology of normal aging of the human brain, but will inform our understanding our age-dependent diseases, in time fostering the development of new interventions for prevention and treatment of age-dependent diseases

  4. Efficient exact-exchange time-dependent density-functional theory methods and their relation to time-dependent Hartree-Fock.

    Science.gov (United States)

    Hesselmann, Andreas; Görling, Andreas

    2011-01-21

    A recently introduced time-dependent exact-exchange (TDEXX) method, i.e., a response method based on time-dependent density-functional theory that treats the frequency-dependent exchange kernel exactly, is reformulated. In the reformulated version of the TDEXX method electronic excitation energies can be calculated by solving a linear generalized eigenvalue problem while in the original version of the TDEXX method a laborious frequency iteration is required in the calculation of each excitation energy. The lowest eigenvalues of the new TDEXX eigenvalue equation corresponding to the lowest excitation energies can be efficiently obtained by, e.g., a version of the Davidson algorithm appropriate for generalized eigenvalue problems. Alternatively, with the help of a series expansion of the new TDEXX eigenvalue equation, standard eigensolvers for large regular eigenvalue problems, e.g., the standard Davidson algorithm, can be used to efficiently calculate the lowest excitation energies. With the help of the series expansion as well, the relation between the TDEXX method and time-dependent Hartree-Fock is analyzed. Several ways to take into account correlation in addition to the exact treatment of exchange in the TDEXX method are discussed, e.g., a scaling of the Kohn-Sham eigenvalues, the inclusion of (semi)local approximate correlation potentials, or hybrids of the exact-exchange kernel with kernels within the adiabatic local density approximation. The lowest lying excitations of the molecules ethylene, acetaldehyde, and pyridine are considered as examples.

  5. 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.

  6. 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.

  7. Catenin-dependent cadherin function drives divisional segregation of spinal motor neurons.

    Science.gov (United States)

    Bello, Sanusi M; Millo, Hadas; Rajebhosale, Manisha; Price, Stephen R

    2012-01-11

    Motor neurons that control limb movements are organized as a neuronal nucleus in the developing ventral horn of the spinal cord called the lateral motor column. Neuronal migration segregates motor neurons into distinct lateral and medial divisions within the lateral motor column that project axons to dorsal or ventral limb targets, respectively. This migratory phase is followed by an aggregation phase whereby motor neurons within a division that project to the same muscle cluster together. These later phases of motor neuron organization depend on limb-regulated differential cadherin expression within motor neurons. Initially, all motor neurons display the same cadherin expression profile, which coincides with the migratory phase of motor neuron segregation. Here, we show that this early, pan-motor neuron cadherin function drives the divisional segregation of spinal motor neurons in the chicken embryo by controlling motor neuron migration. We manipulated pan-motor neuron cadherin function through dissociation of cadherin binding to their intracellular partners. We found that of the major intracellular transducers of cadherin signaling, γ-catenin and α-catenin predominate in the lateral motor column. In vivo manipulations that uncouple cadherin-catenin binding disrupt divisional segregation via deficits in motor neuron migration. Additionally, reduction of the expression of cadherin-7, a cadherin predominantly expressed in motor neurons only during their migration, also perturbs divisional segregation. Our results show that γ-catenin-dependent cadherin function is required for spinal motor neuron migration and divisional segregation and suggest a prolonged role for cadherin expression in all phases of motor neuron organization.

  8. Invariant mass dependence of two-pion inclusive correlation functions

    International Nuclear Information System (INIS)

    Berger, E.L.; Singer, R.; Thomas, G.H.; Kafka, T.

    1976-06-01

    High energy two-particle inclusive correlations are studied as a function of the invariant mass M of the pair. Using data from 205 GeV/c pp interactions, one compares the correlation functions C(M) for (+-) and (--) pairs of produced pions. Strong positive correlations are observed in both distributions in the form of a broad threshold enhancement at small M. The decrease of C(M) as M increases is interpreted in the Mueller-Regge framework. From the M dependence of C +- one extracts an effective trajectory intercept of roughly α(0) approximately equal to 0.5 +- 0.1, consistent with the (rho,f) pair. For the exotic (--) system, one finds a low intercept, α(0) approximately equal to -0.5. A rho resonance signal is observed above background in C +- (M). Near threshold, effects suggestive of Bose symmetry are seen but are not conclusive. In an exclusive picture, one relates most of the correlation in the threshold region to resonances involving three or more pions. One also examines the joint correlations in M and the azimuthal angle phi

  9. Species-Specific Effects on Ecosystem Functioning Can Be Altered by Interspecific Interactions.

    Science.gov (United States)

    Clare, David S; Spencer, Matthew; Robinson, Leonie A; Frid, Christopher L J

    2016-01-01

    Biological assemblages are constantly undergoing change, with species being introduced, extirpated and experiencing shifts in their densities. Theory and experimentation suggest that the impacts of such change on ecosystem functioning should be predictable based on the biological traits of the species involved. However, interspecific interactions could alter how species affect functioning, with the strength and sign of interactions potentially depending on environmental context (e.g. homogenous vs. heterogeneous conditions) and the function considered. Here, we assessed how concurrent changes to the densities of two common marine benthic invertebrates, Corophium volutator and Hediste diversicolor, affected the ecological functions of organic matter consumption and benthic-pelagic nutrient flux. Complementary experiments were conducted within homogenous laboratory microcosms and naturally heterogeneous field plots. When the densities of the species were increased within microcosms, interspecific interactions enhanced effects on organic matter consumption and reduced effects on nutrient flux. Trait-based predictions of how each species would affect functioning were only consistently supported when the density of the other species was low. In field plots, increasing the density of either species had a positive effect on organic matter consumption (with no significant interspecific interactions) but no effect on nutrient flux. Our results indicate that species-specific effects on ecosystem functioning can be altered by interspecific interactions, which can be either facilitative (positive) or antagonistic (negative) depending on the function considered. The impacts of biodiversity change may therefore not be predictable based solely on the biological traits of the species involved. Possible explanations for why interactions were detected in microcosms but not in the field are discussed.

  10. Species-Specific Effects on Ecosystem Functioning Can Be Altered by Interspecific Interactions.

    Directory of Open Access Journals (Sweden)

    David S Clare

    Full Text Available Biological assemblages are constantly undergoing change, with species being introduced, extirpated and experiencing shifts in their densities. Theory and experimentation suggest that the impacts of such change on ecosystem functioning should be predictable based on the biological traits of the species involved. However, interspecific interactions could alter how species affect functioning, with the strength and sign of interactions potentially depending on environmental context (e.g. homogenous vs. heterogeneous conditions and the function considered. Here, we assessed how concurrent changes to the densities of two common marine benthic invertebrates, Corophium volutator and Hediste diversicolor, affected the ecological functions of organic matter consumption and benthic-pelagic nutrient flux. Complementary experiments were conducted within homogenous laboratory microcosms and naturally heterogeneous field plots. When the densities of the species were increased within microcosms, interspecific interactions enhanced effects on organic matter consumption and reduced effects on nutrient flux. Trait-based predictions of how each species would affect functioning were only consistently supported when the density of the other species was low. In field plots, increasing the density of either species had a positive effect on organic matter consumption (with no significant interspecific interactions but no effect on nutrient flux. Our results indicate that species-specific effects on ecosystem functioning can be altered by interspecific interactions, which can be either facilitative (positive or antagonistic (negative depending on the function considered. The impacts of biodiversity change may therefore not be predictable based solely on the biological traits of the species involved. Possible explanations for why interactions were detected in microcosms but not in the field are discussed.

  11. Evaluation of exchange-correlation functionals for time-dependent density functional theory calculations on metal complexes.

    Science.gov (United States)

    Holland, Jason P; Green, Jennifer C

    2010-04-15

    The electronic absorption spectra of a range of copper and zinc complexes have been simulated by using time-dependent density functional theory (TD-DFT) calculations implemented in Gaussian03. In total, 41 exchange-correlation (XC) functionals including first-, second-, and third-generation (meta-generalized gradient approximation) DFT methods were compared in their ability to predict the experimental electronic absorption spectra. Both pure and hybrid DFT methods were tested and differences between restricted and unrestricted calculations were also investigated by comparison of analogous neutral zinc(II) and copper(II) complexes. TD-DFT calculated spectra were optimized with respect to the experimental electronic absorption spectra by use of a Matlab script. Direct comparison of the performance of each XC functional was achieved both qualitatively and quantitatively by comparison of optimized half-band widths, root-mean-squared errors (RMSE), energy scaling factors (epsilon(SF)), and overall quality-of-fit (Q(F)) parameters. Hybrid DFT methods were found to outperform all pure DFT functionals with B1LYP, B97-2, B97-1, X3LYP, and B98 functionals providing the highest quantitative and qualitative accuracy in both restricted and unrestricted systems. Of the functionals tested, B1LYP gave the most accurate results with both average RMSE and overall Q(F) 0.990) for the copper complexes. The XC functional performance in spin-restricted TD-DFT calculations on the zinc complexes was found to be slightly worse. PBE1PBE, mPW1PW91 and B1LYP gave the most accurate results with typical RMSE and Q(F) values between 5.3 and 7.3%, and epsilon(SF) around 0.930. These studies illustrate the power of modern TD-DFT calculations for exploring excited state transitions of metal complexes. 2009 Wiley Periodicals, Inc.

  12. Reproductive function and biological dosimetry prospective study of young thyroid differentiated cancer patients treated with I-131

    International Nuclear Information System (INIS)

    Di Giorgio, Marina; Vallerga, Maria B.; Taja, Maria R.; Radl, Analia; Chebel, Graciela; Fadel, Ana M.; Gutierrez, Silvia; Normandi, Eduardo; Levalle, Oscar; Kundt, Miriam

    2008-01-01

    Full text: The administration of I-131 in the management of differentiated thyroid cancer (DTC) is a well established practice. As the spermatogonia is highly sensitive to radiation, large doses of internal radiation could result in adverse effects on reproductive function such as oligo/azoospermia and infertility. During spermiogenesis, mammalian chromatin undergoes replacement of nuclear histones by protamines, which yields a DNA sixfold more highly condensed in spermatozoa than in mitotic chromosomes. The structure of this highly packaged chromatin shows a low binding capacity for several fluoro chromes and dyes such as chromo mycin A 3 (CMA 3 ). The aim of this study is to assess the correlation between reproductive function (endocrine and exocrine testicular function, and levels of CMA 3 stainability) and biological dosimetry in a prospective study of 4 young DTC patients treated with I-131. In this context, a background level of CMA 3 binding in mature human sperm was established. It revealed a variable accessibility of CMA 3 to the DNA that is dependant on packaging quality and thus, indicative of protamine deficiency. The identification of altered stainability suggests DNA damage as well as epigenetic effects, which may be indicators of male infertility. Transient impairment of spermatogenesis associated with an increase in FSH, an altered spermiogram and even azoospermia was observed after the administration of cumulative activities. Overall, testosterone levels were preserved, except in one case, which presented a drastically diminished value associated with an increase in LH level. As peripheral blood lymphocytes and spermatogonia have equivalent radiosensitivity (interphase death) we hypothesize that the knowledge of DNA damage recovery in peripheral lymphocytes could correlate with spermatogonia recovery and with FSH evolution. Therefore, a prospective study on the decline of unstable chromosome aberrations is being conducted, considering the damage

  13. How to measure load-dependent kinetics of individual motor molecules without a force clamp

    DEFF Research Database (Denmark)

    Sung, J.; Mortensen, Kim; Spudich, J.A.

    2017-01-01

    Single-molecule force spectroscopy techniques, including optical trapping, magnetic trapping, and atomic force microscopy, have provided unprecedented opportunities to understand biological processes at the smallest biological length scales. For example, they have been used to elucidate the molec......Single-molecule force spectroscopy techniques, including optical trapping, magnetic trapping, and atomic force microscopy, have provided unprecedented opportunities to understand biological processes at the smallest biological length scales. For example, they have been used to elucidate...... functions at the single molecule level, such as conformational changes and force-generation of individual motor proteins or force-dependent kinetics in molecular interactions. Here, we describe a new method, “Harmonic Force Spectroscopy (HFS).” With a conventional dual-beam optical trap and a simple...... concepts, experimental setup, step-by-step experimental protocol, theory, data analysis, and results....

  14. Measuring the evolutionary rewiring of biological networks.

    Directory of Open Access Journals (Sweden)

    Chong Shou

    Full Text Available We have accumulated a large amount of biological network data and expect even more to come. Soon, we anticipate being able to compare many different biological networks as we commonly do for molecular sequences. It has long been believed that many of these networks change, or "rewire", at different rates. It is therefore important to develop a framework to quantify the differences between networks in a unified fashion. We developed such a formalism based on analogy to simple models of sequence evolution, and used it to conduct a systematic study of network rewiring on all the currently available biological networks. We found that, similar to sequences, biological networks show a decreased rate of change at large time divergences, because of saturation in potential substitutions. However, different types of biological networks consistently rewire at different rates. Using comparative genomics and proteomics data, we found a consistent ordering of the rewiring rates: transcription regulatory, phosphorylation regulatory, genetic interaction, miRNA regulatory, protein interaction, and metabolic pathway network, from fast to slow. This ordering was found in all comparisons we did of matched networks between organisms. To gain further intuition on network rewiring, we compared our observed rewirings with those obtained from simulation. We also investigated how readily our formalism could be mapped to other network contexts; in particular, we showed how it could be applied to analyze changes in a range of "commonplace" networks such as family trees, co-authorships and linux-kernel function dependencies.

  15. Self-consistent DFT +U method for real-space time-dependent density functional theory calculations

    Science.gov (United States)

    Tancogne-Dejean, Nicolas; Oliveira, Micael J. T.; Rubio, Angel

    2017-12-01

    We implemented various DFT+U schemes, including the Agapito, Curtarolo, and Buongiorno Nardelli functional (ACBN0) self-consistent density-functional version of the DFT +U method [Phys. Rev. X 5, 011006 (2015), 10.1103/PhysRevX.5.011006] within the massively parallel real-space time-dependent density functional theory (TDDFT) code octopus. We further extended the method to the case of the calculation of response functions with real-time TDDFT+U and to the description of noncollinear spin systems. The implementation is tested by investigating the ground-state and optical properties of various transition-metal oxides, bulk topological insulators, and molecules. Our results are found to be in good agreement with previously published results for both the electronic band structure and structural properties. The self-consistent calculated values of U and J are also in good agreement with the values commonly used in the literature. We found that the time-dependent extension of the self-consistent DFT+U method yields improved optical properties when compared to the empirical TDDFT+U scheme. This work thus opens a different theoretical framework to address the nonequilibrium properties of correlated systems.

  16. Dilution thermodynamics of the biologically relevant cation mixtures

    International Nuclear Information System (INIS)

    Kaczyński, Marek; Borowik, Tomasz; Przybyło, Magda; Langner, Marek

    2014-01-01

    Graphical abstract: - Highlights: • Dilution energetics of Ca 2+ can be altered by the aqueous phase ionic composition. • Dissipated heat upon Ca 2+ dilution is drastically reduced in the K + presence. • Reduction of the enthalpy change upon Ca 2+ dilution is K + concentration dependent. • The cooperativity of Ca 2+ hydration might be of great biological relevance providing a thermodynamic argument for the specific ionic composition of the intracellular environment. - Abstract: The ionic composition of intracellular space is rigorously controlled by a variety of processes consuming large quantities of energy. Since the energetic efficiency is an important evolutional criterion, therefore the ion fluxes within the cell should be optimized with respect to the accompanying energy consumption. In the paper we present the experimental evidence that the dilution enthalpies of the biologically relevant ions; i.e. calcium and magnesium depend on the presence of monovalent cations; i.e. sodium and potassium. The heat flow generated during the dilution of ionic mixtures was measured with the isothermal titration calorimetry. When calcium was diluted together with potassium the dilution enthalpy was drastically reduced as the function of the potassium concentration present in the solution. No such effect was observed when the potassium ions were substituted with sodium ones. When the dilution of magnesium was investigated the dependence of the dilution enthalpy on the accompanying monovalent cation was much weaker. In order to interpret experimental evidences the ionic cluster formation is postulated. The specific organization of such cluster should depend on ions charges, sizes and organization of the hydration layers

  17. Mode coupling theory analysis of electrolyte solutions: Time dependent diffusion, intermediate scattering function, and ion solvation dynamics.

    Science.gov (United States)

    Roy, Susmita; Yashonath, Subramanian; Bagchi, Biman

    2015-03-28

    A self-consistent mode coupling theory (MCT) with microscopic inputs of equilibrium pair correlation functions is developed to analyze electrolyte dynamics. We apply the theory to calculate concentration dependence of (i) time dependent ion diffusion, (ii) intermediate scattering function of the constituent ions, and (iii) ion solvation dynamics in electrolyte solution. Brownian dynamics with implicit water molecules and molecular dynamics method with explicit water are used to check the theoretical predictions. The time dependence of ionic self-diffusion coefficient and the corresponding intermediate scattering function evaluated from our MCT approach show quantitative agreement with early experimental and present Brownian dynamic simulation results. With increasing concentration, the dispersion of electrolyte friction is found to occur at increasingly higher frequency, due to the faster relaxation of the ion atmosphere. The wave number dependence of intermediate scattering function, F(k, t), exhibits markedly different relaxation dynamics at different length scales. At small wave numbers, we find the emergence of a step-like relaxation, indicating the presence of both fast and slow time scales in the system. Such behavior allows an intriguing analogy with temperature dependent relaxation dynamics of supercooled liquids. We find that solvation dynamics of a tagged ion exhibits a power law decay at long times-the decay can also be fitted to a stretched exponential form. The emergence of the power law in solvation dynamics has been tested by carrying out long Brownian dynamics simulations with varying ionic concentrations. The solvation time correlation and ion-ion intermediate scattering function indeed exhibit highly interesting, non-trivial dynamical behavior at intermediate to longer times that require further experimental and theoretical studies.

  18. Designing synthetic biology.

    Science.gov (United States)

    Agapakis, Christina M

    2014-03-21

    Synthetic biology is frequently defined as the application of engineering design principles to biology. Such principles are intended to streamline the practice of biological engineering, to shorten the time required to design, build, and test synthetic gene networks. This streamlining of iterative design cycles can facilitate the future construction of biological systems for a range of applications in the production of fuels, foods, materials, and medicines. The promise of these potential applications as well as the emphasis on design has prompted critical reflection on synthetic biology from design theorists and practicing designers from many fields, who can bring valuable perspectives to the discipline. While interdisciplinary connections between biologists and engineers have built synthetic biology via the science and the technology of biology, interdisciplinary collaboration with artists, designers, and social theorists can provide insight on the connections between technology and society. Such collaborations can open up new avenues and new principles for research and design, as well as shed new light on the challenging context-dependence-both biological and social-that face living technologies at many scales. This review is inspired by the session titled "Design and Synthetic Biology: Connecting People and Technology" at Synthetic Biology 6.0 and covers a range of literature on design practice in synthetic biology and beyond. Critical engagement with how design is used to shape the discipline opens up new possibilities for how we might design the future of synthetic biology.

  19. 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

  20. Functional impairment of the frontal lobe in methamphetamine dependent patients detected on FDG-PET and WCST

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Yang Tae; Kwon, Do Hoon [Bugok National Hostipal, Changnyeong (Korea, Republic of); Lee, Sang Woo; Seo, Ji Hyoung; Kang, Seong Min; Lee, Jae Tae; Lee, Kyu Bo [Kyungpook National University Hospital, Daeug (Korea, Republic of)

    2007-07-01

    There are mounting evidences from neuropsychological and neuroimaging studies to support the view that patients with substance dependence have abnormalities in prefrontal cortex. However, functional deficits in prefrontal cortex has not been adequately studied in methamphetamine dependence. Therefore, the purpose of this study is to examine whether methamphetamine dependent patients have metabolic abnormalities and executive dysfunction. Twenty-one abstinent methamphetamine dependent patients who were hospitalized in Bugok National Hospital underwent resting FDG-PET, after which they completed computerized versions of the Wisconsin Card Sorting Test (WCST). Brain PET images were obtained 30 minutes after intravenous injection of 370 MBq of 18F-FDG. Significant differences of glucose metabolism were estimated for every voxel using t-statistics on SPM2 implemented in Matlab between methamphetamine dependent patients and age-matched normal controls. FDG-PET revealed significant hypometabolism in the left inferior frontal white matter (Talairach coordinates (x, y, z): -34, 7, 31) in methamphetamine dependent patients compared to the normal controls (uncorrect p<0.001, t>3.39). The nearest gray matter region was the left inferior frontal cortex (Brodmann area 9). Methamphetamine dependent patients completed significantly fewer categories (3.662.19) and made more perseveration errors (22.0411.94) and total errors (44.5719.70) on the WCST compared to the normal controls (p<0.01). These data suggest that patients with methamphetamine dependence have functional impairments in prefrontal cortex.

  1. Functional impairment of the frontal lobe in methamphetamine dependent patients detected on FDG-PET and WCST

    International Nuclear Information System (INIS)

    Kim, Yang Tae; Kwon, Do Hoon; Lee, Sang Woo; Seo, Ji Hyoung; Kang, Seong Min; Lee, Jae Tae; Lee, Kyu Bo

    2007-01-01

    There are mounting evidences from neuropsychological and neuroimaging studies to support the view that patients with substance dependence have abnormalities in prefrontal cortex. However, functional deficits in prefrontal cortex has not been adequately studied in methamphetamine dependence. Therefore, the purpose of this study is to examine whether methamphetamine dependent patients have metabolic abnormalities and executive dysfunction. Twenty-one abstinent methamphetamine dependent patients who were hospitalized in Bugok National Hospital underwent resting FDG-PET, after which they completed computerized versions of the Wisconsin Card Sorting Test (WCST). Brain PET images were obtained 30 minutes after intravenous injection of 370 MBq of 18F-FDG. Significant differences of glucose metabolism were estimated for every voxel using t-statistics on SPM2 implemented in Matlab between methamphetamine dependent patients and age-matched normal controls. FDG-PET revealed significant hypometabolism in the left inferior frontal white matter (Talairach coordinates (x, y, z): -34, 7, 31) in methamphetamine dependent patients compared to the normal controls (uncorrect p 3.39). The nearest gray matter region was the left inferior frontal cortex (Brodmann area 9). Methamphetamine dependent patients completed significantly fewer categories (3.662.19) and made more perseveration errors (22.0411.94) and total errors (44.5719.70) on the WCST compared to the normal controls (p<0.01). These data suggest that patients with methamphetamine dependence have functional impairments in prefrontal cortex

  2. The functional dependence of canopy conductance on water vapor pressure deficit revisited

    Science.gov (United States)

    Fuchs, Marcel; Stanghellini, Cecilia

    2018-03-01

    Current research seeking to relate between ambient water vapor deficit (D) and foliage conductance (g F ) derives a canopy conductance (g W ) from measured transpiration by inverting the coupled transpiration model to yield g W = m - n ln(D) where m and n are fitting parameters. In contrast, this paper demonstrates that the relation between coupled g W and D is g W = AP/D + B, where P is the barometric pressure, A is the radiative term, and B is the convective term coefficient of the Penman-Monteith equation. A and B are functions of g F and of meteorological parameters but are mathematically independent of D. Keeping A and B constant implies constancy of g F . With these premises, the derived g W is a hyperbolic function of D resembling the logarithmic expression, in contradiction with the pre-set constancy of g F . Calculations with random inputs that ensure independence between g F and D reproduce published experimental scatter plots that display a dependence between g W and D in contradiction with the premises. For this reason, the dependence of g W on D is a computational artifact unrelated to any real effect of ambient humidity on stomatal aperture and closure. Data collected in a maize field confirm the inadequacy of the logarithmic function to quantify the relation between canopy conductance and vapor pressure deficit.

  3. Biotin-dependent functions in adiposity: a study of monozygotic twin pairs.

    Science.gov (United States)

    Järvinen, E; Ismail, K; Muniandy, M; Bogl, L H; Heinonen, S; Tummers, M; Miettinen, S; Kaprio, J; Rissanen, A; Ollikainen, M; Pietiläinen, K H

    2016-05-01

    Biotin acts as a coenzyme for carboxylases regulating lipid and amino-acid metabolism. We investigated alterations of the biotin-dependent functions in obesity and the downstream effects of biotin restriction in adipocytes in vitro. Twenty-four monozygotic twin pairs discordant for body mass index (BMI). Mean within-pair difference (heavy-lean co-twin, Δ) of BMI was 6.0 kg m(-2) (range 3.1-15.2 kg m(-)(2)). Adipose tissue (AT) DNA methylation, gene expression of AT and adipocytes, and leukocytes (real-time quantitative PCR), serum biotin, C-reactive protein (CRP) and triglycerides were measured in the twins. Human adipocytes were cultured in low and control biotin concentrations and analyzed for lipid droplet content, mitochondrial morphology and mitochondrial respiration. The gene expression levels of carboxylases, PCCB and MCCC1, were upregulated in the heavier co-twins' leukocytes. ΔPCCB (r=0.91, P=0.0046) and ΔMCCC1 (r=0.79, P=0.036) correlated with ΔCRP within-pairs. Serum biotin levels were lower in the heavier (274 ng l(-1)) than in the lean co-twins (390 ng l(-1), P=0.034). ΔBiotin correlated negatively with Δtriglycerides (r=-0.56, P=0.045) within-pairs. In AT, HLCS and ACACB were hypermethylated and biotin cycle genes HLCS and BTD were downregulated (PBiotin-dependent carboxylases were downregulated (ACACA, ACACB, PCCB, MCCC2 and PC; Pbiotin had decreased lipid accumulation, altered mitochondrial morphology and deficient mitochondrial respiration. Biotin-dependent functions are modified by adiposity independent of genetic effects, and correlate with inflammation and hypertriglyceridemia. Biotin restriction decreases lipid accumulation and respiration, and alters mitochondrial morphology in adipocytes.

  4. [DEVELOPMENT OF FUNCTIONAL AND MORPHOLOGICAL CHANGES OF A PANCREAS DEPENDING ON THE DURATION OF OBSTRUCTIVE CHOLESTASIS].

    Science.gov (United States)

    Belyaev, A N; Kostin, S V; Belyaev, S A

    2015-01-01

    To study the severity and timing of the development of functional (reversible) and morphological (irreversible) disturbances in the pancreas, depending on the duration of obstructive cholestasis. Obstructive jaundice in the experiment 18 dogs modeled by applying the loop stranglehold on the common bile duct, followed by observation for 30 days. We measured total bilirubin and fractions aspartate aminotransferase activity (AST) and alanine aminotransferase (ALT), the contents alpha-amylase, pancreatic lipase, glucose, histological examination of the pancreas (magnification of 100 times and 400). On day 3 the common bile duct obstruction bilirubin increased from 7.1 to 286.8 μmol/l, ALT--from 0.17 to 4.18 μmol*h/l, alpha-amylase from 89 to 186 U/L and lipase--to 68 to 179 U/L. Then there was a slight decrease in the parameters studied with repeated their increase to 15 hours. Morphological changes in the first three days were characterized by reversible (swelling), impaired organ that 14-16 days passed in organic (irreversible) changes. Dynamics of fluctuations in the level of liver enzymes in the pancreas and obstructive cholestasis correlates with morphological abnormalities in the pancreas and fit into the concept of general biological organism's reaction to injury.

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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...

  10. 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.

  11. Mitochondrial function, ornamentation, and immunocompetence.

    Science.gov (United States)

    Koch, Rebecca E; Josefson, Chloe C; Hill, Geoffrey E

    2017-08-01

    Understanding the mechanisms that link ornamental displays and individual condition is key to understanding the evolution and function of ornaments. Immune function is an aspect of individual quality that is often associated with the expression of ornamentation, but a general explanation for why the expression of some ornaments seems to be consistently linked to immunocompetence remains elusive. We propose that condition-dependent ornaments may be linked to key aspects of immunocompetence through co-dependence on mitochondrial function. Mitochondrial involvement in immune function is rarely considered outside of the biomedical literature, but the role of mitochondria as the primary energy producers of the cell and the centres of biosynthesis, the oxidative stress response, and cellular signalling place them at the hub of a variety of immune pathways. A promising new mechanistic explanation for correlations between a wide range of ornamental traits and the properties of individual quality is that mitochondrial function may be the 'shared pathway' responsible for links between ornament production and individual condition. Herein, we first review the role of mitochondria as both signal transducers and metabolic regulators of immune function. We then describe connections between hormonal pathways and mitochondria, with implications for both immune function and the expression of ornamentation. Finally, we explore the possibility that ornament expression may link directly to mitochondrial function. Considering condition-dependent traits within the framework of mitochondrial function has the potential to unify central tenets within the study of sexual selection, eco-immunology, oxidative stress ecology, stress and reproductive hormone biology, and animal physiology. © 2016 Cambridge Philosophical Society.

  12. 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.

  13. 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.

  14. Vibrationally resolved UV/Vis spectroscopy with time-dependent density functional based tight binding

    NARCIS (Netherlands)

    Ruger, R.; Niehaus, T.; van Lenthe, E.; Heine, T.; Visscher, L.

    2016-01-01

    We report a time-dependent density functional based tight-binding (TD-DFTB) scheme for the calculation of UV/Vis spectra, explicitly taking into account the excitation of nuclear vibrations via the adiabatic Hessian Franck-Condon method with a harmonic approximation for the nu- clear wavefunction.

  15. Time dependent density functional theory of light absorption in dense plasmas: application to iron-plasma

    International Nuclear Information System (INIS)

    Grimaldi, F.; Grimaldi-Lecourt, A.; Dharma-Wardana, M.W.C.

    1986-10-01

    The objective of this paper is to present a simple time-dependent calculation of the light absorption cross section for a strongly coupled partially degenerate plasma so as to transcend the usual single-particle picture. This is achieved within the density functional theory (DFT) of plasmas by generalizing the method given by Zangwill and Soven for atomic calculations at zero temperature. The essential feature of the time dependent DFT is the correct treatment of the relaxation of the system under the external field. Exploratory calculations for a Fe-plasma at 100 eV show new features in the absorption cross section which are absent in the usual single particle theory. These arise from inter-shell correlations, channel mixing and self-energy effects. These many-body effects introduce significant modifications to the radiative properties of plasmas and are shown to be efficiently calculable by time dependent density functional theory (TD-DFT)

  16. Time dependent density functional theory of light absorption in dense plasmas: application to iron-plasma

    International Nuclear Information System (INIS)

    Grimaldi, F.; Grimaldi-Lecourt, A.; Dharma-Wardana, M.W.C.

    1985-02-01

    The objective of this paper is to present a simple time-dependent calculation of the light absorption cross section for a strongly coupled partially degenerate plasma so as to transcend the usual single-particle picture. This is achieved within the density functional theory (DFT) of plasmas by generalizing the method given by Zangwill and Soven for atomic calculations at zero temperature. The essential feature of the time dependent DFT is the correct treatment of the relaxation of the system under the external field. Exploratory calculations for an Fe-plasma at 100 eV show new features in the absorption cross section which are absent in the usual single particle theory. These arise from inter-shell correlations, channel mixing and self-energy effects. These many-body effects introduce significant modifications to the radiative properties of plasma and are shown to be efficiently calculable by time dependent density functional theory (TD-DFT)

  17. 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.

  18. Spin-dependent transport and functional design in organic ferromagnetic devices

    Directory of Open Access Journals (Sweden)

    Guichao Hu

    2017-09-01

    Full Text Available Organic ferromagnets are intriguing materials in that they combine ferromagnetic and organic properties. Although challenges in their synthesis still remain, the development of organic spintronics has triggered strong interest in high-performance organic ferromagnetic devices. This review first introduces our theory for spin-dependent electron transport through organic ferromagnetic devices, which combines an extended Su–Schrieffer–Heeger model with the Green’s function method. The effects of the intrinsic interactions in the organic ferromagnets, including strong electron–lattice interaction and spin–spin correlation between π-electrons and radicals, are highlighted. Several interesting functional designs of organic ferromagnetic devices are discussed, specifically the concepts of a spin filter, multi-state magnetoresistance, and spin-current rectification. The mechanism of each phenomenon is explained by transmission and orbital analysis. These works show that organic ferromagnets are promising components for spintronic devices that deserve to be designed and examined in future experiments.

  19. Differences in functional connectivity between alcohol dependence and internet gaming disorder.

    Science.gov (United States)

    Han, Ji Won; Han, Doug Hyun; Bolo, Nicolas; Kim, BoAh; Kim, Boong Nyun; Renshaw, Perry F

    2015-02-01

    Internet gaming disorder (IGD) and alcohol dependence (AD) have been reported to share clinical characteristics including craving and over-engagement despite negative consequences. However, there are also clinical factors that differ between individuals with IGD and those with AD in terms of chemical intoxication, prevalence age, and visual and auditory stimulation. We assessed brain functional connectivity within the prefrontal, striatum, and temporal lobe in 15 patients with IGD and in 16 patients with AD. Symptoms of depression, anxiety, and the attention deficit hyperactivity disorder were assessed in patients with IGD and in patients with AD. Both AD and IGD subjects have positive functional connectivity between the dorsolateral prefrontal cortex (DLPFC), cingulate, and cerebellum. In addition, both groups have negative functional connectivity between the DLPFC and the orbitofrontal cortex. However, the AD subjects have positive functional connectivity between the DLPFC, temporal lobe and striatal areas while IGD subjects have negative functional connectivity between the DLPFC, temporal lobe and striatal areas. AD and IGD subjects may share deficits in executive function, including problems with self-control and adaptive responding. However, the negative connectivity between the DLPFC and the striatal areas in IGD subjects, different from the connectivity observed in AD subjects, may be due to the earlier prevalence age, different comorbid diseases as well as visual and auditory stimulation. Copyright © 2014 Elsevier Ltd. All rights reserved.

  20. Differences in functional connectivity between alcohol dependence and internet gaming disorder

    Science.gov (United States)

    Han, Ji Won; Han, Doug Hyun; Bolo, Nicolas; Kim, BoAh; Kim, Boong Nyun; Renshaw, Perry F.

    2017-01-01

    Introduction Internet gaming disorder (IGD) and alcohol dependence (AD) have been reported to share clinical characteristics including craving and over-engagement despite negative consequences. However, there are also clinical factors that differ between individuals with IGD and those with AD in terms of chemical intoxication, prevalence age, and visual and auditory stimulation. Methods We assessed brain functional connectivity within the prefrontal, striatum, and temporal lobe in 15 patients with IGD and in 16 patients with AD. Symptoms of depression, anxiety, and the attention deficit hyperactivity disorder were assessed in patients with IGD and in patients with AD. Results Both AD and IGD subjects have positive functional connectivity between the dorsolateral prefrontal cortex (DLPFC), cingulate, and cerebellum. In addition, both groups have negative functional connectivity between the DLPFC and the orbitofrontal cortex. However, the AD subjects have positive functional connectivity between the DLPFC, temporal lobe and striatal areas while IGD subjects have negative functional connectivity between the DLPFC, temporal lobe and striatal areas. Conclusions AD and IGD subjects may share deficits in executive function, including problems with self-control and adaptive responding. However, the negative connectivity between the DLPFC and the striatal areas in IGD subjects, different from the connectivity observed in AD subjects, may be due to the earlier prevalence age, different comorbid diseases as well as visual and auditory stimulation. PMID:25282597

  1. Using synthetic biology to distinguish and overcome regulatory and functional barriers related to nitrogen fixation.

    Directory of Open Access Journals (Sweden)

    Xia Wang

    Full Text Available Biological nitrogen fixation is a complex process requiring multiple genes working in concert. To date, the Klebsiella pneumoniae nif gene cluster, divided into seven operons, is one of the most studied systems. Its nitrogen fixation capacity is subject to complex cascade regulation and physiological limitations. In this report, the entire K. pneumoniae nif gene cluster was reassembled as operon-based BioBrick parts in Escherichia coli. It provided ~100% activity of native K. pneumoniae system. Based on the expression levels of these BioBrick parts, a T7 RNA polymerase-LacI expression system was used to replace the σ(54-dependent promoters located upstream of nif operons. Expression patterns of nif operons were critical for the maximum activity of the recombinant system. By mimicking these expression levels with variable-strength T7-dependent promoters, ~42% of the nitrogenase activity of the σ(54-dependent nif system was achieved in E. coli. When the newly constructed T7-dependent nif system was challenged with different genetic and physiological conditions, it bypassed the original complex regulatory circuits, with minor physiological limitations. Therefore, we have successfully replaced the nif regulatory elements with a simple expression system that may provide the first step for further research of introducing nif genes into eukaryotic organelles, which has considerable potentials in agro-biotechnology.

  2. 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.

  3. Glial cell biology in the Great Lakes region.

    Science.gov (United States)

    Feinstein, Douglas L; Skoff, Robert P

    2016-03-31

    We report on the tenth bi-annual Great Lakes Glial meeting, held in Traverse City, Michigan, USA, September 27-29 2015. The GLG meeting is a small conference that focuses on current research in glial cell biology. The array of functions that glial cells (astrocytes, microglia, oligodendrocytes, Schwann cells) play in health and disease is constantly increasing. Despite this diversity, GLG meetings bring together scientists with common interests, leading to a better understanding of these cells. This year's meeting included two keynote speakers who presented talks on the regulation of CNS myelination and the consequences of stress on Schwann cell biology. Twenty-two other talks were presented along with two poster sessions. Sessions covered recent findings in the areas of microglial and astrocyte activation; age-dependent changes to glial cells, Schwann cell development and pathology, and the role of stem cells in glioma and neural regeneration.

  4. 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...

  5. 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...

  6. 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.

  7. An Investigation into the Effects of Interface Stress and Interfacial Arrangement on Temperature Dependent Thermal Properties of a Biological and a Biomimetic Material

    Energy Technology Data Exchange (ETDEWEB)

    Tomar, Vikas [Purdue Univ., West Lafayette, IN (United States)

    2015-01-12

    A significant effort in the biomimetic materials research is on developing materials that can mimic and function in the same way as biological tissues, on bio-inspired electronic circuits, on bio-inspired flight structures, on bio-mimetic materials processing, and on structural biomimetic materials, etc. Most structural biological and biomimetic material properties are affected by two primary factors: (1) interfacial interactions between an organic and an inorganic phase usually in the form of interactions between an inorganic mineral phase and organic protein network; and (2) structural arrangement of the constituents. Examples are exoskeleton structures such as spicule, nacre, and crustacean exoskeletons. A significant effort is being directed towards making synthetic biomimetic materials based on a manipulation of the above two primary factors. The proposed research is based on a hypothesis that in synthetic materials with biomimetic morphology thermal conductivity, k, (how fast heat is carried away) and thermal diffusivity, D, (how fast a material’s temperature rises: proportional to the ratio of k and heat capacity) can be engineered to be either significantly low or significantly high based on a combination of chosen interface orientation and interfacial arrangement in comparison to conventional material microstructures with the same phases and phase volume fractions. METHOD DEVELOPMENT 1. We have established a combined Raman spectroscopy and nanomechanical loading based experimental framework to perform environment (liquid vs. air vs. vacuum) dependent and temperature dependent (~1000 degree-C) in-situ thermal diffusivity measurements in biomaterials at nanoscale to micron scale along with the corresponding analytical theoretic calculations. (Zhang and Tomar, 2013) 2. We have also established a new classical molecular simulation based framework to measure thermal diffusivity in biomolecular interfaces. We are writing a publication currently (Qu and Tomar

  8. Biological couplings: Classification and characteristic rules

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    The phenomena that biological functions originate from biological coupling are the important biological foundation of multiple bionics and the significant discoveries in the bionic fields. In this paper, the basic concepts related to biological coupling are introduced from the bionic viewpoint. Constitution, classification and characteristic rules of biological coupling are illuminated, the general modes of biological coupling studies are analyzed, and the prospects of multi-coupling bionics are predicted.

  9. Dependence of Au- production upon the target work function in a plasma-sputter-type negative ion source

    International Nuclear Information System (INIS)

    Okabe, Yushirou; Sasao, Mamiko; Fujita, Junji; Yamaoka, Hitoshi; Wada, Motoi.

    1991-01-01

    A method to measure the work function of the target surface in a plasma-sputter-type negative ion source has been developed. The method can determine the work function by measuring the photoelectric current induced by two lasers (He-Ne, Ar + laser). The dependence of Au - production upon the work function of the target surface in the ion source was studied using this method. The time variation of the target work function and Au - production rate were measured during the cesium coverage decrease due to the plasma ion sputtering. The observed minimum work function of a cesiated gold surface in an Ar plasma was 1.3 eV. At the same time, the negative ion production rate (Au - current/target current) took the maximum value. The negative ion production rate indicated the same dependence on the incident ion energy as that of the sputtering rate when the work function was constant. (author)

  10. Radiation oncology - Linking technology and biology in the treatment of cancer

    International Nuclear Information System (INIS)

    Coleman, C. Norman

    2002-01-01

    Technical advances in radiation oncology including CT-simulation, 3D-conformal and intensity-modulated radiation therapy (IMRT) delivery techniques, and brachytherapy have allowed greater treatment precision and dose escalation. The ability to intensify treatment requires the identification of the critical targets within the treatment field, recognizing the unique biology of tumor, stroma and normal tissue. Precision is technology based while accuracy is biologically based. Therefore, the intensity of IMRT will undoubtedly mean an increase in both irradiation dose and the use of biological agents, the latter considered in the broadest sense. Radiation oncology has the potential and the opportunity to provide major contributions to the linkage between molecular and functional imaging, molecular profiling and novel therapeutics for the emerging molecular targets for cancer treatment. This process of 'credentialing' of molecular targets will require multi disciplinary imaging teams, clinicians and basic scientists. Future advances will depend on the appropriate integration of biology into the training of residents, continuing post graduate education, participation in innovative clinical research and commitment to the support of basic research as an essential component of the practice of radiation oncology

  11. 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.

  12. 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.

  13. Transverse momentum dependent (TMD) parton distribution functions. Status and prospects

    International Nuclear Information System (INIS)

    Angeles-Martinez, R.; Bacchetta, A.; Pavia Univ.; Balitsky, I.I.

    2015-07-01

    We provide a concise overview on transverse momentum dependent (TMD) parton distribution functions, their application to topical issues in high-energy physics phenomenology, and their theoretical connections with QCD resummation, evolution and factorization theorems. We illustrate the use of TMDs via examples of multi-scale problems in hadronic collisions. These include transverse momentum q T spectra of Higgs and vector bosons for low q T , and azimuthal correlations in the production of multiple jets associated with heavy bosons at large jet masses. We discuss computational tools for TMDs, and present an application of a new tool, TMDlib, to parton density fits and parameterizations.

  14. Time-dependent density functional theory for nonlinear properties of open-shell systems.

    Science.gov (United States)

    Rinkevicius, Zilvinas; Jha, Prakash Chandra; Oprea, Corneliu I; Vahtras, Olav; Agren, Hans

    2007-09-21

    This paper presents response theory based on a spin-restricted Kohn-Sham formalism for computation of time-dependent and time-independent nonlinear properties of molecules with a high spin ground state. The developed approach is capable to handle arbitrary perturbations and constitutes an efficient procedure for evaluation of electric, magnetic, and mixed properties. Apart from presenting the derivation of the proposed approach, we show results from illustrating calculations of static and dynamic hyperpolarizabilities of small Si(3n+1)H(6n+3) (n=0,1,2) clusters which mimic Si(111) surfaces with dangling bond defects. The results indicate that the first hyperpolarizability tensor components of Si(3n+1)H(6n+3) have an ordering compatible with the measurements of second harmonic generation in SiO2/Si(111) interfaces and, therefore, support the hypothesis that silicon surface defects with dangling bonds are responsible for this phenomenon. The results exhibit a strong dependence on the quality of basis set and exchange-correlation functional, showing that an appropriate set of diffuse functions is required for reliable predictions of the first hyperpolarizability of open-shell compounds.

  15. 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.

  16. Mathematical model for evaluation of dose-rate effect on biological responses to low dose γ-radiation

    International Nuclear Information System (INIS)

    Ogata, H.; Kawakami, Y.; Magae, J.

    2003-01-01

    Full text: To evaluate quantitative dose-response relationship on the biological response to radiation, it is necessary to consider a model including cumulative dose, dose-rate and irradiation time. In this study, we measured micronucleus formation and [ 3 H] thymidine uptake in human cells as indices of biological response to gamma radiation, and analyzed mathematically and statistically the data for quantitative evaluation of radiation risk at low dose/low dose-rate. Effective dose (ED x ) was mathematically estimated by fitting a general function of logistic model to the dose-response relationship. Assuming that biological response depends on not only cumulative dose but also dose-rate and irradiation time, a multiple logistic function was applied to express the relationship of the three variables. Moreover, to estimate the effect of radiation at very low dose, we proposed a modified exponential model. From the results of fitting curves to the inhibition of [ 3 H] thymidine uptake and micronucleus formation, it was obvious that ED 50 in proportion of inhibition of [ 3 H] thymidine uptake increased with longer irradiation time. As for the micronuclei, ED 30 also increased with longer irradiation times. These results suggest that the biological response depends on not only total dose but also irradiation time. The estimated response surface using the three variables showed that the biological response declined sharply when the dose-rate was less than 0.01 Gy/h. These results suggest that the response does not depend on total cumulative dose at very low dose-rates. Further, to investigate the effect of dose-rate within a wider range, we analyzed the relationship between ED x and dose-rate. Fitted curves indicated that ED x increased sharply when dose-rate was less than 10 -2 Gy/h. The increase of ED x signifies the decline of the response or the risk and suggests that the risk approaches to 0 at infinitely low dose-rate

  17. Age- and sex-dependent model for estimating radioiodine dose to a normal thyroid

    International Nuclear Information System (INIS)

    Killough, G.G.; Eckerman, K.F.

    1985-01-01

    This paper describes the derivation of an age- and sex-dependent model of radioiodine dosimetry in the thyroid and the application of the model to estimating the thyroid dose for each of 4215 patients who were exposed to 131 I in diagnostic and therapeutic procedures. The model was made to conform to these data requirements by the use of age-specific estimates of the biological half-time of iodine in the thyroid and an age- and sex-dependent representation of the mass of the thyroid. Also, it was assumed that the thyroid burden was maximum 24 hours after administration (the 131 I dose is not critically sensitive to this assumption). The metabolic model is of the form A(t) = K[exp(-μ 1 t) - exp(-μ 2 t)] (μCi), where μ 1 = lambda/sub r/ + lambda/sub i//sup b/ (i = 1, 2), lambda/sub r/ is the radiological decay-rate coefficient, and lambda/sub i//sup b/ are biological removal rate coefficients. The values of lambda/sub i//sup b/ are determined by solving a nonlinear equation that depends on assumptions about the time of maximum uptake and the eventual biological loss rate (through which age dependence enters). The value of K may then be calculated from knowledge of the uptake at a particular time. The dosimetric S-factor (rad/μCi-day) is based on specific absorbed fractions for photons of energy ranging from 0.01 to 4.0 MeV for thyroid masses from 1.29 to 19.6 g; the functional form of the S-factor also involves the thyroid mass explicitly, through which the dependence on age and sex enters. An analysis of sensitivity of the model to uncertainties in the thyroid mass and the biological removal rate for several age groups is reported. The model could prove useful in the dosimetry of very short-lived radioiodines. Tables of age- and sex-dependent coefficients are provided to enable readers to make their own calculations. 12 refs., 5 figs., 4 tabs

  18. The dependence of relative biological effectiveness from LET

    International Nuclear Information System (INIS)

    Savich, A.V.

    1985-01-01

    A dependence of radiation-chemical yields of DNA injuries on the LET value is found for two transformations - one and two-strand breaks of it. It is shown that the yield of one-strand breaks decreases with the increase of LET value, and the quantity of two-strand breaks at first increases reaching the maximum value within the LET range from 100 up to 150 eV/nm and then decreases. The considered semiempiric theories of the RBE dependences on LET permits using the experimentally determined parameters characterizing radiosensitivity, to estimate the efficiency of the effect of ionizing radiation on cells at different doses, types of radiation and levels of saturation with oxygen. The stage of the cell cycle is also taken into account

  19. Functional dependency between the logistics security system and the MySAP ERP in metallurgy

    OpenAIRE

    Ranitović, P.; Tepić, G.; Matić, B.; Sremac, S.; Vukadinović, V.

    2013-01-01

    MySAP ERP - Enterprise Resource Planning (system - solution which provides a whole set of functions for the business analytics, finance, human resources management, logistics and corporate services) has developed from SAP R/3. It is one of the main products of the SAP AG German multinational company and as such, it is a very important element of the international industrial and technological security system. By defining the functional dependency between the security systems (logistics securit...

  20. Space-time dependent couplings In N = 1 SUSY gauge theories: Anomalies and central functions

    International Nuclear Information System (INIS)

    Babington, J.; Erdmenger, J.

    2005-01-01

    We consider N = 1 supersymmetric gauge theories in which the couplings are allowed to be space-time dependent functions. Both the gauge and the superpotential couplings become chiral superfields. As has recently been shown, a new topological anomaly appears in models with space-time dependent gauge coupling. Here we show how this anomaly may be used to derive the NSVZ β-function in a particular, well-determined renormalisation scheme, both without and with chiral matter. Moreover we extend the topological anomaly analysis to theories coupled to a classical curved superspace background, and use it to derive an all-order expression for the central charge c, the coefficient of the Weyl tensor squared contribution to the conformal anomaly. We also comment on the implications of our results for the central charge a expected to be of relevance for a four-dimensional C-theorem. (author)

  1. Art and brain: insights from neuropsychology, biology and evolution.

    Science.gov (United States)

    Zaidel, Dahlia W

    2010-02-01

    Art is a uniquely human activity associated fundamentally with symbolic and abstract cognition. Its practice in human societies throughout the world, coupled with seeming non-functionality, has led to three major brain theories of art. (1) The localized brain regions and pathways theory links art to multiple neural regions. (2) The display of art and its aesthetics theory is tied to the biological motivation of courtship signals and mate selection strategies in animals. (3) The evolutionary theory links the symbolic nature of art to critical pivotal brain changes in Homo sapiens supporting increased development of language and hierarchical social grouping. Collectively, these theories point to art as a multi-process cognition dependent on diverse brain regions and on redundancy in art-related functional representation.

  2. Erythrocyte signal transduction pathways, their oxygenation dependence and functional significance.

    Science.gov (United States)

    Barvitenko, Nadezhda N; Adragna, Norma C; Weber, Roy E

    2005-01-01

    Erythrocytes play a key role in human and vertebrate metabolism. Tissue O2 supply is regulated by both hemoglobin (Hb)-O2 affinity and erythrocyte rheology, a key determinant of tissue perfusion. Oxygenation-deoxygenation transitions of Hb may lead to re-organization of the cytoskeleton and signalling pathways activation/deactivation in an O2-dependent manner. Deoxygenated Hb binds to the cytoplasmic domain of the anion exchanger band 3, which is anchored to the cytoskeleton, and is considered a major mechanism underlying the oxygenation-dependence of several erythrocyte functions. This work discusses the multiple modes of Hb-cytoskeleton interactions. In addition, it reviews the effects of Mg2+, 2,3-diphosphoglycerate, NO, shear stress and Ca2+, all factors accompanying the oxygenation-deoxygenation cycle in circulating red cells. Due to the extensive literature on the subject, the data discussed here, pertain mainly to human erythrocytes whose O2 affinity is modulated by 2,3-diphosphoglycerate, ectothermic vertebrate erythrocytes that use ATP, and to bird erythrocytes that use inositol pentaphosphate. Copyright 2005 S. Karger AG, Basel.

  3. 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

  4. Identifying Statistical Dependence in Genomic Sequences via Mutual Information Estimates

    Directory of Open Access Journals (Sweden)

    Wojciech Szpankowski

    2007-12-01

    Full Text Available Questions of understanding and quantifying the representation and amount of information in organisms have become a central part of biological research, as they potentially hold the key to fundamental advances. In this paper, we demonstrate the use of information-theoretic tools for the task of identifying segments of biomolecules (DNA or RNA that are statistically correlated. We develop a precise and reliable methodology, based on the notion of mutual information, for finding and extracting statistical as well as structural dependencies. A simple threshold function is defined, and its use in quantifying the level of significance of dependencies between biological segments is explored. These tools are used in two specific applications. First, they are used for the identification of correlations between different parts of the maize zmSRp32 gene. There, we find significant dependencies between the 5′ untranslated region in zmSRp32 and its alternatively spliced exons. This observation may indicate the presence of as-yet unknown alternative splicing mechanisms or structural scaffolds. Second, using data from the FBI's combined DNA index system (CODIS, we demonstrate that our approach is particularly well suited for the problem of discovering short tandem repeats—an application of importance in genetic profiling.

  5. TIMOC-ESP, Time-Dependent Response Function by Monte-Carlo with Interface to Program TIMOC-72

    International Nuclear Information System (INIS)

    Jaarsma, R.; Perlando, J.M.; Rief, H.

    1981-01-01

    1 - Description of problem or function: TIMOC-ESP is an 'Event Scanning Program' to analyse the events (collision or boundary crossing parameters) of Monte Carlo particle transport problems. It is a modular program and belongs to the TIMOC code system. Whilst TIMOC-72 deals with stationary problems, the time-dependence is dealt with in ESP. TIMOC-ESP is primarily designed to calculate the time-dependent response functions such as energy-dependent fluxes and currents at interfaces. 2 - Method of solution: The output of TIMOC-72 is transferred to TIMOC-ESP using a data set which acts as an interface between the two programs. Time dependent transport events are sampled at each crossing of any specified boundary in TIMOC. TIMOC-72 provides the parameters for ESP which are: - time of the event; - neutron weight; - cosine of the angle between the flight direction and the normal to the surface; - the indices of both regions; - the history number. Fundamentally, three time options are permitted by ESP, which give the current, the angular flux and the time-integrated flux functions between two specified regions. An eventual extension to other quantities is simple and straight- forward - ESP will accept input data for other options such as the calculation of the point flux, the collision density and the flux derived from this estimator, but the coding required for these calculations has yet to be implemented (1977). 3 - Restrictions on the complexity of the problem: The number of parameters must be between 5 and 50. The number of time intervals is at most 50

  6. Lysosomal function is involved in 17β-estradiol-induced estrogen receptor α degradation and cell proliferation.

    Science.gov (United States)

    Totta, Pierangela; Pesiri, Valeria; Marino, Maria; Acconcia, Filippo

    2014-01-01

    The homeostatic control of the cellular proteome steady-state is dependent either on the 26S proteasome activity or on the lysosome function. The sex hormone 17β-estradiol (E2) controls a plethora of biological functions by binding to the estrogen receptor α (ERα), which is both a nuclear ligand-activated transcription factor and also an extrinsic plasma membrane receptor. Regulation of E2-induced physiological functions (e.g., cell proliferation) requires the synergistic activation of both transcription of estrogen responsive element (ERE)-containing genes and rapid extra-nuclear phosphorylation of many different signalling kinases (e.g., ERK/MAPK; PI3K/AKT). Although E2 controls ERα intracellular content and activity via the 26S proteasome-mediated degradation, biochemical and microscopy-based evidence suggests a possible cross-talk among lysosomes and ERα activities. Here, we studied the putative localization of endogenous ERα to lysosomes and the role played by lysosomal function in ERα signalling. By using confocal microscopy and biochemical assays, we report that ERα localizes to lysosomes and to endosomes in an E2-dependent manner. Moreover, the inhibition of lysosomal function obtained by chloroquine demonstrates that, in addition to 26S proteasome-mediated receptor elimination, lysosome-based degradation also contributes to the E2-dependent ERα breakdown. Remarkably, the lysosome function is further involved in those ERα activities required for E2-dependent cell proliferation while it is dispensable for ERα-mediated ERE-containing gene transcription. Our discoveries reveal a novel lysosome-dependent degradation pathway for ERα and show a novel biological mechanism by which E2 regulates ERα cellular content and, as a consequence, cellular functions.

  7. Protein kinase inhibitor peptide (PKI): a family of endogenous neuropeptides that modulate neuronal cAMP-dependent protein kinase function.

    Science.gov (United States)

    Dalton, George D; Dewey, William L

    2006-02-01

    Signal transduction cascades involving cAMP-dependent protein kinase are highly conserved among a wide variety of organisms. Given the universal nature of this enzyme it is not surprising that cAMP-dependent protein kinase plays a critical role in numerous cellular processes. This is particularly evident in the nervous system where cAMP-dependent protein kinase is involved in neurotransmitter release, gene transcription, and synaptic plasticity. Protein kinase inhibitor peptide (PKI) is an endogenous thermostable peptide that modulates cAMP-dependent protein kinase function. PKI contains two distinct functional domains within its amino acid sequence that allow it to: (1) potently and specifically inhibit the activity of the free catalytic subunit of cAMP-dependent protein kinase and (2) export the free catalytic subunit of cAMP-dependent protein kinase from the nucleus. Three distinct PKI isoforms (PKIalpha, PKIbeta, PKIgamma) have been identified and each isoform is expressed in the brain. PKI modulates neuronal synaptic activity, while PKI also is involved in morphogenesis and symmetrical left-right axis formation. In addition, PKI also plays a role in regulating gene expression induced by cAMP-dependent protein kinase. Future studies should identify novel physiological functions for endogenous PKI both in the nervous system and throughout the body. Most interesting will be the determination whether functional differences exist between individual PKI isoforms which is an intriguing possibility since these isoforms exhibit: (1) cell-type specific tissue expression patterns, (2) different potencies for the inhibition of cAMP-dependent protein kinase activity, and (3) expression patterns that are hormonally, developmentally and cell-cycle regulated. Finally, synthetic peptide analogs of endogenous PKI will continue to be invaluable tools that are used to elucidate the role of cAMP-dependent protein kinase in a variety of cellular processes throughout the nervous

  8. Voxel Scale Complex Networks of Functional Connectivity in the Rat Brain: Neurochemical State Dependence of Global and Local Topological Properties

    Directory of Open Access Journals (Sweden)

    Adam J. Schwarz

    2012-01-01

    Full Text Available Network analysis of functional imaging data reveals emergent features of the brain as a function of its topological properties. However, the brain is not a homogeneous network, and the dependence of functional connectivity parameters on neuroanatomical substrate and parcellation scale is a key issue. Moreover, the extent to which these topological properties depend on underlying neurochemical changes remains unclear. In the present study, we investigated both global statistical properties and the local, voxel-scale distribution of connectivity parameters of the rat brain. Different neurotransmitter systems were stimulated by pharmacological challenge (d-amphetamine, fluoxetine, and nicotine to discriminate between stimulus-specific functional connectivity and more general features of the rat brain architecture. Although global connectivity parameters were similar, mapping of local connectivity parameters at high spatial resolution revealed strong neuroanatomical dependence of functional connectivity in the rat brain, with clear differentiation between the neocortex and older brain regions. Localized foci of high functional connectivity independent of drug challenge were found in the sensorimotor cortices, consistent with the high neuronal connectivity in these regions. Conversely, the topological properties and node roles in subcortical regions varied with neurochemical state and were dependent on the specific dynamics of the different functional processes elicited.

  9. 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.

  10. Endothelial RIG-I activation impairs endothelial function

    International Nuclear Information System (INIS)

    Asdonk, Tobias; Motz, Inga; Werner, Nikos; Coch, Christoph; Barchet, Winfried; Hartmann, Gunther; Nickenig, Georg; Zimmer, Sebastian

    2012-01-01

    Highlights: ► RIG-I activation impairs endothelial function in vivo. ► RIG-I activation alters HCAEC biology in vitro. ► EPC function is affected by RIG-I stimulation in vitro. -- Abstract: Background: Endothelial dysfunction is a crucial part of the chronic inflammatory atherosclerotic process and is mediated by innate and acquired immune mechanisms. Recent studies suggest that pattern recognition receptors (PRR) specialized in immunorecognition of nucleic acids may play an important role in endothelial biology in a proatherogenic manner. Here, we analyzed the impact of endothelial retinoic acid inducible gene I (RIG-I) activation upon vascular endothelial biology. Methods and results: Wild type mice were injected intravenously with 32.5 μg of the RIG-ligand 3pRNA (RNA with triphosphate at the 5′end) or polyA control every other day for 7 days. In 3pRNA-treated mice, endothelium-depended vasodilation was significantly impaired, vascular oxidative stress significantly increased and circulating endothelial microparticle (EMP) numbers significantly elevated compared to controls. To gain further insight in RIG-I dependent endothelial biology, cultured human coronary endothelial cells (HCAEC) and endothelial progenitor cells (EPC) were stimulated in vitro with 3pRNA. Both cells types express RIG-I and react with receptor upregulation upon stimulation. Reactive oxygen species (ROS) formation is enhanced in both cell types, whereas apoptosis and proliferation is not significantly affected in HCAEC. Importantly, HCAEC release significant amounts of proinflammatory cytokines in response to RIG-I stimulation. Conclusion: This study shows that activation of the cytoplasmatic nucleic acid receptor RIG-I leads to endothelial dysfunction. RIG-I induced endothelial damage could therefore be an important pathway in atherogenesis.

  11. 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.

  12. Haemocompatibility Of Non-Functionalized And Plasmachemical Functionalized Detonation Nanodiamond Particles

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    Mitura K.

    2015-09-01

    Full Text Available The purpose of this paper is to present the innovative design of microwave plasma system for modification of detonation nanodiamond particles (DNP using a special rotating drum placed inside the reactor. Nanodiamond particles manufactured by detonation method reveal the biological activity depending on surface functionalization. Plasmachemical modification of detonation nanodiamond particles gives the possibility of controlling surface of nanodiamonds particles in biological tests. In this paper we would like to compare detonation nanodiamond (the grain sizes from 2 to 5 nm with modified detonation nanodiamond in rotary reactor chamber, by microwave plasma activated chemical vapour deposition (MW PACVD method in materials research (Raman and FT-IR spectroscopy and in vitro examinations with full of human blood. The results indicate haemocompatibility of non-modified detonation nanodiamond and modified nanodiamond by MW PACVD method in rotary reactor chamber (modified ND-3 and the presence of haemolysis in commercial detonation nanodiamond.

  13. Optimized effective potential in real time: Problems and prospects in time-dependent density-functional theory

    International Nuclear Information System (INIS)

    Mundt, Michael; Kuemmel, Stephan

    2006-01-01

    The integral equation for the time-dependent optimized effective potential (TDOEP) in time-dependent density-functional theory is transformed into a set of partial-differential equations. These equations only involve occupied Kohn-Sham orbitals and orbital shifts resulting from the difference between the exchange-correlation potential and the orbital-dependent potential. Due to the success of an analog scheme in the static case, a scheme that propagates orbitals and orbital shifts in real time is a natural candidate for an exact solution of the TDOEP equation. We investigate the numerical stability of such a scheme. An approximation beyond the Krieger-Li-Iafrate approximation for the time-dependent exchange-correlation potential is analyzed

  14. The function of communities in protein interaction networks at multiple scales

    Directory of Open Access Journals (Sweden)

    Jones Nick S

    2010-07-01

    Full Text Available Abstract Background If biology is modular then clusters, or communities, of proteins derived using only protein interaction network structure should define protein modules with similar biological roles. We investigate the link between biological modules and network communities in yeast and its relationship to the scale at which we probe the network. Results Our results demonstrate that the functional homogeneity of communities depends on the scale selected, and that almost all proteins lie in a functionally homogeneous community at some scale. We judge functional homogeneity using a novel test and three independent characterizations of protein function, and find a high degree of overlap between these measures. We show that a high mean clustering coefficient of a community can be used to identify those that are functionally homogeneous. By tracing the community membership of a protein through multiple scales we demonstrate how our approach could be useful to biologists focusing on a particular protein. Conclusions We show that there is no one scale of interest in the community structure of the yeast protein interaction network, but we can identify the range of resolution parameters that yield the most functionally coherent communities, and predict which communities are most likely to be functionally homogeneous.

  15. Molecular wave function and effective adiabatic potentials calculated by extended multi-configuration time-dependent Hartree-Fock method

    Energy Technology Data Exchange (ETDEWEB)

    Kato, Tsuyoshi; Ide, Yoshihiro; Yamanouchi, Kaoru [Department of Chemistry, School of Science, The University of Tokyo, 7-3-1, Hongo Bunkyo-ku, Tokyo, 113-0033 (Japan)

    2015-12-31

    We first calculate the ground-state molecular wave function of 1D model H{sub 2} molecule by solving the coupled equations of motion formulated in the extended multi-configuration time-dependent Hartree-Fock (MCTDHF) method by the imaginary time propagation. From the comparisons with the results obtained by the Born-Huang (BH) expansion method as well as with the exact wave function, we observe that the memory size required in the extended MCTDHF method is about two orders of magnitude smaller than in the BH expansion method to achieve the same accuracy for the total energy. Second, in order to provide a theoretical means to understand dynamical behavior of the wave function, we propose to define effective adiabatic potential functions and compare them with the conventional adiabatic electronic potentials, although the notion of the adiabatic potentials is not used in the extended MCTDHF approach. From the comparison, we conclude that by calculating the effective potentials we may be able to predict the energy differences among electronic states even for a time-dependent system, e.g., time-dependent excitation energies, which would be difficult to be estimated within the BH expansion approach.

  16. Biological-based and physical-based optimization for biological evaluation of prostate patient's plans

    Science.gov (United States)

    Sukhikh, E.; Sheino, I.; Vertinsky, A.

    2017-09-01

    Modern modalities of radiation treatment therapy allow irradiation of the tumor to high dose values and irradiation of organs at risk (OARs) to low dose values at the same time. In this paper we study optimal radiation treatment plans made in Monaco system. The first aim of this study was to evaluate dosimetric features of Monaco treatment planning system using biological versus dose-based cost functions for the OARs and irradiation targets (namely tumors) when the full potential of built-in biological cost functions is utilized. The second aim was to develop criteria for the evaluation of radiation dosimetry plans for patients based on the macroscopic radiobiological criteria - TCP/NTCP. In the framework of the study four dosimetric plans were created utilizing the full extent of biological and physical cost functions using dose calculation-based treatment planning for IMRT Step-and-Shoot delivery of stereotactic body radiation therapy (SBRT) in prostate case (5 fractions per 7 Gy).

  17. Educational Attainment is not a Good Proxy for Cognitive Function in Methamphetamine Dependence

    Science.gov (United States)

    Dean, Andy C.; Hellemann, Gerhard; Sugar, Catherine A.; London, Edythe D.

    2014-01-01

    We sought to test the hypothesis that methamphetamine use interferes with both the quantity and quality of one's education, such that the years of education obtained by methamphetamine dependent individuals serves to underestimate general cognitive functioning and overestimate the quality of academic learning. Thirty-six methamphetamine-dependent participants and 42 healthy comparison subjects completed cognitive tests and self-report measures in Los Angeles, California. An overall cognitive battery score was used to assess general cognition, and vocabulary knowledge was used as a proxy for the quality of academic learning. Linear regression procedures were used for analyses. Supporting the hypothesis that methamphetamine use interferes with the quantity of education, we found that a) earlier onset of methamphetamine use was associated with fewer years of education (p battery score (p < .01); and c) greater differences between methamphetamine-dependent participants' predicted and actual educational attainment were associated with an earlier onset of MA use (p ≤ .01). Supporting the hypothesis that methamphetamine use interferes with the quality of education, years of education received prior to the onset of methamphetamine use was a better predictor of a proxy for academic learning, vocabulary knowledge, than was the total years of education obtained. Results support the hypothesis that methamphetamine use interferes with the quantity and quality of educational exposure, leading to under- and overestimation of cognitive function and academic learning, respectively. PMID:22206606

  18. Educational attainment is not a good proxy for cognitive function in methamphetamine dependence.

    Science.gov (United States)

    Dean, Andy C; Hellemann, Gerhard; Sugar, Catherine A; London, Edythe D

    2012-06-01

    We sought to test the hypothesis that methamphetamine use interferes with both the quantity and quality of one's education, such that the years of education obtained by methamphetamine dependent individuals serves to underestimate general cognitive functioning and overestimate the quality of academic learning. Thirty-six methamphetamine-dependent participants and 42 healthy comparison subjects completed cognitive tests and self-report measures in Los Angeles, California. An overall cognitive battery score was used to assess general cognition, and vocabulary knowledge was used as a proxy for the quality of academic learning. Linear regression procedures were used for analyses. Supporting the hypothesis that methamphetamine use interferes with the quantity of education, we found that (a) earlier onset of methamphetamine use was associated with fewer years of education (pbattery score (p<.01); and (c) greater differences between methamphetamine-dependent participants' predicted and actual educational attainment were associated with an earlier onset of MA use (p≤.01). Supporting the hypothesis that methamphetamine use interferes with the quality of education, years of education received prior to the onset of methamphetamine use was a better predictor of a proxy for academic learning, vocabulary knowledge, than was the total years of education obtained. Results support the hypothesis that methamphetamine use interferes with the quantity and quality of educational exposure, leading to under- and overestimation of cognitive function and academic learning, respectively. Copyright © 2011. Published by Elsevier Ireland Ltd.

  19. Use and management of the natural resources of the Colombian Amazon rain forest: a biological approach

    Directory of Open Access Journals (Sweden)

    Angela Yaneth Landínez Torres

    2013-12-01

    Full Text Available This study analyzes the main features associated with biological use practices and management of forest resources in the Colombian Amazon. The theoretical cut proposal contrasts biological level, the forms of appropriation of forest resources in indigenous and urban contexts depending on the importance that such activity involves the establishment of management strategies biodiversity in Colombia. In this way, provides an integrative perspective that will address conflict situations considering environmental factors not only biological but cultural in various scenarios , to give sustenance to the decisions made and provide a reasonable treatment that enables the implementation of environmental regulation mechanisms in especially in areas such as strategic biological Colombian Amazon. Finally, reflect on the importance of facilitating the functional analysis of the connections and interrelationships of ecosystem components, including human communities, sketching involving both biological and social guidelines for sustainable use of biodiversity.

  20. Biologically Costly Altruism Depends on Emotional Closeness among Step but Not Half or Full Sibling

    Directory of Open Access Journals (Sweden)

    Paola Bressan

    2009-01-01

    Full Text Available We studied altruistic behaviors of varying biological cost (high, medium, and low among siblings of varying genetic relatedness (full, half, and step. In agreement with inclusive fitness theory, the relative importance of either reliable (such as co-residence or heuristic (such as emotional closeness kinship cues depended crucially on the costs of help. When help did not endanger the altruist's life, thus making reciprocation possible, emotional closeness was the strongest predictor of altruism; perceived physical and psychological similarity to the sibling amplified altruistic behavior via their association with emotional closeness. When help endangered the altruist's life, thus making reciprocation unlikely, the strongest predictor of altruism was the ancestrally valid kinship cue of co-residence duration. Emotional closeness predicted costly altruism only for step siblings; its effects were nonsignificant when siblings were genetically related. Our findings support the idea that emotional closeness promotes costly altruistic behavior by serving as a surrogate kinship cue when more reliable cues are missing.

  1. Time-dependent density functional theory beyond Kohn-Sham Slater determinants.

    Science.gov (United States)

    Fuks, Johanna I; Nielsen, Søren E B; Ruggenthaler, Michael; Maitra, Neepa T

    2016-08-03

    When running time-dependent density functional theory (TDDFT) calculations for real-time simulations of non-equilibrium dynamics, the user has a choice of initial Kohn-Sham state, and typically a Slater determinant is used. We explore the impact of this choice on the exchange-correlation potential when the physical system begins in a 50 : 50 superposition of the ground and first-excited state of the system. We investigate the possibility of judiciously choosing a Kohn-Sham initial state that minimizes errors when adiabatic functionals are used. We find that if the Kohn-Sham state is chosen to have a configuration matching the one that dominates the interacting state, this can be achieved for a finite time duration for some but not all such choices. When the Kohn-Sham system does not begin in a Slater determinant, we further argue that the conventional splitting of the exchange-correlation potential into exchange and correlation parts has limited value, and instead propose a decomposition into a "single-particle" contribution that we denote v, and a remainder. The single-particle contribution can be readily computed as an explicit orbital-functional, reduces to exchange in the Slater determinant case, and offers an alternative to the adiabatic approximation as a starting point for TDDFT approximations.

  2. Scaffolded biology.

    Science.gov (United States)

    Minelli, Alessandro

    2016-09-01

    Descriptions and interpretations of the natural world are dominated by dichotomies such as organism vs. environment, nature vs. nurture, genetic vs. epigenetic, but in the last couple of decades strong dissatisfaction with those partitions has been repeatedly voiced and a number of alternative perspectives have been suggested, from perspectives such as Dawkins' extended phenotype, Turner's extended organism, Oyama's Developmental Systems Theory and Odling-Smee's niche construction theory. Last in time is the description of biological phenomena in terms of hybrids between an organism (scaffolded system) and a living or non-living scaffold, forming unit systems to study processes such as reproduction and development. As scaffold, eventually, we can define any resource used by the biological system, especially in development and reproduction, without incorporating it as happens in the case of resources fueling metabolism. Addressing biological systems as functionally scaffolded systems may help pointing to functional relationships that can impart temporal marking to the developmental process and thus explain its irreversibility; revisiting the boundary between development and metabolism and also regeneration phenomena, by suggesting a conceptual framework within which to investigate phenomena of regular hypermorphic regeneration such as characteristic of deer antlers; fixing a periodization of development in terms of the times at which a scaffolding relationship begins or is terminated; and promoting plant galls to legitimate study objects of developmental biology.

  3. Impaired Perception of Biological Motion in Parkinson’s Disease

    Science.gov (United States)

    Jaywant, Abhishek; Shiffrar, Maggie; Roy, Serge; Cronin-Golomb, Alice

    2016-01-01

    Objective We examined biological motion perception in Parkinson’s disease (PD). Biological motion perception is related to one’s own motor function and depends on the integrity of brain areas affected in PD, including posterior superior temporal sulcus. If deficits in biological motion perception exist, they may be specific to perceiving natural/fast walking patterns that individuals with PD can no longer perform, and may correlate with disease-related motor dysfunction. Method 26 non-demented individuals with PD and 24 control participants viewed videos of point-light walkers and scrambled versions that served as foils, and indicated whether each video depicted a human walking. Point-light walkers varied by gait type (natural, parkinsonian) and speed (0.5, 1.0, 1.5 m/s). Participants also completed control tasks (object motion, coherent motion perception), a contrast sensitivity assessment, and a walking assessment. Results The PD group demonstrated significantly less sensitivity to biological motion than the control group (pperception (p=.02, Cohen’s d=.68). There was no group difference in coherent motion perception. Although individuals with PD had slower walking speed and shorter stride length than control participants, gait parameters did not correlate with biological motion perception. Contrast sensitivity and coherent motion perception also did not correlate with biological motion perception. Conclusion PD leads to a deficit in perceiving biological motion, which is independent of gait dysfunction and low-level vision changes, and may therefore arise from difficulty perceptually integrating form and motion cues in posterior superior temporal sulcus. PMID:26949927

  4. Biology of primate relaxin: A paracrine signal in early pregnancy?

    Directory of Open Access Journals (Sweden)

    Hayes Eric S

    2004-06-01

    Full Text Available Abstract Relaxin is a peptide hormone that exerts numerous effects in a variety of tissues across a broad range of species. Although first identified more than 75 years ago interest in relaxin biology has waxed and waned over the years consistent with peaks and troughs of new experimental data on its wide-ranging biological effects and advances in relaxin enabling technologies. Recent insights into species-dependent differences in relaxin biology during pregnancy have once again stimulated a relative surge of interest in the study of relaxin's reproductive biology. Identification and pharmacological characterization of orphaned relaxin receptors and exploration of its paracrine effects on pregnancy using genomic and proteomic technologies have succeeded in fueling current interest in relaxin research. Primates and non-primate vertebrates exhibit very disparate profiles of relaxin genomics, proteomics and functional biology. Non-human primates appear to exhibit a very close similarity to humans with respect to relaxin reproductive biology but the similarities and subtle differences are only just beginning to be understood. We, and others, have shown that relaxin produces significant changes to the non-human primate endometrium during the peri-implantation period that are consistent with relaxin's long perceived role as a paracrine modulator of pregnancy. The purpose of this review is to summarize the reproductive biology of relaxin in non-human primates with a specific emphasis on the paracrine role of ovarian and endometrial relaxin during embryo implantation and early pregnancy.

  5. Temperature and directional dependences of the infrared dielectric function of free standing silicon nanowire

    Energy Technology Data Exchange (ETDEWEB)

    Kazan, M.; Bruyant, A.; Sedaghat, Z.; Arnaud, L.; Blaize, S.; Royer, P. [Laboratoire de Nanotechnologie et d' Instrumentation Optique, Institut Charles Delaunay, Universite de Technologie de Troyes, CNRS FRE 2848, 12 Rue Marie Curie, 10010 Troyes, Cedex (France)

    2011-03-15

    An approach to calculate the infrared dielectric function of semiconductor nanostructures is presented and applied to silicon (Si) nanowires (NW's). The phonon modes symmetries and frequencies are calculated by means of the elastic continuum medium theory. The modes strengths and damping are calculated from a model for lattice dynamics and perturbation theory. The data are used in anisotropic Lorentz oscillator model to generate the temperature and directional dependences of the infrared dielectric function of free standing Si NW's. Our results showed that in the direction perpendicular to the NW axis, the complex dielectric function is identical to that of bulk Si. However, along the NW axis, the infrared dielectric function is a strong function of the wavelength. (copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  6. Determining the functional form of density dependence: deductive approaches for consumer-resource systems having a single resource.

    Science.gov (United States)

    Abrams, Peter A

    2009-09-01

    Consumer-resource models are used to deduce the functional form of density dependence in the consumer population. A general approach to determining the form of consumer density dependence is proposed; this involves determining the equilibrium (or average) population size for a series of different harvest rates. The relationship between a consumer's mortality and its equilibrium population size is explored for several one-consumer/one-resource models. The shape of density dependence in the resource and the shape of the numerical and functional responses all tend to be "inherited" by the consumer's density dependence. Consumer-resource models suggest that density dependence will very often have both concave and convex segments, something that is impossible under the commonly used theta-logistic model. A range of consumer-resource models predicts that consumer population size often declines at a decelerating rate with mortality at low mortality rates, is insensitive to or increases with mortality over a wide range of intermediate mortalities, and declines at a rapidly accelerating rate with increased mortality when mortality is high. This has important implications for management and conservation of natural populations.

  7. Towards functional 3D T-ray imaging

    International Nuclear Information System (INIS)

    Ferguson, Bradley; Wang, Shaohong; Gray, Doug; Abbott, Derek; Zhang, X-C

    2002-01-01

    We review the recent development of T-ray computed tomography, a terahertz imaging technique that allows the reconstruction of the three-dimensional refractive index profile of weakly scattering objects. Terahertz pulse imaging is used to obtain images of the target at multiple projection angles and the filtered backprojection algorithm enables the reconstruction of the object's frequency-dependent refractive index. The application of this technique to a biological bone sample and a plastic test structure is demonstrated. The structure of each target is accurately resolved and the frequency-dependent refractive index is determined. The frequency-dependent information may potentially be used to extract functional information from the target, to uniquely identify different materials or to diagnose medical conditions

  8. Exploring new biological functions of amyloids: bacteria cell agglutination mediated by host protein aggregation.

    Directory of Open Access Journals (Sweden)

    Marc Torrent

    Full Text Available Antimicrobial proteins and peptides (AMPs are important effectors of the innate immune system that play a vital role in the prevention of infections. Recent advances have highlighted the similarity between AMPs and amyloid proteins. Using the Eosinophil Cationic Protein as a model, we have rationalized the structure-activity relationships between amyloid aggregation and antimicrobial activity. Our results show how protein aggregation can induce bacteria agglutination and cell death. Using confocal and total internal reflection fluorescence microscopy we have tracked the formation in situ of protein amyloid-like aggregates at the bacteria surface and on membrane models. In both cases, fibrillar aggregates able to bind to amyloid diagnostic dyes were detected. Additionally, a single point mutation (Ile13 to Ala can suppress the protein amyloid behavior, abolishing the agglutinating activity and impairing the antimicrobial action. The mutant is also defective in triggering both leakage and lipid vesicle aggregation. We conclude that ECP aggregation at the bacterial surface is essential for its cytotoxicity. Hence, we propose here a new prospective biological function for amyloid-like aggregates with potential biological relevance.

  9. Multifunctional and biologically active matrices from multicomponent polymeric solutions

    Science.gov (United States)

    Kiick, Kristi L. (Inventor); Yamaguchi, Nori (Inventor)

    2010-01-01

    The present invention relates to a biologically active functionalized electrospun matrix to permit immobilization and long-term delivery of biologically active agents. In particular the invention relates to a functionalized polymer matrix comprising a matrix polymer, a compatibilizing polymer and a biomolecule or other small functioning molecule. In certain aspects the electrospun polymer fibers comprise at least one biologically active molecule functionalized with low molecular weight heparin. Examples of active molecules that may be used with the multicomponent polymer of the invention include, for example, a drug, a biopolymer, for example a growth factor, a protein, a peptide, a nucleotide, a polysaccharide, a biological macromolecule or the like. The invention is further directed to the formation of functionalized crosslinked matrices, such as hydrogels, that include at least one functionalized compatibilizing polymer capable of assembly.

  10. Mechanism of bactericidal activity of Silver Nitrate - a concentration dependent bi-functional molecule

    Directory of Open Access Journals (Sweden)

    Sureshbabu Ram Kumar Pandian

    2010-10-01

    Full Text Available Silver nitrate imparts different functions on bacteria depending upon its concentration. At lower concentration it induced synthesis of nanoparticles, whereas at higher concentrations it induced cell death. Bacillus licheniformis was used as model system. The MIC was 5 mM, and it induced catalase production, apoptotic body formation and DNA fragmentation.

  11. Sequential double excitations from linear-response time-dependent density functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Mosquera, Martín A.; Ratner, Mark A.; Schatz, George C., E-mail: g-schatz@northwestern.edu [Department of Chemistry, Northwestern University, 2145 Sheridan Rd., Evanston, Illinois 60208 (United States); Chen, Lin X. [Department of Chemistry, Northwestern University, 2145 Sheridan Rd., Evanston, Illinois 60208 (United States); Chemical Sciences and Engineering Division, Argonne National Laboratory, 9700 South Cass Ave., Lemont, Illinois 60439 (United States)

    2016-05-28

    Traditional UV/vis and X-ray spectroscopies focus mainly on the study of excitations starting exclusively from electronic ground states. However there are many experiments where transitions from excited states, both absorption and emission, are probed. In this work we develop a formalism based on linear-response time-dependent density functional theory to investigate spectroscopic properties of excited states. We apply our model to study the excited-state absorption of a diplatinum(II) complex under X-rays, and transient vis/UV absorption of pyrene and azobenzene.

  12. Functional capacity and dependency in transfer and dressing are associated with depressive symptoms in older people

    Directory of Open Access Journals (Sweden)

    Boström G

    2014-02-01

    Full Text Available Gustaf Boström,1 Mia Conradsson,1 Erik Rosendahl,1,2 Peter Nordström,1 Yngve Gustafson,1 Håkan Littbrand1,21Department of Community Medicine and Rehabilitation, Geriatric Medicine, Umeå University, Umeå, Sweden; 2Department of Community Medicine and Rehabilitation, Physiotherapy, Umeå University, Umeå, SwedenBackground: This study examined associations between depressive symptoms and functional capacity, overall dependency in personal activities of daily living (ADLs, and dependency in individual ADL tasks, respectively, in people with a high mean age, large range of functional capacity, and wide spectrum of dependency in ADLs.Methods: Cross-sectional data from three studies were used. A total of 392 individuals living in community and residential care facilities were included. Mean age was 86.2 years, 72% were women, 75% were dependent in ADLs, 42% had depression, and 39% had dementia. Depressive symptoms were assessed with the 15-item Geriatric Depression Scale (GDS-15, functional capacity with the Berg Balance Scale (BBS, and ADLs with the Barthel ADL Index. Multiple linear regression analyses with comprehensive adjustments were performed between GDS-15 and BBS, GDS-15 and Barthel ADL Index, and GDS-15 and each individual ADL task, separately.Results: GDS-15 score was associated with BBS score (unstandardized b =-0.03, P=0.008, but not with Barthel ADL Index score (unstandardized b =-0.07, P=0.068. No significant interaction effects of sex, dementia, or living conditions were found in these associations. Among individual ADL tasks, dependency in transfer (unstandardized b =-1.03, P=0.007 and dressing (unstandardized b =-0.70, P=0.035 were associated with depressive symptoms.Conclusion: Functional capacity seems to be independently associated with depressive symptoms in older people living in community and residential care facilities, whereas overall ADL performance may not be associated. Dependency in the individual ADL tasks of

  13. Transverse momentum dependent fragmenting jet functions with applications to quarkonium production

    Energy Technology Data Exchange (ETDEWEB)

    Bain, Reggie; Makris, Yiannis; Mehen, Thomas [Department of Physics, Duke University,Science Dr., Box 90305, Durham, NC 27708 (United States)

    2016-11-23

    We introduce the transverse momentum dependent fragmenting jet function (TMDFJF), which appears in factorization theorems for cross sections for jets with an identified hadron. These are functions of z, the hadron’s longitudinal momentum fraction, and transverse momentum, p{sub ⊥}, relative to the jet axis. In the framework of Soft-Collinear Effective Theory (SCET) we derive the TMDFJF from both a factorized SCET cross section and the TMD fragmentation function defined in the literature. The TMDFJFs are factorized into distinct collinear and soft-collinear modes by matching onto SCET{sub +}. As TMD calculations contain rapidity divergences, both the renormalization group (RG) and rapidity renormalization group (RRG) must be used to provide resummed calculations with next-to-leading-logarithm prime (NLL’) accuracy. We apply our formalism to the production of J/ψ within jets initiated by gluons. In this case the TMDFJF can be calculated in terms of NRQCD (Non-relativistic quantum chromodynamics) fragmentation functions. We find that when the J/ψ carries a significant fraction of the jet energy, the p{sub T} and z distributions differ for different NRQCD production mechanisms. Another observable with discriminating power is the average angle that the J/ψ makes with the jet axis.

  14. Polynomial fuzzy model-based control systems stability analysis and control synthesis using membership function dependent techniques

    CERN Document Server

    Lam, Hak-Keung

    2016-01-01

    This book presents recent research on the stability analysis of polynomial-fuzzy-model-based control systems where the concept of partially/imperfectly matched premises and membership-function dependent analysis are considered. The membership-function-dependent analysis offers a new research direction for fuzzy-model-based control systems by taking into account the characteristic and information of the membership functions in the stability analysis. The book presents on a research level the most recent and advanced research results, promotes the research of polynomial-fuzzy-model-based control systems, and provides theoretical support and point a research direction to postgraduate students and fellow researchers. Each chapter provides numerical examples to verify the analysis results, demonstrate the effectiveness of the proposed polynomial fuzzy control schemes, and explain the design procedure. The book is comprehensively written enclosing detailed derivation steps and mathematical derivations also for read...

  15. Is functional dependence of Duchenne muscular dystrophy patients determinant of the quality of life and burden of their caregivers?

    Directory of Open Access Journals (Sweden)

    Maria Clara Drummond Soares de Moura

    2015-01-01

    Full Text Available Objective The relationship between functional dependence and quality of life (QOL in Duchenne muscular dystrophy (DMD patients and burden and QOL in caregivers is not clear. This study investigated possible relationships between functional dependence/QOL of DMD patients and QOL/burden of caregivers. Method This study included 35 boys (6-17 years and respective caregivers (above 21 years. Caregivers answered to World Health Organization Quality of Life and Zarit Burden Interview questionnaires. Patients were assessed with the Motor Function Measure and the Autoquestionnaire Qualité de vie Enfant Imagé. Spearman correlations and linear regressions were run to investigate relationships between the variables. Results The occurrence of lower QOL and higher burden among the caregivers of patients with Duchenne muscular dystrophy was evidenced. The functional dependence of patients was not considered a determinant factor. Higher caregivers’ burden was related to lower caregivers’ QOL and to higher patients’ ages.

  16. Understanding Biological Regulation Through Synthetic Biology.

    Science.gov (United States)

    Bashor, Caleb J; Collins, James J

    2018-03-16

    Engineering synthetic gene regulatory circuits proceeds through iterative cycles of design, building, and testing. Initial circuit designs must rely on often-incomplete models of regulation established by fields of reductive inquiry-biochemistry and molecular and systems biology. As differences in designed and experimentally observed circuit behavior are inevitably encountered, investigated, and resolved, each turn of the engineering cycle can force a resynthesis in understanding of natural network function. Here, we outline research that uses the process of gene circuit engineering to advance biological discovery. Synthetic gene circuit engineering research has not only refined our understanding of cellular regulation but furnished biologists with a toolkit that can be directed at natural systems to exact precision manipulation of network structure. As we discuss, using circuit engineering to predictively reorganize, rewire, and reconstruct cellular regulation serves as the ultimate means of testing and understanding how cellular phenotype emerges from systems-level network function. Expected final online publication date for the Annual Review of Biophysics Volume 47 is May 20, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

  17. Arctigenin inhibits osteoclast differentiation and function by suppressing both calcineurin-dependent and osteoblastic cell-dependent NFATc1 pathways.

    Science.gov (United States)

    Yamashita, Teruhito; Uehara, Shunsuke; Udagawa, Nobuyuki; Li, Feng; Kadota, Shigetoshi; Esumi, Hiroyasu; Kobayashi, Yasuhiro; Takahashi, Naoyuki

    2014-01-01

    -forming activity of osteoclast-like cells cultured on dentin slices. These results suggest that arctigenin induces a dominant negative species of NFATc1, which inhibits osteoclast differentiation and function by suppressing both calcineurin-dependent and osteoblastic cell-dependent NFATc1 pathways.

  18. Arctigenin Inhibits Osteoclast Differentiation and Function by Suppressing Both Calcineurin-Dependent and Osteoblastic Cell-Dependent NFATc1 Pathways

    Science.gov (United States)

    Yamashita, Teruhito; Uehara, Shunsuke; Udagawa, Nobuyuki; Li, Feng; Kadota, Shigetoshi; Esumi, Hiroyasu; Kobayashi, Yasuhiro; Takahashi, Naoyuki

    2014-01-01

    -forming activity of osteoclast-like cells cultured on dentin slices. These results suggest that arctigenin induces a dominant negative species of NFATc1, which inhibits osteoclast differentiation and function by suppressing both calcineurin-dependent and osteoblastic cell-dependent NFATc1 pathways. PMID:24465763

  19. Arctigenin inhibits osteoclast differentiation and function by suppressing both calcineurin-dependent and osteoblastic cell-dependent NFATc1 pathways.

    Directory of Open Access Journals (Sweden)

    Teruhito Yamashita

    pit-forming activity of osteoclast-like cells cultured on dentin slices. These results suggest that arctigenin induces a dominant negative species of NFATc1, which inhibits osteoclast differentiation and function by suppressing both calcineurin-dependent and osteoblastic cell-dependent NFATc1 pathways.

  20. Dependency distance: A new perspective on syntactic patterns in natural languages

    Science.gov (United States)

    Liu, Haitao; Xu, Chunshan; Liang, Junying

    2017-07-01

    Dependency distance, measured by the linear distance between two syntactically related words in a sentence, is generally held as an important index of memory burden and an indicator of syntactic difficulty. Since this constraint of memory is common for all human beings, there may well be a universal preference for dependency distance minimization (DDM) for the sake of reducing memory burden. This human-driven language universal is supported by big data analyses of various corpora that consistently report shorter overall dependency distance in natural languages than in artificial random languages and long-tailed distributions featuring a majority of short dependencies and a minority of long ones. Human languages, as complex systems, seem to have evolved to come up with diverse syntactic patterns under the universal pressure for dependency distance minimization. However, there always exist a small number of long-distance dependencies in natural languages, which may reflect some other biological or functional constraints. Language system may adapt itself to these sporadic long-distance dependencies. It is these universal constraints that have shaped such a rich diversity of syntactic patterns in human languages.