WorldWideScience

Sample records for biomolecular screening applications

  1. Scanning probe and micropatterning approaches for biomolecular screening applications

    CERN Document Server

    Wilde, L M

    2002-01-01

    Force mapping using atomic force microscopy (AFM) allows for the simultaneous acquisition of topography and probe-sample interaction data. For example, AFM probes functionalised with an antigen can be employed to map the spatial distribution of recognition events on a substrate functionalised with the complementary specific antibody. However, this technique is currently limited to the detection of a single receptor-ligand species. Were the detection of multiple receptor-ligand interactions possible, AFM force mapping would offer greater scope as a sensitive tool for bioassay and screening applications. This thesis outlines developments in probe and substrate immobilisation methods to facilitate this process. We have developed an immobilisation strategy, which allows two antigen species, human serum albumin (HSA) and the beta subunit of human chorionic gonadotropin (beta hCG) to be simultaneously present on an AFM probe. Single point force spectroscopy results have revealed the ability of such probes to discri...

  2. Application of Nanodiamonds in Biomolecular Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    Ping Cheng

    2010-03-01

    Full Text Available The combination of nanodiamond (ND with biomolecular mass spectrometry (MS makes rapid, sensitive detection of biopolymers from complex biosamples feasible. Due to its chemical inertness, optical transparency and biocompatibility, the advantage of NDs in MS study is unique. Furthermore, functionalization on the surfaces of NDs expands their application in the fields of proteomics and genomics for specific requirements greatly. This review presents methods of MS analysis based on solid phase extraction and elution on NDs and different application examples including peptide, protein, DNA, glycan and others. Owing to the quick development of nanotechnology, surface chemistry, new MS methods and the intense interest in proteomics and genomics, a huge increase of their applications in biomolecular MS analysis in the near future can be predicted.

  3. Biomolecular logic systems: applications to biosensors and bioactuators

    Science.gov (United States)

    Katz, Evgeny

    2014-05-01

    The paper presents an overview of recent advances in biosensors and bioactuators based on the biocomputing concept. Novel biosensors digitally process multiple biochemical signals through Boolean logic networks of coupled biomolecular reactions and produce output in the form of YES/NO response. Compared to traditional single-analyte sensing devices, biocomputing approach enables a high-fidelity multi-analyte biosensing, particularly beneficial for biomedical applications. Multi-signal digital biosensors thus promise advances in rapid diagnosis and treatment of diseases by processing complex patterns of physiological biomarkers. Specifically, they can provide timely detection and alert to medical emergencies, along with an immediate therapeutic intervention. Application of the biocomputing concept has been successfully demonstrated for systems performing logic analysis of biomarkers corresponding to different injuries, particularly exemplified for liver injury. Wide-ranging applications of multi-analyte digital biosensors in medicine, environmental monitoring and homeland security are anticipated. "Smart" bioactuators, for example for signal-triggered drug release, were designed by interfacing switchable electrodes and biocomputing systems. Integration of novel biosensing and bioactuating systems with the biomolecular information processing systems keeps promise for further scientific advances and numerous practical applications.

  4. DockScreen: A Database of In Silico Biomolecular Interactions to Support Computational Toxicology

    Directory of Open Access Journals (Sweden)

    Michael-Rock Goldsmith

    2014-01-01

    Full Text Available We have developed DockScreen, a database of in silico biomolecular interactions designed to enable rational molecular toxicological insight within a computational toxicology framework. This database is composed of chemical/target (receptor and enzyme binding scores calculated by molecular docking of more than 1000 chemicals into 150 protein targets and contains nearly 135 thousand unique ligand/target binding scores. Obtaining this dataset was achieved using eHiTS (Simbiosys Inc., a fragment-based molecular docking approach with an exhaustive search algorithm, on a heterogeneous distributed high-performance computing framework. The chemical landscape covered in DockScreen comprises selected environmental and therapeutic chemicals. The target landscape covered in DockScreen was selected based on the availability of high-quality crystal structures that covered the assay space of phase I ToxCast in vitro assays. This in silico data provides continuous information that establishes a means for quantitatively comparing, on a structural biophysical basis, a chemical’s profile of biomolecular interactions. The combined minimum-score chemical/target matrix is provided.

  5. Electrochemical sensor for multiplex screening of genetically modified DNA: identification of biotech crops by logic-based biomolecular analysis.

    Science.gov (United States)

    Liao, Wei-Ching; Chuang, Min-Chieh; Ho, Ja-An Annie

    2013-12-15

    Genetically modified (GM) technique, one of the modern biomolecular engineering technologies, has been deemed as profitable strategy to fight against global starvation. Yet rapid and reliable analytical method is deficient to evaluate the quality and potential risk of such resulting GM products. We herein present a biomolecular analytical system constructed with distinct biochemical activities to expedite the computational detection of genetically modified organisms (GMOs). The computational mechanism provides an alternative to the complex procedures commonly involved in the screening of GMOs. Given that the bioanalytical system is capable of processing promoter, coding and species genes, affirmative interpretations succeed to identify specified GM event in terms of both electrochemical and optical fashions. The biomolecular computational assay exhibits detection capability of genetically modified DNA below sub-nanomolar level and is found interference-free by abundant coexistence of non-GM DNA. This bioanalytical system, furthermore, sophisticates in array fashion operating multiplex screening against variable GM events. Such a biomolecular computational assay and biosensor holds great promise for rapid, cost-effective, and high-fidelity screening of GMO.

  6. Recent applications of AC electrokinetics in biomolecular analysis on microfluidic devices.

    Science.gov (United States)

    Sasaki, Naoki

    2012-01-01

    AC electrokinetics is a generic term that refers to an induced motion of particles and fluids under nonuniform AC electric fields. The AC electric fields are formed by application of AC voltages to microelectrodes, which can be easily integrated into microfluidic devices by standard microfabrication techniques. Moreover, the magnitude of the motion is large enough to control the mass transfer on the devices. These advantages are attractive for biomolecular analysis on the microfluidic devices, in which the characteristics of small space and microfluidics have been mainly employed. In this review, I describe recent applications of AC electrokinetics in biomolecular analysis on microfluidic devices. The applications include fluid pumping and mixing by AC electrokinetic flow, and manipulation of biomolecules such as DNA and proteins by various AC electrokinetic techniques. Future prospects for highly functional biomolecular analysis on microfluidic devices with the aid of AC electrokinetics are also discussed.

  7. Markov propagation of allosteric effects in biomolecular systems: application to GroEL–GroES

    OpenAIRE

    Chennubhotla, Chakra; Bahar, Ivet

    2006-01-01

    We introduce a novel approach for elucidating the potential pathways of allosteric communication in biomolecular systems. The methodology, based on Markov propagation of ‘information' across the structure, permits us to partition the network of interactions into soft clusters distinguished by their coherent stochastics. Probabilistic participation of residues in these clusters defines the communication patterns inherent to the network architecture. Application to bacterial chaperonin complex ...

  8. Rational Design of Biomolecular Templates for Synthesizing Multifunctional Noble Metal Nanoclusters toward Personalized Theranostic Applications.

    Science.gov (United States)

    Yu, Yong; Mok, Beverly Y L; Loh, Xian Jun; Tan, Yen Nee

    2016-08-01

    Biomolecule-templated or biotemplated metal nanoclusters (NCs) are ultrasmall (<2 nm) metal (Au, Ag) particles stabilized by a certain type of biomolecular template (e.g., peptides, proteins, and DNA). Due to their unique physiochemical properties, biotemplated metal NCs have been widely used in sensing, imaging, delivery and therapy. The overwhelming applications in these individual areas imply the great promise of harnessing biotemplated metal NCs in more advanced biomedical aspects such as theranostics. Although applications of biotemplated metal NCs as theranostic agents are trending, the rational design of biomolecular templates suitable for the synthesis of multifunctional metal NCs for theranostics is comparatively underexplored. This progress report first identifies the essential attributes of biotemplated metal NCs for theranostics by reviewing the state-of-art applications in each of the four modalities of theranostics, namely sensing, imaging, delivery and therapy. To achieve high efficacy in these modalities, we elucidate the design principles underlying the use of biomolecules (proteins, peptides and nucleic acids) to control the NC size, emission color and surface chemistries for post-functionalization of therapeutic moieties. We then propose a unified strategy to engineer biomolecular templates that combine all these modalities to produce multifunctional biotemplated metal NCs that can serve as the next-generation personalized theranostic agents.

  9. Surface-enhanced Raman spectroscopy bioanalytical, biomolecular and medical applications

    CERN Document Server

    Procházka, Marek

    2016-01-01

    This book gives an overview of recent developments in RS and SERS for sensing and biosensing considering also limitations, possibilities and prospects of this technique. Raman scattering (RS) is a widely used vibrational technique providing highly specific molecular spectral patterns. A severe limitation for the application of this spectroscopic technique lies in the low cross section of RS. Surface-enhanced Raman scattering (SERS) spectroscopy overcomes this problem by 6-11 orders of magnitude enhancement compared with the standard RS for molecules in the close vicinity of certain rough metal surfaces. Thus, SERS combines molecular fingerprint specificity with potential single-molecule sensitivity. Due to the recent development of new SERS-active substrates, labeling and derivatization chemistry as well as new instrumentations, SERS became a very promising tool for many varied applications, including bioanalytical studies and sensing. Both intrinsic and extrinsic SERS biosensing schemes have been employed to...

  10. Biomolecular crystals for material applications and a mechanistic study of an iron oxide nanoparticle synthesis

    Science.gov (United States)

    Falkner, Joshua Charles

    The three projects within this work address the difficulties of controlling biomolecular crystal formats (i.e. size and shape), producing 3-D ordered composite materials from biomolecular crystal templates, and understanding the mechanism of a practical iron oxide synthesis. The unifying thread consistent throughout these three topics is the development of methods to manipulate nanomaterials using a bottom-up approach. Biomolecular crystals are nanometer to millimeter sized crystals that have well ordered mesoporous solvent channels. The overall physical dimensions of these crystals are highly dependent on crystallization conditions. The controlled growth of micro- and nanoprotein crystals was studied to provide new pathways for creating smaller crystalline protein materials. This method produced tetragonal hen egg-white lysozyme crystals (250--100,000 nm) with near monodisperse size distributions (membranes or templates. In this work, the porous structure of larger cowpea mosaic virus crystals was used to template metal nanoparticle growth within the body centered cubic crystalline network. The final composite material was found to have long range ordering of palladium and platinum nonocrystal aggregates (10nm) with symmetry consistent to the virus template. Nanoparticle synthesis itself is an immense field of study with an array of diverse applications. The final piece of this work investigates the mechanism behind a previously developed iron oxide synthesis to gain more understanding and direction to future synthesis strategies. The particle growth mechanism was found to proceed by the formation of a solvated iron(III)oleate complex followed by a reduction of iron (III) to iron (II). This unstable iron(II) nucleates to form a wustite (FeO) core which serves as an epitaxial surface for the magnetite (Fe3O4) shell growth. This method produces spherical particles (6-60nm) with relative size distributions of less than 15%.

  11. Overcoming the solubility limit with solubility-enhancement tags: successful applications in biomolecular NMR studies

    International Nuclear Information System (INIS)

    Although the rapid progress of NMR technology has significantly expanded the range of NMR-trackable systems, preparation of NMR-suitable samples that are highly soluble and stable remains a bottleneck for studies of many biological systems. The application of solubility-enhancement tags (SETs) has been highly effective in overcoming solubility and sample stability issues and has enabled structural studies of important biological systems previously deemed unapproachable by solution NMR techniques. In this review, we provide a brief survey of the development and successful applications of the SET strategy in biomolecular NMR. We also comment on the criteria for choosing optimal SETs, such as for differently charged target proteins, and recent new developments on NMR-invisible SETs.

  12. Advances in biomolecular surface meshing and its applications to mathematical modeling

    Institute of Scientific and Technical Information of China (English)

    CHEN MinXin; LU BenZhuo

    2013-01-01

    In the field of molecular modeling and simulation,molecular surface meshes are necessary for many problems,such as molecular structure visualization and analysis,docking problem and implicit solvent modeling and simulation.Recently,with the developments of advanced mathematical modeling in the field of implicit solvent modeling and simulation,providing surface meshes with good qualities efficiently for large real biomolecular systems becomes an urgent issue beyond its traditional purposes for visualization and geometry analyses for molecular structure.In this review,we summarize recent works on this issue.First,various definitions of molecular surfaces and corresponding meshing methods are introduced.Second,our recent meshing tool,TMSmesh,and its performances are presented.Finally,we show the applications of the molecular surface mesh in implicit solvent modeling and simulations using boundary element method (BEM) and finite element method (FEM).

  13. Biomolecular ligands screening using radiation damping difference WaterLOGSY spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Sun Peng; Jiang Xianwang; Jiang Bin; Zhang Xu, E-mail: zhangxu@wipm.ac.cn; Liu Maili, E-mail: ml.liu@wipm.ac.cn [Chinese Academy of Sciences, Wuhan Center for Magnetic Resonance, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics (China)

    2013-07-15

    Water-ligand observed via gradient spectroscopy (WaterLOGSY) is a widely used nuclear magnetic resonance method for ligand screening. The crucial procedure for the effectiveness of WaterLOGSY is selective excitation of the water resonance. The selective excitation is conventionally achieved by using long selective pulse, which causes partial saturation of the water magnetization leading to reduction of sensitivity, in addition to time consuming and error prone. Therefore, many improvements have been made to enhance the sensitivity and robustness of the method. Here we propose an alternative selective excitation scheme for WaterLOGSY by utilizing radiation damping effect. The pulse scheme starts simply with a hard inversion pulse, instead of selective pulse or pulse train, followed by a pulse field gradient to control the radiation damping effect. The rest parts of the pulse scheme are similar to conventional WaterLOGSY. When the gradient pulse is applied immediately after the inversion pulse, the radiation damping effect is suppressed, and all of the magnetization is inversed. When the gradient pulse and the inversion pulse are about 10-20 ms apart, the radiation damping effect remains active and drives the water magnetization toward +z-axis, resulting in selective non-inversion of the water magnetization. By taking the differences of the spectra obtained under these two conditions, one should get the result of WaterLOGSY. The method is demonstrated to be simple, robust and sensitive for ligand screening.

  14. Biomolecular ligands screening using radiation damping difference WaterLOGSY spectroscopy.

    Science.gov (United States)

    Sun, Peng; Jiang, Xianwang; Jiang, Bin; Zhang, Xu; Liu, Maili

    2013-07-01

    Water-ligand observed via gradient spectroscopy (WaterLOGSY) is a widely used nuclear magnetic resonance method for ligand screening. The crucial procedure for the effectiveness of WaterLOGSY is selective excitation of the water resonance. The selective excitation is conventionally achieved by using long selective pulse, which causes partial saturation of the water magnetization leading to reduction of sensitivity, in addition to time consuming and error prone. Therefore, many improvements have been made to enhance the sensitivity and robustness of the method. Here we propose an alternative selective excitation scheme for WaterLOGSY by utilizing radiation damping effect. The pulse scheme starts simply with a hard inversion pulse, instead of selective pulse or pulse train, followed by a pulse field gradient to control the radiation damping effect. The rest parts of the pulse scheme are similar to conventional WaterLOGSY. When the gradient pulse is applied immediately after the inversion pulse, the radiation damping effect is suppressed, and all of the magnetization is inversed. When the gradient pulse and the inversion pulse are about 10-20 ms apart, the radiation damping effect remains active and drives the water magnetization toward +z-axis, resulting in selective non-inversion of the water magnetization. By taking the differences of the spectra obtained under these two conditions, one should get the result of WaterLOGSY. The method is demonstrated to be simple, robust and sensitive for ligand screening. PMID:23740293

  15. Global analysis of time-resolved fluorescence microspectroscopy and applications in biomolecular studies

    NARCIS (Netherlands)

    Laptenok, S.

    2009-01-01

    Understanding the properties of biomolecular networks is of central importance in life sciences. Optical microscopy has been very useful to determine the sub-cellular localisation of proteins but it cannot reveal whether proteins interact with one another. Micro-spectroscopic techniques (combining m

  16. Hazard screening application guide

    International Nuclear Information System (INIS)

    The basic purpose of hazard screening is to group precesses, facilities, and proposed modifications according to the magnitude of their hazards so as to determine the need for and extent of follow on safety analysis. A hazard is defined as a material, energy source, or operation that has the potential to cause injury or illness in human beings. The purpose of this document is to give guidance and provide standard methods for performing hazard screening. Hazard screening is applied to new and existing facilities and processes as well as to proposed modifications to existing facilities and processes. The hazard screening process evaluates an identified hazards in terms of the effects on people, both on-site and off-site. The process uses bounding analyses with no credit given for mitigation of an accident with the exception of certain containers meeting DOT specifications. The process is restricted to human safety issues only. Environmental effects are addressed by the environmental program. Interfaces with environmental organizations will be established in order to share information

  17. PUPIL: A Software Integration System for Multi-Scale QM/MM-MD Simulations and Its Application to Biomolecular Systems.

    Science.gov (United States)

    Torras, Juan; Roberts, Benjamin P; Seabra, Gustavo M; Trickey, Samuel B

    2015-01-01

    PUPIL (Program for User Package Interfacing and Linking) implements a distinctive multi-scale approach to hybrid quantum mechanical/molecular mechanical molecular dynamics (QM/MM-MD) simulations. Originally developed to interface different external programs for multi-scale simulation with applications in the materials sciences, PUPIL is finding increasing use in the study of complex biological systems. Advanced MD techniques from the external packages can be applied readily to a hybrid QM/MM treatment in which the forces and energy for the QM region can be computed by any of the QM methods available in any of the other external packages. Here, we give a survey of PUPIL design philosophy, main features, and key implementation decisions, with an orientation to biomolecular simulation. We discuss recently implemented features which enable highly realistic simulations of complex biological systems which have more than one active site that must be treated concurrently. Examples are given.

  18. Design of Flow Systems for Improved Networking and Reduced Noise in Biomolecular Signal Processing in Biocomputing and Biosensing Applications

    Directory of Open Access Journals (Sweden)

    Arjun Verma

    2016-07-01

    Full Text Available We consider flow systems that have been utilized for small-scale biomolecular computing and digital signal processing in binary-operating biosensors. Signal measurement is optimized by designing a flow-reversal cuvette and analyzing the experimental data to theoretically extract the pulse shape, as well as reveal the level of noise it possesses. Noise reduction is then carried out numerically. We conclude that this can be accomplished physically via the addition of properly designed well-mixing flow-reversal cell(s as an integral part of the flow system. This approach should enable improved networking capabilities and potentially not only digital but analog signal-processing in such systems. Possible applications in complex biocomputing networks and various sense-and-act systems are discussed.

  19. Design of Flow Systems for Improved Networking and Reduced Noise in Biomolecular Signal Processing in Biocomputing and Biosensing Applications.

    Science.gov (United States)

    Verma, Arjun; Fratto, Brian E; Privman, Vladimir; Katz, Evgeny

    2016-07-05

    We consider flow systems that have been utilized for small-scale biomolecular computing and digital signal processing in binary-operating biosensors. Signal measurement is optimized by designing a flow-reversal cuvette and analyzing the experimental data to theoretically extract the pulse shape, as well as reveal the level of noise it possesses. Noise reduction is then carried out numerically. We conclude that this can be accomplished physically via the addition of properly designed well-mixing flow-reversal cell(s) as an integral part of the flow system. This approach should enable improved networking capabilities and potentially not only digital but analog signal-processing in such systems. Possible applications in complex biocomputing networks and various sense-and-act systems are discussed.

  20. Design of Flow Systems for Improved Networking and Reduced Noise in Biomolecular Signal Processing in Biocomputing and Biosensing Applications.

    Science.gov (United States)

    Verma, Arjun; Fratto, Brian E; Privman, Vladimir; Katz, Evgeny

    2016-01-01

    We consider flow systems that have been utilized for small-scale biomolecular computing and digital signal processing in binary-operating biosensors. Signal measurement is optimized by designing a flow-reversal cuvette and analyzing the experimental data to theoretically extract the pulse shape, as well as reveal the level of noise it possesses. Noise reduction is then carried out numerically. We conclude that this can be accomplished physically via the addition of properly designed well-mixing flow-reversal cell(s) as an integral part of the flow system. This approach should enable improved networking capabilities and potentially not only digital but analog signal-processing in such systems. Possible applications in complex biocomputing networks and various sense-and-act systems are discussed. PMID:27399702

  1. Grid computing and biomolecular simulation.

    Science.gov (United States)

    Woods, Christopher J; Ng, Muan Hong; Johnston, Steven; Murdock, Stuart E; Wu, Bing; Tai, Kaihsu; Fangohr, Hans; Jeffreys, Paul; Cox, Simon; Frey, Jeremy G; Sansom, Mark S P; Essex, Jonathan W

    2005-08-15

    Biomolecular computer simulations are now widely used not only in an academic setting to understand the fundamental role of molecular dynamics on biological function, but also in the industrial context to assist in drug design. In this paper, two applications of Grid computing to this area will be outlined. The first, involving the coupling of distributed computing resources to dedicated Beowulf clusters, is targeted at simulating protein conformational change using the Replica Exchange methodology. In the second, the rationale and design of a database of biomolecular simulation trajectories is described. Both applications illustrate the increasingly important role modern computational methods are playing in the life sciences.

  2. Variational Methods for Biomolecular Modeling

    CERN Document Server

    Wei, Guo-Wei

    2016-01-01

    Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the identification of essential energetic components, the optimal parametrization of energies, and the efficient computational implementation of energy variation or minimization. Given the fact that complex biomolecular systems are structurally non-uniform and their interactions occur through contact interfaces, their free energies are associated with various interfaces as well, such as solute-solvent interface, molecular binding interface, lipid domain interface, and membrane surfaces. This fact motivates the inclusion of interface geometry, particular its curvatures, to the parametrization of free energies. Applications of such interface geometry based energetic variational principles are illustrated through three concrete topics: the multiscale modeling of biomolecular electrosta...

  3. Biomolecular EPR spectroscopy

    CERN Document Server

    Hagen, Wilfred Raymond

    2008-01-01

    Comprehensive, Up-to-Date Coverage of Spectroscopy Theory and its Applications to Biological SystemsAlthough a multitude of books have been published about spectroscopy, most of them only occasionally refer to biological systems and the specific problems of biomolecular EPR (bioEPR). Biomolecular EPR Spectroscopy provides a practical introduction to bioEPR and demonstrates how this remarkable tool allows researchers to delve into the structural, functional, and analytical analysis of paramagnetic molecules found in the biochemistry of all species on the planet. A Must-Have Reference in an Intrinsically Multidisciplinary FieldThis authoritative reference seamlessly covers all important bioEPR applications, including low-spin and high-spin metalloproteins, spin traps and spin lables, interaction between active sites, and redox systems. It is loaded with practical tricks as well as do's and don'ts that are based on the author's 30 years of experience in the field. The book also comes with an unprecedented set of...

  4. Stable isotope applications in biomolecular structure and mechanisms. A meeting to bring together producers and users of stable-isotope-labeled compounds to assess current and future needs

    Energy Technology Data Exchange (ETDEWEB)

    Trewhella, J.; Cross, T.A.; Unkefer, C.J. [eds.

    1994-12-01

    Knowledge of biomolecular structure is a prerequisite for understanding biomolecular function, and stable isotopes play an increasingly important role in structure determination of biological molecules. The first Conference on Stable Isotope Applications in Biomolecular Structure and Mechanisms was held in Santa Fe, New Mexico, March 27--31, 1994. More than 120 participants from 8 countries and 44 institutions reviewed significant developments, discussed the most promising applications for stable isotopes, and addressed future needs and challenges. Participants focused on applications of stable isotopes for studies of the structure and function of proteins, peptides, RNA, and DNA. Recent advances in NMR techniques neutron scattering, EPR, and vibrational spectroscopy were highlighted in addition to the production and synthesis of labeled compounds. This volume includes invited speaker and poster presentations as well as a set of reports from discussion panels that focused on the needs of the scientific community and the potential roles of private industry, the National Stable Isotope Resource, and the National High Magnetic Field Laboratory in serving those needs. This is the leading abstract. Individual papers are processed separately for the database.

  5. Stable isotope applications in biomolecular structure and mechanisms. A meeting to bring together producers and users of stable-isotope-labeled compounds to assess current and future needs

    International Nuclear Information System (INIS)

    Knowledge of biomolecular structure is a prerequisite for understanding biomolecular function, and stable isotopes play an increasingly important role in structure determination of biological molecules. The first Conference on Stable Isotope Applications in Biomolecular Structure and Mechanisms was held in Santa Fe, New Mexico, March 27--31, 1994. More than 120 participants from 8 countries and 44 institutions reviewed significant developments, discussed the most promising applications for stable isotopes, and addressed future needs and challenges. Participants focused on applications of stable isotopes for studies of the structure and function of proteins, peptides, RNA, and DNA. Recent advances in NMR techniques neutron scattering, EPR, and vibrational spectroscopy were highlighted in addition to the production and synthesis of labeled compounds. This volume includes invited speaker and poster presentations as well as a set of reports from discussion panels that focused on the needs of the scientific community and the potential roles of private industry, the National Stable Isotope Resource, and the National High Magnetic Field Laboratory in serving those needs. This is the leading abstract. Individual papers are processed separately for the database

  6. Application of isothermal titration calorimetry for characterizing thermodynamic parameters of biomolecular interactions: peptide self-assembly and protein adsorption case studies.

    Science.gov (United States)

    Kabiri, Maryam; Unsworth, Larry D

    2014-10-13

    The complex nature of macromolecular interactions usually makes it very hard to identify the molecular-level mechanisms that ultimately dictate the result of these interactions. This is especially evident in the case of biological systems, where the complex interaction of molecules in various situations may be responsible for driving biomolecular interactions themselves but also has a broader effect at the cell and/or tissue level. This review will endeavor to further the understanding of biomolecular interactions utilizing the isothermal titration calorimetry (ITC) technique for thermodynamic characterization of two extremely important biomaterial systems, viz., peptide self-assembly and nonfouling polymer-modified surfaces. The advantages and shortcomings of this technique will be presented along with a thorough review of the recent application of ITC to these two areas. Furthermore, the controversies associated with the enthalpy-entropy compensation effect as well as thermodynamic equilibrium state for such interactions will be discussed.

  7. Development of Cellulose-Based, Nanostructured, Conductive Paper for Biomolecular Extraction and Energy Storage Applications

    OpenAIRE

    Razaq, Aamir

    2011-01-01

    Conductive paper materials consisting of conductive polymers and cellulose are promising for high-tech applications (energy storage and biosciences) due to outstanding aspects of environmental friendliness, mechanical flexibility, electrical conductivity and efficient electroactive behavior. Recently, a conductive composite paper material was developed by covering the individual nanofibers of cellulose from the green algae Cladophora with a polypyrrole (PPy) layer. The PPy-Cladophora cellulos...

  8. Biosensors with Built-In Biomolecular Logic Gates for Practical Applications

    Directory of Open Access Journals (Sweden)

    Yu-Hsuan Lai

    2014-08-01

    Full Text Available Molecular logic gates, designs constructed with biological and chemical molecules, have emerged as an alternative computing approach to silicon-based logic operations. These molecular computers are capable of receiving and integrating multiple stimuli of biochemical significance to generate a definitive output, opening a new research avenue to advanced diagnostics and therapeutics which demand handling of complex factors and precise control. In molecularly gated devices, Boolean logic computations can be activated by specific inputs and accurately processed via bio-recognition, bio-catalysis, and selective chemical reactions. In this review, we survey recent advances of the molecular logic approaches to practical applications of biosensors, including designs constructed with proteins, enzymes, nucleic acids, nanomaterials, and organic compounds, as well as the research avenues for future development of digitally operating “sense and act” schemes that logically process biochemical signals through networked circuits to implement intelligent control systems.

  9. Biomolecular urease thin films grown by laser techniques for blood diagnostic applications

    International Nuclear Information System (INIS)

    Matrix assisted pulsed laser evaporation (MAPLE) was used for growing urease thin films designed for bio-sensor applications in clinical diagnostics. The targets exposed to laser radiation were made from a frozen composite manufactured by dissolving biomaterials in distilled water. We used a UV KrF* (λ = 248 nm, τFWHM ≅ 30 ns, ν = 10 Hz) excimer source for multipulse laser irradiation of the frozen targets cooled with Peltier elements. The laser source was operated at an incident fluence of 0.4 J/cm2. Urease activity and kinetics were assayed by the Worthington method that monitors urea hydrolysis by coupling ammonia production to a glutamate dehydrogenase reaction. A decrease in absorbance was measured at 340 nm and correlated with the enzymatic activity of urease. We show that the urease films obtained by MAPLE techniques remain active up to three months after deposition.

  10. Applicability of carbon and boron nitride nanotubes as biosensors: Effect of biomolecular adsorption on the transport properties of carbon and boron nitride nanotubes

    Science.gov (United States)

    Zhong, Xiaoliang; Mukhopadhyay, Saikat; Gowtham, S.; Pandey, Ravindra; Karna, Shashi P.

    2013-04-01

    The effect of molecular adsorption on the transport properties of single walled carbon and boron nitride nanotubes (CNTs and BNNTs) is investigated using density functional theory and non-equilibrium Green's function methods. The calculated I-V characteristics predict noticeable changes in the conductivity of semiconducting BNNTs due to physisorption of nucleic acid base molecules. Specifically, guanine which binds to the side wall of BNNT significantly enhances its conductivity by introducing conduction channels near the Fermi energy of the bioconjugated system. For metallic CNTs, a large background current masks relatively small changes in current due to the biomolecular adsorption. The results therefore suggest the suitability of BNNTs for biosensing applications.

  11. Biomolecular Science (Fact Sheet)

    Energy Technology Data Exchange (ETDEWEB)

    2012-04-01

    A brief fact sheet about NREL Photobiology and Biomolecular Science. The research goal of NREL's Biomolecular Science is to enable cost-competitive advanced lignocellulosic biofuels production by understanding the science critical for overcoming biomass recalcitrance and developing new product and product intermediate pathways. NREL's Photobiology focuses on understanding the capture of solar energy in photosynthetic systems and its use in converting carbon dioxide and water directly into hydrogen and advanced biofuels.

  12. Conducting polymer based biomolecular electronic devices

    Indian Academy of Sciences (India)

    B D Malhotra; Rahul Singhal

    2003-08-01

    Biomolecular electronics is rapidly evolving from physics, chemistry, biology, electronics and information technology. Organic materials such as proteins, pigments and conducting polymers have been considered as alternatives for carrying out the functions that are presently being performed by semiconductor silicon. Conducting polymers such as polypyrroles, polythiophenes and polyanilines have been projected for applications for a wide range of biomolecular electronic devices such as optical, electronic, drug-delivery, memory and biosensing devices. Our group has been actively working towards the application of conducting polymers to Schottky diodes, metal–insulator–semiconductor (MIS) devices and biosensors for the past 10 years. This paper is a review of some of the results obtained at our laboratory in the area of conducting polymer biomolecular electronics.

  13. Programming in Biomolecular Computation:

    DEFF Research Database (Denmark)

    Hartmann, Lars; Jones, Neil; Simonsen, Jakob Grue;

    2011-01-01

    Our goal is to provide a top-down approach to biomolecular computation. In spite of widespread discussion about connections between biology and computation, one question seems notable by its absence: Where are the programs? We identify a number of common features in programming that seem...... conspicuously absent from the literature on biomolecular computing; to partially redress this absence, we introduce a model of computation that is evidently programmable, by programs reminiscent of low-level computer machine code; and at the same time biologically plausible: its functioning is defined...... by a single and relatively small set of chemical-like reaction rules. Further properties: the model is stored-program: programs are the same as data, so programs are not only executable, but are also compilable and interpretable. It is universal: all computable functions can be computed (in natural ways...

  14. Bipolar electrochemistry for high throughput screening applications

    OpenAIRE

    Munktell, Sara

    2016-01-01

    Bipolar electrochemistry is an interesting concept for high throughput screening techniques due to the ability to induce gradients in a range of materials and their properties, such as composition, particle size, or dopant levels, among many others. One of the key advantages of the method is the ability to test, create or modify materials without the need for a direct electrical connection. In this thesis, the viability of this method has been explored for a range of possible applications, su...

  15. Science Letters: Demonstration of a new biosensing concept for immunodiagnostic applications based on change in surface conductance of antibodies after biomolecular interactions

    Institute of Scientific and Technical Information of China (English)

    VASHIST Sandeep Kumar; KAUR Inderpreet; BAJPAI Ram Prakash; BHARADWAJ Lalit Mohan; TEWARI Rupinder; RAITERI Roberto

    2006-01-01

    We report an important observation that the surface conductivity of antibody layer immobilized on polylysine-coated glass substrate decreases upon the formation of complex with their specific antigens. This change in conductivity has been observed for both monoclonal and polyclonal antibodies. The conductance of monoclonal mouse IgG immobilized on polylysine-coated glass substrate changed from 1.02×l0-8 Ω-1 to 1.41×l0-11 Ω-1 at 10 V when complex is formed due to the specific biomolecular interactions with rabbit anti-mouse IgG F(ab')2. Similar behavior was observed when the same set up was tested in two clinical assays: (1) anti-Leishmania antigen polyclonal antibodies taken from Kala Azar positive patient serum interacting with Leishmania promastigote antigen, and (2) anti-p21 polyclonal antibodies interacting with p21 antigen. The proposed concept can represent a new immunodiagnostic technique and may have wide ranging applications in biosensors and nanobiotechnology too.

  16. Programming in Biomolecular Computation

    DEFF Research Database (Denmark)

    Hartmann, Lars; Jones, Neil; Simonsen, Jakob Grue

    2010-01-01

    Our goal is to provide a top-down approach to biomolecular computation. In spite of widespread discussion about connections between biology and computation, one question seems notable by its absence: Where are the programs? We introduce a model of computation that is evidently programmable......, by programs reminiscent of low-level computer machine code; and at the same time biologically plausible: its functioning is defined by a single and relatively small set of chemical-like reaction rules. Further properties: the model is stored-program: programs are the same as data, so programs are not only...... in a strong sense: a universal algorithm exists, that is able to execute any program, and is not asymptotically inefficient. A prototype model has been implemented (for now in silico on a conventional computer). This work opens new perspectives on just how computation may be specified at the biological level....

  17. Improving interactive TV experience using second screen mobile applications

    OpenAIRE

    Mu, Mu; Knowles, William; Mauthe, Andreas Ulrich; Sani, Yusuf; Race, Nicholas John Paul

    2015-01-01

    The past two decades have seen a shift in the multimedia consumption behaviours from that of collectivism and passivity, to individualism and activity. This paper introduces the architectural design, implementation and user evaluation of a second screen application, which is designed to supersede the traditional user control interface for primary screen interaction. We describe how NSMobile, our second screen application, can be used as a pervasive multimedia platform by integrating user expe...

  18. Event Detection and Sub-state Discovery from Bio-molecular Simulations Using Higher-Order Statistics: Application To Enzyme Adenylate Kinase

    OpenAIRE

    Ramanathan, Arvind; Savol, Andrej J.; Agarwal, Pratul K.; Chennubhotla, Chakra S.

    2012-01-01

    Biomolecular simulations at milli-second and longer timescales can provide vital insights into functional mechanisms. Since post-simulation analyses of such large trajectory data-sets can be a limiting factor in obtaining biological insights, there is an emerging need to identify key dynamical events and relating these events to the biological function online, that is, as simulations are progressing. Recently, we have introduced a novel computational technique, quasi-anharmonic analysis (QAA)...

  19. Development of a nanomaterial bio-screening platform for neurological applications.

    Science.gov (United States)

    Jenkins, Stuart Iain; Roach, Paul; Chari, Divya Maitreyi

    2015-01-01

    Nanoparticle platforms are being intensively investigated for neurological applications. Current biological models used to identify clinically relevant materials have major limitations, e.g. technical/ethical issues with live animal experimentation, failure to replicate neural cell diversity, limited control over cellular stoichiometries and poor reproducibility. High-throughput neuro-mimetic screening systems are required to address these challenges. We describe an advanced multicellular neural model comprising the major non-neuronal/glial cells of the central nervous system (CNS), shown to account for ~99.5% of CNS nanoparticle uptake. This model offers critical advantages for neuro-nanomaterials testing while reducing animal use: one primary source and culture medium for all cell types, standardized biomolecular corona formation and defined/reproducible cellular stoichiometry. Using dynamic time-lapse imaging, we demonstrate in real-time that microglia (neural immune cells) dramatically limit particle uptake in other neural subtypes (paralleling post-mortem observations after nanoparticle injection in vivo), highlighting the utility of the system in predicting neural handling of biomaterials. PMID:25101878

  20. Micro and Nanotechnologies Enhanced Biomolecular Sensing

    Directory of Open Access Journals (Sweden)

    Tza-Huei Wang

    2013-07-01

    Full Text Available This editorial summarizes some of the recent advances of micro and nanotechnology-based tools and devices for biomolecular detection. These include the incorporation of nanomaterials into a sensor surface or directly interfacing with molecular probes to enhance target detection via more rapid and sensitive responses, and the use of self-assembled organic/inorganic nanocomposites that inhibit exceptional spectroscopic properties to enable facile homogenous assays with efficient binding kinetics. Discussions also include some insight into microfluidic principles behind the development of an integrated sample preparation and biosensor platform toward a miniaturized and fully functional system for point of care applications.

  1. Police Applicant Screening: An Analogue Study.

    Science.gov (United States)

    Costello, Raymond M.; And Others

    1982-01-01

    Studied the effect of different base rates of a target phenomenon on psychometric efficiency when an explicit decision-making rule was used to evaluate police officers. Concluded that numerous predictive indices would be required to screen such a heterogeneous population. (Author/JAC)

  2. Organic & Biomolecular Chemistry

    OpenAIRE

    Zhang, Wenyu; Bryson, David I.; Crumpton, Jason B.; Wynn, Jessica; Santos, Webster L.

    2013-01-01

    On-bead high-throughput screening of a medium-sized (1000_2000 Da) branched peptideboronic acid (BPBA) library consisting of 46 656 unique sequences against HIV-1 RRE RNA generated peptides with binding affinities in the low micromolar range. In particular, BPBA1 had a Kd of 1.4 _M with RRE IIB, preference for RNA over DNA (27 fold), and selectivity of up to >75 fold against a panel of RRE IIB variants. Structure_activity studies suggest that the boronic acid moiety and ͐branching in peptide...

  3. Abstractions for biomolecular computations

    CERN Document Server

    Okunoye, Babatunde O

    2008-01-01

    Deoxyribonucleic acid is increasingly being understood to be an informational molecule, capable of information processing.It has found application in the determination of non-deterministic algorithms and in the design of molecular computing devices. This is a theoretical analysis of the mathematical properties and relations of the molecules which constituting DNA, which explains in part why DNA is a successful computing molecule.

  4. Micro- and nanodevices integrated with biomolecular probes

    Science.gov (United States)

    Alapan, Yunus; Icoz, Kutay; Gurkan, Umut A.

    2016-01-01

    Understanding how biomolecules, proteins and cells interact with their surroundings and other biological entities has become the fundamental design criterion for most biomedical micro- and nanodevices. Advances in biology, medicine, and nanofabrication technologies complement each other and allow us to engineer new tools based on biomolecules utilized as probes. Engineered micro/nanosystems and biomolecules in nature have remarkably robust compatibility in terms of function, size, and physical properties. This article presents the state of the art in micro- and nanoscale devices designed and fabricated with biomolecular probes as their vital constituents. General design and fabrication concepts are presented and three major platform technologies are highlighted: microcantilevers, micro/nanopillars, and microfluidics. Overview of each technology, typical fabrication details, and application areas are presented by emphasizing significant achievements, current challenges, and future opportunities. PMID:26363089

  5. Application of TruScreen in detecting ASCUS patients

    Institute of Scientific and Technical Information of China (English)

    Weihong Li; Yu Guo; Haiyan Niu; Song Jin; Li Wang

    2011-01-01

    Objective:To explore the application of cervical cancer screening system, TruScreen in detecting atypical squamous cell of undetermined significance(ASCUS) patients.Methods: A total of42 cases were selected, who were diagnosed asASCUSby thinprep cytologic test(TCT). Area from site15 to20, site21 to32 were detected by TruScreen. And the result was compared with those of cases which had positive pathological result of cervical biopsy.Results:There were 16 cases with abnormal pathological result inASCUS cases, including 6 cases with cervical intraepithelial neoplasia(CIN) Ⅰ,6 cases withCINⅡ,3 cases withCINⅢ and 1 case with infiltrating carcinoma. The consistency betweenTCT and pathological test was38.10% (16/42). The positive rate of TruScreen at site15-20 was 61.91% (26/42). There was significant difference in consistency with pathological test betweenTCT and TruScreen (x2=4.762,P=0.029). The positive rate of TruScreen at site21-32 was66.67% (28/42)(Kappa=0.181,P=0.016). There was significant difference in consistency with pathological test betweenTCT and TruScreen(x2=9.4919,P=0.002).And no case was missed when site 21-32 of patients withCIN栻 and above were detected by TruScreen. Conclusions:TruScreen is effective in detectingASCUS patients.

  6. Biomolecular simulation on thousands of processors

    Science.gov (United States)

    Phillips, James Christopher

    Classical molecular dynamics simulation is a generally applicable method for the study of biomolecular aggregates of proteins, lipids, and nucleic acids. As experimental techniques have revealed the structures of larger and more complex biomolecular machines, the time required to complete even a single meaningful simulation of such systems has become prohibitive. We have developed the program NAMD to simulate systems of 50,000--500,000 atoms efficiently with full electrostatics on parallel computers with 1000 and more processors. NAMD's scalability is achieved through latency tolerant adaptive message-driven execution and measurement-based load balancing. NAMD is implemented in C++ and uses object-oriented design and threads to shield the basic algorithms from the necessary complexity of high-performance parallel execution. Apolipoprotein A-I is the primary protein constituent of high density lipoprotein particles, which transport cholesterol in the bloodstream. In collaboration with A. Jonas, we have constructed and simulated models of the nascent discoidal form of these particles, providing theoretical insight to the debate regarding the lipid-bound structure of the protein. Recently, S. Sligar and coworkers have created 10 nm phospholipid bilayer nanoparticles comprising a small lipid bilayer disk solubilized by synthetic membrane scaffold proteins derived from apolipoprotein A-I. Membrane proteins may be embedded in the water-soluble disks, with various medical and technological applications. We are working to develop variant scaffold proteins that produce disks of greater size, stability, and homogeneity. Our simulations have demonstrated a significant deviation from idealized cylindrical structure, and are being used in the interpretation of small angle x-ray scattering data.

  7. Application of Plagiarism Screening Software in the Chemical Engineering Curriculum

    Science.gov (United States)

    Cooper, Matthew E.; Bullard, Lisa G.

    2014-01-01

    Plagiarism is an area of increasing concern for written ChE assignments, such as laboratory and design reports, due to ease of access to text and other materials via the internet. This study examines the application of plagiarism screening software to four courses in a university chemical engineering curriculum. The effectiveness of plagiarism…

  8. Biomolecular Detection employing the Interferometric Reflectance Imaging Sensor (IRIS)

    OpenAIRE

    Carlos A Lopez; George G Daaboul; Ahn, Sunmin; Reddington, Alexander P.; Monroe, Margo R.; Zhang, Xirui; Irani, Rostem J.; Yu, Chunxiao; Genco, Caroline A.; Cretich, Marina; Chiari, Marcella; Goldberg, Bennett B.; Connor, John H.; Ünlü, M. Selim

    2011-01-01

    The sensitive measurement of biomolecular interactions has use in many fields and industries such as basic biology and microbiology, environmental/agricultural/biodefense monitoring, nanobiotechnology, and more. For diagnostic applications, monitoring (detecting) the presence, absence, or abnormal expression of targeted proteomic or genomic biomarkers found in patient samples can be used to determine treatment approaches or therapy efficacy. In the research arena, information on molecular aff...

  9. Event Detection and Sub-state Discovery from Bio-molecular Simulations Using Higher-Order Statistics: Application To Enzyme Adenylate Kinase

    Science.gov (United States)

    Ramanathan, Arvind; Savol, Andrej J.; Agarwal, Pratul K.; Chennubhotla, Chakra S.

    2012-01-01

    Biomolecular simulations at milli-second and longer timescales can provide vital insights into functional mechanisms. Since post-simulation analyses of such large trajectory data-sets can be a limiting factor in obtaining biological insights, there is an emerging need to identify key dynamical events and relating these events to the biological function online, that is, as simulations are progressing. Recently, we have introduced a novel computational technique, quasi-anharmonic analysis (QAA) (PLoS One 6(1): e15827), for partitioning the conformational landscape into a hierarchy of functionally relevant sub-states. The unique capabilities of QAA are enabled by exploiting anharmonicity in the form of fourth-order statistics for characterizing atomic fluctuations. In this paper, we extend QAA for analyzing long time-scale simulations online. In particular, we present HOST4MD - a higher-order statistical toolbox for molecular dynamics simulations, which (1) identifies key dynamical events as simulations are in progress, (2) explores potential sub-states and (3) identifies conformational transitions that enable the protein to access those sub-states. We demonstrate HOST4MD on micro-second time-scale simulations of the enzyme adenylate kinase in its apo state. HOST4MD identifies several conformational events in these simulations, revealing how the intrinsic coupling between the three sub-domains (LID, CORE and NMP) changes during the simulations. Further, it also identifies an inherent asymmetry in the opening/closing of the two binding sites. We anticipate HOST4MD will provide a powerful and extensible framework for detecting biophysically relevant conformational coordinates from long time-scale simulations. PMID:22733562

  10. Integrative NMR for biomolecular research.

    Science.gov (United States)

    Lee, Woonghee; Cornilescu, Gabriel; Dashti, Hesam; Eghbalnia, Hamid R; Tonelli, Marco; Westler, William M; Butcher, Samuel E; Henzler-Wildman, Katherine A; Markley, John L

    2016-04-01

    NMR spectroscopy is a powerful technique for determining structural and functional features of biomolecules in physiological solution as well as for observing their intermolecular interactions in real-time. However, complex steps associated with its practice have made the approach daunting for non-specialists. We introduce an NMR platform that makes biomolecular NMR spectroscopy much more accessible by integrating tools, databases, web services, and video tutorials that can be launched by simple installation of NMRFAM software packages or using a cross-platform virtual machine that can be run on any standard laptop or desktop computer. The software package can be downloaded freely from the NMRFAM software download page ( http://pine.nmrfam.wisc.edu/download_packages.html ), and detailed instructions are available from the Integrative NMR Video Tutorial page ( http://pine.nmrfam.wisc.edu/integrative.html ). PMID:27023095

  11. Application of neural networks to waste site screening

    International Nuclear Information System (INIS)

    Waste site screening requires knowledge of the actual concentrations of hazardous materials and rates of flow around and below the site with time. The present approach consists primarily of drilling boreholes near contaminated sites and chemically analyzing the extracted physical samples and processing the data. This is expensive and time consuming. The feasibility of using neural network techniques to reduce the cost of waste site screening was investigated. Two neural network techniques, gradient descent back propagation and fully recurrent back propagation were utilized. The networks were trained with data received from Westinghouse Hanford Corporation. The results indicate that the network trained with the fully recurrent technique shows satisfactory generalization capability. The predicted results are close to the results obtained from a mathematical flow prediction model. It is possible to develop a new tool to predict the waste plume, thus substantially reducing the number of the bore sites and samplings. There are a variety of applications for this technique in environmental site screening and remediation. One of the obvious applications would be for optimum well siting. A neural network trained from the existing sampling data could be utilized to decide where would be the best position for the next bore site. Other applications are discussed in the report

  12. [Advances in biomolecular machine: methane monooxygenases].

    Science.gov (United States)

    Lu, Jixue; Wang, Shizhen; Fang, Baishan

    2015-07-01

    Methane monooxygenases (MMO), regarded as "an amazing biomolecular machine", catalyze the oxidation of methane to methanol under aerobic conditions. MMO catalyze the oxidation of methane elaborately, which is a novel way to catalyze methane to methanol. Furthermore, MMO can inspire the biomolecular machine design. In this review, we introduced MMO including structure, gene and catalytic mechanism. The history and the taxonomy of MMO were also introduced. PMID:26647577

  13. Microwave spectroscopy of biomolecular building blocks.

    Science.gov (United States)

    Alonso, José L; López, Juan C

    2015-01-01

    Microwave spectroscopy, considered as the most definitive gas phase structural probe, is able to distinguish between different conformational structures of a molecule, because they have unique spectroscopic constants and give rise to distinct individual rotational spectra.Previously, application of this technique was limited to molecular specimens possessing appreciable vapor pressures, thus discarding the possibility of studying many other molecules of biological importance, in particular those with high melting points, which had a tendency to undergo thermal reactions, and ultimately degradation, upon heating.Nowadays, the combination of laser ablation with Fourier transform microwave spectroscopy techniques, in supersonic jets, has enabled the gas-phase study of such systems. In this chapter, these techniques, including broadband spectroscopy, as well as results of their application into the study of the conformational panorama and structure of biomolecular building blocks, such as amino acids, nucleic bases, and monosaccharides, are briefly discussed, and with them, the tools for conformational assignation - rotational constants, nuclear quadrupole coupling interaction, and dipole moment. PMID:25721775

  14. Rapid screening of potential metallic glasses for biomedical applications

    International Nuclear Information System (INIS)

    This paper presents a rapid screening process to select potential titanium and zirconium based metallic glasses (MGs) for bio-material applications. Electrochemical activity of 7 MGs including 6 bulk metallic glasses and 1 thin-film deposited MG in simulation body and human serum is first inspected. A low-voltage potential state test is also developed to simulate the cell membrane potential that the implant MGs will suffer. Results show that the MGs composed of Ti65Si15Ta10Zr10 and Ta57Zr23Cu12Ti8 exhibit excellent electrochemical stability in both simulation body fluid and human serum. In addition, the copper content in the MGs plays an important role on the electrochemical activity. MGs with the copper content higher than 17.5% show significant electrochemical responses. The cytotoxicity of the solid MG samples and the corrosion released ions are also evaluated by an in-vitro MTT test utilizing the murine bone marrow stem cells. Results indicate that all the solid MG samples show no acute cytotoxicity yet the corrosion released ions show significant toxicity for murine bone marrow stem cells. The rapid screening process developed in the present study suggests that the Ti65Si15Ta10Zr10 metallic glass has high potential for biomedical applications due to its good electrochemical stability and very low cytotoxicity. - Highlights: • A rapid electrochemical cycle screening process is proposed. • This process can select potential metallic glasses for bio-material applications. • The Ti65Si15Ta10Zr10 metallic glass exhibits the best response and high potential

  15. A review of current sleep screening applications for smartphones

    International Nuclear Information System (INIS)

    Sleep disorders are a common problem and contribute to a wide range of healthcare issues. The societal and financial costs of sleep disorders are enormous. Sleep-related disorders are often diagnosed with an overnight sleep test called a polysomnogram, or sleep study involving the measurement of brain activity through the electroencephalogram. Other parameters monitored include oxygen saturation, respiratory effort, cardiac activity (through the electrocardiogram), as well as video recording, sound and movement activity. Monitoring can be costly and removes the patients from their normal sleeping environment, preventing repeated unbiased studies. The recent increase in adoption of smartphones, with high quality on-board sensors has led to the proliferation of many sleep screening applications running on the phone. However, with the exception of simple questionnaires, no existing sleep-related application available for smartphones is based on scientific evidence. This paper reviews the existing smartphone applications landscape used in the field of sleep disorders and proposes possible advances to improve screening approaches. (topical review)

  16. Integrated Spintronic Platforms for Biomolecular Recognition Detection

    Science.gov (United States)

    Martins, V. C.; Cardoso, F. A.; Loureiro, J.; Mercier, M.; Germano, J.; Cardoso, S.; Ferreira, R.; Fonseca, L. P.; Sousa, L.; Piedade, M. S.; Freitas, P. P.

    2008-06-01

    This paper covers recent developments in magnetoresistive based biochip platforms fabricated at INESC-MN, and their application to the detection and quantification of pathogenic waterborn microorganisms in water samples for human consumption. Such platforms are intended to give response to the increasing concern related to microbial contaminated water sources. The presented results concern the development of biological active DNA chips and protein chips and the demonstration of the detection capability of the present platforms. Two platforms are described, one including spintronic sensors only (spin-valve based or magnetic tunnel junction based), and the other, a fully scalable platform where each probe site consists of a MTJ in series with a thin film diode (TFD). Two microfluidic systems are described, for cell separation and concentration, and finally, the read out and control integrated electronics are described, allowing the realization of bioassays with a portable point of care unit. The present platforms already allow the detection of complementary biomolecular target recognition with 1 pM concentration.

  17. Virtual screening of electron acceptor materials for organic photovoltaic applications

    Science.gov (United States)

    Halls, Mathew D.; Djurovich, Peter J.; Giesen, David J.; Goldberg, Alexander; Sommer, Jonathan; McAnally, Eric; Thompson, Mark E.

    2013-10-01

    Virtual screening involves the generation of structure libraries, automated analysis to predict properties related to application performance and subsequent screening to identify lead systems and estimate critical structure-property limits across a targeted chemical design space. This approach holds great promise for informing experimental discovery and development efforts for next-generation materials, such as organic semiconductors. In this work, the virtual screening approach is illustrated for nitrogen-substituted pentacene molecules to identify systems for development as electron acceptor materials for use in organic photovoltaic (OPV) devices. A structure library of tetra-azapentacenes (TAPs) was generated by substituting four nitrogens for CH at 12 sites on the pentacene molecular framework. Molecular properties (e.g. ELUMO, Eg and μ) were computed for each candidate structure using hybrid DFT at the B3LYP/6-311G** level of theory. The resulting TAPs library was then analyzed with respect to intrinsic properties associated with OPV acceptor performance. Marcus reorganization energies for charge transport for the most favorable TAP candidates were then calculated to further determine suitability as OPV electron acceptors. The synthesis, characterization and OPV device testing of TAP materials is underway, guided by these results.

  18. Flourescence from Gas-Phase Biomolecular Ions

    DEFF Research Database (Denmark)

    Nielsen, Steen Brøndsted

    2013-01-01

    from experiments on dye-derivatised biomolecular ions that provide important information on folding/unfolding processes and local structural changes are presented. Examples included here are a model DNA duplex, the Trp-cage protein, polyproline peptides, and the cytochrome c heme protein. The chapter......This chapter deals with measurements of fluorescence from electronically excited biomolecular ions where there are no interactions with an external environment. Biomolecules with no natural fluorophores are labelled with a dye for such experiments. First, some of the advantages, but also...

  19. Role of biomolecular logic systems in biosensors and bioactuators

    Science.gov (United States)

    Mailloux, Shay; Katz, Evgeny

    2014-09-01

    An overview of recent advances in biosensors and bioactuators based on biocomputing systems is presented. Biosensors digitally process multiple biochemical signals through Boolean logic networks of coupled biomolecular reactions and produce an output in the form of a YES/NO response. Compared to traditional single-analyte sensing devices, the biocomputing approach enables high-fidelity multianalyte biosensing, which is particularly beneficial for biomedical applications. Multisignal digital biosensors thus promise advances in rapid diagnosis and treatment of diseases by processing complex patterns of physiological biomarkers. Specifically, they can provide timely detection and alert medical personnel of medical emergencies together with immediate therapeutic intervention. Application of the biocomputing concept has been successfully demonstrated for systems performing logic analysis of biomarkers corresponding to different injuries, particularly as exemplified for liver injury. Wide-ranging applications of multianalyte digital biosensors in medicine, environmental monitoring, and homeland security are anticipated. "Smart" bioactuators, for signal-triggered drug release, for example, were designed by interfacing switchable electrodes with biocomputing systems. Integration of biosensing and bioactuating systems with biomolecular information processing systems advances the potential for further scientific innovations and various practical applications.

  20. Advances in integrative modeling of biomolecular complexes

    NARCIS (Netherlands)

    Karaca, E.; Bonvin, A.M.J.J.

    2013-01-01

    High-resolution structural information is needed in order to unveil the underlying mechanistic of biomolecular function. Due to the technical limitations or the nature of the underlying complexes, acquiring atomic resolution information is difficult for many challenging systems, while, often, low-re

  1. Transition metal bioconjugates with an organometallic link between the metal and the biomolecular scaffold

    OpenAIRE

    Monney, Angèle; Albrecht, Martin

    2013-01-01

    This overview compiles recent advances in the synthesis and application of organometallic bioconjugates that comprise a metal–carbon linkage between the metal and the biomolecular scaffold. This specific area of bioorganometallic chemistry has been spurred by the discovery of naturally occurring bioorganometallic compounds and afforded organometallic bioconjugates from transition metals binding to amino acids, nucleic acids and other biomolecules. These artificial bioorganometallic compounds ...

  2. Computer Programming and Biomolecular Structure Studies: A Step beyond Internet Bioinformatics

    Science.gov (United States)

    Likic, Vladimir A.

    2006-01-01

    This article describes the experience of teaching structural bioinformatics to third year undergraduate students in a subject titled "Biomolecular Structure and Bioinformatics." Students were introduced to computer programming and used this knowledge in a practical application as an alternative to the well established Internet bioinformatics…

  3. Microfluidic-Enabled Print-to-Screen Platform for High-Throughput Screening of Combinatorial Chemotherapy.

    Science.gov (United States)

    Ding, Yuzhe; Li, Jiannan; Xiao, Wenwu; Xiao, Kai; Lee, Joyce; Bhardwaj, Urvashi; Zhu, Zijie; Digiglio, Philip; Yang, Gaomai; Lam, Kit S; Pan, Tingrui

    2015-10-20

    Since the 1960s, combination chemotherapy has been widely utilized as a standard method to treat cancer. However, because of the potentially enormous number of drug candidates and combinations, conventional identification methods of the effective drug combinations are usually associated with significantly high operational costs, low throughput screening, laborious and time-consuming procedures, and ethical concerns. In this paper, we present a low-cost, high-efficiency microfluidic print-to-screen (P2S) platform, which integrates combinatorial screening with biomolecular printing for high-throughput screening of anticancer drug combinations. This P2S platform provides several distinct advantages and features, including automatic combinatorial printing, high-throughput parallel drug screening, modular disposable cartridge, and biocompatibility, which can potentially speed up the entire discovery cycle of potent drug combinations. Microfluidic impact printing utilizing plug-and-play microfluidic cartridges is experimentally characterized with controllable droplet volume and accurate positioning. Furthermore, the combinatorial print-to-screen assay is demonstrated in a proof-of-concept biological experiment which can identify the positive hits among the entire drug combination library in a parallel and rapid manner. Overall, this microfluidic print-to-screen platform offers a simple, low-cost, high-efficiency solution for high-throughput large-scale combinatorial screening and can be applicable for various emerging applications in drug cocktail discovery. PMID:26334956

  4. Perspective: Coarse-grained models for biomolecular systems

    Science.gov (United States)

    Noid, W. G.

    2013-09-01

    By focusing on essential features, while averaging over less important details, coarse-grained (CG) models provide significant computational and conceptual advantages with respect to more detailed models. Consequently, despite dramatic advances in computational methodologies and resources, CG models enjoy surging popularity and are becoming increasingly equal partners to atomically detailed models. This perspective surveys the rapidly developing landscape of CG models for biomolecular systems. In particular, this review seeks to provide a balanced, coherent, and unified presentation of several distinct approaches for developing CG models, including top-down, network-based, native-centric, knowledge-based, and bottom-up modeling strategies. The review summarizes their basic philosophies, theoretical foundations, typical applications, and recent developments. Additionally, the review identifies fundamental inter-relationships among the diverse approaches and discusses outstanding challenges in the field. When carefully applied and assessed, current CG models provide highly efficient means for investigating the biological consequences of basic physicochemical principles. Moreover, rigorous bottom-up approaches hold great promise for further improving the accuracy and scope of CG models for biomolecular systems.

  5. MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations

    Science.gov (United States)

    Vergara-Perez, Sandra; Marucho, Marcelo

    2016-01-01

    One of the most used and efficient approaches to compute electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation. There are several software packages available that solve the PB equation for molecules in aqueous electrolyte solutions. Most of these software packages are useful for scientists with specialized training and expertise in computational biophysics. However, the user is usually required to manually take several important choices, depending on the complexity of the biological system, to successfully obtain the numerical solution of the PB equation. This may become an obstacle for researchers, experimentalists, even students with no special training in computational methodologies. Aiming to overcome this limitation, in this article we present MPBEC, a free, cross-platform, open-source software that provides non-experts in the field an easy and efficient way to perform biomolecular electrostatic calculations on single processor computers. MPBEC is a Matlab script based on the Adaptative Poisson-Boltzmann Solver, one of the most popular approaches used to solve the PB equation. MPBEC does not require any user programming, text editing or extensive statistical skills, and comes with detailed user-guide documentation. As a unique feature, MPBEC includes a useful graphical user interface (GUI) application which helps and guides users to configure and setup the optimal parameters and approximations to successfully perform the required biomolecular electrostatic calculations. The GUI also incorporates visualization tools to facilitate users pre- and post-analysis of structural and electrical properties of biomolecules.

  6. Improvements in continuum modeling for biomolecular systems

    CERN Document Server

    Qiao, Yu

    2015-01-01

    Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the Poisson-Boltzmann (PB)/Poisson-Nernst-Planck (PNP) equations has made great contributions towards simulation of these processes. However, the model has shortcomings in its commonly used form and cannot capture (or cannot accurately capture) some important physical properties of biological systems. Considerable efforts have been made to improve the continuum model to account for discrete particle interactions and to make progress in numerical methods to provide accurate and efficient simulation. This review will summarize recent main improvements in continuum modeling for biomolecular systems, with focus on the size-modified models, the coupling of the classical density functional theory and PNP equations, the coupling of polar and nonpolar interactions, and numerical progress.

  7. A statistical mechanical description of biomolecular hydration

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-02-01

    We present an efficient and accurate theoretical description of the structural hydration of biological macromolecules. The hydration of molecules of almost arbitrary size (tRNA, antibody-antigen complexes, photosynthetic reaction centre) can be studied in solution and in the crystal environment. The biomolecular structure obtained from x-ray crystallography, NMR, or modeling is required as input information. The structural arrangement of water molecules near a biomolecular surface is represented by the local water density analogous to the corresponding electron density in an x-ray diffraction experiment. The water-density distribution is approximated in terms of two- and three-particle correlation functions of solute atoms with water using a potentials-of-mean-force expansion.

  8. Visualization of confocal microscopic biomolecular data

    Science.gov (United States)

    Liu, Zhanping; Moorhead, Robert J., II

    2005-04-01

    Biomolecular visualization facilitates insightful interpretation of molecular structures and complex mechanisms underlying bio-chemical processes. Effective visualization techniques are required to deal with confocal microscopic biomolecular data in which intricate structures, fine features, and obscure patterns might be overlooked without sophisticated data processing and image synthesis. This paper presents major challenges in visualizing confocal microscopic biomolecular data, followed by a survey of related work. We then introduce a case study conducted to investigate the interaction between two proteins contained in a budding yeast saccharomyces cerevisiae by embedding custom modules in Amira. The multi-channel confocal microscopic volume data was first processed using an exponential operator to correct z-drop artifacts introduced during data acquisition. Channel correlation was then exploited to extract the overlap between the proteins as a new channel to represent the interaction while a statistical method was employed to compute the intensity of interaction to locate hot spots. To take advantage of crisp surface representation of region boundaries by iso-surfaces and visually pleasing translucent delineation of dense volumes by volume rendering, we adopted hybrid rendering that incorporates these two methods to display clear-cut protein boundaries, amorphous interior materials, and the scattered interaction in the same view volume with suppressed and highlighted parts selected by the user. The highlighted overlap helped biologists learn where the interaction happens and how it spreads, particularly when the volume was investigated in an immersive Cave Automatic Virtual Environment (CAVE) for intuitive comprehension of the data.

  9. Biomolecular interactions: essential instrumentation methods.

    Science.gov (United States)

    Messina, Paula Veronica; Ruso, Juan Manuel

    2013-01-01

    The main goal of this review is to outline the basic principles and applications of the broad range of modern biophysical technical methods used to study the different aspects of protein–ligand interactions by discussing such aspects as newer systems, unusual approaches and highly used techniques.

  10. Barcoded microchips for biomolecular assays.

    Science.gov (United States)

    Zhang, Yi; Sun, Jiashu; Zou, Yu; Chen, Wenwen; Zhang, Wei; Xi, Jianzhong Jeff; Jiang, Xingyu

    2015-01-20

    Multiplexed assay of analytes is of great importance for clinical diagnostics and other analytical applications. Barcode-based bioassays with the ability to encode and decode may realize this goal in a straightforward and consistent manner. We present here a microfluidic barcoded chip containing several sets of microchannels with different widths, imitating the commonly used barcode. A single barcoded microchip can carry out tens of individual protein/nucleic acid assays (encode) and immediately yield all assay results by a portable barcode reader or a smartphone (decode). The applicability of a barcoded microchip is demonstrated by human immunodeficiency virus (HIV) immunoassays for simultaneous detection of three targets (anti-gp41 antibody, anti-gp120 antibody, and anti-gp36 antibody) from six human serum samples. We can also determine seven pathogen-specific oligonucleotides by a single chip containing both positive and negative controls.

  11. The Dutch periodontal screening index validation and its application in The Netherlands

    NARCIS (Netherlands)

    U. van der Velden

    2009-01-01

    Objective: To provide evidence that the Dutch periodontal screening index (DPSI) is a valuable tool for the screening of the periodontal status and to evaluate the application of the DPSI by general practitioners in the Netherlands. Material and methods: To assess the validity of the DPSI, an availa

  12. Biomolecular Assembly of Gold Nanocrystals

    Energy Technology Data Exchange (ETDEWEB)

    Micheel, Christine Marya [Univ. of California, Berkeley, CA (United States)

    2005-05-20

    Over the past ten years, methods have been developed to construct discrete nanostructures using nanocrystals and biomolecules. While these frequently consist of gold nanocrystals and DNA, semiconductor nanocrystals as well as antibodies and enzymes have also been used. One example of discrete nanostructures is dimers of gold nanocrystals linked together with complementary DNA. This type of nanostructure is also known as a nanocrystal molecule. Discrete nanostructures of this kind have a number of potential applications, from highly parallel self-assembly of electronics components and rapid read-out of DNA computations to biological imaging and a variety of bioassays. My research focused in three main areas. The first area, the refinement of electrophoresis as a purification and characterization method, included application of agarose gel electrophoresis to the purification of discrete gold nanocrystal/DNA conjugates and nanocrystal molecules, as well as development of a more detailed understanding of the hydrodynamic behavior of these materials in gels. The second area, the development of methods for quantitative analysis of transmission electron microscope data, used computer programs written to find pair correlations as well as higher order correlations. With these programs, it is possible to reliably locate and measure nanocrystal molecules in TEM images. The final area of research explored the use of DNA ligase in the formation of nanocrystal molecules. Synthesis of dimers of gold particles linked with a single strand of DNA possible through the use of DNA ligase opens the possibility for amplification of nanostructures in a manner similar to polymerase chain reaction. These three areas are discussed in the context of the work in the Alivisatos group, as well as the field as a whole.

  13. Simulation of Parallel Logical Operations with Biomolecular Computing

    Directory of Open Access Journals (Sweden)

    Mahnaz Kadkhoda

    2008-01-01

    Full Text Available Biomolecular computing is the computational method that uses the potential of DNA as a parallel computing device. DNA computing can be used to solve NP-complete problems. An appropriate application of DNA computation is large-scale evaluation of parallel computation models such as Boolean Circuits. In this study, we present a molecular-based algorithm for evaluation of Nand-based Boolean Circuits. The contribution of this paper is that the proposed algorithm has been implemented using only three molecular operations and the number of passes in each level is decreased to less than half of previously addressed in the literature. Thus, the proposed algorithm is much easier to implement in the laboratory.

  14. Perspective: Markov Models for Long-Timescale Biomolecular Dynamics

    CERN Document Server

    Schwantes, Christian R; Pande, Vijay S

    2014-01-01

    Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is insufficient, as researchers must be able to transform the data in a simulation trajectory into specific scientific insights. Although this analysis step has often been taken for granted, it deserves further attention as large-scale simulations become increasingly routine. In this perspective, we discuss the application of Markov models to the analysis of large-scale biomolecular simulations. We draw attention to recent improvements in the construction of these models as well as several important open issues. In addition, we highlight recent theoretical advances that pave the way for a new generation of models of molecular kinetics.

  15. A globally applicable screening model for detecting individuals with undiagnosed diabetes

    DEFF Research Database (Denmark)

    Vistisen, Dorte; Lee, Crystal M Y; Colagiuri, Stephen;

    2012-01-01

    Current risk scores for undiagnosed diabetes are additive in structure. We sought to derive a globally applicable screening model based on established non-invasive risk factors for diabetes but with a more flexible structure....

  16. Nanotube-Based Chemical and Biomolecular Sensors

    Institute of Scientific and Technical Information of China (English)

    J.Koh; B.Kim; S.Hong; H.Lim; H.C.Choi

    2008-01-01

    We present a brief review about recent results regarding carbon nanotube (CNT)-based chemical and biomolecular sensors. For the fabrication of CNT-based sensors, devices containing CNT channels between two metal electrodes are first fabricated usually via chemical vapor deposition (CVD) process or "surface programmed assembly" method. Then, the CNT surfaces are often functionalized to enhance the selectivity of the sensors. Using this process, highly-sensitive CNT-based sensors can be fabricated for the selective detection of various chemical and biological molecules such as hydrogen, ammonia, carbon monoxide, chlorine gas, DNA, glucose, alcohol, and proteins.

  17. Azurin for Biomolecular Electronics: a Reliability Study

    Science.gov (United States)

    Bramanti, Alessandro; Pompa, Pier Paolo; Maruccio, Giuseppe; Calabi, Franco; Arima, Valentina; Cingolani, Roberto; Corni, Stefano; Di Felice, Rosa; De Rienzo, Francesca; Rinaldi, Ross

    2005-09-01

    The metalloprotein azurin, used in biomolecular electronics, is investigated with respect to its resilience to high electric fields and ambient conditions, which are crucial reliability issues. Concerning the effect of electric fields, two models of different complexity agree indicating an unexpectedly high robustness. Experiments in device-like conditions confirm that no structural modifications occur, according to fluorescence spectra, even after a 40-min exposure to tens of MV/m. Ageing is then investigated experimentally, at ambient conditions and without field, over several days. Only a small conformational rearrangement is observed in the first tens of hours, followed by an equilibrium state.

  18. Scalable Molecular Dynamics for Large Biomolecular Systems

    Directory of Open Access Journals (Sweden)

    Robert K. Brunner

    2000-01-01

    Full Text Available We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program NAMD. With an object-based hybrid force and spatial decomposition scheme, and an aggressive measurement-based predictive load balancing framework, we have attained speeds and speedups that are much higher than any reported in literature so far. The paper first summarizes the broad methodology we are pursuing, and the basic parallelization scheme we used. It then describes the optimizations that were instrumental in increasing performance, and presents performance results on benchmark simulations.

  19. Hazard screening application guide. Safety Analysis Report Update Program

    Energy Technology Data Exchange (ETDEWEB)

    None

    1992-06-01

    The basic purpose of hazard screening is to group precesses, facilities, and proposed modifications according to the magnitude of their hazards so as to determine the need for and extent of follow on safety analysis. A hazard is defined as a material, energy source, or operation that has the potential to cause injury or illness in human beings. The purpose of this document is to give guidance and provide standard methods for performing hazard screening. Hazard screening is applied to new and existing facilities and processes as well as to proposed modifications to existing facilities and processes. The hazard screening process evaluates an identified hazards in terms of the effects on people, both on-site and off-site. The process uses bounding analyses with no credit given for mitigation of an accident with the exception of certain containers meeting DOT specifications. The process is restricted to human safety issues only. Environmental effects are addressed by the environmental program. Interfaces with environmental organizations will be established in order to share information.

  20. Application of neural networks to waste site screening

    Energy Technology Data Exchange (ETDEWEB)

    Dabiri, A.E.; Kraft, T.; Hilton, J.M. [Science Applications International Corp., San Diego, CA (United States)

    1993-03-01

    Waste site screening requires knowledge of the actual concentrations of hazardous materials and rates of flow around and below the site with time. The present approach to site screening consists primarily of drilling, boreholes near contaminated site and chemically analyzing the extracted physical samples and processing the data. In addition, hydraulic and geochemical soil properties are obtained so that numerical simulation models can be used to interpret and extrapolate the field data. The objective of this work is to investigate the feasibility of using neural network techniques to reduce the cost of waste site screening. A successful technique may lead to an ability to reduce the number of boreholes and the number of samples analyzed from each borehole to properly screen the waste site. The analytic tool development described here is inexpensive because it makes use of neural network techniques that can interpolate rapidly and which can learn how to analyze data rather than having to be explicitly programmed. In the following sections, data collection and data analyses will be described, followed by a section on different neural network techniques used. The results will be presented and compared with mathematical model. Finally, the last section will summarize the research work performed and make several recommendations for future work.

  1. Systematic evaluation of bundled SPC water for biomolecular simulations.

    Science.gov (United States)

    Gopal, Srinivasa M; Kuhn, Alexander B; Schäfer, Lars V

    2015-04-01

    molecules between the active site and the bulk. Our results form a basis for assessing the accuracy that can be expected from bundled SPC water models. At the same time, this study also highlights the importance of evaluating beforehand the effects of water bundling on the biomolecular system of interest for a particular multiscale simulation application.

  2. ssDNA-Functionalized Nanoceria: A Redox-Active Aptaswitch for Biomolecular Recognition.

    Science.gov (United States)

    Bülbül, Gonca; Hayat, Akhtar; Andreescu, Silvana

    2016-04-01

    Quantification of biomolecular binding events is a critical step for the development of biorecognition assays for diagnostics and therapeutic applications. This paper reports the design of redox-active switches based on aptamer conjugated nanoceria for detection and quantification of biomolecular recognition. It is shown that the conformational transition state of the aptamer on nanoceria, combined with the redox properties of these particles can be used to create surface based structure switchable aptasensing platforms. Changes in the redox properties at the nanoceria surface upon binding of the ssDNA and its target analyte enables rapid and highly sensitive measurement of biomolecular interactions. This concept is demonstrated as a general applicable method to the colorimetric detection of DNA binding events. An example of a nanoceria aptaswitch for the colorimetric sensing of Ochratoxin A (OTA) and applicability to other targets is provided. The system can sensitively and selectivity detect as low as 0.15 × 10(-9) m OTA. This novel assay is simple in design and does not involve oligonucleotide labeling or elaborate nanoparticle modification steps. The proposed mechanism discovered here opens up a new way of designing optical sensing methods based on aptamer recognition. This approach can be broadly applicable to many bimolecular recognition processes and related applications. PMID:26844813

  3. Bio-molecular sensors based on guided mode resonance filters

    Science.gov (United States)

    Saleem, M. R.; Ali, R.; Honkanen, S.; Turunen, J.

    2016-08-01

    In this work a low surface roughness and homogenous, high refractive index, and amorphous TiO2 layer on corrugated structures of diffractive optical element is coated by Atomic Layer Deposition (ALD) for biosensors. The design of Guided Mode Resonance Filters (GMRFs) is based on refractive indices and thicknesses of the waveguide biomolecular layers. The designed spectral shifts are calculated by Fourier Modal Method (FMM) and depend on the magnitude of the variations in refractive index of the biomolecular layer on waveguide structures. Furthermore, the sensitivity of the biomolecular sensors depends on the thickness of biomolecular layer and periodicity of the structures. The waveguide structures designed for larger periods show an enhancement in the sensitivity (nm/RIU) of the biomolecular sensor at longer wavelengths. The periodicities of nanophotonic structures are varied from 300 to 500 nm in design calculations with predominance of increase in effective index of the structure to support leaky waveguide modes.

  4. Computational Screening of Materials for Water Splitting Applications

    DEFF Research Database (Denmark)

    Castelli, Ivano Eligio

    has been applied to guide the search for new materials. The main descriptors of the properties relevant for the screening are: heat of formation, electronic bandgap, and positions of the band edges with respect to the red-ox levels of water. A recently implemented exchange-correlation functional......, called GLLB-SC, has been used for the estimation of the bandgaps. Firstly, a screening procedure has been applied to 19000 cubic perovskite structures. These are obtained by combining 52 metals together with oxygen, nitrogen, sulfur and fluorine as anions. 32 promising materials have been found...... Project database, which is based on the experimental ICSD database, and the bandgaps were calculated with focus on finding materials with potential as light harvesters. 24 materials have been proposed for the one-photon water splitting and 23 for the two-photon mechanism. Another method to obtain energy...

  5. Coassembly of aromatic dipeptides into biomolecular necklaces.

    Science.gov (United States)

    Yuran, Sivan; Razvag, Yair; Reches, Meital

    2012-11-27

    This paper describes the formation of complex peptide-based structures by the coassembly of two simple peptides, the diphenylalanine peptide and its tert-butyl dicarbonate (Boc) protected analogue. Each of these peptides can self-assemble into a distinct architecture: the diphenylalanine peptide into tubular structures and its analogue into spheres. Integrated together, these peptides coassemble into a construction of beaded strings, where spherical assemblies are connected by elongated elements. Electron and scanning force microscopy demonstrated the morphology of these structures, which we termed "biomolecular necklaces". Additional experiments indicated the reversibility of the coassembly process and the stability of the structures. Furthermore, we suggest a possible mechanism of formation for the biomolecular necklaces. Our suggestion is based on the necklace model for polyelectrolyte chains, which proposes that a necklace structure appears as a result of counterion condensation on the backbone of a polyelectrolyte. Overall, the approach of coassembly, demonstrated using aromatic peptides, can be adapted to any peptides and may lead to the development and discovery of new self-assembled architectures formed by peptides and other biomolecules. PMID:23061818

  6. Improvements in continuum modeling for biomolecular systems

    Science.gov (United States)

    Yu, Qiao; Ben-Zhuo, Lu

    2016-01-01

    Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the Poisson- Boltzmann (PB)/Poisson-Nernst-Planck (PNP) equations has made great contributions towards simulation of these processes. However, the model has shortcomings in its commonly used form and cannot capture (or cannot accurately capture) some important physical properties of the biological systems. Considerable efforts have been made to improve the continuum model to account for discrete particle interactions and to make progress in numerical methods to provide accurate and efficient simulations. This review will summarize recent main improvements in continuum modeling for biomolecular systems, with focus on the size-modified models, the coupling of the classical density functional theory and the PNP equations, the coupling of polar and nonpolar interactions, and numerical progress. Project supported by the National Natural Science Foundation of China (Grant No. 91230106) and the Chinese Academy of Sciences Program for Cross & Cooperative Team of the Science & Technology Innovation.

  7. Biomolecular detection with a thin membrane transducer.

    Science.gov (United States)

    Cha, Misun; Shin, Jaeha; Kim, June-Hyung; Kim, Ilchaek; Choi, Junbo; Lee, Nahum; Kim, Byung-Gee; Lee, Junghoon

    2008-06-01

    We present a thin membrane transducer (TMT) that can detect nucleic acid based biomolecular reactions including DNA hybridization and protein recognition by aptamers. Specific molecular interactions on an extremely thin and flexible membrane surface cause the deflection of the membrane due to surface stress change which can be measured by a compact capacitive circuit. A gold-coated thin PDMS membrane assembled with metal patterned glass substrate is used to realize the capacitive detection. It is demonstrated that perfect match and mismatch hybridizations can be sharply discriminated with a 16-mer DNA oligonucleotide immobilized on the gold-coated surface. While the mismatched sample caused little capacitance change, the perfectly matched sample caused a well-defined capacitance decrease vs. time due to an upward deformation of the membrane by a compressive surface stress. Additionally, the TMT demonstrated the single nucleotide polymorphism (SNP) capabilities which enabled a detection of mismatching base pairs in the middle of the sequence. It is intriguing that the increase of capacitance, therefore a downward deflection due to tensile stress, was observed with the internal double mismatch hybridization. We further present the detection of thrombin protein through ligand-receptor type recognition with 15-mer thrombin aptamer as a receptor. Key aspects of this detection such as the effect of concentration variation are investigated. This capacitive thin membrane transducer presents a completely new approach for detecting biomolecular reactions with high sensitivity and specificity without molecular labelling and optical measurement. PMID:18497914

  8. [Research on the Screening Method of Soil Remediation Technology at Contaminated Sites and Its Application].

    Science.gov (United States)

    Bai, Li-ping; Luo, Yun; Liu, Li; Zhou, You-ya; Yan, Zeng-guang; Li, Fa-sheng

    2015-11-01

    Soil remediation technology screening is an important procedure in the supervision of contaminated sites. The efficiency and costs of contaminated site remediation will be directly affected by the applicability of soil remediation technology. The influencing factors include characteristics of contaminants, site conditions, remediation time and costs should be considered to determine the most applicable remediation technology. The remediation technology screening was commonly evaluated by the experienced expert in China, which limited the promotion and application of the decision making method. Based on the supervision requirements of contaminated sites and the research status at home and abroad, the screening method includes preliminary screening and explicit evaluation was suggested in this paper. The screening index system was constructed, and the extension theory was used to divide the technology grade. The extension theory could solve the problem of human interference in the evaluation process and index value assignment. A chromium residue contaminated site in China was selected as the study area, and the applicable remediation technologies were suggested by the screening method. The research results could provide a scientific and technological support for the supervision and management of contaminated sites in China.

  9. [Research on the Screening Method of Soil Remediation Technology at Contaminated Sites and Its Application].

    Science.gov (United States)

    Bai, Li-ping; Luo, Yun; Liu, Li; Zhou, You-ya; Yan, Zeng-guang; Li, Fa-sheng

    2015-11-01

    Soil remediation technology screening is an important procedure in the supervision of contaminated sites. The efficiency and costs of contaminated site remediation will be directly affected by the applicability of soil remediation technology. The influencing factors include characteristics of contaminants, site conditions, remediation time and costs should be considered to determine the most applicable remediation technology. The remediation technology screening was commonly evaluated by the experienced expert in China, which limited the promotion and application of the decision making method. Based on the supervision requirements of contaminated sites and the research status at home and abroad, the screening method includes preliminary screening and explicit evaluation was suggested in this paper. The screening index system was constructed, and the extension theory was used to divide the technology grade. The extension theory could solve the problem of human interference in the evaluation process and index value assignment. A chromium residue contaminated site in China was selected as the study area, and the applicable remediation technologies were suggested by the screening method. The research results could provide a scientific and technological support for the supervision and management of contaminated sites in China. PMID:26911012

  10. Application Of Active Screen Method For Ion Nitriding Efficiency Improvement

    Directory of Open Access Journals (Sweden)

    Ogórek M.

    2015-06-01

    Full Text Available Paper presents the research of austenitic steel AISI 304 after ion nitriding at 400°C and at t =4h, for the two different variants of samples distribution in the working plasma reactive chamber tube. In order to assess the effectiveness of ion nitriding variants emission spectroscopy – GDOES, surface hardness tests, microstructure research (LM of nitrided layers were made. It has been found that the use of active screens increases the surface layer thickness and depth of nitrogen diffusion into austenitic steel 304.

  11. The application of tandem mass spectrometry to neonatal screening for inherited disorders of intermediary metabolism.

    Science.gov (United States)

    Chace, Donald H; Kalas, Theodore A; Naylor, Edwin W

    2002-01-01

    This review is intended to serve as a practical guide for geneticists to current applications of tandem mass spectrometry to newborn screening. By making dried-blood spot analysis more sensitive, specific, reliable, and inclusive, tandem mass spectrometry has improved the newborn detection of inborn errors of metabolism. Its innate ability to detect and quantify multiple analytes from one prepared blood specimen in a single analysis permits broad recognition of amino acid, fatty acid, and organic acid disorders. An increasing number of newborn screening programs are either utilizing or conducting pilot studies with tandem mass spectrometry. It is therefore imperative that the genetics community be familiar with tandem mass spectrometric newborn screening.

  12. CRISPR-Cas9 for medical genetic screens: applications and future perspectives.

    Science.gov (United States)

    Xue, Hui-Ying; Ji, Li-Juan; Gao, Ai-Mei; Liu, Ping; He, Jing-Dong; Lu, Xiao-Jie

    2016-02-01

    CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats-CRISPR associated nuclease 9) systems have emerged as versatile and convenient (epi)genome editing tools and have become an important player in medical genetic research. CRISPR-Cas9 and its variants such as catalytically inactivated Cas9 (dead Cas9, dCas9) and scaffold-incorporating single guide sgRNA (scRNA) have been applied in various genomic screen studies. CRISPR screens enable high-throughput interrogation of gene functions in health and diseases. Compared with conventional RNAi screens, CRISPR screens incur less off-target effects and are more versatile in that they can be used in multiple formats such as knockout, knockdown and activation screens, and can target coding and non-coding regions throughout the genome. This powerful screen platform holds the potential of revolutionising functional genomic studies in the near future. Herein, we introduce the mechanisms of (epi)genome editing mediated by CRISPR-Cas9 and its variants, introduce the procedures and applications of CRISPR screen in functional genomics, compare it with conventional screen tools and at last discuss current challenges and opportunities and propose future directions.

  13. Biomolecular Structure Determination with Divide and Concur

    Science.gov (United States)

    Kallus, Yoav; Elser, Veit

    2009-03-01

    Divide and concur (D-C) is a general computational approach, designed for the solution of highly frustrated problems. Recently applied to the problems of disk packing, the kissing number problem, and 3-SAT, it was competitive or outperformed special-purpose methods.ootnotetextS. Gravel and V. Elser, Phys. Rev. E 78, 036706 (2008) We present a method for applying the D-C framework to the problem of biomolecular structure determination. From a list of geometric constraints on groups of atoms in the molecule, we construct a deterministic iterative map that efficiently searches for structures simultaneously satisfying all constraints. As our method eschews an energy function and its minimization to focus on geometric constraints, it can very naturally integrate with the geometric constraints due to chemistry and physics, experimental constraints due to NMR data or many other experimental or biological hints. We present some results of our method.

  14. Biomolecular Markers in Cancer of the Tongue

    Directory of Open Access Journals (Sweden)

    Daris Ferrari

    2009-01-01

    Full Text Available The incidence of tongue cancer is increasing worldwide, and its aggressiveness remains high regardless of treatment. Genetic changes and the expression of abnormal proteins have been frequently reported in the case of head and neck cancers, but the little information that has been published concerning tongue tumours is often contradictory. This review will concentrate on the immunohistochemical expression of biomolecular markers and their relationships with clinical behaviour and prognosis. Most of these proteins are associated with nodal stage, tumour progression and metastases, but there is still controversy concerning their impact on disease-free and overall survival, and treatment response. More extensive clinical studies are needed to identify the patterns of molecular alterations and the most reliable predictors in order to develop tailored anti-tumour strategies based on the targeting of hypoxia markers, vascular and lymphangiogenic factors, epidermal growth factor receptors, intracytoplasmatic signalling and apoptosis.

  15. Nonequilibrium phase transitions in biomolecular signal transduction

    Science.gov (United States)

    Smith, Eric; Krishnamurthy, Supriya; Fontana, Walter; Krakauer, David

    2011-11-01

    We study a mechanism for reliable switching in biomolecular signal-transduction cascades. Steady bistable states are created by system-size cooperative effects in populations of proteins, in spite of the fact that the phosphorylation-state transitions of any molecule, by means of which the switch is implemented, are highly stochastic. The emergence of switching is a nonequilibrium phase transition in an energetically driven, dissipative system described by a master equation. We use operator and functional integral methods from reaction-diffusion theory to solve for the phase structure, noise spectrum, and escape trajectories and first-passage times of a class of minimal models of switches, showing how all critical properties for switch behavior can be computed within a unified framework.

  16. Climate risk screening tools and their application: A guide to the guidance

    Energy Technology Data Exchange (ETDEWEB)

    Traerup, S.; Olhoff, A.

    2011-07-01

    Climate risk screening is an integral part of efforts to ascertain current and future vulnerabilities and risks related to climate change. It is a prerequisite for identifying and designing adaptation measures, and an important element in the process of integrating, or mainstreaming, climate change adaptation into development project, planning and policy processes. There is an increasing demand and attention among national stakeholders in developing countries to take into account potential implications of climate variability and change for planning and prioritizing of development strategies and activities. Subsequently, there is a need for user friendly guidance on climate risk screening tools and their potentials for application that targets developing country stakeholders. This need is amplified by the sheer volume of climate change mainstreaming guidance documents and risk screening and assessment tools available and currently under development. Against this background, this paper sets out to provide potential users in developing countries, including project and programme developers and managers, with an informational entry point to climate risk screening tools. The emphasis in this report is on providing: 1) An overview of available climate risk screening and assessment tools along with indications of the tools available and relevant for specific purposes and contexts (Section 3). 2) Examples of application of climate risk screening and assessment tools along with links to further information (Section 4). Before turning to the respective sections on available climate risk screening tools and examples of their application, a delimitation of the tools included in this paper is included in Section 2. This section also provides a brief overview of how climate screening and related tools fit into decision making steps at various planning and decision making levels in conjunction with an outline of overall considerations to make when choosing a tool. The paper is

  17. Full-scale testing of a new sand control screen for SAGD applications

    Energy Technology Data Exchange (ETDEWEB)

    Hamilton, K.A. [C-FER Technologies, Edmonton, AB (Canada); Woiceshyn, G. [Absolute Completion Technologies, Calgary, AB (Canada); Caulfield, I. [Schlumberger, Calgary, AB (Canada)

    2009-07-01

    This paper described a sand control screen developed for use in thermal applications for horizontal wells. The screen consists of several 25.4 diameter fusion-bonded metal laminate (FMBL) cartridges that are flush-mounted and secured into machined holes in the base pipe wall. A 2-stage evaluation of the screen's performance was conducted using finite element analysis (FEA) and full-scale mechanical testing to measure the screen's mechanical strength and assess the structural performance of the screen's individual FMBL cartridges. Cartridge ejection tests, full-scale burst tests, and full-scale thermal cyclic loading tests were conducted to determine the force required to eject the cartridges from the base pipe under various temperature and pressure regimes. Results of the study showed that the screen provides 3 times more torsional rigidity and twice the collapse strength of conventional slotted liners placed under similar load conditions. Field tests will be conducted to further assess the control screen's performance. 4 refs., 22 figs.

  18. Screening of zonal isolation agents for SAGD EOR applications

    OpenAIRE

    Danyalov, Asset

    2012-01-01

    Utilization of Steam Assisted Gravity Drainage (SAGD) features is currently one of the most widely applied technologies for production of bitumen oil in Canadian oil sand fields. However, as in most oil and gas reservoirs, the bitumen oil reservoirs also differ depending on their reservoir structure; for the Surmont field case in Athabasca oil sands region, the lack of natural sealing and presence of overlying thief zones became a point of concern for a conventional application of the SAGD me...

  19. Using the PSI to Screen Job Applicants with a Criminal History.

    Science.gov (United States)

    Terris, William; Jones, John W.

    Employee crime in the workplace is a common and rapidly growing problem in the United States. A new deterrent to such crime is the use of psychological tests to screen job applicants. The Personnel Selection Inventory (PSI), a psychological test measuring tendencies toward dishonesty, violence, and drug abuse was administered to job applicants…

  20. Applications in radiation therapy of a scintillating screen viewed by a CCD camera

    NARCIS (Netherlands)

    Schippers, J.M.; Boon, S.N.; van Luijk, P.

    2002-01-01

    A two-dimensional (2D) dosimetry system has been designed for position-sensitive dose-measurement applications in modem radiation therapy. The system consists of a scintillating screen (Gd2O2S:Tb), observed by a low-noise CCD camera with a long integration time. The system allows reliable and accura

  1. Biomolecular detection employing the Interferometric Reflectance Imaging Sensor (IRIS).

    Science.gov (United States)

    Lopez, Carlos A; Daaboul, George G; Ahn, Sunmin; Reddington, Alexander P; Monroe, Margo R; Zhang, Xirui; Irani, Rostem J; Yu, Chunxiao; Genco, Caroline A; Cretich, Marina; Chiari, Marcella; Goldberg, Bennett B; Connor, John H; Ünlü, M Selim

    2011-01-01

    The sensitive measurement of biomolecular interactions has use in many fields and industries such as basic biology and microbiology, environmental/agricultural/biodefense monitoring, nanobiotechnology, and more. For diagnostic applications, monitoring (detecting) the presence, absence, or abnormal expression of targeted proteomic or genomic biomarkers found in patient samples can be used to determine treatment approaches or therapy efficacy. In the research arena, information on molecular affinities and specificities are useful for fully characterizing the systems under investigation. Many of the current systems employed to determine molecular concentrations or affinities rely on the use of labels. Examples of these systems include immunoassays such as the enzyme-linked immunosorbent assay (ELISA), polymerase chain reaction (PCR) techniques, gel electrophoresis assays, and mass spectrometry (MS). Generally, these labels are fluorescent, radiological, or colorimetric in nature and are directly or indirectly attached to the molecular target of interest. Though the use of labels is widely accepted and has some benefits, there are drawbacks which are stimulating the development of new label-free methods for measuring these interactions. These drawbacks include practical facets such as increased assay cost, reagent lifespan and usability, storage and safety concerns, wasted time and effort in labelling, and variability among the different reagents due to the labelling processes or labels themselves. On a scientific research basis, the use of these labels can also introduce difficulties such as concerns with effects on protein functionality/structure due to the presence of the attached labels and the inability to directly measure the interactions in real time. Presented here is the use of a new label-free optical biosensor that is amenable to microarray studies, termed the Interferometric Reflectance Imaging Sensor (IRIS), for detecting proteins, DNA, antigenic material

  2. A multiscale modeling approach for biomolecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Bowling, Alan, E-mail: bowling@uta.edu; Haghshenas-Jaryani, Mahdi, E-mail: mahdi.haghshenasjaryani@mavs.uta.edu [The University of Texas at Arlington, Department of Mechanical and Aerospace Engineering (United States)

    2015-04-15

    This paper presents a new multiscale molecular dynamic model for investigating the effects of external interactions, such as contact and impact, during stepping and docking of motor proteins and other biomolecular systems. The model retains the mass properties ensuring that the result satisfies Newton’s second law. This idea is presented using a simple particle model to facilitate discussion of the rigid body model; however, the particle model does provide insights into particle dynamics at the nanoscale. The resulting three-dimensional model predicts a significant decrease in the effect of the random forces associated with Brownian motion. This conclusion runs contrary to the widely accepted notion that the motor protein’s movements are primarily the result of thermal effects. This work focuses on the mechanical aspects of protein locomotion; the effect ATP hydrolysis is estimated as internal forces acting on the mechanical model. In addition, the proposed model can be numerically integrated in a reasonable amount of time. Herein, the differences between the motion predicted by the old and new modeling approaches are compared using a simplified model of myosin V.

  3. The fidelity of dynamic signaling by noisy biomolecular networks.

    Directory of Open Access Journals (Sweden)

    Clive G Bowsher

    Full Text Available Cells live in changing, dynamic environments. To understand cellular decision-making, we must therefore understand how fluctuating inputs are processed by noisy biomolecular networks. Here we present a general methodology for analyzing the fidelity with which different statistics of a fluctuating input are represented, or encoded, in the output of a signaling system over time. We identify two orthogonal sources of error that corrupt perfect representation of the signal: dynamical error, which occurs when the network responds on average to other features of the input trajectory as well as to the signal of interest, and mechanistic error, which occurs because biochemical reactions comprising the signaling mechanism are stochastic. Trade-offs between these two errors can determine the system's fidelity. By developing mathematical approaches to derive dynamics conditional on input trajectories we can show, for example, that increased biochemical noise (mechanistic error can improve fidelity and that both negative and positive feedback degrade fidelity, for standard models of genetic autoregulation. For a group of cells, the fidelity of the collective output exceeds that of an individual cell and negative feedback then typically becomes beneficial. We can also predict the dynamic signal for which a given system has highest fidelity and, conversely, how to modify the network design to maximize fidelity for a given dynamic signal. Our approach is general, has applications to both systems and synthetic biology, and will help underpin studies of cellular behavior in natural, dynamic environments.

  4. Introduction and Application of Electrochemical Sensors Based on Screen-Printed Technology

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@ We report here the development of chemical sensors based on screen-printed technology in our research group to solve major analytical problems in environmental and clinical aspects. The purpose of the research is aimed at the enhancement of selectivity and sensitivity for analysis and monitoring of pollutants and analytes using novel chenically modified screen-printed electrodes. For example, an enzyme reactor coupled with a copper-plated screen-printed carbon electrode (CuSPE) was developed for glucose sensing. The electrocatalytic reduction of enzymatically produced H2O2 at the CuSPE was determined by flow injection analysis (FIA) in pH 7.4 PBS. The proposed method was applied to determine glucose content in fruit juice and clinical sample and satisfactory results with good recoveries were obtained. A thoroughly kinetics and mechanism study was also done for those systems that are verified in analytical applications.

  5. Introduction and Application of Electrochemical Sensors Based on Screen-Printed Technology

    Institute of Scientific and Technical Information of China (English)

    ZEN; Jyh-Myng

    2001-01-01

    We report here the development of chemical sensors based on screen-printed technology in our research group to solve major analytical problems in environmental and clinical aspects. The purpose of the research is aimed at the enhancement of selectivity and sensitivity for analysis and monitoring of pollutants and analytes using novel chenically modified screen-printed electrodes. For example, an enzyme reactor coupled with a copper-plated screen-printed carbon electrode (CuSPE) was developed for glucose sensing. The electrocatalytic reduction of enzymatically produced H2O2 at the CuSPE was determined by flow injection analysis (FIA) in pH 7.4 PBS. The proposed method was applied to determine glucose content in fruit juice and clinical sample and satisfactory results with good recoveries were obtained. A thoroughly kinetics and mechanism study was also done for those systems that are verified in analytical applications.  ……

  6. Biomolecular Modification of Inorganic Crystal Growth

    Energy Technology Data Exchange (ETDEWEB)

    De Yoreo, J J

    2007-04-27

    The fascinating shapes and hierarchical designs of biomineralized structures are an inspiration to materials scientists because of the potential they suggest for biomolecular control over materials synthesis. Conversely, the failure to prevent or limit tissue mineralization in the vascular, skeletal, and urinary systems is a common source of disease. Understanding the mechanisms by which organisms direct or limit crystallization has long been a central challenge to the biomineralization community. One prevailing view is that mineral-associated macromolecules are responsible for either inhibiting crystallization or initiating and stabilizing non-equilibrium crystal polymorphs and morphologies through interactions between anionic moieties and cations in solution or at mineralizing surfaces. In particular, biomolecules that present carboxyl groups to the growing crystal have been implicated as primary modulators of growth. Here we review the results from a combination of in situ atomic force microscopy (AFM) and molecular modeling (MM) studies to investigate the effect of specific interactions between carboxylate-rich biomolecules and atomic steps on crystal surfaces during the growth of carbonates, oxalates and phosphates of calcium. Specifically, we how the growth kinetics and morphology depend on the concentration of additives that include citrate, simple amino acids, synthetic Asp-rich polypeptides, and naturally occurring Asp-rich proteins found in both functional and pathological mineral tissues. The results reveal a consistent picture of shape modification in which stereochemical matching of modifiers to specific atomic steps drives shape modification. Inhibition and other changes in growth kinetics are shown to be due to a range of mechanisms that depend on chemistry and molecular size. Some effects are well described by classic crystal growth theories, but others, such as step acceleration due to peptide charge and hydrophylicity, were previously unrealized

  7. Discoveries and application of prostate-specific antigen, and some proposals to optimize prostate cancer screening

    Directory of Open Access Journals (Sweden)

    Tokudome S

    2016-05-01

    Full Text Available Shinkan Tokudome,1 Ryosuke Ando,2 Yoshiro Koda,3 1Department of Nutritional Epidemiology, National Institute of Health and Nutrition, Shinjuku-ku, Tokyo, 2Department of Nephro-urology, Nagoya City University Graduate School of Medical Sciences, Mizuho-ku, Nagoya, 3Department of Forensic Medicine and Human Genetics, Kurume University School of Medicine, Kurume, Japan Abstract: The discoveries and application of prostate-specific antigen (PSA have been much appreciated because PSA-based screening has saved millions of lives of prostate cancer (PCa patients. Historically speaking, Flocks et al first identified antigenic properties in prostate tissue in 1960. Then, Barnes et al detected immunologic characteristics in prostatic fluid in 1963. Hara et al characterized γ-semino-protein in semen in 1966, and it has been proven to be identical to PSA. Subsequently, Ablin et al independently reported the presence of precipitation antigens in the prostate in 1970. Wang et al purified the PSA in 1979, and Kuriyama et al first applied an enzyme-linked immunosorbent assay for PSA in 1980. However, the positive predictive value with a cutoff figure of 4.0 ng/mL appeared substantially low (~30%. There are overdiagnoses and overtreatments for latent/low-risk PCa. Controversies exist in the PCa mortality-reducing effects of PSA screening between the European Randomized Study of Screening for Prostate Cancer (ERSPC and the US Prostate, Lung, Colorectal, and Ovarian (PLCO Cancer Screening Trial. For optimizing PCa screening, PSA-related items may require the following: 1 adjustment of the cutoff values according to age, as well as setting limits to age and screening intervals; 2 improving test performance using doubling time, density, and ratio of free: total PSA; and 3 fostering active surveillance for low-risk PCa with monitoring by PSA value. Other items needing consideration may include the following: 1 examinations of cell proliferation and cell cycle markers

  8. Computational screening of metal organic frameworks for mixed matrix membrane applications

    OpenAIRE

    Keskin, Seda; Eruçar, İlknur

    2012-01-01

    1 Computational Screening of Metal Organic Frameworks for Mixed Matrix Membrane Applications Ilknur Erucar† and Seda Keskin‡* †Department of Computational Sciences and Engineering, Koç University, 34450, Istanbul, Turkey ‡Department of Chemical and Biological Engineering, Koç University, 34450, Istanbul, Turkey Submitted to Journal of Membrane Science Abstract In this study, detailed molecular simulations were used to examine the challenge of selecting metal organic...

  9. In situ monitoring of biomolecular processes in living systems using surface-enhanced Raman scattering

    Science.gov (United States)

    Altunbek, Mine; Kelestemur, Seda; Culha, Mustafa

    2015-12-01

    Surface-enhanced Raman scattering (SERS) continues to strive to gather molecular level information from dynamic biological systems. It is our ongoing effort to utilize the technique for understanding of the biomolecular processes in living systems such as eukaryotic and prokaryotic cells. In this study, the technique is investigated to identify cell death mechanisms in 2D and 3D in vitro cell culture models, which is a very important process in tissue engineering and pharmaceutical applications. Second, in situ biofilm formation monitoring is investigated to understand how microorganisms respond to the environmental stimuli, which inferred information can be used to interfere with biofilm formation and fight against their pathogenic activity.

  10. Nanoscale field effect transistor for biomolecular signal amplification

    CERN Document Server

    Chen, Yu; Hong, Mi K; Erramilli, Shyamsunder; Rosenberg, Carol; Mohanty, Pritiraj

    2008-01-01

    We report amplification of biomolecular recognition signal in lithographically defined silicon nanochannel devices. The devices are configured as field effect transistors (FET) in the reversed source-drain bias region. The measurement of the differential conductance of the nanowire channels in the FET allows sensitive detection of changes in the surface potential due to biomolecular binding. Narrower silicon channels demonstrate higher sensitivity to binding due to increased surface-to-volume ratio. The operation of the device in the negative source-drain region demonstrates signal amplification. The equivalence between protein binding and change in the surface potential is described.

  11. Acoustic Droplet Ejection Applications for High-Throughput Screening of Infectious Agents.

    Science.gov (United States)

    Rasmussen, Lynn; White, E Lucile; Bostwick, James R

    2016-02-01

    When acoustic droplet ejection technology was first introduced for high-throughput applications, it was used primarily for dispensing compounds dissolved in DMSO. The high precision and accuracy achieved for low-volume transfers in this application were noted by those working outside of the compound management area, and interest was generated in expanding the scope of the technology to include other liquid types. Later-generation instruments included calibrations for several aqueous buffers that were applicable to the life sciences. The High Throughput Screening Center at Southern Research has made use of this range of liquid calibrations for the Infectious Disease Program. The original calibration for DMSO has allowed the preparation of assay-ready plates that can be sent to remote locations. This process was used as part of the collaboration between Southern Research and Galveston National Laboratory, University of Texas Medical Branch, to develop high-throughput screening for biological safety level 4 containment and to provide compounds for two pilot screens that were run there with BSL-4-level pathogens. The aqueous calibrations have been instrumental in miniaturizing assays used for infectious disease, such as qPCR, tissue culture infectious dose 50, and bacterial motility, to make them compatible with HTS operations. PMID:26663786

  12. Electroanalytical applications of screen-printable surfactant-induced sol-gel graphite composites

    Energy Technology Data Exchange (ETDEWEB)

    Guadalupe, Ana R. (San Juan, PR); Guo, Yizhu (San Juan, PR)

    2001-05-15

    A process for preparing sol-gel graphite composite electrodes is presented. This process preferably uses the surfactant bis(2-ethylhexyl) sulfosuccinate (AOT) and eliminates the need for a cosolvent, an acidic catalyst, a cellulose binder and a thermal curing step from prior art processes. Fabrication of screen-printed electrodes by this process provides a simple approach for electroanalytical applications in aqueous and nonaqueous solvents. Examples of applications for such composite electrodes produced from this process include biochemical sensors such as disposable, single-use glucose sensors and ligand modified composite sensors for metal ion sensitive sensors.

  13. Development and applicability of a ready-to-use PCR system for GMO screening.

    Science.gov (United States)

    Rosa, Sabrina F; Gatto, Francesco; Angers-Loustau, Alexandre; Petrillo, Mauro; Kreysa, Joachim; Querci, Maddalena

    2016-06-15

    With the growing number of GMOs introduced to the market, testing laboratories have seen their workload increase significantly. Ready-to-use multi-target PCR-based detection systems, such as pre-spotted plates (PSP), reduce analysis time while increasing capacity. This paper describes the development and applicability to GMO testing of a screening strategy involving a PSP and its associated web-based Decision Support System. The screening PSP was developed to detect all GMOs authorized in the EU in one single PCR experiment, through the combination of 16 validated assays. The screening strategy was successfully challenged in a wide inter-laboratory study on real-life food/feed samples. The positive outcome of this study could result in the adoption of a PSP screening strategy across the EU; a step that would increase harmonization and quality of GMO testing in the EU. Furthermore, this system could represent a model for other official control areas where high-throughput DNA-based detection systems are needed.

  14. Microengineering methods for cell-based microarrays and high-throughput drug-screening applications

    International Nuclear Information System (INIS)

    Screening for effective therapeutic agents from millions of drug candidates is costly, time consuming, and often faces concerns due to the extensive use of animals. To improve cost effectiveness, and to minimize animal testing in pharmaceutical research, in vitro monolayer cell microarrays with multiwell plate assays have been developed. Integration of cell microarrays with microfluidic systems has facilitated automated and controlled component loading, significantly reducing the consumption of the candidate compounds and the target cells. Even though these methods significantly increased the throughput compared to conventional in vitro testing systems and in vivo animal models, the cost associated with these platforms remains prohibitively high. Besides, there is a need for three-dimensional (3D) cell-based drug-screening models which can mimic the in vivo microenvironment and the functionality of the native tissues. Here, we present the state-of-the-art microengineering approaches that can be used to develop 3D cell-based drug-screening assays. We highlight the 3D in vitro cell culture systems with live cell-based arrays, microfluidic cell culture systems, and their application to high-throughput drug screening. We conclude that among the emerging microengineering approaches, bioprinting holds great potential to provide repeatable 3D cell-based constructs with high temporal, spatial control and versatility.

  15. Development and applicability of a ready-to-use PCR system for GMO screening.

    Science.gov (United States)

    Rosa, Sabrina F; Gatto, Francesco; Angers-Loustau, Alexandre; Petrillo, Mauro; Kreysa, Joachim; Querci, Maddalena

    2016-06-15

    With the growing number of GMOs introduced to the market, testing laboratories have seen their workload increase significantly. Ready-to-use multi-target PCR-based detection systems, such as pre-spotted plates (PSP), reduce analysis time while increasing capacity. This paper describes the development and applicability to GMO testing of a screening strategy involving a PSP and its associated web-based Decision Support System. The screening PSP was developed to detect all GMOs authorized in the EU in one single PCR experiment, through the combination of 16 validated assays. The screening strategy was successfully challenged in a wide inter-laboratory study on real-life food/feed samples. The positive outcome of this study could result in the adoption of a PSP screening strategy across the EU; a step that would increase harmonization and quality of GMO testing in the EU. Furthermore, this system could represent a model for other official control areas where high-throughput DNA-based detection systems are needed. PMID:26868555

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

    Science.gov (United States)

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

    2016-01-01

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

  17. Biomolecular detection using a metal semiconductor field effect transistor

    Science.gov (United States)

    Estephan, Elias; Saab, Marie-Belle; Buzatu, Petre; Aulombard, Roger; Cuisinier, Frédéric J. G.; Gergely, Csilla; Cloitre, Thierry

    2010-04-01

    In this work, our attention was drawn towards developing affinity-based electrical biosensors, using a MESFET (Metal Semiconductor Field Effect Transistor). Semiconductor (SC) surfaces must be prepared before the incubations with biomolecules. The peptides route was adapted to exceed and bypass the limits revealed by other types of surface modification due to the unwanted unspecific interactions. As these peptides reveal specific recognition of materials, then controlled functionalization can be achieved. Peptides were produced by phage display technology using a library of M13 bacteriophage. After several rounds of bio-panning, the phages presenting affinities for GaAs SC were isolated; the DNA of these specific phages were sequenced, and the peptide with the highest affinity was synthesized and biotinylated. To explore the possibility of electrical detection, the MESFET fabricated with the GaAs SC were used to detect the streptavidin via the biotinylated peptide in the presence of the bovine Serum Albumin. After each surface modification step, the IDS (current between the drain and the source) of the transistor was measured and a decrease in the intensity was detected. Furthermore, fluorescent microscopy was used in order to prove the specificity of this peptide and the specific localisation of biomolecules. In conclusion, the feasibility of producing an electrical biosensor using a MESFET has been demonstrated. Controlled placement, specific localization and detection of biomolecules on a MESFET transistor were achieved without covering the drain and the source. This method of functionalization and detection can be of great utility for biosensing application opening a new way for developing bioFETs (Biomolecular Field-Effect Transistor).

  18. Time-resolved methods in biophysics. 9. Laser temperature-jump methods for investigating biomolecular dynamics.

    Science.gov (United States)

    Kubelka, Jan

    2009-04-01

    Many important biochemical processes occur on the time-scales of nanoseconds and microseconds. The introduction of the laser temperature-jump (T-jump) to biophysics more than a decade ago opened these previously inaccessible time regimes up to direct experimental observation. Since then, laser T-jump methodology has evolved into one of the most versatile and generally applicable methods for studying fast biomolecular kinetics. This perspective is a review of the principles and applications of the laser T-jump technique in biophysics. A brief overview of the T-jump relaxation kinetics and the historical development of laser T-jump methodology is presented. The physical principles and practical experimental considerations that are important for the design of the laser T-jump experiments are summarized. These include the Raman conversion for generating heating pulses, considerations of size, duration and uniformity of the temperature jump, as well as potential adverse effects due to photo-acoustic waves, cavitation and thermal lensing, and their elimination. The laser T-jump apparatus developed at the NIH Laboratory of Chemical Physics is described in detail along with a brief survey of other laser T-jump designs in use today. Finally, applications of the laser T-jump in biophysics are reviewed, with an emphasis on the broad range of problems where the laser T-jump methodology has provided important new results and insights into the dynamics of the biomolecular processes.

  19. Facing and Overcoming Sensitivity Challenges in Biomolecular NMR Spectroscopy

    DEFF Research Database (Denmark)

    Ardenkjær-Larsen, Jan Henrik; Boebinger, Gregory S.; Comment, Arnaud;

    2015-01-01

    In the Spring of 2013, NMR spectroscopists convened at the Weizmann Institute in Israel to brainstorm on approaches to improve the sensitivity of NMR experiments, particularly when applied in biomolecular settings. This multi‐author interdisciplinary Review presents a state‐of‐the‐art description...

  20. The HADDOCK web server for data-driven biomolecular docking

    NARCIS (Netherlands)

    de Vries, S.J.; van Dijk, M.; Bonvin, A.M.J.J.

    2010-01-01

    Computational docking is the prediction or modeling of the three-dimensional structure of a biomolecular complex, starting from the structures of the individual molecules in their free, unbound form. HADDOC K is a popular docking program that takes a datadriven approach to docking, with support for

  1. From dynamics to structure and function of model biomolecular systems

    NARCIS (Netherlands)

    Fontaine-Vive-Curtaz, F.

    2007-01-01

    The purpose of this thesis was to extend recent works on structure and dynamics of hydrogen bonded crystals to model biomolecular systems and biological processes. The tools that we have used are neutron scattering (NS) and density functional theory (DFT) and force field (FF) based simulation method

  2. Screening and metamodeling of computer experiments with functional outputs. Application to thermal-hydraulic computations

    CERN Document Server

    Auder, Benjamin; Iooss, Bertrand; Marques, Michel

    2010-01-01

    To perform uncertainty, sensitivity or optimization analysis on scalar variables calculated by a cpu time expensive computer code, a widely accepted methodology consists in first identifying the most influential uncertain inputs (by screening techniques), and then in replacing the cpu time expensive model by a cpu inexpensive mathematical function, called a metamodel. This paper extends this methodology to the functional output case, for instance when the model output variables are curves. The screening approach is based on the analysis of variance and principal component analysis of output curves. The functional metamodeling consists in a curve classification step, a dimension reduction step, then a classical metamodeling step. An industrial nuclear reactor application (dealing with uncertainties in the pressurized thermal shock analysis) illustrates all these steps.

  3. Discoveries and application of prostate-specific antigen, and some proposals to optimize prostate cancer screening

    Science.gov (United States)

    Tokudome, Shinkan; Ando, Ryosuke; Koda, Yoshiro

    2016-01-01

    The discoveries and application of prostate-specific antigen (PSA) have been much appreciated because PSA-based screening has saved millions of lives of prostate cancer (PCa) patients. Historically speaking, Flocks et al first identified antigenic properties in prostate tissue in 1960. Then, Barnes et al detected immunologic characteristics in prostatic fluid in 1963. Hara et al characterized γ-semino-protein in semen in 1966, and it has been proven to be identical to PSA. Subsequently, Ablin et al independently reported the presence of precipitation antigens in the prostate in 1970. Wang et al purified the PSA in 1979, and Kuriyama et al first applied an enzyme-linked immunosorbent assay for PSA in 1980. However, the positive predictive value with a cutoff figure of 4.0 ng/mL appeared substantially low (∼30%). There are overdiagnoses and overtreatments for latent/low-risk PCa. Controversies exist in the PCa mortality-reducing effects of PSA screening between the European Randomized Study of Screening for Prostate Cancer (ERSPC) and the US Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial. For optimizing PCa screening, PSA-related items may require the following: 1) adjustment of the cutoff values according to age, as well as setting limits to age and screening intervals; 2) improving test performance using doubling time, density, and ratio of free: total PSA; and 3) fostering active surveillance for low-risk PCa with monitoring by PSA value. Other items needing consideration may include the following: 1) examinations of cell proliferation and cell cycle markers in biopsy specimens; 2) independent quantification of Gleason grading; 3) developing ethnicity-specific staging nomograms based on tumor stage, PSA value, and Gleason score; 4) delineation of the natural history; 5) revisiting the significance of the androgen/testosterone hypothesis; and 6) devoting special attention to individuals with a certain genetic predisposition. Finally

  4. Discoveries and application of prostate-specific antigen, and some proposals to optimize prostate cancer screening.

    Science.gov (United States)

    Tokudome, Shinkan; Ando, Ryosuke; Koda, Yoshiro

    2016-01-01

    The discoveries and application of prostate-specific antigen (PSA) have been much appreciated because PSA-based screening has saved millions of lives of prostate cancer (PCa) patients. Historically speaking, Flocks et al first identified antigenic properties in prostate tissue in 1960. Then, Barnes et al detected immunologic characteristics in prostatic fluid in 1963. Hara et al characterized γ-semino-protein in semen in 1966, and it has been proven to be identical to PSA. Subsequently, Ablin et al independently reported the presence of precipitation antigens in the prostate in 1970. Wang et al purified the PSA in 1979, and Kuriyama et al first applied an enzyme-linked immunosorbent assay for PSA in 1980. However, the positive predictive value with a cutoff figure of 4.0 ng/mL appeared substantially low (∼30%). There are overdiagnoses and overtreatments for latent/low-risk PCa. Controversies exist in the PCa mortality-reducing effects of PSA screening between the European Randomized Study of Screening for Prostate Cancer (ERSPC) and the US Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial. For optimizing PCa screening, PSA-related items may require the following: 1) adjustment of the cutoff values according to age, as well as setting limits to age and screening intervals; 2) improving test performance using doubling time, density, and ratio of free: total PSA; and 3) fostering active surveillance for low-risk PCa with monitoring by PSA value. Other items needing consideration may include the following: 1) examinations of cell proliferation and cell cycle markers in biopsy specimens; 2) independent quantification of Gleason grading; 3) developing ethnicity-specific staging nomograms based on tumor stage, PSA value, and Gleason score; 4) delineation of the natural history; 5) revisiting the significance of the androgen/testosterone hypothesis; and 6) devoting special attention to individuals with a certain genetic predisposition. Finally

  5. A self-regulating biomolecular comparator for processing oscillatory signals.

    Science.gov (United States)

    Agrawal, Deepak K; Franco, Elisa; Schulman, Rebecca

    2015-10-01

    While many cellular processes are driven by biomolecular oscillators, precise control of a downstream on/off process by a biochemical oscillator signal can be difficult: over an oscillator's period, its output signal varies continuously between its amplitude limits and spends a significant fraction of the time at intermediate values between these limits. Further, the oscillator's output is often noisy, with particularly large variations in the amplitude. In electronic systems, an oscillating signal is generally processed by a downstream device such as a comparator that converts a potentially noisy oscillatory input into a square wave output that is predominantly in one of two well-defined on and off states. The comparator's output then controls downstream processes. We describe a method for constructing a synthetic biochemical device that likewise produces a square-wave-type biomolecular output for a variety of oscillatory inputs. The method relies on a separation of time scales between the slow rate of production of an oscillatory signal molecule and the fast rates of intermolecular binding and conformational changes. We show how to control the characteristics of the output by varying the concentrations of the species and the reaction rates. We then use this control to show how our approach could be applied to process different in vitro and in vivo biomolecular oscillators, including the p53-Mdm2 transcriptional oscillator and two types of in vitro transcriptional oscillators. These results demonstrate how modular biomolecular circuits could, in principle, be combined to build complex dynamical systems. The simplicity of our approach also suggests that natural molecular circuits may process some biomolecular oscillator outputs before they are applied downstream. PMID:26378119

  6. Interacting with the biomolecular solvent accessible surface via a haptic feedback device

    Directory of Open Access Journals (Sweden)

    Hayward Steven

    2009-10-01

    Full Text Available Abstract Background From the 1950s computer based renderings of molecules have been produced to aid researchers in their understanding of biomolecular structure and function. A major consideration for any molecular graphics software is the ability to visualise the three dimensional structure of the molecule. Traditionally, this was accomplished via stereoscopic pairs of images and later realised with three dimensional display technologies. Using a haptic feedback device in combination with molecular graphics has the potential to enhance three dimensional visualisation. Although haptic feedback devices have been used to feel the interaction forces during molecular docking they have not been used explicitly as an aid to visualisation. Results A haptic rendering application for biomolecular visualisation has been developed that allows the user to gain three-dimensional awareness of the shape of a biomolecule. By using a water molecule as the probe, modelled as an oxygen atom having hard-sphere interactions with the biomolecule, the process of exploration has the further benefit of being able to determine regions on the molecular surface that are accessible to the solvent. This gives insight into how awkward it is for a water molecule to gain access to or escape from channels and cavities, indicating possible entropic bottlenecks. In the case of liver alcohol dehydrogenase bound to the inhibitor SAD, it was found that there is a channel just wide enough for a single water molecule to pass through. Placing the probe coincident with crystallographic water molecules suggests that they are sometimes located within small pockets that provide a sterically stable environment irrespective of hydrogen bonding considerations. Conclusion By using the software, named HaptiMol ISAS (available from http://www.haptimol.co.uk, one can explore the accessible surface of biomolecules using a three-dimensional input device to gain insights into the shape and water

  7. Engineering intracellular active transport systems as in vivo biomolecular tools.

    Energy Technology Data Exchange (ETDEWEB)

    Bachand, George David; Carroll-Portillo, Amanda

    2006-11-01

    Active transport systems provide essential functions in terms of cell physiology and metastasis. These systems, however, are also co-opted by invading viruses, enabling directed transport of the virus to and from the cell's nucleus (i.e., the site of virus replication). Based on this concept, fundamentally new approaches for interrogating and manipulating the inner workings of living cells may be achievable by co-opting Nature's active transport systems as an in vivo biomolecular tool. The overall goal of this project was to investigate the ability to engineer kinesin-based transport systems for in vivo applications, specifically the collection of effector proteins (e.g., transcriptional regulators) within single cells. In the first part of this project, a chimeric fusion protein consisting of kinesin and a single chain variable fragment (scFv) of an antibody was successfully produced through a recombinant expression system. The kinesin-scFv retained both catalytic and antigenic functionality, enabling selective capture and transport of target antigens. The incorporation of a rabbit IgG-specific scFv into the kinesin established a generalized system for functionalizing kinesin with a wide range of target-selective antibodies raised in rabbits. The second objective was to develop methods of isolating the intact microtubule network from live cells as a platform for evaluating kinesin-based transport within the cytoskeletal architecture of a cell. Successful isolation of intact microtubule networks from two distinct cell types was demonstrated using glutaraldehyde and methanol fixation methods. This work provides a platform for inferring the ability of kinesin-scFv to function in vivo, and may also serve as a three-dimensional scaffold for evaluating and exploiting kinesin-based transport for nanotechnological applications. Overall, the technology developed in this project represents a first-step in engineering active transport system for in vivo

  8. Applications in radiation therapy of a scintillating screen viewed by a CCD camera

    CERN Document Server

    Schippers, J M; Luijk, P V

    2002-01-01

    A two-dimensional (2D) dosimetry system has been designed for position-sensitive dose-measurement applications in modern radiation therapy. The system consists of a scintillating screen (Gd sub 2 O sub 2 S : Tb), observed by a low-noise CCD camera with a long integration time. The system allows reliable and accurate simultaneous 2D imaging of therapeutic dose distributions in the scintillator with sub millimeter spatial resolution. This system has been applied successfully at different applications in radiation therapy. Results of dose measurements in a treatment modality using a scanning proton beam are reported. It is shown that a quick and reliable measurement can be done. The screen+CCD system has proven to perform accurate dosimetry in applications where beams with a small (1-5 mm) diameter are used and where absolute dosimetry by means of standard ionization chambers is not possible due to their relatively large size. For the routine measurements of the alignment of therapeutic beams with respect to the...

  9. Cathode material for lithium ion accumulators prepared by screen printing for Smart Textile applications

    Science.gov (United States)

    Syrový, T.; Kazda, T.; Syrová, L.; Vondrák, J.; Kubáč, L.; Sedlaříková, M.

    2016-03-01

    The presented study is focused on the development of LiFePO4 based cathode for thin and flexible screen printed secondary lithium based accumulators. An ink formulation was developed for the screen printing technique, which enabled mass production of accumulator's cathode for Smart Label and Smart Textile applications. The screen printed cathode was compared with an electrode prepared by the bar coating technique using an ink formulation based on the standard approach of ink composition. Obtained LiFePO4 cathode layers were characterized by scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS) and galvanostatic charge/discharge measurements at different loads. The discharge capacity, capacity retention and stability at a high C rate of the LiFePO4 cathode were improved when Super P and PVDF were replaced by conductive polymers PEDOT:PSS. The achieved capacity during cycling at various C rates was approximately the same at the beginning and at the end, and it was about 151 mAh/g for cycling under 1C. The obtained results of this novelty electrode layer exceed the parameters of several electrode layers based on LiFePO4 published in literature in terms of capacity, cycling stability and overcomes them in terms of simplicity/industrial process ability of cathode layer fabrication and electrode material preparation.

  10. Application of the Morris method for screening the influential parameters of fuzzy controllers applied to WWTPs

    DEFF Research Database (Denmark)

    Ruano, M.V.; Ribes, J.; Ferrer, J,;

    2011-01-01

    In this paper,we evaluate the application of a sensitivity analysis to help fine-tuning a fuzzy controller for a biological nitrogen and phosphorus removal (BNPR) plant. The Morris Screeningmethod is proposed and evaluated as a prior step to obtain the parameter significance ranking. First...... the optimal repetition number for each study in question. With the proper r found, the Morris Screening helped identify the parameter significance ranking, thereby facilitating the calibration of fuzzy controllers,which containmany parameters that need to be adjusted for different wastewater treatment plant...

  11. Survey and screening of intermediate-size photovoltaic total energy and electric applications

    Energy Technology Data Exchange (ETDEWEB)

    Rattin, E.J.

    1978-08-01

    One of the principal objectives of this photovoltaic mission analysis effort has been to identify and evaluate applications for photovoltaic solar energy conversion that could lead to significant contributions to the national energy supply and that would provide attractive opportunities for application experiments aimed at stimulating the adoption of photovoltaic technology. The scope of the study has included applications both for electric-only photovoltaic (PV) systems and for photovoltaic total energy systems (PTES), i.e., systems that provide both photovoltaic electricity and solar thermal energy to meet all or part of the energy demand at a single load point or a group of related load points. In either case, both flat-plate and concentrating systems have been considered and it has been assumed that the thermal energy is collected in and transported by the fluid used in an active cooling system for the photovoltaic cells. Because the efficiency of photovoltaic devices decreases rapidly with increasing temperature and because the operational lifetime of such devices is reduced by prolonged operation at elevated temperatures, a practical upper limit of about 200/sup 0/C (400/sup 0/F) was assumed for the temperature at which arrays can be allowed to be operated. This limitation, in turn, places an upper bound on the temperature at which solar thermal energy is available in PTES applications. An initial screening aimed at identifying the most promising applications has therefore been required, with the expectation that detailed evaluation will be made of only the higher-ranking candidates. A description of the screening procedure that was adopted and a discussion of the results are presented.

  12. Combining vibrational biomolecular spectroscopy with chemometric techniques for the study of response and sensitivity of molecular structures/functional groups mainly related to lipid biopolymer to various processing applications.

    Science.gov (United States)

    Yu, Gloria Qingyu; Yu, Peiqiang

    2015-09-01

    The objectives of this project were to (1) combine vibrational spectroscopy with chemometric multivariate techniques to determine the effect of processing applications on molecular structural changes of lipid biopolymer that mainly related to functional groups in green- and yellow-type Crop Development Centre (CDC) pea varieties [CDC strike (green-type) vs. CDC meadow (yellow-type)] that occurred during various processing applications; (2) relatively quantify the effect of processing applications on the antisymmetric CH3 ("CH3as") and CH2 ("CH2as") (ca. 2960 and 2923 cm(-1), respectively), symmetric CH3 ("CH3s") and CH2 ("CH2s") (ca. 2873 and 2954 cm(-1), respectively) functional groups and carbonyl C=O ester (ca. 1745 cm(-1)) spectral intensities as well as their ratios of antisymmetric CH3 to antisymmetric CH2 (ratio of CH3as to CH2as), ratios of symmetric CH3 to symmetric CH2 (ratio of CH3s to CH2s), and ratios of carbonyl C=O ester peak area to total CH peak area (ratio of C=O ester to CH); and (3) illustrate non-invasive techniques to detect the sensitivity of individual molecular functional group to the various processing applications in the recently developed different types of pea varieties. The hypothesis of this research was that processing applications modified the molecular structure profiles in the processed products as opposed to original unprocessed pea seeds. The results showed that the different processing methods had different impacts on lipid molecular functional groups. Different lipid functional groups had different sensitivity to various heat processing applications. These changes were detected by advanced molecular spectroscopy with chemometric techniques which may be highly related to lipid utilization and availability. The multivariate molecular spectral analyses, cluster analysis, and principal component analysis of original spectra (without spectral parameterization) are unable to fully distinguish the structural differences in the

  13. Combining vibrational biomolecular spectroscopy with chemometric techniques for the study of response and sensitivity of molecular structures/functional groups mainly related to lipid biopolymer to various processing applications.

    Science.gov (United States)

    Yu, Gloria Qingyu; Yu, Peiqiang

    2015-09-01

    The objectives of this project were to (1) combine vibrational spectroscopy with chemometric multivariate techniques to determine the effect of processing applications on molecular structural changes of lipid biopolymer that mainly related to functional groups in green- and yellow-type Crop Development Centre (CDC) pea varieties [CDC strike (green-type) vs. CDC meadow (yellow-type)] that occurred during various processing applications; (2) relatively quantify the effect of processing applications on the antisymmetric CH3 ("CH3as") and CH2 ("CH2as") (ca. 2960 and 2923 cm(-1), respectively), symmetric CH3 ("CH3s") and CH2 ("CH2s") (ca. 2873 and 2954 cm(-1), respectively) functional groups and carbonyl C=O ester (ca. 1745 cm(-1)) spectral intensities as well as their ratios of antisymmetric CH3 to antisymmetric CH2 (ratio of CH3as to CH2as), ratios of symmetric CH3 to symmetric CH2 (ratio of CH3s to CH2s), and ratios of carbonyl C=O ester peak area to total CH peak area (ratio of C=O ester to CH); and (3) illustrate non-invasive techniques to detect the sensitivity of individual molecular functional group to the various processing applications in the recently developed different types of pea varieties. The hypothesis of this research was that processing applications modified the molecular structure profiles in the processed products as opposed to original unprocessed pea seeds. The results showed that the different processing methods had different impacts on lipid molecular functional groups. Different lipid functional groups had different sensitivity to various heat processing applications. These changes were detected by advanced molecular spectroscopy with chemometric techniques which may be highly related to lipid utilization and availability. The multivariate molecular spectral analyses, cluster analysis, and principal component analysis of original spectra (without spectral parameterization) are unable to fully distinguish the structural differences in the

  14. The interplay of intrinsic and extrinsic bounded noises in biomolecular networks.

    Directory of Open Access Journals (Sweden)

    Giulio Caravagna

    Full Text Available After being considered as a nuisance to be filtered out, it became recently clear that biochemical noise plays a complex role, often fully functional, for a biomolecular network. The influence of intrinsic and extrinsic noises on biomolecular networks has intensively been investigated in last ten years, though contributions on the co-presence of both are sparse. Extrinsic noise is usually modeled as an unbounded white or colored gaussian stochastic process, even though realistic stochastic perturbations are clearly bounded. In this paper we consider Gillespie-like stochastic models of nonlinear networks, i.e. the intrinsic noise, where the model jump rates are affected by colored bounded extrinsic noises synthesized by a suitable biochemical state-dependent Langevin system. These systems are described by a master equation, and a simulation algorithm to analyze them is derived. This new modeling paradigm should enlarge the class of systems amenable at modeling. We investigated the influence of both amplitude and autocorrelation time of a extrinsic Sine-Wiener noise on: (i the Michaelis-Menten approximation of noisy enzymatic reactions, which we show to be applicable also in co-presence of both intrinsic and extrinsic noise, (ii a model of enzymatic futile cycle and (iii a genetic toggle switch. In (ii and (iii we show that the presence of a bounded extrinsic noise induces qualitative modifications in the probability densities of the involved chemicals, where new modes emerge, thus suggesting the possible functional role of bounded noises.

  15. Physics at the biomolecular interface fundamentals for molecular targeted therapy

    CERN Document Server

    Fernández, Ariel

    2016-01-01

    This book focuses primarily on the role of interfacial forces in understanding biological phenomena at the molecular scale. By providing a suitable statistical mechanical apparatus to handle the biomolecular interface, the book becomes uniquely positioned to address core problems in molecular biophysics. It highlights the importance of interfacial tension in delineating a solution to the protein folding problem, in unravelling the physico-chemical basis of enzyme catalysis and protein associations, and in rationally designing molecular targeted therapies. Thus grounded in fundamental science, the book develops a powerful technological platform for drug discovery, while it is set to inspire scientists at any level in their careers determined to address the major challenges in molecular biophysics. The acknowledgment of how exquisitely the structure and dynamics of proteins and their aqueous environment are related attests to the overdue recognition that biomolecular phenomena cannot be effectively understood w...

  16. Single-Molecule Pull-down FRET (SiMPull-FRET) to dissect the mechanisms of biomolecular machines

    Science.gov (United States)

    Kahlscheuer, Matthew L.; Widom, Julia; Walter, Nils G.

    2016-01-01

    Spliceosomes are multi-megadalton RNA-protein complexes responsible for the faithful removal of non-coding segments (introns) from pre-messenger RNAs (pre-mRNAs), a process critical for the maturation of eukaryotic mRNAs for subsequent translation by the ribosome. Both the spliceosome and ribosome, as well as many other RNA and DNA processing machineries, contain central RNA components that endow biomolecular complexes with precise, sequence-specific nucleic acid recognition and versatile structural dynamics. Single molecule fluorescence (or Förster) resonance energy transfer (smFRET) microscopy is a powerful tool for the study of local and global conformational changes of both simple and complex biomolecular systems involving RNA. The integration of biochemical tools such as immunoprecipitation with advanced methods in smFRET microscopy and data analysis has opened up entirely new avenues towards studying the mechanisms of biomolecular machines isolated directly from complex biological specimens such as cell extracts. Here we detail the general steps for using prism-based total internal reflection fluorescence (TIRF) microscopy in exemplary single molecule pull-down FRET (SiMPull-FRET) studies of the yeast spliceosome and discuss the broad application potential of this technique. PMID:26068753

  17. Association of Biomolecular Resource Facilities Survey: Service Laboratory Funding

    OpenAIRE

    Ogorzalek Loo, Rachel; Nicolet, Charles M.; Niece, Ronald L.; Young, Mary; Simpson, John T.

    2009-01-01

    In 2007, The Association of Biomolecular Resource Facilities (ABRF) Survey Committee surveyed the ABRF membership and scientists at-large concerning the current state of funding in service-oriented laboratories. Questions pertained to services offered, cost recovery, capital equipment funding, and future outlook. The web-based survey, available for 3 weeks, achieved participation from 209 respondents in 13 countries, 77% of which represented academic laboratories. Most respondents (75%) direc...

  18. Dynamic Presentation of Immobilized Ligands Regulated through Biomolecular Recognition

    OpenAIRE

    Liu, Bo; Liu, Yang; Riesberg, Jeremiah J.; Shen, Wei

    2010-01-01

    To mimic the dynamic regulation of signaling ligands immobilized on extracellular matrices or on the surfaces of neighboring cells for guidance of cell behavior and fate selection, we have harnessed biomolecular recognition in combination with polymer engineering to create dynamic surfaces on which the accessibility of immobilized ligands to cell surface receptors can be reversibly interconverted under physiological conditions. The cell-adhesive RGD peptide is chosen as a model ligand. RGD is...

  19. Genetically Engineered Protein Modules: Development and Applications in Anti-Viral Agent Screening and Cancer Marker Detection

    OpenAIRE

    Biswas, Payal

    2010-01-01

    ABSTRACT OF THE DISSERTATION Genetically Engineered Protein Modules: Development and Applications in Anti-Viral Agent Screening and Cancer Marker Detection byPayal BiswasDoctor of Philosophy Cell Molecular and Developmental Biology Graduate ProgramUniversity of California, Riverside, August 2010Dr. Wilfred Chen, ChairpersonOne of the most critical aspects in drug discovery is the bioactivity screening assay, by which compounds that most effectively inhibit the target are identified. During t...

  20. Screening CO

    NARCIS (Netherlands)

    Ramírez, A.; Hagedoorn, S.; Kramers, L.; Wildenborg, T.; Hendriks, C.

    2010-01-01

    This paper describes the development and application of a methodology to screen and rank Dutch reservoirs suitable for long-term large scale CO2 storage. The screening focuses on off- and on-shore individual aquifers, gas and oil fields. In total 176 storage reservoirs have been taken int

  1. Retroactivity in the Context of Modularly Structured Biomolecular Systems

    Science.gov (United States)

    Pantoja-Hernández, Libertad; Martínez-García, Juan Carlos

    2015-01-01

    Synthetic biology has intensively promoted the technical implementation of modular strategies in the fabrication of biological devices. Modules are considered as networks of reactions. The behavior displayed by biomolecular systems results from the information processes carried out by the interconnection of the involved modules. However, in natural systems, module wiring is not a free-of-charge process; as a consequence of interconnection, a reactive phenomenon called retroactivity emerges. This phenomenon is characterized by signals that propagate from downstream modules (the modules that receive the incoming signals upon interconnection) to upstream ones (the modules that send the signals upon interconnection). Such retroactivity signals, depending of their strength, may change and sometimes even disrupt the behavior of modular biomolecular systems. Thus, analysis of retroactivity effects in natural biological and biosynthetic systems is crucial to achieve a deeper understanding of how this interconnection between functionally characterized modules takes place and how it impacts the overall behavior of the involved cell. By discussing the modules interconnection in natural and synthetic biomolecular systems, we propose that such systems should be considered as quasi-modular. PMID:26137457

  2. A Sensor-Enabled Smartphone Application to Collect Eating Behavior Data for Population Screening.

    Science.gov (United States)

    Maramis, Christos; Moulos, Ioannis; Ioakeimidis, Ioannis; Nolstam, Jenny; Lekka, Irini; Bergh, Cecilia; Maglaveras, Nicos

    2016-01-01

    The worldwide extent of obesity and eating disorders (ED) today highlights the necessity for efficient treatment, but also early prevention of eating-related diseases. A promising category of therapeutic and preventive interventions comes from the domain of behavioral informatics (BI), whose purpose is to monitor and modify harmful behaviors - unhealthy eating in the particular case - with the help of information and communication technologies. Smartphones have already shown great promise in delivering such BI interventions in the field of obesity and ED. In fact, plenty of smartphone applications aiming to monitor and support the change of eating behavior with the help of built-in or external sensors have been proposed in the scientific literature. However, to the best of our knowledge, no smartphone application up to date has been designed to collect eating behavior data for the purpose of population screening against obesity or ED. In this work we describe a novel, sensor-enabled smartphone application that captures in-meal behavioral data from multiple subjects in a brief data collection process, with the end goal of recording, in detail, the user's eating style throughout a cooked meal. These data can later be employed for assessing the subjects' risk for obesity or ED. The proposed application has undergone preliminary evaluation with respect to its usability and technical soundness, yielding promising results. PMID:27225568

  3. A Sensor-Enabled Smartphone Application to Collect Eating Behavior Data for Population Screening.

    Science.gov (United States)

    Maramis, Christos; Moulos, Ioannis; Ioakeimidis, Ioannis; Nolstam, Jenny; Lekka, Irini; Bergh, Cecilia; Maglaveras, Nicos

    2016-01-01

    The worldwide extent of obesity and eating disorders (ED) today highlights the necessity for efficient treatment, but also early prevention of eating-related diseases. A promising category of therapeutic and preventive interventions comes from the domain of behavioral informatics (BI), whose purpose is to monitor and modify harmful behaviors - unhealthy eating in the particular case - with the help of information and communication technologies. Smartphones have already shown great promise in delivering such BI interventions in the field of obesity and ED. In fact, plenty of smartphone applications aiming to monitor and support the change of eating behavior with the help of built-in or external sensors have been proposed in the scientific literature. However, to the best of our knowledge, no smartphone application up to date has been designed to collect eating behavior data for the purpose of population screening against obesity or ED. In this work we describe a novel, sensor-enabled smartphone application that captures in-meal behavioral data from multiple subjects in a brief data collection process, with the end goal of recording, in detail, the user's eating style throughout a cooked meal. These data can later be employed for assessing the subjects' risk for obesity or ED. The proposed application has undergone preliminary evaluation with respect to its usability and technical soundness, yielding promising results.

  4. Applicability of Screening Tests for Oxytetracycline in the Milk of Three Breeds of Goats.

    Science.gov (United States)

    Attaie, Rahmat; Bsharat, Mohammed; Mora-Gutierrez, Adela

    2016-06-01

    Antibiotics are widely used in animal husbandry, and the presence of antibiotic residues in milk is a health hazard. The objectives of this study were to determine residual amounts of oxytetracycline in the milk of three breeds of goats using high-pressure liquid chromatography (HPLC) analysis and screening tests. It was also essential to explore the safe withdrawal period of oxytetracycline in lactating goats and examine the applicability of Charm ROSA and SNAP screening tests. The qualitative results of these tests were compared with the quantitative results of the HPLC method. Fifteen milking does, five each from the Alpine, LaMancha, and Nubian breeds, were selected from the herd at Prairie View A&M University. Milk samples containing antibiotic residues were deproteinized by HCl and acetonitrile, and then oxytetracycline was extracted from the supernatant. The residues of oxytetracycline in goat's milk up to 110 h after injection were qualitatively detected using the Charm ROSA test. Similarly, the SNAP test detected the antibiotic residues in milk up to 110 h after treatment. The HPLC results indicated that oxytetracycline residues in milk from Alpine goats were below the tolerance level (300 ng/ml) 82 h after drug treatment (72 h for LaManchas, 58 h for Nubians); however, the results of the screening tests would indicate longer withdrawal periods for milk from the breeds of goats studied, which would result in economic losses to goat's milk producers. The results of this study also indicated that oxytetracycline was not stable in raw goat's milk at refrigeration temperature or during pasteurization and that the concentrations decreased significantly. Commercial goat's milk is usually exposed to several hours of refrigeration and then to pasteurization. The results of this study indicated that, if oxytetracycline was present in raw goat's milk, the concentration would decrease significantly before it was marketed.

  5. Theoretical Screening of Mixed Solid Sorbent for Applications to CO2 Capture Technology

    Energy Technology Data Exchange (ETDEWEB)

    Duan, Yuhua

    2014-01-01

    Since current technologies for capturing CO2 to fight global climate change are still too energy intensive, there is a critical need for development of new materials that can capture CO2 reversibly with acceptable energy costs. Accordingly, solid sorbents have been proposed to be used for CO2 capture applications through a reversible chemical transformation. By combining thermodynamic database mining with first principles density functional theory and phonon lattice dynamics calculations, a theoretical screening methodology to identify the most promising CO2 sorbent candidates from the vast array of possible solid materials has been proposed and validated. The calculated thermodynamic properties of different classes of solid materials versus temperature and pressure changes were further used to evaluate the equilibrium properties for the CO2 adsorption/desorption cycles. According to the requirements imposed by the pre- and post- combustion technologies and based on our calculated thermodynamic properties for the CO2 capture reactions by the solids of interest, we were able to screen only those solid materials for which lower capture energy costs are expected at the desired pressure and temperature conditions. Only those selected CO2 sorbent candidates were further considered for experimental validations. The ab initio thermodynamic technique has the advantage of identifying thermodynamic properties of CO2 capture reactions without any experimental input beyond crystallographic structural information of the solid phases involved. Such methodology not only can be used to search for good candidates from existing database of solid materials, but also can provide some guidelines for synthesis new materials. In this presentation, we apply our screening methodology to mixing solid systems to adjust the turnover temperature to help on developing CO2 capture Technologies.

  6. Applicability of Screening Tests for Oxytetracycline in the Milk of Three Breeds of Goats.

    Science.gov (United States)

    Attaie, Rahmat; Bsharat, Mohammed; Mora-Gutierrez, Adela

    2016-06-01

    Antibiotics are widely used in animal husbandry, and the presence of antibiotic residues in milk is a health hazard. The objectives of this study were to determine residual amounts of oxytetracycline in the milk of three breeds of goats using high-pressure liquid chromatography (HPLC) analysis and screening tests. It was also essential to explore the safe withdrawal period of oxytetracycline in lactating goats and examine the applicability of Charm ROSA and SNAP screening tests. The qualitative results of these tests were compared with the quantitative results of the HPLC method. Fifteen milking does, five each from the Alpine, LaMancha, and Nubian breeds, were selected from the herd at Prairie View A&M University. Milk samples containing antibiotic residues were deproteinized by HCl and acetonitrile, and then oxytetracycline was extracted from the supernatant. The residues of oxytetracycline in goat's milk up to 110 h after injection were qualitatively detected using the Charm ROSA test. Similarly, the SNAP test detected the antibiotic residues in milk up to 110 h after treatment. The HPLC results indicated that oxytetracycline residues in milk from Alpine goats were below the tolerance level (300 ng/ml) 82 h after drug treatment (72 h for LaManchas, 58 h for Nubians); however, the results of the screening tests would indicate longer withdrawal periods for milk from the breeds of goats studied, which would result in economic losses to goat's milk producers. The results of this study also indicated that oxytetracycline was not stable in raw goat's milk at refrigeration temperature or during pasteurization and that the concentrations decreased significantly. Commercial goat's milk is usually exposed to several hours of refrigeration and then to pasteurization. The results of this study indicated that, if oxytetracycline was present in raw goat's milk, the concentration would decrease significantly before it was marketed. PMID:27296606

  7. Theoretical Screening of Mixed Solid Sorbent for Applications to CO{sub 2} Capture Technology

    Energy Technology Data Exchange (ETDEWEB)

    Duan, Yuhua

    2014-03-30

    Since current technologies for capturing CO{sub 2} to fight global climate change are still too energy intensive, there is a critical need for development of new materials that can capture CO{sub 2} reversibly with acceptable energy costs. Accordingly, solid sorbents have been proposed to be used for CO{sub 2} capture applications through a reversible chemical transformation. By combining thermodynamic database mining with first principles density functional theory and phonon lattice dynamics calculations, a theoretical screening methodology to identify the most promising CO{sub 2} sorbent candidates from the vast array of possible solid materials has been proposed and validated. The calculated thermodynamic properties of different classes of solid materials versus temperature and pressure changes were further used to evaluate the equilibrium properties for the CO{sub 2} adsorption/desorption cycles. According to the requirements imposed by the pre- and post- combustion technologies and based on our calculated thermodynamic properties for the CO{sub 2} capture reactions by the solids of interest, we were able to screen only those solid materials for which lower capture energy costs are expected at the desired pressure and temperature conditions. Only those selected CO{sub 2} sorbent candidates were further considered for experimental validations. The ab initio thermodynamic technique has the advantage of identifying thermodynamic properties of CO{sub 2} capture reactions without any experimental input beyond crystallographic structural information of the solid phases involved. Such methodology not only can be used to search for good candidates from existing database of solid materials, but also can provide some guidelines for synthesis new materials. In this presentation, we apply our screening methodology to mixing solid systems to adjust the turnover temperature to help on developing CO{sub 2} capture Technologies.

  8. Fourier-transform infrared spectroscopy for rapid screening and live-cell monitoring: application to nanotoxicology

    Energy Technology Data Exchange (ETDEWEB)

    Sundaram, S. K.; Sacksteder, Colette A.; Weber, T. J.; Riley, Brian J.; Addleman, Raymond S.; Harrer, Bruce J.; Peterman, John W.

    2013-01-01

    A significant challenge to realize the full potential of nanotechnology for therapeutic and diagnostic applications is to understand and evaluate how live-cells interact with an external stimulus, e.g., a nanosized particle (NSP), and the toxicity and broad risk associated with these stimuli. NSPs are increasingly used in medicine with largely undetermined hazards in complex cell dynamics and environments. It is difficult to capture the complexity and dynamics of these interactions by following an omics-based approach exclusively, which are expensive and time-consuming. Additionally, this approach needs destructive sampling methods. Live-cell attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectrometry is well suited to provide noninvasive approach to provide rapid screening of cellular responses to potentially toxic NSPs or any stimuli. Herein we review the technical basis of the approach, the instrument configuration and interface with the biological media, and various effects that impact the data, data analysis, and toxicity. Our preliminary results on live-cell monitoring show promise for rapid screening the NSPs.

  9. Application of intraoperative round window electrocochleography for screening the patients with auditory neuropathy

    Institute of Scientific and Technical Information of China (English)

    WANG Lin-e; WANG Zhen; ZHANG Dao-xing; CAO Ke-li

    2009-01-01

    Background Most patients with auditory neuropathy (AN) could receive good even the best effects after cochlear implantation. How to diagnose AN objectively and accurately is very important, In this study, we screened the patients with AN according to the presence or absence of compound action potential (CAP) of intraoperative round window electrocochleography (RW ECochG).Methods Intraoperative RW ECochG was performed on 32 patients with profound sensorineural deafness, who had normal cochlea during cochlear implantation surgery under general anesthesia in the standard operating room. The cochlear microphonic (CM) and CAP of RW ECochG was observed and recorded.Results The presence of CM but the absence of CAP of RW ECochG occurred in 12 among the 32 patients. They were suspected to suffer from AN. The rest patients who had CM and CAP of RW ECochG were thought not to suffer from AN.Conclusion Application of intraoperative RW ECochG during the cochlear implantation surgery may objectively and accurately screen the patients with AN, and can give a meaningful clue for implanted device working.

  10. Computational Studies on Biomolecular Diffusion and Electrostatics

    OpenAIRE

    Wang, Nuo

    2015-01-01

    As human understandings of physics, chemistry and biology converge and the development of computers proceeds, computational chemistry or computational biophysics has become a substantial field of research. It serves to explore the fundamentals of life and also has extended applications in the field of medicine. Among the many aspects of computational chemistry, this Ph. D. work focuses on the numerical methods for studying diffusion and electrostatics of biomolecules at the nanoscale. Diffusi...

  11. Efficient Theoretical Screening of Solid Sorbents for CO2 Capture Applications*

    Energy Technology Data Exchange (ETDEWEB)

    Duan, Yuhua; Luebke, David; Pennline, Henry

    2012-03-31

    By combining thermodynamic database mining with first principles density functional theory and phonon lattice dynamics calculations, a theoretical screening methodology to identify the most promising CO2 sorbent candidates from the vast array of possible solid materials has been proposed and validated. The ab initio thermodynamic technique has the advantage of allowing identification of thermodynamic properties of CO2 capture reactions without any experimental input beyond crystallographic structural information of the solid phases involved. For a given solid, the first step is to attempt to extract thermodynamic properties from thermodynamic databases and the available literatures. If the thermodynamic properties of the compound of interest are unknown, an ab initio thermodynamic approach is used to calculate them. These properties expressed conveniently as chemical potentials and heat of reactions, which obtained either from databases or from calculations, are further used for computing the thermodynamic reaction equilibrium properties of the CO2 absorption/desorption cycles. Only those solid materials for which lower capture energy costs are predicted at the desired process conditions are selected as CO2 sorbent candidates and are further considered for experimental validations. Solid sorbents containing alkali and alkaline earth metals have been reported in several previous studies to be good candidates for CO2 sorbent applications due to their high CO2 absorption capacity at moderate working temperatures. In addition to introducing our computational screening procedure, in this presentation we will summarize our results for solid systems composed by alkali and alkaline earth metal oxides, hydroxides, and carbon- ates/bicarbonates to validate our methodology. Additionally, applications of our computational method to mixed solid systems of Li2O with SiO2/ZrO2 with different mixing ratios, our preliminary results showed that increasing the Li2O/SiO2 ratio in

  12. Label-free screening of single biomolecules through resistive pulse sensing technology for precision medicine applications

    Science.gov (United States)

    Harrer, S.; Kim, S. C.; Schieber, C.; Kannam, S.; Gunn, N.; Moore, S.; Scott, D.; Bathgate, R.; Skafidas, S.; Wagner, J. M.

    2015-05-01

    systems genomics has to be accompanied by an equally strong effort to develop next-generation DNA-sequencing and next-generation drug screening and design platforms. In that context lab-on-a-chip devices utilizing nanopore- and nanochannel based resistive pulse-sensing technology for DNA-sequencing and protein screening applications occupy a key role. This paper describes the status quo of resistive pulse sensing technology for these two application areas with a special focus on current technology trends and challenges ahead.

  13. Enhanced semiempirical QM methods for biomolecular interactions

    Directory of Open Access Journals (Sweden)

    Nusret Duygu Yilmazer

    2015-01-01

    Full Text Available Recent successes and failures of the application of ‘enhanced’ semiempirical QM (SQM methods are reviewed in the light of the benefits and backdraws of adding dispersion (D and hydrogen-bond (H correction terms. We find that the accuracy of SQM-DH methods for non-covalent interactions is very often reported to be comparable to dispersion-corrected density functional theory (DFT-D, while computation times are about three orders of magnitude lower. SQM-DH methods thus open up a possibility to simulate realistically large model systems for problems both in life and materials science with comparably high accuracy.

  14. Enhanced semiempirical QM methods for biomolecular interactions.

    Science.gov (United States)

    Yilmazer, Nusret Duygu; Korth, Martin

    2015-01-01

    Recent successes and failures of the application of 'enhanced' semiempirical QM (SQM) methods are reviewed in the light of the benefits and backdraws of adding dispersion (D) and hydrogen-bond (H) correction terms. We find that the accuracy of SQM-DH methods for non-covalent interactions is very often reported to be comparable to dispersion-corrected density functional theory (DFT-D), while computation times are about three orders of magnitude lower. SQM-DH methods thus open up a possibility to simulate realistically large model systems for problems both in life and materials science with comparably high accuracy. PMID:25848495

  15. Cellular automata modelling of biomolecular networks dynamics.

    Science.gov (United States)

    Bonchev, D; Thomas, S; Apte, A; Kier, L B

    2010-01-01

    The modelling of biological systems dynamics is traditionally performed by ordinary differential equations (ODEs). When dealing with intracellular networks of genes, proteins and metabolites, however, this approach is hindered by network complexity and the lack of experimental kinetic parameters. This opened the field for other modelling techniques, such as cellular automata (CA) and agent-based modelling (ABM). This article reviews this emerging field of studies on network dynamics in molecular biology. The basics of the CA technique are discussed along with an extensive list of related software and websites. The application of CA to networks of biochemical reactions is exemplified in detail by the case studies of the mitogen-activated protein kinase (MAPK) signalling pathway, the FAS-ligand (FASL)-induced and Bcl-2-related apoptosis. The potential of the CA method to model basic pathways patterns, to identify ways to control pathway dynamics and to help in generating strategies to fight with cancer is demonstrated. The different line of CA applications presented includes the search for the best-performing network motifs, an analysis of importance for effective intracellular signalling and pathway cross-talk. PMID:20373215

  16. Biomolecular ion detection using high-temperature superconducting MgB2 strips

    Science.gov (United States)

    Zen, N.; Shibata, H.; Mawatari, Y.; Koike, M.; Ohkubo, M.

    2015-06-01

    Superconducting strip ion detectors (SSIDs) are promising for realization of ideal ion detection with 100% efficiency and nanosecond-scale time response in time-of-flight mass spectrometry. We have detected single biomolecular ions in the keV range using a 10-nm-thick and 250-nm-wide strip of a high temperature superconductor, magnesium diboride (MgB2), at temperatures of up to 13 K. The output pulse shape is explained remarkably well using circuit simulations and time-dependent Ginzburg-Landau simulations coupled with a heat diffusion equation. The simulations show that the hot spot model is applicable to the proposed MgB2-SSIDs and the normal region expansion is completed within 16 ps, which corresponds to a maximum length of 1010 nm.

  17. A program to calculate non-bonded interaction energy in biomolecular aggregates.

    Science.gov (United States)

    Sundaram, K; Prasad, C V

    1982-02-01

    This paper describes a program to calculate intermolecular as well as intramolecular electronic potential energy resulting from non-bonded interactions. The underlying theory is obtained by the application of Rayleigh-Schroedinger perturbation theory to non-overlap regions of a molecular system. The rigorous theoretical expressions for the energy terms are simplified by approximations consistent with those commonly employed in semi-empirical molecular orbital theories. The program is particularly suited for the study of biomolecular assemblies, and in situations where insight into contributions to total energy from various component interaction types is desired. The inclusion of the non-additive dispersion effects in this approach makes it especially interesting for the study of cooperative phenomena in the light of a recent finding [1]. PMID:7067416

  18. Application of pre-participation cardiovascular screening guidelines to novice older runners and endurance athletes

    Directory of Open Access Journals (Sweden)

    Justin R Abbatemarco

    2016-01-01

    Full Text Available Objectives: Despite robust growth in participation in marathons and endurance sports among older individuals, guidance regarding pre-participation cardiovascular evaluation of these athletes is lacking. The objective of this study was to assess the utility of currently available pre-participation cardiovascular evaluation guidelines as applied to a cohort of older novice endurance athletes. Methods: We applied data from 1457 novice runners and endurance athletes aged 35 years and older to two pre-participation screening tools, the American Heart Association/American College of Sports Medicine Pre-Participation Questionnaire and the 2001 Working Group recommendations for pre-participation screening of masters athletes (2001 Masters. Results: Application of the American Heart Association/American College of Sports Medicine Pre-Participation Questionnaire identified 42.1% for which pre-participation cardiovascular evaluation was indicated. Of those who met criteria, 51.5% reported completion of a healthcare evaluation. Application of the 2001 Masters guidelines identified 75.2% who qualified for pre-participation electrocardiogram and 34.0% for pre-participation stress testing. Of those who met 2001 Masters criteria for pre-participation testing, 43.7% and 24.6% underwent recommended electrocardiogram and stress testing, respectively. While there was modest concordance with recommendations for pre-participation evaluations based on both American Heart Association/American College of Sports Medicine Pre-Participation Questionnaire and 2001 Masters, only athlete age was independently associated with completion of a pre-participation healthcare evaluation and only athlete age and athlete’s participation in marathons were independently associated with pre-participation stress testing. Conclusion: Among older novice endurance athletes, application of the American Heart Association/American College of Sports Medicine Pre-Participation Questionnaire

  19. Application of pre-participation cardiovascular screening guidelines to novice older runners and endurance athletes

    Science.gov (United States)

    Abbatemarco, Justin R; Bennett, Courtney; Bell, Adrian J; Dunne, Laura; Matsumura, Martin E

    2016-01-01

    Objectives: Despite robust growth in participation in marathons and endurance sports among older individuals, guidance regarding pre-participation cardiovascular evaluation of these athletes is lacking. The objective of this study was to assess the utility of currently available pre-participation cardiovascular evaluation guidelines as applied to a cohort of older novice endurance athletes. Methods: We applied data from 1457 novice runners and endurance athletes aged 35 years and older to two pre-participation screening tools, the American Heart Association/American College of Sports Medicine Pre-Participation Questionnaire and the 2001 Working Group recommendations for pre-participation screening of masters athletes (2001 Masters). Results: Application of the American Heart Association/American College of Sports Medicine Pre-Participation Questionnaire identified 42.1% for which pre-participation cardiovascular evaluation was indicated. Of those who met criteria, 51.5% reported completion of a healthcare evaluation. Application of the 2001 Masters guidelines identified 75.2% who qualified for pre-participation electrocardiogram and 34.0% for pre-participation stress testing. Of those who met 2001 Masters criteria for pre-participation testing, 43.7% and 24.6% underwent recommended electrocardiogram and stress testing, respectively. While there was modest concordance with recommendations for pre-participation evaluations based on both American Heart Association/American College of Sports Medicine Pre-Participation Questionnaire and 2001 Masters, only athlete age was independently associated with completion of a pre-participation healthcare evaluation and only athlete age and athlete’s participation in marathons were independently associated with pre-participation stress testing. Conclusion: Among older novice endurance athletes, application of the American Heart Association/American College of Sports Medicine Pre-Participation Questionnaire and 2001 Masters

  20. Scanning probe and optical tweezer investigations of biomolecular interactions

    Energy Technology Data Exchange (ETDEWEB)

    Rigby-Singleton, Shellie

    2002-07-01

    A complex array of intermolecular forces controls the interactions between and within biological molecules. The desire to empirically explore the fundamental forces has led to the development of several biophysical techniques. Of these, the atomic force microscope (AFM) and the optical tweezers have been employed throughout this thesis to monitor the intermolecular forces involved in biomolecular interactions. The AFM is a well-established force sensing technique capable of measuring biomolecular interactions at a single molecule level. However, its versatility has not been extrapolated to the investigation of a drug-enzyme complex. The energy landscape for the force induced dissociation of the DHFR-methotrexate complex was studied. Revealing an energy barrier to dissociation located {approx}0.3 nm from the bound state. Unfortunately, the AFM has a limited range of accessible loading rates and in order to profile the complete energy landscape alternative force sensing instrumentation should be considered, for example the BFP and optical tweezers. Thus, this thesis outlines the development and construction an optical trap capable of measuring intermolecular forces between biomolecules at the single molecule level. To demonstrate the force sensing abilities of the optical set up, proof of principle measurements were performed which investigate the interactions between proteins and polymer surfaces subjected to varying degrees of argon plasma treatment. Complementary data was gained from measurements performed independently by the AFM. Changes in polymer resistance to proteins as a response to changes in polymer surface chemistry were detected utilising both AFM and optical tweezers measurements. Finally, the AFM and optical tweezers were employed as ultrasensitive biosensors. Single molecule investigations of the antibody-antigen interaction between the cardiac troponin I marker and its complementary antibody, reveals the impact therapeutic concentrations of heparin

  1. Engineering biomolecular microenvironments for cell instructive biomaterials.

    Science.gov (United States)

    Custódio, Catarina A; Reis, Rui L; Mano, João F

    2014-06-01

    Engineered cell instructive microenvironments with the ability to stimulate specific cellular responses are a topic of high interest in the fabrication and development of biomaterials for application in tissue engineering. Cells are inherently sensitive to the in vivo microenvironment that is often designed as the cell "niche." The cell "niche" comprising the extracellular matrix and adjacent cells, influences not only cell architecture and mechanics, but also cell polarity and function. Extensive research has been performed to establish new tools to fabricate biomimetic advanced materials for tissue engineering that incorporate structural, mechanical, and biochemical signals that interact with cells in a controlled manner and to recapitulate the in vivo dynamic microenvironment. Bioactive tunable microenvironments using micro and nanofabrication have been successfully developed and proven to be extremely powerful to control intracellular signaling and cell function. This Review is focused in the assortment of biochemical signals that have been explored to fabricate bioactive cell microenvironments and the main technologies and chemical strategies to encode them in engineered biomaterials with biological information.

  2. Application of PET and PET/CT imaging for cancer screening

    International Nuclear Information System (INIS)

    The aim of this study was to evaluate the potential application of 18F-fluorodeoxyglucose (FDG) Positron Emission Tomography (PET) and PET/CT for cancer screening in asymptomatic individuals. Methods: The subjects consisted of 3631 physical check up examinees (1947 men, 1684 women; mean age ±SD, 52.1±8.2 y) with non-specific medical histories. Whole-body FDG PET (or PET/CT), ultrasound and tumor markers were performed on all patients. Focal hypermetabolic areas with intensities equal to or exceeding the level of FDG uptake in the brain and bladder were considered abnormal and interpreted as neoplasia. Follow-up periods were longer than one year. Results: Among the 3631 FDG PET (including 1687 PET/CT), ultrasound and tumor markers examinations, malignant tumors were discovered in 47 examinees (1.29%). PET findings were true-positive in 38 of the 47 cancers (80.9%). In addition, 32 of the 47 cancers were performed with the PET-CT scan. PET detected cancer lesions in 28 of the 32 examinees. However, the CT detected cancer lesions in only 15 of 32 examinees. Conclusion: The sensitivity of FDG PET in the detection of a wide variety of cancers is high. Most cancer can be detected with FDG PET in a resectable stage. CT of the PET/CT for localization and characteristics of the lesion shows an increased specificity of the PET scan. Using ultrasound and tumor markers may complement the PET scan in cancer screening for hepatic and urologic neoplasms. (authors)

  3. Theoretical description of biomolecular hydration - Application to A-DNA

    Energy Technology Data Exchange (ETDEWEB)

    Garcia, A.E.; Hummer, G. [Los Alamos National Laboratory, NM (United States); Soumpasis, D.M. [Max Planck Inst. for Biophysical Chemistry, Goettingen (Germany)

    1994-12-31

    The local density of water molecules around a biomolecule is constructed from calculated two- and three-points correlation functions of polar solvents in water using a Potential-of-Mean-Force (PMF) expansion. As a simple approximation, the hydration of all polar (including charged) groups in a biomolecule is represented by the hydration of water oxygen in bulk water, and the effect of non-polar groups on hydration are neglected, except for excluded volume effects. Pair and triplet correlation functions are calculated by molecular dynamics simulations. We present calculations of the structural hydration for ideal A-DNA molecules with sequences [d(CG){sub 5}]{sub 2} and [d(C{sub 5}G{sub 5})]{sub 2}. We find that this method can accurately reproduce the hydration patterns of A-DNA observed in neutron diffraction experiments on oriented DNA fibers.

  4. A Seoul-Fluor-based bioprobe for lipid droplets and its application in image-based high throughput screening.

    Science.gov (United States)

    Kim, Eunha; Lee, Sanghee; Park, Seung Bum

    2012-02-25

    We developed a novel fluorescent bioprobe (SF44) that can specifically visualize the cellular lipid droplets in in vitro and in vivo systems and illustrated the mechanistic rationale of its fluorogenic property. Its application to image-based high throughput screening led us to the identification of a new small-molecule modulator of lipid droplet formation.

  5. Evaluation of kinetic constants of biomolecular interaction on optical surface plasmon resonance sensor with Newton Iteration Method

    Science.gov (United States)

    Zhao, Yuanyuan; Jiang, Guoliang; Hu, Jiandong; Hu, Fengjiang; Wei, Jianguang; Shi, Liang

    2010-10-01

    In the immunology, there are two important types of biomolecular interaction: antigens-antibodies and receptors-ligands. Monitoring the response rate and affinity of biomolecular interaction can help analyze the protein function, drug discover, genomics and proteomics research. Moreover the association rate constant and dissociation rate constant of receptors-ligands are the important parameters for the study of signal transmission between cells. Recent advances in bioanalyzer instruments have greatly simplified the measurement of the kinetics of molecular interactions. Non-destructive and real-time monitoring the response to evaluate the parameters between antigens and antibodies can be performed by using optical surface plasmon resonance (SPR) biosensor technology. This technology provides a quantitative analysis that is carried out rapidly with label-free high-throughput detection using the binding curves of antigens-antibodies. Consequently, the kinetic parameters of interaction between antigens and antibodies can be obtained. This article presents a low cost integrated SPR-based bioanalyzer (HPSPR-6000) designed by ourselves. This bioanalyzer is mainly composed of a biosensor TSPR1K23, a touch-screen monitor, a microprocessor PIC24F128, a microflow cell with three channels, a clamp and a photoelectric conversion device. To obtain the kinetic parameters, sensorgrams may be modeled using one of several binding models provided with BIAevaluation software 3.0, SensiQ or Autolab. This allows calculation of the association rate constant (ka) and the dissociation rate constant (kd). The ratio of ka to kd can be used to estimate the equilibrium constant. Another kind is the analysis software OriginPro, which can process the obtained data by nonlinear fitting and then get some correlative parameters, but it can't be embedded into the bioanalyzer, so the bioanalyzer don't support the use of OriginPro. This paper proposes a novel method to evaluate the kinetic parameters

  6. MOCVD ZnO/Screen Printed Ag Back Reflector for Flexible Thin Film Silicon Solar Cell Application

    Directory of Open Access Journals (Sweden)

    Amornrat Limmanee

    2014-01-01

    Full Text Available We have prepared Ag back electrode by screen printing technique and developed MOCVD ZnO/screen printed Ag back reflector for flexible thin film silicon solar cell application. A discontinuity and poor contact interface between the MOCVD ZnO and screen printed Ag layers caused poor open circuit voltage (Voc and low fill factor (FF; however, an insertion of a thin sputtered ZnO layer at the interface could solve this problem. The n type hydrogenated amorphous silicon (a-Si:H film is preferable for the deposition on the surface of MOCVD ZnO film rather than the microcrystalline film due to its less sensitivity to textured surface, and this allowed an improvement in the FF. The n-i-p flexible amorphous silicon solar cell using the MOCVD ZnO/screen printed Ag back reflector showed an initial efficiency of 6.2% with Voc=0.86 V, Jsc=12.4 mA/cm2, and FF = 0.58 (1 cm2. The identical quantum efficiency and comparable performance to the cells using conventional sputtered Ag back electrode have verified the potential of the MOCVD ZnO/screen printed Ag back reflector and possible opportunity to use the screen printed Ag thick film for flexible thin film silicon solar cells.

  7. Protein hydrogels with engineered biomolecular recognition

    Science.gov (United States)

    Mi, Lixin

    water soluble and swelling. The RGD cell adhesion tripeptide has been inserted into the polyelectrolyte region by site-directed mutagenesis. Two dimensional human foreskin fibroblast cultures have shown that the RGD-containing protein surface is bioactive in promoting cell attachment, cell signaling, and cytoskeleton organization. The protein and the cell recognize and interact at molecular level. Collectively, these findings indicate that this bioactive protein hydrogel system is a promising biomaterial for mammalian cell culture. This research may provide insights for the rational development of bioactive ECM for specific cell and tissue engineering applications.

  8. [Low field nuclear magnetic resonance for rapid quantitation of microalgae lipid and its application in high throughput screening].

    Science.gov (United States)

    Liu, Tingting; Yang, Yi; Wang, Zejian; Zhuang, Yingping; Chu, Ju; Guoi, Meijin

    2016-03-01

    A rapid and accurate determination method of lipids in microalgae plays a significant role in an efficient breeding process for high-lipid production of microalgae. Using low field nuclear magnetic resonance (LF-NMR), we developed a direct quantitative method for cellular lipids in Chlorella protothecoides cells. The LF-NMR signal had a linear relationship with the lipid content in the microalgae cells for both dry cell samples and algal broth samples (R2 > 0.99). These results indicated that we could use this method for accurate determination of microalgal lipids. Although LF-NMR is a rapid and easy lipid determination method in comparison to conventional methods, low efficiency would limit its application in high throughput screening. Therefore, we developed a novel combined high throughput screening method for high-lipid content mutants of C. protothecoides. Namely, we initially applied Nile red staining method for semi-quantification of lipid in the pre-screening process, and following with LF-NMR method for accurate lipid determination in re-screening process. Finally, we adopted this novel screening method in the breeding process of high-lipid content heterotrophic cells of C. protothecoides. From 3 098 mutated strains 108 high-lipid content strains were selected through pre-screening process, and then 9 mutants with high-lipid production were obtained in the re-screening process. In a consequence, with heterotrophical cultivation of 168 h, the lipid concentration could reach 5 g/L, and the highest lipid content exceeded 20% (W/W), which was almost two-fold to that of the wild strain. All these results demonstrated that the novel breeding process was reliable and feasible for improving the screening efficiency. PMID:27349121

  9. web cellHTS2: A web-application for the analysis of high-throughput screening data

    Directory of Open Access Journals (Sweden)

    Boutros Michael

    2010-04-01

    Full Text Available Abstract Background The analysis of high-throughput screening data sets is an expanding field in bioinformatics. High-throughput screens by RNAi generate large primary data sets which need to be analyzed and annotated to identify relevant phenotypic hits. Large-scale RNAi screens are frequently used to identify novel factors that influence a broad range of cellular processes, including signaling pathway activity, cell proliferation, and host cell infection. Here, we present a web-based application utility for the end-to-end analysis of large cell-based screening experiments by cellHTS2. Results The software guides the user through the configuration steps that are required for the analysis of single or multi-channel experiments. The web-application provides options for various standardization and normalization methods, annotation of data sets and a comprehensive HTML report of the screening data analysis, including a ranked hit list. Sessions can be saved and restored for later re-analysis. The web frontend for the cellHTS2 R/Bioconductor package interacts with it through an R-server implementation that enables highly parallel analysis of screening data sets. web cellHTS2 further provides a file import and configuration module for common file formats. Conclusions The implemented web-application facilitates the analysis of high-throughput data sets and provides a user-friendly interface. web cellHTS2 is accessible online at http://web-cellHTS2.dkfz.de. A standalone version as a virtual appliance and source code for platforms supporting Java 1.5.0 can be downloaded from the web cellHTS2 page. web cellHTS2 is freely distributed under GPL.

  10. Development and Implementation of a Smartphone Application to Promote Physical Activity and Reduce Screen-Time in Adolescent Boys

    OpenAIRE

    Lubans, David R; Smith, Jordan J.; Skinner, Geoff; Morgan, Philip J

    2014-01-01

    Purpose: To describe the development and implementation of a smartphone application (app) designed to promote physical activity and reduce screen-time in adolescent boys considered “at-risk” of obesity. Methods: An app was developed to support the delivery of a face-to-face school-based obesity prevention program known as the “Active Teen Leaders Avoiding Screen-time” (ATLAS) program. ATLAS was guided by self-determination theory and social cognitive theory and evaluated using a cluster ra...

  11. Development and Implementation of a Smartphone Application to Promote Physical Activity and Reduce Screen-time in Adolescent Boys

    OpenAIRE

    David Revalds Lubans; Jordan eSmith; Geoff eSkinner; Philip James Morgan

    2014-01-01

    Purpose: The primary aim is to describe the development and implementation of a smartphone application (app) designed to promote physical activity and reduce screen-time in adolescent boys ‘at risk’ of obesity from low-income communities.Methods: An app was developed to support the delivery of a face-to-face school-based obesity prevention program known as the ‘Active Teen Leaders Avoiding Screen-time’ (ATLAS) program. ATLAS was guided by self-determination theory and social cognitive theory ...

  12. Application of experimental modal analysis technique to structural design of linear vibrating screen

    Institute of Scientific and Technical Information of China (English)

    LI Wen-ying(李文英); MI Zhao-yang(米朝阳); WU Wang-guo(武望国); XIONG Shi-bo(熊诗波)

    2004-01-01

    A large model of the screen was mounted in the laboratory for studying its modal performance. The model is suspended with steel ropes. Modal test was carried out with artificially exciting by 500 g impacting hammer and 100 kg exciting force shaker respectively. Synthesis and correction of the modal parameters are obtained from both testing methods. Design faults of vibrating screen were determined based on the analysis and dynamic correction of structure approaches about the screen was put forward finally.

  13. Knowledge based cluster ensemble for cancer discovery from biomolecular data.

    Science.gov (United States)

    Yu, Zhiwen; Wongb, Hau-San; You, Jane; Yang, Qinmin; Liao, Hongying

    2011-06-01

    The adoption of microarray techniques in biological and medical research provides a new way for cancer diagnosis and treatment. In order to perform successful diagnosis and treatment of cancer, discovering and classifying cancer types correctly is essential. Class discovery is one of the most important tasks in cancer classification using biomolecular data. Most of the existing works adopt single clustering algorithms to perform class discovery from biomolecular data. However, single clustering algorithms have limitations, which include a lack of robustness, stability, and accuracy. In this paper, we propose a new cluster ensemble approach called knowledge based cluster ensemble (KCE) which incorporates the prior knowledge of the data sets into the cluster ensemble framework. Specifically, KCE represents the prior knowledge of a data set in the form of pairwise constraints. Then, the spectral clustering algorithm (SC) is adopted to generate a set of clustering solutions. Next, KCE transforms pairwise constraints into confidence factors for these clustering solutions. After that, a consensus matrix is constructed by considering all the clustering solutions and their corresponding confidence factors. The final clustering result is obtained by partitioning the consensus matrix. Comparison with single clustering algorithms and conventional cluster ensemble approaches, knowledge based cluster ensemble approaches are more robust, stable and accurate. The experiments on cancer data sets show that: 1) KCE works well on these data sets; 2) KCE not only outperforms most of the state-of-the-art single clustering algorithms, but also outperforms most of the state-of-the-art cluster ensemble approaches.

  14. Programming in Biomolecular Computation: Programs, Self-Interpretation and Visualisation

    Directory of Open Access Journals (Sweden)

    J.G. Simonsen

    2011-01-01

    Full Text Available Our goal is to provide a top-down approach to biomolecular computation. In spite of widespread discussion about connections between biology and computation, one question seems notable by its absence: Where are the programs? We identify a number of common features in programming that seem conspicuously absent from the literature on biomolecular computing; to partially redress this absence, we introduce a model of computation that is evidently programmable, by programs reminiscent of low-level computer machine code; and at the same time biologically plausible: its functioning is defined by a single and relatively small set of chemical-like reaction rules. Further properties: the model is stored-program: programs are the same as data, so programs are not only executable, but are also compilable and interpretable. It is universal: all computable functions can be computed (in natural ways and without arcane encodings of data and algorithm; it is also uniform: new ``hardware'' is not needed to solve new problems; and (last but not least it is Turing complete in a strong sense: a universal algorithm exists, that is able to execute any program, and is not asymptotically inefficient.

  15. REPROVIS-DB: a benchmark system for ligand-based virtual screening derived from reproducible prospective applications.

    Science.gov (United States)

    Ripphausen, Peter; Wassermann, Anne Mai; Bajorath, Jürgen

    2011-10-24

    Benchmark calculations are essential for the evaluation of virtual screening (VS) methods. Typically, classes of known active compounds taken from the medicinal chemistry literature are divided into reference molecules (search templates) and potential hits that are added to background databases assumed to consist of compounds not sharing this activity. Then VS calculations are carried out, and the recall of known active compounds is determined. However, conventional benchmarking is affected by a number of problems that reduce its value for method evaluation. In addition to often insufficient statistical validation and the lack of generally accepted evaluation standards, the artificial nature of typical benchmark settings is often criticized. Retrospective benchmark calculations generally overestimate the potential of VS methods and do not scale with their performance in prospective applications. In order to provide additional opportunities for benchmarking that more closely resemble practical VS conditions, we have designed a publicly available compound database (DB) of reproducible virtual screens (REPROVIS-DB) that organizes information from successful ligand-based VS applications including reference compounds, screening databases, compound selection criteria, and experimentally confirmed hits. Using the currently available 25 hand-selected compound data sets, one can attempt to reproduce successful virtual screens with other than the originally applied methods and assess their potential for practical applications.

  16. The Application of Eddy Current Transducer for Testing Movement Locus of Shaker Screen

    Institute of Scientific and Technical Information of China (English)

    Zhu Pingyu; Lao Chuanjun; Zhang Wei; Li Xuejun

    2007-01-01

    Shaker screen is one of important equipments in the industry of oil, metallurgy, coal and timbering. The movement locus of shaker screen affects the capacity and efficiency of shaker screen to split the solid particle from crude ore directly .To test movement of shaker locus, two eddy current transducers are employed. A discussion of the usage of these eddy current transducer to test and acceleration sensors will be made. The experiment results from a real elliptic shaker screen have good agree with the design requirements.

  17. Applicability of ELISA to screen for dioxin-like PCBs in retail fish

    Energy Technology Data Exchange (ETDEWEB)

    Tsutsumi, T.; Amakura, Y.; Sasaki, K.; Maitani, T. [National Institute of Health Sciences, Tokyo (Japan); Okuyama, A.; Mizukami, H. [EnBioTec Laboratories Co., Ltd., Tokyo (Japan); Tanioka, Y.; Ueda, K.; Sakata, K. [Daiichi Fine Chemical Co., Ltd., Toyama (Japan)

    2004-09-15

    The group of dioxin-like PCBs, consisting of four non-ortho PCBs and eight mono-ortho PCBs, is classified among the dioxins. Humans are considerably exposed to dioxin through consumption of fish in Japan. The TEQ contribution of dioxin-like PCBs in fish is dominant, contributing about 70% of the total TEQ. Therefore, it is important to reveal TEQ levels of dioxin-like PCBs as well as PCDD/Fs in retail fish. HRGC/HRMS is currently the most widely used method to determine levels of dioxin-like PCBs. This method is very reliable and highly sensitive, but it is also timeconsuming and requires expensive equipment and highly trained analysts. One possible alternative method for screening dioxin-like PCBs is a bioassay, such as an ELISA. We recently developed an ELISA kit using a monoclonal antibody (MAb) specific to 2,3{sup '},4,4{sup '},5-pentachlorobiphenyl (PCB 118). PCB 118 is generally the most abundant isomer among dioxin-like PCBs in fish, although it has a relatively small contribution to the total TEQ derived from dioxin-like PCBs. Based on our HRGC/HRMS data, we found that the concentrations of PCB 118 correlated well to the TEQ levels of dioxin-like PCBs in retail fish (r>0.85, n = 181). Here, we examined the application of the ELISA kit in determining TEQ levels of dioxin-like PCBs in retail fish.

  18. An ontology for pharmaceutical ligands and its application for in silico screening and library design.

    Science.gov (United States)

    Schuffenhauer, Ansgar; Zimmermann, Jürg; Stoop, Ruedi; van der Vyver, Jan-Jan; Lecchini, Steffano; Jacoby, Edgar

    2002-01-01

    Annotation efforts in biosciences have focused in past years mainly on the annotation of genomic sequences. Only very limited effort has been put into annotation schemes for pharmaceutical ligands. Here we propose annotation schemes for the ligands of four major target classes, enzymes, G protein-coupled receptors (GPCRs), nuclear receptors (NRs), and ligand-gated ion channels (LGICs), and outline their usage for in silico screening and combinatorial library design. The proposed schemes cover ligand functionality and hierarchical levels of target classification. The classification schemes are based on those established by the EC, GPCRDB, NuclearDB, and LGICDB. The ligands of the MDL Drug Data Report (MDDR) database serve as a reference data set of known pharmacologically active compounds. All ligands were annotated according to the schemes when attribution was possible based on the activity classification provided by the reference database. The purpose of the ligand-target classification schemes is to allow annotation-based searching of the ligand database. In addition, the biological sequence information of the target is directly linkable to the ligand, hereby allowing sequence similarity-based identification of ligands of next homologous receptors. Ligands of specified levels can easily be retrieved to serve as comprehensive reference sets for cheminformatics-based similarity searches and for design of target class focused compound libraries. Retrospective in silico screening experiments within the MDDR01.1 database, searching for structures binding to dopamine D2, all dopamine receptors and all amine-binding class A GPCRs using known dopamine D2 binding compounds as a reference set, have shown that such reference sets are in particular useful for the identification of ligands binding to receptors closely related to the reference system. The potential for ligand identification drops with increasing phylogenetic distance. The analysis of the focus of a tertiary

  19. Establishment of a P-glycoprotein substrate screening model and its preliminary application

    Institute of Scientific and Technical Information of China (English)

    Yi Wang; Jiang Cao; Su Zeng

    2004-01-01

    AIM: To establish a high P-glycoprotein (P-gp) expressing cell line as a model for studying drug absorption and distribution, and to explore the preliminary application of this screening model.METHODS: A full-length MDR1 cDNA fragment in plasmid pMDRA1 was first subcloned into plasmid pET28a(+), then MDR1 cDNA was cut from the recombinant plasmid with double-digestion and ligated into the mammalian expression vector pcDNA3.1(+). The recombinant plasmid pcDNA3.1(+)/MDR1 was transfected into breast cancer cell line Bcap37using the Superfect transfection reagent. Several stably transfected clones were obtained after selection with G418.Real-time fluorescent quantitative RT- PCR and Western blot methods were used to detect the expression of P-gp, and the cellular location of the expressed protein was determined by immunohistochemical staining. Drug sensitivity assay was used to evaluate the biological function of expressed P-gp.Concentration of quercetin in cells was determined by highperformance liquid chromatography (HPLC).RESULTS: The recombinant plasmid was confirmed to be inserted in the correct orientation by restrictive enzyme digestion and DNA sequencing. Real-time fluorescent quantitative RT-PCR showed a higher level of P-cp mRNA in transfected cells compared to that in the control cells, and the Western blot result also indicated that P-gp expression in transfected cells was higher than that in control cells. The immunohistochemical staining showed that the expressed P-gp was localized on cell membranes. Drug sensitivity assay showed that the IC50 for adriamycin and colchicine of the transfected cells was higher than that of the control cells.The concentration of quercetin in model cells was lower than that in control cells by HPLC. After P-gp inhibitor verapamil was administered, the concentration of quercetin in model cells was increased.CONCLUSION: A high P-gp expressing ceil line can be established, which could provide a suitable in vitro model system for

  20. Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads

    Science.gov (United States)

    Stone, John E.; Hallock, Michael J.; Phillips, James C.; Peterson, Joseph R.; Luthey-Schulten, Zaida; Schulten, Klaus

    2016-01-01

    Many of the continuing scientific advances achieved through computational biology are predicated on the availability of ongoing increases in computational power required for detailed simulation and analysis of cellular processes on biologically-relevant timescales. A critical challenge facing the development of future exascale supercomputer systems is the development of new computing hardware and associated scientific applications that dramatically improve upon the energy efficiency of existing solutions, while providing increased simulation, analysis, and visualization performance. Mobile computing platforms have recently become powerful enough to support interactive molecular visualization tasks that were previously only possible on laptops and workstations, creating future opportunities for their convenient use for meetings, remote collaboration, and as head mounted displays for immersive stereoscopic viewing. We describe early experiences adapting several biomolecular simulation and analysis applications for emerging heterogeneous computing platforms that combine power-efficient system-on-chip multi-core CPUs with high-performance massively parallel GPUs. We present low-cost power monitoring instrumentation that provides sufficient temporal resolution to evaluate the power consumption of individual CPU algorithms and GPU kernels. We compare the performance and energy efficiency of scientific applications running on emerging platforms with results obtained on traditional platforms, identify hardware and algorithmic performance bottlenecks that affect the usability of these platforms, and describe avenues for improving both the hardware and applications in pursuit of the needs of molecular modeling tasks on mobile devices and future exascale computers.

  1. 膨胀筛管防砂技术研究%Application of expandable screen pipe technology for sand control

    Institute of Scientific and Technical Information of China (English)

    沈琛; 宁学涛; 朱海波; 唐明

    2011-01-01

    膨胀筛管技术是一种新兴的防砂技术,介绍了大通径膨胀筛管悬挂器、带有割缝的膨胀螺纹及具有变径功能的膨胀工具等膨胀筛管的几个关键技术.大通径膨胀筛管悬挂器能够确保变径膨胀工具的顺利下入,带有割缝的螺纹膨胀后与筛管本体具有一样大小的内径,变径膨胀工具使得膨胀筛管可以紧贴井壁,减少砂粒的运移和冲蚀.膨胀筛管技术在两口套损井中的防砂应用表明,在满足选井条件的情况下,采用膨胀筛管可以获得较好的生产效果,筛管膨胀后紧贴套管内壁,膨胀后筛管内径比普通筛管内径大,有利于增大泄油面积,提高油井产量.%Expandable Screen Technology is a new sand control technique. Expandable hanger with larger diameter, expandable screw with slot and expansion tool with diameter variable features are several key technologies of expandable screen. Expandable hanger with larger diameter enables the diameter variable expansion tool to run into the well successfully, the slotted thread after expansion has the same diameter with expandable screen, and The adjustable expansion tool makes expandable screen close to the wall, which can reduce the migration of sand and erosion. In this paper, the study on the slotted expandable thread, expandable hanger and the development of adjustable expansion tool, ground-based testing and underground simulation testing of expandable screen were introduced. This application of expandable screen technology in two damaged casing for the sand control illustrated that adopting expandable tube can get favorable productivity after meeting the requirement of selecting well condition. The expandable screen touching the inwall of the casing for which the inner diameter of expandable screen is bigger than that of conventional screen pipe, is helpful to enlarge the drainage area and enhance oil well productivity.

  2. The biomolecular corona of nanoparticles in circulating biological media

    Science.gov (United States)

    Pozzi, D.; Caracciolo, G.; Digiacomo, L.; Colapicchioni, V.; Palchetti, S.; Capriotti, A. L.; Cavaliere, C.; Zenezini Chiozzi, R.; Puglisi, A.; Laganà, A.

    2015-08-01

    When nanoparticles come into contact with biological media, they are covered by a biomolecular `corona', which confers a new identity to the particles. In all the studies reported so far nanoparticles are incubated with isolated plasma or serum that are used as a model for protein adsorption. Anyway, bodily fluids are dynamic in nature so the question arises on whether the incubation protocol, i.e. dynamic vs. static incubation, could affect the composition and structure of the biomolecular corona. Here we let multicomponent liposomes interact with fetal bovine serum (FBS) both statically and dynamically, i.e. in contact with circulating FBS (~40 cm s-1). The structure and composition of the liposome-protein corona, as determined by dynamic light scattering, electrophoretic light scattering and liquid chromatography tandem mass spectrometry, were found to be dependent on the incubation protocol. Specifically, following dynamic exposure to FBS, multicomponent liposomes were less enriched in complement proteins and appreciably more enriched in apolipoproteins and acute phase proteins (e.g. alpha-1-antitrypsin and inter-alpha-trypsin inhibitor heavy chain H3) that are involved in relevant interactions between nanoparticles and living systems. Supported by our results, we speculate that efficient predictive modeling of nanoparticle behavior in vivo will require accurate knowledge of nanoparticle-specific protein fingerprints in circulating biological media.When nanoparticles come into contact with biological media, they are covered by a biomolecular `corona', which confers a new identity to the particles. In all the studies reported so far nanoparticles are incubated with isolated plasma or serum that are used as a model for protein adsorption. Anyway, bodily fluids are dynamic in nature so the question arises on whether the incubation protocol, i.e. dynamic vs. static incubation, could affect the composition and structure of the biomolecular corona. Here we let

  3. Biomolecular Simulation of Base Excision Repair and Protein Signaling

    Energy Technology Data Exchange (ETDEWEB)

    Straatsma, TP; McCammon, J A; Miller, John H; Smith, Paul E; Vorpagel, Erich R; Wong, Chung F; Zacharias, Martin W

    2006-03-03

    The goal of the Biomolecular Simulation of Base Excision Repair and Protein Signaling project is to enhance our understanding of the mechanism of human polymerase-β, one of the key enzymes in base excision repair (BER) and the cell-signaling enzymes cyclic-AMP-dependent protein kinase. This work used molecular modeling and simulation studies to specifically focus on the • dynamics of DNA and damaged DNA • dynamics and energetics of base flipping in DNA • mechanism and fidelity of nucleotide insertion by BER enzyme human polymerase-β • mechanism and inhibitor design for cyclic-AMP-dependent protein kinase. Molecular dynamics simulations and electronic structure calculations have been performed using the computer resources at the Molecular Science Computing Facility at the Environmental Molecular Sciences Laboratory.

  4. Insights into cancer severity from biomolecular interaction mechanisms

    Science.gov (United States)

    Raimondi, Francesco; Singh, Gurdeep; Betts, Matthew J.; Apic, Gordana; Vukotic, Ranka; Andreone, Pietro; Stein, Lincoln; Russell, Robert B.

    2016-01-01

    To attain a deeper understanding of diseases like cancer, it is critical to couple genetics with biomolecular mechanisms. High-throughput sequencing has identified thousands of somatic mutations across dozens of cancers, and there is a pressing need to identify the few that are pathologically relevant. Here we use protein structure and interaction data to interrogate nonsynonymous somatic cancer mutations, identifying a set of 213 molecular interfaces (protein-protein, -small molecule or –nucleic acid) most often perturbed in cancer, highlighting several potentially novel cancer genes. Over half of these interfaces involve protein-small-molecule interactions highlighting their overall importance in cancer. We found distinct differences in the predominance of perturbed interfaces between cancers and histological subtypes and presence or absence of certain interfaces appears to correlate with cancer severity. PMID:27698488

  5. Structure and Interactions of Isolated Biomolecular Building Blocks.

    Science.gov (United States)

    de Vries, Mattanjah

    2006-03-01

    We investigate biomolecular building blocks and their clusters with each other and with water on a single molecular level. The motivation is the need to distinguish between intrinsic molecular properties and those that result from the biological environment. This is achieved by a combination of laser desorption and jet cooling, applied to aromatic amino acids, small peptides containing those, nucleobases and nucleosides. This approach is coupled with a number of laser spectroscopic techniques, including resonant multi-photon ionization, spectral hole burning and infra-red ion-dip spectroscopy. We will discuss examples illustrating how information can be obtained on spatial structure of individual biomolecules, including peptide conformations and details of DNA base-pairing.

  6. PRELIMINARY APPLICATION OF WHOLE BODY DIFFUSION WEIGHTED IMAGING IN SCREENING METASTASIS

    Institute of Scientific and Technical Information of China (English)

    Yong-jing Guan; Hua-wei Ling; Ke-min Chen

    2008-01-01

    Objective To investigate the feasibility of whole body diffusion weighted imaging (WB-DWI) in screening metastasis.Methods WB-DWI was performed in 24 patients diagnosed with various types of primary tumors. The three-dimensional maximum intensity projection reconstruction and black-and-white flip technique were used to observe metastatic lesions, and the results were compared with those of bone scintigraphy. Results By WB-DWI scanning sequence at b = 800 s/mm2, all the bone lesions found by bone scintigraphy in the cohort were well identified, and other lesions of soft tissue and organs were also well demonstrated. Its screening capability was equivalent with bone scintigraphy in screening metastases in bones (P = 0.062). Conclusion WB-DWI was practicable with the parameter settings attempted in metastases screening.

  7. Application of Imaging-Based Assays in Microplate Formats for High-Content Screening.

    Science.gov (United States)

    Fogel, Adam I; Martin, Scott E; Hasson, Samuel A

    2016-01-01

    The use of multiparametric microscopy-based screens with automated analysis has enabled the large-scale study of biological phenomena that are currently not measurable by any other method. Collectively referred to as high-content screening (HCS), or high-content analysis (HCA), these methods rely on an expanding array of imaging hardware and software automation. Coupled with an ever-growing amount of diverse chemical matter and functional genomic tools, HCS has helped open the door to a new frontier of understanding cell biology through phenotype-driven screening. With the ability to interrogate biology on a cell-by-cell basis in highly parallel microplate-based platforms, the utility of HCS continues to grow as advancements are made in acquisition speed, model system complexity, data management, and analysis systems. This chapter uses an example of screening for genetic factors regulating mitochondrial quality control to exemplify the practical considerations in developing and executing high-content campaigns. PMID:27317002

  8. Technological features of application of nanophotonic elements of packaging by screen printing

    OpenAIRE

    Сарапулова, Ольга Олександрівна; Шерстюк, Валентин Петрович

    2013-01-01

    The technological parameters that affect the process of producing printed packaging with nanophotonic elements were defined. The factors and parameters of manufacturing coatings based on nanosized zinc oxide with photoluminescent properties for producing active and intelligent (smart) packaging by screen printing were studied. The formation of luminescent coatings by screen printing on polypropylene films was carried out and parameters of deposition process and photoluminescence properties of...

  9. The application and use of chemical space mapping to interpret crystallization screening results

    OpenAIRE

    Snell, Edward H.; Nagel, Ray M.; Wojtaszcyk, Ann; O’Neill, Hugh; Wolfley, Jennifer L.; Joseph R Luft

    2008-01-01

    Macromolecular crystallization screening is an empirical process. It often begins by setting up experiments with a number of chemically diverse cocktails designed to sample chemical space known to promote crystallization. Where a potential crystal is seen a refined screen is set up, optimizing around that condition. By using an incomplete factorial sampling of chemical space to formulate the cocktails and presenting the results graphically, it is possible to readily identify trends relevant t...

  10. Neuroblastoma Screening

    Science.gov (United States)

    ... Health Professional Neuroblastoma Treatment Neuroblastoma Screening Research Neuroblastoma Screening (PDQ®)–Patient Version What is screening? Go to Health Professional Version Screening is looking ...

  11. Video Screen Capture Basics

    Science.gov (United States)

    Dunbar, Laura

    2014-01-01

    This article is an introduction to video screen capture. Basic information of two software programs, QuickTime for Mac and BlueBerry Flashback Express for PC, are also discussed. Practical applications for video screen capture are given.

  12. Application effect of TruScreen system in cervical cancer screening%TruScreen系统在宫颈癌筛查中的应用效果

    Institute of Scientific and Technical Information of China (English)

    李佩; 王金声; 康媛

    2016-01-01

    Objective To investigate the effect of TruScreen (TS) system as applied in cervical cancer screening. Method 368 patients were included in the retrospective analysis, and were randomized into TS group or TCT group, with 184 cases in each. The TS group was tested with TS detection, while the TCT group was administered with Thin Prep cytology test (TCT), and the effect of the two tests were compared with histopathology as the diagnostic standard. Result The detection sensitivity, specificity and the positive rate of the TS and TCT group were 93.2%and 100%, 76.0%and 75.0%, 64.7% and 55.7%, respectively. Conclusion TS detection is as good as TCT detection in cervical cancer screening, which is clinically applicable.%目的:探讨宫颈癌筛查系统TruScreen(TS)在宫颈癌筛查中的应用效果。方法回顾性分析368例检查者,分为TS检测组和TCT检测组,每组184例,TS检测组行TS检测,TCT检测组行液基薄层细胞学(TCT)检测,以组织病理学为诊断标准,比较TS与TCT检查在宫颈癌筛查中的应用效果。结果 TS检测组与TCT检测组检测敏感度分别为93.2%、100%,特异度分别为76.0%、75.0%,阳性符合率分别为64.7%、55.7%。结论 TS检测与TCT检测在宫颈癌筛查中具有相似的检测效果,值得临床推广和运用。

  13. Differential geometry-based solvation and electrolyte transport models for biomolecular modeling: a review

    OpenAIRE

    Wei, Guo Wei; Baker, Nathan A.

    2014-01-01

    This chapter reviews the differential geometry-based solvation and electrolyte transport for biomolecular solvation that have been developed over the past decade. A key component of these methods is the differential geometry of surfaces theory, as applied to the solvent-solute boundary. In these approaches, the solvent-solute boundary is determined by a variational principle that determines the major physical observables of interest, for example, biomolecular surface area, enclosed volume, el...

  14. HER2 Targeting Peptides Screening and Applications in Tumor Imaging and Drug Delivery

    Science.gov (United States)

    Geng, Lingling; Wang, Zihua; Jia, Xiangqian; Han, Qiuju; Xiang, Zhichu; Li, Dan; Yang, Xiaoliang; Zhang, Di; Bu, Xiangli; Wang, Weizhi; Hu, Zhiyuan; Fang, Qiaojun

    2016-01-01

    Herein, computational-aided one-bead-one-compound (OBOC) peptide library design combined with in situ single-bead sequencing microarray methods were successfully applied in screening peptides targeting at human epidermal growth factor receptor-2 (HER2), a biomarker of human breast cancer. As a result, 72 novel peptides clustered into three sequence motifs which are PYL***NP, YYL***NP and PPL***NP were acquired. Particularly one of the peptides, P51, has nanomolar affinity and high specificity for HER2 in ex vivo and in vivo tests. Moreover, doxorubicin (DOX)-loaded liposome nanoparticles were modified with peptide P51 or P25 and demonstrated to improve the targeted delivery against HER2 positive cells. Our study provides an efficient peptide screening method with a combination of techniques and the novel screened peptides with a clear binding site on HER2 can be used as probes for tumor imaging and targeted drug delivery. PMID:27279916

  15. Application of Autofluorescence Endoscopy for Colorectal Cancer Screening: Rationale and an Update

    Directory of Open Access Journals (Sweden)

    Hiroyuki Aihara

    2012-01-01

    Full Text Available As the result of basic researches, several intravital fluorophores have been determined so far in human colorectal tissue. Autofluorescence endoscopy (AFE can detect slight alterations in their distribution and concentration during the colorectal carcinogenesis process and, thus facilitate noninvasive screening colonoscopies without the need for fluorescent substances or staining reagents to be administered. While detecting faint autofluorescence intensity by conventional fiberoptic endoscopy remains challenging, the latest AFE system with high-resolution videoendoscope capabilities enables such detection by using a false-color display algorithm. To this end, the diagnostic benefits of AFE have been reported in several multicenter randomized controlled studies of colorectal cancer (CRC screening and differential diagnosis. CRC screening using the latest AFE technology could, therefore, lead to future reductions in CRC mortality.

  16. Application of isothermal titration calorimeter for screening bitterness-suppressing molecules of quinine.

    Science.gov (United States)

    Zhang, Yifan; Zhu, Youwei; Zhao, Na; Wu, Jinhui; Hu, Yiqiao

    2016-01-01

    Bitterness-suppressing molecules have drawn ever-increasing attention these years for some unique advantages like low molecular weight, tastelessness and no interference on drug bioavailability. L-Arg was reported to suppress the bitterness of quinine, and we happened to find that the suppressing effects could be demonstrated by isothermal titration calorimeter (ITC). In this study, we investigated the possibility of using ITC to screen bitterness-suppressing molecules for quinine. Among the amino acids we screened, L-Lys bond quinine with high affinity. The results of ITC correlated well with the results of human sensory experiments. L-Arg and L-Lys could suppress the bitterness of quinine while other amino acids could not. Therefore, ITC has the potential to screen bitterness-suppressing molecules.

  17. 大屏幕拼接技术及其应用%Large-Screen Splicing Technology and Its Applications

    Institute of Scientific and Technical Information of China (English)

    卢光义

    2009-01-01

    大屏幕拼接技术是现代计算机图形处理技术和各种显示技术的有机结合,实现多路独立视频信号和计算机信号同时直通显示,单元无级缩放、画中画显示,网络计算机信号快速显示,高分辨率全屏显示,灵活缩放显示、大画面跨屏清晰显示,超高分辨率图像、视频、计算机、网络信号综合显示等.广泛用于部队、武警、公安指挥中心、政府视频会议系统、企业生产调度中心等场合.该文主要介绍DLP、MPDP、LED三种主流大屏幕拼接技术的原理、结构和实际运用.%Splicing technology is a large-screen graphics of modern computer technology and the organic integration of display technology to achieve an independent multi-channel video signal and computer signal through at the same time show that no unit-level zoom, pic-ture-in-picture display, network computer signal quickly revealed that high-resolution the rate of full-screen display, flexible scaling showed that the screen to clearly indicate that cross-screen, ultra-high-resohition images, video, computer, network signal integrated dis-play. Widely used in troops, armed police, public security command center, the Government Video Conference System, business centers, production scheduling occasions. In this paper, DLP, MPDP, LED splicing of three large-screen technology to mainstream the principles, structure and practical appli-cation.

  18. Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations.

    Science.gov (United States)

    Takada, Shoji; Kanada, Ryo; Tan, Cheng; Terakawa, Tsuyoshi; Li, Wenfei; Kenzaki, Hiroo

    2015-12-15

    Due to hierarchic nature of biomolecular systems, their computational modeling calls for multiscale approaches, in which coarse-grained (CG) simulations are used to address long-time dynamics of large systems. Here, we review recent developments and applications of CG modeling methods, focusing on our methods primarily for proteins, DNA, and their complexes. These methods have been implemented in the CG biomolecular simulator, CafeMol. Our CG model has resolution such that ∼10 non-hydrogen atoms are grouped into one CG particle on average. For proteins, each amino acid is represented by one CG particle. For DNA, one nucleotide is simplified by three CG particles, representing sugar, phosphate, and base. The protein modeling is based on the idea that proteins have a globally funnel-like energy landscape, which is encoded in the structure-based potential energy function. We first describe two representative minimal models of proteins, called the elastic network model and the classic Go̅ model. We then present a more elaborate protein model, which extends the minimal model to incorporate sequence and context dependent local flexibility and nonlocal contacts. For DNA, we describe a model developed by de Pablo's group that was tuned to well reproduce sequence-dependent structural and thermodynamic experimental data for single- and double-stranded DNAs. Protein-DNA interactions are modeled either by the structure-based term for specific cases or by electrostatic and excluded volume terms for nonspecific cases. We also discuss the time scale mapping in CG molecular dynamics simulations. While the apparent single time step of our CGMD is about 10 times larger than that in the fully atomistic molecular dynamics for small-scale dynamics, large-scale motions can be further accelerated by two-orders of magnitude with the use of CG model and a low friction constant in Langevin dynamics. Next, we present four examples of applications. First, the classic Go̅ model was used to

  19. Cost-Effective Fabrication of Wettability Gradient Copper Surface by Screen Printing and its Application to Condensation Heat Transfer

    Science.gov (United States)

    Leu, Tzong-Shyng; Huang, Hung-Ming; Huang, Ding-Jun

    2016-06-01

    In this paper, wettability gradient pattern is applied to condensation heat transfer on a copper tube surface. For this application, the vital issue is how to fabricate gradient patterns on a curve tube surface to accelerate the droplet collection efficiently. For this purpose, novel fabrication processes are developed to form wettability gradient patterns on a curve copper tube surface by using roller screen printing surface modification techniques. The roller screen printing surface modification techniques can easily realize wettability gradient surfaces with superhydrophobicity and superhydrophilicity on a copper tube surface. Experimental results show the droplet nucleation sites, movement and coalescence toward the collection areas can be effectively controlled which can assist in removing the condensation water from the surface. The effectiveness of droplet collection is appropriate for being applied to condensation heat transfer in the foreseeable future.

  20. From Evidence to Decision Support in Cancer Screening; Application of Miscan Models

    NARCIS (Netherlands)

    R. Boer (Rob)

    2000-01-01

    textabstractMaking decisions to introduce or change cancer screening that are based on observed evidence is not straight forward. Even if there is evidence available from randomised controlled trials that clearly proves a reduction in mortality from the cancer in question, there are still several is

  1. APPLICATION OF EMPORE C-8 EXTRACTION DISKS FOR SCREENING URINE IN SYSTEMATIC TOXICOLOGICAL ANALYSIS

    NARCIS (Netherlands)

    ENSING, K; FRANKE, JP; TEMMINK, A; CHEN, XH; DEZEEUW, RA

    1992-01-01

    Solid-phase extraction (SPE) by means of disposable columns has become a widely accepted technique for sample pretreatment in toxicology, both for directed analyses and for screening analyses. However, the sample capacity in SPE is usually limited to a few millilitres. Therefore, we have investigate

  2. The CALUX bioassay: current status of its application to screening food and feed

    NARCIS (Netherlands)

    Hoogenboom, L.A.P.; Goeyens, L.; Carbonnelle, S.; Loco, van J.; Beernaert, H.; Baeyens, W.; Traag, W.A.; Bovee, T.F.H.; Jacobs, G.; Schoeters, G.

    2006-01-01

    The CALUX bioassay is at present the best screening method for dioxins and dioxin-like (dl) polychlorinated biphenyls (PCBs) in food and feed, and the only assay used in routine monitoring and during larger incidents. Furthermore, the use of bioassays in addition to chemical reference methods allows

  3. Life-Stage Physiologically-Based Pharmacokinetic (PBPK) Model Applications to Screen Environmental Hazards.

    Science.gov (United States)

    This presentation discusses methods used to extrapolate from in vitro high-throughput screening (HTS) toxicity data for an endocrine pathway to in vivo for early life stages in humans, and the use of a life stage PBPK model to address rapidly changing physiological parameters. A...

  4. Construction of the Application Systems for Universal Education in Architectural Heritage – Multimedia Touch Screen Desk System

    Directory of Open Access Journals (Sweden)

    Sato Reika

    2016-01-01

    Full Text Available The importance of popular education in architectural heritage is well known. It is an effective method for public education to develop applications that utilize digital copy of architectural heritage. We provide a case study focusing on the historical buildings of Toji Temple in Kyoto, Japan. We digitize the historical buildings in both overall construction and detailed structures. We build a demonstration and operating system using multimedia technologies such as multimedia touch screen desk system. The system will produce 3D digital models of architectural heritage with high resolution and use advanced technology to develop a variety of demonstration applications that can enhance your presentation and ease operation. The users can also have more opportunities and ways to improve their interests in learning and understanding about the architectural heritage knowledge, hence finding new ways to further improve the methodology of architectural heritage education with the application of multimedia interactive technologies and digital copy of historical buildings.

  5. Function of Amphiphilic Biomolecular Machines: Elastic Protein-based Polymers

    Science.gov (United States)

    Urry, Dan W.

    2000-03-01

    Elastic protein-based polymers function as biomolecular machines due to inverse temperature transitions of hydrophobic folding and assembly. The transitions occur either on raising the temperature from below to above the transition temperature, Tt, or on isothermally lowering Tt from above to below an operating temperature. The inverse temperature transition involves a decrease in entropy of the polymer component of the system on raising the temperature and a larger increase in solvent entropy on hydrophobic association. Tt depends on the quantity of hydrophobic hydration that undergoes transition to bulk water. Designed amphiphilic polymers perform free energy transductions involving the intensive variables of mechanical force, pressure, temperature, chemical potential, electrochemical potential and electromagnetic radiation and define a set of five axioms for their function as machines. The physical basis for these diverse energy conversions is competition for hydration between apolar (hydrophobic) and polar (e.g., charged) moieties. The effectiveness of these Tt-type entropic elastic protein-based machines is due to repeating peptide sequences that form regular, dynamic repeating structures and exhibit damping of backbone torsional oscillations on extension.

  6. [Biobanking and Biomolecular Resources Research Infrastructure (BBMRI). Implications for pathology].

    Science.gov (United States)

    Viertler, C; Zatloukal, K

    2008-11-01

    High quality human biological samples (e.g. blood, tissue or DNA) with associated, well documented clinical and research data are key resources for advancement of life sciences, biotechnology, clinical medicine, drug development and also molecular pathology. Millions of samples of diseased tissues have been collected in the context of routine histopathological diagnosis and are stored in the archives of hospitals and institutes of pathology. A concerted effort is necessary to overcome the current fragmentation of the European biobanking community in order to tap the full research potential of existing biobanks. A pan-European research infrastructure for biobanking and biomolecular resources (BBMRI) is currently in its planning phase. The mission is to link and provide access to local biobanks of different formats, including tissue collections, harmonize standards, establish operational procedures which properly consider ethical, legal, societal aspects, and to secure sustainable funding. Pathology plays a key role in development and administration of tissue banks and is, thus, a major partner for collaboration, expertise and construction of this pan-European research infrastructure.

  7. A programmable biomolecular computing machine with bacterial phenotype output.

    Science.gov (United States)

    Kossoy, Elizaveta; Lavid, Noa; Soreni-Harari, Michal; Shoham, Yuval; Keinan, Ehud

    2007-07-23

    The main advantage of autonomous biomolecular computing devices over electronic computers is their ability to interact directly with biological systems. No interface is required since all components of molecular computers, including hardware, software, input, and output are molecules that interact in solution along a cascade of programmable chemical events. Here, we demonstrate for the first time that the output of a computation preduced by a molecular finite automaton can be a visible bacterial phenotype. Our 2-symbol-2-state finite automaton utilized linear double-stranded DNA inputs that were prepared by inserting a string of six base pair symbols into the lacZ gene on the pUC18 plasmid. The computation resulted in a circular plasmid that differed from the original pUC18 by either a 9 base pair (accepting state) or 11 base pair insert (unaccepting state) within the lacZ alpha region gene. Upon transformation and expression of the resultant plasmids in E. coli, the accepting state was represented by production of functional beta-galactosidase and formation of blue colonies on X-gal medium. In contrast, the unaccepting state was represented by white colonies due to a shift in the open reading frame of lacZ. PMID:17562552

  8. Stochastic Simulation of Biomolecular Networks in Dynamic Environments.

    Directory of Open Access Journals (Sweden)

    Margaritis Voliotis

    2016-06-01

    Full Text Available Simulation of biomolecular networks is now indispensable for studying biological systems, from small reaction networks to large ensembles of cells. Here we present a novel approach for stochastic simulation of networks embedded in the dynamic environment of the cell and its surroundings. We thus sample trajectories of the stochastic process described by the chemical master equation with time-varying propensities. A comparative analysis shows that existing approaches can either fail dramatically, or else can impose impractical computational burdens due to numerical integration of reaction propensities, especially when cell ensembles are studied. Here we introduce the Extrande method which, given a simulated time course of dynamic network inputs, provides a conditionally exact and several orders-of-magnitude faster simulation solution. The new approach makes it feasible to demonstrate-using decision-making by a large population of quorum sensing bacteria-that robustness to fluctuations from upstream signaling places strong constraints on the design of networks determining cell fate. Our approach has the potential to significantly advance both understanding of molecular systems biology and design of synthetic circuits.

  9. Preparation of a YAG:Ce phosphor glass by screen-printing technology and its application in LED packaging.

    Science.gov (United States)

    Yang, Liang; Chen, Mingxiang; Lv, Zhicheng; Wang, Simin; Liu, Xiaogang; Liu, Sheng

    2013-07-01

    A simple and practical method for preparing phosphor glass is proposed. Phosphor distribution and element analysis are investigated by optical microscope and field emission scanning electron microscope (FE-SEM). The phosphor particles dispersed in the matrix are vividly observed, and their distributions are uniform. Spectrum distribution and color coordinates dependent on the thickness of the screen-printed phosphor layer coupled with a blue light emitting diode (LED) chip are studied. The luminous efficacy of the 75 μm printed phosphor-layer phosphor glass packaged white LED is 81.24 lm/W at 350 mA. This study opens up many possibilities for applications using the phosphor glass on a selected chip in which emission is well absorbed by all phosphors. The screen-printing technique also offers possibilities for the design and engineering of complex phosphor layers on glass substrates. Phosphor screen-printing technology allows the realization of high stability and thermal conductivity for the phosphor layer. This phosphor glass method provides many possibilities for LED packing, including thin-film flip chip and remote phosphor technology. PMID:23811889

  10. A First Application of Enzyme-Linked Immunosorbent Assay for Screening Cyclodiene Insecticides in Ground Water

    Science.gov (United States)

    Dombrowski, T.R.; Thurman, E.M.; Mohrman, G.B.

    1996-01-01

    A commercially available enzyme-linked immunosorbent assay (ELISA) plate kit for screening of cyclodiene insecticides (aldrin, chlordane, dieldrin, endosulfan, endrin, and heptachlor) was evaluated for sensitivity, cross reactivity, and overall performance using groundwater samples from a contaminated site. Ground-water contaminants included several pesticide compounds and their manufacturing byproducts, as well as many other organic and inorganic compounds. Cross-reactivity studies were carried out for the cyclodiene compounds, and results were compared to those listed by the manufacturer. Data obtained were used to evaluate the sensitivity of the ELISA kit to the cyclodiene compounds in ground water samples with a contaminated matrix. The method quantitation limit for the ELISA kit was 15 ??g/L (as chlordane). Of the 56 ground-water samples analyzed using the ELISA plate kits, more than 85% showed cyclodiene insecticide contamination. The ELISA kit showed excellent potential as a screening tool for sites with suspected groundwater contamination by insecticides.

  11. Possible application of RIA-TEST-T4 (URVJT-Kosice) in congenital hypothyroidism screening

    International Nuclear Information System (INIS)

    Using a kit for serum thyroxine level estimation (RIA-TEST-T4) commercially made by the Kosice Institute of Radioecology and Applied Nuclear Techniques, the authors modified a version for thyroxine level determination in dry blood drops. Within the 30 to 60 ng.ml-1 range, i.e.; well within the region necessary for congenital hypothyroidism screening, sensitivity proved to be 36 imp.s-1.ng-1.ml. Accuracy at 20 ng.ml-1 was 13%, at 50 ng.ml-1 - 8%, and at 70 ng.ml-1 - 7.6%. Compared with imported kits the cost of examination of one neonate was relatively low. The method lends itself well to mechanization, and screening evaluation time can be reduced to a few minutes. (author)

  12. Application of ATP-bioluminescence assay for screening chemotherapeutic agents of ovarian cancer chemotherapy

    International Nuclear Information System (INIS)

    To evaluate the feasibility of using ATP-bioluminescence assay for tumor chemosensitivity testing in vitro, authors selected the A2780 cell line as a model and established the suitable assay condition. Screening chemotherapeutic agents of ovarian cancer in vitro were preliminarily researched. Using this assay, dose-response curve was detected in cell line treated with these agents. The result showed that the coefficients of variation for assay ranged from 0.2% to 8.2%, which means high reproducibility. It can measured ATP content of as few as forty cells. The thermal stability of the luciferin-luciferase system was high enough used in industry. The predictable accuracy rate is about 90.6%. This study demonstrated ATP-bioluminescence assay is a reliable, reproducible and sensitive method. It can provide a technical base for screening sensitive chemotherapeutic agents in clinic

  13. Risk factors for breast cancer with applications to selection for the prevalence screen.

    OpenAIRE

    Alexander, F. E.; Roberts, M. M.; Huggins, A

    1987-01-01

    There have been many studies of individual risk factors for breast cancer; most of the factors concerned may be broadly grouped into demographic and dietary, reproductive history, endocrine related, family history of breast cancer, and previous history of breast disease. Some of these studies have examined the combined effect of these factors. The present case-control study does this in the context of a randomised controlled trial of breast cancer screening. The relative risks that we have ob...

  14. Screening for ligninolytic enzymes from autochthonous fungi and applications for decolorization of Remazole Marine Blue

    OpenAIRE

    Erden, Emre; Ucar, M. Cigdem; Gezer, Tekin; Pazarlioglu, Nurdan Kasikara

    2009-01-01

    This study presents new and alternative fungal strains for the production of ligninolytic enzymes which have great potential to use in industrial and biotechnological processes. Thirty autochthonous fungal strains were harvested from Bornova-Izmir in Turkiye. In the fresh fruitbody extracts laccase, manganese peroxidase and lignin peroxidase activities, which are the principal enzymes responsible for ligninocellulose degradation by Basidiomycetes, were screened. Spores of some of the basidiom...

  15. Microengineering Methods for Cell Based Microarrays and High-Throughput Drug Screening Applications

    OpenAIRE

    Xu, Feng; Wu, Jinhui; Wang, Shuqi; Durmus, Naside Gozde; Gurkan, Umut Atakan; Demirci, Utkan

    2011-01-01

    Screening for effective therapeutic agents from millions of drug candidates is costly, time-consuming and often face ethical concerns due to extensive use of animals. To improve cost-effectiveness, and to minimize animal testing in pharmaceutical research, in vitro monolayer cell microarrays with multiwell plate assays have been developed. Integration of cell microarrays with microfluidic systems have facilitated automated and controlled component loading, significantly reducing the consumpti...

  16. Application of stress susceptibility index for drought tolerance screening of tomato populations

    Directory of Open Access Journals (Sweden)

    Zdravković Jasmina

    2013-01-01

    Full Text Available Investigation comprised 41 tomato genotypes originating from the population of domestic and domesticated genotypes collected in Serbia and belonging to the tomato collection of the Institute of Vegetable Crop Science, Smederevska Palanka. The aim of collection screening was to choose the genotypes tolerant to drought during plant intensive growth stage, whereby the process of selection would set out to obtain the recombinant genotypes for this abiotic factor. The screening criteria were established for genotype divergence in plant height and shoot-root ratio under conditions of optimal irrigation regime and drought. Divergence was estimated using cluster analysis with Euclidean distance as a measure of distance, with a complete gene attachment to grouping. Drought tolerance is expressed by the stress susceptibility index (SSI. Various results were obtained based on the screening of genotypes grown under optimal and dry conditions. As a measure of stress susceptibility, based on SSI, genotypes having different drought tolerance level were determined. On the grounds of the analyses carried out, 10 genotypes were segregated (G102, G104, G107, G109, G110, G119, G125, G126, G128 and G141 to represent a basis to obtain the recombinant genotypes and to initiate the selection for drought resistance. [Projekat Ministarstva nauke Republike Srbije, br. TR 31005 i br. TR 31059

  17. A Quick-responsive DNA Nanotechnology Device for Bio-molecular Homeostasis Regulation

    Science.gov (United States)

    Wu, Songlin; Wang, Pei; Xiao, Chen; Li, Zheng; Yang, Bing; Fu, Jieyang; Chen, Jing; Wan, Neng; Ma, Cong; Li, Maoteng; Yang, Xiangliang; Zhan, Yi

    2016-01-01

    Physiological processes such as metabolism, cell apoptosis and immune responses, must be strictly regulated to maintain their homeostasis and achieve their normal physiological functions. The speed with which bio-molecular homeostatic regulation occurs directly determines the ability of an organism to adapt to conditional changes. To produce a quick-responsive regulatory system that can be easily utilized for various types of homeostasis, a device called nano-fingers that facilitates the regulation of physiological processes was constructed using DNA origami nanotechnology. This nano-fingers device functioned in linked open and closed phases using two types of DNA tweezers, which were covalently coupled with aptamers that captured specific molecules when the tweezer arms were sufficiently close. Via this specific interaction mechanism, certain physiological processes could be simultaneously regulated from two directions by capturing one biofactor and releasing the other to enhance the regulatory capacity of the device. To validate the universal application of this device, regulation of the homeostasis of the blood coagulant thrombin was attempted using the nano-fingers device. It was successfully demonstrated that this nano-fingers device achieved coagulation buffering upon the input of fuel DNA. This nano-device could also be utilized to regulate the homeostasis of other types of bio-molecules. PMID:27506964

  18. Nanoscale Biomolecular Detection Limit for Gold Nanoparticles Based on Near-Infrared Response

    Directory of Open Access Journals (Sweden)

    Mario D’Acunto

    2012-01-01

    Full Text Available Gold nanoparticles have been widely used during the past few years in various technical and biomedical applications. In particular, the resonance optical properties of nanometer-sized particles have been employed to design biochips and biosensors used as analytical tools. The optical properties of nonfunctionalized gold nanoparticles and core-gold nanoshells play a crucial role for the design of biosensors where gold surface is used as a sensing component. Gold nanoparticles exhibit excellent optical tunability at visible and near-infrared frequencies leading to sharp peaks in their spectral extinction. In this paper, we study how the optical properties of gold nanoparticles and core-gold nanoshells are changed as a function of different sizes, shapes, composition, and biomolecular coating with characteristic shifts towards the near-infrared region. We show that the optical tenability can be carefully tailored for particle sizes falling in the range 100–150 nm. The results should improve the design of sensors working at the detection limit.

  19. Solving the 0/1 Knapsack Problem by a Biomolecular DNA Computer

    Directory of Open Access Journals (Sweden)

    Hassan Taghipour

    2013-01-01

    Full Text Available Solving some mathematical problems such as NP-complete problems by conventional silicon-based computers is problematic and takes so long time. DNA computing is an alternative method of computing which uses DNA molecules for computing purposes. DNA computers have massive degrees of parallel processing capability. The massive parallel processing characteristic of DNA computers is of particular interest in solving NP-complete and hard combinatorial problems. NP-complete problems such as knapsack problem and other hard combinatorial problems can be easily solved by DNA computers in a very short period of time comparing to conventional silicon-based computers. Sticker-based DNA computing is one of the methods of DNA computing. In this paper, the sticker based DNA computing was used for solving the 0/1 knapsack problem. At first, a biomolecular solution space was constructed by using appropriate DNA memory complexes. Then, by the application of a sticker-based parallel algorithm using biological operations, knapsack problem was resolved in polynomial time.

  20. Potential-of-mean-force description of ionic interactions and structural hydration in biomolecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Hummer, G.; Garcia, A.E. [Los Alamos National Lab., NM (United States). Theoretical Biology and Biophysics Group; Soumpasis, D.M. [Max-Planck-Inst for Biophysical Chemistry, Goettingen (Germany). Biocomputation Group

    1994-10-01

    To understand the functioning of living organisms on a molecular level, it is crucial to dissect the intricate interplay of the immense number of biological molecules. Most of the biochemical processes in cells occur in a liquid environment formed mainly by water and ions. This solvent environment plays an important role in biological systems. The potential-of-mean-force (PMF) formalism attempts to describe quantitatively the interactions of the solvent with biological macromolecules on the basis of an approximate statistical-mechanical representation. At its current status of development, it deals with ionic effects on the biomolecular structure and with the structural hydration of biomolecules. The underlying idea of the PMF formalism is to identify the dominant sources of interactions and incorporate these interactions into the theoretical formalism using PMF`s (or particle correlation functions) extracted from bulk-liquid systems. In the following, the authors shall briefly outline the statistical-mechanical foundation of the PMF formalism and introduce the PMF expansion formalism, which is intimately linked to superposition approximations for higher-order particle correlation functions. The authors shall then sketch applications, which describe the effects of the ionic environment on nucleic-acid structure. Finally, the authors shall present the more recent extension of the PMF idea to describe quantitatively the structural hydration of biomolecules. Results for the interface of ice and water and for the hydration of deoxyribonucleic acid (DNA) will be discussed.

  1. Computational Recipe for Efficient Description of Large-Scale Conformational Changes in Biomolecular Systems.

    Science.gov (United States)

    Moradi, Mahmoud; Tajkhorshid, Emad

    2014-07-01

    Characterizing large-scale structural transitions in biomolecular systems poses major technical challenges to both experimental and computational approaches. On the computational side, efficient sampling of the configuration space along the transition pathway remains the most daunting challenge. Recognizing this issue, we introduce a knowledge-based computational approach toward describing large-scale conformational transitions using (i) nonequilibrium, driven simulations combined with work measurements and (ii) free energy calculations using empirically optimized biasing protocols. The first part is based on designing mechanistically relevant, system-specific reaction coordinates whose usefulness and applicability in inducing the transition of interest are examined using knowledge-based, qualitative assessments along with nonequilirbrium work measurements which provide an empirical framework for optimizing the biasing protocol. The second part employs the optimized biasing protocol resulting from the first part to initiate free energy calculations and characterize the transition quantitatively. Using a biasing protocol fine-tuned to a particular transition not only improves the accuracy of the resulting free energies but also speeds up the convergence. The efficiency of the sampling will be assessed by employing dimensionality reduction techniques to help detect possible flaws and provide potential improvements in the design of the biasing protocol. Structural transition of a membrane transporter will be used as an example to illustrate the workings of the proposed approach.

  2. FINDSITE(X): a structure-based, small molecule virtual screening approach with application to all identified human GPCRs.

    Science.gov (United States)

    Zhou, Hongyi; Skolnick, Jeffrey

    2012-06-01

    We have developed FINDSITE(X), an extension of FINDSITE, a protein threading based algorithm for the inference of protein binding sites, biochemical function and virtual ligand screening, that removes the limitation that holo protein structures (those containing bound ligands) of a sufficiently large set of distant evolutionarily related proteins to the target be solved; rather, predicted protein structures and experimental ligand binding information are employed. To provide the predicted protein structures, a fast and accurate version of our recently developed TASSER(VMT), TASSER(VMT)-lite, for template-based protein structural modeling applicable up to 1000 residues is developed and tested, with comparable performance to the top CASP9 servers. Then, a hybrid approach that combines structure alignments with an evolutionary similarity score for identifying functional relationships between target and proteins with binding data has been developed. By way of illustration, FINDSITE(X) is applied to 998 identified human G-protein coupled receptors (GPCRs). First, TASSER(VMT)-lite provides updates of all human GPCR structures previously modeled in our lab. We then use these structures and the new function similarity detection algorithm to screen all human GPCRs against the ZINC8 nonredundant (TC identity > 30% to the target from the binding data library) on a 168 human GPCR set with known binding data, the average enrichment factor in the top 1% of the compound library (EF(0.01)) is 22.7, whereas EF(0.01) by FINDSITE is 7.1. For virtual screening when just the target and its native ligands are excluded, the average EF(0.01) reaches 41.4. We also analyze off-target interactions for the 168 protein test set. All predicted structures, virtual screening data and off-target interactions for the 998 human GPCRs are available at http://cssb.biology.gatech.edu/skolnick/webservice/gpcr/index.html .

  3. Improvement of Virtual Screening Predictions using Computational Intelligence Methods

    OpenAIRE

    Cano, Gaspar; García Rodríguez, José; Pérez Sánchez, Horacio

    2014-01-01

    Virtual Screening (VS) methods can considerably aid clinical research, predicting how ligands interact with drug targets. However, the accuracy of most VS methods is constrained by limitations in the scoring function that describes biomolecular interactions, and even nowadays these uncertainties are not completely understood. In order to improve accuracy of scoring functions used in most VS methods we propose a hybrid novel approach where neural networks (NNET) and support vector machines (SV...

  4. Network target for screening synergistic drug combinations with application to traditional Chinese medicine

    Directory of Open Access Journals (Sweden)

    Zhang Ningbo

    2011-06-01

    Full Text Available Abstract Background Multicomponent therapeutics offer bright prospects for the control of complex diseases in a synergistic manner. However, finding ways to screen the synergistic combinations from numerous pharmacological agents is still an ongoing challenge. Results In this work, we proposed for the first time a “network target”-based paradigm instead of the traditional "single target"-based paradigm for virtual screening and established an algorithm termed NIMS (Network target-based Identification of Multicomponent Synergy to prioritize synergistic agent combinations in a high throughput way. NIMS treats a disease-specific biological network as a therapeutic target and assumes that the relationship among agents can be transferred to network interactions among the molecular level entities (targets or responsive gene products of agents. Then, two parameters in NIMS, Topology Score and Agent Score, are created to evaluate the synergistic relationship between each given agent combinations. Taking the empirical multicomponent system traditional Chinese medicine (TCM as an illustrative case, we applied NIMS to prioritize synergistic agent pairs from 63 agents on a pathological process instanced by angiogenesis. The NIMS outputs can not only recover five known synergistic agent pairs, but also obtain experimental verification for synergistic candidates combined with, for example, a herbal ingredient Sinomenine, which outperforms the meet/min method. The robustness of NIMS was also showed regarding the background networks, agent genes and topological parameters, respectively. Finally, we characterized the potential mechanisms of multicomponent synergy from a network target perspective. Conclusions NIMS is a first-step computational approach towards identification of synergistic drug combinations at the molecular level. The network target-based approaches may adjust current virtual screen mode and provide a systematic paradigm for facilitating the

  5. Screening Protocol for Iodine-Specific Getters in YMP-Related Invert Applications

    International Nuclear Information System (INIS)

    This document defines a standardized screening protocol for use in developing iodine ''getters'' for placement in the proposed YMP-repository invert. The work was funded by the US Department of Energy (DOE), Office of Civilian Radioactive Waste Management (OCRWM), Office of Science and Technology International (S and T) during 2004-2005. First, the likely environmental conditions in the invert are reviewed as a basis for defining the thermal and geochemical regimes in which a getter must function. These considerations, then, served as the basis for laying out a hierarchy of materials screening tests (Table 1). An experimental design for carrying out these screening tests follows next. Finally, the latter half of the document develops methods for preparing test solutions with chemistries that relate to various aspects of the YMP-repository environment (or, at least to such representations as were available from program documents late in 2004). Throughout the document priority was given to defining procedures that would quickly screen out unpromising candidate materials with a minimum amount of labor. Hence, the proposed protocol relies on batch tests over relatively short times, and on a hierarchy of short pre-test conditioning steps. So as not to repeat the mistakes (and frustrations) encountered in the past (notably in preparing WIPP test brines) particular care was also given to developing standardized test solution recipes that could be prepared easily and reproducibly. This document is principally intended for use as a decision-making tool in evaluating and planning research activities. It is explicitly NOT a roadmap for qualifying getters for actual placement in the repository. That would require a comprehensive test plan and a substantial consensus building effort. This document is also not intended to provide a complete list of all the tests that individuals may wish to carry out. Various materials will have their own peculiar concerns that will call for

  6. High voltage series resonant inverter ion engine screen supply. [SCR series resonant inverter for space applications

    Science.gov (United States)

    Biess, J. J.; Inouye, L. Y.; Shank, J. H.

    1974-01-01

    A high-voltage, high-power LC series resonant inverter using SCRs has been developed for an Ion Engine Power Processor. The inverter operates within 200-400Vdc with a maximum output power of 2.5kW. The inverter control logic, the screen supply electrical and mechanical characteristics, the efficiency and losses in power components, regulation on the dual feedback principle, the SCR waveforms and the component weight are analyzed. Efficiency of 90.5% and weight density of 4.1kg/kW are obtained.

  7. Compression force behaviours: An exploration of the beliefs and values influencing the application of breast compression during screening mammography

    International Nuclear Information System (INIS)

    This research project investigated the compression behaviours of practitioners during screening mammography. The study sought to provide a qualitative understanding of ‘how’ and ‘why’ practitioners apply compression force. With a clear conflict in the existing literature and little scientific evidence base to support the reasoning behind the application of compression force, this research project investigated the application of compression using a phenomenological approach. Following ethical approval, six focus group interviews were conducted at six different breast screening centres in England. A sample of 41 practitioners were interviewed within the focus groups together with six one-to-one interviews of mammography educators or clinical placement co-ordinators. The findings revealed two broad humanistic and technological categories consisting of 10 themes. The themes included client empowerment, white-lies, time for interactions, uncertainty of own practice, culture, power, compression controls, digital technology, dose audit-safety nets, numerical scales. All of these themes were derived from 28 units of significant meaning (USM). The results demonstrate a wide variation in the application of compression force, thus offering a possible explanation for the difference between practitioner compression forces found in quantitative studies. Compression force was applied in many different ways due to individual practitioner experiences and behaviour. Furthermore, the culture and the practice of the units themselves influenced beliefs and attitudes of practitioners in compression force application. The strongest recommendation to emerge from this study was the need for peer observation to enable practitioners to observe and compare their own compression force practice to that of their colleagues. The findings are significant for clinical practice in order to understand how and why compression force is applied

  8. Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models and ontology.

    Science.gov (United States)

    Thibault, J C; Roe, D R; Eilbeck, K; Cheatham Iii, T E; Facelli, J C

    2015-01-01

    Biomolecular simulations aim to simulate structure, dynamics, interactions, and energetics of complex biomolecular systems. With the recent advances in hardware, it is now possible to use more complex and accurate models, but also reach time scales that are biologically significant. Molecular simulations have become a standard tool for toxicology and pharmacology research, but organizing and sharing data - both within the same organization and among different ones - remains a substantial challenge. In this paper we review our recent work leading to the development of a comprehensive informatics infrastructure to facilitate the organization and exchange of biomolecular simulations data. Our efforts include the design of data models and dictionary tools that allow the standardization of the metadata used to describe the biomedical simulations, the development of a thesaurus and ontology for computational reasoning when searching for biomolecular simulations in distributed environments, and the development of systems based on these models to manage and share the data at a large scale (iBIOMES), and within smaller groups of researchers at laboratory scale (iBIOMES Lite), that take advantage of the standardization of the meta data used to describe biomolecular simulations. PMID:26387907

  9. Content adaptive screen image scaling

    OpenAIRE

    Zhai, Yao; Wang, Qifei; Lu, Yan; Li, Shipeng

    2015-01-01

    This paper proposes an efficient content adaptive screen image scaling scheme for the real-time screen applications like remote desktop and screen sharing. In the proposed screen scaling scheme, a screen content classification step is first introduced to classify the screen image into text and pictorial regions. Afterward, we propose an adaptive shift linear interpolation algorithm to predict the new pixel values with the shift offset adapted to the content type of each pixel. The shift offse...

  10. Assessment of the potential for refinery applications of inorganic membrane technology: An identification and screening analysis. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, H.E.; Schulman, B.L.

    1993-05-01

    Commercial application of membrane technology in the separation of gas, liquid, and solid streams has grown to a business with worldwide revenues exceeding $1 billion annually. Use of organic membranes for industrial gas separation, particularly in the refining industry, is one of the major growth areas. However, organic membranes based on polymeric separation barriers, are susceptible to damage by liquids, and careful precautions must be taken to retain the system integrity. Researchers are currently developing small pore sized inorganic membranes which may substantially increase the efficiency and economics in selected refinery separation applications. Expected advantages of these advanced inorganic membranes include high permeability, high selectivity, and low manufacturing cost. SFA Pacific conducted a screening analysis to identify applications for inorganic membrane technology in the petroleum refining industry and their potential cost advantages over competing separation systems. Two meetings were held in connection with this project. Copies of Viewgraphs presented by SFA Pacific at these meetings are attached in Appendices A and C. Potential high priority applications and market impacts of advanced inorganic membrane technology in the refining industry are addressed in this report, and include the following areas: Competitive separation technologies; application of those technologies; incentives for inorganic membranes; market benefits and impacts of inorganic membranes.

  11. Bridging Nano- and Microtribology in Mechanical and Biomolecular Layers

    Science.gov (United States)

    Tomala, Agnieszka; Göçerler, Hakan; Gebeshuber, Ille C.

    The physical and chemical composition of surfaces determine various important properties of solids such as corrosion rates, adhesive properties, frictional properties, catalytic activity, wettability, contact potential and - finally and most importantly - failure mechanisms. Very thin, weak layers (of man-made and biological origin) on much harder substrates that reduce friction are the focus of the micro- and nanotribological investigations presented in this chapter.Biomolecular layers fulfil various functions in organs of the human body. Examples comprise the skin that provides a protective physical barrier between the body and the environment, preventing unwanted inward and outward passage of water and electrolytes, reducing penetration by destructive chemicals, arresting the penetration of microorganisms and external antigens and absorbing radiation from the sun, or the epithelium of the cornea that blocks the passage of foreign material, such as dust, water and bacteria, into the eye and that contributes to the lubrication layer that ensures smooth movement of the eyelids over the eyeballs.Monomolecular thin films, additive-derived reaction layers and hard coatings are widely used to tailor tribological properties of surfaces. Nanotribological investigations on these substrates can reveal novel properties regarding the orientation of chemisorbed additive layers, development of rubbing films with time and the relation of frictional properties to surface characteristics in diamond coatings.Depending on the questions to be answered with the tribological research, various micro- and nanotribological measurement methods are applied, including scanning probe microscopy (AFM, FFM), scanning electron microscopy, microtribometer investigations, angle-resolved photoelectron spectroscopy and optical microscopy. Thoughts on the feasibility of a unified approach to energy-dissipating systems and how it might be reached (touching upon new ways of scientific publishing

  12. Vision Screening

    Science.gov (United States)

    ... offer vision screening programs for children. At what age should a child have his or her vision screened? Vision screening ... a child fails a vision screening at any age, the child should be referred for a comprehensive eye examination. ...

  13. Computational methods to study the structure and dynamics of biomolecules and biomolecular processes from bioinformatics to molecular quantum mechanics

    CERN Document Server

    2014-01-01

    Since the second half of the 20th century machine computations have played a critical role in science and engineering. Computer-based techniques have become especially important in molecular biology, since they often represent the only viable way to gain insights into the behavior of a biological system as a whole. The complexity of biological systems, which usually needs to be analyzed on different time- and size-scales and with different levels of accuracy, requires the application of different approaches, ranging from comparative analysis of sequences and structural databases, to the analysis of networks of interdependence between cell components and processes, through coarse-grained modeling to atomically detailed simulations, and finally to molecular quantum mechanics. This book provides a comprehensive overview of modern computer-based techniques for computing the structure, properties and dynamics of biomolecules and biomolecular processes. The twenty-two chapters, written by scientists from all over t...

  14. Effects of "Like Type" Sex Pairings between Applicants-Principals and Type of Focal Position Considered at the Screening Stage of the Selection Process

    Science.gov (United States)

    Young, I. Phillip

    2005-01-01

    This study addresses the screening decisions for a national random sample of high school principals as viewed from the attraction-similarity theory of interpersonal perceptions. Independent variables are the sex of principals, sex of applicants, and the type of focal positions sought by hypothetical job applicants (teacher or counselor). Dependent…

  15. Toward the discovery of functional transthyretin amyloid inhibitors: application of virtual screening methods.

    Science.gov (United States)

    Simões, Carlos J V; Mukherjee, Trishna; Brito, Rui M M; Jackson, Richard M

    2010-10-25

    Inhibition of amyloid fibril formation by stabilization of the native form of the protein transthyretin (TTR) is a viable approach for the treatment of familial amyloid polyneuropathy that has been gaining momentum in the field of amyloid research. The TTR stabilizer molecules discovered to date have shown efficacy at inhibiting fibrilization in vitro but display impairing issues of solubility, affinity for TTR in the blood plasma and/or adverse effects. In this study we present a benchmark of four protein- and ligand-based virtual screening (VS) methods for identifying novel TTR stabilizers: (i) two-dimensional (2D) similarity searches with chemical hashed, pharmacophore, and UNITY fingerprints, (ii) 3D searches based on shape, chemical, and electrostatic similarity, (iii) LigMatch, a new ligand-based method which uses multiple templates and combines 3D geometric hashing with a 2D preselection process, and (iv) molecular docking to consensus X-ray crystal structures of TTR. We illustrate the potential of the best-performing VS protocols to retrieve promising new leads by ranking a tailored library of 2.3 million commercially available compounds. Our predictions show that the top-scoring molecules possess distinctive features from the known TTR binders, holding better solubility, fraction of halogen atoms, and binding affinity profiles. To the best of our knowledge, this is the first attempt to rationalize the utilization of a large battery of in silico screening techniques toward the identification of a new generation of TTR amyloid inhibitors.

  16. Application of epidemiologic studies of radiation-induced breast cancer to mammographic screening guidelines

    International Nuclear Information System (INIS)

    The question of benefit/risk ratio for the mammographic screening of asymptomatic women has been under intense scrutiny for several years. The studies of radiogenic breast cancer show good agreement in the quantitative estimation of the magnitude of radiation risks, in spite of the variations among the several studies in radiation quality factors, exposure fractionation, and the background population rate of breast cancer. There is a report indicating no evidence for the synergism between radiation and benign breast disease, late menopause, or the family history of breast cancer. According to the report, the radiogenic breast cancer risk is 3-fold higher in nulliparous women as compared with parous women. The analyses of lifetime risks and benefits suggest that the choice of an additive vs. multiplicative risk model is not crucial. The benefit/risk ratio shows strong age dependence which agrees well with the current U.S. guidelines, namely that the routine mammographic screening of the general population of asymptomatic women is recommended only after age of 50. (Yamashita, S.)

  17. Investigation of physical properties of screen printed nanosized ZnO films for optoelectronic applications

    Science.gov (United States)

    Zargar, Rayees Ahmad; Arora, Manju; Khurram Hafiz, Aurangzeb

    2015-04-01

    Nanosized ZnO particles derived from chemical co-precipitation route were used for casting ZnO films by screen printing method followed by sintering at two different temperatures. The variation in structural, optical and electrical properties of these films with temperature have been investigated by XRD, SEM, FTIR, Raman, UV-VIS, EPR and four probe analytical techniques. XRD patterns of these films exhibit polycrystalline nature with hexagonal wurtzite structure and SEM images reveal the smooth, dense and without any cracks/damage porous surface morphology. Infrared transmission spectra shows peaks pertaining to Zn-O stretching modes and their multiphonon modes. While Raman spectra exhibited strong peaks of E2 (high) phonon and overtone of surface phonon mode at 429 cm-1 and 1144 cm-1 respectively with weak components of LO and TO branches. The direct band gap energy of these films showed narrowing of band gap from 3.21 eV to 3.12 eV on increasing sintering temperature from 500 °C to 600 °C. DC conductivity measurements confirmed semiconducting behaviour and showed lowering of activation energy. EPR spectra showed single narrow line resonance signal of g-value ~ 1.9469 due to oxygen vacancies which are produced during synthesis of ZnO nanoparticles by sol-gel process. These studies revealed that on increasing sintering temperature the crystallinity of the film improves with reduction in lattice deformations in these screen printed ZnO films.

  18. A novel screening system based on VanX-mediated autolysis-Application to Gaussia luciferase.

    Science.gov (United States)

    Wu, Nan; Kamioka, Tetsuya; Kuroda, Yutaka

    2016-07-01

    We report a novel bacterial screening protocol based on co-expressing the target protein with VanX, an enzyme which mediates Escherichia coli's autolysis and the release of the target protein into the culture medium, thereby facilitating activity measurement and screening from crude medium. This protocol as assessed with 19 Gaussia luciferase (GLuc) expressing colonies, was able to detect bioluminescence wavelength shift as small as 1.5 nm. We demonstrate the performance and versatility of this protocol by applying it to a semi-rational search for GLuc variants with red-shifted bioluminescence. Six GLuc's sites, F113, I114, W143, L144, A149, and F151, were randomly mutated, and for each site, 50 colonies were cultivated in 3 mL samples, from which bioluminescence was measured without purification. We identified two GLuc single mutation red-shifted variants: W143V and L144A. Their red shifted bioluminescence and biophysical/biochemical properties were confirmed using HPLC purified variants. Biotechnol. Bioeng. 2016;113: 1413-1420. © 2015 Wiley Periodicals, Inc. PMID:26694096

  19. Multiple Features Based Approach to Extract Bio-molecular Event Triggers Using Conditional Random Field

    Directory of Open Access Journals (Sweden)

    Amit Majumder

    2012-11-01

    Full Text Available The purpose of Biomedical Natural Language Processing (BioNLP is to capture biomedical phenomena from textual data by extracting relevant entities, information and relations between biomedical entities (i.e. proteins and genes. In general, in most of the published papers, only binary relations were extracted. In a recent past, the focus is shifted towards extracting more complex relations in the form of bio-molecular events that may include several entities or other relations. In this paper we propose an approach that enables event trigger extraction of relatively complex bio-molecular events. We approach this problem as a detection of bio-molecular event trigger using the well-known algorithm, namely Conditional Random Field (CRF. We apply our experiments on development set. It shows the overall average recall, precision and F-measure values of 64.27504%, 69.97559% and 67.00429%, respectively for the event detection.

  20. Robust ridge regression estimators for nonlinear models with applications to high throughput screening assay data.

    Science.gov (United States)

    Lim, Changwon

    2015-03-30

    Nonlinear regression is often used to evaluate the toxicity of a chemical or a drug by fitting data from a dose-response study. Toxicologists and pharmacologists may draw a conclusion about whether a chemical is toxic by testing the significance of the estimated parameters. However, sometimes the null hypothesis cannot be rejected even though the fit is quite good. One possible reason for such cases is that the estimated standard errors of the parameter estimates are extremely large. In this paper, we propose robust ridge regression estimation procedures for nonlinear models to solve this problem. The asymptotic properties of the proposed estimators are investigated; in particular, their mean squared errors are derived. The performances of the proposed estimators are compared with several standard estimators using simulation studies. The proposed methodology is also illustrated using high throughput screening assay data obtained from the National Toxicology Program. PMID:25490981

  1. Applicability of the ParaDNA(®) Screening System to Seminal Samples.

    Science.gov (United States)

    Tribble, Nicholas D; Miller, Jamie A D; Dawnay, Nick; Duxbury, Nicola J

    2015-05-01

    Seminal fluid represents a common biological material recovered from sexual assault crime scenes. Such samples can be prescreened using different techniques to determine cell type and relative amount before submitting for full STR profiling. The ParaDNA(®) Screening System is a novel forensic test which identifies the presence of DNA through amplification and detection of two common STR loci (D16S539 and TH01) and the Amelogenin marker. The detection of the Y allele in samples could provide a useful tool in the triage and submission of sexual assault samples by enforcement authorities. Male template material was detected on a range of common sexual assault evidence items including cotton pillow cases, condoms, swab heads and glass surfaces and shows a detection limit of 1 in 1000 dilution of neat semen. These data indicate this technology has the potential to be a useful tool for the detection of male donor DNA in sexual assault casework. PMID:25739746

  2. Immobilization of Acetylcholinesterase on Screen-Printed Electrodes. Application to the Determination of Arsenic(III

    Directory of Open Access Journals (Sweden)

    M. Julia Arcos-Martínez

    2010-03-01

    Full Text Available Enzymatic amperometric procedures for measuring arsenic, based on the inhibitive action of this metal on acetylcholinesterase enzyme activity, have been developed. Screen-printed carbon electrodes (SPCEs were used with acetylcholinesterase covalently bonded directly to its surface. The amperometric response of acetylcholinesterase was affected by the presence of arsenic ions, which caused a decrease in the current intensity. The experimental optimum working conditions of pH, substrate concentration and potential applied, were established. Under these conditions, repeatability and reproducibility of biosensors were determined, reaching values below 4% in terms of relative standard deviation. The detection limit obtained for arsenic was 1.1 × 10−8 M for Ach/SPCE biosensor. Analysis of the possible effect of the presence of foreign ions in the solution was performed. The method was applied to determine levels of arsenic in spiked tap water samples.

  3. Application of handheld and portable spectrometers for screening acrylamide content in commercial potato chips.

    Science.gov (United States)

    Ayvaz, Huseyin; Rodriguez-Saona, Luis E

    2015-05-01

    The most common methods for acrylamide analysis in foods require the use of LC-MS/MS and GC-MS. Although these methods have great analytical performance, they need intensive sample preparation, highly specialised instrumentation, and are time consuming. In this study, portable and handheld infrared spectrometers were evaluated as rapid methods for screening acrylamide in potato chips and their performances were compared to those of benchtop infrared systems. The acrylamide content of 64 commercial potato chips (169-2453 μg/kg) was determined by LC-MS/MS. Spectral data were collected using mid-infrared (MIR) and near-infrared (NIR) spectrometers. Partial least squares regression (PLSR) calibration models were developed to predict acrylamide levels. Overall, good linear correlation was found between the predicted acrylamide levels and actual measured acrylamide concentrations by LC-MS/MS (rPred > 0.90 and SEP potato chips. PMID:25529665

  4. In vivo models of cardiac diseases: application to drug development and screening.

    Science.gov (United States)

    Rokutan, Hirofumi; Anker, Stefan D; Springer, Jochen

    2010-01-01

    Cardiac disease is the top cause of human mortality in the Western world. Current drug therapy for cardiac disease has been established via experimental studies using a variety of in vivo animal models. The purpose of this review is to discuss the features (advantages and limitations) of the mainly used in vivo models of cardiac disease and provide the reader with an overview of how they can be utilized in the development and screening of cardiac drugs. A search for articles focusing on and including in vivo models for the main areas of cardiac diseases was performed on PubMed. We also searched the reference lists of identified articles for further original articles. Large and small animal models including genetically modified ones have made accomplishments in the process of cardiac drug development with different clinical relevance. However, there is still a clear need for lessening the gap between human and experimental models by improving in vivo models.

  5. Application of Short Screening Tools for Post-Traumatic Stress Disorder in the Korean Elderly Population

    Science.gov (United States)

    Jang, Yu Jin; Chung, Hae Gyung; Choi, Jin Hee; Kim, Tae Yong; So, Hyung Seok

    2016-01-01

    Objective Post-traumatic stress disorder (PTSD) is often missed or incorrectly diagnosed in primary care settings. Although brief screening instruments may be useful in detecting PTSD, an adequate validation study has not been conducted with older adults. This study aimed to evaluate the reliability and validity of the Korean version of the primary care PTSD screen (PC-PTSD) and single-item PTSD screener (SIPS) in elderly veterans. Methods The PC-PTSD and SIPS assessments were translated into Korean, with a back-translation to the original language to verify accuracy. Vietnamese war veterans [separated into a PTSD group (n=41) and a non-PTSD group (n=99)] participated in several psychometric assessments, including the Korean versions of the PC-PTSD (PC-PTSD-K), SIPS (SIPS-K), a structured clinical interview from the Diagnostic and Statistical Manual of Mental Disorders-IV(SCID), and PTSD checklist(PCL). Results The PC-PTSD-K showed high internal consistency (Cronbach α=0.76), and the test-retest reliability of the PC-PTSD-K and SIPS-K were also high (r=0.97 and r=0.91, respectively). A total score of 3 from the PC-PTSD-K yielded the highest diagnostic efficiency, with sensitivity and specificity values of 0.90 and 0.86, respectively. The 'bothered a lot' response level from the SIPS-K showed the highest diagnostic efficiency, with sensitivity and specificity values of 0.85 and 0.89, respectively. Conclusion Our findings suggest that both PC-PTSD-K and SIPS-K have good psychometric properties with high validity and reliability for detecting PTSD symptoms in elderly Korean veterans. However, further research will be necessary to increase our understanding of PTSD characteristics in diverse groups with different types of trauma.

  6. Isolation of self Printing paste from Plant Seeds and Its Application in Simultaneous Burn-out and Screen Printing technique

    Directory of Open Access Journals (Sweden)

    J.I.Abd –El Thalouth

    2016-02-01

    Full Text Available Printing pastes containing eco-friendly galactomannan gum and safety natural dye were isolated simultaneously in one step process from tara plant seeds using sodium hydroxide solution. The effect of concentrations of sodium hydroxide on the rheological properties of the isolated printing pastes were thoroughly investigated. Technological evaluation of the obtained pastes to act as screen printing paste and burn-out style paste to be used in printing five different blends as well as pure wool was achieved. The results were evaluated via measuring the % loss in weight, K/S of the coloured area and tensile strength for the printed area. The results obtained reviles that all the isolated pastes are characterized by non-Newtonian pseudoplastic behaviour, and its apparent viscosity depends on the concentration of sodium hydroxide and also on the time of storing. The prepared pastes could be used successfully as a screen printing paste and burn-out paste simultaneously. The % loss in weight increases by increasing sodium hydroxide concentration and/or the portion of wool in the blend. The K/S of the printed area depends on the nature of the component of the blend and higher on protenic fabrics than that of cellulosic. Unique colour and attractive texture could be achieved using the current technique. It is also found that as the concentration of sodium hydroxide increases, the % loss in tensile strength increases specially for woolen blends, however the decreases is not high and satisfactory for industrial application.

  7. Synthesis of carbon nanotubes using screen-printing catalyst and its application for a field emission device

    Energy Technology Data Exchange (ETDEWEB)

    Chiang, Wang-Ta; Su, Shui-Hsiang; Wu, Cheng-Yu; Yokoyama, Meiso [Department of Electronic Engineering, I-Shou University, No. 1, Sec. 1, Syuecheng Rd., Dashu Township, Kaohsiung County 840 (China)

    2010-04-15

    Iron nitrate (Fe(NO{sub 3}){sub 3}.9H{sub 2}O) catalyst is screen-printed over silicon substrates and efficiently utilized to catalyze the synthesis of carbon nanotubes (CNTs) by thermal chemical vapor deposition (CVD). The concentration of iron nitrate influences the particle size distribution of the Fe catalyst, which determines the morphology of the obtained CNT arrays. H{sub 2} is introduced in varying concentrations in a CH{sub 4}/N{sub 2} mixed gas during the synthesis of the CNTs, from which CNTs with uniform diameter distribution are grown. A field emission device that employs CNTs as emitters exhibits a current density of 9 mA/cm{sup 2} at an electrical field of 1.2 V/{mu}m. This work demonstrates the potential to synthesize CNTs using a screen-printed catalyst, which is a requirement for field emitter application at a large size. (copyright 2010 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  8. Designing for Small Screens: Learning Objects for Educational Applications via Handheld Mobile Technologies

    OpenAIRE

    Churchill, D

    2006-01-01

    This presentation discusses an ongoing study into issues relevant to the design of learning objects for educational applications via PDA devices. The specific areas of inquiry in this study are: the kinds of learning objects that are effective for PDA delivery; contexts for their effective educational applications; and learning object designs that overcome the limitations of the small display area characteristic of this kind of technology. Data from the study suggests that a learning object e...

  9. iBIOMES: managing and sharing biomolecular simulation data in a distributed environment.

    Science.gov (United States)

    Thibault, Julien C; Facelli, Julio C; Cheatham, Thomas E

    2013-03-25

    Biomolecular simulations, which were once batch queue or compute limited, have now become data analysis and management limited. In this paper we introduce a new management system for large biomolecular simulation and computational chemistry data sets. The system can be easily deployed on distributed servers to create a mini-grid at the researcher's site. The system not only offers a simple data deposition mechanism but also a way to register data into the system without moving the data from their original location. Any registered data set can be searched and downloaded using a set of defined metadata for molecular dynamics and quantum mechanics and visualized through a dynamic Web interface.

  10. Output-input ratio in thermally fluctuating biomolecular machines.

    Science.gov (United States)

    Kurzynski, Michal; Torchala, Mieczyslaw; Chelminiak, Przemyslaw

    2014-01-01

    Biological molecular machines are proteins that operate under isothermal conditions and hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free energy-donating (input) reaction and the free energy-accepting (output) one. Most if not all biologically active proteins display a slow stochastic dynamics of transitions between a variety of conformational substates composing their native state. This makes the description of the enzymatic reaction kinetics in terms of conventional rate constants insufficient. In the steady state, upon taking advantage of the assumption that each reaction proceeds through a single pair (the gate) of transition conformational substates of the enzyme-substrates complex, the degree of coupling between the output and the input reaction fluxes has been expressed in terms of the mean first-passage times on a conformational transition network between the distinguished substates. The theory is confronted with the results of random-walk simulations on the five-dimensional hypercube. The formal proof is given that, for single input and output gates, the output-input degree of coupling cannot exceed unity. As some experiments suggest such exceeding, looking for the conditions for increasing the degree of coupling value over unity challenges the theory. Performed simulations of random walks on several model networks involving more extended gates indicate that the case of the degree of coupling value higher than 1 is realized in a natural way on critical branching trees extended by long-range shortcuts. Such networks are scale-free and display the property of the small world. For short-range shortcuts, the networks are scale-free and fractal, representing a reasonable model for biomolecular machines displaying tight coupling, i.e., the degree of coupling equal exactly to unity. A hypothesis is stated that the protein conformational transition networks, as

  11. E-recruitment and Applicant Tracking System : New age of technology based applicant screening. Threat or opportunity?

    OpenAIRE

    Gagua, Levan

    2015-01-01

    The purpose of this study was to provide reader with in-depth information of new technological instruments, which recruiters apply in order mitigate application data. This study examines how applicant tracking system has integrated in Finnish organizations´ human resource department and how it helps managing labour force. This case study was executed in nature of qualitative research, where subjected organizations were interviewed via telephone and e-mail conversations. Findings wer...

  12. Conceptual design of thermal energy storage systems for near term electric utility applications. Volume 1: Screening of concepts

    Science.gov (United States)

    Hausz, W.; Berkowitz, B. J.; Hare, R. C.

    1978-01-01

    Over forty thermal energy storage (TES) concepts gathered from the literature and personal contacts were studied for their suitability for the electric utility application of storing energy off-peak discharge during peak hours. Twelve selections were derived from the concepts for screening; they used as storage media high temperature water (HTW), hot oil, molten salts, and packed beds of solids such as rock. HTW required pressure containment by prestressed cast-iron or concrete vessels, or lined underground cavities. Both steam generation from storage and feedwater heating from storage were studied. Four choices were made for further study during the project. Economic comparison by electric utility standard cost practices, and near-term availability (low technical risk) were principal criteria but suitability for utility use, conservation potential, and environmental hazards were considered.

  13. Application of MoS2 modified screen-printed electrodes for highly sensitive detection of bovine serum albumin.

    Science.gov (United States)

    Kukkar, Manil; Sharma, Ashish; Kumar, Parveen; Kim, Ki-Hyun; Deep, Akash

    2016-10-01

    The present work reports the application of a new molybdenum disulphide (MoS2)-based electrochemical platform for highly sensitive quantitation of an iron-binding protein, bovine serum albumin (BSA). The gold screen-printed electrodes were modified with MoS2 nanoflakes, followed by bioconjugation with anti-BSA antibodies. Using the above bioelectrode, cyclic voltammetric analysis was carried out in the presence of a Fe(3+)/Fe(2+) redox probe which exhibited a linear response of peak current with varying concentrations of BSA up to 10 ng/mL (with a detection limit of 0.006 ng/mL). This study is novel in that it shows a considerable enhancement of signal during electrochemical sensing of a protein. PMID:27639148

  14. A commentary on iPS cells: potential applications in autologous transplantation, study of illnesses and drug screening.

    Science.gov (United States)

    Romano, Gaetano; Morales, Fátima; Marino, Ignazio R; Giordano, Antonio

    2014-02-01

    Undoubtedly, the focus of the field of stem cell research is predominantly aimed at the artificial reprogramming of human somatic cells for the production of induced pluripotent stem (iPS) cells. This relatively new technology may circumvent the ethical issues of using human embryonic stem (hES) cells for the potential applications in cell replacement therapy. Besides such ethical issues, iPS cell technology offers the advantage of obtaining patient-derived tissues and/or cells, which may be utilized for autologous transplantation and tissue regeneration, investigation of a variety of human illnesses and for the screening of new drugs. The field of stem cell research has placed a major emphasis in understanding the genetic and epigenetic codes for pluripotency, in order to control and optimize autologous transplantation techniques and avoid teratoma formation.

  15. EXPLORING THE IMPACT OF APPLICANTS’ GENDER AND RELIGION ON PRINCIPALS’ SCREENING DECISIONS FOR ASSISTANT PRINCIPAL APPLICANTS

    Directory of Open Access Journals (Sweden)

    SUSAN C. BON

    2009-02-01

    Full Text Available In this experimental study, a national random sample of high school principals (stratified by gender were asked to evaluate hypothetical applicants whose resumes varied by religion (Jewish, Catholic, nondenominational and gender (male, female for employment as assistant principals. Results reveal that male principals rate all applicants higher than female principals and that the gender and religion of applicants failed to negatively or positively affect principals’ evaluations. These results suggest that discrimination based on an applicant’s gender and religion failed to be manifested during the pre-interview stage of the selection process. The paper concludes with a theoretical discussion of the distinction between explicit and implicit prejudice, and encourages future researchers to investigate the potential impact of prejudice on employment selection decisions and to consider whether schools should promote diversity in leadership positions.

  16. Maryland Power Plant Siting Project: an application of the ORNL-Land Use Screening Procedure

    Energy Technology Data Exchange (ETDEWEB)

    Dobson, J.E.

    1975-01-01

    Since 1974 the Resource Analysis Group in the Regional and Urban Studies Section of the Oak Ridge National Laboratory (ORNL) has been engaged in developing a procedure for regional and local siting analysis known as the ORNL Land Use Screening Procedure (LUSP). This document is the final report of the Maryland Power Plant Siting Project (MPPSP) in which the ORNL LUSP was used to identify candidate areas for power plant sites in northern Maryland. Numerous candidate areas are identified on the basis of four different siting objectives: the minimization of adverse ecologic impact, the minimization of adverse socioeconomic impact, the minimization of construction and operating costs, and a composite of all siting objectives. Siting criteria have been defined for each of these objectives through group processing techniques administered to four different groups of siting specialists. The siting priorities and opinions of each group have been expressed quantitatively and applied to a geographic information system containing 52 variables for each 91.8-acre cell in the northern eight counties of Maryland.

  17. Synthesis and screening of N-acyl thiolated chitosans for antibacterial applications.

    Science.gov (United States)

    Croce, Matteo; Conti, Simona; Maake, Caroline; Patzke, Greta R

    2016-10-20

    Low-molecular weight chitosan-thioglycolic acid has shown significant antibacterial properties against different microorganisms. In order to explore the potential and structure-activity relationships of newly synthesized alkyl thiomers, chitosan has been functionalized with a series of thio-acids with increasing alkyl chain length. All thiomers were characterized with special emphasis on the determination of their degree of deacetylation and substitution, as well as on their molecular weight and amount of thiol groups. The pre-screened chitosan-thiomers were further investigated with plate counting on Pseudomonas aeruginosa, Streptococcus sobrinus and Streptococcus mutans. Furthermore, LIVE/DEAD assays supported the efficiency of chitosan-thiomers against the above microorganisms. All fully characterized chitosan-thiomers showed comparable or enhanced antimicrobial activity compared to pristine chitosan. Our comprehensive approach paves the way to detailed explorations of much sought-after structure activity relationships in the complex chitosan parameter room, starting from correlations between alkyl chain length and antimicrobial activity. PMID:27474669

  18. Magnetic induction imaging with optical atomic magnetometers: towards applications to screening and surveillance

    Science.gov (United States)

    Marmugi, Luca; Hussain, Sarah; Deans, Cameron; Renzoni, Ferruccio

    2015-10-01

    We propose a new approach, based on optical atomic magnetometers and magnetic induction tomography (MIT), for remote and non-invasive detection of conductive targets. Atomic magnetometers overcome the main limitations of conventional MIT instrumentation, in particular their poor low-frequency sensitivity, their large size and their limited scalability. Moreover, atomic magnetometers have been proven to reach extremely high sensitivities, with an improvement of up to 7 orders of magnitude in the 50 MHz to DC band, with respect to a standard pick-up coil of the same size. In the present scheme, an oscillating magnetic field induces eddy currents in a conductive target and laser-pumped atomic magnetometers, either stand-alone or in an array, detect the response of the objects. A phase-sensitive detection scheme rejects the background, allowing remote detection of the secondary field and, thus, mapping of objects, hidden in cargos, underwater or underground. The potential for extreme sensitivity, miniaturization, dynamic range and array operation paves the way to a new generation of non-invasive, active detectors for surveillance, as well as for real-time cargo screening.

  19. Screening efficiency and screen length of a linear vibrating screen using DEM 3D simulation

    Institute of Scientific and Technical Information of China (English)

    Wang Guifeng; Tong Xin

    2011-01-01

    The effect of screen length on the screening efficiency of particles is studied under various single parameter conditions including frequency,amplitude,vibration angle,and screen inclination.The Discrete Element Method (DEM) has been used to simulate the screening process.A functional relationship between screening efficiency and screen length is established.It is shown that screening efficiency and screen length have a complicated exponential relationship.Relationships between them are profoundly discussed and conclusions are easily drawn:low values of the parameters do not benefit screening; screening efficiency generally increases with screen length; screening efficiency reaches a plateau when these parameters are in range frequently encountered in practical applications.

  20. Screening instruments for monitoring market power in wholesale electricity markets: Lessons from applications in Germany

    OpenAIRE

    Bataille, Marc; Steinmetz, Alexander; Thorwarth, Susanne

    2014-01-01

    While liberalization in energy markets has been a widely successful process all over the world, incumbents often still hold a dominant position. Thus, electricity wholesale markets are subject to market surveillance. Nevertheless, consolidated findings on abusive practices of market power and their cause and effect in wholesale electricity markets are scarce and non-controversial market monitoring practices fail to exist. Our application of the established measure of market concentration RSI ...

  1. Enhancing fan experience during live sports broadcasts through second screen applications

    OpenAIRE

    Centieiro, Pedro Miguel da Fonseca

    2015-01-01

    When sports fans attend live sports events, they usually engage in social experiences with friends, family members and other fans at the venue sharing the same affiliation. However, fans watching the same event through a live television broadcast end up not feeling so emotionally connected with the athletes and other fans as they would if they were watching it live, together with thousands of other fans. With this in mind, we seek to create mobile applications that deliver engaging social exp...

  2. Conformation of bovine submaxillary mucin layers on hydrophobic surface as studied by biomolecular probes

    DEFF Research Database (Denmark)

    Pakkanen, Kirsi I.; Madsen, Jan Busk; Lee, Seunghwan

    2015-01-01

    In the present study, the conformational changes of bovine submaxillary mucin (BSM) adsorbed on a hydrophobic surface (polystyrene (PS)) as a function of concentration in bulk solution (up to 2mg/mL) have been investigated with biomolecular probe-based approaches, including bicinchoninic acid (BC...

  3. Optical Coherence Tomography and Biomolecular Imaging with Coherent Raman Scattering Microscopy

    DEFF Research Database (Denmark)

    Andersson-Engels, Stefan; Andersen, Peter E.

    2014-01-01

    The Special Section on Selected Topics in Biophotonics: Optical Coherence Tomography and Biomolecular Imaging with Coherent Raman Scattering Microscopy comprises two invited review papers and several contributed papers from the summer school Biophotonics ’13, as well as contributed papers within...

  4. Health Screening

    Science.gov (United States)

    Screenings are tests that look for diseases before you have symptoms. Screening tests can find diseases early, when they're easier to treat. You can get some screenings in your doctor's office. Others need special equipment, ...

  5. Immune cell-based screening assay for response to anticancer agents: applications in pharmacogenomics

    Directory of Open Access Journals (Sweden)

    Frick A

    2015-02-01

    Full Text Available Amber Frick,1 Yuri Fedoriw,2 Kristy Richards,3,4 Blossom Damania,3,5 Bethany Parks,6 Oscar Suzuki,1 Cristina S Benton,1 Emmanuel Chan,1 Russell S Thomas,7 Tim Wiltshire1,3 1Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, 2Department of Pathology and Laboratory Medicine, School of Medicine, 3Lineberger Comprehensive Cancer Center, School of Medicine, 4Department of Genetics, School of Medicine, 5Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC, USA; 6The Hamner Institutes for Health Sciences, 7Environmental Protection Agency, Research Triangle Park, NC, USA Background: Interpatient variability in immune and chemotherapeutic cytotoxic responses is likely due to complex genetic differences and is difficult to ascertain in humans. Through the use of a panel of genetically diverse mouse inbred strains, we developed a drug screening platform aimed at examining interstrain differences in viability on normal, noncancerous immune cells following chemotherapeutic cytotoxic insult. Drug effects were investigated by comparing selective chemotherapeutic agents, such as BEZ-235 and selumetinib, against conventional cytotoxic agents targeting multiple pathways, including doxorubicin and idarubicin. Methods: Splenocytes were isolated from 36 isogenic strains of mice using standard procedures. Of note, the splenocytes were not stimulated to avoid attributing responses to pathways involved with cellular stimulation rather than toxicity. Cells were incubated with compounds on a nine-point logarithmic dosing scale ranging from 15 nM to 100 µM (37°C, 5% CO2. At 4 hours posttreatment, cells were labeled with antibodies and physiological indicator dyes and fixed with 4% paraformaldehyde. Cellular phenotypes (eg, viability were collected and analyzed using flow cytometry. Dose-response curves with response normalized to the zero dose as a function of log concentration

  6. Screening of various low-grade biomass materials for low temperature gasification: Method development and application

    DEFF Research Database (Denmark)

    Thomsen, Tobias Pape; Ravenni, Giulia; Holm, Jens Kai;

    2015-01-01

    method and the subsequent use of the method to identify promising e but currently unproven, low-grade biomass resources for conversion in Pyroneer systems. The technical assessment is conducted by comparing the results from a series of physical-mechanical and thermochemical experiments to a set of proven...... references. The technical assessment is supplemented by an evaluation of practical application and overall energy balance. Applying the developed method to 4 references and 18 unproven low-grade potential fuels, indicated that one of these unproven candidates was most likely unsuited for Pyroneer...

  7. Development and Implementation of a Smartphone Application to Promote Physical Activity and Reduce Screen-time in Adolescent Boys

    Directory of Open Access Journals (Sweden)

    David Revalds Lubans

    2014-05-01

    Full Text Available Purpose: The primary aim is to describe the development and implementation of a smartphone application (app designed to promote physical activity and reduce screen-time in adolescent boys ‘at risk’ of obesity from low-income communities.Methods: An app was developed to support the delivery of a face-to-face school-based obesity prevention program known as the ‘Active Teen Leaders Avoiding Screen-time’ (ATLAS program. ATLAS was guided by self-determination theory and social cognitive theory and evaluated using a cluster randomized controlled trial with 361 boys (12.7± 0.5 years in 14 secondary schools. Following the completion of the study, participants in the intervention group completed a process evaluation questionnaire and focus groups were conducted with 42 students to explore their general perceptions of the ATLAS program and their experience with the smartphone app. Barriers and challenges encountered in the development, implementation and evaluation of the app are also described.Results: Participation in the study was not contingent on ownership of a smartphone, but 70% of participants in the intervention group reported having access to a smartphone or tablet device. Focus group participants reported an enjoyment of the program, and felt that it had provided them with new skills, techniques, and routines for the future. However, their engagement with the smartphone app was limited, due to a variety of reasons. Barriers to the implementation and evaluation of the app included limited access to smartphone devices, technical problems with the push notifications, lack of access to usage data and the challenges of maintaining participants’ interest in using the app.Conclusions: Although participants reported high levels of satisfaction with the ATLAS program in general, the smartphone app was not used extensively. Additional strategies and features may be needed to enhance engagement in adolescent boys.

  8. High throughput ratio imaging to profile caspase activity: potential application in multiparameter high content apoptosis analysis and drug screening.

    Directory of Open Access Journals (Sweden)

    Jeena Joseph

    Full Text Available Recent advancement in the area of green fluorescent protein techniques coupled with microscopic imaging has significantly contributed in defining and dissecting subcellular changes of apoptosis with high spatio-temporal resolution. Although single cell based studies using EGFP and associated techniques have provided valuable information of initiation and hierarchical changes of apoptosis, they are yet to be exploited for multiparameter cell based real time analysis for possible drug screening or pathway defining in a high throughput manner. Here we have developed multiple cancer cell lines expressing FRET sensors for active caspases and adapted them for high throughput live cell ratio imaging, enabling high content image based multiparameter analysis. Sensitivity of the system to detect live cell caspase activation was substantiated by confocal acceptor bleaching as well as wide field FRET imaging. Multiple caspase-specific activities of DEVDase, IETDase and LEHDase were analysed simultaneously with other decisive events of cell death. Through simultaneous analysis of caspase activation by FRET ratio change coupled with detection of mitochondrial membrane potential loss or superoxide generation, we identified several antitumor agents that induced caspase activation with or without membrane potential loss or superoxide generation. Also, cells that escaped the initial drug-induced caspase activation could be easily followed up for defining long term fate. Employing such a revisit imaging strategy of the same area, we have tracked the caspase surviving fractions with multiple drugs and its subsequent response to retreatment, revealing drug-dependent diverging fate of surviving cells. This thereby indicates towards a complex control of drug induced tumor resistance. The technique described here has wider application in both screening of compound libraries as well as in defining apoptotic pathways by linking multiple signaling to identify non

  9. Relaxing the electrostatic screening effect by patterning vertically-aligned silicon nanowire arrays into bundles for field emission application

    Energy Technology Data Exchange (ETDEWEB)

    Hung, Yung-Jr, E-mail: yungjrhung@gmail.com [Department of Electronic Engineering, National Taiwan University of Science and Technology, No. 43, Sec. 4, Keelung Rd., Taipei 106, Taiwan, ROC (China); Department of Photonics, National Sun Yat-sen University, No. 70, Lienhai Rd., Kaohsiung 80424, Taiwan, ROC (China); Graduate Institute of Electro-Optical Engineering, National Taiwan University of Science and Technology, No. 43, Sec. 4, Keelung Rd., Taipei 106, Taiwan, ROC (China); Lee, San-Liang [Department of Electronic Engineering, National Taiwan University of Science and Technology, No. 43, Sec. 4, Keelung Rd., Taipei 106, Taiwan, ROC (China); Graduate Institute of Electro-Optical Engineering, National Taiwan University of Science and Technology, No. 43, Sec. 4, Keelung Rd., Taipei 106, Taiwan, ROC (China); Beng, Looi Choon [Faculty of Engineering, Multimedia University, Jalan Multimedia, 63100 Cyberjaya, Selangor (Malaysia); Chang, Hsuan-Chen [Department of Electronic Engineering, National Taiwan University of Science and Technology, No. 43, Sec. 4, Keelung Rd., Taipei 106, Taiwan, ROC (China); Graduate Institute of Electro-Optical Engineering, National Taiwan University of Science and Technology, No. 43, Sec. 4, Keelung Rd., Taipei 106, Taiwan, ROC (China); Huang, Yung-Jui [Graduate Institute of Electro-Optical Engineering, National Taiwan University of Science and Technology, No. 43, Sec. 4, Keelung Rd., Taipei 106, Taiwan, ROC (China); Lee, Kuei-Yi; Huang, Ying-Sheng [Department of Electronic Engineering, National Taiwan University of Science and Technology, No. 43, Sec. 4, Keelung Rd., Taipei 106, Taiwan, ROC (China); Graduate Institute of Electro-Optical Engineering, National Taiwan University of Science and Technology, No. 43, Sec. 4, Keelung Rd., Taipei 106, Taiwan, ROC (China)

    2014-04-01

    Top-down fabrication strategies are proposed and demonstrated to realize arrays of vertically-aligned silicon nanowire bundles and bundle arrays of carbon nanotube–silicon nanowire (CNT–SiNW) heterojunctions, aiming for releasing the electrostatic screening effect and improving the field emission characteristics. The trade-off between the reduction in the electrostatic screening effect and the decrease of emission sites leads to an optimal SiNW bundle arrangement which enables the lowest turn-on electric field of 1.4 V/μm and highest emission current density of 191 μA/cm{sup 2} among all testing SiNW samples. Benefiting from the superior thermal and electrical properties of CNTs and the flexible patterning technologies available for SiNWs, bundle arrays of CNT–SiNW heterojunctions show improved and highly-uniform field emission with a lower turn-on electric field of 0.9 V/μm and higher emission current density of 5.86 mA/cm{sup 2}. The application of these materials and their corresponding fabrication approaches is not limited to the field emission but can be used for a variety of emerging fields like nanoelectronics, lithium-ion batteries, and solar cells. - Highlights: • Aligned silicon nanowire (SiNW) bundle arrays are realized with top-down methods. • Growing carbon nanotubes atop SiNW bundle arrays enable uniform field emission. • A turn-on field of 0.9 V/μm and an emission current of > 5 mA/cm{sup 2} are achieved.

  10. LED屏幕工作原理及其在电视演播室的应用%The Mechanism of LED Screen and Application in TV Studios

    Institute of Scientific and Technical Information of China (English)

    刘畅

    2013-01-01

      The mechanism of LED screen and technical parameters were introduced along with its application in basic structure for TV Studios.%  介绍了LED屏幕的工作原理和技术指标,及其在电视台演播室的基础架构和应用。

  11. Convection-diffusion driven concentration gradients in nanolitre droplets for microfluidic screening applications

    Science.gov (United States)

    Thakur, Raviraj; Amin, Ahmed; Wereley, Steven

    2014-11-01

    Ability to generate a concentration gradients in emulsified aqueous droplets is a highly desired feature for several lab-on-chip applications. Numerous schemes exists for generating concentration gradients in continuous flow devices such as Y junctions, split-and-recombine techniques, etc. However, varying the sample concentration in emulsified droplets is quite challenging. In this work, we have developed a scheme for generating and controlling concentration gradients in programmable multi-layer PDMS microfluidic chips. Briefly, a high concentration sample is injected into a steady stream of buffer. The buffer with the sample pulse and an immiscible oil phase are flowed through a T-junction in an alternate manner. As the sample pulse advances, the combined effect of diffusion and convection produced dispersion of sample pulse in streamwise direction. This continuous gradient stream is split into discrete droplets at the T-junction. Pulsatile flow condition are maintained using on-chip diaphragm peristaltic pumps. The problem can be thought of an extension of Taylor-Aris dispersion with laminar pulsatile flow in rectangular channels. The concentration profile is found to be dependent upon the frequency of pulsatile flow and thus can be fine-tuned according to application needs. Theoretical framework is established for pump regimes that correlates the diffusion coefficients of the input samples with the resultant concentration profiles.

  12. Theoretical analysis of screened heat pipes for medium and high temperature solar applications

    International Nuclear Information System (INIS)

    A mathematical model is applied to study the cylindrical heat pipes (HPs) behaviour when it is exposed to higher heat input at the evaporator for solar collector applications. The steady state analytical model includes two-dimensional heat conduction in the wall, the liquid flow in the wick and vapour hydrodynamics, and can be used to evaluate the working limits and to optimize the HP. The results of the analytical model are compared with numerical and experimental results available in literature, with good agreement. The effects of heat transfer coefficient, power input, evaporator length, pipe diameter, wick thickness and effective pore radius on the vapour temperature, maximum pressure drop and maximum heat transfer capability (HTC) of the HP are studied. The analysis shows that wick thickness plays an important role in the enhancement of HTC. Results show that it is possible to improve HTC of a HP by selecting the appropriate wick thickness, effective pore radius, and evaporator length. The parametric investigations are aimed to determine working limits and thermal performance of HP for medium temperature solar collector application

  13. Environmental Application of Reporter-Genes Based Biosensors for Chemical Contamination Screening

    Directory of Open Access Journals (Sweden)

    Matejczyk Marzena

    2014-12-01

    Full Text Available The paper presents results of research concerning possibilities of applications of reporter-genes based microorganisms, including the selective presentation of defects and advantages of different new scientific achievements of methodical solutions in genetic system constructions of biosensing elements for environmental research. The most robust and popular genetic fusion and new trends in reporter genes technology – such as LacZ (β-galactosidase, xylE (catechol 2,3-dioxygenase, gfp (green fluorescent proteins and its mutated forms, lux (prokaryotic luciferase, luc (eukaryotic luciferase, phoA (alkaline phosphatase, gusA and gurA (β-glucuronidase, antibiotics and heavy metals resistance are described. Reporter-genes based biosensors with use of genetically modified bacteria and yeast successfully work for genotoxicity, bioavailability and oxidative stress assessment for detection and monitoring of toxic compounds in drinking water and different environmental samples, surface water, soil, sediments.

  14. Decision-making in healthcare: a practical application of partial least square path modelling to coverage of newborn screening programmes

    Directory of Open Access Journals (Sweden)

    Fischer Katharina E

    2012-08-01

    Full Text Available Abstract Background Decision-making in healthcare is complex. Research on coverage decision-making has focused on comparative studies for several countries, statistical analyses for single decision-makers, the decision outcome and appraisal criteria. Accounting for decision processes extends the complexity, as they are multidimensional and process elements need to be regarded as latent constructs (composites that are not observed directly. The objective of this study was to present a practical application of partial least square path modelling (PLS-PM to evaluate how it offers a method for empirical analysis of decision-making in healthcare. Methods Empirical approaches that applied PLS-PM to decision-making in healthcare were identified through a systematic literature search. PLS-PM was used as an estimation technique for a structural equation model that specified hypotheses between the components of decision processes and the reasonableness of decision-making in terms of medical, economic and other ethical criteria. The model was estimated for a sample of 55 coverage decisions on the extension of newborn screening programmes in Europe. Results were evaluated by standard reliability and validity measures for PLS-PM. Results After modification by dropping two indicators that showed poor measures in the measurement models’ quality assessment and were not meaningful for newborn screening, the structural equation model estimation produced plausible results. The presence of three influences was supported: the links between both stakeholder participation or transparency and the reasonableness of decision-making; and the effect of transparency on the degree of scientific rigour of assessment. Reliable and valid measurement models were obtained to describe the composites of ‘transparency’, ‘participation’, ‘scientific rigour’ and ‘reasonableness’. Conclusions The structural equation model was among the first applications of PLS-PM to

  15. Screening of matrices and fibers for reinforced thermoplastics intended for dental applications.

    Science.gov (United States)

    Goldberg, A J; Burstone, C J; Hadjinikolaou, I; Jancar, J

    1994-02-01

    Plastics reinforced with continuous fibers (FRC) are being developed for dental applications, such as prosthodontic frameworks and orthodontic retainers. Flexure properties, stress relaxation and hydrolytic stability of FRC based on six thermoplastic matrices, three types of fibers, and three fiber volume fractions were evaluated. Samples with clinically relevant dimensions were tested. Polycarbonate was the preferred matrix material. Polycarbonate reinforced with 42 volume percent glass fibers exhibited the highest combination of flexure modulus (17.9 +/- 2.6 GPa), flexure strength (426 +/- 40 MPa), reinforcing efficiency (0.79), and resistance to stress relaxation. No statistically significant difference was observed between E and S2 glass reinforced composites under the experimental conditions used. Kevlar reinforced materials exhibited a low flexure modulus and strength. The apparent flexure moduli of all composites decreased with span length in the range of clinical interest. Generally, the prevalent mode of failure for all FRC investigated was brittle failure under flexure loading. Relatively large sample-to-sample variation in both composition and properties indicated that improved fabrication methods will be needed in future studies. The combination of good flexure properties, formability, and translucency suggests that novel appliance designs for dentistry are feasible with FRC, but further studies of its properties and particularly the effects of fiber/matrix interfacial quality are needed.

  16. Relfection on the Application of LED Screen in the CCTV Spring Festival Gala%对央视春晚应用LED显示屏的思考

    Institute of Scientific and Technical Information of China (English)

    徐瀛弢

    2013-01-01

    探讨LED显示屏与节目内容如何有机融合、LED显示屏在舞美中定位和作用,以及其对灯光设计产生的影响,反思LED显示屏在电视舞美中的应用。%From the three aspects of integration of LED screen and program contents, its location and function in the stage art, and its influence on the lighting design, the application of LED screen in TV stage art was deeply pondered over.

  17. Direct electrochemical reduction of graphene oxide on ionic liquid doped screen-printed electrode and its electrochemical biosensing application.

    Science.gov (United States)

    Ping, Jianfeng; Wang, Yixian; Fan, Kai; Wu, Jian; Ying, Yibin

    2011-10-15

    A novel electrochemical biosensing platform using electrochemically reduced graphene oxide (ER-GNO) modified electrode was proposed. This modified electrode was prepared by one-step electrodeposition of the exfoliated GNO sheets onto the ionic liquid doped screen-printed electrode (IL-SPE). The resulting ER-GNO/IL-SPE brought new capabilities for electrochemical devices by combining the advantages of ER-GNO and disposable electrode. Two important biomolecules, nicotinamide adenine dinucleotide (NADH) and hydrogen peroxide (H(2)O(2)), were employed to study the electrochemical performance of the ER-GNO/IL-SPE, which exhibited more favorable electron transfer kinetics than the bare IL-SPE. On the basis of the greatly enhanced electrochemical reactivity of H(2)O(2) at the developed electrode, ER-GNO and glucose oxidase constructed disposable biosensor showed better analytical performance for the glucose detection compared with the IL-SPE based biosensor. The linear range for the detection of glucose was from 5.0 μM to 12.0 mM with a detection limit of 1.0 μM. This work provides a useful avenue for implementing ER-GNO as a new generation of electrochemical transducer in disposable electrode, which could expand the scope of graphene constructed electrochemical biosensing devices and hold great promise for routine sensing applications. PMID:21807494

  18. The Rapid and Sensitive Quantitative Determination of Galactose by Combined Enzymatic and Colorimetric Method: Application in Neonatal Screening.

    Science.gov (United States)

    Kianmehr, Anvarsadat; Mahrooz, Abdolkarim; Ansari, Javad; Oladnabi, Morteza; Shahbazmohammadi, Hamid

    2016-05-01

    The quantitative measurement of galactose in blood is essential for the early diagnosis, treatment, and dietary monitoring of galactosemia patients. In this communication, we aimed to develop a rapid, sensitive, and cost-effective combined method for galactose determination in dry blood spots. This procedure was based on the combination of enzymatic reactions of galactose dehydrogenase (GalDH), dihydrolipoyl dehydrogenase (DLD), and alkaline phosphates with a colorimetric system. The incubation time and the concentration of enzymes used in new method were also optimized. The analytical performance was studied by the precision, recovery, linearity, and sensitivity parameters. Statistical analysis was applied to method comparison experiment. The regression equation and correlation coefficient (R (2)) were Y = 0.0085x + 0.032 and R (2) = 0.998, respectively. This assay exhibited a recovery in the range of 91.7-114.3 % and had the limit detection of 0.5 mg/dl for galactose. The between-run coefficient of variation (CV) was between 2.6 and 11.1 %. The within-run CV was between 4.9 and 9.2 %. Our results indicated that the new and reference methods were in agreement because no significant biases exist between them. Briefly, a quick and reliable combined enzymatic and colorimetric assay was presented for application in newborn mass screening and monitoring of galactosemia patients. PMID:26821257

  19. CdS/CdTe solar cells by the screen-printing-sintering technique: Fabrication, photovoltaic properties and applications

    Energy Technology Data Exchange (ETDEWEB)

    Ikegami, Seiji

    1988-01-15

    CdS/CdTe solar cells are fabricated on a borosilicate glass substrate by successively repeating screen printing and sintering (heating) in a belt furnace pastes of CdS, cadmium plus tellurium, carbon, silver plus indium and silver. In various sizes of solar cells, the highest efficiencies have been achieved for II-VI compound solar cells. The present solar cells have a spectral sensitivity up to a slightly longer wavelength than that of the usual CdS/CdTe solar cells. This may be due to the formation of CdS/sub x/Te/sub 1-x/ mixed crystals during the sintering of CdTe. In reliability tests under rooftop conditions, no remarkable change in the output power was observed in encapsulated solar cells over 800 days. From the results of accelerated tests on unencapsulated solar cells, a waterproof-type structure for the present solar cell module is required. The present solar cells and modules are now on the market for both indoor use and outdoor use; this is the first experience of the use of II-VI compound solar cells. Efforts to expand their application are being continued.

  20. Effective screening strategy using ensembled pharmacophore models combined with cascade docking: application to p53-MDM2 interaction inhibitors.

    Science.gov (United States)

    Xue, Xin; Wei, Jin-Lian; Xu, Li-Li; Xi, Mei-Yang; Xu, Xiao-Li; Liu, Fang; Guo, Xiao-Ke; Wang, Lei; Zhang, Xiao-Jin; Zhang, Ming-Ye; Lu, Meng-Chen; Sun, Hao-Peng; You, Qi-Dong

    2013-10-28

    Protein-protein interactions (PPIs) play a crucial role in cellular function and form the backbone of almost all biochemical processes. In recent years, protein-protein interaction inhibitors (PPIIs) have represented a treasure trove of potential new drug targets. Unfortunately, there are few successful drugs of PPIIs on the market. Structure-based pharmacophore (SBP) combined with docking has been demonstrated as a useful Virtual Screening (VS) strategy in drug development projects. However, the combination of target complexity and poor binding affinity prediction has thwarted the application of this strategy in the discovery of PPIIs. Here we report an effective VS strategy on p53-MDM2 PPI. First, we built a SBP model based on p53-MDM2 complex cocrystal structures. The model was then simplified by using a Receptor-Ligand complex-based pharmacophore model considering the critical binding features between MDM2 and its small molecular inhibitors. Cascade docking was subsequently applied to improve the hit rate. Based on this strategy, we performed VS on NCI and SPECS databases and successfully discovered 6 novel compounds from 15 hits with the best, compound 1 (NSC 5359), K(i) = 180 ± 50 nM. These compounds can serve as lead compounds for further optimization. PMID:24050442

  1. A Simplified Method for Gene Knockout and Direct Screening of Recombinant Clones for Application in Paenibacillus polymyxa.

    Directory of Open Access Journals (Sweden)

    Seong-Bin Kim

    Full Text Available Paenibacillus polymyxa is a bacterium widely used in agriculture, industry, and environmental remediation because it has multiple functions including nitrogen fixation and produces various biologically active compounds. Among these compounds are the antibiotics polymyxins, and the bacterium is currently being reassessed for medical application. However, a lack of genetic tools for manipulation of P. polymyxa has limited our understanding of the biosynthesis of these compounds.To facilitate an understanding of the genetic determinants of the bacterium, we have developed a system for marker exchange mutagenesis directly on competent cells of P. polymyxa under conditions where homologous recombination is enhanced by denaturation of the suicide plasmid DNA. To test this system, we targeted P. polymyxa α-and β-amylase genes for disruption. Chloramphenicol or erythromycin resistance genes were inserted into the suicide plasmid pGEM7Z-f+ (Promega. To mediate homologous recombination and replacement of the targeted genes with the antibiotic resistance genes nucleotide sequences of the α-and β-amylase genes were cloned into the plasmid flanking the antibiotic resistance genes.We have created a simple system for targeted gene deletion in P. polymyxa E681. We propose that P. polymyxa isogenic mutants could be developed using this system of marker exchange mutagenesis. α-and β-amylase genes provide a useful tool for direct recombinant screening in P. polymyxa.

  2. Design and screening of a glial cell-specific, cell penetrating peptide for therapeutic applications in multiple sclerosis.

    Directory of Open Access Journals (Sweden)

    Corey Heffernan

    Full Text Available Multiple Sclerosis (MS is an autoimmune, neurodegenerative disease of the central nervous system (CNS characterized by demyelination through glial cell loss. Current and proposed therapeutic strategies to arrest demyelination and/or promote further remyelination include: (i modulation of the host immune system; and/or (ii transplantation of myelinating/stem or progenitor cells to the circulation or sites of injury. However, significant drawbacks are inherent with both approaches. Cell penetrating peptides (CPP are short amino acid sequences with an intrinsic ability to translocate across plasma membranes, and theoretically represent an attractive vector for delivery of therapeutic peptides or nanoparticles to glia to promote cell survival or remyelination. The CPPs described to date are commonly non-selective in the cell types they transduce, limiting their therapeutic application in vivo. Here, we describe a theoretical framework for design of a novel CPP sequence that selectively transduces human glial cells (excluding non-glial cell types, and conduct preliminary screens of purified, recombinant CPPs with immature and matured human oligodendrocytes and astrocytes, and two non-glial cell types. A candidate peptide, termed TD2.2, consistently transduced glial cells, was significantly more effective at transducing immature oligodendrocytes than matured progeny, and was virtually incapable of transducing two non-glial cell types: (i human neural cells and (ii human dermal fibroblasts. Time-lapse confocal microscopy confirms trafficking of TD2.2 (fused to EGFP to mature oligodendrocytes 3-6 hours after protein application in vitro. We propose selectivity of TD2.2 for glial cells represents a new therapeutic strategy for the treatment of glial-related disease, such as MS.

  3. Constructing Bio-molecular Databases on a DNA-based Computer

    CERN Document Server

    Chang, Weng-Long; Ho,; Guo, Minyi

    2007-01-01

    Codd [Codd 1970] wrote the first paper in which the model of a relational database was proposed. Adleman [Adleman 1994] wrote the first paper in which DNA strands in a test tube were used to solve an instance of the Hamiltonian path problem. From [Adleman 1994], it is obviously indicated that for storing information in molecules of DNA allows for an information density of approximately 1 bit per cubic nm (nanometer) and a dramatic improvement over existing storage media such as video tape which store information at a density of approximately 1 bit per 1012 cubic nanometers. This paper demonstrates that biological operations can be applied to construct bio-molecular databases where data records in relational tables are encoded as DNA strands. In order to achieve the goal, DNA algorithms are proposed to perform eight operations of relational algebra (calculus) on bio-molecular relational databases, which include Cartesian product, union, set difference, selection, projection, intersection, join and division. Fu...

  4. PREFACE: India-Japan Workshop on Biomolecular Electronics & Organic Nanotechnology for Environment Preservation

    Science.gov (United States)

    Onoda, Mitsuyoshi; Malhotra, Bansi D.

    2012-04-01

    The 'India-Japan Workshop on Biomolecular Electronics & Organic Nanotechnology for Environment Preservation' (IJWBME 2011) will be held on 7-10 December 2011 at EGRET Himeji, Himeji, Hyogo, Japan. This workshop was held for the first time on 17-19 December 2009 at NPL, New Delhi. Keeping in mind the importance of organic nanotechnology and biomolecular electronics for environmental preservation and their anticipated impact on the economics of both the developing and the developed world, IJWBME 2009 was jointly organized by the Department of Biological Functions, Graduate School of Life Sciences and Systems Engineering, the Kyushu Institute of Technology (KIT), Kitakyushu, Japan, and the Department of Science & Technology Centre on Biomolecular Electronics (DSTCBE), National Physical Laboratory (NPL). Much progress in the field of biomolecular electronics and organic nanotechnology for environmental preservation is expected for the 21st Century. Organic optoelectronic devices, such as organic electroluminescent devices, organic thin-film transistors, organic sensors, biological systems and so on have especially attracted much attention. The main purpose of this workshop is to provide an opportunity for researchers interested in biomolecular electronics and organic nanotechnology for environmental preservation, to come together in an informal and friendly atmosphere and exchange technical knowledge and experience. We are sure that this workshop will be very useful and fruitful for all participants in summarizing the recent progress in biomolecular electronics and organic nanotechnology for environmental preservation and preparing new ground for the next generation. Many papers have been submitted from India and Japan and more than 30 papers have been accepted for presentation. The main topics of interest are as follows: Bioelectronics Biomolecular Electronics Fabrication Techniques Self-assembled Monolayers Nano-sensors Environmental Monitoring Organic Devices

  5. Biochemical filter with sigmoidal response: increasing the complexity of biomolecular logic.

    Science.gov (United States)

    Privman, Vladimir; Halámek, Jan; Arugula, Mary A; Melnikov, Dmitriy; Bocharova, Vera; Katz, Evgeny

    2010-11-11

    The first realization of a designed, rather than natural, biochemical filter process is reported and analyzed as a promising network component for increasing the complexity of biomolecular logic systems. Key challenge in biochemical logic research has been achieving scalability for complex network designs. Various logic gates have been realized, but a "toolbox" of analog elements for interconnectivity and signal processing has remained elusive. Filters are important as network elements that allow control of noise in signal transmission and conversion. We report a versatile biochemical filtering mechanism designed to have sigmoidal response in combination with signal-conversion process. Horseradish peroxidase-catalyzed oxidation of chromogenic electron donor by H(2)O(2) was altered by adding ascorbate, allowing to selectively suppress the output signal, modifying the response from convex to sigmoidal. A kinetic model was developed for evaluation of the quality of filtering. The results offer improved capabilities for design of scalable biomolecular information processing systems.

  6. Effect of antibody modifications on its biomolecular binding as determined by surface plasmon resonance.

    Science.gov (United States)

    Vashist, Sandeep Kumar

    2012-02-01

    A surface plasmon resonance (SPR)-based procedure was developed to determine the effect of antibody modifications on its biomolecular binding behavior. Mouse immunoglobulin G (IgG) was immobilized on a protein A-functionalized gold-coated SPR chip. Goat anti-mouse IgG and its various commercially available modifications (i.e., conjugated with atto 550, atto 647, tetramethylrhodamine isothiocyanate [TRITC], horseradish peroxidase [HRP], or biotin) were employed in exactly the same concentration for the detection of mouse IgG. The various modifications of goat anti-mouse IgG decreased its biomolecular binding to mouse IgG in the order of unmodified>HRP-labeled>atto 550-labeled>biotinylated>TRITC-labeled>atto 647-labeled. PMID:22093612

  7. Effects of Application of Social Marketing Theory and the Health Belief Model in Promoting Cervical Cancer Screening among Targeted Women in Sisaket Province, Thailand.

    Science.gov (United States)

    Wichachai, Suparp; Songserm, Nopparat; Akakul, Theerawut; Kuasiri, Chanapong

    2016-01-01

    Cervical cancer is a major public health problem in Thailand, being ranked second only to breast cancer. Thai women have been reported to have a low rate of cervical cancer screening (27.7% of the 80% goal of WHO). We therefore aimed to apply the social marketing theory and health belief model in promoting cervical cancer screening in Kanthararom District, Sisaket Province. A total of 92 from 974 targeted women aged 3060 years were randomly divided into two groups. The experimental group underwent application of social marketing theory and a health belief model program promoting cervical cancer screening while the control group received normal services. Two research tools were used: (1) application of social marketing theory and health belief model program and (2) questionnaire used to evaluate perceptions of cervical cancer. Descriptive and inferential statistics including paired sample ttest and independent ttest were used to analyze the data. After the program had been used, the mean score of perception of cervical cancer of experimental group was at a higher level (x=4.09; S.D. =0.30), than in the control group (x=3.82; S.D. =0.20) with statistical significance (psocial marketing and the health belief model be used to promote cervical cancer screening in targeted women and it can be promoted as a guideline for other health services, especially in health promotion and disease prevention.

  8. Bridge- and Solvent-Mediated Intramolecular Electronic Communications in Ubiquinone-Based Biomolecular Wires

    OpenAIRE

    Liu, Xiao-Yuan; Ma, Wei; Zhou, Hao; Cao, Xiao-Ming; Long, Yi-Tao

    2015-01-01

    Intramolecular electronic communications of molecular wires play a crucial role for developing molecular devices. In the present work, we describe different degrees of intramolecular electronic communications in the redox processes of three ubiquinone-based biomolecular wires (Bis-CoQ0s) evaluated by electrochemistry and Density Functional Theory (DFT) methods in different solvents. We found that the bridges linkers have a significant effect on the electronic communications between the two pe...

  9. Extension of the GLYCAM06 Biomolecular Force Field to Lipids, Lipid Bilayers and Glycolipids

    OpenAIRE

    Tessier, Matthew B; DeMarco, Mari L.; Yongye, Austin B.; Woods, Robert J.

    2008-01-01

    GLYCAM06 is a generalisable biomolecular force field that is extendible to diverse molecular classes in the spirit of a small-molecule force field. Here we report parameters for lipids, lipid bilayers and glycolipids for use with GLYCAM06. Only three lipid-specific atom types have been introduced, in keeping with the general philosophy of transferable parameter development. Bond stretching, angle bending, and torsional force constants were derived by fitting to quantum mechanical data for a c...

  10. Atomic force microscopy of self-assembled biomolecular structures and their interaction with metallic nanoparticles.

    OpenAIRE

    Gysemans, Maarten

    2009-01-01

    We applied AFM to study biomolecular wires, both out of interest in thei r biological functions and in the framework of nanotechnology based fabr ication. We have focused on two different kinds of protein wires: Insuli n fibrils and microtubules. Microtubules are an important constituent of the cytoskeleton and fulfill multiple vital functions in the cell. Insu lin fibrils on the other hand are amyloid fibrils without a clear biolog ical role, but with intriguing polymerization properties tha...

  11. Assembly of single wall carbon nanotube-metal nanohybrids using biomolecular components

    Science.gov (United States)

    Kim, Sang Nyon; Slocik, Joseph M.; Naik, Rajesh R.

    2010-08-01

    Biomaterials such as nucleic acids and proteins can be exploited to create higher order structures. The biomolecular components such as DNA and peptides have been used to assemble nanoparticles with high fidelity. Here, we use DNA and peptides, and their preferential interaction with inorganic and carbon nanomaterials to form homogeneous hybrids. The enhanced binding of Pt ions to both DNA and peptide functionalized nanoparticles mediates the assembly of carbon nanotubes functionalized with DNA with peptide coated gold nanoparticles.

  12. Changes in biomolecular profile in a single nucleolus during cell fixation.

    Science.gov (United States)

    Kuzmin, Andrey N; Pliss, Artem; Prasad, Paras N

    2014-11-01

    Fixation of biological sample is an essential technique applied in order to "freeze" in time the intracellular molecular content. However, fixation induces changes of the cellular molecular structure, which mask physiological distribution of biomolecules and bias interpretation of results. Accurate, sensitive, and comprehensive characterization of changes in biomolecular composition, occurring during fixation, is crucial for proper analysis of experimental data. Here we apply biomolecular component analysis for Raman spectra measured in the same nucleoli of HeLa cells before and after fixation by either formaldehyde solution or by chilled ethanol. It is found that fixation in formaldehyde does not strongly affect the Raman spectra of nucleolar biomolecular components, but may significantly decrease the nucleolar RNA concentration. At the same time, ethanol fixation leads to a proportional increase (up to 40%) in concentrations of nucleolar proteins and RNA, most likely due to cell shrinkage occurring in the presence of coagulant fixative. Ethanol fixation also triggers changes in composition of nucleolar proteome, as indicated by an overall reduction of the α-helical structure of proteins and increase in the concentration of proteins containing the β-sheet conformation. We conclude that cross-linking fixation is a more appropriate protocol for mapping of proteins in situ. At the same time, ethanol fixation is preferential for studies of RNA-containing macromolecules. We supplemented our quantitative Raman spectroscopic measurements with mapping of the protein and lipid macromolecular groups in live and fixed cells using coherent anti-Stokes Raman scattering nonlinear optical imaging.

  13. Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning.

    Science.gov (United States)

    Cole, Daniel J; Vilseck, Jonah Z; Tirado-Rives, Julian; Payne, Mike C; Jorgensen, William L

    2016-05-10

    Molecular mechanics force fields, which are commonly used in biomolecular modeling and computer-aided drug design, typically treat nonbonded interactions using a limited library of empirical parameters that are developed for small molecules. This approach does not account for polarization in larger molecules or proteins, and the parametrization process is labor-intensive. Using linear-scaling density functional theory and atoms-in-molecule electron density partitioning, environment-specific charges and Lennard-Jones parameters are derived directly from quantum mechanical calculations for use in biomolecular modeling of organic and biomolecular systems. The proposed methods significantly reduce the number of empirical parameters needed to construct molecular mechanics force fields, naturally include polarization effects in charge and Lennard-Jones parameters, and scale well to systems comprised of thousands of atoms, including proteins. The feasibility and benefits of this approach are demonstrated by computing free energies of hydration, properties of pure liquids, and the relative binding free energies of indole and benzofuran to the L99A mutant of T4 lysozyme. PMID:27057643

  14. An improved simple polarisable water model for use in biomolecular simulation

    Energy Technology Data Exchange (ETDEWEB)

    Bachmann, Stephan J.; Gunsteren, Wilfred F. van, E-mail: wfvgn@igc.phys.chem.ethz.ch [Laboratory of Physical Chemistry, ETH Zürich, CH-8093 Zürich (Switzerland)

    2014-12-14

    The accuracy of biomolecular simulations depends to some degree on the accuracy of the water model used to solvate the biomolecules. Because many biomolecules such as proteins are electrostatically rather inhomogeneous, containing apolar, polar, and charged moieties or side chains, a water model should be able to represent the polarisation response to a local electrostatic field, while being compatible with the force field used to model the biomolecules or protein. The two polarisable water models, COS/G2 and COS/D, that are compatible with the GROMOS biomolecular force fields leave room for improvement. The COS/G2 model has a slightly too large dielectric permittivity and the COS/D model displays a much too slow dynamics. The proposed COS/D2 model has four interaction sites: only one Lennard-Jones interaction site, the oxygen atom, and three permanent charge sites, the two hydrogens, and one massless off-atom site that also serves as charge-on-spring (COS) polarisable site with a damped or sub-linear dependence of the induced dipole on the electric field strength for large values of the latter. These properties make it a cheap and yet realistic water model for biomolecular solvation.

  15. MRSA Screening

    Science.gov (United States)

    ... limited. Home Visit Global Sites Search Help? MRSA Screening Share this page: Was this page helpful? Formal name: Methicillin resistant Staphylococcus aureus Screening Related tests: Wound Culture At a Glance Test ...

  16. Genome-wide screening and identification of new Trypanosoma cruzi antigens with potential application for chronic Chagas disease diagnosis.

    Directory of Open Access Journals (Sweden)

    João Luís Reis-Cunha

    Full Text Available The protozoan Trypanosoma cruzi is the etiologic agent of Chagas disease, an infection that afflicts approximately 8 million people in Latin America. Diagnosis of chronic Chagas disease is currently based on serological tests because this condition is usually characterized by high anti-T. cruzi IgG titers and low parasitemia. The antigens used in these assays may have low specificity due to cross reactivity with antigens from related parasite infections, such as leishmaniasis, and low sensitivity caused by the high polymorphism among T. cruzi strains. Therefore, the identification of new T. cruzi-specific antigens that are conserved among the various parasite discrete typing units (DTUs is still required. In the present study, we have explored the hybrid nature of the T. cruzi CL Brener strain using a broad genome screening approach to select new T. cruzi antigens that are conserved among the different parasite DTUs and that are absent in other trypanosomatid species. Peptide arrays containing the conserved antigens with the highest epitope prediction scores were synthesized, and the reactivity of the peptides were tested by immunoblot using sera from C57BL/6 mice chronically infected with T. cruzi strains from the TcI, TcII or TcVI DTU. The two T. cruzi proteins that contained the most promising peptides were expressed as recombinant proteins and tested in ELISA experiments with sera from chagasic patients with distinct clinical manifestations: those infected with T. cruzi from different DTUs and those with cutaneous or visceral leishmaniasis. These proteins, named rTc_11623.20 and rTc_N_10421.310, exhibited 94.83 and 89.66% sensitivity, 98.2 and 94.6% specificity, respectively, and a pool of these 2 proteins exhibited 96.55% sensitivity and 98.18% specificity. This work led to the identification of two new antigens with great potential application in the diagnosis of chronic Chagas disease.

  17. Cancer screening

    OpenAIRE

    Krishna Prasad

    1987-01-01

    Cancer screening is a means to detect cancer early with the goal of decreasing morbidity and mortality. At present, there is a reasonable consensus regarding screening for breast, cervical and colorectal cances and the role of screening is under trial in case of cancers of the lung,  ovaries and prostate. On the other hand, good screening tests are not available for some of the commonest cancers in India like the oral, pharyngeal, esophageal and stomach cancers.

  18. A multivariate cure model for left-censored and right-censored data with application to colorectal cancer screening patterns.

    Science.gov (United States)

    Hagar, Yolanda C; Harvey, Danielle J; Beckett, Laurel A

    2016-08-30

    We develop a multivariate cure survival model to estimate lifetime patterns of colorectal cancer screening. Screening data cover long periods of time, with sparse observations for each person. Some events may occur before the study begins or after the study ends, so the data are both left-censored and right-censored, and some individuals are never screened (the 'cured' population). We propose a multivariate parametric cure model that can be used with left-censored and right-censored data. Our model allows for the estimation of the time to screening as well as the average number of times individuals will be screened. We calculate likelihood functions based on the observations for each subject using a distribution that accounts for within-subject correlation and estimate parameters using Markov chain Monte Carlo methods. We apply our methods to the estimation of lifetime colorectal cancer screening behavior in the SEER-Medicare data set. Copyright © 2016 John Wiley & Sons, Ltd. PMID:26990553

  19. Biomolecular coronas provide the biological identity of nanosized materials

    NARCIS (Netherlands)

    Monopoli, Marco P; Åberg, Christoffer; Salvati, Anna; Dawson, Kenneth A

    2012-01-01

    The search for understanding the interactions of nanosized materials with living organisms is leading to the rapid development of key applications, including improved drug delivery by targeting nanoparticles, and resolution of the potential threat of nanotechnological devices to organisms and the en

  20. Production and detection of neutral molecular beams : from single amino acids to biomolecular complexes

    International Nuclear Information System (INIS)

    This thesis presents a laser desorption source for neutral organic molecules and clusters as well as the first exploration of a superconducting single photon detector for the detection of massive neutral particles. Whereas the source can produce beams of biomolecules for various gas-phase applications, the detector can be used to overcome the current post- ionization detection mass limit of neutral molecules. The aim of our work is to produce and detect neutral molecular gas-phase beams, ranging from small amino acids overlarge polypeptides to massive complexes. The purpose of creating these beams is to use them for quantum optics experiments, like near field matter wave interference and its applications in metrology. Standard effusive sources usually lack the ability to cool the evaporated organic molecules fast enough to prevent fragmentation. In contrast to that, the presented laser desorption source cools the initially evaporated molecules by embedding them into a supersonic seed gas beam. The mixing of the seed gas and the desorbed molecules is implemented both in free expansion as well as inside a closed mixing channel. The desorbed neutral molecules are detected by photo-ionization using UV (266 nm) and FUV (157 nm) light followed by time-of-flight mass spectrometry. For the amino acid tryptophan (204amu) and for the antibiotic polypeptide gramicidin (1884amu) the ion yields for both photo-ionization wavelengths are examined and the ionization cross sections for the UV wavelength are measured. In case of tryptophan the ionization yield is comparable for both wavelengths, whereas gramicidin is detected fifteen times more efficiently under VUV ionization than for UV ionization at equal intensity. Desorption of heavier molecules than gramicidin never resulted in a detectable ion yield, which confirms the known inefficiency for the post-ionization of isolated large organic molecules [1-3]. The desorption source is also used for the formation of large neutral

  1. Double-gated spectral snapshots for biomolecular fluorescence

    International Nuclear Information System (INIS)

    A versatile method to take femtosecond spectral snapshots of fluorescence has been developed based on a double gating technique in the combination of an optical Kerr gate and an image intensifier as an electrically driven gate set in front of a charge-coupled device detector. The application of a conventional optical-Kerr-gate method is limited to molecules with the short fluorescence lifetime up to a few hundred picoseconds, because long-lifetime fluorescence itself behaves as a source of the background signal due to insufficiency of the extinction ratio of polarizers employed for the Kerr gate. By using the image intensifier with the gate time of 200 ps, we have successfully suppressed the background signal and overcome the application limit of optical-Kerr-gate method. The system performance has been demonstrated by measuring time-resolved fluorescence spectra for laser dye solution and the riboflavin solution as a typical sample of biomolecule

  2. Application of Atomic Dielectric Resonance Spectroscopy for the screening of blood samples from patients with clinical variant and sporadic CJD

    Directory of Open Access Journals (Sweden)

    Ironside James W

    2007-08-01

    Full Text Available Abstract Background Sub-clinical variant Creutzfeldt-Jakob disease (vCJD infection and reports of vCJD transmission through blood transfusion emphasise the need for blood screening assays to ensure the safety of blood and transplanted tissues. Most assays aim to detect abnormal prion protein (PrPSc, although achieving required sensitivity is a challenge. Methods We have used innovative Atomic Dielectric Resonance Spectroscopy (ADRS, which determines dielectric properties of materials which are established by reflectivity and penetration of radio/micro waves, to analyse blood samples from patients and controls to identify characteristic ADR signatures unique to blood from vCJD and to sCJD patients. Initial sets of blood samples from vCJD, sCJD, non-CJD neurological diseases and normal healthy adults (blood donors were screened as training samples to determine group-specific ADR characteristics, and provided a basis for classification of blinded sets of samples. Results Blood sample groups from vCJD, sCJD, non-CJD neurological diseases and normal healthy adults (blood donors screened by ADRS were classified with 100% specificity and sensitivity, discriminating these by a co-variance expert analysis system. Conclusion ADRS appears capable of recognising and discriminating serum samples from vCJD, sCJD, non-CJD neurological diseases, and normal healthy adults, and might be developed to provide a system for primary screening or confirmatory assay complementary to other screening systems.

  3. A Barcode-Free Combinatorial Screening Platform for Matrix Metalloproteinase Screening

    OpenAIRE

    Rane, Tushar D.; Zec, Helena C.; Wang, Tza-Huei

    2014-01-01

    Application of droplet microfluidics to combinatorial screening applications remains elusive because of the need for composition-identifying unique barcodes. Here we propose a barcode-free continuous flow droplet microfluidic platform to suit the requirements of combinatorial screening applications. We demonstrate robust and repeatable functioning of this platform with matrix metalloproteinase activity screening as a sample application.

  4. Application of screen-printed biosensor in food analysis%丝网印刷生物传感器在食品分析中的应用

    Institute of Scientific and Technical Information of China (English)

    臧帅; 刘珒; 卢蓝蓝; 孙远明; 刘英菊; 雷红涛

    2013-01-01

    Screen-printed biosensor had been widely applied in food analysis due to its various advantages including low cost,short time-consuming and miniaturization compared with other physicochemical methods.This review focused on the basic configurations of screen-printing electrode and their applications especially in food analysis.Additionally,a general overview of the potential application of screen-printed biosensor in the food analysis field was also addressed.%丝网印刷生物传感器因其成本低,耗时短,微型化等优点,近年来在食品分析领域得到广泛应用.本文对丝网印刷电极的原理、制作过程进行了介绍,并综述了丝网印刷生物传感器在食品分析领域的研究进展,探讨了其在食品分析领域的应用前景.

  5. Calculation of the importance of quality factors in braille application process on labels by screen UV-varnishes

    Directory of Open Access Journals (Sweden)

    Vyacheslav Repeta

    2014-09-01

    Full Text Available Oriented graph has been drawn in the article according to fixed factors of the quality of applying Braille screen printing on the label by screen UV-varnishes. Using hierarchical representation of relationships between factors in the form of oriented graphs we have ranked the factors of the screen printing process of Braille elements by UV-varnishes and calculated their corresponding coefficients. We have found that the most ranked are such factors as the surface energy of the printing material, the printing speed, the temperature of UV-varnish and its viscosity. Received results of ranking will enable to synthesize the model of the process’ priority factors and to reveal the possibilities of regulations of geometrical parameters of the tactile font elements.

  6. Application of a cocktail approach to screen cytochrome P450 BM3 libraries for metabolic activity and diversity.

    Science.gov (United States)

    Reinen, Jelle; Postma, Geert; Tump, Cornelis; Bloemberg, Tom; Engel, Jasper; Vermeulen, Nico P E; Commandeur, Jan N M; Honing, Maarten

    2016-02-01

    In the present study, the validity of using a cocktail screening method in combination with a chemometrical data mining approach to evaluate metabolic activity and diversity of drug-metabolizing bacterial Cytochrome P450 (CYP) BM3 mutants was investigated. In addition, the concept of utilizing an in-house-developed library of CYP BM3 mutants as a unique biocatalytic synthetic tool to support medicinal chemistry was evaluated. Metabolic efficiency of the mutant library towards a selection of CYP model substrates, being amitriptyline (AMI), buspirone (BUS), coumarine (COU), dextromethorphan (DEX), diclofenac (DIC) and norethisterone (NET), was investigated. First, metabolic activity of a selection of CYP BM3 mutants was screened against AMI and BUS. Subsequently, for a single CYP BM3 mutant, the effect of co-administration of multiple drugs on the metabolic activity and diversity towards AMI and BUS was investigated. Finally, a cocktail of AMI, BUS, COU, DEX, DIC and NET was screened against the whole in-house CYP BM3 library. Different validated quantitative and qualitative (U)HPLC-MS/MS-based analytical methods were applied to screen for substrate depletion and targeted product formation, followed by a more in-depth screen for metabolic diversity. A chemometrical approach was used to mine all data to search for unique metabolic properties of the mutants and allow classification of the mutants. The latter would open the possibility of obtaining a more in-depth mechanistic understanding of the metabolites. The presented method is the first MS-based method to screen CYP BM3 mutant libraries for diversity in combination with a chemometrical approach to interpret results and visualize differences between the tested mutants. PMID:26753974

  7. Application of a cocktail approach to screen cytochrome P450 BM3 libraries for metabolic activity and diversity.

    Science.gov (United States)

    Reinen, Jelle; Postma, Geert; Tump, Cornelis; Bloemberg, Tom; Engel, Jasper; Vermeulen, Nico P E; Commandeur, Jan N M; Honing, Maarten

    2016-02-01

    In the present study, the validity of using a cocktail screening method in combination with a chemometrical data mining approach to evaluate metabolic activity and diversity of drug-metabolizing bacterial Cytochrome P450 (CYP) BM3 mutants was investigated. In addition, the concept of utilizing an in-house-developed library of CYP BM3 mutants as a unique biocatalytic synthetic tool to support medicinal chemistry was evaluated. Metabolic efficiency of the mutant library towards a selection of CYP model substrates, being amitriptyline (AMI), buspirone (BUS), coumarine (COU), dextromethorphan (DEX), diclofenac (DIC) and norethisterone (NET), was investigated. First, metabolic activity of a selection of CYP BM3 mutants was screened against AMI and BUS. Subsequently, for a single CYP BM3 mutant, the effect of co-administration of multiple drugs on the metabolic activity and diversity towards AMI and BUS was investigated. Finally, a cocktail of AMI, BUS, COU, DEX, DIC and NET was screened against the whole in-house CYP BM3 library. Different validated quantitative and qualitative (U)HPLC-MS/MS-based analytical methods were applied to screen for substrate depletion and targeted product formation, followed by a more in-depth screen for metabolic diversity. A chemometrical approach was used to mine all data to search for unique metabolic properties of the mutants and allow classification of the mutants. The latter would open the possibility of obtaining a more in-depth mechanistic understanding of the metabolites. The presented method is the first MS-based method to screen CYP BM3 mutant libraries for diversity in combination with a chemometrical approach to interpret results and visualize differences between the tested mutants.

  8. The Spatial Distribution of Hepatitis C Virus Infections and Associated Determinants—An Application of a Geographically Weighted Poisson Regression for Evidence-Based Screening Interventions in Hotspots

    Science.gov (United States)

    Kauhl, Boris; Heil, Jeanne; Hoebe, Christian J. P. A.; Schweikart, Jürgen; Krafft, Thomas; Dukers-Muijrers, Nicole H. T. M.

    2015-01-01

    Background Hepatitis C Virus (HCV) infections are a major cause for liver diseases. A large proportion of these infections remain hidden to care due to its mostly asymptomatic nature. Population-based screening and screening targeted on behavioural risk groups had not proven to be effective in revealing these hidden infections. Therefore, more practically applicable approaches to target screenings are necessary. Geographic Information Systems (GIS) and spatial epidemiological methods may provide a more feasible basis for screening interventions through the identification of hotspots as well as demographic and socio-economic determinants. Methods Analysed data included all HCV tests (n = 23,800) performed in the southern area of the Netherlands between 2002–2008. HCV positivity was defined as a positive immunoblot or polymerase chain reaction test. Population data were matched to the geocoded HCV test data. The spatial scan statistic was applied to detect areas with elevated HCV risk. We applied global regression models to determine associations between population-based determinants and HCV risk. Geographically weighted Poisson regression models were then constructed to determine local differences of the association between HCV risk and population-based determinants. Results HCV prevalence varied geographically and clustered in urban areas. The main population at risk were middle-aged males, non-western immigrants and divorced persons. Socio-economic determinants consisted of one-person households, persons with low income and mean property value. However, the association between HCV risk and demographic as well as socio-economic determinants displayed strong regional and intra-urban differences. Discussion The detection of local hotspots in our study may serve as a basis for prioritization of areas for future targeted interventions. Demographic and socio-economic determinants associated with HCV risk show regional differences underlining that a one

  9. The urgent need for universally applicable simple screening procedures and diagnostic criteria for gestational diabetes mellitus - lessons from projects funded by the World Diabetes Foundation

    DEFF Research Database (Denmark)

    Nielsen, Karoline Kragelund; de Courten, Maximilian; Kapur, Anil

    2012-01-01

    Background: To address the risks of adverse pregnancy outcomes and future type 2 diabetes associated with gestational diabetes mellitus (GDM), its early detection and timely treatment is essential. In the absence of an international consensus, multiple different guidelines on screening...... and diagnosis of GDM have existed for a long time. This may be changing with the publication of the recommendations by the International Association of Diabetes and Pregnancy Study Groups. However, none of these guidelines take into account evidence from or ground realities of resource-poor settings. Objective......: This study aimed to investigate whether GDM projects supported by the World Diabetes Foundation in developing countries utilize any of the internationally recommended guidelines for screening and diagnosis of GDM, explore experiences on applicability and usefulness of the guidelines and barriers if any...

  10. Research Focus towards biomolecular medicines development: An overview

    Directory of Open Access Journals (Sweden)

    K Ramalingam

    2011-04-01

    Full Text Available Research towards molecular medicines development for noninfectious diseases such as cardio-vascular diseases, cancer, diabetes, neuro-degenerative diseases and musculo-skeletal joint inflammatory disorders (arthritis needs a fresh impetus, in view of the developments in the assessment of the therapeutic proteins such as interferons, cytokines, interleukins, erythropoietin H, somatostatin, defensins, tumor necrosis factor, monoclonal antibodies, polyclonal antibodies, lectins etc. The new therapeutic strategies like gene therapy and cell based/stem cell therapy augment the efficacy of the various bimolecular proteins and their application towards clinical management of the diseases. The above research areas also imply a shift in the existing paradigm of both the clinical and therapeutic evaluation.

  11. Towards a calculus of biomolecular complexes at equilibrium.

    Science.gov (United States)

    Mjolsness, Eric

    2007-07-01

    An overview is presented of the construction and use of algebraic partition functions to represent the equilibrium statistical mechanics of multimolecular complexes and their action within a larger regulatory network. Unlike many applications of equilibrium statistical mechanics, multimolecular complexes may operate with various subsets of their components present and connected to the others, the rest remaining in solution. Thus they are variable-structure systems. This aspect of their behavior may be accounted for by the use of 'fugacity' variables as a representation within the partition functions. Four principles are proposed by which the combinatorics of molecular complex construction can be reflected in the construction of their partition functions. The corresponding algebraic operations on partition functions are multiplication, addition, function composition and a less commonly used operation called contraction. Each has a natural interpretation in terms of probability distributions on multimolecular structures. Possible generalizations to nonequilibrium statistical mechanics are briefly discussed.

  12. Revisions of the Fish Invasiveness Screening Kit (FISK) for its application in warmer climatic zones, with particular reference to peninsular Florida.

    Science.gov (United States)

    Lawson, Larry L; Hill, Jeffrey E; Vilizzi, Lorenzo; Hardin, Scott; Copp, Gordon H

    2013-08-01

    The initial version (v1) of the Fish Invasiveness Scoring Kit (FISK) was adapted from the Weed Risk Assessment of Pheloung, Williams, and Halloy to assess the potential invasiveness of nonnative freshwater fishes in the United Kingdom. Published applications of FISK v1 have been primarily in temperate-zone countries (Belgium, Belarus, and Japan), so the specificity of this screening tool to that climatic zone was not noted until attempts were made to apply it in peninsular Florida. To remedy this shortcoming, the questions and guidance notes of FISK v1 were reviewed and revised to improve clarity and extend its applicability to broader climatic regions, resulting in changes to 36 of the 49 questions. In addition, upgrades were made to the software architecture of FISK to improve overall computational speed as well as graphical user interface flexibility and friendliness. We demonstrate the process of screening a fish species using FISK v2 in a realistic management scenario by assessing the Barcoo grunter Scortum barcoo (Terapontidae), a species whose management concerns are related to its potential use for aquaponics in Florida. The FISK v2 screening of Barcoo grunter placed the species into the lower range of medium risk (score = 5), suggesting it is a permissible species for use in Florida under current nonnative species regulations. Screening of the Barcoo grunter illustrates the usefulness of FISK v2 as a proactive tool serving to inform risk management decisions, but the low level of confidence associated with the assessment highlighted a dearth of critical information on this species.

  13. Effects of Application of Social Marketing Theory and the Health Belief Model in Promoting Cervical Cancer Screening among Targeted Women in Sisaket Province, Thailand.

    Science.gov (United States)

    Wichachai, Suparp; Songserm, Nopparat; Akakul, Theerawut; Kuasiri, Chanapong

    2016-01-01

    Cervical cancer is a major public health problem in Thailand, being ranked second only to breast cancer. Thai women have been reported to have a low rate of cervical cancer screening (27.7% of the 80% goal of WHO). We therefore aimed to apply the social marketing theory and health belief model in promoting cervical cancer screening in Kanthararom District, Sisaket Province. A total of 92 from 974 targeted women aged 3060 years were randomly divided into two groups. The experimental group underwent application of social marketing theory and a health belief model program promoting cervical cancer screening while the control group received normal services. Two research tools were used: (1) application of social marketing theory and health belief model program and (2) questionnaire used to evaluate perceptions of cervical cancer. Descriptive and inferential statistics including paired sample ttest and independent ttest were used to analyze the data. After the program had been used, the mean score of perception of cervical cancer of experimental group was at a higher level (x=4.09; S.D. =0.30), than in the control group (x=3.82; S.D. =0.20) with statistical significance (presearch demonstrated an appropriate communication process in behavioral modification to prevent cervical cancer. It can be recommended that this program featuring social marketing and the health belief model be used to promote cervical cancer screening in targeted women and it can be promoted as a guideline for other health services, especially in health promotion and disease prevention. PMID:27510000

  14. Revisions of the Fish Invasiveness Screening Kit (FISK) for its application in warmer climatic zones, with particular reference to peninsular Florida.

    Science.gov (United States)

    Lawson, Larry L; Hill, Jeffrey E; Vilizzi, Lorenzo; Hardin, Scott; Copp, Gordon H

    2013-08-01

    The initial version (v1) of the Fish Invasiveness Scoring Kit (FISK) was adapted from the Weed Risk Assessment of Pheloung, Williams, and Halloy to assess the potential invasiveness of nonnative freshwater fishes in the United Kingdom. Published applications of FISK v1 have been primarily in temperate-zone countries (Belgium, Belarus, and Japan), so the specificity of this screening tool to that climatic zone was not noted until attempts were made to apply it in peninsular Florida. To remedy this shortcoming, the questions and guidance notes of FISK v1 were reviewed and revised to improve clarity and extend its applicability to broader climatic regions, resulting in changes to 36 of the 49 questions. In addition, upgrades were made to the software architecture of FISK to improve overall computational speed as well as graphical user interface flexibility and friendliness. We demonstrate the process of screening a fish species using FISK v2 in a realistic management scenario by assessing the Barcoo grunter Scortum barcoo (Terapontidae), a species whose management concerns are related to its potential use for aquaponics in Florida. The FISK v2 screening of Barcoo grunter placed the species into the lower range of medium risk (score = 5), suggesting it is a permissible species for use in Florida under current nonnative species regulations. Screening of the Barcoo grunter illustrates the usefulness of FISK v2 as a proactive tool serving to inform risk management decisions, but the low level of confidence associated with the assessment highlighted a dearth of critical information on this species. PMID:23035930

  15. β2-Adrenoceptor affinity chromatography and its application in the screening of the active compounds from Semen Armeniacae Amarum

    Institute of Scientific and Technical Information of China (English)

    ZHENG XiaoHui; ZHAO XinFeng; YANG Rong; WANG ShiXiang; WEI YinMao; ZHENG JianBin

    2008-01-01

    β2-Adrenoceptor (β2-AR) was purified from the rabbit lung tissue by sepharose-salbutamol affinity chromatographic column. To prepare the β2-AR stationary phase, β2-AR was evenly immobilized on the surface of macro-pore silica with a mild chemical coupling method through covalent bond. The reten-tion properties of β2-AR stationary phase were characterized by four ligands, salbutamol sulfate, noradrenaline bitartrate, adrenaline hydrochloride and propranolol hydrochloride, to establish the β2-AR affinity chromatography. Then, the method was used to screen the active compounds from the total extracts of Semen Armeniacae Amarum. The results showed that β2-AR on the surface of the sta-tionary phase could keep its original bioactivity and selectivity. Amygdalin retained in the chroma-tographic column was proved to be the active compound of the total extracts of Semen Armeniacae Amarum. Compared with the existing chromatographic screening approaches, this method showed a good stability and high selectivity. The active compounds which could interact with β2-AR in traditional Chinese medicine (TCM) could be screened efficiently by this method, providing a new way to screen the active compounds in complicated samples such as TCM.

  16. Formulation and screen printing of water based conductive flake silver pastes onto green ceramic tapes for electronic applications

    International Nuclear Information System (INIS)

    Highlights: ► Formulation of water-based pastes. ► Viscosity, yield stress, elastic and viscous modulus determination. ► Screen printing onto green ceramic tapes. ► Rheology effect on line dimensions and electrical properties. ► Resistivity ∼18–33 nΩ m. Minimum width ∼60 μm after sintering. - Abstract: Environmentally friendly, water-based silver pastes, adapted for screen printing, were formulated with different silver contents (67–75%). These pastes allowed screen printing onto low temperature co-fired ceramic (LTCC) of narrow conductive tracks with a 60 μm line width and a 3 × 10−8 Ω m electrical resistivity. Inks were formulated with a mixture of spherical and flake shape silver particles with 2–4 μm mean diameter. Rheological behaviour of pastes was studied in order to determine its effect on printed lines properties. Prepared inks were then screen printed and sintered under normal atmosphere at 875 °C. As expected, electrical properties depended on silver content. Resistivity values varying from 1.6 × 10−8 to 3.3 × 10−8 Ω m were calculated over 36.3 cm line length. These values are very close to bulk silver resistivity (1.6 × 10−8 Ω m). Compared to previous research and commercial pastes, the newly formulated pastes reached equivalent or even better conductivities with lower silver content (70% by weight).

  17. Raman spectroscopy detects biomolecular changes associated with nanoencapsulated hesperetin treatment in experimental oral carcinogenesis

    Science.gov (United States)

    Gurushankar, K.; Gohulkumar, M.; Kumar, Piyush; Krishna, C. Murali; Krishnakumar, N.

    2016-03-01

    Recently it has been shown that Raman spectroscopy possesses great potential in the investigation of biomolecular changes of tumor tissues with therapeutic drug response in a non-invasive and label-free manner. The present study is designed to investigate the antitumor effect of hespertin-loaded nanoparticles (HETNPs) relative to the efficacy of native hesperetin (HET) in modifying the biomolecular changes during 7,12-dimethyl benz(a)anthracene (DMBA)-induced oral carcinogenesis using a Raman spectroscopic technique. Significant differences in the intensity and shape of the Raman spectra between the control and the experimental tissues at 1800-500 cm-1 were observed. Tumor tissues are characterized by an increase in the relative amount of proteins, nucleic acids, tryptophan and phenylalanine and a decrease in the percentage of lipids when compared to the control tissues. Further, oral administration of HET and its nanoparticulates restored the status of the lipids and significantly decreased the levels of protein and nucleic acid content. Treatment with HETNPs showed a more potent antitumor effect than treatment with native HET, which resulted in an overall reduction in the intensity of several biochemical Raman bands in DMBA-induced oral carcinogenesis being observed. Principal component and linear discriminant analysis (PC-LDA), together with leave-one-out cross validation (LOOCV) on Raman spectra yielded diagnostic sensitivities of 100%, 80%, 91.6% and 65% and specificities of 100%, 65%, 60% and 55% for classification of control versus DMBA, DMBA versus DMBA  +  HET, DMBA versus DMBA  +  HETNPs and DMBA  +  HET versus DMBA  +  HETNPs treated tissue groups, respectively. These results further demonstrate that Raman spectroscopy associated with multivariate statistical algorithms could be a valuable tool for developing a comprehensive understanding of the process of biomolecular changes, and could reveal the signatures of the

  18. Biomolecular Deuteration for Neutron Structural Biology and Dynamics.

    Science.gov (United States)

    Haertlein, Michael; Moulin, Martine; Devos, Juliette M; Laux, Valerie; Dunne, Orla; Forsyth, V Trevor

    2016-01-01

    Neutron scattering studies provide important information in structural biology that is not accessible using other approaches. The uniqueness of the technique, and its complementarity with X-ray scattering, is greatest when full use is made of deuterium labeling. The ability to produce tailor-made deuterium-labeled biological macromolecules allows neutron studies involving solution scattering, crystallography, reflection, and dynamics to be optimized in a manner that has major impact on the scope, quality, and throughput of work in these areas. Deuteration facilities have now been developed at many neutron centres throughout the world; these are having a crucial effect on neutron studies in the life sciences and on biologically related studies in soft matter. This chapter describes methods that have been developed for the efficient production of deuterium-labeled samples for a wide range of neutron scattering applications. Examples are given that illustrate the use of these samples for each of the main techniques. Perspectives for biological deuterium labeling are discussed in relation to developments at current facilities and those that are planned in the future.

  19. Multiresolution persistent homology for excessively large biomolecular datasets

    Science.gov (United States)

    Xia, Kelin; Zhao, Zhixiong; Wei, Guo-Wei

    2015-10-01

    Although persistent homology has emerged as a promising tool for the topological simplification of complex data, it is computationally intractable for large datasets. We introduce multiresolution persistent homology to handle excessively large datasets. We match the resolution with the scale of interest so as to represent large scale datasets with appropriate resolution. We utilize flexibility-rigidity index to access the topological connectivity of the data set and define a rigidity density for the filtration analysis. By appropriately tuning the resolution of the rigidity density, we are able to focus the topological lens on the scale of interest. The proposed multiresolution topological analysis is validated by a hexagonal fractal image which has three distinct scales. We further demonstrate the proposed method for extracting topological fingerprints from DNA molecules. In particular, the topological persistence of a virus capsid with 273 780 atoms is successfully analyzed which would otherwise be inaccessible to the normal point cloud method and unreliable by using coarse-grained multiscale persistent homology. The proposed method has also been successfully applied to the protein domain classification, which is the first time that persistent homology is used for practical protein domain analysis, to our knowledge. The proposed multiresolution topological method has potential applications in arbitrary data sets, such as social networks, biological networks, and graphs.

  20. Multiresolution persistent homology for excessively large biomolecular datasets

    Energy Technology Data Exchange (ETDEWEB)

    Xia, Kelin; Zhao, Zhixiong [Department of Mathematics, Michigan State University, East Lansing, Michigan 48824 (United States); Wei, Guo-Wei, E-mail: wei@math.msu.edu [Department of Mathematics, Michigan State University, East Lansing, Michigan 48824 (United States); Department of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824 (United States); Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (United States)

    2015-10-07

    Although persistent homology has emerged as a promising tool for the topological simplification of complex data, it is computationally intractable for large datasets. We introduce multiresolution persistent homology to handle excessively large datasets. We match the resolution with the scale of interest so as to represent large scale datasets with appropriate resolution. We utilize flexibility-rigidity index to access the topological connectivity of the data set and define a rigidity density for the filtration analysis. By appropriately tuning the resolution of the rigidity density, we are able to focus the topological lens on the scale of interest. The proposed multiresolution topological analysis is validated by a hexagonal fractal image which has three distinct scales. We further demonstrate the proposed method for extracting topological fingerprints from DNA molecules. In particular, the topological persistence of a virus capsid with 273 780 atoms is successfully analyzed which would otherwise be inaccessible to the normal point cloud method and unreliable by using coarse-grained multiscale persistent homology. The proposed method has also been successfully applied to the protein domain classification, which is the first time that persistent homology is used for practical protein domain analysis, to our knowledge. The proposed multiresolution topological method has potential applications in arbitrary data sets, such as social networks, biological networks, and graphs.

  1. Conformational thermodynamics of biomolecular complexes: The histogram-based method

    Science.gov (United States)

    Das, Amit; Sikdar, Samapan; Ghosh, Mahua; Chakrabarti, J.

    2015-09-01

    Conformational changes in biomacromolecules govern majority of biological processes. Complete characterization of conformational contributions to thermodynamics of complexation of biomacromolecules has been challenging. Although, advances in NMR relaxation experiments and several computational studies have revealed important aspects of conformational entropy changes, efficient and large-scale estimations still remain an intriguing facet. Recent histogram-based method (HBM) offers a simple yet rigorous route to estimate both conformational entropy and free energy changes from same set of histograms in an efficient manner. The HBM utilizes the power of histograms which can be generated as accurately as desired from an arbitrarily large sample space from atomistic simulation trajectories. Here we discuss some recent applications of the HBM, using dihedral angles of amino acid residues as conformational variables, which provide good measure of conformational thermodynamics of several protein-peptide complexes, obtained from NMR, metal-ion binding to an important metalloprotein, interfacial changes in protein-protein complex and insight to protein function, coupled with conformational changes. We conclude the paper with a few future directions worth pursuing.

  2. Plucked Human Hair Shafts and Biomolecular Medical Research

    Directory of Open Access Journals (Sweden)

    Kevin Schembri

    2013-01-01

    Full Text Available The hair follicle is a skin integument at the boundary between an organism and its immediate environment. The biological role of the human hair follicle has lost some of its ancestral importance. However, an indepth investigation of this miniorgan reveals hidden complexity with huge research potential. An essential consideration when dealing with human research is the awareness of potential harm and thus the absolute need not to harm—a rule aptly qualified by the Latin term “primum non nocere” (first do no harm. The plucked hair shaft offers such advantages. The use of stem cells found in hair follicles cells is gaining momentum in the field of regenerative medicine. Furthermore, current diagnostic and clinical applications of plucked hair follicles include their use as autologous and/or three-dimensional epidermal equivalents, together with their utilization as surrogate tissue in pharmacokinetic and pharmacodynamics studies. Consequently, the use of noninvasive diagnostic procedures on hair follicle shafts, posing as a surrogate molecular model for internal organs in the individual patient for a spectrum of human disease conditions, can possibly become a reality in the near future.

  3. Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks

    DEFF Research Database (Denmark)

    Soberano de Oliveira, Ana Paula; Patil, Kiran Raosaheb; Nielsen, Jens

    2008-01-01

    Factors, Reporter Proteins and Reporter Complexes, and use this to decipher the logic of regulatory circuits playing a key role in yeast glucose repression and human diabetes. Conclusion: Reporter Features offer the opportunity to identify regulatory hot-spots in bio-molecular interaction networks...... that are significantly affected between or across conditions. Results of the Reporter Feature analysis not only provide a snapshot of the transcriptional regulatory program but also are biologically easy to interpret and provide a powerful way to generate new hypotheses. Our Reporter Features analyses of yeast glucose...

  4. Surface-plasmon-enhanced fluorescence from periodic quantum dot arrays through distance control using biomolecular linkers

    International Nuclear Information System (INIS)

    We have developed a protein-enabled strategy to fabricate quantum dot (QD) nanoarrays where up to a 15-fold increase in surface-plasmon-enhanced fluorescence has been achieved. This approach permits a comprehensive control both laterally (via lithographically defined gold nanoarrays) and vertically (via the QD-metal distance) of the collectively behaving assemblies of QDs and gold nanoarrays by way of biomolecular recognition. Specifically, we demonstrated the spectral tuning of plasmon resonant metal nanoarrays and self-assembly of protein-functionalized QDs in a stepwise fashion with a concomitant incremental increase in separation from the metal surface through biotin-streptavidin spacer units.

  5. The use of gold nanoparticle aggregation for DNA computing and logic-based biomolecular detection

    Energy Technology Data Exchange (ETDEWEB)

    Lee, In-Hee; Yang, Kyung-Ae; Zhang, Byoung-Tak [School of Computer Science and Engineering, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-742 (Korea, Republic of); Lee, Ji-Hoon [Center for Bioinformation Technology, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-742 (Korea, Republic of); Park, Ji-Yoon; Chai, Young Gyu [Division of Molecular and Life Sciences, Hanyang University, 1271 Sa-dong, Sangnok-gu, Ansan, Gyeonggi-do 426-791 (Korea, Republic of); Lee, Jae-Hoon [Fachgebiet Mikrobiologie und Genetik, Institut fuer Biotechnologie, Technische Universitaet Berlin, Gustav-Meyer Allee 25, D-13355 Berlin (Germany)], E-mail: btzhang@bi.snu.ac.kr

    2008-10-01

    The use of DNA molecules as a physical computational material has attracted much interest, especially in the area of DNA computing. DNAs are also useful for logical control and analysis of biological systems if efficient visualization methods are available. Here we present a quick and simple visualization technique that displays the results of the DNA computing process based on a colorimetric change induced by gold nanoparticle aggregation, and we apply it to the logic-based detection of biomolecules. Our results demonstrate its effectiveness in both DNA-based logical computation and logic-based biomolecular detection.

  6. GLYCAM06: a generalizable biomolecular force field. Carbohydrates.

    Science.gov (United States)

    Kirschner, Karl N; Yongye, Austin B; Tschampel, Sarah M; González-Outeiriño, Jorge; Daniels, Charlisa R; Foley, B Lachele; Woods, Robert J

    2008-03-01

    A new derivation of the GLYCAM06 force field, which removes its previous specificity for carbohydrates, and its dependency on the AMBER force field and parameters, is presented. All pertinent force field terms have been explicitly specified and so no default or generic parameters are employed. The new GLYCAM is no longer limited to any particular class of biomolecules, but is extendible to all molecular classes in the spirit of a small-molecule force field. The torsion terms in the present work were all derived from quantum mechanical data from a collection of minimal molecular fragments and related small molecules. For carbohydrates, there is now a single parameter set applicable to both alpha- and beta-anomers and to all monosaccharide ring sizes and conformations. We demonstrate that deriving dihedral parameters by fitting to QM data for internal rotational energy curves for representative small molecules generally leads to correct rotamer populations in molecular dynamics simulations, and that this approach removes the need for phase corrections in the dihedral terms. However, we note that there are cases where this approach is inadequate. Reported here are the basic components of the new force field as well as an illustration of its extension to carbohydrates. In addition to reproducing the gas-phase properties of an array of small test molecules, condensed-phase simulations employing GLYCAM06 are shown to reproduce rotamer populations for key small molecules and representative biopolymer building blocks in explicit water, as well as crystalline lattice properties, such as unit cell dimensions, and vibrational frequencies. PMID:17849372

  7. An optics-based variable-temperature assay system for characterizing thermodynamics of biomolecular reactions on solid support

    Energy Technology Data Exchange (ETDEWEB)

    Fei, Yiyan; Landry, James P.; Zhu, X. D., E-mail: xdzhu@physics.ucdavis.edu [Department of Physics, University of California, One Shields Avenue, Davis, California 95616 (United States); Li, Yanhong; Yu, Hai; Lau, Kam; Huang, Shengshu; Chokhawala, Harshal A.; Chen, Xi [Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616 (United States)

    2013-11-15

    A biological state is equilibrium of multiple concurrent biomolecular reactions. The relative importance of these reactions depends on physiological temperature typically between 10 °C and 50 °C. Experimentally the temperature dependence of binding reaction constants reveals thermodynamics and thus details of these biomolecular processes. We developed a variable-temperature opto-fluidic system for real-time measurement of multiple (400–10 000) biomolecular binding reactions on solid supports from 10 °C to 60 °C within ±0.1 °C. We illustrate the performance of this system with investigation of binding reactions of plant lectins (carbohydrate-binding proteins) with 24 synthetic glycans (i.e., carbohydrates). We found that the lectin-glycan reactions in general can be enthalpy-driven, entropy-driven, or both, and water molecules play critical roles in the thermodynamics of these reactions.

  8. An optics-based variable-temperature assay system for characterizing thermodynamics of biomolecular reactions on solid support.

    Science.gov (United States)

    Fei, Yiyan; Landry, James P; Li, Yanhong; Yu, Hai; Lau, Kam; Huang, Shengshu; Chokhawala, Harshal A; Chen, Xi; Zhu, X D

    2013-11-01

    A biological state is equilibrium of multiple concurrent biomolecular reactions. The relative importance of these reactions depends on physiological temperature typically between 10 °C and 50 °C. Experimentally the temperature dependence of binding reaction constants reveals thermodynamics and thus details of these biomolecular processes. We developed a variable-temperature opto-fluidic system for real-time measurement of multiple (400-10,000) biomolecular binding reactions on solid supports from 10 °C to 60 °C within ±0.1 °C. We illustrate the performance of this system with investigation of binding reactions of plant lectins (carbohydrate-binding proteins) with 24 synthetic glycans (i.e., carbohydrates). We found that the lectin-glycan reactions in general can be enthalpy-driven, entropy-driven, or both, and water molecules play critical roles in the thermodynamics of these reactions.

  9. Biomolecular interactions probed by fluorescence resonance energy transfer

    Science.gov (United States)

    Lange, Daniela Charlotte

    2000-09-01

    This thesis describes how a physical phenomenon, Fluorescence Resonance Energy Transfer (FRET), can be exploited for the study of interactions between biomolecules. The physical basis of this phenomenon is discussed and it is described how some of its characteristics can be exploited in measurement. A recently introduced method, photobleaching FRET microscopy, was implemented and its image analysis refined to suit our biological context. Further, a new technique is proposed, which combines FRET with confocal laser scanning microscopy to optimize resolution and to allow for 3D-studies in living cells. The first part of this thesis presents the application of FRET to the study of oligomerization of G-protein coupled receptors (GPCRs), which was performed at the Fraser Laboratories at McGill University in Montreal. It is demonstrated how FRET microscopy allowed us to circumvent problems of traditional biochemical approaches and provided the first direct evidence for GPCR oligomerization in intact cells. We found that somatostatin receptors (SSTRs) functionally interact by forming oligomers with their own kind, with different SSTR isoforms, and even with distantly related GPCRs, such as dopamine receptors, the latter of which is breaking with the dogma that GPCRs would only pair up with their own kind. The high sensitivity of the FRET technique allowed us to characterize these interactions under more physiological conditions, which lead to the observation that oligomerization is induced by receptor agonist. We further studied the differential effects of agonists and antagonists on receptor oligomerization, leading to a model for the molecular mechanism underlying agonist/antagonist function and receptor activation. The second part was carried out at the Neurobiology Laboratory of the VA Medical Center in Newington, CT. The objective was to further our understanding of Niemann- Pick type C disease, which is characterized by a defect in intracellular cholesterol

  10. The Cervical Cancer Screening Technique of Application and Progression%子宫颈癌筛查方法的应用及研究进展

    Institute of Scientific and Technical Information of China (English)

    张文娟; 东燕; 孙绪兰; 王萍; 曾燕

    2012-01-01

    Cervical cancer is a common gynecologic tumor and it is the second-leading cause of death from cancer in women worldwide. It is critical to construct a sustainable, reasonable and efficient general survey method for the early detection of precancerosis of Cervical Cancer. At present, cervical cancer screening technique includes: (a) cervical cytological screening (papanicolaou smear, TCT and DNA quantification); (b) visual inspection with acetic acid (VIA) and visual inspection with Lugol'S iodine (VH.I) ; (c) vaginoscopy; (d) HPV detection. The article is to summarize the application and progression of technique for cervical cancer screening.%子宫颈癌是妇科常见恶性肿瘤之一,发病率居女性恶性肿瘤第二位.建立可持续、合理、有效的普查方法,早期发现癌前病变是防治宫颈癌的关键.目前宫颈癌筛查方法有宫颈细胞学筛查(巴氏涂片、液基薄层细胞学检测、细胞DNA定量分析技术)、肉眼观察辅以醋酸白和Lugol碘溶液检测法、阴道镜检查、病毒-HPV检测,本文就当前各种筛查方法的应用及研究进展进行概括.

  11. Reliability of LED Display Screen and Other Application%浅谈LED显示和应用产品的可靠性

    Institute of Scientific and Technical Information of China (English)

    李熹霖

    2012-01-01

    In this article the author advises to express the reliability and lifetime of LED display screen and other application in both MTBF of system and luminous degradation of LED.%本文简要讨论LED显示产品的可靠性的含义,提出应以显示屏系统的MTBF和LED光衰两个特征量来描述LED显示和应用产品的可靠性和寿命。厂家应提供各种规格的箱体的MTBF.这是计算系统MTBF的基础。

  12. Chinese Young Researcher Symposia on Pharmacology (Track 2) Establishment and application of an in vitro embryotoxicity screening test

    Institute of Scientific and Technical Information of China (English)

    YanCHANG; Hai-xiaLIN; Qi-bingMEI; Bei-liQIAN

    2005-01-01

    AIM Developmental toxicity testing to current international guidelines involves exposure of pregnant animals, mostly rats and rabbits, and subsequent assessment of toxic effects in their fetuses. Alternative methods have been developed since 1980s. The most complex assays in this area make distinctive and extensive use of isolated postimplantation rodent embryos which are cultured in vitro during the phase of major organogenesis. The objective of this study is to establish an in vitro embryotoxicity test----based on postimplatation 9.5d whole embryo culture (WEC) and 3T3 cell toxicity. The possibilities for their application as embryotoxicity screens have been investigated.

  13. Application of an in vitro-amplification assay as a novel pre-screening test for compounds inhibiting the aggregation of prion protein scrapie

    OpenAIRE

    Matthias Schmitz; Maria Cramm; Franc Llorens; Niccolò Candelise; Dominik Müller-Cramm; Daniela Varges; Schulz-Schaeffer, Walter J.; Saima Zafar; Inga Zerr

    2016-01-01

    In vitro amplification assays, such as real-time quaking-induced conversion (RT-QuIC) are used to detect aggregation activity of misfolded prion protein (PrP) in brain, cerebrospinal fluid (CSF) and urine samples from patients with a prion disease. We believe that the method also has a much broader application spectrum. In the present study, we applied RT-QuIC as a pre-screening test for substances that potentially inhibit the aggregation process of the cellular PrP (PrPC) to proteinase (PK)-...

  14. Reduction of radiation dose and imaging costs in scoliosis radiography. Application of large-screen image intensifier photofluorography

    Energy Technology Data Exchange (ETDEWEB)

    Manninen, H.; Kiekara, O.; Soimakallio, S.; Vainio, J.

    1988-04-01

    Photofluorography using a large-field image intensifier (Siemens Optilux 57) was applied to scoliosis radiography and compared with a full-size rare-earth screen/film technique. When scoliosis radiography (PA-projection) was performed on 25 adolescent patients, the photofluorographs were found to be of comparable diagnostic quality with full-size films. A close correspondence between the imaging techniques was found in the Cobb angle measurements as well as in the grading of rotation with the pedicle method. The use of photofluorography results in a radiation dose reduction of about one-half and considerable savings in direct imaging costs and archive space. In our opinion the method is particularly well-suited for follow-up and screening evaluation of scoliosis, but in tall patients the image field size of 40 x 40 cm restricts its usefulness as initial examination.

  15. A Teach-Discover-Treat Application of ZincPharmer: An Online Interactive Pharmacophore Modeling and Virtual Screening Tool.

    Directory of Open Access Journals (Sweden)

    David Ryan Koes

    Full Text Available The 2012 Teach-Discover-Treat (TDT community-wide experiment provided a unique opportunity to test prospective virtual screening protocols targeting the anti-malarial target dihydroorotate dehydrogenase (DHODH. Facilitated by ZincPharmer, an open access online interactive pharmacophore search of the ZINC database, the experience resulted in the development of a novel classification scheme that successfully predicted the bound structure of a non-triazolopyrimidine inhibitor, as well as an overall hit rate of 27% of tested active compounds from multiple novel chemical scaffolds. The general approach entailed exhaustively building and screening sparse pharmacophore models comprising of a minimum of three features for each bound ligand in all available DHODH co-crystals and iteratively adding features that increased the number of known binders returned by the query. Collectively, the TDT experiment provided a unique opportunity to teach computational methods of drug discovery, develop innovative methodologies and prospectively discover new compounds active against DHODH.

  16. Screening of the effective cellulose-degradable strain and its application in the production of cellulose bioethanol

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Strains from the cellulose-containing environment were collected. Primary screening(by filter-paper Hutchison solid culture medium and sodium carboxymethylcellulose solid culture medium) and reelection(by filter-paper inorganic salt culture medium and sodium carboxymethylcellulose Congo red culture medium) indicated that five strains obtained were best suited for high performance cellulose degradation. Determination of sodium carboxymethylcellulose activity(CMCA) and filter paper activity(FPA) was accomplis...

  17. Identification of ellagic acid as potent inhibitor of protein kinase CK2: a successful example of a virtual screening application.

    Science.gov (United States)

    Cozza, Giorgio; Bonvini, Paolo; Zorzi, Elisa; Poletto, Giorgia; Pagano, Mario A; Sarno, Stefania; Donella-Deana, Arianna; Zagotto, Giuseppe; Rosolen, Angelo; Pinna, Lorenzo A; Meggio, Flavio; Moro, Stefano

    2006-04-20

    Casein kinase 2 (CK2) is a ubiquitous, essential, and highly pleiotropic protein kinase whose abnormally high constitutive activity is suspected to underlie its pathogenic potential in neoplasia and other diseases. Using a virtual screening approach, we have identified the ellagic acid, a naturally occurring tannic acid derivative, as a novel potent CK2 inhibitor. At present, ellagic acid represents the most potent known CK2 inhibitor (K(i) = 20 nM). PMID:16610779

  18. Effect of sintering temperatures and screen printing types on TiO2 layers in DSSC applications

    Science.gov (United States)

    Supriyanto, Agus; Furqoni, Lutfi; Nurosyid, Fahru; Hidayat, Jojo; Suryana, Risa

    2016-03-01

    Dye-Sensitized Solar Cell (DSSC) is a candidate solar cell, which has a big potential in the future due to its eco-friendly material. This research is conducted to study the effect of sintering temperature and the type of screen-printing toward the characteristics of TiO2 layer as a working electrode in DSSC. TiO2 layers were fabricated using a screen-printing method with a mesh size of T-49, T-55, and T-61. TiO2 layers were sintered at temperatures of 600°C and 650°C for 60 min. DSSC structure was composed of TiO2 as semiconductors, ruthenium complex as dyes, and carbon as counter electrodes. The morphology of TiO2 layer was observed by using Nikon E2 Digital Camera Microscopy. The efficiencies of DSSC were calculated from the I-V curves. The highest efficiency is 0.015% at TiO2 layer fabricated with screen type T-61 and at a sintering temperature of 650°C.

  19. 论LED屏在舞蹈编导中的创新应用%On the innovative application of LED screen in the choreography

    Institute of Scientific and Technical Information of China (English)

    刘爽

    2013-01-01

    LED electronic screen as an information display media in technology era, with its incomparable advantages over traditional choreography and stage effect increasingly applied to modern dance choreographer. Firstly, related to the content of LED screen are summarized, followed by analysis of the coordinated application of LED and other elements, finally proposes the problems and its evasion mode of LED screen for choreography, aims to study and analyze the LED screen can be better used in modern dance choreographer, serve for the more perfect interpretation of dance art, and the better reflect of the connotation.%LED电子屏幕作为高科技时代的一种信息显示媒体,正以其传统舞美无法比拟的优势和舞台效果越来越多地应用到现代舞蹈的编导之中。本文首先对LED屏相关内容进行概述,其次分析了LED与其他元素的协调应用,最后提出LED屏应用于舞蹈编导中存在的问题及其规避方式,旨在通过研究和分析使LED屏能够更好地应用于现代舞蹈编导,服务于舞蹈艺术的更完美诠释和舞蹈内涵的更好体现。

  20. Biomolecular solid state NMR with magic-angle spinning at 25 K

    Science.gov (United States)

    Thurber, Kent R.; Tycko, Robert

    2009-01-01

    A magic-angle spinning (MAS) probe has been constructed which allows the sample to be cooled with helium, while the MAS bearing and drive gases are nitrogen. The sample can be cooled to 25 K using roughly 3 liters/hour of liquid helium, while the 4 mm diameter rotor spins at 6.7 kHz with good stability (±5 Hz) for many hours. Proton decoupling fields up to at least 130 kHz can be applied. This helium-cooled MAS probe enables a variety of one-dimensional and two-dimensional NMR experiments on biomolecular solids and other materials at low temperatures, with signal-to-noise proportional to 1/T. We show examples of low-temperature 13C NMR data for two biomolecular samples, namely the peptide Aβ14–23 in the form of amyloid fibrils and the protein HP35 in frozen glycerol/water solution. Issues related to temperature calibration, spin-lattice relaxation at low temperatures, paramagnetic doping of frozen solutions, and 13C MAS NMR linewidths are discussed. PMID:18922715

  1. Neutral-particle emission in collisions of electrons with biomolecular ions in an electrostatic storage ring

    International Nuclear Information System (INIS)

    Electron-biomolecular ion collisions were studied using an electrostatic storage ring with a merging electron beam device. Biomolecular ions produced by an electrospray ion source and accelerated to 20 keV/charge were injected into the ring after being mass-analyzed. The circulating ion beam was then merged with an electron beam. Neutral reaction products in collisions of electrons with ions were detected by a micro-channel plate outside of the ring. Electron-ion collisions were studied for multiply-deprotonated oligonucleotide and peptide anions as well as singly protonated oligonucleotide and peptide cations. For peptide cations, neutrals were resonantly emitted at an electron energy of around 6.5 eV, which was almost independent of the ion masses. This is deduced to come from electron-ion recombination, resulting in the cleavage of a peptide bond. For DNA oligonucleotide cations, resonant neutral particle emission was also observed. In electron and DNA anion collisions, neutrals started to increase from definite threshold energies, where the threshold energies increased in proportion to the ion charge. The same was found for peptide anions. The origin of this phenomenon is discussed

  2. The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes.

    Science.gov (United States)

    van Zundert, G C P; Rodrigues, J P G L M; Trellet, M; Schmitz, C; Kastritis, P L; Karaca, E; Melquiond, A S J; van Dijk, M; de Vries, S J; Bonvin, A M J J

    2016-02-22

    The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modeling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process. This has been at the core of our information-driven docking approach HADDOCK. We present here the updated version 2.2 of the HADDOCK portal, which offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in a user-friendly interface. With well over 6000 registered users and 108,000 jobs served, an increasing fraction of which on grid resources, we hope that this timely upgrade will help the community to solve important biological questions and further advance the field. The HADDOCK2.2 Web server is freely accessible to non-profit users at http://haddock.science.uu.nl/services/HADDOCK2.2.

  3. Submicrometer Hall sensors for detection of magnetic nanoparticles in biomolecular sensing

    Science.gov (United States)

    Mihajlovic, Goran; Xiong, P.; von Molnar, S.; Ohtani, K.; Ohno, H.; Field, M.; Sullivan, G. J.

    2006-03-01

    Significant progress has been made in the recent years in synthesis and biomolecular functionalization of magnetic nanoparticles. These magnetic bio-nanolabels can be utilized as protein or gene markers in biomolecular sensing assays, in contrast to the much larger micron sized magnetic beads that are usually limited to cell labeling. However, the low magnetic moments of individual nanoparticles (10^4-10^5 μB) render their sensitive detection still a challenging task. In order to address this issue we are developing miniaturized Hall sensors from InAs/AlSb quantum well semiconductor heterostructures with active Hall cross areas down to 300 nm x 300 nm. Our preliminary characterization measurements performed at room temperature show functional devices with magnetic field resolution < 100 μT/√Hz at frequencies above 100 Hz, yielding a moment sensitivity ˜ 10^5 μB. In addition to the progress in improving the moment sensitivity of the submicrometer Hall detectors, we will also present efforts in device integration with on-chip microcoils for the generation of local magnetic excitation fields. Results on nanoparticle detection will also be presented.

  4. The detection of specific biomolecular interactions with micro-Hall magnetic sensors

    Science.gov (United States)

    Manandhar, Pradeep; Chen, Kan-Sheng; Aledealat, Khaled; Mihajlović, Goran; Yun, C. Steven; Field, Mark; Sullivan, Gerard J.; Strouse, Geoffrey F.; Bryant Chase, P.; von Molnár, Stephan; Xiong, Peng

    2009-09-01

    The detection of reagent-free specific biomolecular interactions through sensing of nanoscopic magnetic labels provides one of the most promising routes to biosensing with solid-state devices. In particular, Hall sensors based on semiconductor heterostructures have shown exceptional magnetic moment sensitivity over a large dynamic field range suitable for magnetic biosensing using superparamagnetic labels. Here we demonstrate the capability of such micro-Hall sensors to detect specific molecular binding using biotin-streptavidin as a model system. We apply dip-pen nanolithography to selectively biotinylate the active areas of InAs micro-Hall devices with nanoscale precision. Specific binding of complementarily functionalized streptavidin-coated superparamagnetic beads to the Hall crosses occurs via molecular recognition, and magnetic detection of the assembled beads is achieved at room temperature using phase sensitive micro-Hall magnetometry. The experiment constitutes the first unambiguous demonstration of magnetic detection of specific biomolecular interactions with semiconductor micro-Hall sensors, and the selective molecular functionalization and resulting localized bead assembly demonstrate the possibility of multiplexed sensing of multiple target molecules using a single device with an array of micro-Hall sensors.

  5. Lung Cancer Screening.

    Science.gov (United States)

    Wu, Geena X; Raz, Dan J

    2016-01-01

    Lung cancer is the leading cause of cancer mortality in the United States and worldwide. Since lung cancer outcomes are dependent on stage at diagnosis with early disease resulting in longer survival, the goal of screening is to capture lung cancer in its early stages when it can be treated and cured. Multiple studies have evaluated the use of chest X-ray (CXR) with or without sputum cytologic examination for lung cancer screening, but none has demonstrated a mortality benefit. In contrast, the multicenter National Lung Screening Trial (NLST) from the United States found a 20 % reduction in lung cancer mortality following three consecutive screenings with low-dose computed tomography (LDCT) in high-risk current and former smokers. Data from European trials are not yet available. In addition to a mortality benefit, lung cancer screening with LDCT also offers a unique opportunity to promote smoking cessation and abstinence and may lead to the diagnoses of treatable chronic diseases, thus decreasing the overall disease burden. The risks of lung cancer screening include overdiagnosis, radiation exposure, and false-positive results leading to unnecessary testing and possible patient anxiety and distress. However, the reduction in lung cancer mortality is a benefit that outweighs the risks and major health organizations currently recommend lung cancer screening using age, smoking history, and quit time criteria derived from the NLST. Although more research is needed to clearly define and understand the application and utility of lung cancer screening in the general population, current data support that lung cancer screening is effective and should be offered to eligible beneficiaries. PMID:27535387

  6. Thermo-responsive cell culture carriers based on poly(vinyl methyl ether)—the effect of biomolecular ligands to balance cell adhesion and stimulated detachment

    Science.gov (United States)

    Teichmann, Juliane; Nitschke, Mirko; Pette, Dagmar; Valtink, Monika; Gramm, Stefan; Härtel, Frauke V.; Noll, Thomas; Funk, Richard H. W.; Engelmann, Katrin; Werner, Carsten

    2015-08-01

    Two established material systems for thermally stimulated detachment of adherent cells were combined in a cross-linked polymer blend to merge favorable properties. Through this approach poly(N-isopropylacrylamide) (PNiPAAm) with its superior switching characteristic was paired with a poly(vinyl methyl ether)-based composition that allows adjusting physico-chemical and biomolecular properties in a wide range. Beyond pure PNiPAAm, the proposed thermo-responsive coating provides thickness, stiffness and swelling behavior, as well as an apposite density of reactive sites for biomolecular functionalization, as effective tuning parameters to meet specific requirements of a particular cell type regarding initial adhesion and ease of detachment. To illustrate the strength of this approach, the novel cell culture carrier was applied to generate transplantable sheets of human corneal endothelial cells (HCEC). Sheets were grown, detached, and transferred onto planar targets. Cell morphology, viability and functionality were analyzed by immunocytochemistry and determination of transepithelial electrical resistance (TEER) before and after sheet detachment and transfer. HCEC layers showed regular morphology with appropriate TEER. Cells were positive for function-associated marker proteins ZO-1, Na+/K+-ATPase, and paxillin, and extracellular matrix proteins fibronectin, laminin and collagen type IV before and after transfer. Sheet detachment and transfer did not impair cell viability. Subsequently, a potential application in ophthalmology was demonstrated by transplantation onto de-endothelialized porcine corneas in vitro. The novel thermo-responsive cell culture carrier facilitates the generation and transfer of functional HCEC sheets. This paves the way to generate tissue engineered human corneal endothelium as an alternative transplant source for endothelial keratoplasty.

  7. Screening for Panic Disorder

    Science.gov (United States)

    ... Conference & Education Membership Journal & Multimedia Resources Awards Consumers Screening for Panic Disorder Main navigation FAQs Screen Yourself Screening for Depression Screening for Generalized Anxiety Disorder (GAD) ...

  8. Application of Two Kinds of Coal Classification Screening in Coal Preparation Plant%浅析两种原煤分级筛在洗煤厂的应用

    Institute of Scientific and Technical Information of China (English)

    梁学朋

    2015-01-01

    Combined with the application situation of Bohou screening and sine powerful screening in Xingtai Mine Coal Preparation Plant, this paper mainly conducted comparative analysis of their different characteristics, summed up that compared with the Bohou screening, the sine powerful screening can improve the screening rate, increase the broken raw coal processing capacity, and also can improve the handling capacity.%本文主要针对博后筛和正弦强力筛的不同特点,结合两种分级筛在邢台矿洗煤厂的使用情况,进行对比分析,总结出相对于博后筛,强力正弦筛可以提高透筛率,提高筛分破碎的原煤处理量,同时还能提高处理能力。

  9. Hypertension screening

    Science.gov (United States)

    Foulke, J. M.

    1975-01-01

    An attempt was made to measure the response to an announcement of hypertension screening at the Goddard Space Center, to compare the results to those of previous statistics. Education and patient awareness of the problem were stressed.

  10. Airport Screening

    Science.gov (United States)

    ... ionizing radiation for security screening individuals [online]. Health Physics Society Position Statement. 2009. Available at http: / / hps. org/ documents/ securityscreening_ ps017- 1. pdf. Accessed 7 January 2011. Interagency Steering Committee on ...

  11. From the application of antibiotics to antibiotic residues in liquid manures and digestates: A screening study in one European center of conventional pig husbandry.

    Science.gov (United States)

    Widyasari-Mehta, Arum; Hartung, Susen; Kreuzig, Robert

    2016-07-15

    In conventional pig husbandry, antibiotics are frequently applied. Together with excreta, antibiotic residues enter liquid manures finally used as organic soil fertilizers or input materials for biogas plants. Therefore, this first screening study was performed to survey the application patterns of antibiotics from fall 2011 until spring 2013. Manures and digestates were then analyzed for selected antibiotic residues from spring 2012 to 2013. The data analysis of veterinary drug application documents revealed the use of 34 different antibiotics belonging to 11 substance classes at 21 farms under study. Antibiotics, particularly tetracyclines, frequently administered to larger pig groups were detected in manure samples up to higher mg kg(-1) dry weight (DW) concentrations. Antibiotic residues in digestates, furthermore, show that a full removal capacity cannot be guaranteed through the anaerobic digestion process in biogas plants. PMID:27088209

  12. Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studies

    Directory of Open Access Journals (Sweden)

    Schalkwyk Leonard C

    2007-07-01

    Full Text Available Abstract Background Genetic influences underpinning complex traits are thought to involve multiple quantitative trait loci (QTLs of small effect size. Detection of such QTL associations requires systematic screening of large numbers of DNA markers within large sample populations. Using pooled DNA on SNP microarrays to screen for allelic frequency differences between groups such as cases and controls (called SNP Microarray and Pooling, or SNP-MaP has been validated as an efficient solution on both 10 k and 100 k platforms. We demonstrate that this approach can be effectively applied to the truly genomewide Affymetrix GeneChip® Mapping 500 K Array. Results In comparisons between five independent DNA pools (N ~200 per pool on separate Affymetrix GeneChip® Mapping 500 K Array sets, we show that, for SNPs with minor allele frequencies > 0.05, the reliability of the rank order of estimated allele frequencies, assessed as the average correlation between allele frequency estimates across the DNA pools, was 0.948 (average mean difference across the five pools = 0.069. Similarly, validity of the SNP-MaP approach was demonstrated by a rank-order correlation of 0.937 (average mean difference = 0.095 between the average DNA pool allele frequency estimates and the allele frequencies of an independent (CEPH sample of 60 unrelated individually genotyped subjects. Conclusion We conclude that SNP-MaP can be extended for use on the Affymetrix GeneChip® Mapping 500 K Array, providing a cost-effective, reliable and valid initial screen of 500 K SNP microarrays in genomewide association scans.

  13. An unbiased method to build benchmarking sets for ligand-based virtual screening and its application to GPCRs.

    Science.gov (United States)

    Xia, Jie; Jin, Hongwei; Liu, Zhenming; Zhang, Liangren; Wang, Xiang Simon

    2014-05-27

    Benchmarking data sets have become common in recent years for the purpose of virtual screening, though the main focus had been placed on the structure-based virtual screening (SBVS) approaches. Due to the lack of crystal structures, there is great need for unbiased benchmarking sets to evaluate various ligand-based virtual screening (LBVS) methods for important drug targets such as G protein-coupled receptors (GPCRs). To date these ready-to-apply data sets for LBVS are fairly limited, and the direct usage of benchmarking sets designed for SBVS could bring the biases to the evaluation of LBVS. Herein, we propose an unbiased method to build benchmarking sets for LBVS and validate it on a multitude of GPCRs targets. To be more specific, our methods can (1) ensure chemical diversity of ligands, (2) maintain the physicochemical similarity between ligands and decoys, (3) make the decoys dissimilar in chemical topology to all ligands to avoid false negatives, and (4) maximize spatial random distribution of ligands and decoys. We evaluated the quality of our Unbiased Ligand Set (ULS) and Unbiased Decoy Set (UDS) using three common LBVS approaches, with Leave-One-Out (LOO) Cross-Validation (CV) and a metric of average AUC of the ROC curves. Our method has greatly reduced the "artificial enrichment" and "analogue bias" of a published GPCRs benchmarking set, i.e., GPCR Ligand Library (GLL)/GPCR Decoy Database (GDD). In addition, we addressed an important issue about the ratio of decoys per ligand and found that for a range of 30 to 100 it does not affect the quality of the benchmarking set, so we kept the original ratio of 39 from the GLL/GDD.

  14. A Bayesian Approach to Calibrating High-Throughput Virtual Screening Results and Application to Organic Photovoltaic Materials

    CERN Document Server

    Pyzer-Knapp, Edward O; Aspuru-Guzik, Alan

    2015-01-01

    A novel approach for calibrating quantum-chemical properties determined as part of a high-throughput virtual screen to experimental analogs is presented. Information on the molecular graph is extracted through the use of extended connectivity fingerprints, and exploited using a Gaussian process to calibrate both electronic properties such as frontier orbital energies, and optical gaps and device properties such as short circuit current density, open circuit voltage and power conversion efficiency. The Bayesian nature of this process affords a value for uncertainty in addition to each calibrated value. This allows the researcher to gain intuition about the model as well as the ability to respect its bounds.

  15. Screening of the effective cellulose-degradable strain and its application in the production of cellulose bioethanol

    Institute of Scientific and Technical Information of China (English)

    Peng-fei Gao; Dai-di Fan; Pei Ma; Yan-e Luo; Xiao-xuan Ma; Chen-hui Zhu; Jun-feng Hui

    2009-01-01

    Strains from the cellulose-containing environment were collected. Primary screening(by filter-paper Hutchison solid culture medium and sodium carboxymethylcellulose solid culture medium) and reelection(by filter-paper inorganic salt culture medium and sodium carboxymethylcellulosc Congo red coltnre medium) indicated that five strains obtained were best suited for high performance cellulose degradation. Determination of sodium carboxymethylcellulose activity(CMCA) and filter paper activity(FPA) was accomplished for each of the five. The strongest of the five in CMCA and FPA was applied to the production of cellulose bioethanol by separate hydrolysis and fermentation(SHF) and simultaneous saccharification and fermentation(SSF) respectively.

  16. Application of docking and QM/MM-GBSA rescoring to screen for novel Myt1 kinase inhibitors.

    Science.gov (United States)

    Wichapong, Kanin; Rohe, Alexander; Platzer, Charlott; Slynko, Inna; Erdmann, Frank; Schmidt, Matthias; Sippl, Wolfgang

    2014-03-24

    Identification of compounds that can bind to a target protein with high affinity is a nontrivial task in structure-based drug design. Several approaches ranging from simple scoring methods to more computationally demanding methods are usually applied for this purpose. In the current work, we used ligand docking in combination with QM/MM-GBSA, MM-GBSA, and MM-PBSA rescoring to discriminate between active and inactive Myt1 kinase inhibitors. Results show that QM/MM-GBSA rescoring performs better than normal docking scores or MM-GBSA rescoring in classifying active and inactive inhibitors. We also applied QM/MM-GBSA rescoring to estimate the binding affinities of compounds from different virtual screening runs. To prove our approach and to confirm its predictive power, a few compounds which were predicted to be active were purchased and experimentally tested. Among the five selected compounds, three showed significant inhibition of recombinant Myt1. PD-173952, which yielded a favorable QM/MM-GBSA binding free energy, showed a K(i) value of 8.1 nM. In addition, two compounds, PD-180970 and saracatinib, showed inhibition at the low micromolar level. Thus, the developed protocol might be useful for further virtual screening experiments to better discriminate between active and inactive compounds and to further optimize the identified hits. PMID:24490903

  17. HCC screening; HCC-Screening

    Energy Technology Data Exchange (ETDEWEB)

    Albrecht, T. [Charite-Unversitaetsmedizin,Freie Universitaet und Humboldt-Universitaet zu Berlin, Klinik und Hochschulambulanz fuer Radiologie und Nuklearmedizin,Campus Benjamin Franklin, Berlin (Germany)

    2008-01-15

    Hepatocellular carcinoma (HCC) is one of the most frequently diagnosed tumour diseases throughout the world. In the vast majority of cases those affected are high-risk patients with chronic viral hepatitis and/or liver cirrhosis, which means there is a clearly identifiable target group for HCC screening. With resection, transplantation, and interventional procedures for local ablation, following early diagnosis curative treatment options are available with which 5-year survival rates of over 60% can be reached. Such early diagnosis is a reality only in a minority of patients, however, and in the majority of cases the disease is already in an advanced stage at diagnosis. One of the objects of HCC screening is diagnosis in an early stage when curative treatment is still possible. Precisely this is achieved by screening, so that the proportion of patients treated with curative intent is decisively higher. There is not yet any clear evidence as to whether this leads to a lowering of the mortality of HCC. As lower mortality is the decisive indicator of success for a screening programme the benefit of HCC screening has so far been neither documented nor refuted. Nonetheless, in large regions of the world it is the practice for high-risk patients to undergo HCC screening in the form of twice-yearly ultrasound examination and determination of AFP. (orig.) [German] Das hepatozellulaere Karzinom (HCC) ist eine der weltweit haeufigsten Tumorerkrankungen. Es tritt in der grossen Mehrzahl der Faelle bei Hochrisikopatienten mit chronischer Virushepatitis bzw. Leberzirrhose auf, woraus sich eine klar identifizierbare Zielgruppe fuer das HCC-Screening ergibt. Mit der Resektion, der Transplantation und interventionellen lokal ablativen Verfahren stehen bei rechtzeitiger Diagnosestellung kurative Therapieoptionen zur Verfuegung, die 5-Jahres-Ueberlebensraten von >60% erreichen. Diese rechtzeitige Diagnosestellung erfolgt jedoch nur bei einer Minderzahl der Patienten, waehrend die

  18. Using Nature's "Tricks" To Rationally Tune the Binding Properties of Biomolecular Receptors.

    Science.gov (United States)

    Ricci, Francesco; Vallée-Bélisle, Alexis; Simon, Anna J; Porchetta, Alessandro; Plaxco, Kevin W

    2016-09-20

    The biosensor community has long focused on achieving the lowest possible detection limits, with specificity (the ability to differentiate between closely similar target molecules) and sensitivity (the ability to differentiate between closely similar target concentrations) largely being relegated to secondary considerations and solved by the inclusion of cumbersome washing and dilution steps or via careful control experimental conditions. Nature, in contrast, cannot afford the luxury of washing and dilution steps, nor can she arbitrarily change the conditions (temperature, pH, ionic strength) under which binding occurs in the homeostatically maintained environment within the cell. This forces evolution to focus at least as much effort on achieving optimal sensitivity and specificity as on achieving low detection limits, leading to the "invention" of a number of mechanisms, such as allostery and cooperativity, by which the useful dynamic range of receptors can be tuned, extended, narrowed, or otherwise optimized by design, rather than by sample manipulation. As the use of biomolecular receptors in artificial technologies matures (i.e., moves away from multistep, laboratory-bound processes and toward, for example, systems supporting continuous in vivo measurement) and these technologies begin to mimic the reagentless single-step convenience of naturally occurring chemoperception systems, the ability to artificially design receptors of enhanced sensitivity and specificity will likely also grow in importance. Thus motivated, we have begun to explore the adaptation of nature's solutions to these problems to the biomolecular receptors often employed in artificial biotechnologies. Using the population-shift mechanism, for example, we have generated nested sets of receptors and allosteric inhibitors that greatly expanded the normally limited (less than 100-fold) useful dynamic range of unmodified molecular and aptamer beacons, enabling the single-step (e.g., dilution

  19. A method for 3D electron density imaging using single scattered x-rays with application to mammographic screening

    Science.gov (United States)

    Van Uytven, Eric; Pistorius, Stephen; Gordon, Richard

    2008-10-01

    Screening mammography is the current standard in detecting breast cancer. However, its fundamental disadvantage is that it projects a 3D object into a 2D image. Small lesions are difficult to detect when superimposed over layers of normal, heterogeneous tissue. In this work, we examine the potential of single scattered photon electron density imaging in a mammographic environment. Simulating a low-energy (electron density images from a single projection. We have tested the algorithm by imaging parts of a simulated mammographic accreditation phantom containing lesions of various sizes. The results indicate that the group of imaged lesions differ significantly from background breast tissue (p electron density imaging may be a useful diagnostic test for the presence of breast cancer.

  20. Clinical application of low-dose CT combined with computer-aided detection in lung cancer screening

    International Nuclear Information System (INIS)

    Objective: To investigate the clinical value of chest low-dose CT (LDCT) combined with computer-aided detection (CAD) system for lung cancer screening in high risk population. Methods: Two hundred and nineteen healthy candidates underwent 64-slice LDCT scan. All images were reviewed in consensus by two radiologists with 15 years of thoracic CT diagnosis experience. Then the image data were analyzed with CAD alone. Finally images were reviewed by two radiologists with 5 years of CT diagnosis experience with and without CT Viewer software. The sensitivity, false positive rate of CAD for pulmonary nodule detection were calculated. SPSS 11.5 software and Chi-square test were used for the statistics. Results: Of 219 candidates ,104(47.5% ) were detected with lung nodules. There were 366 true nodules confirmed by the senior radiologists. The CAD system detected 271 (74.0%) true nodules and 424 false-positive nodules. The false-positive rate was 1.94/per case. The two junior radiologists indentifid 292 (79.8%), 286(78.1%) nodules without CAD and 336 (91.8%), 333 (91.0%) nodules with CAD respectively. There were significant differences for radiologists in indentifying nodules with or without CAD system (P<0.01). Conclusions: CAD is more sensitive than radiologists for indentifying the nodules in the central area or in the hilar region of the lung. While radiologists are more sensitive for the peripheral and sub-pleural nodules,or ground glass opacity nodules, or nodules smaller than 4 mm. CAD can not be used alone. The detection rate can be improved with the combination of radiologist and CAD in LDCT screen. (authors)

  1. Label-free cardiac contractility monitoring for drug screening applications based on compact high-speed lens-free imaging

    Science.gov (United States)

    Pauwelyn, Thomas; Reumers, Veerle; Vanmeerbeeck, Geert; Stahl, Richard; Janssens, Stefan; Lagae, Liesbet; Braeken, Dries; Lambrechts, Andy

    2015-03-01

    Cardiotoxicity is the major cause of drug withdrawal from the market, despite rigorous toxicity testing during the drug development process. Existing safety screening techniques, some of which are based on simplified cellular assays, others on electrical (impedance) or optical (fluorescent microscopy) measurements, are either too limited in throughput or offer too poor predictability of toxicity to be applied on large numbers of compounds in the early stage of drug development. We present a compact optical system for direct (label-free) monitoring of fast cellular movements that enable low cost and high throughput drug screening. Our system is based on a high-speed lens-free in-line holographic microscope. When compared to a conventional microscope, the system can combine adequate imaging resolution (5.5 μm pixel pitch) with a large field-of-view (63.4 mm2) and high speed (170 fps) to capture physical cell motion in real-time. This combination enables registration of cardiac contractility parameters such as cell contraction frequency, total duration, and rate and duration of both contraction and relaxation. The system also quantifies conduction velocity, which is challenging in existing techniques. Additionally, to complement the imaging hardware we have developed image processing software that extracts all the contractility parameters directly from the raw interference images. The system was tested with varying concentration of the drug verapamil and at 100 nM, showed a decrease in: contraction frequency (-23.3% +/- 13%), total duration (-21% +/- 5%), contraction duration (-19% +/- 6%) and relaxation duration (-21% +/- 8%). Moreover, contraction displacement ceased at higher concentrations.

  2. Effect of temperature and magnetic field on the photocurrent response of biomolecular bulk-hetero junction

    Science.gov (United States)

    Tajima, Hiroyuki; Sekiguchi, Yusuke; Matsuda, Masaki

    2012-02-01

    The photocurrent responses were investigated for the biomolecular bulk-hetero junction of chlorophyll α (Chl-α) and 1-(3-methoxycarbonyl)-propyl-1-phenyl-1-phenyl-(6,6)C61 (PCBM) in the temperature range between 300 K and 1.5 K under the magnetic field up to 8 T. The chopped-light photocurrent decreases on lowering the temperature. Below 10 K, photocurrent decrease was observed under the applied magnetic field. Decay of the photocurrent observed at 10 K was ascribed to the formation of the charged trap under light irradiation. The magnetic field effect (MFE) observed in this device was found to be very similar to that observed in P3HT:PCBM bulk-hetero junction at low temperatures.

  3. Biomolecular papain thin films grown by matrix assisted and conventional pulsed laser deposition: A comparative study

    Science.gov (United States)

    György, E.; Pérez del Pino, A.; Sauthier, G.; Figueras, A.

    2009-12-01

    Biomolecular papain thin films were grown both by matrix assisted pulsed laser evaporation (MAPLE) and conventional pulsed laser deposition (PLD) techniques with the aid of an UV KrF∗ (λ =248 nm, τFWHM≅20 ns) excimer laser source. For the MAPLE experiments the targets submitted to laser radiation consisted on frozen composites obtained by dissolving the biomaterial powder in distilled water at 10 wt % concentration. Conventional pressed biomaterial powder targets were used in the PLD experiments. The surface morphology of the obtained thin films was studied by atomic force microscopy and their structure and composition were investigated by Fourier transform infrared spectroscopy. The possible physical mechanisms implied in the ablation processes of the two techniques, under comparable experimental conditions were identified. The results showed that the growth mode, surface morphology as well as structure of the deposited biomaterial thin films are determined both by the incident laser fluence value as well as target preparation procedure.

  4. A Review of Salam Phase Transition in Protein Amino Acids Implication for Biomolecular Homochirality

    CERN Document Server

    Bai, F; Bai, Fan; Wang, Wenqing

    2002-01-01

    The origin of chirality, closely related to the evolution of life on the earth, has long been debated. In 1991, Abdus Salam suggested a novel approach to achieve biomolecular homochirality by a phase transition. In his subsequent publication, he predicted that this phase transition could eventually change D-amino acids to L-amino acids as C -H bond would break and H atom became a superconductive atom. Since many experiments denied the configuration change in amino acids, Salam hypothesis aroused suspicion. This paper is aimed to provide direct experimental evidence of a phase transition in alanine, valine single crystals but deny the configuration change of D- to L- enantiomers. New views on Salam phase transition are presented to revalidate its great importance in the origin of homochirality.

  5. Settlement specifics: Effective induction of abalone settlement and metamorphosis corresponds to biomolecular composition of natural cues.

    Science.gov (United States)

    Williams, Elizabeth A; Cummins, Scott; Degnan, Sandie M

    2009-07-01

    Chemical signaling plays a major role in shaping life history processes that drive ecology and evolution in marine systems, notably including habitat selection by marine invertebrate larvae that must settle out of the plankton onto the benthos.1 For larvae, the identification of appropriate habitats in which to settle and undergo metamorphosis to the adult form relies heavily on the recognition of cues indicative of a favorable environment. By documenting settlement responses of larvae of the tropical abalone, Haliotis asinina, to a range of coralline algae species, we recently highlighted the species-specific nature of this interaction.2 Here, we demonstrate that this specificity is likely driven by chemical, rather than physical, properties of the algae. Our initial characterization of the surface cell biomarkers from three different algal species shows that inductive cue biomolecular composition correlates with variations in larval settlement response.

  6. Biochemical Filter with Sigmoidal Response: Increasing the Complexity of Biomolecular Logic

    CERN Document Server

    Privman, Vladimir; Arugula, Mary A; Melnikov, Dmitriy; Bocharova, Vera; Katz, Evgeny

    2010-01-01

    The first realization of a designed, rather than natural, biochemical filter process is reported and analyzed as a promising network component for increasing the complexity of biomolecular logic systems. Key challenge in biochemical logic research has been achieving scalability for complex network designs. Various logic gates have been realized, but a "toolbox" of analog elements for interconnectivity and signal processing has remained elusive. Filters are important as network elements that allow control of noise in signal transmission and conversion. We report a versatile biochemical filtering mechanism designed to have sigmoidal response in combination with signal-conversion process. Horseradish peroxidase-catalyzed oxidation of chromogenic electron donor by hydrogen peroxide, was altered by adding ascorbate, allowing to selectively suppress the output signal, modifying the response from convex to sigmoidal. A kinetic model was developed for evaluation of the quality of filtering. The results offer improved...

  7. Screening for Specific Phobias

    Science.gov (United States)

    ... Screening for Posttraumatic Stress Disorder (PTSD) Screening for Social Anxiety Disorder Screening for Specific Phobias Screening for an Anxiety Disorder: Children Screening for an Anxiety Disorder: Family Member Self- ...

  8. Carotid Artery Screening

    Science.gov (United States)

    ... Resources Professions Site Index A-Z Carotid Artery Screening What is carotid artery screening? Who should consider ... about carotid artery screening? What is carotid artery screening? Screening examinations are tests performed to find disease ...

  9. Preconception Carrier Screening

    Science.gov (United States)

    ... Events Advocacy For Patients About ACOG Preconception Carrier Screening Home For Patients Search FAQs Preconception Carrier Screening ... Screening FAQ179, August 2012 PDF Format Preconception Carrier Screening Pregnancy What is preconception carrier screening? What is ...

  10. Biomolecular Characterization of Diazotrophs Isolated from the Tropical Soil in Malaysia

    Directory of Open Access Journals (Sweden)

    Zulkifli H Shamsuddin

    2013-08-01

    Full Text Available This study was conducted to evaluate selected biomolecular characteristics of rice root-associated diazotrophs isolated from the Tanjong Karang rice irrigation project area of Malaysia. Soil and rice plant samples were collected from seven soil series belonging to order Inceptisol (USDA soil taxonomy. A total of 38 diazotrophs were isolated using a nitrogen-free medium. The biochemical properties of the isolated bacteria, such as nitrogenase activity, indoleacetic acid (IAA production and sugar utilization, were measured. According to a cluster analysis of Jaccard’s similarity coefficients, the genetic similarities among the isolated diazotrophs ranged from 10% to 100%. A dendogram constructed using the unweighted pair-group method with arithmetic mean (UPGMA showed that the isolated diazotrophs clustered into 12 groups. The genomic DNA rep-PCR data were subjected to a principal component analysis, and the first four principal components (PC accounted for 52.46% of the total variation among the 38 diazotrophs. The 10 diazotrophs that tested highly positive in the acetylene reduction assay (ARA were identified as Bacillus spp. (9 diazotrophs and Burkholderia sp. (Sb16 using the partial 16S rRNA gene sequence analysis. In the analysis of the biochemical characteristics, three principal components were accounted for approximately 85% of the total variation among the identified diazotrophs. The examination of root colonization using scanning electron microscopy (SEM and transmission electron microscopy (TEM proved that two of the isolated diazotrophs (Sb16 and Sb26 were able to colonize the surface and interior of rice roots and fixed 22%–24% of the total tissue nitrogen from the atmosphere. In general, the tropical soils (Inceptisols of the Tanjong Karang rice irrigation project area in Malaysia harbor a diverse group of diazotrophs that exhibit a large variation of biomolecular characteristics.

  11. Versatile single-molecule multi-color excitation and detection fluorescence setup for studying biomolecular dynamics

    KAUST Repository

    Sobhy, M. A.

    2011-11-07

    Single-molecule fluorescence imaging is at the forefront of tools applied to study biomolecular dynamics both in vitro and in vivo. The ability of the single-molecule fluorescence microscope to conduct simultaneous multi-color excitation and detection is a key experimental feature that is under continuous development. In this paper, we describe in detail the design and the construction of a sophisticated and versatile multi-color excitation and emission fluorescence instrument for studying biomolecular dynamics at the single-molecule level. The setup is novel, economical and compact, where two inverted microscopes share a laser combiner module with six individual laser sources that extend from 400 to 640 nm. Nonetheless, each microscope can independently and in a flexible manner select the combinations, sequences, and intensities of the excitation wavelengths. This high flexibility is achieved by the replacement of conventional mechanical shutters with acousto-optic tunable filter (AOTF). The use of AOTF provides major advancement by controlling the intensities, duration, and selection of up to eight different wavelengths with microsecond alternation time in a transparent and easy manner for the end user. To our knowledge this is the first time AOTF is applied to wide-field total internal reflection fluorescence (TIRF) microscopy even though it has been commonly used in multi-wavelength confocal microscopy. The laser outputs from the combiner module are coupled to the microscopes by two sets of four single-mode optic fibers in order to allow for the optimization of the TIRF angle for each wavelength independently. The emission is split into two or four spectral channels to allow for the simultaneous detection of up to four different fluorophores of wide selection and using many possible excitation and photoactivation schemes. We demonstrate the performance of this new setup by conducting two-color alternating excitation single-molecule fluorescence resonance energy

  12. Graph-theoretical identification of dissociation pathways on free energy landscapes of biomolecular interaction.

    Science.gov (United States)

    Wang, Ling; Stumm, Boris; Helms, Volkhard

    2010-03-01

    Biomolecular association and dissociation reactions take place on complicated interaction free energy landscapes that are still very hard to characterize computationally. For large enough distances, though, it often suffices to consider the six relative translational and rotational degrees of freedom of the two particles treated as rigid bodies. Here, we computed the six-dimensional free energy surface of a dimer of water-soluble alpha-helices by scanning these six degrees of freedom in about one million grid points. In each point, the relative free energy difference was computed as the sum of the polar and nonpolar solvation free energies of the helix dimer and of the intermolecular coulombic interaction energy. The Dijkstra graph algorithm was then applied to search for the lowest cost dissociation pathways based on a weighted, directed graph, where the vertices represent the grid points, the edges connect the grid points and their neighbors, and the weights are the reaction costs between adjacent pairs of grid points. As an example, the configuration of the bound state was chosen as the source node, and the eight corners of the translational cube were chosen as the destination nodes. With the strong electrostatic interaction of the two helices giving rise to a clearly funnel-shaped energy landscape, the eight lowest-energy cost pathways coming from different orientations converge into a well-defined pathway for association. We believe that the methodology presented here will prove useful for identifying low-energy association and dissociation pathways in future studies of complicated free energy landscapes for biomolecular interaction. PMID:19603501

  13. Luminescent screens

    International Nuclear Information System (INIS)

    Luminescent screens which are useful for such purposes as intensifying screens for radiographs are comprised of a support bearing a layer of finely divided particles of a phosphor dispersed in a cross-linked polymeric matrix formed by heat-curing of a coating composition comprising an unsaturated cross-linkable polymer, a polymerizable acrylic monomer, a thermoplastic polyurethane elastomer, and a heat-activatable polymerization initiator. The phosphor layer includes voids formed by evaporation of an evaporable component which is present in the coating composition from which such layer is formed. (author)

  14. Clinical Application of Screening for GJB2 Mutations before Cochlear Implantation in a Heterogeneous Population with High Rate of Autosomal Recessive Nonsyndromic Hearing Loss

    Directory of Open Access Journals (Sweden)

    Masoud Motasaddi Zarandy

    2011-01-01

    Full Text Available Clinical application of mutation screening and its effect on the outcome of cochlear implantation is widely debated. We investigated the effect of mutations in GJB2 gene on the outcome of cochlear implantation in a population with a high rate of consanguineous marriage and autosomal recessive nonsyndromic hearing loss. Two hundred and one children with profound prelingual sensorineural hearing loss were included. Forty-six patients had 35delG in GJB2. Speech awareness thresholds (SATs and speech recognition thresholds (SRTs improved following implantation, but there was no difference in performance between patients with GJB2-related deafness versus control (all >0.10. Both groups had produced their first comprehensible words within the same period of time following implantation (2.27 months in GJB2-related deaf versus 2.62 months in controls, =0.22. Although our findings demonstrate the need to uncover unidentified genetic causes of hereditary deafness, they do not support the current policy for genetic screening before cochlear implantation, nor prove a prognostic value.

  15. Combinatorial solid-phase glycopeptide libraries - Synthesis and application in biomolecular interaction studies and biosensors

    NARCIS (Netherlands)

    Maljaars, C.E.P.

    2006-01-01

    Carbohydrates play vital roles in all forms of life. Attached to proteins and lipids they serve as recognition elements in several biological interaction processes, such as intercellular communication, immune response, viral and parasitical infections, signal transduction, and development. Synthetic

  16. Combinatorial solid-phase glycopeptide libraries - Synthesis and application in biomolecular interaction studies and biosensors

    OpenAIRE

    Maljaars, C.E.P.

    2006-01-01

    Carbohydrates play vital roles in all forms of life. Attached to proteins and lipids they serve as recognition elements in several biological interaction processes, such as intercellular communication, immune response, viral and parasitical infections, signal transduction, and development. Synthetic mimics of natural oligosaccharides have contributed to a better understanding of these complex recognition events. In addition, these mimics can be used to modulate, or intervene in undesired (pat...

  17. Higher-Order Level-Set Method and Its Application in Biomolecular Surfaces Construction

    Institute of Scientific and Technical Information of China (English)

    Chandrajit L. Bajaj; Guo-Liang Xu; Qin Zhang

    2008-01-01

    We present a general framework for a higher-order spline level-set (HLS) method and apply this to biomolecule surfaces construction. Starting from a first order energy functional, we obtain a general level set formulation of geometric partial differential equation, and provide an efficient approach to solving this partial differential equation using a C2 spline basis. We also present a fast cubic spline interpolation algorithm based on convolution and the Z-transform, which exploits the local relationship of interpolatory cubic spline coefficients with respect to given function data values. One example of our HLS method is demonstrated, which is the construction of biomolecule surfaces (an implicit salvation interface) with their individual atomic coordinates and solvated radii as prerequisites.

  18. Recycling wastes: its application in acoustic screens and construction materials; Residuos con necesidad de reciclado: su aplicacion en plantallas acusticas y como materiales de construccion

    Energy Technology Data Exchange (ETDEWEB)

    Santa Coloma, O.; Cortes, A.; Sanchez, J.A.

    1998-12-01

    The activities developed by man are origin of a great variety of wastes. These activities entail both the resource consumption and the generation of wastes. Both aspects are important because of the impact on the environment where man lives. If we focus on our attention on the consumption of natural resources, both economic aspects (every time the resources are more expensive) and its availability (it increases gradually the difficulty to get them). In this sense, it is very important to pro move the plans and programs necessary in order to minimize the wastes through the re utilization and recycling. Two of the options are the application of some wastes in the manufacture of acoustic screens and as construction materials. (Author)

  19. Unified Application of Vapor Screen Flow Visualization and Pressure Sensitive Paint Measurement Techniques to Vortex- and Shock Wave-Dominated Flow Fields

    Science.gov (United States)

    Erickson, Gary E.

    2010-01-01

    Laser vapor screen (LVS) flow visualization and pressure sensitive paint (PSP) techniques were applied in a unified approach to wind tunnel testing of slender wing and missile configurations dominated by vortex flows and shock waves at subsonic, transonic, and supersonic speeds. The off-surface cross-flow patterns using the LVS technique were combined with global PSP surface static pressure mappings to characterize the leading-edge vortices and shock waves that coexist and interact at high angles of attack. The synthesis of LVS and PSP techniques was also effective in identifying the significant effects of passive surface porosity and the presence of vertical tail surfaces on the flow topologies. An overview is given of LVS and PSP applications in selected experiments on small-scale models of generic slender wing and missile configurations in the NASA Langley Research Center (NASA LaRC) Unitary Plan Wind Tunnel (UPWT) and 8-Foot Transonic Pressure Tunnel (8-Foot TPT).

  20. Unified Application Vapor Screen Flow Visualization and Pressure Sensitive Paint Measurement Techniques to Vortex- and Shock Wave-Dominated Flow Fields

    Science.gov (United States)

    Erickson, Gary E.

    2008-01-01

    Laser vapor screen (LVS) flow visualization and pressure sensitive paint (PSP) techniques were applied in a unified approach to wind tunnel testing of slender wing and missile configurations dominated by vortex flows and shock waves at subsonic, transonic, and supersonic speeds. The off-surface cross-flow patterns using the LVS technique were combined with global PSP surface static pressure mappings to characterize the leading-edge vortices and shock waves that coexist and interact at high angles of attack (alpha). The synthesis of LVS and PSP techniques was also effective in identifying the significant effects of passive surface porosity and the presence of vertical tail surfaces on the flow topologies. An overview is given of LVS and PSP applications in selected experiments on small-scale models of generic slender wing and missile configurations in the NASA Langley Research Center (NASA LaRC) Unitary Plan Wind Tunnel (UPWT) and 8-Foot Transonic Pressure Tunnel (8-Foot TPT).

  1. Current screens

    OpenAIRE

    Cubitt, Sean

    2011-01-01

    The architecture of screen design, including LCD, LED and DLP projection, is analysed in terms of the political economy and their aesthetics and phenomenological impacts, in association with the use of codecs as constraining as well as enabling tools in the control and management of visual data transmission.

  2. Hearing Screening

    Science.gov (United States)

    Johnson-Curiskis, Nanette

    2012-01-01

    Hearing levels are threatened by modern life--headsets for music, rock concerts, traffic noises, etc. It is crucial we know our hearing levels so that we can draw attention to potential problems. This exercise requires that students receive a hearing screening for their benefit as well as for making the connection of hearing to listening.

  3. APPLICATION OF VIA IN SCREENING OF CERVICAL DISEASES AMONG WOMEN WORKERS%VIA在女职工体检中的应用

    Institute of Scientific and Technical Information of China (English)

    高琨; 李力; 梁欢欢; 黄玲莎

    2011-01-01

    [目的]评价在女职工体检中采用醋酸肉眼观察法(VIA)的筛查宫颈病变的效果.[方法]对737位女职工进行妇科检查,同时采用VIA及巴氏涂片法进行宫颈病变的筛查,评价两种方法的宫颈病变检出率.[结果]参检率为75.20%(737/980),参检妇女关于癌症的知晓率为62.5%;宫颈癌的筛查方法的知晓率为42.5%,其中宫颈细胞学检查知晓率为36.5%;人乳头瘤病毒知晓率为19%;CIN Ⅱ级以上病变的检出率VIA法为0.54%(4/737);巴氏涂片法为0,两种检查方法比较差异有统计学意义(P<0.05).[结论]大多数妇女对宫颈癌症的防治知识了解甚少,需加强知识的普及:应用VIA联合巴氏涂片法进行宫颈癌的初筛可进一步提高癌前病变的检出率.%[ Objective] To explore feasibilities of visual inspection with acetic acid ( VIA) in screening of cervical diseases among women workers. [Methods] 737 female workers were screened by using VIA and Pap smear screening for cervical lesions. The detection rates of cervical lesions were evaluated. [ Results] Participation rate was 75.20% (737/980). The rate of awareness about cancer in the women worker was 62.5%, and the rate of awareness about screening methods for cervical cancer was 36.5%, in which the rate of awareness of cervical cy(t)ology was 42.5%, and 19% knew human papillomavirus. CIN Ⅱ lesion detection rate was 0.54% by using VIA method, but we did not find cases by the Pap smear screening. Comparing two methods,there was a significant difference (P< 0.05). [Conclusion] Most of the women poorly understand ahout the prevention and treatment of cervical cancer, so we should strengthen the popularization of health knowledge. Application of VIA method combined Pap smear screening for cervical cancer may further improve the detection rate of precancerous lesions.

  4. Spray-Deposited Large-Area Copper Nanowire Transparent Conductive Electrodes and Their Uses for Touch Screen Applications.

    Science.gov (United States)

    Chu, Hsun-Chen; Chang, Yen-Chen; Lin, Yow; Chang, Shu-Hao; Chang, Wei-Chung; Li, Guo-An; Tuan, Hsing-Yu

    2016-05-25

    Large-area conducting transparent conducting electrodes (TCEs) were prepared by a fast, scalable, and low-cost spray deposition of copper nanowire (CuNW) dispersions. Thin, long, and pure copper nanowires were obtained via the seed-mediated growth in an organic solvent-based synthesis. The mean length and diameter of nanowires are, respectively, 37.7 μm and 46 nm, corresponding to a high-mean-aspect ratio of 790. These wires were spray-deposited onto a glass substrate to form a nanowire conducting network which function as a TCE. CuNW TCEs exhibit high-transparency and high-conductivity since their relatively long lengths are advantageous in lowering in the sheet resistance. For example, a 2 × 2 cm(2) transparent nanowire electrode exhibits transmittance of T = 90% with a sheet resistance as low as 52.7 Ω sq(-1). Large-area sizes (>50 cm(2)) of CuNW TCEs were also prepared by the spray coating method and assembled as resistive touch screens that can be integrated with a variety of devices, including LED lighting array, a computer, electric motors, and audio electronic devices, showing the capability to make diverse sizes and functionalities of CuNW TCEs by the reported method. PMID:27144911

  5. Facile fabrication of CdSe/CdS quantum dots and their application on the screening of colorectal cancer

    Energy Technology Data Exchange (ETDEWEB)

    Cao, Hongfeng; Dong, Quanjin, E-mail: qjdong1508@163.com [Zhejiang Provincial People’s Hospital, Department of Colorectal Surgery (China); Hu, Li [Nanjing University of Science and Technology, School of Environmental and Biological Engineering (China); Tu, Shiliang; Chai, Rui; Dai, Qiaoqiong [Zhejiang Provincial People’s Hospital, Department of Colorectal Surgery (China)

    2015-11-15

    In this paper, a facile aqueous route to water-soluble CdSe/CdS quantum dots (QDs) under mild conditions has been developed. The samples were characterized by means of transmission electron microscopy, energy-dispersive X-ray spectroscopy, and photoluminescence (PL) spectroscopy. The PL property of the QDs can be controlled by adjusting the reaction time. The CdSe/CdS QDs after 48-h reaction with size of 5 nm have the strongest PL intensity located at 553 nm, and the highest quantum yield of 19.9 %. The obtained QDs were applied for the colorectal cancer screening. The QDs could be conjugated with antibody of aldo-keto reductase family 1, member B10 (AKR1B10) for the detection of AKR1B10. The AKR1B10 in PBS/5 % serum solution with concentration of 1 ng/mL could be well calibrated, and the limit of detection could be lower than 0.05 ng/mL.

  6. Development and application of a SYBR green RT-PCR for first line screening and quantification of porcine sapovirus infection

    Directory of Open Access Journals (Sweden)

    Mauroy Axel

    2012-10-01

    Full Text Available Abstract Background Sapoviruses are single stranded positive sense RNA viruses belonging to the family Caliciviridae. The virus is detected in different species including the human and the porcine species as an enteric pathogen causing asymptomatic to symptomatic enteritis. In this study, we report the development of a rapid real time qRT-PCR based on SYBR Green chemistry for the diagnosis of porcine sapovirus infection in swine. Results The method allows the detection of porcine sapoviruses and the quantification of the genomic copies present in stool samples. During its development, the diagnostic tool showed good correlation compared with the gold standard conventional RT-PCR and was ten-fold more sensitive. When the method was applied to field samples, porcine noroviruses from genogroup 2 genotype 11b were also detected. The method was also applied to swine samples from the Netherlands that were positive for PoSaV infection. Phylogenetic results obtained from the samples showed that PoSaV sequences were genetically related to the currently described genogroup III, to the proposed genogroup VII and also to the MI-QW19 sequence (close to the human SaV sequences. Conclusions A rapid, sensitive, and reliable diagnosis method was developed for porcine sapovirus diagnosis. It correlated with the gold standard conventional RT-PCR. Specificity was good apart for genogroup 2 genotype 11b porcine noroviruses. As a first line screening diagnosis method, it allows a quicker and easier decision on doubtful samples.

  7. Electrochemical properties of the acetaminophen on the screen printed carbon electrode towards the high performance practical sensor applications.

    Science.gov (United States)

    Karikalan, Natarajan; Karthik, Raj; Chen, Shen-Ming; Velmurugan, Murugan; Karuppiah, Chelladurai

    2016-12-01

    Acetaminophen is a non-steroidal anti-inflammatory drug used as an antipyretic agent for the alternative to aspirin. Conversely, the overdoses of acetaminophen can cause hepatic toxicity and kidney damage. Hence, the determination of acetaminophen receives much more attention in biological samples and also in pharmaceutical formulations. Here, we report a rapid and sensitive detection of the acetaminophen based on the bare (unmodified) screen printed carbon electrode (BSPCE) and its electrochemistry was studied in various pHs. From the observed results, the mechanism of the electro-oxidation of acetaminophen was derived for various pHs. The acetaminophen is not stable in strong acidic and strong alkaline media, which is hydrolyzed and hydroxylated. However, it is stable in intermediate pHs due to the dimerization of acetaminophen. The kinetics of the acetaminophen oxidation was briefly studied and documented in the schemes. In addition, the surface morphology and disorders of BSPCE was probed by scanning electron microscope (SEM) and Raman spectroscopy. Moreover, the BSPCE determined the acetaminophen with the linear concentration ranging from 0.05 to 190μM and the lower detection limit of 0.013μM. Besides that it reveals the good recoveries towards the pharmaceutical samples and shows the excellent selectivity, sensitivity and stability. To the best of our knowledge, this is the better performance compare to the previously reported unmodified acetaminophen sensors. PMID:27552419

  8. The application of the Escherichia coli giant spheroplast for drug screening with automated planar patch clamp system

    Directory of Open Access Journals (Sweden)

    Kyoko Kikuchi

    2015-09-01

    Full Text Available Kv2.1, the voltage-gated ion channel, is ubiquitously expressed in variety of tissues and dysfunction of this ion channel is responsible for multiple diseases. Electrophysiological properties of ion channels are so far characterized with eukaryotic cells using the manual patch clamp which requires skilful operators and expensive equipments. In this research, we created a simple and sensitive drug screen method using bacterial giant spheroplasts and the automated patch clamp which does not require special skills. We expressed a eukaryotic voltage-gated ion channel Kv2.1 in Escherichia coli using prokaryotic codon, and prepared giant spheroplasts large enough for the patch clamp. Human Kv2.1 currents were successfully recorded from giant spheroplasts with the automated system, and Kv2.1-expressed E. coli spheroplasts could steadily reacted to the dose–response assay with TEA and 4-AP. Collectively, our results indicate for the first time that the bacterial giant spheroplast can be applied for practical pharmaceutical assay using the automated patch clamp.

  9. Development of a capillary electrophoresis method for analyzing adenosine deaminase and purine nucleoside phosphorylase and its application in inhibitor screening.

    Science.gov (United States)

    Qi, Yanfei; Li, Youxin; Bao, James J

    2016-08-01

    A novel capillary electrophoresis (CE) method was developed for simultaneous analysis of adenosine deaminase (ADA) and purine nucleoside phosphorylase (PNP) in red blood cells (RBCs). The developed method considered and took advantage of the natural conversion from the ADA product, inosine to hypoxanthine. The transformation ratio was introduced for ADA and PNP analysis to obtain more reliable results. After optimizing the enzymatic incubation and electrophoresis separation conditions, the determined activities of ADA and PNP in 12 human RBCs were 0.237-0.833 U/ml and 9.013-10.453 U/ml packed cells, respectively. The analysis of ADA in mice RBCs indicated that there was an apparent activity difference between healthy and hepatoma mice. In addition, the proposed method was also successfully applied in the inhibitor screening from nine traditional Chinese medicines, and data showed that ADA activities were strongly inhibited by Rhizoma Chuanxiong and Angelica sinensis. The inhibition effect of Angelica sinensis on ADA is first reported here and could also inhibit PNP activity. PMID:27173606

  10. Application of a NMR-based untargeted quantitative metabonomic approach to screen for illicit salbutamol administration in cattle.

    Science.gov (United States)

    Tang, Chaohua; Zhang, Kai; Liang, Xiaowei; Zhao, Qingyu; Zhang, Junmin

    2016-07-01

    The use of metabonomic methodologies to identify illicit salbutamol administration in cattle has not been previously investigated. In this study, a nuclear magnetic resonance (NMR)-based untargeted quantitative metabonomic approach was applied to discriminate biofluid samples (plasma and urine) obtained from cattle before and after salbutamol treatment. Six male cattle (265.7 ± 3.9 kg) were fed salbutamol (0.15 mg/kg body weight) for 21 consecutive days. Plasma and urine samples were collected before and after treatment. By the use of targeted profiling, 46 and 43 metabolites in plasma and urine, respectively, were quantified, of which 9 and 11 metabolites were significantly affected (P plot (VIP) scores of glucose and lactate in plasma, and urine, hippurate, acetate, glycine, formate, n-phenylacetyl, benzoate, and phenylacetate in urine were >1.0, which implies that these metabolites may serve as potential biomarkers for salbutamol treatment. These findings suggest the potential value of NMR-based untargeted quantitative metabonomic methodologies for plasma and urine analyses as a screening technique for detection of illicit salbutamol usage in cattle. PMID:27116419

  11. Electrochemical Sensors Based on Screen-Printed Electrodes: The Use of Phthalocyanine Derivatives for Application in VFA Detection

    Science.gov (United States)

    Ndiaye, Amadou L.; Delile, Sébastien; Brunet, Jérôme; Varenne, Christelle; Pauly, Alain

    2016-01-01

    Here, we report on the use of electrochemical methods for the detection of volatiles fatty acids (VFAs), namely acetic acid. We used tetra-tert-butyl phthalocyanine (PcH2-tBu) as the sensing material and investigated its electroanalytical properties by means of cyclic voltammetry (CV) and square wave voltammetry (SWV). To realize the electrochemical sensing system, the PcH2-tBu has been dropcast-deposited on carbon (C) orgold (Au)screen-printed electrodes (SPEs) and characterized by cyclic voltammetry and scanning electron microscopy (SEM). The SEM analysis reveals that the PcH2-tBu forms mainly aggregates on the SPEs. The modified electrodes are used for the detection of acetic acid and present a linear current increase when the acetic acid concentration increases. The Cmodified electrode presents a limit of detection (LOD) of 25.77 mM in the range of 100 mM–400 mM, while the Aumodified electrode presents an LOD averaging 40.89 mM in the range of 50 mM–300 mM. When the experiment is realized in a buffered condition, theCmodified electrode presents a lower LOD, which averagesthe 7.76 mM. A pronounced signal decay attributed to an electrode alteration is observed in the case of the gold electrode. This electrode alteration severely affects the coating stability. This alteration is less perceptible in the case of the carbon electrode. PMID:27598214

  12. STOPP (Screening Tool of Older Persons' potentially inappropriate Prescriptions): application to acutely ill elderly patients and comparison with Beers' criteria.

    LENUS (Irish Health Repository)

    Gallagher, Paul

    2012-02-03

    Introduction: STOPP (Screening Tool of Older Persons\\' potentially inappropriate Prescriptions) is a new, systems-defined medicine review tool. We compared the performance of STOPP to that of established Beers\\' criteria in detecting potentially inappropriate medicines (PIMs) and related adverse drug events (ADEs) in older patients presenting for hospital admission. METHODS: we prospectively studied 715 consecutive acute admissions to a university teaching hospital. Diagnoses, reason for admission and concurrent medications were recorded. STOPP and Beers\\' criteria were applied. PIMs with clear causal connection or contribution to the principal reason for admission were determined. RESULTS: median patient age (interquartile range) was 77 (72-82) years. Median number of prescription medicines was 6 (range 0-21). STOPP identified 336 PIMs affecting 247 patients (35%), of whom one-third (n = 82) presented with an associated ADE. Beers\\' criteria identified 226 PIMs affecting 177 patients (25%), of whom 43 presented with an associated ADE. STOPP-related PIMs contributed to 11.5% of all admissions. Beers\\' criteria-related PIMs contributed to significantly fewer admissions (6%). CONCLUSION: STOPP criteria identified a significantly higher proportion of patients requiring hospitalisation as a result of PIM-related adverse events than Beers\\' criteria. This finding has significant implications for hospital geriatric practice.

  13. The Future of Prenatal Diagnosis and Screening

    OpenAIRE

    Eugene Pergament

    2014-01-01

    The future of prenatal diagnosis and screening lies in developing clinical approaches and laboratory technologies applicable to genetic analyses and therapeutic interventions during embryonic development.

  14. 3D electron density imaging using single scattered x rays with application to breast CT and mammographic screening

    Science.gov (United States)

    van Uytven, Eric Peter

    Screening mammography is the current standard in detecting breast cancer. However, its fundamental disadvantage is that it projects a 3D object into a 2D image. Small lesions are difficult to detect when superimposed over layers of normal tissue. Commercial Computed Tomography (CT) produces a true 3D image yet has a limited role in mammography due to relatively low resolution and contrast. With the intent of enhancing mammography and breast CT, we have developed an algorithm which can produce 3D electron density images using a single projection. Imaging an object with x rays produces a characteristic scattered photon spectrum at the detector plane. A known incident beam spectrum, beam shape, and arbitrary 3D matrix of electron density values enable a theoretical scattered photon distribution to be calculated. An iterative minimization algorithm is used to make changes to the electron density voxel matrix to reduce regular differences between the theoretical and the experimentally measured distributions. The object is characterized by the converged electron density image. This technique has been validated in simulation using data produced by the EGSnrc Monte Carlo code system. At both mammographic and CT energies, a scanning polychromatic pencil beam was used to image breast tissue phantoms containing lesion-like inhomogeneities. The resulting Monte Carlo data is processed using a Nelder-Mead iterative algorithm (MATLAB) to produce the 3D matrix of electron density values. Resulting images have confirmed the ability of the algorithm to detect various 1x1x2.5 mm3 lesions with calcification content as low as 0.5% (p<0.005) at a dose comparable to mammography.

  15. Development of a voltammetric assay, using screen-printed electrodes, for clonazepam and its application to beverage and serum samples.

    Science.gov (United States)

    Honeychurch, Kevin C; Brooks, Joshua; Hart, John P

    2016-01-15

    This paper describes the development of an electrochemical assay based on screen-printed carbon sensors for the determination of clonazepam in serum and in wine. The cyclic voltammetric behaviour of the drug was investigated and the effects of pH and scan rate on the peak current and peak potential determined. Two reduction peaks were recorded on the initial negative going scan, which were considered to result from the 2e(-), 2 H(+) reduction of the 4,5-azomethine and from the 4e(-), 4 H(+) reduction of the 7-NO2 to a hydroxylamine. On the return positive going scan an oxidation peak was seen, which was considered to result from the 2e(-), 2 H(+) oxidation (O1) of the hydroxylamine to the corresponding nitroso species. At pH 11 the solution of clonazepam was found to turn from clear to yellow in colour and the voltammetric signal of the O1 oxidation process was found to be adsorptive in nature, this was exploited in the development of an adsorptive stripping voltammetric assay. Experimental conditions were then optimised for the differential pulse adsorptive voltammetric measurement of clonazepam in wine and serum samples. It was shown that these analyses could be performed on only 100µL of sample which was deposited on the sensor surface. Mean recoveries of 79.53% (%CV=9.88%) and 88.22% (%CV=14.1%) were calculated for wine fortified with 3.16µg/mL and serum fortified with 12.6µg/mL. PMID:26592640

  16. Large scale, highly conductive and patterned transparent films of silver nanowires on arbitrary substrates and their application in touch screens

    International Nuclear Information System (INIS)

    The application of silver nanowire films as transparent conductive electrodes has shown promising results recently. In this paper, we demonstrate the application of a simple spray coating technique to obtain large scale, highly uniform and conductive silver nanowire films on arbitrary substrates. We also integrated a polydimethylsiloxane (PDMS)-assisted contact transfer technique with spray coating, which allowed us to obtain large scale high quality patterned films of silver nanowires. The transparency and conductivity of the films was controlled by the volume of the dispersion used in spraying and the substrate area. We note that the optoelectrical property, σDC/σOp, for various films fabricated was in the range 75-350, which is extremely high for transparent thin film compared to other candidate alternatives to doped metal oxide film. Using this method, we obtain silver nanowire films on a flexible polyethylene terephthalate (PET) substrate with a transparency of 85% and sheet resistance of 33 Ω/sq, which is comparable to that of tin-doped indium oxide (ITO) on flexible substrates. In-depth analysis of the film shows a high performance using another commonly used figure-of-merit, ΦTE. Also, Ag nanowire film/PET shows good mechanical flexibility and the application of such a conductive silver nanowire film as an electrode in a touch panel has been demonstrated.

  17. Development and application of rapid screening technology and its evaluation and authentication profiles%快速筛选技术的评价验证

    Institute of Scientific and Technical Information of China (English)

    赵博; 张庆合; 李红梅

    2014-01-01

    快速筛选技术是指包括样品制备在内,能够在较短时间内出具检测结果的行为,也称之为快速检测技术。随着我国食品安全问题广受关注,快速筛选技术便成为研究的重点。快速检测目前主要应用于食品中农、兽药残留,微生物致病菌,营养成分,不明污染物等针对食品安全的现场快速检测及常规检测。本文介绍了分子光谱法、免疫分析方法、酶抑制法和生物传感器等几种快速筛选技术的研究进展以及在食品安全检测等领域的应用。随着快速筛选技术的不断发展使得快速检测方法及其相关仪器产品种类越来越多且原理复杂,快速检测方法的质量控制和方法验证显得尤为重要。本文重点阐述了快速筛选技术与方法的评价验证,其主要技术参数包括:敏感度、阴性和阳性界限值的准确性、选择性和特异性、检出限、定量限、重复性和再现性等,并对其发展前景进行了展望。%Rapid screening technology means, including sample preparation, a kind of technology to be able to issue the test results in a short time. It was also defined as rapid detection technology. It was mainly used in food, pesticide, veterinary drug residues, microbial pathogens, nutrients, and unknown contaminants, etc. Rapid screening technology had become the focus of research as well as the food safety in our country. Several technologies of the rapid screening method were mainly introduced, including molecular spectrometry, immunoassay, enzyme inhibition method, and biological sensors,etc. With the continuous development of rapid screening technology, rapid detection methods and related equipment products appeared more and more, and their quality control and validation method turned to be particularly important. In this paper, the development and application of the rapid screening technology in food safety were expounded as well as its evaluation methods

  18. 快速筛选技术的评价验证%Development and application of rapid screening technology and its evaluation and authentication profiles

    Institute of Scientific and Technical Information of China (English)

    赵博; 张庆合; 李红梅

    2014-01-01

    Rapid screening technology means, including sample preparation, a kind of technology to be able to issue the test results in a short time. It was also defined as rapid detection technology. It was mainly used in food, pesticide, veterinary drug residues, microbial pathogens, nutrients, and unknown contaminants, etc. Rapid screening technology had become the focus of research as well as the food safety in our country. Several technologies of the rapid screening method were mainly introduced, including molecular spectrometry, immunoassay, enzyme inhibition method, and biological sensors,etc. With the continuous development of rapid screening technology, rapid detection methods and related equipment products appeared more and more, and their quality control and validation method turned to be particularly important. In this paper, the development and application of the rapid screening technology in food safety were expounded as well as its evaluation methods. Its main technical parameters included sensitivity, the accuracy of the negative and positive threshold, selectivity and specificity, detection limit, quantitative limit, repeatability and reproducibility, etc. The development in the future was prospected as well.%快速筛选技术是指包括样品制备在内,能够在较短时间内出具检测结果的行为,也称之为快速检测技术。随着我国食品安全问题广受关注,快速筛选技术便成为研究的重点。快速检测目前主要应用于食品中农、兽药残留,微生物致病菌,营养成分,不明污染物等针对食品安全的现场快速检测及常规检测。本文介绍了分子光谱法、免疫分析方法、酶抑制法和生物传感器等几种快速筛选技术的研究进展以及在食品安全检测等领域的应用。随着快速筛选技术的不断发展使得快速检测方法及其相关仪器产品种类越来越多且原理复杂,快速检测方法的质量控制和方法验证显得尤为重

  19. Mathematical Models of the Sinusoidal Screen Family

    Directory of Open Access Journals (Sweden)

    Tajana Koren

    2011-06-01

    Full Text Available In this paper we will define a family of sinusoidal screening elements and explore the possibilities of their application in graphic arts, securities printing and design solutions in photography and typography editing. For this purpose mathematical expressions of sinusoidal families were converted into a Postscript language. The introduction of a random variable results in a countless number of various mutations which cannot be repeated without knowing the programming code itself. The use of the family of screens in protection of securities is thus of great importance. Other possible application of modulated sinusoidal screens is related to the large format color printing. This paper will test the application of sinusoidal screens in vector graphics, pixel graphics and typography. The development of parameters in the sinusoidal screen element algorithms gives new forms defined within screening cells with strict requirements of coverage implementation. Individual solutions include stochastic algorithms, as well as the autonomy of screening forms in regard to multicolor printing channels.

  20. Application of Clinical Aging Indicators for the Assessment of Neurological Health via Screening Among Residents of the Almaty Region

    Directory of Open Access Journals (Sweden)

    Erkin Nurguzhayev

    2014-12-01

    Full Text Available Introduction. Life expectancy at birth is considered to be a primary indicator of public health success. However, an increase in life expectancy is meaningless if it is not accompanied by an equivalent increase in the number of life years without disability such as physical, cognitive, and psychological abilities. The main consequences of disease leading to neurological dysfunction are directly related to issues such as the inability to walk, talk, learn, live in society, or take care of oneself. The objective of the study was to conduct a medical examination of elderly people as a part of the scientific program "Development of a model (program of anti-aging to provide active longevity of elderly people of Kazakhstan.”Methods. As part of a pilot study, we assessed the presence of the following clinical indicators of aging: cognitive impairment (MMSE test, pyramidal symptoms,and  ataxia. We conducted medical examination (screening among 150 elderly persons in Almaty City Polyclinic #8 and 287 elderly persons in Central Regional Clinic of Rayimbek Area, Almaty region aged 45 and above.Results. The results show that the intensity of changes is directly dependent on the age of the study groups. The cognitive function is the most affected and depends on the age of examinees. The changes are more expressed among residents of Almaty region. The average MMSE score in Almaty was 28.2 (age group of 45-49 years and 25.8 (age group of 80 and above, and 27.3 and 24.0 respectively  in Almaty region. The various symptoms among residents of Almaty tend to stabilize after 65 years, however, the frequency of ataxia continues to grow and increases significantly after 75 years.Conclusions. Considering that important risk factors of neurological disorders are cerebrovascular diseases of various origins (primarily hypertension, atherosclerosis, and diabetes, an adequate treatment of these diseases will increase a healthy lifespan. Furthermore, it is necessary to

  1. Nutritional screening tools application in a general hospital: a comparative study Aplicação de instrumentos de triagem nutricional em hospital geral: um estudo comparativo

    Directory of Open Access Journals (Sweden)

    Janaína Damasceno Bezerra

    2012-05-01

    Full Text Available Introduction: There are many nutritional screening tools and it becomes difficult to choose which one is the best to be used in clinical nutrition practice. Objective: To compare five nutritional screening tools (MST, NRS-2002, MUST, MNA and MNA-SF in adults and elderly hospitalized. Materials and Methods: A cross-sectional study, with the application of nutritional screening tools in adult and elderly patients in the first 48 hours of hospitalization was performed. Nutritional risk occurrence between adult and elderly patients was compared. Statistical analyses were performed using descriptive data and a non-parametric test (Man Whitney. Results: We evaluated 77 patients, 51 (66.2% adults and 26 (33.8% elderly, aged 53.6 (standard deviation of 17.9 years, with female predominance (53.2%. The main reasons for hospitalization were neoplasia and nephrolithotripsy. Overall, one quarter of patients was at nutritional risk. Nutritional risk in adults was detected with similarity by MUST and MST. However it was underestimated by NRS-2002. The MNA and MNA-SF, exclusively for the elderly, also had similar result to detect nutritional risk. In relation to the time of application, the MNA was the instrument with longer application time. Conclusion: Considering the higher detection of patients with nutritional risk, the easiness and the lower application time, we suggest, respectively, MUST and MNA-SF to be used in adult and elderly patients admitted in this hospital.Introdução: Com inúmeros instrumentos de triagem nutricional existentes, é difícil eleger o mais adequado para os protocolos de nutrição hospitalar. Objetivo: Comparar cinco instrumentos de triagem nutricional (MST, NRS-2002, MUST, MNA e MNA-SF em adultos e idosos hospitalizados. Materiais e Métodos: Nesse estudo transversal, cinco instrumentos de triagem nutricional foram aplicados aos pacientes nas primeiras 48 horas de internação hospitalar. A ocorrência de risco nutricional

  2. Application Value of Chest Digital Radiography with High KV in Health Screening%高千伏胸部摄影在健康体检的应用

    Institute of Scientific and Technical Information of China (English)

    严贵华; 梁克树

    2013-01-01

      目的:探讨直接数字化X线摄影(digital radiography,DR)胸部高千伏摄影在健康体检的应用价值及优势。方法:在健康体检胸部摄影中随机分组,分别采用高千伏技术和普通千伏技术,由多位有经验的影像科医师、技师评价影像质量,比较两组一次成功率和受检者曝光量。结果:高千伏组甲级片占92.0%,普通千伏组甲级片占84.0%;高千伏胸部摄片一次成功率99.6%,普通千伏胸部摄片一次成功率98.5%;高千伏技术个体曝光量是普通千伏个体曝光量的1/3。结论:在健康体检中行DR胸部摄影,采用高千伏技术在提高影像质量,降低曝光量,减少受检者辐射剂量,延长机器使用寿命等方面有明显优势。%Objective:To study the application value and advantage of chest digital radiography with high KV(kilovolt)in health screening. Method:High KV digital radiography and general KV radiography were adopted in two health screening groups which were divided randomly.The image qualities were evaluated by several experienced radiologists and radiographers.one time success rate and exposure value were also compared.Result:The image qualities of High KV group with its class A was 92.0%and the one of general KV group with its class A was 84.0%. one time success rate with High KV group was 99.6%and the one with general KV group was 98.5%.The individual exposure value with High KV group was 1/3 of the one with general KV group.Conclusion:Chest radiography with high KV in health screening has clear advantages in improving image quality,reducing radiation to the physical examination people and extending the service life of the machine.

  3. Detection and kinetic studies of triplex formation by oligodeoxynucleotides using real-time biomolecular interaction analysis (BIA).

    OpenAIRE

    Bates, P. J.; Dosanjh, H. S.; S. Kumar; Jenkins, T. C.; Laughton, C A; Neidle, S

    1995-01-01

    Real-time biomolecular interaction analysis (BIA) has been applied to triplex formation between oligodeoxynucleotides. 5'-Biotinylated oligonucleotides were immobilised on the streptavidin-coated surface of a biosensor chip and subsequently hybridised to their complementary strand. Sequence-specific triplex formation was observed when a suitable third-strand oligopyrimidine was injected over the surface-bound duplex. In addition, a single-stranded oligonucleotide immobilised on the chip surfa...

  4. 住院患者营养风险筛查及其临床应用%Nutritional Risk Screening and the Clinical Applications on Hospitalized Patients

    Institute of Scientific and Technical Information of China (English)

    刘彩虹

    2012-01-01

    Nutritional risk screening (NRS )2002 is an effective tool to predict the clinical outcome of hospitalized patients and determine whether nutrition intervention is needed,which is recommended as a nutritional risk screening tool of first choice for hospitalized patients. NRS as a basis for nutritional support, plays an important role in improvement of clinical outcome, reducing medical costs and the waste of resources and benefiting the patients. At present, irrationality still exists in clinical nutrition support. Here is to make a review' on the definition of NRS2002, scoring methods and clinical applications at home and abroad, in order to provide a reference for clinical practitioners to achieve the purpose of rational use of nutritional support.%营养风险筛查(NRS2002)可以预测住院患者的临床结局,作为判断是否需要营养干预的一种有效工具,被推荐为住院患者NRS的首选工具.NRS作为营养支持依据,具有改善患者临床结局,减少医疗费用,降低资源浪费的良好作用,并使患者从中获益.目前营养支持在临床应用中仍存在不合理性.现对NRS2002的定义、评分方法和国内外临床应用情况等予以综述,以期为临床工作者提供参考,达到合理应用营养支持的目的.

  5. 基于信息甄别的预订货策略研究%The Application of Information Screening in Early Order Commitment

    Institute of Scientific and Technical Information of China (English)

    蒋龙珠; 江志斌; 储熠斌; 耿娜

    2012-01-01

    以一个制造商一个经销商组成的二级供应链为研究对象,在信息不对称条件下从制造商的角度,基于信息经济学理论建立了供应链的利润函数的信息甄别解析模型.提出了预订货激励契约.对其有效原因进行了分析并解释了契约关键参数的意义.得出了制造商的最优产量决策机制.结论表明:在信息不对称条件下,制造商可利用预订货价改变经销商的利润函数结构,通过信息甄别机制对经销商的预订购量进行判断以获得真实的市场需求信息.%A two-stage supply chain of one manufacture and one agency are studied under the condition of asymmetric information from the view of manufacture. By application of information screening in Early Order Commitment ( EOC) , the analytic models of the supply chain profit function is proposed based on the information economics theory. An incentive contract is proposed, analyzed its effect, explain its key index, and given out the optimal production volume. Conclusions demonstrate that the manufacture can re-structure the agency' s profit function by means of EOC price, and get the credible demand information from screening the agency' s purchase quantity under asymmetric information condition.

  6. Fragment screening: an introduction.

    Science.gov (United States)

    Leach, Andrew R; Hann, Michael M; Burrows, Jeremy N; Griffen, Ed J

    2006-09-01

    There are clearly many different philosophies associated with adapting fragment screening into mainstream Drug Discovery Lead Generation strategies. Scientists at Astex, for instance, focus entirely on strategies involving use of X-ray crystallography and NMR. However, AstraZeneca uses a number of different fragment screening strategies. One approach is to screen a 2000 compound fragment set (with close to "lead-like" complexity) at 100 microM in parallel with every HTS such that the data are obtained on the entire screening collection at 10 microM plus the extra samples at 100 microM; this provides valuable compound potency data in a concentration range that is usually unexplored. The fragments are then screen-specific "privileged structures" that can be searched for in the rest of the HTS output and other databases as well as having synthesis follow-up. A typical workflow for a fragment screen within AstraZeneca is shown below (Figure 24) and highlights the desirability (particularly when screening >100 microM) for NMR and X-ray information to validate weak hits and give information on how to optimise them. In this chapter, we have provided an introduction to the theoretical and practical issues associated with the use of fragment methods and lead-likeness. Fragment-based approaches are still in an early stage of development and are just one of many interrelated techniques that are now used to identify novel lead compounds for drug development. Fragment based screening has some advantages, but like every other drug hunting strategy will not be universally applicable. There are in particular some practical challenges associated with fragment screening that relate to the generally lower level of potency that such compounds initially possess. Considerable synthetic effort has to be applied for post-fragment screening to build the sort of potency that would be expected to be found from a traditional HTS. However, if there are no low-hanging fruit in a screening

  7. Development of polarizable models for molecular mechanical calculations. 3. Polarizable water models conforming to Thole polarization screening schemes.

    Science.gov (United States)

    Wang, Jun; Cieplak, Piotr; Cai, Qin; Hsieh, Meng-Juei; Wang, Junmei; Duan, Yong; Luo, Ray

    2012-07-19

    As an integrated step toward a coherent polarizable force field for biomolecular modeling, we analyzed four polarizable water models to evaluate their consistencies with the Thole polarization screening schemes utilized in our latest Amber polarizable force field. Specifically, we studied the performance of both the Thole linear and exponential schemes in these water models to assess their abilities to reproduce experimental water properties. The analysis shows that the tested water models reproduce most of the room-temperature properties of liquid water reasonably well but fall short of reproducing the dynamic properties and temperature-dependent properties. This study demonstrates the necessity to further fine-tune water polarizable potentials for more robust polarizable force fields for biomolecular simulations.

  8. Prenatal Screening Using Maternal Markers

    Directory of Open Access Journals (Sweden)

    Howard Cuckle

    2014-05-01

    Full Text Available Maternal markers are widely used to screen for fetal neural tube defects (NTDs, chromosomal abnormalities and cardiac defects. Some are beginning to broaden prenatal screening to include pregnancy complications such as pre-eclampsia. The methods initially developed for NTDs using a single marker have since been built upon to develop high performance multi-maker tests for chromosomal abnormalities. Although cell-free DNA testing is still too expensive to be considered for routine application in public health settings, it can be cost-effective when used in combination with existing multi-maker marker tests. The established screening methods can be readily applied in the first trimester to identify pregnancies at high risk of pre-eclampsia and offer prevention though aspirin treatment. Prenatal screening for fragile X syndrome might be adopted more widely if the test was to be framed as a form of maternal marker screening.

  9. Quadruple screen test

    Science.gov (United States)

    ... screen; Multiple marker screening; AFP plus; Triple screen test; AFP maternal; MSAFP; 4-marker screen ... This test is most often done between the 15th and 22nd weeks of the pregnancy. It is most accurate ...

  10. Quadruple screen test

    Science.gov (United States)

    ... screen; Multiple marker screening; AFP plus; Triple screen test; AFP maternal; MSAFP; 4-marker screen; Down syndrome - ... This test is most often done between the 15th and 22nd weeks of the pregnancy. It is most accurate ...

  11. Autism Screening and Diagnosis

    Science.gov (United States)

    ... Websites About Us Information For... Media Policy Makers Screening and Diagnosis Language: English Español (Spanish) Recommend on ... two steps: Developmental Screening Comprehensive Diagnostic Evaluation Developmental Screening Developmental screening is a short test to tell ...

  12. Designer DNA Architectures: Applications in Nanomedicine

    OpenAIRE

    Arun Richard Chandrasekaran

    2016-01-01

    DNA has been used as a material for the construction of nanoscale objects. These nanostructures are programmable and allow the conjugation of biomolecular guests to improve their functionality. DNA nanostructures display a wide variety of characteristics, such as cellular permeabil‐ ity, biocompatibility and stability, and responsiveness to external stimuli, making them excellent candidates for applications in nanomedicine.

  13. 糖尿病足筛查表格的设计及应用%The design and application of diabetic foot screening form

    Institute of Scientific and Technical Information of China (English)

    欧召容; 梁赤波

    2014-01-01

    Objective To detect risk factors of diabetic foot through diabetic foot screening,and take countermeasures timely to reduce the incidence of diabetic foot.Methods Designed diabetic foot screening form according to the diagnostic criteria,prevention strategies of diabetic foot,and document literature.Applied diabetic foot screen to 358 cases of diabetic under the charge of Changan Community Health Service Center,who were randomly divided into control group and observation group based on dangerous level,with 179 cases in each group.Two groups were under observation for 1 year respectively.Control group received conventional management,while observation group received hierarchical management according to dangerous level.Results Screening results:① the risk of diabetic foot occurred in 277 patients (77.4%) in this study,multiple risk factors in 183 cases,single risk factor in 94 cases.② There were 51 cases of high-risk foot,77 cases of moderate-risk foot,149 cases of low-risk foot,and 81 cases of normal foot.There was statistically significant difference in the incidence of diabetic foot (high,moderate and low risk foot) before and after the intervention in observation group (P < 0.01),no statistically significant difference in control group (P > 0.05).Conclusions Patients with diabetic have a high risk of diabetic foot.So it is necessary to strengthen community screening of diabetic foot,and carry out appropriate management according to dangerous level to prevent the occurrence of diabetic foot.Diabetic foot screening table is simple,convenient,economic and applicable in clinical application,worthy of clinical promotion.%目的 通过对糖尿病足的筛查,早期发现糖尿病足的危险因素,针对病因及时采取针对性的措施,减少糖尿病足的发生.方法 依据糖尿病足的诊断标准和预防策略这两根主线,再结合查阅文献资料设计糖尿病足的筛查表.对长安社区纳入管理的358例糖尿病患者进行糖尿

  14. Application research of HPV test in screening of cervical lesions%HPV检测在宫颈病变筛查中的应用价值研究

    Institute of Scientific and Technical Information of China (English)

    揭艳频

    2014-01-01

    目的:探讨HPV检测在宫颈病变筛查中的应用价值。方法选择2011年2月-2013年6月本院门诊及体检的500例女性HPV检测的患者,分别给予HPV的TCT和DNA检测,并于病理组织检查结果进行比较。结果随着病变等级的升高, HPV DNA感染率逐渐升高。 TCT检测的阳性率为15.4%,HPV DNA检测的阳性率为35.2%,病理检测的阳性率为19.6%;TCT检测的灵敏度为44.90%,HPV DNA检测的灵敏度为83.67%,两组间差异有统计学意义(P<0.05)。结论 HPV DNA检测的灵敏度高于TCT检测,但两者各有优势,在宫颈病变筛查中的应用价值较高。%Objective To explore the application of HPV test in screening of cervical lesions. Methods 500 cases of female pa-tients with HPV tested in our hospital outpatient service and the physical examination from February 2011 to June 2013were se-lected, they were given the HPV TCT and DNA tested respectively, the examination results was compared with histopathologic. Results With the increase of level of lesion, the HPV DNA infection rate increased. TCT detection positive rate was 15.4%, HPV DNA detection positive rate was 35.2%, the pathological d detection positive rate was 19.6%;TCT detection sensitivity of 44.90%, the HPV DNA sensitivity of 83.67%, the differences between the two groups was statistically significant (P<0.05). Conclusion HPV DNA detection sensitivity is higher than the TCT detection, but they have their own advantages and high application value in screening of cervical lesions.

  15. Application of health-based screening levels to ground-water quality data in a state-scale pilot effort

    Science.gov (United States)

    Toccalino, Patricia L.; Norman, Julia E.; Phillips, Robyn H.; Kauffman, Leon J.; Stackelberg, Paul E.; Nowell, Lisa H.; Krietzman, Sandra J.; Post, Gloria B.

    2004-01-01

    A state-scale pilot effort was conducted to evaluate a Health-Based Screening Level (HBSL) approach developed for communicating findings from the U.S. Geological Survey (USGS) National Water-Quality Assessment Program in a human-health context. Many aquifers sampled by USGS are used as drinking-water sources, and water-quality conditions historically have been assessed by comparing measured contaminant concentrations to established drinking-water standards and guidelines. Because drinking-water standards and guidelines do not exist for many analyzed contaminants, HBSL values were developed collaboratively by the USGS, U.S. Environmental Protection Agency (USEPA), New Jersey Department of Environmental Protection, and Oregon Health & Science University, using USEPA toxicity values and USEPA Office of Water methodologies. The main objective of this report is to demonstrate the use of HBSL approach as a tool for communicating water-quality data in a human-health context by conducting a retrospective analysis of ground-water quality data from New Jersey. Another important objective is to provide guidance on the use and interpretation of HBSL values and other human-health benchmarks in the analyses of water-quality data in a human-health context. Ground-water samples collected during 1996-98 from 30 public-supply, 82 domestic, and 108 monitoring wells were analyzed for 97 pesticides and 85 volatile organic compounds (VOCs). The occurrence of individual pesticides and VOCs was evaluated in a human-health context by calculating Benchmark Quotients (BQs), defined as ratios of measured concentrations of regulated compounds (that is, compounds with Federal or state drinking-water standards) to Maximum Contaminant Level (MCL) values and ratios of measured concentrations of unregulated compounds to HBSL values. Contaminants were identified as being of potential human-health concern if maximum detected concentrations were within a factor of 10 of the associated MCL or HBSL

  16. Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components.

    Science.gov (United States)

    Pardee, Keith; Green, Alexander A; Takahashi, Melissa K; Braff, Dana; Lambert, Guillaume; Lee, Jeong Wook; Ferrante, Tom; Ma, Duo; Donghia, Nina; Fan, Melina; Daringer, Nichole M; Bosch, Irene; Dudley, Dawn M; O'Connor, David H; Gehrke, Lee; Collins, James J

    2016-05-19

    The recent Zika virus outbreak highlights the need for low-cost diagnostics that can be rapidly developed for distribution and use in pandemic regions. Here, we report a pipeline for the rapid design, assembly, and validation of cell-free, paper-based sensors for the detection of the Zika virus RNA genome. By linking isothermal RNA amplification to toehold switch RNA sensors, we detect clinically relevant concentrations of Zika virus sequences and demonstrate specificity against closely related Dengue virus sequences. When coupled with a novel CRISPR/Cas9-based module, our sensors can discriminate between viral strains with single-base resolution. We successfully demonstrate a simple, field-ready sample-processing workflow and detect Zika virus from the plasma of a viremic macaque. Our freeze-dried biomolecular platform resolves important practical limitations to the deployment of molecular diagnostics in the field and demonstrates how synthetic biology can be used to develop diagnostic tools for confronting global health crises. PAPERCLIP. PMID:27160350

  17. A method for rapid quantitative assessment of biofilms with biomolecular staining and image analysis.

    Science.gov (United States)

    Larimer, Curtis; Winder, Eric; Jeters, Robert; Prowant, Matthew; Nettleship, Ian; Addleman, Raymond Shane; Bonheyo, George T

    2016-01-01

    The accumulation of bacteria in surface-attached biofilms can be detrimental to human health, dental hygiene, and many industrial processes. Natural biofilms are soft and often transparent, and they have heterogeneous biological composition and structure over micro- and macroscales. As a result, it is challenging to quantify the spatial distribution and overall intensity of biofilms. In this work, a new method was developed to enhance the visibility and quantification of bacterial biofilms. First, broad-spectrum biomolecular staining was used to enhance the visibility of the cells, nucleic acids, and proteins that make up biofilms. Then, an image analysis algorithm was developed to objectively and quantitatively measure biofilm accumulation from digital photographs and results were compared to independent measurements of cell density. This new method was used to quantify the growth intensity of Pseudomonas putida biofilms as they grew over time. This method is simple and fast, and can quantify biofilm growth over a large area with approximately the same precision as the more laborious cell counting method. Stained and processed images facilitate assessment of spatial heterogeneity of a biofilm across a surface. This new approach to biofilm analysis could be applied in studies of natural, industrial, and environmental biofilms.

  18. Toxicity evaluation of PEDOT/biomolecular composites intended for neural communication electrodes

    Energy Technology Data Exchange (ETDEWEB)

    Asplund, M; Thaning, E; Von Holst, H [Division of Neuronic Engineering, School of Technology and Health, Royal Institute of Technology, SE-14152 Huddinge (Sweden); Lundberg, J [Section for Neuroradiology, R2:02 NKK-lab, Department of Clinical Neuroscience, Karolinska Institutet, Karolinska University Hospital, Solna, SE-171 76, Stockholm (Sweden); Sandberg-Nordqvist, A C [Section of Clinical CNS Research, Department of Clinical Neuroscience, Karolinska Institutet, Karolinska University Hospital, Solna, SE-171 76, Stockholm (Sweden); Kostyszyn, B [Center for Hearing and Communication Research, Department of Clinical Neuroscience, Karolinska Institutet, Karolinska University Hospital, M1:01, SE-171 76 Stockholm (Sweden); Inganaes, O, E-mail: maria.asplund@sth.kth.s [Biomolecular and Organic Electronics, IFM, Linkoeping University, SE-581 83 Linkoeping (Sweden)

    2009-08-15

    Electrodes coated with the conducting polymer poly(3,4-ethylene dioxythiophene) (PEDOT) possess attractive electrochemical properties for stimulation or recording in the nervous system. Biomolecules, added as counter ions in electropolymerization, could further improve the biomaterial properties, eliminating the need for surfactant counter ions in the process. Such PEDOT/biomolecular composites, using heparin or hyaluronic acid, have previously been investigated electrochemically. In the present study, their biocompatibility is evaluated. An agarose overlay assay using L929 fibroblasts, and elution and direct contact tests on human neuroblastoma SH-SY5Y cells are applied to investigate cytotoxicity in vitro. PEDOT:heparin was further evaluated in vivo through polymer-coated implants in rodent cortex. No cytotoxic response was seen to any of the PEDOT materials tested. The examination of cortical tissue exposed to polymer-coated implants showed extensive glial scarring irrespective of implant material (Pt:polymer or Pt). However, quantification of immunological response, through distance measurements from implant site to closest neuron and counting of ED1+ cell density around implant, was comparable to those of platinum controls. These results indicate that PEDOT:heparin surfaces were non-cytotoxic and show no marked difference in immunological response in cortical tissue compared to pure platinum controls.

  19. Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components.

    Science.gov (United States)

    Pardee, Keith; Green, Alexander A; Takahashi, Melissa K; Braff, Dana; Lambert, Guillaume; Lee, Jeong Wook; Ferrante, Tom; Ma, Duo; Donghia, Nina; Fan, Melina; Daringer, Nichole M; Bosch, Irene; Dudley, Dawn M; O'Connor, David H; Gehrke, Lee; Collins, James J

    2016-05-19

    The recent Zika virus outbreak highlights the need for low-cost diagnostics that can be rapidly developed for distribution and use in pandemic regions. Here, we report a pipeline for the rapid design, assembly, and validation of cell-free, paper-based sensors for the detection of the Zika virus RNA genome. By linking isothermal RNA amplification to toehold switch RNA sensors, we detect clinically relevant concentrations of Zika virus sequences and demonstrate specificity against closely related Dengue virus sequences. When coupled with a novel CRISPR/Cas9-based module, our sensors can discriminate between viral strains with single-base resolution. We successfully demonstrate a simple, field-ready sample-processing workflow and detect Zika virus from the plasma of a viremic macaque. Our freeze-dried biomolecular platform resolves important practical limitations to the deployment of molecular diagnostics in the field and demonstrates how synthetic biology can be used to develop diagnostic tools for confronting global health crises. PAPERCLIP.

  20. A method for rapid quantitative assessment of biofilms with biomolecular staining and image analysis.

    Science.gov (United States)

    Larimer, Curtis; Winder, Eric; Jeters, Robert; Prowant, Matthew; Nettleship, Ian; Addleman, Raymond Shane; Bonheyo, George T

    2016-01-01

    The accumulation of bacteria in surface-attached biofilms can be detrimental to human health, dental hygiene, and many industrial processes. Natural biofilms are soft and often transparent, and they have heterogeneous biological composition and structure over micro- and macroscales. As a result, it is challenging to quantify the spatial distribution and overall intensity of biofilms. In this work, a new method was developed to enhance the visibility and quantification of bacterial biofilms. First, broad-spectrum biomolecular staining was used to enhance the visibility of the cells, nucleic acids, and proteins that make up biofilms. Then, an image analysis algorithm was developed to objectively and quantitatively measure biofilm accumulation from digital photographs and results were compared to independent measurements of cell density. This new method was used to quantify the growth intensity of Pseudomonas putida biofilms as they grew over time. This method is simple and fast, and can quantify biofilm growth over a large area with approximately the same precision as the more laborious cell counting method. Stained and processed images facilitate assessment of spatial heterogeneity of a biofilm across a surface. This new approach to biofilm analysis could be applied in studies of natural, industrial, and environmental biofilms. PMID:26643074

  1. AFMPB: An adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems

    Science.gov (United States)

    Lu, Benzhuo; Cheng, Xiaolin; Huang, Jingfang; McCammon, J. Andrew

    2013-11-01

    A Fortran program package is introduced for rapid evaluation of the electrostatic potentials and forces in biomolecular systems modeled by the linearized Poisson-Boltzmann equation. The numerical solver utilizes a well-conditioned boundary integral equation (BIE) formulation, a node-patch discretization scheme, a Krylov subspace iterative solver package with reverse communication protocols, and an adaptive new version of the fast multipole method in which the exponential expansions are used to diagonalize the multipole-to-local translations. The program and its full description, as well as several closely related libraries and utility tools are available at http://lsec.cc.ac.cn/~lubz/afmpb.html and a mirror site at http://mccammon.ucsd.edu/. This paper is a brief summary of the program: the algorithms, the implementation and the usage. Restrictions: Only three or six significant digits options are provided in this version. Unusual features: Most of the codes are in Fortran77 style. Memory allocation functions from Fortran90 and above are used in a few subroutines. Additional comments: The current version of the codes is designed and written for single core/processor desktop machines. Check http://lsec.cc.ac.cn/lubz/afmpb.html for updates and changes. Running time: The running time varies with the number of discretized elements (N) in the system and their distributions. In most cases, it scales linearly as a function of N.

  2. Amplified Immunoassay of Human IgG Using Real-time Biomolecular Interaction Analysis (BIA) Technology

    Institute of Scientific and Technical Information of China (English)

    PEI,Ren-Jun(裴仁军); CUI,Xiao-Qiang(崔小强); YANG,Xiu-Rong(杨秀荣); WANG,Er-Kang(汪尔康)

    2002-01-01

    An automated biomolecular interaction analysis instrument (BIAcore) based on surface plasmon resonance (SPR) has been used to determine human immunoglobulin G (IgG) in real time. Polyclonal anti-human IgG antibody was covalently immobilized to a carboxymethyldextran-modified gold film surface. The samples of human IgG prepared in HBS buffer were poured over the immobilized surface. The signal amplification antibody was applied to amplify the response signal. After each measurement, the surface was regenerated with 0.1 mol/L H3PO4. The assay was rapid, requiring only 30 min for antibody immobilization and 20 min for each subsequent process of immune binding, antibody amplification and regeneration. The antibody immobilized surface had good response to human IgG in the range of 0.12-60 nmol/L with a detection limit of 60 pmoL/L. The same antibody immobilized surface could be used for more than 110 cycles of binding, amplificafion and regeneration. The results demonstrate that the sensitivity, specificity and reproducibility of amplified immunoassay using real-time BIA technology are satisfactory.

  3. Biomolecular environment, quantification, and intracellular interaction of multifunctional magnetic SERS nanoprobes.

    Science.gov (United States)

    Büchner, Tina; Drescher, Daniela; Merk, Virginia; Traub, Heike; Guttmann, Peter; Werner, Stephan; Jakubowski, Norbert; Schneider, Gerd; Kneipp, Janina

    2016-08-15

    Multifunctional composite nanoprobes consisting of iron oxide nanoparticles linked to silver and gold nanoparticles, Ag-Magnetite and Au-Magnetite, respectively, were introduced by endocytic uptake into cultured fibroblast cells. The cells containing the non-toxic nanoprobes were shown to be displaceable in an external magnetic field and can be manipulated in microfluidic channels. The distribution of the composite nanostructures that are contained in the endosomal system is discussed on the basis of surface-enhanced Raman scattering (SERS) mapping, quantitative laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) micromapping, and cryo soft X-ray tomography (cryo soft-XRT). Cryo soft-XRT of intact, vitrified cells reveals that the composite nanoprobes form intra-endosomal aggregates. The nanoprobes provide SERS signals from the biomolecular composition of their surface in the endosomal environment. The SERS data indicate the high stability of the nanoprobes and of their plasmonic properties in the harsh environment of endosomes and lysosomes. The spectra point at the molecular composition at the surface of the Ag-Magnetite and Au-Magnetite nanostructures that is very similar to that of other composite structures, but different from the composition of pure silver and gold SERS nanoprobes used for intracellular investigations. As shown by the LA-ICP-MS data, the uptake efficiency of the magnetite composites is approximately two to three times higher than that of the pure gold and silver nanoparticles. PMID:27353290

  4. A coarse-grained model for the simulations of biomolecular interactions in cellular environments

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao, E-mail: yinghao.wu@einstein.yu.edu [Department of Systems and Computational Biology, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, New York 10461 (United States)

    2014-02-07

    The interactions of bio-molecules constitute the key steps of cellular functions. However, in vivo binding properties differ significantly from their in vitro measurements due to the heterogeneity of cellular environments. Here we introduce a coarse-grained model based on rigid-body representation to study how factors such as cellular crowding and membrane confinement affect molecular binding. The macroscopic parameters such as the equilibrium constant and the kinetic rate constant are calibrated by adjusting the microscopic coefficients used in the numerical simulations. By changing these model parameters that are experimentally approachable, we are able to study the kinetic and thermodynamic properties of molecular binding, as well as the effects caused by specific cellular environments. We investigate the volumetric effects of crowded intracellular space on bio-molecular diffusion and diffusion-limited reactions. Furthermore, the binding constants of membrane proteins are currently difficult to measure. We provide quantitative estimations about how the binding of membrane proteins deviates from soluble proteins under different degrees of membrane confinements. The simulation results provide biological insights to the functions of membrane receptors on cell surfaces. Overall, our studies establish a connection between the details of molecular interactions and the heterogeneity of cellular environments.

  5. Biomolecular Nano-Flow-Sensor to Measure Near-Surface Flow

    Directory of Open Access Journals (Sweden)

    Noji Hiroyuki

    2009-01-01

    Full Text Available Abstract We have proposed and experimentally demonstrated that the measurement of the near-surface flow at the interface between a liquid and solid using a 10 nm-sized biomolecular motor of F1-ATPase as a nano-flow-sensor. For this purpose, we developed a microfluidic test-bed chip to precisely control the liquid flow acting on the F1-ATPase. In order to visualize the rotation of F1-ATPase, several hundreds nanometer-sized particle was immobilized at the rotational axis of F1-ATPase to enhance the rotation to be detected by optical microscopy. The rotational motion of F1-ATPase, which was immobilized on an inner surface of the test-bed chip, was measured to obtain the correlation between the near-surface flow and the rotation speed of F1-ATPase. As a result, we obtained the relationship that the rotation speed of F1-ATPase was linearly decelerated with increasing flow velocity. The mechanism of the correlation between the rotation speed and the near-surface flow remains unclear, however the concept to use biomolecule as a nano-flow-sensor was proofed successfully. (See supplementary material 1 Electronic supplementary material The online version of this article (doi:10.1007/s11671-009-9479-3 contains supplementary material, which is available to authorized users. Click here for file

  6. Extension of the GLYCAM06 Biomolecular Force Field to Lipids, Lipid Bilayers and Glycolipids.

    Science.gov (United States)

    Tessier, Matthew B; Demarco, Mari L; Yongye, Austin B; Woods, Robert J

    2008-01-01

    GLYCAM06 is a generalisable biomolecular force field that is extendible to diverse molecular classes in the spirit of a small-molecule force field. Here we report parameters for lipids, lipid bilayers and glycolipids for use with GLYCAM06. Only three lipid-specific atom types have been introduced, in keeping with the general philosophy of transferable parameter development. Bond stretching, angle bending, and torsional force constants were derived by fitting to quantum mechanical data for a collection of minimal molecular fragments and related small molecules. Partial atomic charges were computed by fitting to ensemble-averaged quantum-computed molecular electrostatic potentials.In addition to reproducing quantum mechanical internal rotational energies and experimental valence geometries for an array of small molecules, condensed-phase simulations employing the new parameters are shown to reproduce the bulk physical properties of a DMPC lipid bilayer. The new parameters allow for molecular dynamics simulations of complex systems containing lipids, lipid bilayers, glycolipids, and carbohydrates, using an internally consistent force field. By combining the AMBER parameters for proteins with the GLYCAM06 parameters, it is also possible to simulate protein-lipid complexes and proteins in biologically relevant membrane-like environments. PMID:22247593

  7. Bio-objectifying European bodies: standardisation of biobanks in the Biobanking and Biomolecular Resources Research Infrastructure.

    Science.gov (United States)

    Tamminen, Sakari

    2015-01-01

    The article traces the genealogy of the Minimum Information About Biobank Data Sharing model, created in the European Biobanking and Biomolecular Resources Research Infrastructure to facilitate collaboration among biobanks and to foster the exchange of biological samples and data. This information model is aimed at the identification of biobanks; unification of databases; and objectification of the information, samples, and related studies - to create a completely new 'bio-object infrastructure' within the EU. The paper discusses key challenges in creating a 'universal' information model of such a kind, the most important technical translations of European research policy needed for a standardised model for biobank information, and how this model creates new bio-objects. The author claims that this amounts to redefinition of biobanks and technical governance over virtually bio-objectified European populations. It is argued here that old governance models based on the nation-state need radical reconsideration so that we are prepared for a new and changing situation wherein bodies of information that lack organs flow from one database to another with a click of a mouse. PMID:26626620

  8. Indirect readout in protein-peptide recognition: a different story from classical biomolecular recognition.

    Science.gov (United States)

    Yu, Hua; Zhou, Peng; Deng, Maolin; Shang, Zhicai

    2014-07-28

    Protein-peptide interactions are prevalent and play essential roles in many living activities. Peptides recognize their protein partners by direct nonbonded interactions and indirect adjustment of conformations. Although processes of protein-peptide recognition have been comprehensively studied in both sequences and structures recently, flexibility of peptides and the configuration entropy penalty in recognition did not get enough attention. In this study, 20 protein-peptide complexes and their corresponding unbound peptides were investigated by molecular dynamics simulations. Energy analysis revealed that configurational entropy penalty introduced by restriction of the degrees of freedom of peptides in indirect readout process of protein-peptide recognition is significant. Configurational entropy penalty has become the main content of the indirect readout energy in protein-peptide recognition instead of deformation energy which is the main source of the indirect readout energy in classical biomolecular recognition phenomena, such as protein-DNA binding. These results provide us a better understanding of protein-peptide recognition and give us some implications in peptide ligand design.

  9. Magneto-optical relaxation measurements for the characterization of biomolecular interactions

    International Nuclear Information System (INIS)

    Measurements of the magneto-optical relaxation of ferrofluids (MORFF) were applied as a novel homogeneous immunoassay for the investigation of biomolecular interactions. The technique is based on magnetic nanoparticles (MNP) functionalized with antibodies. The relaxation time of the optical birefringence that occurs when a pulsed magnetic field is applied to the nanoparticle suspension depends on the particle size. This enables the detection of particle aggregates formed after the addition of the antigen coupling partner. MORFF size measurements on the original ferrofluid and its fractions obtained by magnetic fractionation are comparable with results from other methods such as atomic force microscopy and photon correlation spectroscopy. In kinetic studies, the binding properties of five antigens and their polyclonal antibodies were investigated: human immunoglobulin G (hIgG), human immunoglobulin M (hIgM), human Eotaxin (hEotaxin), human carcinoembryonic antigen (hCEA), and human insulin (hInsulin). The enlargement of the relaxation time observed during the coupling experiments is expressed in terms of a size distribution function, which includes MNP monomers as well as aggregates. The kinetic process can be described by a model of stepwise polymerization. The kinetic parameters obtained are compared to results of surface plasmon resonance measurements

  10. Bridge- and Solvent-Mediated Intramolecular Electronic Communications in Ubiquinone-Based Biomolecular Wires

    Science.gov (United States)

    Liu, Xiao-Yuan; Ma, Wei; Zhou, Hao; Cao, Xiao-Ming; Long, Yi-Tao

    2015-05-01

    Intramolecular electronic communications of molecular wires play a crucial role for developing molecular devices. In the present work, we describe different degrees of intramolecular electronic communications in the redox processes of three ubiquinone-based biomolecular wires (Bis-CoQ0s) evaluated by electrochemistry and Density Functional Theory (DFT) methods in different solvents. We found that the bridges linkers have a significant effect on the electronic communications between the two peripheral ubiquinone moieties and solvents effects are limited and mostly depend on the nature of solvents. The DFT calculations for the first time indicate the intensity of the electronic communications during the redox processes rely on the molecular orbital elements VL for electron transfer (half of the energy splitting of the LUMO and LUMO+1), which is could be affected by the bridges linkers. The DFT calculations also demonstrates the effect of solvents on the latter two-electron transfer of Bis-CoQ0s is more significant than the former two electrons transfer as the observed electrochemical behaviors of three Bis-CoQ0s. In addition, the electrochemistry and theoretical calculations reveal the intramolecular electronic communications vary in the four-electron redox processes of three Bis-CoQ0s.

  11. An Atomic Force Microscope with Dual Actuation Capability for Biomolecular Experiments

    Science.gov (United States)

    Sevim, Semih; Shamsudhin, Naveen; Ozer, Sevil; Feng, Luying; Fakhraee, Arielle; Ergeneman, Olgaç; Pané, Salvador; Nelson, Bradley J.; Torun, Hamdi

    2016-06-01

    We report a modular atomic force microscope (AFM) design for biomolecular experiments. The AFM head uses readily available components and incorporates deflection-based optics and a piezotube-based cantilever actuator. Jetted-polymers have been used in the mechanical assembly, which allows rapid manufacturing. In addition, a FeCo-tipped electromagnet provides high-force cantilever actuation with vertical magnetic fields up to 0.55 T. Magnetic field calibration has been performed with a micro-hall sensor, which corresponds well with results from finite element magnetostatics simulations. An integrated force resolution of 1.82 and 2.98 pN, in air and in DI water, respectively was achieved in 1 kHz bandwidth with commercially available cantilevers made of Silicon Nitride. The controller and user interface are implemented on modular hardware to ensure scalability. The AFM can be operated in different modes, such as molecular pulling or force-clamp, by actuating the cantilever with the available actuators. The electromagnetic and piezoelectric actuation capabilities have been demonstrated in unbinding experiments of the biotin-streptavidin complex.

  12. A new source for quantum optics with biomolecules and biomolecular clusters

    Science.gov (United States)

    Marksteiner, Markus; Haslinger, Philipp; Ulbricht, Hendrik; Arndt, Markus

    2008-03-01

    We present recent progress towards matter wave experiments with amino acids, polypeptides and large biomolecular clusters. All successful experiments on macromolecule interferometry so far, with fullerenes, fullerene derivates and large perfluoroalkyl-functionalized azobenzenes used effusive beam sources. The combination of Stark deflectometry with quantum interferometry also allowed us to create a new device for precisely measuring electric susceptibilities of large molecules in the gas phase. In order to apply quantum interference to molecules of biological interest, we have now implemented a pulsed laser desorption source. The combination of UV laser desorption into an intense noble gas jet and single-photon ionization by a VUV excimer laser (157nm) allows us to observe intense neutral jets of amino acids (e.g. Tryptophan), nucleotides (e.g. Guanin) and polypeptides ranging from tri-peptides to Gramicidin. Remarkably, we also found a new method for producing large neutral amino acid clusters, such as for instance Trp30, with masses exceeding 6000 amu: the addition of alkaline Earth salts in the desorption process leads to the inclusion of at least one metal atom per complex and is sufficient to catalyze the cluster formation process.

  13. Calculating free-energy profiles in biomolecular systems from fast nonequilibrium processes

    Science.gov (United States)

    Forney, Michael W.; Janosi, Lorant; Kosztin, Ioan

    2008-11-01

    Often gaining insight into the functioning of biomolecular systems requires to follow their dynamics along a microscopic reaction coordinate (RC) on a macroscopic time scale, which is beyond the reach of current all atom molecular dynamics (MD) simulations. A practical approach to this inherently multiscale problem is to model the system as a fictitious overdamped Brownian particle that diffuses along the RC in the presence of an effective potential of mean force (PMF) due to the rest of the system. By employing the recently proposed FR method [I. Kosztin , J. Chem. Phys. 124, 064106 (2006)], which requires only a small number of fast nonequilibrium MD simulations of the system in both forward and time reversed directions along the RC, we reconstruct the PMF: (1) of deca-alanine as a function of its end-to-end distance, and (2) that guides the motion of potassium ions through the gramicidin A channel. In both cases the computed PMFs are found to be in good agreement with previous results obtained by different methods. Our approach appears to be about one order of magnitude faster than the other PMF calculation methods and, in addition, it also provides the position-dependent diffusion coefficient along the RC. Thus, the obtained PMF and diffusion coefficient can be used in an overdamped Brownian model to estimate important characteristics of the studied systems, e.g., the mean folding time of the stretched deca-alanine and the mean diffusion time of the potassium ion through gramicidin A.

  14. Calculating free energy profiles in biomolecular systems from fast non-equilibrium processes

    CERN Document Server

    Forney, Michael; Kosztin, Ioan

    2008-01-01

    Often gaining insight into the functioning of biomolecular systems requires to follow their dynamics along a microscopic reaction coordinate (RC) on a macroscopic time scale, which is beyond the reach of current all atom molecular dynamics (MD) simulations. A practical approach to this inherently multiscale problem is to model the system as a fictitious overdamped Brownian particle that diffuses along the RC in the presence of an effective potential of mean force (PMF) due to the rest of the system. By employing the recently proposed FR method [I. Kosztin et al., J. of Chem. Phys. 124, 064106 (2006)], which requires only a small number of fast nonequilibrium MD simulations of the system in both forward and time reversed directions along the RC, we reconstruct the PMF: (1) of deca-alanine as a function of its end-to-end distance, and (2) that guides the motion of potassium ions through the gramicidin A channel. In both cases the computed PMFs are found to be in good agreement with previous results obtained by ...

  15. Drug Transport Microdevice Mimicking an Idealized Nanoscale Bio-molecular Motor

    Institute of Scientific and Technical Information of China (English)

    Jae Hwan Lee; Ramana M. Pidaparti

    2011-01-01

    Molecular motors are nature's nano-devices and the essential agents of movement that are an integral part of many living organisms.The supramolecular motor,called Nuclear Pore Complex (NPC),controls the transport of all cellular material between the cytoplasm and the nucleus that occurs naturally in biological cells of many organisms.In order to understand the design characteristics of the NPC,we developed a microdevice for drug/fluidic transport mimicking the coarse-grained representation of the NPC geometry through computational fluid dynamic analysis and optimization.Specifically,the role of the central plug in active fluidic/particle transport and passive transport (without central plug) was investigated.Results of flow rate,pressure and velocity profiles obtained from the models indicate that the central plug plays a major role in transport through this biomolecular machine.The results of this investigation show that fluidic transport and flow passages are important factors in designing NPC based nano- and micro-devices for drug delivery.

  16. A smartphone-based colorimetric reader for bioanalytical applications using the screen-based bottom illumination provided by gadgets.

    Science.gov (United States)

    Vashist, Sandeep Kumar; van Oordt, Thomas; Schneider, E Marion; Zengerle, Roland; von Stetten, Felix; Luong, John H T

    2015-05-15

    A smartphone-based colorimetric reader (SBCR) was developed using a Samsung Galaxy SIII mini, a gadget (iPAD mini, iPAD4 or iPhone 5s), integrated with a custom-made dark hood and base holder assembly. The smartphone equipped with a back camera (5 megapixels resolution) was used for colorimetric imaging via the hood and base-holder assembly. A 96- or 24-well microtiter plate (MTP) was positioned on the gadget's screensaver that provides white light-based bottom illumination only in the specific regions corresponding to the bottom of MTP's wells. The pixel intensity of the captured images was determined by an image processing algorithm. The developed SBCR was evaluated and compared with a commercial MTP reader (MTPR) for three model assays: our recently developed human C-reactive protein sandwich enzyme-linked immunosorbent assay (ELISA), horseradish peroxidase direct ELISA, and bicinchoninic acid protein estimation assay. SBCR had the same precision, dynamic range, detection limit and sensitivity as MTPR for all three assays. With advanced microfabrication and data processing, SBCR will become more compact, lighter, inexpensive and enriched with more features. Therefore, SBCR with a remarkable computing power could be an ideal point-of-care (POC) colorimetric detection device for the next-generation of cost-effective POC diagnostics, immunoassays and diversified bioanalytical applications.

  17. A smartphone-based colorimetric reader for bioanalytical applications using the screen-based bottom illumination provided by gadgets.

    Science.gov (United States)

    Vashist, Sandeep Kumar; van Oordt, Thomas; Schneider, E Marion; Zengerle, Roland; von Stetten, Felix; Luong, John H T

    2015-05-15

    A smartphone-based colorimetric reader (SBCR) was developed using a Samsung Galaxy SIII mini, a gadget (iPAD mini, iPAD4 or iPhone 5s), integrated with a custom-made dark hood and base holder assembly. The smartphone equipped with a back camera (5 megapixels resolution) was used for colorimetric imaging via the hood and base-holder assembly. A 96- or 24-well microtiter plate (MTP) was positioned on the gadget's screensaver that provides white light-based bottom illumination only in the specific regions corresponding to the bottom of MTP's wells. The pixel intensity of the captured images was determined by an image processing algorithm. The developed SBCR was evaluated and compared with a commercial MTP reader (MTPR) for three model assays: our recently developed human C-reactive protein sandwich enzyme-linked immunosorbent assay (ELISA), horseradish peroxidase direct ELISA, and bicinchoninic acid protein estimation assay. SBCR had the same precision, dynamic range, detection limit and sensitivity as MTPR for all three assays. With advanced microfabrication and data processing, SBCR will become more compact, lighter, inexpensive and enriched with more features. Therefore, SBCR with a remarkable computing power could be an ideal point-of-care (POC) colorimetric detection device for the next-generation of cost-effective POC diagnostics, immunoassays and diversified bioanalytical applications. PMID:25168283

  18. Application of DNA Hybridization Biosensor as a Screening Method for the Detection of Genetically Modified Food Components

    Directory of Open Access Journals (Sweden)

    Marian Filipiak

    2008-03-01

    Full Text Available An electrochemical biosensor for the detection of genetically modified food components is presented. The biosensor was based on 21-mer single-stranded oligonucleotide (ssDNA probe specific to either 35S promoter or nos terminator, which are frequently present in transgenic DNA cassettes. ssDNA probe was covalently attached by 5’-phosphate end to amino group of cysteamine self-assembled monolayer (SAM on gold electrode surface with the use of activating reagents – water soluble 1-ethyl-3(3’- dimethylaminopropyl-carbodiimide (EDC and N-hydroxy-sulfosuccinimide (NHS. The hybridization reaction on the electrode surface was detected via methylene blue (MB presenting higher affinity to ssDNA probe than to DNA duplex. The electrode modification procedure was optimized using 19-mer oligoG and oligoC nucleotides. The biosensor enabled distinction between DNA samples isolated from soybean RoundupReady® (RR soybean and non-genetically modified soybean. The frequent introduction of investigated DNA sequences in other genetically modified organisms (GMOs give a broad perspectives for analytical application of the biosensor.

  19. Intensifying screens in transaxial tomography

    International Nuclear Information System (INIS)

    This patent claim by Agfa-Gevaert relates to a method for the production of transaxial tomographs, a combination of materials therefor and X-ray intensifying screens incorporating at least one reflecting element for use in transaxial tomography, wherein the exposure of a photographic silver halide emulsion material proceeds at an angle within the range of 20 to 100 in conjunction with an X-ray fluorescent intensifying screen including an ultra-violet and/or visible radiation reflective coating or sheet to increase the radiation output of the screen and to reduce the exposure time and radiation dose e.g. in medical X-ray applications. (author)

  20. The Configuration and the Application Programming of the Multi-screen Display under Windows 98%Windows 98下多屏显示的配置及应用编程技术

    Institute of Scientific and Technical Information of China (English)

    李芳; 郭兴旺

    2001-01-01

    介绍了Windows 98下一台计算机带多个显示器以扩大显示桌面的系统配置方法,论述了一机多屏环境下应用程序的开发技术,并给出用VB编写的例子程序。%Under Windows 98 a computer can drive several screens to magnify the display desk. The article introduces the system configuration and the application programming of the multi-screen display, and gives a sample program in Visual Basic.

  1. Design and Application of a New Type of Rocking Bar Screening Device%一种摇杆式筛分器的设计与应用

    Institute of Scientific and Technical Information of China (English)

    高顺利; 陈继富; 颛孙伟

    2011-01-01

    介绍一种新型的摇杆式筛分器,解决了传统筛分器存在的噪声大,故障率高,筛分效率低的问题,也改善了可维修性性能.%This paper introduces a new type of rocking bar screening device, which is used to solve large noise, high failure rate, low the screening efficiency and high maintenance of the traditional screening device.

  2. Development of a Clinical Forecasting Model to Predict Comorbid Depression Among Diabetes Patients and an Application in Depression Screening Policy Making

    OpenAIRE

    Jin, Haomiao; Wu, Shinyi; Di Capua, Paul

    2015-01-01

    Introduction Depression is a common but often undiagnosed comorbid condition of people with diabetes. Mass screening can detect undiagnosed depression but may require significant resources and time. The objectives of this study were 1) to develop a clinical forecasting model that predicts comorbid depression among patients with diabetes and 2) to evaluate a model-based screening policy that saves resources and time by screening only patients considered as depressed by the clinical forecasting...

  3. Real-Time, Label-Free Detection of Biomolecular Interactions in Sandwich Assays by the Oblique-Incidence Reflectivity Difference Technique

    Directory of Open Access Journals (Sweden)

    Yung-Shin Sun

    2014-12-01

    Full Text Available One of the most important goals in proteomics is to detect the real-time kinetics of diverse biomolecular interactions. Fluorescence, which requires extrinsic tags, is a commonly and widely used method because of its high convenience and sensitivity. However, in order to maintain the conformational and functional integrality of biomolecules, label-free detection methods are highly under demand. We have developed the oblique-incidence reflectivity difference (OI-RD technique for label-free, kinetic measurements of protein-biomolecule interactions. Incorporating the total internal refection geometry into the OI-RD technique, we are able to detect as low as 0.1% of a protein monolayer, and this sensitivity is comparable with other label-free techniques such as surface plasmon resonance (SPR. The unique advantage of OI-RD over SPR is no need for dielectric layers. Moreover, using a photodiode array as the detector enables multi-channel detection and also eliminates the over-time signal drift. In this paper, we demonstrate the applicability and feasibility of the OI-RD technique by measuring the kinetics of protein-protein and protein-small molecule interactions in sandwich assays.

  4. Data Mining Approaches for Genomic Biomarker Development: Applications Using Drug Screening Data from the Cancer Genome Project and the Cancer Cell Line Encyclopedia.

    Directory of Open Access Journals (Sweden)

    David G Covell

    Full Text Available Developing reliable biomarkers of tumor cell drug sensitivity and resistance can guide hypothesis-driven basic science research and influence pre-therapy clinical decisions. A popular strategy for developing biomarkers uses characterizations of human tumor samples against a range of cancer drug responses that correlate with genomic change; developed largely from the efforts of the Cancer Cell Line Encyclopedia (CCLE and Sanger Cancer Genome Project (CGP. The purpose of this study is to provide an independent analysis of this data that aims to vet existing and add novel perspectives to biomarker discoveries and applications. Existing and alternative data mining and statistical methods will be used to a evaluate drug responses of compounds with similar mechanism of action (MOA, b examine measures of gene expression (GE, copy number (CN and mutation status (MUT biomarkers, combined with gene set enrichment analysis (GSEA, for hypothesizing biological processes important for drug response, c conduct global comparisons of GE, CN and MUT as biomarkers across all drugs screened in the CGP dataset, and d assess the positive predictive power of CGP-derived GE biomarkers as predictors of drug response in CCLE tumor cells. The perspectives derived from individual and global examinations of GEs, MUTs and CNs confirm existing and reveal unique and shared roles for these biomarkers in tumor cell drug sensitivity and resistance. Applications of CGP-derived genomic biomarkers to predict the drug response of CCLE tumor cells finds a highly significant ROC, with a positive predictive power of 0.78. The results of this study expand the available data mining and analysis methods for genomic biomarker development and provide additional support for using biomarkers to guide hypothesis-driven basic science research and pre-therapy clinical decisions.

  5. Data Mining Approaches for Genomic Biomarker Development: Applications Using Drug Screening Data from the Cancer Genome Project and the Cancer Cell Line Encyclopedia.

    Science.gov (United States)

    Covell, David G

    2015-01-01

    Developing reliable biomarkers of tumor cell drug sensitivity and resistance can guide hypothesis-driven basic science research and influence pre-therapy clinical decisions. A popular strategy for developing biomarkers uses characterizations of human tumor samples against a range of cancer drug responses that correlate with genomic change; developed largely from the efforts of the Cancer Cell Line Encyclopedia (CCLE) and Sanger Cancer Genome Project (CGP). The purpose of this study is to provide an independent analysis of this data that aims to vet existing and add novel perspectives to biomarker discoveries and applications. Existing and alternative data mining and statistical methods will be used to a) evaluate drug responses of compounds with similar mechanism of action (MOA), b) examine measures of gene expression (GE), copy number (CN) and mutation status (MUT) biomarkers, combined with gene set enrichment analysis (GSEA), for hypothesizing biological processes important for drug response, c) conduct global comparisons of GE, CN and MUT as biomarkers across all drugs screened in the CGP dataset, and d) assess the positive predictive power of CGP-derived GE biomarkers as predictors of drug response in CCLE tumor cells. The perspectives derived from individual and global examinations of GEs, MUTs and CNs confirm existing and reveal unique and shared roles for these biomarkers in tumor cell drug sensitivity and resistance. Applications of CGP-derived genomic biomarkers to predict the drug response of CCLE tumor cells finds a highly significant ROC, with a positive predictive power of 0.78. The results of this study expand the available data mining and analysis methods for genomic biomarker development and provide additional support for using biomarkers to guide hypothesis-driven basic science research and pre-therapy clinical decisions.

  6. 胸片和临床症状肺结核筛查的应用价值%Application Value of Chest X-Ray and Clinical Symptoms of Pulmonary Tuberculosis Screening

    Institute of Scientific and Technical Information of China (English)

    张延安

    2014-01-01

    Objective: To evaluate the value of clinical application of chest X-ray and clinical symptoms of pulmonary TB screening. Methods:All objects by symptoms, chest X-ray screening questionnaire (CXR), and (or) sputum smear or culture. Results:There were abnormal CXR sensitivity was 94%, specificity was 73%. The sensitivity of screening with symptoms was 90%, the specificity was 32%. Smear microscopy failed to increase the suspicious patients, joint symptoms and CXR screening sensitivity was 100%, specificity was 65%. Conclusion:Only by CXR screening showed that the accuracy of screening compared with symptoms of high, combined with CXR and symptom screening has the highest sensitivity.%目的:评估胸片和临床症状对肺TB筛查的应用价值。方法:所有对象经症状问卷筛查、胸片(CXR)、和(或)痰涂片或培养。结果:存在CXR异常者敏感性为94%,特异性为73%。症状筛查结合的敏感性为90%,特异性为32%。涂片显微镜检查未能增加可疑病人,联合症状和CXR筛查敏感性达100%,特异性达65%。结论:仅用CXR筛查即呈现较单纯症状筛查高的准确度,联合CXR和症状筛查有最高的敏感性。

  7. Comparison of Four Kinds of Nutritional Screening Tools in Clinical Application of General Surgery Pa-tients Application%4种营养筛查工具在普外科患者中应用的比较

    Institute of Scientific and Technical Information of China (English)

    包学智; 田伟军

    2015-01-01

    目的:使用NRS2002和SGA、MNA、NRI 4种工具对普外科入院患者进行营养状态调查,比较4种工具的适用性和一致性以及每种工具所得筛查结果和临床结局的关系。方法:采用连续取样方法选取天津医科大学总医院普外科收治的125名患者为研究对象,当患者入院第2 d分别应用NRS2002和SGA、MNA、NRI进行营养筛查和评估,并比较每种工具所得筛查结果和临床结局的关系。结果:入院NRS2002、SGA及MNA适用性91.91%,NRI适用性91.18%,4种方法对患者营养风险的评价具有一致性。将BMI≤18.5或ALB≤30 g/L作为营养不良的一个标准,4种评价工具与该标准的一致性较差。NRS2002、SGA筛查结果和临床结局的关系最为密切。结论:4种营养评价工具均适用于普外科营养不足的筛查。NRS2002、SGA筛查结果和临床结局的关系最为密切。%Objective NRS2002, SGA, MNA and NRI are used to screen nutritional risk of general surgery hospitalized patients, then to compare their applicability and consistency and analyze the effect in clinical out⁃comes of NRS results with respect to each tool. Methods The 125 patients hospitalized in General Hospital of Tianjin Medical University from June to September 2014 were chosen as object of study, to screen and evalu⁃ate nutritional risk of patients by NRS 2002, SGA, MNA and NRI, respectively, on the second hospital day. Then to compare the consistency of NRS results with respect to the four tools on clinical outcomes. Results The applicabilities of hospital NRS2002, SGA, MNA and NRI were alternatively 91.91%,91.91%,91.91% and 91.18%.The evaluation of patients’NRS corresponding to different four tools was consistent. Let BMI≤18.5 or ALB≤30 g/L be one standard of malnutrition, the consistency of four evaluation tools and the standard was poor. The effects of screening results of NRS2002 and SGA on clinical outcomes were most closely related. Conclusion

  8. 彩超在乳腺疾病筛查中的应用价值%Application value of color Doppler ultrasound in screening of breast diseases

    Institute of Scientific and Technical Information of China (English)

    徐亚丽

    2016-01-01

    Objective:To discuss the application value of color Doppler ultrasound in screening of breast diseases.Methods:Screening and diagnosis of breast diseases with two dimensional ultrasound and color Doppler,the diagnosis and treatment of positive cases were offered,and the diagnosis and pathological results were compared,the diagnosis and treatment were followed up. Results:In 8 014 healthy people,colour exceeds clew 2 081 cases of breast hyperplasia,341 cases of mammary gland fibroma, breast intraductal papilloma 148 cases,29 cases of breast cysts,mastitis in 1 case,4 cases of breast cancer,benign breast lesions 105 cases.Conclusion:Normal breast tissues and breast benign lesions were significantly different in the ultrasonic images,and the color Doppler ultrasound has the characteristics of non-invasive,simple,safe,repeatable and accurate.%目的:探讨彩超在乳腺疾病筛查中的临床应用价值.方法:用二维超声及彩色多普勒对乳腺疾病进行筛查诊断,对阳性病例及时提供诊治建议,并对其钼靶诊断及病理学结果进行对照分析,对诊治过程进行随访.结果:在 8 014例体检者中,彩超提示乳腺增生2 081例,乳腺纤维瘤341例,乳腺导管内乳头状瘤148例,乳腺囊肿29例,乳腺炎1例,乳腺癌4例,乳腺良性病变105例.结论:正常乳腺组织、乳腺良性恶性病变在超声声像图中有显著的差异,彩超具有无创、简捷、安全、可重复、准确性高等特点.

  9. Application value of color Doppler ultrasound in screening of breast diseases%彩超在乳腺疾病筛查中的应用价值

    Institute of Scientific and Technical Information of China (English)

    徐亚丽

    2016-01-01

    目的:探讨彩超在乳腺疾病筛查中的临床应用价值.方法:用二维超声及彩色多普勒对乳腺疾病进行筛查诊断,对阳性病例及时提供诊治建议,并对其钼靶诊断及病理学结果进行对照分析,对诊治过程进行随访.结果:在 8 014例体检者中,彩超提示乳腺增生2 081例,乳腺纤维瘤341例,乳腺导管内乳头状瘤148例,乳腺囊肿29例,乳腺炎1例,乳腺癌4例,乳腺良性病变105例.结论:正常乳腺组织、乳腺良性恶性病变在超声声像图中有显著的差异,彩超具有无创、简捷、安全、可重复、准确性高等特点.%Objective:To discuss the application value of color Doppler ultrasound in screening of breast diseases.Methods:Screening and diagnosis of breast diseases with two dimensional ultrasound and color Doppler,the diagnosis and treatment of positive cases were offered,and the diagnosis and pathological results were compared,the diagnosis and treatment were followed up. Results:In 8 014 healthy people,colour exceeds clew 2 081 cases of breast hyperplasia,341 cases of mammary gland fibroma, breast intraductal papilloma 148 cases,29 cases of breast cysts,mastitis in 1 case,4 cases of breast cancer,benign breast lesions 105 cases.Conclusion:Normal breast tissues and breast benign lesions were significantly different in the ultrasonic images,and the color Doppler ultrasound has the characteristics of non-invasive,simple,safe,repeatable and accurate.

  10. Screening and identification of phospholipase-producing strains and their applications%产磷脂酶菌株的筛选鉴定及其应用

    Institute of Scientific and Technical Information of China (English)

    姜芳燕; 王金梅; 戴大章; 李春

    2012-01-01

    采用磷脂平板初筛和摇瓶复筛,从富油土样中筛选得到一株产磷脂酶菌株BIT-18.经菌株形态特征、生理生化特征及16S rRNA序列分析,鉴定其为荧光假单胞菌(Pseudomonas fluorescens).以磷脂标准品(1-棕榈酰-2-油酰-Sn-甘油-3-磷脂酰胆碱)为底物,通过气相色谱分析反应产物的脂肪酸成分,定性鉴定P.fluorescens BIT-18表达的磷脂酶为B型磷脂酶.该酶为低温酶,最适温度和pH值分别为25℃和6.5,低浓度的金属离子有利于其酶促反应进行.以磷脂酶B为催化剂在自制间歇式反应器中对大豆油进行酶法脱胶,在加酶量500 U·kg-,加水量2%,温度40℃,pH 4.7的条件下反应6h,脱胶油磷含量由90.1 mg·kg-降至4.6 mg· kg-1,脱胶率高达94.9%,显示出良好的应用前景.%Using soybean phospholipids as substrates, one strain which expressed phospholipase was screened out from the oil-rich soil sample by preliminary screening of plate cultivation and re-screening of shake flask fermentation. According to the morphological characteristics, physiochemical properties, and 16S rRNA sequences, the strain BIT-18 was identified as Pseudomonas fluorescens. Synthetic phosphatecholine (l-palmitoyl-2-oleoyl phosphatecholine) was used as substrate, then the fatty acid compositions of hydrolyzates were analyzed by gas chromatography, and the phospholipase from BIT-18 was determined as phospholipase B. This enzyme could not tolerate a high temperature. The optimal conditions for the enzymatic reaction were 251 and pH 6. 5, and low concentrations of metal ions were good for trigging its reaction. The phospholipase B from BIT-18 was used as catalyst for the degumming of soybean oil in a self-made batch reactor. The optimal conditions were phospholipase B dosage of 500 U · kg-1 and 2% water, and reaction at 40℃ , pH 4. 7 for 6 h. The residual phosphorus content of degummed oil decreased from 90. 1 mg · kg-1 to 4. 6 mg · kg-1, with the degumming rate as

  11. Application of Fuzzy Comprehensive Evaluation in Formulation Screening%模糊综合评价法在处方筛选中的应用研究Δ

    Institute of Scientific and Technical Information of China (English)

    李龙龙; 郝鹏彬; 王文鹏; 冯玉康; 屈云萍; 姜国志; 李振江

    2015-01-01

    OBJECTIVE:To investigate the application of fuzzy comprehensive evaluation in formulation screening. METH-ODS:Taking Compound paracetamol and chlorphenamine maleate granules as model drug,based on single factor experiment,L9(34) orthogonal test was used to screen the formulation with the amount of aspartame,hawthorn powder essence,milk powder essence and saccharose as factors,using dissolution rate of caffeine as index. The granules prepared by 9 kinds of formulation in orthogonal test were evaluated with fuzzy comprehensive evaluation in terms of taste,aroma,color and dissolubility. The optimized formula-tion was validated and compared with original formulation. RESULTS:The formulation 5 was the optimal choice in both orthogo-nal test and fuzzy comprehensive evaluation,and obtained same results. Compared with sensory comprehensive score (63.12) and dissolution rate of caffeine (91.3%) in original formulation,two indicators of optimized formulation in 3 tests were 84.00 and 99.07% in average (RSD<2.0%,n=3). CONCLUSIONS:Fuzzy comprehensive evaluation can be used for the formulation screening of sensory evaluation index. It is scientific and accurate.%目的:探讨模糊综合评价法在处方筛选中的应用。方法:以复方氨酚那敏颗粒为模型药物,在单因素试验基础上,以阿司帕坦、山楂粉末香精、鲜奶精粉末香精、蔗糖加入量为因素,咖啡因溶出度为指标,进行4因素3水平正交试验设计筛选处方;应用模糊综合评价法对正交试验9个处方所制颗粒从滋味、香气、色泽、溶化性方面进行感官评价。对优选处方进行验证试验并与原处方进行比较。结果:正交试验与模糊综合评价的最优处方均为处方5,结果一致;与原处方的感官综合得分和咖啡因溶出度(63.12分、91.3%)比较,优选处方3次验证试验中2个指标的平均值分别为84.00分、99.07%(RSD<2.0%,n=3)。结论:模糊综合评价

  12. Scaling analysis of bio-molecular dynamics derived from elastic incoherent neutron scattering experiments

    Science.gov (United States)

    Doster, W.; Nakagawa, H.; Appavou, M. S.

    2013-07-01

    Numerous neutron scattering studies of bio-molecular dynamics employ a qualitative analysis of elastic scattering data and atomic mean square displacements. We provide a new quantitative approach showing that the intensity at zero energy exchange can be a rich source of information of bio-structural fluctuations on a pico- to nano-second time scale. Elastic intensity scans performed either as a function of the temperature (back-scattering) and/or by varying the instrumental resolution (time of flight spectroscopy) yield the activation parameters of molecular motions and the approximate structural correlation function in the time domain. The two methods are unified by a scaling function, which depends on the ratio of correlation time and instrumental resolution time. The elastic scattering concept is illustrated with a dynamic characterization of alanine-dipeptide, protein hydration water, and water-coupled protein motions of lysozyme, per-deuterated c-phycocyanin (CPC) and hydrated myoglobin. The complete elastic scattering function versus temperature, momentum exchange, and instrumental resolution is analyzed instead of focusing on a single cross-over temperature of mean square displacements at the apparent onset temperature of an-harmonic motions. Our method predicts the protein dynamical transition (PDT) at Td from the collective (α) structural relaxation rates of the solvation shell as input. By contrast, the secondary (β) relaxation enhances the amplitude of fast local motions in the vicinity of the glass temperature Tg. The PDT is specified by step function in the elastic intensity leading from elastic to viscoelastic dynamic behavior at a transition temperature Td.

  13. Morbillivirus infection in cetaceans stranded along the Italian coastline: pathological, immunohistochemical and biomolecular findings.

    Science.gov (United States)

    Di Guardo, Giovanni; Di Francesco, Cristina Esmeralda; Eleni, Claudia; Cocumelli, Cristiano; Scholl, Francesco; Casalone, Cristina; Peletto, Simone; Mignone, Walter; Tittarelli, Cristiana; Di Nocera, Fabio; Leonardi, Leonardo; Fernández, Antonio; Marcer, Federica; Mazzariol, Sandro

    2013-02-01

    Morbilliviruses are recognized as biological agents highly impacting the health and conservation status of free-ranging cetaceans worldwide, as clearly exemplified by the two Dolphin Morbillivirus (DMV) epidemics of 1990-1992 and 2006-2008 among Mediterranean striped dolphins (Stenella coeruleoalba). After these two epidemics, morbilliviral infection (MI) cases with peculiar neurobiological features were reported in striped dolphins stranded along the Spanish coastline. Affected cetaceans showed a subacute-to-chronic, non-suppurative encephalitis, with brain lesions strongly resembling those found in human "subacute sclerosing panencephalitis" and "old dog encephalitis". Brain was the only tissue in which morbilliviral antigen and/or genome could be detected. Beside a case of morbilliviral encephalitis in a striped dolphin's calf stranded in 2009, we observed 5 additional MI cases in 2 striped dolphins, 1 bottlenose dolphin (Tursiops truncatus) and 2 fin whales (Balaenoptera physalus), all stranded in 2011 along the Italian coastline. Noteworthy, 3 of these animals (2 striped dolphins and 1 bottlenose dolphin) showed immunohistochemical (IHC) and/or biomolecular (PCR) evidence of morbilliviral antigen and/or genome exclusively in their brain, with 1 striped dolphin and 1 bottlenose dolphin also exhibiting a non-suppurative encephalitis. Furthermore, simultaneous IHC and PCR evidence of a Toxoplasma gondii coinfection was obtained in 1 fin whale. The above results are consistent with those reported in striped dolphins after the two MI epidemics of 1990-92 and 2006-2008, with evidence of morbilliviral antigen and/or genome being found exclusively in the brain tissue from affected animals.

  14. Scaling analysis of bio-molecular dynamics derived from elastic incoherent neutron scattering experiments

    Energy Technology Data Exchange (ETDEWEB)

    Doster, W. [Physik-Department, Technische Universität München, D-85748 Garching (Germany); Nakagawa, H. [Jülich Centre for Neutron Science, Forschungszentrum Jülich GmbH, Outstation at MLZ, Lichtenbergstraße 1, 85747 Garching (Germany); Japan Atomic Energy Agency, Quantum Beam Science Directorate, Tokai, Ibaraki 319-1195 (Japan); Appavou, M. S. [Jülich Centre for Neutron Science, Forschungszentrum Jülich GmbH, Outstation at MLZ, Lichtenbergstraße 1, 85747 Garching (Germany)

    2013-07-28

    Numerous neutron scattering studies of bio-molecular dynamics employ a qualitative analysis of elastic scattering data and atomic mean square displacements. We provide a new quantitative approach showing that the intensity at zero energy exchange can be a rich source of information of bio-structural fluctuations on a pico- to nano-second time scale. Elastic intensity scans performed either as a function of the temperature (back-scattering) and/or by varying the instrumental resolution (time of flight spectroscopy) yield the activation parameters of molecular motions and the approximate structural correlation function in the time domain. The two methods are unified by a scaling function, which depends on the ratio of correlation time and instrumental resolution time. The elastic scattering concept is illustrated with a dynamic characterization of alanine-dipeptide, protein hydration water, and water-coupled protein motions of lysozyme, per-deuterated c-phycocyanin (CPC) and hydrated myoglobin. The complete elastic scattering function versus temperature, momentum exchange, and instrumental resolution is analyzed instead of focusing on a single cross-over temperature of mean square displacements at the apparent onset temperature of an-harmonic motions. Our method predicts the protein dynamical transition (PDT) at T{sub d} from the collective (α) structural relaxation rates of the solvation shell as input. By contrast, the secondary (β) relaxation enhances the amplitude of fast local motions in the vicinity of the glass temperature T{sub g}. The PDT is specified by step function in the elastic intensity leading from elastic to viscoelastic dynamic behavior at a transition temperature T{sub d}.

  15. Scaling analysis of bio-molecular dynamics derived from elastic incoherent neutron scattering experiments

    International Nuclear Information System (INIS)

    Numerous neutron scattering studies of bio-molecular dynamics employ a qualitative analysis of elastic scattering data and atomic mean square displacements. We provide a new quantitative approach showing that the intensity at zero energy exchange can be a rich source of information of bio-structural fluctuations on a pico- to nano-second time scale. Elastic intensity scans performed either as a function of the temperature (back-scattering) and/or by varying the instrumental resolution (time of flight spectroscopy) yield the activation parameters of molecular motions and the approximate structural correlation function in the time domain. The two methods are unified by a scaling function, which depends on the ratio of correlation time and instrumental resolution time. The elastic scattering concept is illustrated with a dynamic characterization of alanine-dipeptide, protein hydration water, and water-coupled protein motions of lysozyme, per-deuterated c-phycocyanin (CPC) and hydrated myoglobin. The complete elastic scattering function versus temperature, momentum exchange, and instrumental resolution is analyzed instead of focusing on a single cross-over temperature of mean square displacements at the apparent onset temperature of an-harmonic motions. Our method predicts the protein dynamical transition (PDT) at Td from the collective (α) structural relaxation rates of the solvation shell as input. By contrast, the secondary (β) relaxation enhances the amplitude of fast local motions in the vicinity of the glass temperature Tg. The PDT is specified by step function in the elastic intensity leading from elastic to viscoelastic dynamic behavior at a transition temperature Td

  16. Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields.

    Science.gov (United States)

    Yoo, Jejoong; Wilson, James; Aksimentiev, Aleksei

    2016-10-01

    Calcium ions (Ca(2+) ) play key roles in various fundamental biological processes such as cell signaling and brain function. Molecular dynamics (MD) simulations have been used to study such interactions, however, the accuracy of the Ca(2+) models provided by the standard MD force fields has not been rigorously tested. Here, we assess the performance of the Ca(2+) models from the most popular classical force fields AMBER and CHARMM by computing the osmotic pressure of model compounds and the free energy of DNA-DNA interactions. In the simulations performed using the two standard models, Ca(2+) ions are seen to form artificial clusters with chloride, acetate, and phosphate species; the osmotic pressure of CaAc2 and CaCl2 solutions is a small fraction of the experimental values for both force fields. Using the standard parameterization of Ca(2+) ions in the simulations of Ca(2+) -mediated DNA-DNA interactions leads to qualitatively wrong outcomes: both AMBER and CHARMM simulations suggest strong inter-DNA attraction whereas, in experiment, DNA molecules repel one another. The artificial attraction of Ca(2+) to DNA phosphate is strong enough to affect the direction of the electric field-driven translocation of DNA through a solid-state nanopore. To address these shortcomings of the standard Ca(2+) model, we introduce a custom model of a hydrated Ca(2+) ion and show that using our model brings the results of the above MD simulations in quantitative agreement with experiment. Our improved model of Ca(2+) can be readily applied to MD simulations of various biomolecular systems, including nucleic acids, proteins and lipid bilayer membranes. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 752-763, 2016. PMID:27144470

  17. An Analysis of Biomolecular Force Fields for Simulations of Polyglutamine in Solution

    Energy Technology Data Exchange (ETDEWEB)

    Fluitt, Aaron M. [Univ. of Chicago, IL (United States); de Pablo, Juan J. [Argonne National Lab. (ANL), Argonne, IL (United States)

    2015-09-01

    Polyglutamine (polyQ) peptides are a useful model system for biophysical studies of protein folding and aggregation, both for their intriguing aggregation properties and their own relevance to human disease. The genetic expansion of a polyQ tract triggers the formation of amyloid aggregates associated with nine neurodegenerative diseases. Several clearly identifiable and separable factors, notably the length of the polyQ tract, influence the mechanism of aggregation, its associated kinetics, and the ensemble of structures formed. Atomistic simulations are well positioned to answer open questions regarding the thermodynamics and kinetics of polyQ folding and aggregation. The additional, explicit representation of water permits deeper investigation of the role of solvent dynamics, and it permits a direct comparison of simulation results with infrared spectroscopy experiments. The generation of meaningful simulation results hinges on satisfying two essential criteria: achieving sufficient conformational sampling to draw statistically valid conclusions, and accurately reproducing the intermolecular forces that govern system structure and dynamics. In this work, we examine the ability of 12 biomolecular force fields to reproduce the properties of a simple, 30-residue polyQ peptide (Q30) in explicit water. In addition to secondary and tertiary structure, we consider generic structural properties of polymers that provide additional dimensions for analysis of the highly degenerate disordered states of the molecule. We find that the 12 force fields produce a wide range of predictions. We identify AMBER ff99SB, AMBER ff99SB*, and OPLS-AA/L to be most suitable for studies of polyQ folding and aggregation.

  18. Trade-off between responsiveness and noise suppression in biomolecular system responses to environmental cues.

    Directory of Open Access Journals (Sweden)

    Alexander V Ratushny

    2011-06-01

    Full Text Available When living systems detect changes in their external environment their response must be measured to balance the need to react appropriately with the need to remain stable, ignoring insignificant signals. Because this is a fundamental challenge of all biological systems that execute programs in response to stimuli, we developed a generalized time-frequency analysis (TFA framework to systematically explore the dynamical properties of biomolecular networks. Using TFA, we focused on two well-characterized yeast gene regulatory networks responsive to carbon-source shifts and a mammalian innate immune regulatory network responsive to lipopolysaccharides (LPS. The networks are comprised of two different basic architectures. Dual positive and negative feedback loops make up the yeast galactose network; whereas overlapping positive and negative feed-forward loops are common to the yeast fatty-acid response network and the LPS-induced network of macrophages. TFA revealed remarkably distinct network behaviors in terms of trade-offs in responsiveness and noise suppression that are appropriately tuned to each biological response. The wild type galactose network was found to be highly responsive while the oleate network has greater noise suppression ability. The LPS network appeared more balanced, exhibiting less bias toward noise suppression or responsiveness. Exploration of the network parameter space exposed dramatic differences in system behaviors for each network. These studies highlight fundamental structural and dynamical principles that underlie each network, reveal constrained parameters of positive and negative feedback and feed-forward strengths that tune the networks appropriately for their respective biological roles, and demonstrate the general utility of the TFA approach for systems and synthetic biology.

  19. Enthalpy-entropy compensation in biomolecular halogen bonds measured in DNA junctions.

    Science.gov (United States)

    Carter, Megan; Voth, Andrea Regier; Scholfield, Matthew R; Rummel, Brittany; Sowers, Lawrence C; Ho, P Shing

    2013-07-23

    Interest in noncovalent interactions involving halogens, particularly halogen bonds (X-bonds), has grown dramatically in the past decade, propelled by the use of X-bonding in molecular engineering and drug design. However, it is clear that a complete analysis of the structure-energy relationship must be established in biological systems to fully exploit X-bonds for biomolecular engineering. We present here the first comprehensive experimental study to correlate geometries with their stabilizing potentials for fluorine (F), chlorine (Cl), bromine (Br), or iodine (I) X-bonds in a biological context. For these studies, we determine the single-crystal structures of DNA Holliday junctions containing halogenated uracil bases that compete X-bonds against classic hydrogen bonds (H-bonds), estimate the enthalpic energies of the competing interactions in the crystal system through crystallographic titrations, and compare the enthalpic and entropic energies of bromine and iodine X-bonds in solution by differential scanning calorimetry. The culmination of these studies demonstrates that enthalpic stabilization of X-bonds increases with increasing polarizability from F to Cl to Br to I, which is consistent with the σ-hole theory of X-bonding. Furthermore, an increase in the X-bonding potential is seen to direct the interaction toward a more ideal geometry. However, the entropic contributions to the total free energies must also be considered to determine how each halogen potentially contributes to the overall stability of the interaction. We find that bromine has the optimal balance between enthalpic and entropic energy components, resulting in the lowest free energy for X-bonding in this DNA system. The X-bond formed by iodine is more enthalpically stable, but this comes with an entropic cost, which we attribute to crowding effects. Thus, the overall free energy of an X-bonding interaction balances the stabilizing electrostatic effects of the σ-hole against the competing

  20. Biomolecularly capped uniformly sized nanocrystalline materials: glutathione-capped ZnS nanocrystals

    Science.gov (United States)

    Torres-Martínez, Claudia L.; Nguyen, Liem; Kho, Richard; Bae, Weon; Bozhilov, Krassimir; Klimov, Victor; Mehra, Rajesh K.

    1999-09-01

    Micro-organisms such as bacteria and yeasts form CdS to detoxify toxic cadmium ions. Frequently, CdS particles formed in yeasts and bacteria were found to be associated with specific biomolecules. It was later determined that these biomolecules were present at the surface of CdS. This coating caused a restriction in the growth of CdS particles and resulted in the formation of nanometre-sized semiconductors (NCs) that exhibited typical quantum confinement properties. Glutathione and related phytochelatin peptides were shown to be the biomolecules that capped CdS nanocrystallites synthesized by yeasts Candida glabrata and Schizosaccharomyces pombe. Although early studies showed the existence of specific biochemical pathways for the synthesis of biomolecularly capped CdS NCs, these NCs could be formed in vitro under appropriate conditions. We have recently shown that cysteine and cysteine-containing peptides such as glutathione and phytochelatins can be used in vitro to dictate the formation of discrete sizes of CdS and ZnS nanocrystals. We have evolved protocols for the synthesis of ZnS or CdS nanocrystals within a narrow size distribution range. These procedures involve three steps: (1) formation of metallo-complexes of cysteine or cysteine-containing peptides, (2) introduction of stoichiometric amounts of inorganic sulfide into the metallo-complexes to initiate the formation of nanocrystallites and finally (3) size-selective precipitation of NCs with ethanol in the presence of Na+. The resulting NCs were characterized by optical spectroscopy, high-resolution transmission electron microscopy (HRTEM), x-ray diffraction and electron diffraction. HRTEM showed that the diameter of the ZnS-glutathione nanocrystals was 3.45+/-0.5 nm. X-ray diffraction and electron diffraction analyses indicated ZnS-glutathione to be hexagonal. Photocatalytic studies suggest that glutathione-capped ZnS nanocrystals prepared by our procedure are highly efficient in degrading a test model

  1. Application of screen-printed microband biosensors to end-point measurements of glucose and cell numbers in HepG2 cell culture.

    Science.gov (United States)

    Pemberton, R M; Xu, J; Pittson, R; Biddle, N; Drago, G A; Jackson, S K; Hart, J P

    2009-02-15

    Microband glucose biosensors were produced by insulating and sectioning through a screen-printed, water-based carbon electrode containing cobalt phthalocyanine redox mediator and glucose oxidase enzyme. Under quiescent conditions at 37 degrees C, at an operating potential of +0.4V, they produced an amperometric response to glucose in buffer solutions with a sensitivity of 26.4 nA/mM and a linear range of 0.45 to 9.0 mM. An optimal pH value of 8.5 was obtained under these conditions, and a value for activation energy of 40.55 kJ mol(-1) was calculated. In culture medium (pH 7.3), a sensitivity of 13 nA/mM was obtained and the response was linear up to 5 mM with a detection limit of 0.5 mM. The working concentration was up to 20 mM glucose with a precision of 11.3% for replicate biosensors (n=4). The microband biosensors were applied to determine end-point glucose concentrations in culture medium by monitoring steady-state current responses 400 s after transfer of the biosensors into different sample solutions. In conjunction with cultures of HepG2 (human Caucasian hepatocyte carcinoma) cells, current responses obtained in 24-h supernatants showed an inverse correlation (R(2)=0.98) with cell number, indicating that the biosensors were applicable for monitoring glucose metabolism by cells and of quantifying cell number. Glucose concentrations determined using the biosensor assay were in good agreement, for concentrations up to 20mM, with those determined spectrophotometrically (R(2)=0.99). This method of end-point glucose determination was used to provide an estimated rate of glucose uptake for HepG2 cells of 7.9 nmol/(10(6) cells min) based on a 24-h period in culture. PMID:19027709

  2. An Overview of High Throughput Biological Screening Methods and Its Application%高通量生物分析技术及应用研究进展

    Institute of Scientific and Technical Information of China (English)

    翟绪昭; 王广彬; 赵亮涛; 曾海娟; 李建武; 丁承超; 宋春美; 刘箐

    2016-01-01

    基因组学、蛋白组学、代谢组学等研究的兴起使得大量生物数据的快速获取和分析变得更加重要。传统的生物分析方法大多耗时、费力,已无法满足现代生命科学研究对海量生物信息的需要。高通量分析技术是快速获取大量生物信息的重要手段。对微阵列芯片、微流控芯片、焦磷酸测序、荧光偏振免疫分析、量子点荧光免疫分析等高通量生物分析技术进行了综述,简述了近几年高通量生物分析技术的研究重点和研究成果,并对其在食品安全、医学等方面的应用进行了简要介绍。%The emergence of genomics,proteomics,metabolomics and other molecular biology studies makes the rapid attainment and assessment of large amounts of biological data become extremely important. The traditional detection methods are time-consuming and laborious, and cannot satisfy the needs of contemporary biological science research for massive biological information. High Throughput Screening(HTS) methods are significant means of quick attainment of massive biological information. This paper will make an overview of microarray chip, microfluidic chip,pyrosequencing,fluorescence polarization immunoassay,quantum dot fluorescence immunoassay and multiple PCR, outline research focus and research results of HTS methods in recent years,and briefly introduce its application in food safety,medicine and other fields.

  3. 胚胎植入前遗传学筛查的临床应用%Clinical Application of Preimplantation Genetic Screening

    Institute of Scientific and Technical Information of China (English)

    张倩; 郑叶; 颜军昊

    2014-01-01

    With the development of assisted reproductive technology and genetic analysis technology, the preimplantation genetic screening (PGS) is used to detect the numerical chromosomal abnormalities (aneuploid) in embryos, so as to improve pregnancy outcomes of in vitro fertilization-embryo transfer (IVF-ET). New methods and technologies have been used in PGS, such as blastocyst stage biopsy, comparative genomic hybridization, microarrays and next generation sequencing, which increase the diagnose accuracy and decrease the risk of misdiagnosis. At the same time, PGS is also facing many challenges. The clinical application of PGS was reviewed in this article.%随着辅助生殖技术和遗传学分析技术的发展,胚胎植入前遗传学筛查应用于胚胎染色体数目异常(非整倍体)检测,以期改善体外受精-胚胎移植的妊娠结局。新方法、新技术不断出现并应用于胚胎植入前遗传学筛查中,如囊胚期活检、比较基因组杂交技术、微阵列技术、第二代测序技术等,显著增加了诊断准确性,减少误诊风险。同时,胚胎植入前遗传学筛查的广泛应用也面临许多挑战。综述该领域的应用进展和面临的挑战。

  4. Lung Cancer Screening

    Science.gov (United States)

    ... Treatment Lung Cancer Prevention Lung Cancer Screening Research Lung Cancer Screening (PDQ®)–Patient Version What is screening? Go ... These are called diagnostic tests . General Information About Lung Cancer Key Points Lung cancer is a disease in ...

  5. Skin Cancer Screening

    Science.gov (United States)

    ... Genetics of Skin Cancer Skin Cancer Screening Research Skin Cancer Screening (PDQ®)–Patient Version What is screening? Go ... These are called diagnostic tests . General Information About Skin Cancer Key Points Skin cancer is a disease in ...

  6. What Is Carrier Screening?

    Science.gov (United States)

    ... you want to learn. Search form Search Carrier screening You are here Home Testing & Services Testing for ... help you make the decision. What Is Carrier Screening? Carrier screening checks if a person is a " ...

  7. Application of Sweat Patch Screening for 16 Drugs and Metabolites Using a Fast and Highly Selective LC-MS/MS Method

    NARCIS (Netherlands)

    Koster, Remco A.; Alffenaar, Jan-Willem C.; Greijdanus, Ben; VanDerNagel, Joanneke E. L.; Uges, Donald R. A.

    2014-01-01

    Background: To facilitate the monitoring of drug abuse by patients, a method was developed and validated for fast and highly selective screening for amphetamine, methamphetamine, 3,4-methylenedioxymethamphetamine, methylenedioxyamphetamine, methylenedioxyethylamphetamine, methylphenidate, cocaine, b

  8. Four Principles to Consider Before Advising Women on Screening Mammography

    OpenAIRE

    Keen, John D; Jørgensen, Karsten J

    2015-01-01

    Abstract This article reviews four important screening principles applicable to screening mammography in order to facilitate informed choice. The first principle is that screening may help, hurt, or have no effect. In order to reduce mortality and mastectomy rates, screening must reduce the rate of advanced disease, which likely has not happened. Through overdiagnosis, screening produces substantial harm by increasing both lumpectomy and mastectomy rates, which offsets the often-promised bene...

  9. Four Principles to Consider Before Advising Women on Screening Mammography

    DEFF Research Database (Denmark)

    Keen, John D; Juhl Jørgensen, Karsten

    2015-01-01

    screening cannot reliably correct for selection bias. The final principle is that accounting for tumor biology is important for accurate estimates of lead time, and the potential benefit from screening. Since "early detection" is actually late in a tumor's lifetime, the time window when screen detection......This article reviews four important screening principles applicable to screening mammography in order to facilitate informed choice. The first principle is that screening may help, hurt, or have no effect. In order to reduce mortality and mastectomy rates, screening must reduce the rate of advanced...

  10. HPV基因分型检测在宫颈癌筛查中的应用%The Application of HPV Genotypes in Screening of Cervical Cancer

    Institute of Scientific and Technical Information of China (English)

    肖凤静; 苏明权; 杨柳; 马越云; 郝晓柯

    2012-01-01

    Objective: To explore the application value of HPV genotyped technology in screening of cervical cancer. Methods: Reverse dot blot hybridization was used to demonstrate the HPV genotypes, there were 23 genotypes including low-risk type and high-risk type. Results: In 98 samples, 38 cases were infected by HPV and the positive rate was 38.8%. The prevalence of HPV infection in the chronic cervicitis, CIN I, CIN II, CIN III and SCC was 30.4% (14/46), 15.4% (4/26), 71.4%(10/14), 75%(6/8) and 100% (4/4) respectively. The order of type-specific prevalence was HPV43, 11, 6, 31, 42 and 51 in the chronic cervicitis, HPV35, 16, 52, 53 and 59 in CIN I; HPV 16,6,11 and 51 in CIN II , HPV 16,18,31 and 53 in CIN III while the distribution order in SCC was HPV 1 6, followed by HPV52, 18, 33, 58, 59 and 66. Conclusions: Continuous HPV infection has a close relationship with cervical disease. Detection of HPV gene type provides great help for clinical screening, diagnosis, treatment and prognosis of cervical disease detection.%目的:探讨人乳头瘤病毒(human papilloma virus,HPV)基因分型技术在宫颈癌筛查中的临床应用价值.方法:采用反向斑点杂交法对HPV基因型进行分析,包括低危型(如6、11、42、43、44型等)和高危型(如16、18、31、33、35、MM4型等)共23个型别.结果:98例样本中检出HPV阳性者38例,23种基因型中共检出15种HPV型别,HPV总感染率38.8%(38/98).慢性宫颈炎患者中HPV感染率30.4% (14/46),检测到的HPV亚型主要是HPV43,11,6,42,31和51(其中HPV6,42,31,51检出率一致).CIN I患者HPV感染率15.4%(4/26),最常见的HPV亚型为HPV35,其次为HPV16,52,53和59(其中16,52,53,59检出率一致).CIN Ⅱ患者HPV感染率71.4%(10/14),以HPV16,6,11,51等亚型最常见.CINⅢ患者HPV感染率75%(6/8),HPV亚型以HPV16,18,31,53为主.SCC患者HPV阳性率为100%(4/4),HPV16检测率最高,其次为HPV52,18,33,58,59和66.结论:持续的HPV感染与宫颈疾病有着密切的关

  11. Prenatal screening and genetics

    DEFF Research Database (Denmark)

    Alderson, P; Aro, A R; Dragonas, T;

    2001-01-01

    Although the term 'genetic screening' has been used for decades, this paper discusses how, in its most precise meaning, genetic screening has not yet been widely introduced. 'Prenatal screening' is often confused with 'genetic screening'. As we show, these terms have different meanings, and we...... examine definitions of the relevant concepts in order to illustrate this point. The concepts are i) prenatal, ii) genetic screening, iii) screening, scanning and testing, iv) maternal and foetal tests, v) test techniques and vi) genetic conditions. So far, prenatal screening has little connection...... with precisely defined genetics. There are benefits but also disadvantages in overstating current links between them in the term genetic screening. Policy making and professional and public understandings about screening could be clarified if the distinct meanings of prenatal screening and genetic screening were...

  12. Fragment Descriptors in Virtual Screening

    CERN Document Server

    Baskin, Igor I

    2013-01-01

    This article reviews the application of fragment descriptors at different stages of virtual screening: filtering, similarity search, and direct activity assessment using QSAR/QSPR models. Several case studies are considered. It is demonstrated that the power of fragment descriptors stems from their universality, very high computational efficiency, simplicity of interpretation and versatility.

  13. Unraveling the biomolecular snapshots of mitosis in healthy and cancer cells using plasmonically-enhanced Raman spectroscopy.

    Science.gov (United States)

    Panikkanvalappil, Sajanlal R; Hira, Steven M; Mahmoud, Mahmoud A; El-Sayed, Mostafa A

    2014-11-12

    Owing to the dynamic and complex nature of mitosis, precise and timely executions of biomolecular events are critical for high fidelity cell division. In this context, visualization of such complex events at the molecular level can provide vital information on the biomolecular processes in abnormal cells. Here, we explored the plasmonically enhanced light scattering properties of functionalized gold nanocubes (AuNCs) together with surface-enhanced Raman spectroscopy (SERS) to unravel the complex and dynamic biological processes involved in mitosis of healthy and cancerous cells from its molecular perspectives. By monitoring various stages of mitosis using SERS, we noticed that relatively high rate of conversion of mitotic proteins from their α-helix structure to β-sheet conformation is likely in the cancer cells during meta-, ana-, and telophases. Unique biochemical modifications to the lipid and amino acid moieties, associated with the observed protein conformational modifications, were also identified. However, in healthy cells, the existence of proteins in their β conformation was momentary and was largely in the α-helix form. The role of abnormal conformational modifications of mitotic proteins on the development of anomalous mitotic activities was further confirmed by looking at plasmonic nanoparticle-induced cytokinesis failure in cancer cells. Our findings illustrate the vast possibilities of SERS in real-time tracking of complex, subtle, and momentary modifications of biomolecules in live cells, which could provide new insights to the role of protein conformation dynamics during mitosis on the development of cancer and many other diseases.

  14. A simple knowledge-based mining method for exploring hidden key molecules in a human biomolecular network

    Directory of Open Access Journals (Sweden)

    Tsuji Shingo

    2012-09-01

    Full Text Available Abstract Background In the functional genomics analysis domain, various methodologies are available for interpreting the results produced by high-throughput biological experiments. These methods commonly use a list of genes as an analysis input, and most of them produce a more complicated list of genes or pathways as the results of the analysis. Although there are several network-based methods, which detect key nodes in the network, the results tend to include well-studied, major hub genes. Results To mine the molecules that have biological meaning but to fewer degrees than major hubs, we propose, in this study, a new network-based method for selecting these hidden key molecules based on virtual information flows circulating among the input list of genes. The human biomolecular network was constructed from the Pathway Commons database, and a calculation method based on betweenness centrality was newly developed. We validated the method with the ErbB pathway and applied it to practical cancer research data. We were able to confirm that the output genes, despite having fewer edges than major hubs, have biological meanings that were able to be invoked by the input list of genes. Conclusions The developed method, named NetHiKe (Network-based Hidden Key molecule miner, was able to detect potential key molecules by utilizing the human biomolecular network as a knowledge base. Thus, it is hoped that this method will enhance the progress of biological data analysis in the whole-genome research era.

  15. Real-time and label-free detection of biomolecular interactions by oblique-incidence reflectivity difference method

    Science.gov (United States)

    Wang, Xu; Lu, Heng; Dai, Jun; Wen, Juan; Yuan, Kun; Lü, Hui-Bin; Jin, Kui-Juan; Zhou, Yue-Liang; Yang, Guo-Zhen

    2011-01-01

    We successfully conduct the label-free and real-time detection of the interactions between epoxy groups and rabbit IgG and 5' CTT CAG GTC ATG AGC CTG AT 3' oligonucleotide, and between the hybridization of 5' CTT CAG GTC ATG AGC CTG AT 3' and its complementary 3' GAA GTC CAG TAC TCG GAC TA 5' oligonucleotide, by the oblique-incidence reflectivity difference (OI-RD) method. The dynamic curves of OI-RD signals, corresponding to the kinetic processes of biomolecular combination or hybridization, are acquired. In our case, the combination of epoxy groups with rabbit IgG and 5' CTT CAG GTC ATG AGC CTG AT 3' oligonucleotide need almost one and a half hours and about two hundred seconds, respectively; and the hybridization of the two oligonucleotides needs about five hundred seconds. The experimental results show that the OI-RD is a promising method for the real-time and label-free detection of biomolecular interactions.

  16. Application of computer aids drug screening in new drug design and development%计算机模拟药物筛选在新药设计与开发中的应用

    Institute of Scientific and Technical Information of China (English)

    黄牛

    2001-01-01

    The development of computer technology, molecular pharmacology and molecular biology promoted the technique of in silico drug screening (virtual screening) used in the drug discovery. The in silico drug screening could be used for diversity screening and/or focussed screening. In present paper, the principles, characteristics and methods of computer aids drug screening were briefly described.

  17. Non-Ewald methods: theory and applications to molecular systems

    OpenAIRE

    Fukuda, Ikuo; Nakamura, Haruki

    2012-01-01

    Several non-Ewald methods for calculating electrostatic interactions have recently been developed, such as the Wolf method, the reaction field method, the pre-averaging method, and the zero-dipole summation method, for molecular dynamics simulations of various physical systems, including biomolecular systems. We review the theories of these approaches and their potential applications to molecular simulations, and discuss their relationships.

  18. 24 CFR 983.255 - Tenant screening.

    Science.gov (United States)

    2010-04-01

    ...) OFFICE OF ASSISTANT SECRETARY FOR PUBLIC AND INDIAN HOUSING, DEPARTMENT OF HOUSING AND URBAN DEVELOPMENT... suitability for tenancy. However, the PHA may opt to screen applicants for family behavior or suitability for... in 25 CFR part 5, subpart L, apply to tenant screening....

  19. Suppressor Screens in Arabidopsis.

    Science.gov (United States)

    Li, Xin; Zhang, Yuelin

    2016-01-01

    Genetic screens have proven to be a useful tool in the dissection of biological processes in plants. Specifically, suppressor screens have been widely used to study signal transduction pathways. Here we provide a detailed protocol for ethyl methanesulfonate (EMS) mutagenesis used in our suppressor screens in Arabidopsis and discuss the basic principles behind suppressor screen design and downstream analyses. PMID:26577776

  20. Prenatal screening and genetics

    NARCIS (Netherlands)

    Alderson, P.; Aro, A.R.; Dragonas, T.; Ettorre, E.; Hemminki, E.; Jalinoja, P.; Santalahti, P.; Tijmstra, T.

    2001-01-01

    Although the term 'genetic screening' has been used for decades, this paper discusses how, in its most precise meaning, genetic screening has not yet been widely introduced. 'Prenatal screening' is often confused with 'genetic screening'. As we show, these terms have different meanings, and we exami

  1. 营养风险筛查2002的临床应用和分析%Clinical application of Nutritional Risk Screening 2002

    Institute of Scientific and Technical Information of China (English)

    孙志慧; 胡若梅; 万津颖

    2009-01-01

    Objective To evaluate the clinical application of Nutritional Risk Screening 2002 (NRS 2002) in inpatients.Methods Totally 400 inpatients who were admitted to Tianjin Tianhe Hospital from Novem- ber 2008 to March 2009 were enrolled in this study.Physical examinations,including body height and body meas-urement,were performed the next morning after admission.The nutritional status was evaluated with NRS 2002.Results In all 400 inpatients.NRS 2002 was strongly practicable in 306 patients (76.5%) and weakly practica-ble in 94 patients (23.5%);Ninety-six patients (24.0%) had nutritional risks,which were most common in the department of internal medicine and the Department of neurology.The average age of patients with nutritional risks was (79.0±11.4) years,which was significantly higher than that of patients without nutritional risks [(58.1±15.8) years] (P<0.01).Conclusion NRS 2002 is effective and practicable in evaluating the nutritional status of inpatient.%目的 评估营养风险筛查2002 (NRS 2002)在住院患者营养筛查中的应用价值.方法 以2008年11月-2009年3月天津天和医院新住院患者400例为研究对象,在入院后第2天清晨测定身高、体重,详细记录病史及患者情况,采用NRS 2002对患者进行营养风险评价并进行分析.结果 400例患者中,306例为强适用(76.5%),94例为弱适用(23.5%);96例(24.0%)存在营养风险,其中普通内科(38.3%)和神经科(31.8%)患者的发生率居前两位.有营养风险患者的平均年龄为(79.0±11.4)岁,明显高于无营养风险患者的(58.1±15.8)岁(P<0.01).结论 NRS 2002可有效用于筛查住院患者的营养状况.

  2. Design and Application of Intelligent LED Information Display Screen%智能LED信息显示屏控制系统设计与应用

    Institute of Scientific and Technical Information of China (English)

    汪岚

    2011-01-01

    In regard to the issues including information can not be update off-line, the splash screen which was caused by conflict between reading-writing frame cache and scanning, an intelligent LED display control system design method was presented based on ATMEGA32. In hardware section, MBI5026 was used to enhance the driver ability, and ADXL202 was used to build up the abilities of gravity recognition and automatic information display rotation. In software section, Chinese input-PINYIN, real time information display was available in the program, a scanning optimal model is also established. By setting up the parameters of numbers of row-column and numbers of scanning optimally, the scanning speed can be improved to its maximum capacity. Experimental results show that the system has great advantages, including the brightness can be adjusted intelligently, the external circuit is simple and easy to install and upgrade. In short, it is an excellent application for engineering.%针对传统点阵显示屏显示内容难以脱机更新、读写数据缓冲和扫描速度不匹配容易造成闪屏的问题,介绍了一种以ATMEGA32为核心的可旋转式智能LED信息显示屏控制系统的设计方案.硬件上利用MBI5026提升显示驱动能力,并利用ADXL202实现重力识别和显示信息自动转向的旋转功能.软件上利用编程实现汉字拼音输入功能,实时更新显示信息,还构建了行列扫描优化模型,根据模型最优解合理设置行列扫描数目和次数,可在现有硬件资源的基础上将扫描速度提升至最优状态.实践证明,系统具有显示亮度智能调节、外围电路简单和易安装升级等优点,有很好的工程实用价值.

  3. Assessment of xenoestrogenic exposure by a biomarker approach: application of the E-Screen bioassay to determine estrogenic response of serum extracts

    Directory of Open Access Journals (Sweden)

    Weihe Pal

    2003-10-01

    Full Text Available Abstract Background Epidemiological documentation of endocrine disruption is complicated by imprecise exposure assessment, especially when exposures are mixed. Even if the estrogenic activity of all compounds were known, the combined effect of possible additive and/or inhibiting interaction of xenoestrogens in a biological sample may be difficult to predict from chemical analysis of single compounds alone. Thus, analysis of mixtures allows evaluation of combined effects of chemicals each present at low concentrations. Methods We have developed an optimized in vitro E-Screen test to assess the combined functional estrogenic response of human serum. The xenoestrogens in serum were separated from endogenous steroids and pharmaceuticals by solid-phase extraction followed by fractionation by high-performance liquid chromatography. After dissolution of the isolated fraction in ethanol-DMSO, the reconstituted extract was added with estrogen-depleted fetal calf serum to MCF-7 cells, the growth of which is stimulated by estrogen. After a 6-day incubation on a microwell plate, cell proliferation was assessed and compared with the effect of a 17-beta-estradiol standard. Results and conclusions To determine the applicability of this approach, we assessed the estrogenicity of serum samples from 30 pregnant and 60 non-pregnant Danish women thought to be exposed only to low levels of endocrine disruptors. We also studied 211 serum samples from pregnant Faroese women, whose marine diet included whale blubber that contain a high concentration of persistent halogenated pollutants. The estrogenicity of the serum from Danish controls exceeded the background in 22.7 % of the cases, while the same was true for 68.1 % of the Faroese samples. The increased estrogenicity response did not correlate with the lipid-based concentrations of individual suspected endocrine disruptors in the Faroese samples. When added along with the estradiol standard, an indication of an

  4. Study on Application of Screening Technology to Urban River Dredging Sludge Disposal%筛分技术在城市河道疏浚污泥处置中的应用研究

    Institute of Scientific and Technical Information of China (English)

    杨玉岭; 黄锦城; 赖佑贤

    2015-01-01

    The paper studies the application of screening technology to urban studies river sludge. Based on the analysis of the engineering properties of urban river sludge, the application of different screening equipment to urban is discussed comprehensively. Meanwhile, the screening technology is applied to the project practice, which has obtained a good effect, and provides reference for the problems encountered in the urban river sludge disposal.%对筛分技术应用于城市河道污泥进行探索研究,在对城市河道污泥的工程特性分析的基础上,对不同的筛分设备用于城市河道污泥进行全面分析,并将筛分技术应用于工程实践中,取得了良好的效果,为城市河道污泥预处置中遇到的难题提供了良好借鉴。

  5. The influence of spirituality and religiosity on breast cancer screening delay in African American women: application of the Theory of Reasoned Action and Planned Behavior (TRA/TPB).

    Science.gov (United States)

    Gullate, Mary

    2006-01-01

    African American women (AAW) are 25% more likely to present with late stage breast cancer and 20% more likely to die from their disease than Caucasian women. Researchers report that a treatment delay of 3 months is a significant factor in breast cancer mortality. Socioeconomic factors, lack of access and knowledge, spiritual and religious beliefs, fear and fatalism are reported as contributing factors to screening delays. Studies have primarily applied the Health Belief Model (HBM) and modified versions like the Champion HBM to preventive health practices. Neither have significant inclusion of spirituality or religiosity. The TRA/TPB focus on beliefs, intent and attitude as individual determinants of the likelihood of performing a specific behavior; but have not had wide utility in studies related to screening delays among AAW. This paper explores the utility of applying the TRA/TPB as the theoretical framework for determining cultural relevance of spirituality and religiosity to screening delays among AAW.

  6. Screening for Impaired Cognitive Domains in a Large Parkinson's Disease Population and Its Application to the Diagnostic Procedure for Parkinson's Disease Dementia

    Directory of Open Access Journals (Sweden)

    Kouichi Ohta

    2014-05-01

    Full Text Available Background: Dementia is a new focus of research on improved treatment for Parkinson's disease (PD. In 2007, a screening tool for PD dementia (PD-D was developed by the Movement Disorder Society (Level I testing, which still requires verification by a large population study. Methods: We conducted a cross-sectional and multicenter study including 13 institutions administering the Mini-Mental State Examination (MMSE and Montreal Cognitive Assessment (MoCA to 304 PD patients (mean age: 70.6 ± 8.3 years; mean Hoehn and Yahr stage: 2.7 ± 0.7. Results: In all, 34.5% of the patients had MMSE scores Conclusions: Level I testing with administration of the MMSE and MoCA is a practical and efficient screening tool for PD-D. However, the phonemic fluency and pentagon copying tests should be replaced by more specific/sensitive ones when screening for PD-D.

  7. An application of Caenorhabditis elegans for drug screening%秀丽隐杆线虫(Caenorhabditis elegans)在药物筛选中的应用

    Institute of Scientific and Technical Information of China (English)

    杨再昌; 杨小生

    2009-01-01

    It is relatively simple and cheap for drug discovery by target-based screen in vitro, but the actions of drugs in vivo do not depend fully on the interactions between drugs and targets. Major reasons preventing many early candidates reaching market are the inappropriate ADME (absorption, distribution, metabolism and excretion) properties and drug-induced toxicity. Now more attentions were paid to the methods of drug screening in vivo. In recent years, C. elegans has been widely used as a drug screening model in drug discovery. The developments of screening for drugs increasing lifespan and antagonizing microbes using C. elegans-baszd assays were mainly discussed in this paper. With the advantages of easily culture, simple tissue structure, and being amenable to high-throughput screening (HTS), C. elegans may turn out to be invaluable in the development of novel screening methods in the future.%基于靶点的体外药物筛选操作相对简单,成本较低,但是由于药物在体内的作用并不仅仅取决于其与靶点的作用程度,吸收、分布、代谢、排泄特征和毒性均会对早期先导物能否进入临床使用产生极大的影响,因此,药物的体内筛选受到重视.本文重点综述了秀丽隐杆线虫(C.elegans)在抗衰老、抗感染药物筛选中的应用情况.秀丽隐杆线虫结构简单、易于培养和可实现高通量筛选,在未来的药物筛选中必将发挥更重要的作用.

  8. Establishment and elementary application of normative screening model in stroke risk group%脑卒中高危人群规范化筛查模式的建立与应用

    Institute of Scientific and Technical Information of China (English)

    钟代曲; 蒋晓江; 沈盈盈; 唐嘉

    2014-01-01

    目的:建立脑卒中高危人群规范化筛查模式,应用于脑卒中高危人群进行筛查与管理,并评价其初步应用效果。方法该科成立脑卒中筛查管理小组,建立规范化脑卒中筛查模式,在门诊及社区人群中开展脑卒中筛查工作,对筛查出的脑卒中高危人群根据脑卒中筛查与干预指南实施为期1年的管控。结果共筛查高危人群9631例,筛查出高危患者1786例,高危患者率为18.55%。对高危患者存在的高危因素实施干预,干预前、后高危患者血糖、血压、血脂、肥胖指数、吸烟、体育锻炼、合理饮食等比较,差异有统计学意义(P<0.05)。结论建立脑卒中规范化筛查模式,对脑卒中高危人群进行专项管理是做好脑卒中筛查与管控工作的重要保障,可降低脑卒中高危人群的危险因素。%Objective To establish the normative screening model and apply it to screen and manage the stroke risk group ,and to observe its application effect .Methods The screening management team in our department was set up for establishing the norma-tive stroke screening model .Then the stroke screening works were carried out in the outpatient department and the community pop-ulation .The screened groups of stroke high risk were implemented the 1-year control according to the guidelines of stroke screening and intervention .Results 9 631 individuals of stroke risk were screened ,among them 1 786 high-risk patients were screened out with a rate of 18 .55% .The interventions on the risk factors existing in the high-risk patients were implemented .The comparison of blood glucose ,blood pressure ,blood fat ,fat index ,smoking ,physical exercise and reasonable diet before and after interventions in the high-risk patients showed statistically significant differences (P<0 .05) .Conclusion Establishment of the normative manage-ment model of stroke screening is the important guarantee to do a good job of

  9. 抗性筛选在抗生素高产菌选育中的应用%Application of Antibiotic- Resistance Screening in Breeding of Antibiotic High-Yield Strains

    Institute of Scientific and Technical Information of China (English)

    戴菲; 李瑾; 黄运红; 付学琴; 龙中儿

    2011-01-01

    The resistance of bacteria to antibiotics has a certain correlation with its ability of producing antibiotics,which provides provide an effective way of directional selection of high-yield strains, namely antibiotic-resistance screening. The mechanism of antibiotic-resistance screening and its application in the mutation breeding of antibiotic high-yield strains were reviewed.%抗生素产生菌的产抗能力与其对抗生素的抗性之间具有一定的相关性,这为抗生素高产菌株的定向筛选提供了一种有效方法,即抗性筛选.综述了抗生素高产菌选育中抗性筛选的机理及其应用.

  10. Dipolar recoupling NMR of biomolecular self-assemblies : determining inter- and intrastrand distances in fibrilized Alzheimer's {betta}-amyloid peptide.

    Energy Technology Data Exchange (ETDEWEB)

    Gregory, D. M.; Senzinger, T. L. S.; Burkoth, T. S.; Miller-Auer, H.; Lynn, D. G.; Meredith, S. C.; Botto, R. E.; Chemistry; Univ. of Chicago

    1998-12-01

    We demonstrate a new method for investigating the structure of self-associating biopolymers using dipolar recoupling NMR techniques. This approach was applied to the study of fibrillar {beta}-amyloid (A{beta}) peptides (the primary component of the plaques of Alzheimer's disease) containing only a single isotopic spin label ({sup 13}C), by employing the DRAWS (dipolar recoupling with a windowless sequence) technique to measure {sup 13}C-{sup 13}C distances. The 'single-label' approach simplified analysis of DRAWS data, since only interstrand contacts are present, without the possibility of any intrastrand contacts. As previously reported [T.L.S. Benzinger, D.M. Gregory, T.S. Burkoth, H. Miller-Auer, D.G. Lynn, R.E. Botto, S.C. Meredith, Proc. Natl. Acad. Sci. 95 (1998) 13407.], contacts of approximately 5 {angstrom} were observed at all residues studied, consistent with an extended parallel {beta}-sheet structure with each amino acid in exact register. Here, we propose that our strategy is completely generalizable, and provides a new approach for characterizing any iterative, self-associating biopolymer. Towards the end of generalizing and refining our approach, in this paper we evaluate several issues raised by our previous analyses. First, we consider the effects of double-quantum (DQ) transverse relaxation processes. Next, we discuss the effects of various multiple-spin geometries on modeling of DRAWS data. Several practical issues are also discussed: these include (1) the use of DQ filtering experiments, either to corroborate DRAWS data, or as a rapid screening assessment of the proper placement of isotopic spin labels; and (2) the comparison of solid samples prepared by either lyophilization or freezing. Finally, data obtained from the use of single labels is compared with that obtained in doubly {sup 13}C-labeled model compounds of known crystal structure. It is shown that such data are obtainable in far more complex peptide molecules. These

  11. 产后抑郁筛查量表中文版在产后抑郁筛查中的应用%Application of the Chinese version of the Postpartum Depression Screening Scale in the screening of postpartum depression

    Institute of Scientific and Technical Information of China (English)

    高明; 王智慧; 傅晓红; 陆丽艳

    2013-01-01

    Objective To compare the value of the Postpartum Depression Screening Scale (PDSS)and the Edinburgh Postnatal Depression scale (EPDS)in the screening of postpartum depression.Methods A total of 378women within 42 days postpartum completed PDSS,the Edinburgh Postnatal Depression Scale (EPDS)and Structured Clinical Interview for DSM-IV-TR Axis I Disorders-Patient Edition (SCID-I/P).The SCID-I/P was regarded the standard for postpartum depression diagnosis.Results The cut-of score for PDSS and EPDS was 76 and 13,respectively.Sensitivity of PDSS was 92.00%,and specificity was 95.25%,with positive predictive value of 77.02% and negative predictive value of 99.01%.Sensitivity of EPDS was 82.30%,and specificity was 81.33%,with positive predictive value of 44.73% and negative predictive value of 97.30%.The sensitivity,specificity and positive predictive value showed significantly difference between PDSS and EPDS (P<0.05),and negative predictive value had no statistical significant differece.Conclusion PDSS scale is more suitable for screening postpartum depression than EPDS scale.%目的 比较产后抑郁筛查量表(PDSS)和爱丁堡产后抑郁量表(EPDS)在产后抑郁筛查中的应用价值.方法 分别采用PDSS、爱丁堡产后抑郁量表(EPDS)及美国精神障碍诊断与统计手册第4版轴Ⅰ障碍定式临床检查患者版(SCID-I/P)对378例产后42 d的妇女进行评定,以SCID-I/P作为产后抑郁诊断标准.结果 将两种量表的临界值分别界定为76分和13分.PDSS的敏感性为92.00%,特异性为95.25%,阳性预测值为77.02%,阴性预测值为99.01%;EPDS的敏感性为82.26%,特异性为81.33%,阳性预测值为44.73%,阴性预测值为97.30%.两种量表特异性和敏感性差异比较有统计学意义(P<0.05).PDSS与EPDS阳性预测值比较差异有统计学意义(P<0.05),阴性预测值比较差异无统计学意义(P>0.05).结论 与EPDS比较,PDSS更适合产后抑郁的筛查.

  12. Measuring the psychosocial consequences of screening

    Directory of Open Access Journals (Sweden)

    Doward Lynda C

    2007-01-01

    Full Text Available Abstract The last three decades have seen a dramatic rise in the implementation of screening programmes for cancer in industrialised countries. However, in contrast to screening for infectious diseases, most cancer screening programmes only have the potential to reduce mortality; they cannot lower the incidence of cancer in a population. In fact, most cancer screening programmes have been shown to increase the incidence of the disease as a consequence of over-diagnosis. A further dilemma of cancer screening programmes is that they do not distinguish between healthy people and those with disease. Rather, they identify a continuum of disease severity. Consequently, many healthy people who have abnormal screening tests are wrongly diagnosed. Indeed, studies have demonstrated that for each screening-prevented death from cancer, at least 200 false-positive results are given. Therefore, screening has the potential to be harmful as well as beneficial. The psychosocial consequences of false-positive screening results cannot be determined by diagnostic tests or by other technical means. Instead, patient reported outcome measures must be employed. To measure the outcomes of screening accurately and comprehensively patient reported outcome measures have to capture; the nature and extent of the psychosocial consequences and how these change over time. The outcome measures used must have high content validity and their psychometric properties should be determined prior to their use in the specific population. In particular it is important to establish unidimensionality, additivity and item ordering through the application of Item Response Theory.

  13. A fluorescent HTS assay for phosphohydrolases based on nucleoside 5'-fluorophosphates: its application in screening for inhibitors of mRNA decapping scavenger and PDE-I.

    Science.gov (United States)

    Baranowski, M R; Nowicka, A; Jemielity, J; Kowalska, J

    2016-05-18

    Several nucleotide-specific phosphohydrolases can cleave P-F bonds in substrate analogues containing a fluorophosphate moiety to release fluoride ions. In this work, by employing a fluoride-sensitive molecular sensor, we harnessed this cleavage reaction to develop a fluorescence assay to screen for phosphohydrolase inhibitors. The assay is rapid, sensitive, and based on simple and synthetically available reagents. The assay was adapted to the high-throughput screening (HTS) format and its utility was demonstrated by screening an 'in-house' library of small nucleotides against two enzymes: DcpS, a metal-independent mRNA decapping pyrophosphatase of the histidine triad (HIT) family; and PDE-I, a divalent cation-dependent nuclease. Our screening results agreed with the known specificities of DcpS and PDE-I, and led to the selection of several inhibitors featuring low-micromolar IC50 values. For DcpS, we also verified the results by using an alternative method with the natural substrate. Notably, the assay presented here is the first fluorescence-based HTS-adaptable assay for DcpS, an established therapeutic target for spinal muscular atrophy. The assay should be useful for phosphohydrolase specificity profiling and inhibitor discovery, particularly in the context of DcpS and other HIT-family enzymes, which play key roles in maintaining cellular functions and have been linked to disease development. PMID:27031609

  14. Screening of lysosomal storage disorders: application of the online trapping-and-cleanup liquid chromatography/mass spectrometry method for mucopolysaccharidosis I.

    Science.gov (United States)

    Ombrone, Daniela; Malvagia, Sabrina; Funghini, Silvia; Giocaliere, Elisa; Della Bona, Maria Luisa; Forni, Giulia; De Luca, Alessio; Villanelli, Fabio; Casetta, Bruno; Guerrini, Renzo; la Marca, Giancarlo

    2013-01-01

    In recent years, new treatments have become available to treat some lysosomal storage disorders (LSDs) and many studies suggest that there is a benefit with starting therapy early. Newborn screening should detect diseases early enough for prompt treatment. Some countries include additional conditions, such as some LSDs, into their newborn screening panels. Mucopolysaccharidosis Type I (MPS I) is an autosomal recessive disorder caused by the deficiency of α-L-iduronidase (IDUA) activity. Currently, enzyme replacement therapy (ERT) or bone marrow transplantation is available and this has raised a growing interest for the development of a newborn screening test. In 2009, we reported a new fast and simplified tandem mass spectrometry-based method for quantifying five enzyme activities on dried blood spots. Here, we describe the inclusion of IDUA activity determination for the simultaneous detection of six lysosomal storage diseases. We have defined reference normal ranges by testing 680 healthy newborns and 240 adults. The assay was checked through three confirmed MPS I patients whose IDUA activity was below the normal range. Reproducibility of the assays has been established by assessing the intra-day and inter-day assay imprecisions. This quick assay has been devised to be implemented in newborn screening by liquid chromatography tandem mass spectrometry.

  15. Microelectroporation device for genomic screening

    Energy Technology Data Exchange (ETDEWEB)

    Perroud, Thomas D.; Renzi, Ronald F.; Negrete, Oscar; Claudnic, Mark R.

    2014-09-09

    We have developed an microelectroporation device that combines microarrays of oligonucleotides, microfluidic channels, and electroporation for cell transfection and high-throughput screening applications (e.g. RNA interference screens). Microarrays allow the deposition of thousands of different oligonucleotides in microscopic spots. Microfluidic channels and microwells enable efficient loading of cells into the device and prevent cross-contamination between different oligonucleotides spots. Electroporation allows optimal transfection of nucleic acids into cells (especially hard-to-transfect cells such as primary cells) by minimizing cell death while maximizing transfection efficiency. This invention has the advantage of a higher throughput and lower cost, while preventing cross-contamination compared to conventional screening technologies. Moreover, this device does not require bulky robotic liquid handling equipment and is inherently safer given that it is a closed system.

  16. CLAD DEGRADATION - FEPS SCREENING ARGUMENTS

    International Nuclear Information System (INIS)

    The purpose of this report is to evaluate and document the screening of the clad degradation features, events, and processes (FEPs) with respect to modeling used to support the Total System Performance Assessment-License Application (TSPA-LA). This report also addresses the effect of certain FEPs on both the cladding and the commercial spent nuclear fuel (CSNF), DOE-owned spent nuclear fuel (DSNF), and defense high-level waste (DHLW) waste forms, as appropriate to address the effects on multiple materials and both components (FEPs 2.1.09.09.0A, 2.1.09.11.0A, 2.1.11.05.0A, 2.1.12.02.0A, and 2.1.12.03.0A). These FEPs are expected to affect the repository performance during the postclosure regulatory period of 10,000 years after permanent closure. Table 1-1 provides the list of cladding FEPs, including their screening decisions (include or exclude). The primary purpose of this report is to identify and document the analysis, screening decision, and TSPA-LA disposition (for included FEPs) or screening argument (for excluded FEPs) for these FEPs related to clad degradation. In some cases, where a FEP covers multiple technical areas and is shared with other FEP reports, this report may provide only a partial technical basis for the screening of the FEP. The full technical basis for shared FEPs is addressed collectively by the sharing FEP reports. The screening decisions and associated TSPA-LA dispositions or screening arguments from all of the FEP reports are cataloged in a project-specific FEPs database

  17. CLAD DEGRADATION - FEPS SCREENING ARGUMENTS

    Energy Technology Data Exchange (ETDEWEB)

    R. Schreiner

    2004-10-21

    The purpose of this report is to evaluate and document the screening of the clad degradation features, events, and processes (FEPs) with respect to modeling used to support the Total System Performance Assessment-License Application (TSPA-LA). This report also addresses the effect of certain FEPs on both the cladding and the commercial spent nuclear fuel (CSNF), DOE-owned spent nuclear fuel (DSNF), and defense high-level waste (DHLW) waste forms, as appropriate to address the effects on multiple materials and both components (FEPs 2.1.09.09.0A, 2.1.09.11.0A, 2.1.11.05.0A, 2.1.12.02.0A, and 2.1.12.03.0A). These FEPs are expected to affect the repository performance during the postclosure regulatory period of 10,000 years after permanent closure. Table 1-1 provides the list of cladding FEPs, including their screening decisions (include or exclude). The primary purpose of this report is to identify and document the analysis, screening decision, and TSPA-LA disposition (for included FEPs) or screening argument (for excluded FEPs) for these FEPs related to clad degradation. In some cases, where a FEP covers multiple technical areas and is shared with other FEP reports, this report may provide only a partial technical basis for the screening of the FEP. The full technical basis for shared FEPs is addressed collectively by the sharing FEP reports. The screening decisions and associated TSPA-LA dispositions or screening arguments from all of the FEP reports are cataloged in a project-specific FEPs database.

  18. Diffusion Monte Carlo applied to weak interactions - hydrogen bonding and aromatic stacking in (bio-)molecular model systems

    Science.gov (United States)

    Fuchs, M.; Ireta, J.; Scheffler, M.; Filippi, C.

    2006-03-01

    Dispersion (Van der Waals) forces are important in many molecular phenomena such as self-assembly of molecular crystals or peptide folding. Calculating this nonlocal correlation effect requires accurate electronic structure methods. Usual density-functional theory with generalized gradient functionals (GGA-DFT) fails unless empirical corrections are added that still need extensive validation. Quantum chemical methods like MP2 and coupled cluster are more accurate, yet limited to rather small systems by their unfavorable computational scaling. Diffusion Monte Carlo (DMC) can provide accurate molecular total energies and remains feasible also for larger systems. Here we apply the fixed-node DMC method to (bio-)molecular model systems where dispersion forces are significant: (dimethyl-) formamide and benzene dimers, and adenine-thymine DNA base pairs. Our DMC binding energies agree well with data from coupled cluster (CCSD(T)), in particular for stacked geometries where GGA-DFT fails qualitatively and MP2 predicts too strong binding.

  19. Biomolecular solvation study of proteins in liquid water by a wide range gigahertz-to-terahertz spectroscopy

    Science.gov (United States)

    Charkhesht, Ali; George, Deepu; Nguyen, Vinh

    Solvent dynamics within biomolecular solvation layers play a major role in enzyme activity, but obtaining an accurate and quantitative picture of solvent activity around proteins is challenging. Due to the strong absorption of water in the gigahertz-to-terahertz frequencies, it is challenging to study properties of the solvent dynamics as well as conformational changes protein in water. We have developed a highly sensitive dielectric gigahertz-to-terahertz frequency-domain spectroscopy system for probing the collective dynamics of proteins and solvent. Using this technique, we investigate the complex dielectric response of bovine serum albumin and lysozyme proteins in aqueous environment on a wide frequency range from 0.1 GHz up to 2 THz. We explore the conformation flexibility of proteins and compare the hydration dynamics around proteins to understand the effects of surface-mediated solvent dynamics, relationships among different measures of interfacial solvent dynamics, and protein-mediated solvent dynamics.

  20. Flavin mononucleotide biomolecular laser: longitudinal mode structure, polarization, and temporal characteristics as probes of local chemical environment.

    Science.gov (United States)

    Rivera, José A; Eden, J Gary

    2016-05-16

    A detailed characterization of the flavin mononucleotide (FMN) biomolecular laser, optically pumped in a stable resonator, is reported here. Photoexcitation of the molecule at 355 nm results in lasing over the ~566.5-573.5 nm spectral region, and the threshold pump energy density is measured to be 110 ± 10 µJ/mm2 for a 10 mM FMN/water solution. Over twenty longitudinal modes are observed when the cavity length L and the energy pump fluence Ep are 375 µm and 300 µJ/mm2, respectively. Partial substitution of glycerol for water as the solvent results in a factor of four reduction in the threshold pump energy fluence (to 2) and a quadrupling of the slope efficiency. This effect is attributed to the O2 - mediated photoconversion of FMN molecules in the triplet state to the singlet species. For pump intensities a factor of 2.5 above threshold, the laser pulse width is ~2 ns FWHM, and the output intensity decays exponentially with a photon lifetime of 1.7 ns. The addition of glycerol to a FMN/water solution also suppresses s-polarized emission (yielding P = 0.78 ± 0.08), presumably as a result of the inhibition of FMN rotational diffusion. The sensitivity of the spectral and optical properties of this and other biomolecular lasers to the chemical environment underscores the value of coherent emission as a biochemical or biomedical diagnostic tool, particularly insofar as molecule-molecule interactions are concerned. PMID:27409906