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. Nanoarchitectonics of biomolecular assemblies for functional applications

    Science.gov (United States)

    Avinash, M. B.; Govindaraju, T.

    2014-10-01

    The stringent processes of natural selection and evolution have enabled extraordinary structure-function properties of biomolecules. Specifically, the archetypal designs of biomolecules, such as amino acids, nucleobases, carbohydrates and lipids amongst others, encode unparalleled information, selectivity and specificity. The integration of biomolecules either with functional molecules or with an embodied functionality ensures an eclectic approach for novel and advanced nanotechnological applications ranging from electronics to biomedicine, besides bright prospects in systems chemistry and synthetic biology. Given this intriguing scenario, our feature article intends to shed light on the emerging field of functional biomolecular engineering.

  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. Nanopatterned structures for biomolecular analysis toward genomic and proteomic applications

    Science.gov (United States)

    Chou, Chia-Fu; Gu, Jian; Wei, Qihuo; Liu, Yingjie; Gupta, Ravi; Nishio, Takeyoshi; Zenhausern, Frederic

    2005-01-01

    We report our fabrication of nanoscale devices using electron beam and nanoimprint lithography (NIL). We focus our study in the emerging fields of NIL, nanophotonics and nanobiotechnology and give a few examples as to how these nanodevices may be applied toward genomic and proteomic applications for molecular analysis. The examples include reverse NIL-fabricated nanofluidic channels for DNA stretching, nanoscale molecular traps constructed from dielectric constrictions for DNA or protein focusing by dielectrophoresis, multi-layer nanoburger and nanoburger multiplets for optimized surface-plasma enhanced Raman scattering for protein detection, and biomolecular motor-based nanosystems. The development of advanced nanopatterning techniques promises reliable and high-throughput manufacturing of nanodevices which could impact significantly on the areas of genomics, proteomics, drug discovery and molecular clinical diagnostics.

  6. 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. PMID:23893064

  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. 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...

  9. 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%.

  10. 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.

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

    Science.gov (United States)

    Zhou, Pei; Wagner, Gerhard

    2010-01-01

    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. PMID:19731047

  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. Phase sensitive spectral domain interferometry for label free biomolecular interaction analysis and biosensing applications

    Science.gov (United States)

    Chirvi, Sajal

    Biomolecular interaction analysis (BIA) plays vital role in wide variety of fields, which include biomedical research, pharmaceutical industry, medical diagnostics, and biotechnology industry. Study and quantification of interactions between natural biomolecules (proteins, enzymes, DNA) and artificially synthesized molecules (drugs) is routinely done using various labeled and label-free BIA techniques. Labeled BIA (Chemiluminescence, Fluorescence, Radioactive) techniques suffer from steric hindrance of labels on interaction site, difficulty of attaching labels to molecules, higher cost and time of assay development. Label free techniques with real time detection capabilities have demonstrated advantages over traditional labeled techniques. The gold standard for label free BIA is surface Plasmon resonance (SPR) that detects and quantifies the changes in refractive index of the ligand-analyte complex molecule with high sensitivity. Although SPR is a highly sensitive BIA technique, it requires custom-made sensor chips and is not well suited for highly multiplexed BIA required in high throughput applications. Moreover implementation of SPR on various biosensing platforms is limited. In this research work spectral domain phase sensitive interferometry (SD-PSI) has been developed for label-free BIA and biosensing applications to address limitations of SPR and other label free techniques. One distinct advantage of SD-PSI compared to other label-free techniques is that it does not require use of custom fabricated biosensor substrates. Laboratory grade, off-the-shelf glass or plastic substrates of suitable thickness with proper surface functionalization are used as biosensor chips. SD-PSI is tested on four separate BIA and biosensing platforms, which include multi-well plate, flow cell, fiber probe with integrated optics and fiber tip biosensor. Sensitivity of 33 ng/ml for anti-IgG is achieved using multi-well platform. Principle of coherence multiplexing for multi

  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. Bioactive membranes for bone regeneration applications: effect of physical and biomolecular signals on mesenchymal stem cell behavior.

    Science.gov (United States)

    Tejeda-Montes, Esther; Smith, Katherine H; Rebollo, Elena; Gómez, Raúl; Alonso, Matilde; Rodriguez-Cabello, J Carlos; Engel, Elisabeth; Mata, Alvaro

    2014-01-01

    This study focuses on the in vitro characterization of bioactive elastin-like recombinamer (ELR) membranes for bone regeneration applications. Four bioactive ELRs exhibiting epitopes designed to promote mesenchymal stem cell adhesion (RGDS), endothelial cell adhesion (REDV), mineralization (HAP), and both cell adhesion and mineralization (HAP-RGDS) were synthesized using standard recombinant protein techniques. The materials were then used to fabricate ELR membranes incorporating a variety of topographical micropatterns including channels, holes and posts. Primary rat mesenchymal stem cells (rMSCs) were cultured on the different membranes and the effects of biomolecular and physical signals on cell adhesion, morphology, proliferation, and differentiation were evaluated. All results were analyzed using a custom-made MATLAB program for high throughput image analysis. Effects on cell morphology were mostly dependent on surface topography, while cell proliferation and cell differentiation were largely dependent on the biomolecular signaling from the ELR membranes. In particular, osteogenic differentiation (evaluated by staining for the osteoblastic marker osterix) was significantly enhanced on cells cultured on HAP membranes. Remarkably, cells growing on membranes containing the HAP sequence in non-osteogenic differentiation media exhibited significant up-regulation of the osteogenic marker as early as day 5, while those growing on fibronectin-coated glass in osteogenic differentiation media did not. These results are part of our ongoing effort to develop an optimized molecularly designed periosteal graft. PMID:24035887

  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

    2016-01-01

    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

  20. Photodamage and the importance of photoprotection in biomolecular-powered device applications.

    Science.gov (United States)

    Vandelinder, Virginia; Bachand, George D

    2014-01-01

    In recent years, an enhanced understanding of the mechanisms underlying photobleaching and photoblinking of fluorescent dyes has led to improved photoprotection strategies, such as reducing and oxidizing systems (ROXS) that reduce blinking and oxygen scavenging systems to reduce bleaching. Excitation of fluorescent dyes can also result in damage to catalytic proteins (e.g., biomolecular motors), affecting the performance of integrated devices. Here, we characterized the motility of microtubules driven by kinesin motor proteins using various photoprotection strategies, including a microfluidic deoxygenation device. Impaired motility of microtubules was observed at high excitation intensities in the absence of photoprotection as well as in the presence of an enzymatic oxygen scavenging system. In contrast, using a polydimethylsiloxane (PDMS) microfluidic deoxygenation device and ROXS, not only were the fluorophores slower to bleach but also moving the velocity and fraction of microtubules over time remained unaffected even at high excitation intensities. Further, we demonstrate the importance of photoprotection by examining the effect of photodamage on the behavior of a switchable mutant of kinesin. Overall, these results demonstrate that improved photoprotection strategies may have a profound impact on functional fluorescently labeled biomolecules in integrated devices. PMID:24350711

  1. 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...

  2. 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.

  3. 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

  4. Biomolecular motors

    Directory of Open Access Journals (Sweden)

    Henry Hess

    2005-12-01

    Here, we give a brief introduction to molecular motors, with an emphasis on motor proteins, describe the challenges in interfacing these bionanomachines with an artificial environment, and provide examples of emerging applications.

  5. Overcoming the Solubility Limit with Solubility-Enhancement Tags: Successful Applications in Biomolecular NMR Studies

    OpenAIRE

    Zhou, Pei; Wagner, Gerhard

    2010-01-01

    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 techniq...

  6. 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...

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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...

  13. 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...

  14. 78 FR 76860 - Contraband Screening for Criminal Justice Applications

    Science.gov (United States)

    2013-12-19

    ... for use by criminal justice and law enforcement for the detection of contraband. Screening technology is widely used by criminal justice practitioners (in particular, correctional facilities) to improve... of Justice Programs Contraband Screening for Criminal Justice Applications AGENCY: National...

  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. Mixture of experts models to exploit global sequence similarity on biomolecular sequence labeling

    OpenAIRE

    2009-01-01

    Background Identification of functionally important sites in biomolecular sequences has broad applications ranging from rational drug design to the analysis of metabolic and signal transduction networks. Experimental determination of such sites lags far behind the number of known biomolecular sequences. Hence, there is a need to develop reliable computational methods for identifying functionally important sites from biomolecular sequences. Results We present a mixture of experts approach to b...

  18. 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...

  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. 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)...

  1. Screening of Aptamers on Microfluidic Systems for Clinical Applications

    OpenAIRE

    Gwo-Bin Lee; Chao-Jyun Huang; Chen-Hsun Weng

    2012-01-01

    The use of microfluidic systems for screening of aptamers and their biomedical applications are reviewed in this paper. Aptamers with different nucleic acid sequences have been extensively studied and the results demonstrated a strong binding affinity to target molecules such that they can be used as promising candidate biomarkers for diagnosis and therapeutics. Recently, the aptamer screening protocol has been conducted with microfluidic-based devices. Furthermore, aptamer affinity screening...

  2. Fast Enrichment Screening for Safeguards Applications

    International Nuclear Information System (INIS)

    Methods for rapid non-destructive uranium enrichment classification of large containers are of importance to safeguards and counter-terrorism agencies. There is a need to quickly categorize and segregate suspect items as 'depleted' or 'enriched' on a 'Go/No Go' basis. Recent improvements in gamma spectroscopy technologies have provided the capability to perform rapid field analysis using portable and hand-held devices such as battery-operated medium and high resolution detectors (including lanthanum halide and high purity germanium). Furthermore a new generation of portal monitors are currently under development with advanced spectroscopic capabilities. Instruments and technologies that were previously the domain of complex lab systems are now widely available as touch-screen 'off-the-shelf' units. Despite such advances, the task of enrichment analysis remains a complex exercise. This is particularly so when surveying large items such as drums and crates containing debris of unknown density and composition contaminated with uranium. The challenge is equally applicable to safeguards inspectors evaluating large items and for interdiction of illicit special nuclear materials in mass transport e.g. shipping containers at ports and borders. The variable shielding, container size, lack of matrix knowledge, wall thickness and self-shielding compound this problem. Performing an accurate assessment within the short count time window demanded of the field operative, leads to the need for a reliable method that can adapt to such conditions and is robust to a wide dynamic range of counting statistics. Several methods are evaluated with reference to the performance metrics defined in applicable standards. The primary issue is to minimize the bias that can result from attenuation effects, particularly as the gamma emissions from U235 are low energy and therefore highly susceptible to absorption in large containers with metal scrap. Use of other radiometric signatures such as

  3. 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.

  4. A mechanical Turing machine: blueprint for a biomolecular computer.

    Science.gov (United States)

    Shapiro, Ehud

    2012-08-01

    We describe a working mechanical device that embodies the theoretical computing machine of Alan Turing, and as such is a universal programmable computer. The device operates on three-dimensional building blocks by applying mechanical analogues of polymer elongation, cleavage and ligation, movement along a polymer, and control by molecular recognition unleashing allosteric conformational changes. Logically, the device is not more complicated than biomolecular machines of the living cell, and all its operations are part of the standard repertoire of these machines; hence, a biomolecular embodiment of the device is not infeasible. If implemented, such a biomolecular device may operate in vivo, interacting with its biochemical environment in a program-controlled manner. In particular, it may 'compute' synthetic biopolymers and release them into its environment in response to input from the environment, a capability that may have broad pharmaceutical and biological applications. PMID:22649583

  5. 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...

  6. Storing and analysing biomolecular contacts

    OpenAIRE

    Walter, Peter

    2011-01-01

    Biomolecular contacts play a crucial role in all areas of life. In particular, protein-protein (PP) interactions are essential for most processes in biological cells. Antigen-antibody recognition, enzyme substrate binding, hormone receptor binding, RNA splicing, DNA replication and signal transduction are just some examples for the rich variety of PP interactions. In the last years modern proteomic methods have helped to get a better understanding of the complexity within living cell and orga...

  7. Models for solvated biomolecular structures

    OpenAIRE

    Cerutti, David

    2007-01-01

    Methods for estimating the structure and energetics of water around biomolecules are presented with the objective of improving the treatment of the biomolecular simulation environment as well as facilitating the use of complex, rigorous water models in the context of structure prediction problems that demand cheap solutions. Salt solutions around biomolecules are studied using an implicit solvent model with explicitly represented ions, revealing that the structure of the ion atmosphere is muc...

  8. Large-screen display technology assessment for military applications

    Science.gov (United States)

    Blaha, Richard J.

    1990-08-01

    Full-color, large screen display systems can enhance military applications that require group presentation, coordinated decisions, or interaction between decision makers. The technology already plays an important role in operations centers, simulation facilities, conference rooms, and training centers. Some applications display situational, status, or briefing information, while others portray instructional material for procedural training or depict realistic panoramic scenes that are used in simulators. While each specific application requires unique values of luminance, resolution, response time, reliability, and the video interface, suitable performance can be achieved with available commercial large screen displays. Advances in the technology of large screen displays are driven by the commercial applications because the military applications do not provide the significant market share enjoyed by high definition television (HDTV), entertainment, advertisement, training, and industrial applications. This paper reviews the status of full-color, large screen display technologies and includes the performance and cost metrics of available systems. For this discussion, performance data is based upon either measurements made by our personnel or extractions from vendors' data sheets.

  9. 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.

  10. 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.

  11. 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…

  12. Effectiveness of Audio on Screen Captures in Software Application Instruction

    Science.gov (United States)

    Veronikas, Susan Walsh; Maushak, Nancy

    2005-01-01

    Presentation of software instruction has been supported by manuals and textbooks consisting of screen captures, but a multimedia approach may increase learning outcomes. This study investigated the effects of modality (text, audio, or dual) on the achievement and attitudes of college students learning a software application through the computer.…

  13. Micro- and nanodevices integrated with biomolecular probes.

    Science.gov (United States)

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

    2015-12-01

    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

  14. 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

  15. 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...

  16. 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

  17. Multislot antenna with a screening backplane for UWB WBAN applications

    OpenAIRE

    Yun-fei Wei; Christophe Roblin

    2012-01-01

    A novel multislot antenna with a conducting backplane reflector (MSA-BP) designed for ultrawideband wireless body area networks (WBANs) applications is presented. The objective is to achieve a desensitization of the antenna behavior regarding the proximity effects of the human body, thanks to the field screening operated by the backplane. Partly because of the latter, the antenna is fed with a tapered CPW. The influence of antenna parameters and human body proximity on the radiation character...

  18. 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

  19. 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

  20. Biomolecular structure refinement using the GROMOS simulation software

    Energy Technology Data Exchange (ETDEWEB)

    Schmid, Nathan; Allison, Jane R.; Dolenc, Jozica; Eichenberger, Andreas P.; Kunz, Anna-Pitschna E.; Gunsteren, Wilfred F. van, E-mail: wfvgn@igc.phys.chem.ethz.ch [Swiss Federal Institute of Technology ETH, Laboratory of Physical Chemistry (Switzerland)

    2011-11-15

    For the understanding of cellular processes the molecular structure of biomolecules has to be accurately determined. Initial models can be significantly improved by structure refinement techniques. Here, we present the refinement methods and analysis techniques implemented in the GROMOS software for biomolecular simulation. The methodology and some implementation details of the computation of NMR NOE data, {sup 3}J-couplings and residual dipolar couplings, X-ray scattering intensities from crystals and solutions and neutron scattering intensities used in GROMOS is described and refinement strategies and concepts are discussed using example applications. The GROMOS software allows structure refinement combining different types of experimental data with different types of restraining functions, while using a variety of methods to enhance conformational searching and sampling and the thermodynamically calibrated GROMOS force field for biomolecular simulation.

  1. Microoptical array projectors for free-form screen applications.

    Science.gov (United States)

    Sieler, M; Fischer, S; Schreiber, P; Dannberg, P; Bräuer, A

    2013-11-18

    The system design of front-projection systems for free-form screens utilizing conventional single-aperture optical layouts always requires a trade-off between system complexity and achievable luminous output. This article presents novel slide pre-processing algorithms based on array projection technology that are able to resolve the design drawbacks for both free-form as well as strongly-inclined planar screen applications by breaking the common contradiction between system simplicity and flux. Starting from describing common design strategies and their drawbacks, the theoretical basics of the novel concept are investigated and applied to raytracing simulations. Experimental results are shown and evaluated regarding their optical performance. PMID:24514382

  2. [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

  3. 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

  4. Rapid screening of potential metallic glasses for biomedical applications

    Energy Technology Data Exchange (ETDEWEB)

    Lin, C.H. [Department of Mechanical and Electro-Mechanical Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan, ROC (China); Huang, C.H. [Department of Materials and Optoelectronic Science, Center for Nanoscience and Nanotechnology, National Sun Yat-Sen University, Kaohsiung, Taiwan, ROC (China); Chuang, J.F. [Department of Mechanical and Electro-Mechanical Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan, ROC (China); Huang, J.C., E-mail: jacobc@mail.nsysu.edu.tw [Department of Materials and Optoelectronic Science, Center for Nanoscience and Nanotechnology, National Sun Yat-Sen University, Kaohsiung, Taiwan, ROC (China); Jang, J.S.C. [Institute of Materials Science and Engineering, Department of Mechanical Engineering, National Central University, Chung-Li, Taiwan, ROC (China); Chen, C.H. [Department of Orthopedics, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan, ROC (China); Department of Orthopedics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan, ROC (China); Orthopedic Research Center, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan, ROC (China)

    2013-12-01

    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 Ti{sub 65}Si{sub 15}Ta{sub 10}Zr{sub 10} and Ta{sub 57}Zr{sub 23}Cu{sub 12}Ti{sub 8} 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 Ti{sub 65}Si{sub 15}Ta{sub 10}Zr{sub 10} 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 Ti{sub 65}Si{sub 15}Ta{sub 10}Zr{sub 10} metallic glass exhibits the best response and high potential.

  5. 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

  6. 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)

  7. 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.

  8. Screening applications in drug discovery based on microfluidic technology.

    Science.gov (United States)

    Eribol, P; Uguz, A K; Ulgen, K O

    2016-01-01

    Microfluidics has been the focus of interest for the last two decades for all the advantages such as low chemical consumption, reduced analysis time, high throughput, better control of mass and heat transfer, downsizing a bench-top laboratory to a chip, i.e., lab-on-a-chip, and many others it has offered. Microfluidic technology quickly found applications in the pharmaceutical industry, which demands working with leading edge scientific and technological breakthroughs, as drug screening and commercialization are very long and expensive processes and require many tests due to unpredictable results. This review paper is on drug candidate screening methods with microfluidic technology and focuses specifically on fabrication techniques and materials for the microchip, types of flow such as continuous or discrete and their advantages, determination of kinetic parameters and their comparison with conventional systems, assessment of toxicities and cytotoxicities, concentration generations for high throughput, and the computational methods that were employed. An important conclusion of this review is that even though microfluidic technology has been in this field for around 20 years there is still room for research and development, as this cutting edge technology requires ingenuity to design and find solutions for each individual case. Recent extensions of these microsystems are microengineered organs-on-chips and organ arrays. PMID:26865904

  9. 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.

  10. 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

  11. Flourescence from Gas-Phase Biomolecular Ions

    DEFF Research Database (Denmark)

    Nielsen, Steen Brøndsted

    2013-01-01

    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 difficul...

  12. 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 ...

  13. 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…

  14. Biomolecular localization: Applications in tissue engineering

    Science.gov (United States)

    Znidarsic, William John

    A carrier material designed for in vivo implantation of cells can be chemically modified to present ligands that interact with cell surface receptors and guide new tissue formation. This study presents a versatile technique for modification of alginate matrices that relies upon molecular coating of nanoparticle surfaces, using a layer-by-layer deposition technique, followed by dispersion of these particles with the alginate gel matrix. The deposition technique results in nanoparticle coatings that present a variety of biological information including organic molecules (e.g. amines, polyacrylic acid (PAA), phosphoproteins, collagen, albumin, and growth factors) and inorganic calcium phosphate (e.g. hydroxyapatite). Results show that incorporation of coated nanoparticles can stimulate cell proliferation when compared with incorporation of un-coated particles and/or free molecules. Because cells incorporated within the volume of the alginate matrix present cell surface receptors that are spatially distributed on the nano-scale, the observed stimulation in proliferation may be a result of changes in local concentration of molecules that are coated on the nanoparticles rather than added in "free form". In the repair of maxillofacial defects, alginate gels are used clinically for the delivery and localization of stem cells. Similar techniques for three-dimensional localization of biomolecules within these constructs may possibly prove beneficial in stimulating positive biological outcomes in vivo.

  15. 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.

  16. 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.

  17. Membrane-based biomolecular smart materials

    International Nuclear Information System (INIS)

    Membrane-based biomolecular materials are a new class of smart material that feature networks of artificial lipid bilayers contained within durable synthetic substrates. Bilayers contained within this modular material platform provide an environment that can be tailored to host an enormous diversity of functional biomolecules, where the functionality of the global material system depends on the type(s) and organization(s) of the biomolecules that are chosen. In this paper, we review a series of biomolecular material platforms developed recently within the Leo Group at Virginia Tech and we discuss several novel coupling mechanisms provided by these hybrid material systems. The platforms developed demonstrate that the functions of biomolecules and the properties of synthetic materials can be combined to operate in concert, and the examples provided demonstrate how the formation and properties of a lipid bilayer can respond to a variety of stimuli including mechanical forces and electric fields

  18. 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.

  19. Socioeconomic Disparities across Ethnicities: An Application to Cervical Cancer Screening

    OpenAIRE

    Walsh, B.; O'Neill, C

    2015-01-01

    Objectives: Our aim is to investigate socioeconomic disparities in cervical cancer screening utilization among and between ethnic groups in the United States. Study Design: Observational study. Methods: Data on 26,338 women aged 21 to 64 years were obtained from the 2007 to 2011 years of the Medical Expenditure Panel Survey. Data on cervical cancer screening utilization in the preceding 12 months and 3 years, and a range of sociodemographic characteristics were included. Analyses were...

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. Perspective: Markov models for long-timescale biomolecular dynamics

    International Nuclear Information System (INIS)

    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

  5. 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.

  6. Biomolecular Assembly of Gold Nanocrystals

    Energy Technology Data Exchange (ETDEWEB)

    Micheel, Christine Marya

    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.

  7. 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......Design new materials for energy production in a photoelectrochemical cell, where water is split into hydrogen and oxygen by solar light, is one possible solution to the problem of increasing energy demand and storage. A screening procedure based on ab-initio density functional theory calculations...... visible light harvesting, 20 for the one-photon and 12 for the two-photon water splitting process. In addition, 16 candidates were suggested for the transparent shielding of the photocatalyst. The problem of corrosion has been addressed for the candidates for the one-photon scheme using Pourbaix diagrams...

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

    OpenAIRE

    Ogórek M.; Frączek T.; Skuza Z.

    2015-01-01

    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 i...

  9. Analyzing biomolecular interactions by variable angle ellipsometry

    Science.gov (United States)

    Wu, Jiun-Yan; Lee, Chih-Kung; Lee, J. H.; Shiue, Shuen-Chen; Lee, Shu-Sheng; Lin, Shiming

    2001-10-01

    In this paper, an innovative ellipsometer is developed and applied to metrology of the biomolecular interaction on a protein biochip. Both the theory, optical and opto-mechanical configurations of this newly developed ellipsometer and methodologies adopted in system design to improve the system performance are presented. It will be shown that by measuring the ellipsometric parameters, the corresponding concentration variation in biochemical reaction can be calculated according to stoichiometry analysis. By applying the variable angle ellipsometry to analysis of a multi-layered sample, the thickness and concentration are resolved. It is believed that the newly developed ellipsometer biosensor is able to undertake an accurate measurement on biomedical interaction.

  10. 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.

  11. 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.

  12. Energy dissipation in biomolecular machines

    Energy Technology Data Exchange (ETDEWEB)

    Lervik, Anders

    2012-07-01

    The operation of a molecular pump, the calcium pump of sarcoplasmic reticulum is studied using mesoscopic non-equilibrium thermodynamics and molecular dynamics. The mesoscopic non-equilibrium thermodynamic description of the pump is compared to the description obtained in the framework of Hill for kinetic enzyme cycles. By comparing these two descriptions at isothermal conditions, they are found to be equivalent. This supports the validity of the mesoscopic approach. An extension of the mesoscopic non-equilibrium framework to also include a heat flux and the corresponding temperature difference is proposed. This can be used to model phenomena such as non-shivering thermogenesis, a process which lack a theoretical description in the kinetic cycle picture. Further, the heat transfer in the calcium pump is studied using molecular dynamics. This is done in order to obtain phenomenological parameters that can be used for the modeling of thermogenesis. A non-stationary non-equilibrium molecular dynamics approach is developed, which may be used to study heat transfer between a small object and the surrounding solvent. This methodology is applied to the calcium pump solvated in water. It is found that the thermal conductivity of the protein is low (0.2 W K-1 m-1) compared to water (0.6 WK-1 m-1). This means that the protein may sustain a large temperature gradient across its structure. The simulations also show that the protein-water surface is important for the heat transfer. The time scale for vibrational energy relaxation is found to be of order 10/100 ps which strengthens the local equilibrium assumption of mesoscopic non-equilibrium thermodynamics. Mesoscopic non-equilibrium thermodynamics is also applied to calculate the thermodynamic efficiency of the calcium pump embedded in lipid bilayers of varying length and from different tissues. This is done in order to show the applicability of mesoscopic non-equilibrium thermodynamics to interpret experimental data. The

  13. 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

  14. [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

  15. 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.

  16. 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.

  17. 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

  18. 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. PMID:26673779

  19. Design and Application of a Novel High-throughput Screening Technique for 1-Deoxynojirimycin

    OpenAIRE

    Jiang, Peixia; Mu, Shanshan; Li, Heng; Li, Youhai; Feng, Congmin; Jin, Jian-Ming; Tang, Shuang-Yan

    2015-01-01

    High-throughput screening techniques for small molecules can find intensive applications in the studies of biosynthesis of these molecules. A sensitive, rapid and cost-effective technique that allows high-throughput screening of endogenous production of the natural iminosugar 1-deoxynojirimycin (1-DNJ), an α-glucosidase inhibitor relevant to the pharmaceutical industry, was developed in this study, based on the inhibitory effects of 1-DNJ on the activity of the β-glycosidase LacS from Sulfolo...

  20. 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

  1. 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.

  2. 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.

  3. Ensemble based convergence assessment of biomolecular trajectories

    CERN Document Server

    Lyman, E; Lyman, Edward; Zuckerman, Daniel M.

    2006-01-01

    Assessing the convergence of a biomolecular simulation is an essential part of any computational investigation. This is because many important quantities (e.g., free energy differences) depend on the relative populations of different conformers; insufficient convergence translates into systematic errors. Here we present a simple method to self-consistently assess the convergence of a simulation. Standard clustering methods first generate a set of reference structures to any desired precision. The trajectory is then classified by proximity to the reference structures, yielding a one-dimensional histogram of structurally distinct populations. Comparing ensembles of different trajectories (or different parts of the same trajectory) built with the same reference structures provides a sensitive, quantitative measure of convergence. Please note: this is a preliminary manuscript, and should be read as such. Comments are most welcome, especially regarding pertinent prior work.

  4. 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.

  5. 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...

  6. Extracting Biomolecular Interactions Using Semantic Parsing of Biomedical Text

    OpenAIRE

    Garg, Sahil; Galstyan, Aram; Hermjakob, Ulf; Marcu, Daniel

    2015-01-01

    We advance the state of the art in biomolecular interaction extraction with three contributions: (i) We show that deep, Abstract Meaning Representations (AMR) significantly improve the accuracy of a biomolecular interaction extraction system when compared to a baseline that relies solely on surface- and syntax-based features; (ii) In contrast with previous approaches that infer relations on a sentence-by-sentence basis, we expand our framework to enable consistent predictions over sets of sen...

  7. 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…

  8. Biomolecular surface construction by PDE transform.

    Science.gov (United States)

    Zheng, Qiong; Yang, Siyang; Wei, Guo-Wei

    2012-03-01

    This work proposes a new framework for the surface generation based on the partial differential equation (PDE) transform. The PDE transform has recently been introduced as a general approach for the mode decomposition of images, signals, and data. It relies on the use of arbitrarily high-order PDEs to achieve the time-frequency localization, control the spectral distribution, and regulate the spatial resolution. The present work provides a new variational derivation of high-order PDE transforms. The fast Fourier transform is utilized to accomplish the PDE transform so as to avoid stringent stability constraints in solving high-order PDEs. As a consequence, the time integration of high-order PDEs can be done efficiently with the fast Fourier transform. The present approach is validated with a variety of test examples in two-dimensional and three-dimensional settings. We explore the impact of the PDE transform parameters, such as the PDE order and propagation time, on the quality of resulting surfaces. Additionally, we utilize a set of 10 proteins to compare the computational efficiency of the present surface generation method and a standard approach in Cartesian meshes. Moreover, we analyze the present method by examining some benchmark indicators of biomolecular surface, that is, surface area, surface-enclosed volume, solvation free energy, and surface electrostatic potential. A test set of 13 protein molecules is used in the present investigation. The electrostatic analysis is carried out via the Poisson-Boltzmann equation model. To further demonstrate the utility of the present PDE transform-based surface method, we solve the Poisson-Nernst-Planck equations with a PDE transform surface of a protein. Second-order convergence is observed for the electrostatic potential and concentrations. Finally, to test the capability and efficiency of the present PDE transform-based surface generation method, we apply it to the construction of an excessively large biomolecule, a

  9. 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

  10. 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.

  11. 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.

  12. 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.  ……

  13. Application of ultrasound in fetal cardiac abnormalitis screening and analyzing of influencing factors

    International Nuclear Information System (INIS)

    Objective: To identify the application value of ultrasound in the screening of fetal cardiac abnormalities and to reduce its affecting factors, in order to maximally decrease the birth of oaf. Methods: Adopting the method of four chamber hearts cross-section and sound beam plane head laterodeviation, 3821 fetal hearts were screened by ultrasonocardiography in middle and late fetal period. The influencing factors were also analyzed. Screening results were compared with the autopsy following induced labor and the ultrasonocardiogram after borne. Results: Total 23 cases of the cardiac anomalies were confirmed by odinopoeia or after borned, 21 cases were diagnosed by antepartum ultrasonocardiography, the detectable rate were 91.3%(21/23). And the complex cardiac anomalies were 19 cases, accounted for 82.61%(19/23), the general malformation were 4 cases, accounted for 17.39%(4/23). In 19 cases of the complex anomalies, 17 cases were diagnosed by antepartum examination in the first time, 2 cases were diagnosed by reexamination, the total detectable rate were 100%(19/19). Conclusion: Ultrasonography is not only non-invasive but also unique method in detecting fetal heart defects. It will help to diagnose definitely the vast majority of congenital malformation in the fetal heart, especially complex malformation in the middle and later fetal period. There are some limitations and chronergy in ultrasonography for the screening of fetal heart defects, which should be followed-up when the fetal appeared 'normal' in the early screening. (authors)

  14. Wastewater screening method for evaluating applicability of zero-valent iron to industrial wastewater

    International Nuclear Information System (INIS)

    This study presents a screening protocol to evaluate the applicability of the ZVI pretreatment to various industrial wastewaters of which major constituents are not identified. The screening protocol consisted of a sequential analysis of UV-vis spectrophotometry, high-performance liquid chromatograph (HPLC), and bioassay. The UV-vis and HPLC analyses represented the potential reductive transformation of unknown constituents in wastewater by the ZVI. The UV-vis and HPLC results were quantified using principal component analysis (PCA) and Euclidian distance (ED). The short-term bioassay was used to assess the increased biodegradability of wastewater constituents after ZVI treatment. The screening protocol was applied to seven different types of real industrial wastewaters. After identifying one wastewater as the best candidate for the ZVI treatment, the benefit of ZVI pretreatment was verified through continuous operation of an integrated iron-sequencing batch reactor (SBR) resulting in the increased organic removal efficiency compared to the control. The iron pretreatment was suggested as an economical option to modify some costly physico-chemical processes in the existing wastewater treatment facility. The screening protocol could be used as a robust strategy to estimate the applicability of ZVI pretreatment to a certain wastewater with unknown composition.

  15. 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

  16. 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

  17. 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...

  18. Expert Systems for Environmental Screening. An Application in the Lower Mekong Basin

    OpenAIRE

    K. Fedra; Winkelbauer, L.; Pantulu, V.R.

    1991-01-01

    This research report describes MEXSES, a rule-based expert system for environmental impact assessment at a screening level, implemented for the analysis of water resources development projects in the Lower Mekong Basin. The report makes a brief review of environmental impact assessment methods and tools. It discusses expert systems technology, with emphasis on environmental applications. The Lower Mekong Basin and its specific environmental problems, as well as the Mekong Secretariat's e...

  19. 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.

  20. 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

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

    Energy Technology Data Exchange (ETDEWEB)

    Xu Feng; Wu Jinhui; Wang Shuqi; Gurkan, Umut Atakan; Demirci, Utkan [Department of Medicine, Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Center for Biomedical Engineering, Brigham and Women' s Hospital, Harvard Medical School, Boston, MA (United States); Durmus, Naside Gozde, E-mail: udemirci@rics.bwh.harvard.edu [School of Engineering and Division of Biology and Medicine, Brown University, Providence, RI (United States)

    2011-09-15

    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.

  2. 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.

  3. An investigation of potential applications of intensifying screens in intraoral radiography

    International Nuclear Information System (INIS)

    In medicine, the somewhat degraded image from the screen/film system is accepted for most diagnostic purposes in the interest of radiation thrift. In dentistry, however, the superb image resolution and sharpness of the radiation-intensive, direct-exposure film is the standard for intraoral radiography. There may be occasions in dental practice where such quality is not necessary, thus making the high level of exposure difficult to justify. In a laboratory study, screen-type radiographs were effectively substituted for ultraspeed film in the monitoring stages of endodontic therapy and as posttreatment films in operative dentistry. Even with a slow system, the radiation exposure was one sixteenth of the usual periapical dose. If clinical trials support these conclusions, only the lack of a practical periapical cassette limits the application of this significant method of radiation reduction to dental practice

  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. 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

  6. 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

  7. 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...

  8. 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.

  9. 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, an...... 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...

  10. 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

  11. 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

  12. 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.

  13. 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

  14. Screening Analysis of Criticality Features, Events, and Processes for License Application

    International Nuclear Information System (INIS)

    This report documents the screening analysis of postclosure criticality features, events, and processes. It addresses the probability of criticality events resulting from degradation processes as well as disruptive events (i.e., seismic, rock fall, and igneous). Probability evaluations are performed utilizing the configuration generator described in ''Configuration Generator Model'', a component of the methodology from ''Disposal Criticality Analysis Methodology Topical Report''. The total probability per package of criticality is compared against the regulatory probability criterion for inclusion of events established in 10 CFR 63.114(d) (consider only events that have at least one chance in 10,000 of occurring over 10,000 years). The total probability of criticality accounts for the evaluation of identified potential critical configurations of all baselined commercial and U.S. Department of Energy spent nuclear fuel waste form and waste package combinations, both internal and external to the waste packages. This criticality screening analysis utilizes available information for the 21-Pressurized Water Reactor Absorber Plate, 12-Pressurized Water Reactor Absorber Plate, 44-Boiling Water Reactor Absorber Plate, 24-Boiling Water Reactor Absorber Plate, and the 5-Defense High-Level Radioactive Waste/U.S. Department of Energy Short waste package types. Where defensible, assumptions have been made for the evaluation of the following waste package types in order to perform a complete criticality screening analysis: 21-Pressurized Water Reactor Control Rod, 5-Defense High-Level Radioactive Waste/U.S. Department of Energy Long, and 2-Multi-Canister Overpack/2-Defense High-Level Radioactive Waste package types. The inputs used to establish probabilities for this analysis report are based on information and data generated for the Total System Performance Assessment for the License Application, where available. This analysis report determines whether criticality is to be

  15. A method to screen and evaluate tissue adhesives for joint repair applications

    Directory of Open Access Journals (Sweden)

    Dehne Tilo

    2012-09-01

    Full Text Available Abstract Background Tissue adhesives are useful means for various medical procedures. Since varying requirements cause that a single adhesive cannot meet all needs, bond strength testing remains one of the key applications used to screen for new products and study the influence of experimental variables. This study was conducted to develop an easy to use method to screen and evaluate tissue adhesives for tissue engineering applications. Method Tissue grips were designed to facilitate the reproducible production of substrate tissue and adhesive strength measurements in universal testing machines. Porcine femoral condyles were used to generate osteochondral test tissue cylinders (substrates of different shapes. Viability of substrates was tested using PI/FDA staining. Self-bonding properties were determined to examine reusability of substrates (n = 3. Serial measurements (n = 5 in different operation modes (OM were performed to analyze the bonding strength of tissue adhesives in bone (OM-1 and cartilage tissue either in isolation (OM-2 or under specific requirements in joint repair such as filling cartilage defects with clinical applied fibrin/PLGA-cell-transplants (OM-3 or tissues (OM-4. The efficiency of the method was determined on the basis of adhesive properties of fibrin glue for different assembly times (30 s, 60 s. Seven randomly generated collagen formulations were analyzed to examine the potential of method to identify new tissue adhesives. Results Viability analysis of test tissue cylinders revealed vital cells (>80% in cartilage components even 48 h post preparation. Reuse (n = 10 of test substrate did not significantly change adhesive characteristics. Adhesive strength of fibrin varied in different test settings (OM-1: 7.1 kPa, OM-2: 2.6 kPa, OM-3: 32.7 kPa, OM-4: 30.1 kPa and was increasing with assembly time on average (2.4-fold. The screening of the different collagen formulations revealed a substance with significant

  16. 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...

  17. 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

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

    Science.gov (United States)

    Caravagna, Giulio; Mauri, Giancarlo; d'Onofrio, Alberto

    2013-01-01

    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. PMID:23437034

  19. Spatially encoded strategies in the execution of biomolecular-oriented 3D NMR experiments

    International Nuclear Information System (INIS)

    Three-dimensional nuclear magnetic resonance (3D NMR) provides one of the foremost analytical tools available for the elucidation of biomolecular structure, function and dynamics. Executing a 3D NMR experiment generally involves scanning a series of time-domain signals S(t3), as a function of two time variables (t1, t2) which need to undergo parametric incrementations throughout independent experiments. Recent years have witnessed extensive efforts towards the acceleration of this kind of experiments. Among the different approaches that have been proposed counts an 'ultrafast' scheme, which distinguishes itself from other propositions by enabling-at least in principle-the acquisition of the complete multidimensional NMR data set within a single transient. 2D protein NMR implementations of this single-scan method have been demonstrated, yet its potential for 3D acquisitions has only been exemplified on model organic compounds. This publication discusses a number of strategies that could make these spatial encoding protocols compatible with 3D biomolecular NMR applications. These include a merging of 2D ultrafast NMR principles with temporal 2D encoding schemes, which can yield 3D HNCO spectra from peptides and proteins within ∼100 s timescales. New processing issues that facilitate the collection of 3D NMR spectra by relying fully on spatial encoding principles are also assessed, and shown capable of delivering HNCO spectra within 1 s timescales. Limitations and prospects of these various schemes are briefly addressed

  20. Group transfer theory of single molecule imaging experiments in the F-ATPase biomolecular motor

    Science.gov (United States)

    Volkan-Kacso, Sandor; Marcus, Rudolph

    I describe a chemo-mechanical theory to treat single molecule imaging and ``stalling'' experiments on the F-ATPase enzyme. This enzyme is an effective stepping biomolecular rotary motor with a rotor shaft and a stator ring. Using group transfer theoretical approach the proposed structure-based theory couples the binding transition of nucleotides in the stator subunits and the physics of torsional elasticity in the rotor. The twisting of the elastic rotor domain acts as a perturbation upon the driving potential, the Gibbs free energy. In the theory, without the use of adjustastable parameters, we predict the rate and equilibrium constant dependence of steps such as ATP binding and phosphate release as a function of manipulated rotor angle. Then we compare these predictions to available data from stalling experiments. Besides treating experiments, the theory can provide guides for atomistic simulations, which could calculate the reorganization parameter and the torsional spring constant. The framework is generic and I discuss its application to other single molecule experiments, such as controlled rotation and other biomolecular motors, including motor-DNA complexes and linear motors.[PNAS, Early Edition, Oct. 19, 2015, doi: 10.1073/pnas.1518489112

  1. 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.

  2. 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

  3. Application of EU guidelines for the validation of screening methods for veterinary drugs.

    Science.gov (United States)

    Stolker, Alida A M Linda

    2012-08-01

    Commission Decision (CD) 2002/657/EC describes detailed rules for method validation within the framework of residue monitoring programmes. The approach described in this CD is based on criteria. For (qualitative) screening methods, the most important criteria is that the CCβ has to be below any regulatory limit. Especially when microbiological or immunochemical methods are involved, the approach described in the CD is not easily applied. For example, by those methods, a large number of analytes (all antibiotics) within several different matrices (meat, milk, fish, eggs, etc.) are detected. It is not completely clear whether all those analytes and all matrices have to be taken into account during method validation. To clarify this, a working group - from EU Reference Laboratories - came up with a practical approach to validate multi-analyte multi-matrix screening methods. It describes how many analyte/matrix combinations have to be tested and how these combinations are selected. Furthermore it describes how to determine CCβ for screening methods in relation to a large list of compounds and maximum residue limits (MRLs). First for each analyte/matrix combination the 'cut-off' level - i.e. the level at which the method separates blanks from contaminated samples - is established. The validation is preferably at the concentration of 50% of the regulatory limit. A minimum set of 20 different samples has to be tested. From the experiences with applying these guidelines it was concluded that the validation approach is very 'practical'; however, there are some remarks. One has to be careful with selecting 'representative' analytes and matrices and it is strongly recommended to collect additional validation data during the routine application of the method. PMID:22851358

  4. 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.

  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. 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

  7. 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...

  8. Quantifying Modularity in the Evolution of Biomolecular Systems

    OpenAIRE

    2004-01-01

    Functional modules are considered the primary building blocks of biomolecular systems. Here we study to what extent functional modules behave cohesively across genomes:That is, are functional modules also evolutionary modules? We probe this question by analyzing for a large collection of functional modules the phyletic patterns of their genes across 110 genomes. The majority of functional modules display limited evolutionary modularity. This result confirms certain comparative genome analyses...

  9. The biomolecular and ultrastructural basis of epidermolysis bullosa:

    OpenAIRE

    Ciolan, Maria; Olariu, Liviu; Solovan, Caius

    2005-01-01

    Transmission electron microscopy, immunoelectron microscopy, immunofluorescence and antigenic mapping have improved our understanding of the dermo-epidermal junction. We have reviewed some ultrastructural and biomolecular aspects related to the dermo-epidermal junction. In part, they are implicated in the pathogenesis of a group of hereditary disorders characterized by skin fragility, collectively known as epidermolysis bullosa (EB). These disorders could benefit in the near future from a gen...

  10. A mechanical Turing machine: blueprint for a biomolecular computer

    OpenAIRE

    Shapiro, Ehud

    2012-01-01

    We describe a working mechanical device that embodies the theoretical computing machine of Alan Turing, and as such is a universal programmable computer. The device operates on three-dimensional building blocks by applying mechanical analogues of polymer elongation, cleavage and ligation, movement along a polymer, and control by molecular recognition unleashing allosteric conformational changes. Logically, the device is not more complicated than biomolecular machines of the living cell, and a...

  11. 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...

  12. Screening and metamodeling of computer experiments with functional outputs. Application to thermal–hydraulic computations

    International Nuclear Information System (INIS)

    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. - Highlights: ► Uncertainty and sensitivity analysis methods are extended to cases of curve outputs. ► For cpu time expensive computer code, we propose a new metamodeling technique. ► The difficult task is the dimensionality reduction one. ► It is applied with success on complex computations related to nuclear reactor safety.

  13. 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.

  14. 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

  15. A globally applicable location-specific screening model for assessing the relative risk of pesticide leaching

    International Nuclear Information System (INIS)

    A screening model of pesticide leaching loss is described which forms part of a multi-criteria risk-based indicator system called PRoMPT (Pesticide Risk Management and Profiling Tool). The leaching model evaluates pesticide fate in soil for any application rate and time of application (including multiple applications), for any land-based location in the world. It considers a generic evaluative environment with fixed dimensions and soil properties. The soil profile is conceptualised as a number of discrete layers. Equilibrium partitioning between adsorbed and dissolved chemical (based on the organic carbon-water partition coefficient [K OC]) is assumed in each time step, in each layer. Non-leaching losses are described using first order kinetics. Drainage is assumed to be uniform throughout the soil profile but varies temporally. The drainage rate, which can be augmented by evapotranspiration-adjusted irrigation, is derived from long-term mean monthly water balance model calculations performed for 30 arc-minute grid cells across the entire ice-free land surface of the earth. Although, such predictions are approximate, they do capture the seasonality and relative magnitude of drainage and allow the model to be applied anywhere, without the need for extensive data compilation. PRoMPT predictions are shown to be consistent with those made by more sophisticated models (PRZM, PELMO and PEARL) for the FOCUS groundwater scenarios

  16. Screening Decisions for a Middle School Assistant Principalship: Effects of Principal's Sex, National Origin of Applicants, and Job Experience of Applicants

    Science.gov (United States)

    Young, I. Phillip; Sever, Wesley Richard

    2011-01-01

    Screening decisions of female and male middle school principals were examined for applicants varying in national origin (Hispanic versus non-Hispanic) and type of job experience (direct versus indirect) for a middle school principalship. Principals' reactions were assessed according to perceived qualifications of applicants, probability of…

  17. 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.

  18. 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...

  19. 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.

  20. 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)

  1. 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

  2. Near-infrared fluorophores as biomolecular probes

    Science.gov (United States)

    Patonay, Gabor; Beckford, Garfield; Strekowski, Lucjan; Henary, Maged; Merid, Yonathan

    2010-02-01

    Near-Infrared (NIR) fluorescence has been valuable in analytical and bioanalytical chemistry. NIR probes and labels have been used for several applications, including hydrophobicity of protein binding sites, DNA sequencing, immunoassays, CE separations, etc. The NIR region (700-1100 nm) has advantages for the spectroscopist due to the inherently lower background interference from the biological matrix and the high molar absorptivities of NIR chromophores. During the studies we report here several NIR dyes were prepared to determine the role of the hydrophobicity of NIR dyes and their charge in binding to amino acids and proteins, e.g., serum albumins. We synthesized NIR dye homologs containing the same chromophore but substituents of varying hydrophobicity. Hydrophobic moieties were represented by alkyl and aryl groups. These NIR dyes of varying hydrophobicity exhibited varying degrees of H-aggregation in aqueous solution indicating that the degree of H-aggregation could be used as an indicator to predict binding characteristics to serum albumins. In order to understand what factors may be important in the binding process, spectral behavior of these varying hydrophobicity dyes were examined in the presence of amino acids. Typical dye structures that exhibit large binding constants to biomolecules were compared in order to optimize applications utilizing non-covalent interactions.

  3. 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.

  4. 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.

  5. 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

  6. ACEMD: Accelerating bio-molecular dynamics in the microsecond time-scale

    CERN Document Server

    Harvey, M J; De Fabritiis, G

    2009-01-01

    The high arithmetic performance and intrinsic parallelism of recent graphical processing units (GPUs) can offer a technological edge for molecular dynamics simulations. ACEMD is a production-class bio-molecular dynamics (MD) simulation program designed specifically for GPUs which is able to achieve supercomputing scale performance of 40 nanoseconds/day for all-atom protein systems with over 23,000 atoms. We illustrate the characteristics of the code, its validation and performance. We also run a microsecond-long trajectory for an all-atom molecular system in explicit TIP3P water on a single workstation computer equipped with just 3 GPUs. This performance on cost effective hardware allows ACEMD to reach microsecond timescales routinely with important implications in terms of scientific applications.

  7. 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

  8. 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.

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

    International Nuclear Information System (INIS)

    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)5]2 and [d(C5G5)]2. We find that this method can accurately reproduce the hydration patterns of A-DNA observed in neutron diffraction experiments on oriented DNA fibers

  10. 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.

  11. 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

  12. Proteomic Serum Biomarkers and Their Potential Application in Cancer Screening Programs

    OpenAIRE

    Deelder, André M; Tollenaar, Rob A. E. M.; Mertens, Bart J.; Yuri E. M. van der Burgt; Anouck Huijbers; Tim J. A. Dekker; Wilma E. Mesker; Berit Velstra

    2010-01-01

    Early diagnosis of cancer is of pivotal importance to reduce disease-related mortality. There is great need for non-invasive screening methods, yet current screening protocols have limited sensitivity and specificity. The use of serum biomarkers to discriminate cancer patients from healthy persons might be a tool to improve screening programs. Mass spectrometry based proteomics is widely applied as a technology for mapping and identifying peptides and proteins in body fluids. One commonly use...

  13. 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...

  14. 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 ...

  15. Proteomic Serum Biomarkers and Their Potential Application in Cancer Screening Programs

    Directory of Open Access Journals (Sweden)

    André M. Deelder

    2010-10-01

    Full Text Available Early diagnosis of cancer is of pivotal importance to reduce disease-related mortality. There is great need for non-invasive screening methods, yet current screening protocols have limited sensitivity and specificity. The use of serum biomarkers to discriminate cancer patients from healthy persons might be a tool to improve screening programs. Mass spectrometry based proteomics is widely applied as a technology for mapping and identifying peptides and proteins in body fluids. One commonly used approach in proteomics is peptide and protein profiling. Here, we present an overview of profiling methods that have the potential for implementation in a clinical setting and in national screening programs.

  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. 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.

  18. 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

  19. 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.

  20. Biomolecular interaction analysis for carbon nanotubes and for biocompatibility prediction.

    Science.gov (United States)

    Chen, Xiaoping; Fang, Jinzhang; Cheng, Yun; Zheng, Jianhui; Zhang, Jingjing; Chen, Tao; Ruan, Benfang Helen

    2016-07-15

    The interactions between carbon nanotubes (CNTs) and biologics have been commonly studied by various microscopy and spectroscopy methods. We tried biomolecular interaction analysis to measure the kinetic interactions between proteins and CNTs. The analysis demonstrated that wheat germ agglutinin (WGA) and other proteins have high affinity toward carboxylated CNT (f-MWCNT) but essentially no binding to normal CNT (p-MWCNT). The binding of f-MWCNT-protein showed dose dependence, and the observed kinetic constants were in the range of 10(-9) to 10(-11) M with very small off-rates (10(-3) to 10(-7) s(-1)), indicating a relatively tight and stable f-MWCNT-protein complex formation. Interestingly in hemolysis assay, p-MWCNT showed good biocompatibility, f-MWCNT caused 30% hemolysis, but WGA-coated f-MWCNT did not show hemolysis. Furthermore, the f-MWCNT-WGA complex demonstrated enhanced cytotoxicity toward cancer cells, perhaps through the glycoproteins expressed on the cells' surface. Taken together, biomolecular interaction analysis is a precise method that might be useful in evaluating the binding affinity of biologics to CNTs and in predicting biological actions. PMID:27108187

  1. PREFACE: Radiation Damage in Biomolecular Systems (RADAM07)

    Science.gov (United States)

    McGuigan, Kevin G.

    2008-03-01

    The annual meeting of the COST P9 Action `Radiation damage in biomolecular systems' took place from 19-22 June 2007 in the Royal College of Surgeons in Ireland, in Dublin. The conference was structured into 5 Working Group sessions: Electrons and biomolecular interactions Ions and biomolecular interactions Radiation in physiological environments Theoretical developments for radiation damage Track structure in cells Each of the five working groups presented two sessions of invited talks. Professor Ron Chesser of Texas Tech University, USA gave a riveting plenary talk on `Mechanisms of Adaptive Radiation Responses in Mammals at Chernobyl' and the implications his work has on the Linear-No Threshold model of radiation damage. In addition, this was the first RADAM meeting to take place after the Alexander Litvenenko affair and we were fortunate to have one of the leading scientists involved in the European response Professor Herwig Paretzke of GSF-Institut für Strahlenschutz, Neuherberg, Germany, available to speak. The remaining contributions were presented in the poster session. A total of 72 scientific contributions (32 oral, 40 poster), presented by 97 participants from 22 different countries, gave an overview on the current progress in the 5 different subfields. A 1-day pre-conference `Early Researcher Tutorial Workshop' on the same topic kicked off on 19 June attended by more than 40 postgrads, postdocs and senior researchers. Twenty papers, based on these reports, are included in this volume of Journal of Physics: Conference Series. All the contributions in this volume were fully refereed, and they represent a sample of the courses, invited talks and contributed talks presented during RADAM07. The interdisciplinary RADAM07 conference brought together researchers from a variety of different fields with a common interest in biomolecular radiation damage. This is reflected by the disparate backgrounds of the authors of the papers presented in these proceedings

  2. 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.

  3. Advancements in in vitro hepatic models: application for drug screening and therapeutics.

    Science.gov (United States)

    Damania, Apeksha; Jain, Era; Kumar, Ashok

    2014-01-01

    The liver is one of the most complex organs in the body, performing a multitude of functions. Liver tissue engineering is a combination of various strategies that aim at generating functional liver tissue that can help restore and/or support the ailing liver as it recuperates. Conventionally, in vitro culture has involved growing cells in different media compositions or layering them on matrices largely composed of native ECM components such as collagen or Matrigel. With recent advances in technology, more sophisticated techniques are being devised that are better equipped to capture distinct features of the liver in an in vivo microenvironment. Three-dimensional (3D) cultures of liver cells in 3D scaffolds, as spheroids or cell sheets, allow for a high degree of cell-cell and cell-matrix interaction and an in vivo-like architecture. More recently, decellularized matrices have been used as scaffolds that support ideal cell-matrix interactions. Microfabrication technologies initially used to pattern semiconductors in the integrated circuit industry have grown out of this field and now encompass a variety of methods to etch patterns onto both 2D and 3D scaffolds to allow incorporation of custom-made features resembling the fluid network and organization in native liver. This improvisation permits for enhanced vascularization and oxygen diffusion to the in vitro liver tissue. In this review, we discuss the various configurations that have been implemented in the in vitro culture of liver cells and their application in liver therapeutics in the form of implantable liver tissue constructs and tools for drug screening. PMID:26202404

  4. Microfluidic Plastic Devices for Single-use Applications in High-Throughput Screening and DNA-Analysis

    OpenAIRE

    Gerlach, Andreas; Knebel, Günther; Guber, A. E.; Heckele, M.; Herrmann, D.; Muslija, A.; Schaller, T.

    2001-01-01

    Microfluidic devices fabricated by mass production offer an immense potential of applications such as high-throughput drug screening, clinical diagnostics and gene analysis [1]. The low unit production costs of plastic substrates make it possible to produce single-use devices, eliminating the need for cleaning and reuse [2]. Fabrication of microfluidic devices can be applied by microtechnical fabrication processes in combination with plastic molding techniques [3]. Basically, replication...

  5. 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.

  6. 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

  7. 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...

  8. Application of four bacterial screening procedures to assess changes in the toxicity of chemicals in mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Dutka, B.J.; Kwan, K.K.

    1982-10-01

    Four microbiological acute toxicity screening test methods with Microtox, Spirillum volutans, Pseudomonas fluorescens and Aeromonas hydrophila were compared using solutions of mixed toxic chemicals. Each toxicity screening test appeared to have its own sensitivity pattern and it would appear unwise to try to assess the presence of toxicants in waters or effluents by a single species test. The battery approach, encompassing two or three genera and involving two to four species, is recommended to assess the potential presence of toxicants more thoroughly.

  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. 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.

  12. 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.

  13. Pushing back the frontiers of mercury speciation using a combination of biomolecular and isotopic signatures: challenge and perspectives.

    Science.gov (United States)

    Pedrero, Zoyne; Donard, Olivier F X; Amouroux, David

    2016-04-01

    Mercury (Hg) pollution is considered a major environmental problem due to the extreme toxicity of Hg. However, Hg metabolic pathways in biota remain elusive. An understanding of these pathways is crucial to elucidating the (eco)toxic effects of Hg and its biogeochemical cycle. The development of a new analytical methodology based on both speciation and natural isotopic fractionation represents a promising approach for metabolic studies of Hg and other metal(loid)s. Speciation provides valuable information about the reactivity and potential toxicity of metabolites, while the use of natural isotopic signature analysis adds a complementary dynamic dimension that allows the life history of the target element to be probed, the source of the target element (i.e., the source of pollution) to be identified, and reactions to be tracked. The resulting combined (bio)molecular and isotopic signature affords precious insight into the behavior of Hg in biota and Hg detoxification mechanisms. In the long term, this highly innovative methodology could be used in life and environmental science studies of metal(loid)s to push back the frontiers of our knowledge in this field. This paper summarizes the current status of the application of Hg speciation and the isotopic signature of Hg at the biomolecular level in living organisms, and discusses potential future uses of this combination of techniques. Graphical Abstract Application of Hg speciation and the isotopic signature of Hg to enhance our understanding of the roles of Hg in metabolic, toxicological, and environmental processes. PMID:26753975

  14. Minimal metabolic pathway structure is consistent with associated biomolecular interactions.

    Science.gov (United States)

    Bordbar, Aarash; Nagarajan, Harish; Lewis, Nathan E; Latif, Haythem; Ebrahim, Ali; Federowicz, Stephen; Schellenberger, Jan; Palsson, Bernhard O

    2014-01-01

    Pathways are a universal paradigm for functionally describing cellular processes. Even though advances in high-throughput data generation have transformed biology, the core of our biological understanding, and hence data interpretation, is still predicated on human-defined pathways. Here, we introduce an unbiased, pathway structure for genome-scale metabolic networks defined based on principles of parsimony that do not mimic canonical human-defined textbook pathways. Instead, these minimal pathways better describe multiple independent pathway-associated biomolecular interaction datasets suggesting a functional organization for metabolism based on parsimonious use of cellular components. We use the inherent predictive capability of these pathways to experimentally discover novel transcriptional regulatory interactions in Escherichia coli metabolism for three transcription factors, effectively doubling the known regulatory roles for Nac and MntR. This study suggests an underlying and fundamental principle in the evolutionary selection of pathway structures; namely, that pathways may be minimal, independent, and segregated. PMID:24987116

  15. Ion irradiation and biomolecular radiation damage II. Indirect effect

    CERN Document Server

    Wang, Wei; Su, Wenhui

    2010-01-01

    It has been reported that damage of genome in a living cell by ionizing radiation is about one-third direct and two-thirds indirect. The former which has been introduced in our last paper, concerns direct energy deposition and ionizing reactions in the biomolecules; the latter results from radiation induced reactive species (mainly radicals) in the medium (mainly water) surrounding the biomolecules. In this review, a short description of ion implantation induced radical formation in water is presented. Then we summarize the aqueous radical reaction chemistry of DNA, protein and their components, followed by a brief introduction of biomolecular damage induced by secondary particles (ions and electron). Some downstream biological effects are also discussed.

  16. Computational and theoretical aspects of biomolecular structure and dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Garcia, A.E.; Berendzen, J.; Catasti, P., Chen, X. [and others

    1996-09-01

    This is the final report for a project that sought to evaluate and develop theoretical, and computational bases for designing, performing, and analyzing experimental studies in structural biology. Simulations of large biomolecular systems in solution, hydrophobic interactions, and quantum chemical calculations for large systems have been performed. We have developed a code that implements the Fast Multipole Algorithm (FMA) that scales linearly in the number of particles simulated in a large system. New methods have been developed for the analysis of multidimensional NMR data in order to obtain high resolution atomic structures. These methods have been applied to the study of DNA sequences in the human centromere, sequences linked to genetic diseases, and the dynamics and structure of myoglobin.

  17. 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

  18. Integration of biomolecular logic gates with field-effect transducers

    International Nuclear Information System (INIS)

    Highlights: → Enzyme-based AND/OR logic gates are integrated with a capacitive field-effect sensor. → The AND/OR logic gates compose of multi-enzyme system immobilised on sensor surface. → Logic gates were activated by different combinations of chemical inputs (analytes). → The logic output (pH change) produced by the enzymes was read out by the sensor. - Abstract: The integration of biomolecular logic gates with field-effect devices - the basic element of conventional electronic logic gates and computing - is one of the most attractive and promising approaches for the transformation of biomolecular logic principles into macroscopically useable electrical output signals. In this work, capacitive field-effect EIS (electrolyte-insulator-semiconductor) sensors based on a p-Si-SiO2-Ta2O5 structure modified with a multi-enzyme membrane have been used for electronic transduction of biochemical signals processed by enzyme-based OR and AND logic gates. The realised OR logic gate composes of two enzymes (glucose oxidase and esterase) and was activated by ethyl butyrate or/and glucose. The AND logic gate composes of three enzymes (invertase, mutarotase and glucose oxidase) and was activated by two chemical input signals: sucrose and dissolved oxygen. The developed integrated enzyme logic gates produce local pH changes at the EIS sensor surface as a result of biochemical reactions activated by different combinations of chemical input signals, while the pH value of the bulk solution remains unchanged. The pH-induced charge changes at the gate-insulator (Ta2O5) surface of the EIS transducer result in an electronic signal corresponding to the logic output produced by the immobilised enzymes. The logic output signals have been read out by means of a constant-capacitance method.

  19. 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

  20. 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.

  1. 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.

  2. Fabrication and characterization of pixelated Gd2O2S:Tb scintillator screens for digital X-ray imaging applications

    International Nuclear Information System (INIS)

    X-ray imaging detectors in combination with scintillator screens have been widely used in digital X-ray imaging applications. Gd2O2S:Tb was used as scintillation material for pixelated scintillator screens based on silicon substrates (wafer) with a micropore array of various dimensions fabricated using the photolithography and deep reactive ion etching (DRIE) process. The relative light output and the modulation transfer function (MTF) of each fabricated scintillator screen were measured by a cooled CCD and compared with those of Lanex screens. The spatial resolution of our scintillator screens was higher but their light outputs were lower than those of Lanex screen probably due to the loss of light at the wall surfaces. Therefore further treatment of the wall surface, such as reflective coating, seems necessary to compensate the light loss.

  3. 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.

  4. 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...

  5. 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

  6. Operationalization and application of “early warning signs” to screen nanomaterials for harmful properties

    DEFF Research Database (Denmark)

    Hansen, Steffen Foss; Nielsen, Kåre Nolde; Knudsen, Nina Østergaard;

    2013-01-01

    endeavors. This paper explores how the first lesson – “Acknowledge and respond to ignorance, uncertainty and risk in technology appraisal” could be applied to screen nanomaterials. In cases of ignorance, uncertainty and risk, the EEA recommends paying particular attention to important warning signs such as...

  7. Operationalization and application of “early warning signs” to screen nanomaterials for harmful properties

    DEFF Research Database (Denmark)

    Hansen, Steffen Foss; Nielsen, K. N.; Knudsen, N.;

    endeavors. This paper explores how the first lesson - “Acknowledge and respond to ignorance, uncertainty and risk in technology appraisal” could be applied to screen nanomaterials. In cases of ignorance, uncertainty and risk, the EEA recommends paying particular attention to important warning signs such as...

  8. 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; Ahrenfeldt, Jesper; Hauggaard-Nielsen, Henrik; Henriksen, Ulrik Birk

    2015-01-01

    This work aims at identifying potential low-grade biomass fuels for a near future Danish CHP system encompassing pretreatment of these fuels by Pyroneer gasification for subsequent conversion of the gas in existing coal-fired boilers. The focus of the work is on development of a suitable screening...

  9. 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

  10. 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.

  11. 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

  12. 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)

  13. SCREENING AND CHARACTERIZATION OF STRESS TOLERANT SACCHAROMYCES CEREVISIAE ISOLATED FROM BREWERY EFFLUENTS FOR ANIMAL PROBIOTIC APPLICATIONS

    Directory of Open Access Journals (Sweden)

    Bhukya Bhima, Sudhakara Reddy Marrivada, Tangutur Anjana Devi , Yerradoddi Ramana Reddy, and Linga Venkateswar Rao*

    2010-12-01

    Full Text Available Based on the colony morphology and microscopic characteristics, 26 yeasts were isolated from different sources including brewery effluents. Initially they were screened for their thermotolerance at 40 0C and only 5 strains were selected. They were later grown in yeast extract peptone dextrose medium to screen their stress tolerance at five different temperatures; at different concentrations of a mixture of acetic, propionic and butyric acids; at different pH; at different concentrations of glucose and bile salts. Based on the growth at different stress conditions, yeast OBV9 was selected and characterized as Saccharomyces cerevisiae by sequencing its 5.8S rRNA gene and internal transcribed spacer (ITS 1 and 2. The sequence obtained was most similar (99% to S. cerevisiae, when it was blast searched in NCBI database and showed a separate branch in phylogenetic analysis.

  14. 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

  15. Justifying age thresholds for mammographic screening: an application of pragma-dialectical argumentation theory.

    Science.gov (United States)

    Schulz, Peter J; Meuffels, Bert

    2012-01-01

    Information campaigns on breast cancer screening in the Netherlands need to convince women above 50 years of age to have biannual mammography, and women below 50 years of age that regular mammograms are not recommended for them. This article reports the results of two experiments in which the construction of the persuasive messages was informed by argumentation-theoretical insights. No differences were found between either statistical and anecdotal evidence or gain- and loss-framing in the attempt to convince women under 50 that they normally do not need regular mammography. A striking contrast emerged, however, between the overwhelming acceptance of breast cancer screening for women above 50 and the relative restraint and reluctance to consent that mammography is usually not recommended for women under 50. The reluctance to accept that regular mammography is not recommended for women under 50 is traced back to ego involvement. PMID:21823968

  16. Evaluation of 14 Organic Solvents and Carriers for Screening Applications in Zebrafish Embryos and Larvae

    OpenAIRE

    Maes, Jan; Verlooy, Lien; Buenafe, Olivia E.; de Witte, Peter A. M.; Esguerra, Camila V.; Crawford, Alexander D.

    2012-01-01

    Zebrafish are rapidly growing in popularity as an in vivo model system for chemical genetics, drug discovery, and toxicology, and more recently also for natural product discovery. Experiments involving the pharmacological evaluation of small molecules or natural product extracts in zebrafish bioassays require the effective delivery of these compounds to embryos and larvae. While most samples to be screened are first solubilized in dimethyl sulfoxide (DMSO), which is then diluted in the embryo...

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

    OpenAIRE

    M. Julia Arcos-Martínez; Olga Domínguez-Renedo; Silvia Sanllorente-Méndez

    2010-01-01

    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 concen...

  18. Enhanced tree-classifier performance by inversion with application to pap smear screening data

    Science.gov (United States)

    Chen, E. T. Y.; Lee, James; Nelson, Alan C.

    1993-07-01

    In this paper, we present an inversion method to enhance a binary decision tree classifier using boundary search of training samples. We want to enhance the training at those points which are close to the boundaries. Selection of these points is based on the Euclidean distance from those centroids close to classification boundaries. The enhanced training using these selected data was compared with training using randomly selected samples. We also applied this method to improve the classification of pap smear screening data.

  19. 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...

  20. 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...

  1. Justifying age thresholds for mammographic screening: an application of pragma-dialectical argumentation theory

    OpenAIRE

    Schulz, Peter J.; Meuffels, Bert

    2015-01-01

    Information campaigns on breast cancer screening in the Netherlands need to convince women above 50 years of age to have biannual mammography, and women below 50 years of age that regular mammograms are not recommended for them. This article reports the results of two experiments in which the construction of the persuasive messages was informed by argumentation-theoretical insights. No differences were found between either statistical and anecdotal evidence or gain- and loss-framing in th...

  2. 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...

  3. Application of electrochemical breath test for detection of Helicobacter pylori in screening of Moscow students.

    Science.gov (United States)

    Kukushkina, I A; Korotkova, O A; Loginov, I A; Vasilieva, E A; Yashina, N V; Anokhina, I V; Kozlov, A V; Tumanova, G M; Tedoradze, R V; Dalin, M V

    2012-01-01

    The incidence of Helicobacter pylori infection is analyzed by the results of screening of first- and fourth-year students of Moscow Institute of Foreign Affairs using HelicoSense Scientific breath test system. Age-related dynamics of the infection in patients examined for the first time has been traced. The data on infection rates in patients after eradication therapy are presented. PMID:22803077

  4. 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

  5. Application of the E-screen assay to test for oestrogenically active substances in swine feed.

    Science.gov (United States)

    Bitsch, N; Körner, W; Postupka, S; Brunn, H

    2001-12-01

    A pig breeder in central Hesse (Germany) noticed the occurrence of enlarged vulvae in female piglets. Intoxication with oestrogenically active substances by contamination of two feed mixes ingested by the mother sows appeared to be a possible cause. Using a combined technique of the DFG analytical method S19 and the E-screen assay, two feed samples were found to contain powerful oestrogenically active compounds. By co-incubation with the anti-oestrogen tamoxifen it could be clearly demonstrated that the oestrogenic activity was mediated by the oestrogen receptor. These results demonstrate that use of the E-screen assay in combination with the DFG analytical method S19 provides a simple and readily usable prescreening method for the routine detection of oestrogenically active compounds in animal feed. The results from the E-screen assay show that the sows ingested 10-80 microg oestradiol equivalents per day in their feed. Because of the bioavailability of these substances, the oestrogenic active compounds seem to be transferred into the milk and passed to the piglets via suckling. The milk of the dam appears to contain this substance in biologically active form and at such high concentrations that the female piglets had enlarged vulvae. PMID:11906561

  6. Self-assembling biomolecular catalysts for hydrogen production

    Science.gov (United States)

    Jordan, Paul C.; Patterson, Dustin P.; Saboda, Kendall N.; Edwards, Ethan J.; Miettinen, Heini M.; Basu, Gautam; Thielges, Megan C.; Douglas, Trevor

    2016-02-01

    The chemistry of highly evolved protein-based compartments has inspired the design of new catalytically active materials that self-assemble from biological components. A frontier of this biodesign is the potential to contribute new catalytic systems for the production of sustainable fuels, such as hydrogen. Here, we show the encapsulation and protection of an active hydrogen-producing and oxygen-tolerant [NiFe]-hydrogenase, sequestered within the capsid of the bacteriophage P22 through directed self-assembly. We co-opted Escherichia coli for biomolecular synthesis and assembly of this nanomaterial by expressing and maturing the EcHyd-1 hydrogenase prior to expression of the P22 coat protein, which subsequently self assembles. By probing the infrared spectroscopic signatures and catalytic activity of the engineered material, we demonstrate that the capsid provides stability and protection to the hydrogenase cargo. These results illustrate how combining biological function with directed supramolecular self-assembly can be used to create new materials for sustainable catalysis.

  7. 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.

  8. 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

  9. SWISS-PROT: connecting biomolecular knowledge via a protein database.

    Science.gov (United States)

    Gasteiger, E; Jung, E; Bairoch, A

    2001-07-01

    With the explosive growth of biological data, the development of new means of data storage was needed. More and more often biological information is no longer published in the conventional way via a publication in a scientific journal, but only deposited into a database. In the last two decades these databases have become essential tools for researchers in biological sciences. Biological databases can be classified according to the type of information they contain. There are basically three types of sequence-related databases (nucleic acid sequences, protein sequences and protein tertiary structures) as well as various specialized data collections. It is important to provide the users of biomolecular databases with a degree of integration between these databases as by nature all of these databases are connected in a scientific sense and each one of them is an important piece to biological complexity. In this review we will highlight our effort in connecting biological information as demonstrated in the SWISS-PROT protein database. PMID:11488411

  10. Deterministic characterization of phase noise in biomolecular oscillators

    International Nuclear Information System (INIS)

    On top of the many external perturbations, cellular oscillators also face intrinsic perturbations due the randomness of chemical kinetics. Biomolecular oscillators, distinct in their parameter sets or distinct in their architecture, show different resilience with respect to such intrinsic perturbations. Assessing this resilience can be done by ensemble stochastic simulations. These are computationally costly and do not permit further insights into the mechanistic cause of the observed resilience. For reaction systems operating at a steady state, the linear noise approximation (LNA) can be used to determine the effect of molecular noise. Here we show that methods based on LNA fail for oscillatory systems and we propose an alternative ansatz. It yields an asymptotic expression for the phase diffusion coefficient of stochastic oscillators. Moreover, it allows us to single out the noise contribution of every reaction in an oscillatory system. We test the approach on the one-loop model of the Drosophila circadian clock. Our results are consistent with those obtained through stochastic simulations with a gain in computational efficiency of about three orders of magnitude

  11. Evaluation of 14 organic solvents and carriers for screening applications in zebrafish embryos and larvae.

    Science.gov (United States)

    Maes, Jan; Verlooy, Lien; Buenafe, Olivia E; de Witte, Peter A M; Esguerra, Camila V; Crawford, Alexander D

    2012-01-01

    Zebrafish are rapidly growing in popularity as an in vivo model system for chemical genetics, drug discovery, and toxicology, and more recently also for natural product discovery. Experiments involving the pharmacological evaluation of small molecules or natural product extracts in zebrafish bioassays require the effective delivery of these compounds to embryos and larvae. While most samples to be screened are first solubilized in dimethyl sulfoxide (DMSO), which is then diluted in the embryo medium, often this method is not sufficient to prevent the immediate or eventual precipitation of the sample. Certain compounds and extracts are also not highly soluble in DMSO. In such instances the use of carriers and/or other solvents might offer an alternative means to achieve the required sample concentration. Towards this end, we determined the maximum tolerated concentration (MTC) of several commonly used solvents and carriers in zebrafish embryos and larvae at various developmental stages. Solvents evaluated for this study included acetone, acetonitrile, butanone, dimethyl formamide, DMSO, ethanol, glycerol, isopropanol, methanol, polyethylene glycol (PEG-400), propylene glycol, and solketal, and carriers included albumin (BSA) and cyclodextrin (2-hydroxypropyl-beta-cyclodextrin, or HPBCD). This study resulted in the identification of polyethylene glycol (PEG400), propylene glycol, and methanol as solvents that were relatively well-tolerated over a range of developmental stages. In addition, our results showed that acetone was well-tolerated by embryos but not by larvae, and 1% cyclodextrin (HPBCD) was well-tolerated by both embryos and larvae, indicating the utility of this carrier for compound screening in zebrafish. However, given the relatively small differences (2-3 fold) between concentrations that are apparently safe and those that are clearly toxic, further studies - e.g. omics analyses -should be carried out to determine which cellular processes and signalling

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. Screen-film-combinations for radiography - present and future spectrum of application

    International Nuclear Information System (INIS)

    From the numbers of radiographs of the different examinations and the total amount of radiological diagnostics in the GDR their possible modification by new imaging techniques is discussed under the aspects of costs and radiation burden. Film-screen-systems are of special importance, because they also will be most frequently used image recording system in future. The importance of their various properties and parameters, methods of determining these parameters as well as future developments are analyzed from the standpoint of practical requirements. (author)

  17. Application of TLC in the Screening of Acarbose-producing Actinomycetes

    OpenAIRE

    Fei Ren; Long Chen; Qunyi Tong

    2014-01-01

    Acarbose is widely used in medicine, such as the treatment of diabetes and obesity. A simple Thin Layer Chromatography (TLC)-scanning technique was developed for the rapid and accurate analysis of acarbose in a large number of fermentation broths of actinomycetes to screen for acarbose producer. The linearity of the acarbose in this way was good within the range from 2 to 10 μg (r2 = 0.9997). This technique didn’t need expensive instrument and complex procedure for the detection of acarbose i...

  18. Powered by DFT: Screening methods that accelerate materials development for hydrogen in metals applications.

    Science.gov (United States)

    Nicholson, Kelly M; Chandrasekhar, Nita; Sholl, David S

    2014-11-18

    CONSPECTUS: Not only is hydrogen critical for current chemical and refining processes, it is also projected to be an important energy carrier for future green energy systems such as fuel cell vehicles. Scientists have examined light metal hydrides for this purpose, which need to have both good thermodynamic properties and fast charging/discharging kinetics. The properties of hydrogen in metals are also important in the development of membranes for hydrogen purification. In this Account, we highlight our recent work aimed at the large scale screening of metal-based systems with either favorable hydrogen capacities and thermodynamics for hydrogen storage in metal hydrides for use in onboard fuel cell vehicles or promising hydrogen permeabilities relative to pure Pd for hydrogen separation from high temperature mixed gas streams using dense metal membranes. Previously, chemists have found that the metal hydrides need to hit a stability sweet spot: if the compound is too stable, it will not release enough hydrogen under low temperatures; if the compound is too unstable, the reaction may not be reversible under practical conditions. Fortunately, we can use DFT-based methods to assess this stability via prediction of thermodynamic properties, equilibrium reaction pathways, and phase diagrams for candidate metal hydride systems with reasonable accuracy using only proposed crystal structures and compositions as inputs. We have efficiently screened millions of mixtures of pure metals, metal hydrides, and alloys to identify promising reaction schemes via the grand canonical linear programming method. Pure Pd and Pd-based membranes have ideal hydrogen selectivities over other gases but suffer shortcomings such as sensitivity to sulfur poisoning and hydrogen embrittlement. Using a combination of detailed DFT, Monte Carlo techniques, and simplified models, we are able to accurately predict hydrogen permeabilities of metal membranes and screen large libraries of candidate alloys

  19. 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.

  20. 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

  1. 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

  2. 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

  3. 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...

  4. 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...

  5. 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. ...

  6. Newborn Screening

    Science.gov (United States)

    ... Role of Laboratories Meet the Scientist Newborn Screening: Family Stories Newborn Screening: Public Health Stories Screening Newborns for Critical ... Quality Assurance Program Newborn Screening Translation Research Initiative Newborn ... Stay Connected Twitter Facebook ...

  7. 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.)

  8. 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

  9. 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.

  10. 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. PMID:20883031

  11. 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…

  12. Development of Screen-Printed Texture-Barrier Paste for Single-Side Texturization of Interdigitated Back-Contact Silicon Solar Cell Applications

    OpenAIRE

    Chi-Cheng Chen; Chin-Lung Cheng; Thou-Jen Whang; Yu-Shun Chiu

    2013-01-01

    Continuous cost reduction of silicon-based solar cells is needed to lower the process time and increase efficiency. To achieve lower costs, screen-printed texture-barrier (SPTB) paste was first developed for single-side texturization (ST) of the interdigitated back-contact (IBC) for silicon-based solar cell applications. The SPTB paste was screen-printed on silicon substrates. The SPTB paste was synthesized from intermixed silicate glass (75 wt %), a resin binder (ethyl cellulose ethoce: 20 w...

  13. Duplication and Divergence Effect on Network Motifs in Undirected Bio-Molecular Networks.

    Science.gov (United States)

    Pei Wang; Jinhu Lu; Xinghuo Yu; Zengrong Liu

    2015-06-01

    Duplication and divergence are two basic evolutionary mechanisms of bio-molecular networks. Real-world bio-molecular networks and their statistical characteristics can be well mimicked by artificial algorithms based on the two mechanisms. Bio-molecular networks consist of network motifs, which act as building blocks of large-scale networks. A fundamental question is how network motifs are evolved from long time evolution and natural selection. By considering the effect of various duplication and divergence strategies, we find that the underlying duplication scheme of the real-world undirected bio-molecular networks would rather follow the anti-preference strategy than the random one. The anti-preference duplication mechanism and the dimerization processes can lead to the formation of various motifs, and robustly conserve proper quantities of motifs in the artificial networks as that in the real-world ones. Furthermore, the anti-preference mechanism and edge deletion divergence can robustly preserve the sparsity of the networks. The investigations reveal the possible evolutionary mechanisms of network motifs in real-world bio-molecular networks, and have potential implications in the design, synthesis and reengineering of biological networks for biomedical purpose. PMID:25203993

  14. 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

  15. Experiment and Modeling of Spatially Indexed Microbead Arrays for High-Throughput Screening Applications

    Science.gov (United States)

    Leary, Thomas; Maldarelli, Charles; Couzis, Alexander

    2011-11-01

    The development of platforms for multiplexed, high throughput screening of the binding interactions of target biomolecules against a library of potential binding probes enables progress in many areas in medicine and biology. Formats in which probes are linked to microbeads arrayed in a microfluidic channel offer high sensitivity, reduced reagent consumption and are easily parallelized for multiplexed detection. This presentation describes a microfluidically assembled microbead array in which beads are streamed through a channel with an array of wells inscribed in the floor of the channel. The beads are captured in the wells via gravity. We demonstrate that an array of beads displaying different receptors can be assembled in this format, indexed by sequential depostion and used for a prototype assay. Solutions for a two dimensional mass transfer model of the conjugation of the probe to the receptor on the bead surface identify kinetically limited regimes which are used to measure the binding kinetics of the prototype assay.

  16. 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.

  17. 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

  18. 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

  19. 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

  20. 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.

  1. 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

  2. Soft Supercharging of Biomolecular Ions in Electrospray Ionization Mass Spectrometry

    Science.gov (United States)

    Chingin, Konstantin; Xu, Ning; Chen, Huanwen

    2014-06-01

    The charge states of biomolecular ions in ESI-MS can be significantly increased by the addition of low-vapor supercharging (SC) reagents into the spraying solution. Despite the considerable interest from the community, the mechanistic aspects of SC are not well understood and are hotly debated. Arguments that denaturation accounts for the increased charging observed in proteins sprayed from aqueous solutions containing SC reagent have been published widely, but often with incomplete or ambiguous supporting data. In this work, we explored ESI MS charging and SC behavior of several biopolymers including proteins and DNA oligonucleotides. Analytes were ionized from 100 mM ammonium acetate (NH4Ac) aqueous buffer in both positive (ESI+) and negative (ESI-) ion modes. SC was induced either with m-NBA or by the elevated temperature of ESI capillary. For all the analytes studied we, found striking differences in the ESI MS response to these two modes of activation. The data suggest that activation with m-NBA results in more extensive analyte charging with lower degree of denaturation. When working solution with m-NBA was analyzed at elevated temperatures, the SC effect from m-NBA was neutralized. Instead, the net SC effect was similar to the SC effect achieved by thermal activation only. Overall, our observations indicate that SC reagents enhance ESI charging of biomolecules via distinctly different mechanism compared with the traditional approaches based on analyte denaturation. Instead, the data support the hypothesis that the SC phenomenon involves a direct interaction between a biopolymer and SC reagent occurring in evaporating ESI droplets.

  3. 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...

  4. Application of screening tools to detect risk of hospital readmission in elderly patients in Valencian Healthcare System (VHS) (Spain).

    Science.gov (United States)

    Doñate-Martínez, Ascensión; Garcés Ferrer, Jorge; Ródenas Rigla, Francisco

    2014-01-01

    The Sustainable Social and Healthcare Model (SSHM) is aimed to establish new care pathways in primary care systems contributing to the decrease of health services use and costs and improve the integration and efficiency of social and health care for elderly people with long-term care (LTC) needs. One of these strategies is the segmentation of population in risk groups through standardized tools. This paper is a retrospective study aimed to determine the viability of the implementation of the screening tools Probability of Repeated Admission - Pra - and The Community Assessment Risk Screen - CARS - to detect patients at risk of hospital readmission in a sample of 500 elderly people (65+) from the VHS in Spain. Patients were recruited from three Health Departments. Data from selected tools and predictive variables were collected through the healthcare database from the VHS. The most important results indicate that both instruments predict with high efficacy the proportion of patients not readmitted (negative predictive value between 91% and 92%). Moreover, the tools performed with a moderate efficiency being the Pra less sensitive (54%) and more specific (81%) than CARS (with a sensitivity and specificity of 64%). Results from this study suggest that the application of instruments as Pra and CARS are of interest to the Valencian Health Administration as they can be a good strategy to improve the management of elderly patients at risk with comorbidities and guiding clinical decision. PMID:25022713

  5. 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.

  6. 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.)

  7. 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...

  8. 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

    use the topology of bio-molecular interaction networks in order to constrain the solution space. Such approaches systematically integrate the existing biological knowledge with the 'omics' data. Results: Here we introduce a hypothesis-driven method that integrates bio-molecular network topology with...... transcriptome data, thereby allowing the identification of key biological features (Reporter Features) around which transcriptional changes are significantly concentrated. We have combined transcriptome data with different biological networks in order to identify Reporter Gene Ontologies, Reporter Transcription...... 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...

  9. 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.

  10. 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...

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. Malignant transformation in vitro: criteria, biological markers, and application in environmental screening of carcinogens

    International Nuclear Information System (INIS)

    Biological markers which distinguish malignantly transformed fibroblasts from their normal counterpart include pleomorphic morphology, lowered requirement for nutritional factors, loss of density inhibition of growth, complex topography as discernible by scanning electron microscopy, loss in surface proteins, incomplete glycosylation of membrane glycolylipids and glycoproteins, increased production of specific proteases, decreased organization of the cytoskeleton, and acquisition of neoantigens. Several of these markers are not consistently found in transformed epithelial cells and therefore cannot serve to distinguish unequivocally neoplastic epithelial cells from the normal counterparts. The only criteria associated with the transformed nature of both fibroblasts and epithelial cells are the ability of the cells to proliferate in semisolid medium and to induce tumors in appropriate hosts. In vitro systems represent a powerful tool for screening the mutagenic/oncogenic potential of physical, chemical, and environmental agents. Fibroblasts rather than epithelial cells are preferred for this purpose at the present time because of the clear-cut phenotypic differences between the normal and the transformed cells. These systems have been useful in establishing that malignant transformation can be induced by doses as low as 1 rad of X rays or 0.1 rad of neutrons, and that fractionation at low dose levelsleads to enhanced transformation. They have been useful in identifying a large number of hazardous chemicals and in evaluating the relationship between the mutagenic and carcinogenic potential of radiation and chemicals

  16. 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.

  17. 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.

  18. From Correlation to Causality: Statistical Approaches to Learning Regulatory Relationships in Large-Scale Biomolecular Investigations.

    Science.gov (United States)

    Ness, Robert O; Sachs, Karen; Vitek, Olga

    2016-03-01

    Causal inference, the task of uncovering regulatory relationships between components of biomolecular pathways and networks, is a primary goal of many high-throughput investigations. Statistical associations between observed protein concentrations can suggest an enticing number of hypotheses regarding the underlying causal interactions, but when do such associations reflect the underlying causal biomolecular mechanisms? The goal of this perspective is to provide suggestions for causal inference in large-scale experiments, which utilize high-throughput technologies such as mass-spectrometry-based proteomics. We describe in nontechnical terms the pitfalls of inference in large data sets and suggest methods to overcome these pitfalls and reliably find regulatory associations. PMID:26731284

  19. 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

  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. Development and application of a screening model for evaluating bioenhanced dissolution in DNAPL source zones

    Science.gov (United States)

    Phelan, Thomas J.; Abriola, Linda M.; Gibson, Jenny L.; Smits, Kathleen M.; Christ, John A.

    2015-12-01

    In-situ bioremediation, a widely applied treatment technology for source zones contaminated with dense non-aqueous phase liquids (DNAPLs), has proven economical and reasonably efficient for long-term management of contaminated sites. Successful application of this remedial technology, however, requires an understanding of the complex interaction of transport, mass transfer, and biotransformation processes. The bioenhancement factor, which represents the ratio of DNAPL mass transfer under microbially active conditions to that which would occur under abiotic conditions, is commonly used to quantify the effectiveness of a particular bioremediation remedy. To date, little research has been directed towards the development and validation of methods to predict bioenhancement factors under conditions representative of real sites. This work extends an existing, first-order, bioenhancement factor expression to systems with zero-order and Monod kinetics, representative of many source-zone scenarios. The utility of this model for predicting the bioenhancement factor for previously published laboratory and field experiments is evaluated. This evaluation demonstrates the applicability of these simple bioenhancement factors for preliminary experimental design and analysis, and for assessment of dissolution enhancement in ganglia-contaminated source zones. For ease of application, a set of nomographs is presented that graphically depicts the dependence of bioenhancement factor on physicochemical properties. Application of these nomographs is illustrated using data from a well-documented field site. Results suggest that this approach can successfully capture field-scale, as well as column-scale, behavior. Sensitivity analyses reveal that bioenhanced dissolution will critically depend on in-situ biomass concentrations.

  3. 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, ...

  4. 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

  5. Patterned direct-write and screen-printing of NIR-to-visible upconverting inks for security applications

    International Nuclear Information System (INIS)

    Two methods of direct-write printing for producing highly resolved features of a polymer impregnated with luminescent upconversion phosphors for security applications are presented. The printed polymer structures range in shape from features to text. The thin polymer features were deposited by direct-write printing of atomized material as well as by screen-printing techniques. These films contain highly luminescent lanthanide-doped, rare-earth nanocrystals, β-NaYF4:3%Er, 17%Yb, which are capped with oleic acid. This capping agent allows the nanocrystals to disperse throughout the films for full detailing of printed features. Upconversion of deposited features was obtained using a 980 nm wavelength laser with emission of upconverted light in the visible region at both 540 and 660 nm. Features were deposited onto high bond paper, Kapton®, and glass to demonstrate possible covert and forensic security printing applications, as they are printed in various features and invisible to ‘naked-eye’ viewing at low concentrations of nanocrystals. (paper)

  6. 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.

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

    International Nuclear Information System (INIS)

    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/cm2 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/cm2. 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/cm2 are achieved

  9. Development of a biomolecular assay for postmortem diagnosis of Taenia saginata Cysticercosis.

    Science.gov (United States)

    Chiesa, Francesco; Dalmasso, Alessandra; Bellio, Alberto; Martinetti, Manuela; Gili, Stefano; Civera, Tiziana

    2010-10-01

    Bovine cysticercosis is caused by the larval stage of the human tapeworm Taenia saginata. According to European data on meat inspection, the prevalence ranges from 0.007% to 6.8%, but the real prevalence is considered to be at least 10 times higher. Laboratory confirmation of the etiological agent is based on gross, stereomicroscopic, and histological examination of submitted specimens. False identifications may occur, possibly because of death and degeneration of cysts, or because taeniid larvae and other tissue parasites, such as Sarcocystis spp., may cause similar macroscopic morphological lesions. Therefore, tests that can warrant sure identification of taeniid lesions and calcified cysts in the muscle are needed. The focus of our study was to develop a suitable postmortem test that could be applied on putative lesions by T. saginata cysticerci, as ambiguously diagnosed after routine meat inspection. In particular, we proposed a biomolecular assay targeting the mitochondrial cytochrome c oxidase subunit I gene (COI). For developing the polymerase chain reaction assay, viable cysts of Cysticercus bovis (n = 10) were used as positive reference samples, and those of Echinococcus granulosus (n = 3), Cysticercus tenuicollis (n = 3), and Sarcocystis spp. (n = 4) as reference negative controls. Further, to evaluate the applicability of the proposed assay, 171 samples of bovine muscular tissue, obtained from local slaughterhouses and containing lesions recognized as T. saginata cysticerci by macroscopic examination, were tested. The proposed test confirmed the diagnosis at postmortem inspection in 94.7% (162/171) of samples. In conclusion, the assay developed in this study, amplifying a short fragment from the mitochondrial gene COI, showed to be suitable for samples containing both viable and degenerating T. saginata cysticerci, yielding an unequivocal diagnosis. PMID:20618079

  10. 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.

  11. 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

  12. 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...

  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. Growth Plate Flow and Metabolism Screening Using MR: A New Application for Specialized MR Sequences

    DEFF Research Database (Denmark)

    Shiguetomi Medina, Juan Manuel; Stødkilde-Jørgensen, Hans; Rahbek, Ole;

    Summary MR Apparent Diffusion Constant and Surface Tension Images can provide an overview of the cell metabolism and flow of the bone growth plate. This is a new application for specialized MR sequences. Introduction Magnetic Resonance imaging (MRI) can be used for studies of joint cartilage as...... derived sequences can be applied to cartilage-like tissue such as growth plate. These sequences provide images that correspond to flow and cell-metabolism. MR imaging provides enough evidence and information about the structure and behavior of the growth plate to propose a standardized protocol for MRI...... signs of ischemic lesions; diffusion tensor images provide information on structure of the tissue and finally measurements of water concentration identifies the areas with highest osteoblast activity. Methods Four normal pig frozen tibiae were studied. Tomography, MR T1 and T2 sequences were performed...

  15. 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

  16. Safe VISITOR: visible, infrared, and terahertz object recognition for security screening application

    Science.gov (United States)

    May, T.; Zieger, G.; Anders, S.; Zakosarenko, V.; Meyer, H.-G.; Schubert, M.; Starkloff, M.; Rößler, M.; Thorwirth, G.; Krause, U.

    2009-05-01

    Security solutions with the purpose to detect hidden objects underneath the clothing of persons are desired in many environments. With the variety of application scenarios criteria like flexibility and mobility become more important. So, many developments trend to focus on cameras, which can image scenes from a distance. This new generation of tools will have the advantage of hidden operation, which is believed by experts to add to the security because of its unpredictability. Such stand-off cameras do have some divergent requirements compared to mm-wave portal scanners. They will benefit from shorter wavelengths because of the higher optical resolution. In contrast to that, the needed transmission properties might become impractical at higher frequencies. A commonly accepted compromise is the use of wavelengths around 0.5mm. However, for stand-off cameras without oversized optical apertures, a resolution around 1cm is a practical limit. For our security camera "Safe VISITOR" (Safe VISible, Infrared and Terhaertz Object recognition) we have chosen to combine images from three different camera modules: a CCD for visible light, a microbolometer for long infrared (14μm) and a superconducting bolometer for 870μm. This combines the highest optical resolution (visible), the unprecedented temperature resolution at infrared and the almost perfect transmission at terahertz. We have built a first prototype and tested it in a field trial. We will present experimental results and try to assess the false error rate of our system.

  17. Tribological behaviour of fine ceramics in screening tests and applications up to 10000C

    International Nuclear Information System (INIS)

    Engineering Ceramics have not only proved its general suitability for structural components exposed to friction and wear, but increasingly turns out to become an essential factor of structural components, used in traditional as well as in modern fields of application or construction. The demand for component surfaces, which are extremely wear and corrosion resistant, has been steadily increasing, not only in high-tech industries. The most important questions for an industry focused on retaining its competitiveness are: Will the use of Engineering Ceramics make it possible to operate unlubricated, maintenance-free machines? Will ceramics become the future friction material? The aim was to qualify - in a research project sponsored by the German Federal Ministry of Research and Technology (BMFT) - the friction and wear behaviour of 9 commercial ceramics. For this purpose, the BAM has developed two types of test rigs: a) high temperature test rigs, b) medium temperature test rigs up to 3500C oil temperature under boundary lubrication (now available commercially). (orig./MM)

  18. Screening test results on potential alternate alloys for VHTGR applications. Advanced Gas Cooled Reactor Materials Program

    International Nuclear Information System (INIS)

    General Electric is working to define and develop the materials technology which will be required for advanced very High Temperature Gas Reactors operating at primary coolant temperatures up to 9500C. The most promising application which has been identified is providing process heat for the reforming of methane. Earlier work had identified Inconel 617 and Alloy 800H as the best of the commercially available alloys for the reformer components. Since these alloys were identified, additional alloys have been developed which may offer improved performance over the above reference reformer alloys. This report presents the results obtained to date on four possible alternate alloys, Nimonic 86, Sanicro 32X, SSS-113-MA, and X 8 NiCrMoNb 16 16, which are being evaluated by General Electric for thermal stability and compatibility with HTGR helium environments. The thermal stabilities of Nimonic 86, Sanicro 32X, and X 8 NiCrMoNb 16 16 have been shown to be good out to maximum exposure times and temperatures of 6000 hours and 9500C, respectively. The thermal stability, as measured by room temperature impact strength, and post exposure ductility of the Japanese developmental alloy SSS-113-MA have been shown to be poor. Measured impact strengths and ductilities below 15 ft-lbs and 10%, respectively, have been observed for this alloy. No conclusions regarding the helium compatibility of the alloys can be made at this time because of the limited data available

  19. A new stoichiometric miniaturization strategy for screening of industrial microbial strains: application to cellulase hyper-producing Trichoderma reesei strains

    OpenAIRE

    Jourdier Etienne; Poughon Laurent; Larroche Christian; Monot Frédéric; Chaabane Fadhel

    2012-01-01

    Abstract Background During bioprocess development, secondary screening is a key step at the boundary between laboratory and industrial conditions. To ensure an effective high-throughput screening, miniaturized laboratory conditions must mimic industrial conditions, especially for oxygen transfer, feeding capacity and pH stabilization. Results A feeding strategy has been applied to develop a simple screening procedure, in which a stoichiometric study is combined with a standard miniaturization...

  20. Screening for acromegaly by application of a simple questionnaire evaluating the enlargement of extremities in adult patients seen at primary health care units.

    Science.gov (United States)

    Rosario, Pedro Weslley; Calsolari, Maria Regina

    2012-06-01

    The objective of this study was to screen for acromegaly by application of a simple questionnaire in patients seen at primary health care units. A total of 17,000 patients of both genders >18 and physiognomy (confirmed by the comparison of photographs), in addition to the enlargement of extremities. The present investigation suggests a much higher prevalence of acromegaly in the adult population than that reported traditionally. We propose that screening based on phenotypic alterations is cost-effective since these changes occur early and almost universally in acromegaly and are uncommon in the general population. PMID:21380935

  1. Analysis of risk indicators and issues associated with applications of screening model for hazardous and radioactive waste sites

    International Nuclear Information System (INIS)

    Risk indicators, such as population risk, maximum individual risk, time of arrival of contamination, and maximum water concentrations, were analyzed to determine their effect on results from a screening model for hazardous and radioactive waste sites. The analysis of risk indicators is based on calculations resulting from exposure to air and waterborne contamination predicted with Multimedia Environmental Pollutant Assessment System (MEPAS) model. The different risk indicators were analyzed, based on constituent type and transport and exposure pathways. Three of the specific comparisons that were made are (1) population-based versus maximum individual-based risk indicators, (2) time of arrival of contamination, and (3) comparison of different threshold assumptions for noncarcinogenic impacts. Comparison of indicators for population- and maximum individual-based human health risk suggests that these two parameters are highly correlated, but for a given problem, one may be more important than the other. The results indicate that the arrival distribution for different levels of contamination reaching a receptor can also be helpful in decisions regarding the use of resources for remediating short- and long-term environmental problems. The addition of information from a linear model for noncarcinogenic impacts allows interpretation of results below the reference dose (RfD) levels that might help in decisions for certain applications. The analysis of risk indicators suggests that important information may be lost by the use of a single indicator to represent public health risk and that multiple indicators should be considered. 15 refs., 8 figs., 1 tab

  2. 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

  3. 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

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. Application of host-specific toxins from fungal plant pathogens as a mass screening measure for disease-resistant genotypes of crop cells

    International Nuclear Information System (INIS)

    Use of pathotoxins to screen disease resistant cells, clones or lines was reviewed and selection strategies of host specific toxin (HST) and it application were described in this report. Successful applications of Alternaria toxins in tomato, Japanese pear and apple were reported, although applications were made by in vivo system. It should be noted that there were opposing reports on reactions of in vitro cultured tomato cell clones to AAL-toxin. The reason for the discrepancy is not clear yet. Differences in bioassay systems and cell lines employed might be possible reasons. (author). 33 refs, 7 figs, 16 tabs

  9. 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. PMID:27510000

  10. An Unbiased Method To Build Benchmarking Sets for Ligand-Based Virtual Screening and its Application To GPCRs

    OpenAIRE

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

    2014-01-01

    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...

  11. 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 ...

  12. Application of parallel liquid chromatography/mass spectrometry for high throughput microsomal stability screening of compound libraries.

    Science.gov (United States)

    Xu, Rongda; Nemes, Csaba; Jenkins, Kelly M; Rourick, Robyn A; Kassel, Daniel B; Liu, Charles Z C

    2002-02-01

    Solution-phase and solid-phase parallel synthesis and high throughput screening have enabled biologically active and selective compounds to be identified at an unprecedented rate. The challenge has been to convert these hits into viable development candidates. To accelerate the conversion of these hits into lead development candidates, early assessment of the physicochemical and pharmacological properties of these compounds is being made. In particular, in vitro absorption, distribution, metabolism, and elimination (ADME) assays are being conducted at earlier and earlier stages of discovery with the goal of reducing the attrition rate of these potential drug candidates as they progress through development. In this report, we present an eight-channel parallel liquid chromatography/mass spectrometry (LC/MS) system in combination with custom Visual Basic and Applescript automated data processing applications for high throughput early ADME. The parallel LC/MS system was configured with one set of gradient LC pumps and an eight-channel multiple probe autosampler. The flow was split equivalently into eight streams before the multiple probe autosampler and recombined after the eight columns and just prior to the mass spectrometer ion source. The system was tested for column-to-column variation and for reproducibility over a 17 h period (approximately 500 injections per column). The variations in retention time and peak area were determined to be less than 2 and 10%, respectively, in both tests. The parallel LC/MS system described permits time-course microsomal incubations (t(o), t5, t15, t30) to be measured in triplicate and enables estimations of t 1/2 microsomal stability. The parallel LC/MS system is capable of analyzing up to 240 samples per hour and permits the complete profiling up to two microtiter plates of compounds per day (i.e., 176 test substrate compounds + sixteen controls). PMID:11841071

  13. 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.

  14. 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...

  15. Micromachining microcarrier-based biomolecular encoding for miniaturized and multiplexed immunoassay.

    Science.gov (United States)

    Zhi, Zheng-liang; Morita, Yasutaka; Hasan, Quamrul; Tamiya, Eiichi

    2003-08-15

    Micromachining techniques, which originated in the microelectronics industry, have been employed to manufacture microparticles bearing an engraved dot-type signature for biomolecular encoding. These metallic microstructures are photolithographically defined and manufactured in a highly reproducible manner. In addition, the code introduced on the particle face is a straightforward visible feature that is easily recognizable with the use of optical microscopy. The number of distinct codes theoretically could be many thousands, depending on the coding element numbers. Such microparticles are, thus, with appropriate surface organic functionalizations, ideal for encoding biomolecular libraries and serving as a platform for developing high-throughput multiplexed bioassay schemes based on suspension array technology. As proof of this statement, we demonstrated that encoded microparticles tagged with antibodies to human immunoglobulin classes are capable, using imaging detection as the interrogating approach, of high sensitivity and high specificity, as well as multiplexed detection of the respective antigens in a microliter-sample volume. PMID:14651038

  16. 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

  17. 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

  18. 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...

  19. 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...

  20. Evaluation of stochastic effects on biomolecular networks using the generalised Nyquist stability criterion

    OpenAIRE

    Kim, J; Bates, D. G.; Postlethwaite, I.

    2008-01-01

    Abstract—Stochastic differential equations are now commonly used to model biomolecular networks in systems biology, and much recent research has been devoted to the development of methods to analyse their stability properties. Stability analysis of such systems may be performed using the Laplace transform, which requires the calculation of the exponential matrix involving time symbolically. However, the calculation of the symbolic exponential matrix is not feasible for problems of even mod...

  1. 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...

  2. The Shadow Map: A General Contact Definition for Capturing the Dynamics of Biomolecular Folding and Function

    OpenAIRE

    Jeffrey K Noel; Whitford, Paul C.; Onuchic, José N.

    2012-01-01

    Structure-based models (SBMs) are simplified models of the biomolecular dynamics that arise from funneled energy landscapes. We recently introduced an all-atom SBM that explicitly represents the atomic geometry of a biomolecule. While this initial study showed the robustness of the all-atom SBM Hamiltonian to changes in many of the energetic parameters, an important aspect, which has not been explored previously, is the definition of native interactions. In this study, we propose a general de...

  3. A Review of Salam Phase Transition in Protein Amino Acids: Implication for Biomolecular Homochirality

    OpenAIRE

    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 arou...

  4. Affinity capillary electrophoresis and density functional theory employed for characterization of (bio)molecular interactions

    Czech Academy of Sciences Publication Activity Database

    Kašička, Václav; Ehala, Sille; Růžička, Martin; Dybal, Jiří; Toman, Petr

    Salzburg: Society of Analytical Chemistry, 2014. OR28. [ISC 2014. International Symposium on Chromatography /30./. 14.09.2014-18.09.2014, Salzburg] R&D Projects: GA ČR(CZ) GAP206/12/0453; GA ČR(CZ) GA13-17224S Institutional support: RVO:61388963 ; RVO:61389013 Keywords : affinity capillary electrophoresis * density functional theory * biomolecular complexes Subject RIV: CB - Analytical Chemistry, Separation

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

    OpenAIRE

    Hayward Steven; Stocks Matthew B; Laycock Stephen D

    2009-01-01

    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 mo...

  6. Biomolecular Self-Defense and Futility of High-Specificity Therapeutic Targeting

    OpenAIRE

    Simon Rosenfeld

    2011-01-01

    Robustness has been long recognized to be a distinctive property of living entities. While a reasonably wide consensus has been achieved regarding the conceptual meaning of robustness, the biomolecular mechanisms underlying this systemic property are still open to many unresolved questions. The goal of this paper is to provide an overview of existing approaches to characterization of robustness in mathematically sound terms. The concept of robustness is discussed in various contexts including...

  7. 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

  8. New product development with the innovative biomolecular sublingual immunotherapy formulations for the management of allergic rhinitis

    Directory of Open Access Journals (Sweden)

    Frati F

    2014-09-01

    Full Text Available Franco Frati,1 Lorenzo Cecchi,2,3 Enrico Scala,4 Erminia Ridolo,5 Ilaria Dell'Albani,1 Eleni Makrì,6 Giovanni Pajno,7 Cristoforo Incorvaia6 1Medical and Scientific Department, Stallergenes, Milan, Italy; 2Interdepartmental Centre of Bioclimatology, University of Florence, Florence, Italy; 3Allergy and Clinical Immunology Section, Azienda Sanitaria di Prato, Prato, Italy; 4Experimental Allergy Unit, IDI-IRCCS, Rome, Italy; 5Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy; 6Allergy/Pulmonary Rehabilitation, ICP Hospital, Milan, Italy; 7Department of Pediatrics, Allergy Unit, University of Messina, Messina, Italy Abstract: The molecular allergy technique, currently defined as component-resolved diagnosis, significantly improved the diagnosis of allergy, allowing for differentiation between molecules actually responsible for clinical symptoms (genuine sensitizers and those simply cross-reacting or shared by several sources (panallergens, thus influencing the appropriate management of a patient's allergy. This also concerns allergen immunotherapy (AIT, which may be prescribed more precisely based on the component-resolved diagnosis results. However, the advance in diagnosis needs to be mirrored in AIT. According to consensus documents and to expectations of specialists, therapy should be based on standardized extracts containing measured amounts of the clinically relevant molecules, ie, the major allergens. The new generation of extracts for sublingual immunotherapy fulfills these requirements and are thus defined as biomolecular (BM. BM refers to natural extracts with a defined content of major allergens in micrograms. All Staloral BM products are indicated for the treatment of allergic rhinitis with or without asthma. The effectiveness of AIT is related to its ability to modify the immunological response of allergic subjects. The 5-grass and house dust mite extracts were evaluated addressing the T helper 1, T

  9. 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

  10. 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.

  11. Synthesis of α-glucosidase-immobilized nanoparticles and their application in screening for α-glucosidase inhibitors.

    Science.gov (United States)

    Xiong, Yejuan; Liu, Qingshan; Yin, Xiaoying

    2016-06-01

    In order to rapidly and accurately screen compounds present in Chinese herbal medicines for α-glucosidase inhibition activity, we have developed a screening strategy which couples the immobilized enzymes with HPLC analysis. First, the core-shell PMMA/CS nanoparticle carrier was prepared by graft polymerization method. Subsequently, α-glucosidase was loaded on the nanoparticles to prepare the immobilized enzyme and construct a screening model. Secondly, the morphology and structure of the core-shell PMMA/CS material were characterized by transmission electron microscopy (TEM) and infrared spectroscopy (IR). The results indicate that the size distribution was uniform for the α-glucosidase-immobilized nanoparticles, with an average particle size of about 239nm. Finally, the α-glucosidase-immobilized nanoparticles were used to screen α-glucosidase inhibitors from extracts of traditional Chinese medicine and from a mixture of pharmacologically active compounds. Extracts of traditional Chinese medicines were analyzed by HPLC method before and after incubation with the immobilized enzyme nanoparticles. Using this method, magnoflorine was selectively separated from methanol extracts of Magnoliae Officinalis Cortex and genistein was selectively separated from a mixture of isoflavone compounds. Both the two compounds have previously been reported to have α-glucosidase inhibitory activity. These results demonstrate that this screening strategy represents a rapid and highly efficient method for the identification of α-glucosidase inhibitors in complex extracts of Chinese herbal medicines. PMID:27085015

  12. Adapting the posterior probability of diagnosis index to enhance evidence-based screening: an application to ADHD in primary care.

    Science.gov (United States)

    Lindhiem, Oliver; Yu, Lan; Grasso, Damion J; Kolko, David J; Youngstrom, Eric A

    2015-04-01

    This study adapts the Posterior Probability of Diagnosis (PPOD) Index for use with screening data. The original PPOD Index, designed for use in the context of comprehensive diagnostic assessments, is overconfident when applied to screening data. To correct for this overconfidence, we describe a simple method for adjusting the PPOD Index to improve its calibration when used for screening. Specifically, we compare the adjusted PPOD Index to the original index and naïve Bayes probability estimates on two dimensions of accuracy, discrimination and calibration, using a clinical sample of children and adolescents (N = 321) whose caregivers completed the Vanderbilt Assessment Scale to screen for attention-deficit/hyperactivity disorder and who subsequently completed a comprehensive diagnostic assessment. Results indicated that the adjusted PPOD Index, original PPOD Index, and naïve Bayes probability estimates are comparable using traditional measures of accuracy (sensitivity, specificity, and area under the curve), but the adjusted PPOD Index showed superior calibration. We discuss the importance of calibration for screening and diagnostic support tools when applied to individual patients. PMID:25000935

  13. A new stoichiometric miniaturization strategy for screening of industrial microbial strains: application to cellulase hyper-producing Trichoderma reesei strains

    Directory of Open Access Journals (Sweden)

    Jourdier Etienne

    2012-05-01

    Full Text Available Abstract Background During bioprocess development, secondary screening is a key step at the boundary between laboratory and industrial conditions. To ensure an effective high-throughput screening, miniaturized laboratory conditions must mimic industrial conditions, especially for oxygen transfer, feeding capacity and pH stabilization. Results A feeding strategy has been applied to develop a simple screening procedure, in which a stoichiometric study is combined with a standard miniaturization procedure. Actually, the knowledge of all nutriments and base or acid requirements leads to a great simplification of pH stabilization issue of miniaturized fed-batch cultures. Applied to cellulase production by Trichoderma reesei, this strategy resulted in a stoichiometric mixed feed of carbon and nitrogen sources. While keeping the pH between shake flask and stirred bioreactor comparable, the developed shake flask protocol reproduced the strain behaviour under stirred bioreactor conditions. Compared to a an already existing miniaturized shake flasks protocol, the cellulase concentration was increased 5-fold, reaching about 10 g L-1. Applied to the secondary screening of several clones, the newly developed protocol succeeded in selecting a clone with a high industrial potential. Conclusions The understanding of a bioprocess stoichiometry contributed to define a simpler and more effective miniaturization. The suggested strategy can potentially be applied to other fed-batch processes, for the screening of either strain collections or experimental conditions.

  14. 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

  15. Operationalization and application of “early warning signs” to screen nanomaterials for harmful properties operationalizationand application of “early warning signs” to screen nanomaterials for harmful properties

    DEFF Research Database (Denmark)

    Hansen, Steffen Foss; Nielsen, K. N.; Knudsen, N.;

    endeavors. This paper explores ho w the first lesson - “Acknowledge and respond to ignorance, uncertainty and risk in techn ology appraisal” could be applied to screen nanomaterials. In cases of ignorance, uncertainty a nd risk, the EEA recommends paying particular attention to important warning signs suc h...

  16. Microfluidic multiculture assay to analyze biomolecular signaling in angiogenesis.

    Science.gov (United States)

    Theberge, Ashleigh B; Yu, Jiaquan; Young, Edmond W K; Ricke, William A; Bushman, Wade; Beebe, David J

    2015-03-17

    Angiogenesis (the formation of blood vessels from existing blood vessels) plays a critical role in many diseases such as cancer, benign tumors, and macular degeneration. There is a need for cell culture methods capable of dissecting the intricate regulation of angiogenesis within the microenvironment of the vasculature. We have developed a microscale cell-based assay that responds to complex pro- and antiangiogenic soluble factors with an in vitro readout for vessel formation. The power of this system over traditional techniques is that we can incorporate the whole milieu of soluble factors produced by cells in situ into one biological readout (vessel formation), even if the identity of the factors is unknown. We have currently incorporated macrophages, endothelial cells, and fibroblasts into the assay, with the potential to include additional cell types in the future. Importantly, the microfluidic platform is simple to operate and multiplex to test drugs targeting angiogenesis in a more physiologically relevant context. As a proof of concept, we tested the effect of an enzyme inhibitor (targeting matrix metalloproteinase 12) on vessel formation; the triculture microfluidic assay enabled us to capture a dose-dependent effect entirely missed in a simplified coculture assay (p < 0.0001). This result underscores the importance of cell-based assays that capture chemical cross-talk occurring between cell types. The microscale dimensions significantly reduce cell consumption compared to conventional well plate platforms, enabling the use of limited primary cells from patients in future investigations and offering the potential to screen therapeutic approaches for individual patients in vitro. PMID:25719435

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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

  2. 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.

    Directory of Open Access Journals (Sweden)

    Boris Kauhl

    Full Text Available 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.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.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.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-size-fits-all approach even within small

  3. 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

  4. 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

  5. Biomolecular surface coating to enhance orthopaedic tissue healing and integration

    OpenAIRE

    Reyes, Catherine D.; Petrie, Timothy A.; Burns, Kellie L.; Schwartz, Zvi; Andrés J. García

    2007-01-01

    Implant osseointegration is a prerequisite for clinical success in orthopaedic and dental applications, many of which are restricted by loosening. Biomaterial surface modification approaches, including calcium-phosphate ceramic coatings and macro/microporosity, have had limited success in promoting integration. To improve osseointegration, titanium surfaces were coated with the GFOGER collagen-mimetic peptide, selectively promoting α2β1 integrin binding, a crucial event for osteoblastic diffe...

  6. 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

  7. 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).

  8. 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.

  9. 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.

  10. Force spectroscopy of biomolecular folding and binding: theory meets experiment

    Science.gov (United States)

    Dudko, Olga

    2015-03-01

    Conformational transitions in biological macromolecules usually serve as the mechanism that brings biomolecules into their working shape and enables their biological function. Single-molecule force spectroscopy probes conformational transitions by applying force to individual macromolecules and recording their response, or ``mechanical fingerprints,'' in the form of force-extension curves. However, how can we decode these fingerprints so that they reveal the kinetic barriers and the associated timescales of a biological process? I will present an analytical theory of the mechanical fingerprints of macromolecules. The theory is suitable for decoding such fingerprints to extract the barriers and timescales. The application of the theory will be illustrated through recent studies on protein-DNA interactions and the receptor-ligand complexes involved in blood clot formation.

  11. 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

  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. 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.

  17. 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.

  18. Multiresolution persistent homology for excessively large biomolecular datasets

    International Nuclear Information System (INIS)

    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

  19. Biomolecular pleiomorphism probed by spatial interpolation of coarse models.

    Science.gov (United States)

    Rusu, Mirabela; Birmanns, Stefan; Wriggers, Willy

    2008-11-01

    In low resolution structures of biological assemblies one can often observe conformational deviations that require a flexible rearrangement of structural domains fitted at the atomic level. We are evaluating interpolation methods for the flexible alignment of atomic models based on coarse models. Spatial interpolation is well established in image-processing and visualization to describe the overall deformation or warping of an object or an image. Combined with a coarse representation of the biological system by feature vectors, such methods can provide a flexible approximation of the molecular structure. We have compared three well-known interpolation techniques and evaluated the results by comparing them with constrained molecular dynamics. One method, inverse distance weighting interpolation, consistently produced models that were nearly indistinguishable on the alpha carbon level from the molecular dynamics results. The method is simple to apply and enables flexing of structures by non-expert modelers. This is useful for the basic interpretation of volumetric data in biological applications such as electron microscopy. The method can be used as a general interpretation tool for sparsely sampled motions derived from coarse models. PMID:18757874

  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. 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...

  2. 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

  3. Dynamics of biomoleculars studied by Rayleigh scattering of Moessbauer radiation and Moessbauer spectroscopy

    International Nuclear Information System (INIS)

    This paper reports on dynamics of biomoleculars, proteins and DNA that plays a role in the supply and the regulation their functional activity, for example, like transducers of oxygen, like enzymes, in photosynthesis and so on. The Mossbauer spectroscopy (MS) and especially Rayleigh Scattering of Mossbauer Radiation (RSMR) permit to obtain the quantitative data on dimensions and times of complex hierarchy of motion in biopolymers and to create correspondent functional models. The scheme of RSMR includes Mossbauer source 57Co, the scatterer---biopolymer, the detector and Mossbauer analyzer (Black absorber---or one-line absorber), that situated before and after the scatterer on definite angle -2θ

  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. 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.

  7. Breast Cancer Screening

    Science.gov (United States)

    ... of Breast & Gynecologic Cancers Breast Cancer Screening Research Breast Cancer Screening (PDQ®)–Patient Version What is screening? Screening ... cancer screening: Cancer Screening Overview General Information About Breast Cancer Key Points Breast cancer is a disease in ...

  8. 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.

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

    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。

  10. 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

  11. 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

  12. 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) ...

  13. 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。

  14. 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.

  15. 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 ...

  16. Development of Screen-Printed Texture-Barrier Paste for Single-Side Texturization of Interdigitated Back-Contact Silicon Solar Cell Applications

    Directory of Open Access Journals (Sweden)

    Chi-Cheng Chen

    2013-10-01

    Full Text Available Continuous cost reduction of silicon-based solar cells is needed to lower the process time and increase efficiency. To achieve lower costs, screen-printed texture-barrier (SPTB paste was first developed for single-side texturization (ST of the interdigitated back-contact (IBC for silicon-based solar cell applications. The SPTB paste was screen-printed on silicon substrates. The SPTB paste was synthesized from intermixed silicate glass (75 wt %, a resin binder (ethyl cellulose ethoce: 20 wt %, and a dispersing agent (fatty acid: 5 wt %. The silicate glass is a necessity for contact formation during firing. A resin binder and a dispersing agent determine the rheology of the SPTB paste. In this work, by modulating various parameters, including post SPTB firing, alkali texturing, and removal of the SPTB, the ST of IBC silicon solar cells was achieved. Since the advantages of the SPTB paste include low toxicity and prompt formation of the texture-barrier, SPTB is potentially suited for simple fabrication at low-cost for solar cell applications. The cost of the SPTB is around $100/kg which is lower than the SiH4/NH3 gas ambient used in plasma-enhanced chemical vapor deposition (PECVD. Thus, the expensive Si3N4 film deposited by PECVD using SiH4 and NH3 gas ambient for silicon solar cells can be replaced by this SPTB.

  17. Label-free detection of biomolecular interaction — DNA — Antimicrobial peptide binding

    DEFF Research Database (Denmark)

    Fojan, Peter; Jensen, Kasper Risgaard; Gurevich, Leonid

    2011-01-01

    molecule. In particular, surface plasmon resonance (SPR) sensors have been already demonstrated suitable for food-safety control, label-free screening for various disease markers in bodily fluids, as well as for real-time continuous monitoring of drug levels in intensive care environment. We envisage such...... sensors to be integrated into wireless communication infrastructure for e-health and environmental monitoring applications. One of the important threats in hospital environment is multi-resistant organisms that are not affected by common antibiotics. The growth of multi-resistant infections spurred an...... interest in Antimicrobial peptides that are active against broad range of infections including bacteria, fungi and viruses and were shown to be capable of treating multi-resistant infection either alone or in combination with the conventional antibiotics. In this paper , we demonstrate an application of...

  18. 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

  19. 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.

  20. 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.

  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. X3DBio2: A visual analysis tool for biomolecular structure comparison

    Science.gov (United States)

    Yi, Hong; Thakur, Sidharth; Sethaphong, Latsavongsakda; Yingling, Yaroslava G.

    2013-01-01

    A major problem in structural biology is the recognition of differences and similarities between related three dimensional (3D) biomolecular structures. Investigating these structure relationships is important not only for understanding of functional properties of biologically significant molecules, but also for development of new and improved materials based on naturally-occurring molecules. We developed a new visual analysis tool, X3DBio2, for 3D biomolecular structure comparison and analysis. The tool is designed for elucidation of structural effects of mutations in proteins and nucleic acids and for assessment of time dependent trajectories from molecular dynamics simulations. X3DBio2 is a freely downloadable open source software and provides tightly integrated features to perform many standard analysis and visual exploration tasks. We expect this tool can be applied to solve a variety of biological problems and illustrate the use of the tool on the example study of the differences and similarities between two proteins of the glycosyltransferase family 2 that synthesize polysaccharides oligomers. The size and conformational distances and retained core structural similarity of proteins SpsA to K4CP represent significant epochs in the evolution of inverting glycosyltransferases.

  3. 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. PMID:26410586

  4. Optimizing water hyperpolarization and dissolution for sensitivity-enhanced 2D biomolecular NMR

    Science.gov (United States)

    Olsen, Greg; Markhasin, Evgeny; Szekely, Or; Bretschneider, Christian; Frydman, Lucio

    2016-03-01

    A recent study explored the use of hyperpolarized water, to enhance the sensitivity of nuclei in biomolecules thanks to rapid proton exchanges with labile amide backbone and sidechain groups. Further optimizations of this approach have now allowed us to achieve proton polarizations approaching 25% in the water transferred into the NMR spectrometer, effective water T1 times approaching 40 s, and a reduction in the dilution demanded for the cryogenic dissolution process. Further hardware developments have allowed us to perform these experiments, repeatedly and reliably, in 5 mm NMR tubes. All these ingredients - particularly the ⩾3000× 1H polarization enhancements over 11.7 T thermal counterparts, long T1 times and a compatibility with high-resolution biomolecular NMR setups - augur well for hyperpolarized 2D NMR studies of peptides, unfolded proteins and intrinsically disordered systems undergoing fast exchanges of their protons with the solvent. This hypothesis is here explored by detailing the provisions that lead to these significant improvements over previous reports, and demonstrating 1D coherence transfer experiments and 2D biomolecular HMQC acquisitions delivering NMR spectral enhancements of 100-500× over their optimized, thermally-polarized, counterparts.

  5. Coupling switches and oscillators as a means to shape cellular signals in biomolecular systems

    International Nuclear Information System (INIS)

    To understand how a complex biomolecular network functions, a decomposition or a reconstruction process of the network is often needed so as to provide new insights into the regulatory mechanisms underlying various dynamical behaviors and also to gain qualitative knowledge of the network. Unfortunately, it seems that there are still no general rules on how to decompose a complex network into simple modules. An alternative resolution is to decompose a complex network into small modules or subsystems with specified functions such as switches and oscillators and then integrate them by analyzing the interactions between them. The main idea of this approach can be illustrated by considering a bidirectionally coupled network in this paper, i.e., coupled Toggle switch and Repressilator, and analyzing the occurrence of various dynamics, although the theoretical principle may hold for a general class of networks. We show that various biomolecular signals can be shaped by regulating the coupling between the subsystems. The approach presented here can be expected to simplify and analyze even more complex biological networks

  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. Microfilter paper method for 17α-hydroxyprogesterone radioimmunoassay: its application for rapid screening for congenital adrenal hyperplasia

    International Nuclear Information System (INIS)

    A new micromethod for measuring a steroid in blood collected on filter paper has been developed. The method is easy and rapid and has the specificity, accuracy and precision of RIA in whole plasma. Less than 20 μl of blood is required, and, therefore, samples may be obtained with heel prick. This method has been applied to the determination of 17α-hydroxyprogesterone (17α-OH-P) for screening patients with congenital adrenal hyperplasia (CAH) due to 21-hydroxylase deficiency. There was excellent correlation (r = .94) between the values of 17α-OH-P obtained by microfilter paper method and those from plasma samples of cord (40 +- 13 ng/ml) and neonatal blood (<3.6 ng/ml) in normal infants. In six neonates at risk for CAH the diagnosis was made utilizing the microfilter paper method. 17α-OH-P concentrations were highly elevated in both filter paper eluates of whole blood (67 to 360 ng/ml of plasma) and simultaneously obtained plasma concentration (74 to 395 ng/ml) in affected infants. The concentrations of 17α-OH-P remained unchanged in dried filter paper blood when stored at room temperature for up to 21 days. Thus, filter paper with dried blood may be sent for steroid assay by mail. The ease with which samples may be transported and the minute amount of sample necessary make this method a promising screening test for CAH

  8. 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

  9. 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

  10. Establish an automated flow injection ESI-MS method for the screening of fragment based libraries: Application to Hsp90.

    Science.gov (United States)

    Riccardi Sirtori, Federico; Caronni, Dannica; Colombo, Maristella; Dalvit, Claudio; Paolucci, Mauro; Regazzoni, Luca; Visco, Carlo; Fogliatto, Gianpaolo

    2015-08-30

    ESI-MS is a well established technique for the study of biopolymers (nucleic acids, proteins) and their non covalent adducts, due to its capacity to detect ligand-target complexes in the gas phase and allows inference of ligand-target binding in solution. In this article we used this approach to investigate the interaction of ligands to the Heat Shock Protein 90 (Hsp90). This enzyme is a molecular chaperone involved in the folding and maturation of several proteins which has been subjected in the last years to intensive drug discovery efforts due to its key role in cancer. In particular, reference compounds, with a broad range of dissociation constants from 40pM to 100μM, were tested to assess the reliability of ESI-MS for the study of protein-ligand complexes. A good agreement was found between the values measured with a fluorescence polarization displacement assay and those determined by mass spectrometry. After this validation step we describe the setup of a medium throughput screening method, based on ESI-MS, suitable to explore interactions of therapeutic relevance biopolymers with chemical libraries. Our approach is based on an automated flow injection ESI-MS method (AFI-MS) and has been applied to screen the Nerviano Medical Sciences proprietary fragment library of about 2000 fragments against Hsp90. In order to discard false positive hits and to discriminate those of them interacting with the N-terminal ATP binding site, competition experiments were performed using a reference inhibitor. Gratifyingly, this group of hits matches with the ligands previously identified by NMR FAXS techniques and confirmed by X-ray co-crystallization experiments. These results support the use of AFI-MS for the screening of medium size libraries, including libraries of small molecules with low affinity typically used in fragment based drug discovery. AFI-MS is a valid alternative to other techniques with the additional opportunities to identify compounds interacting with

  11. 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.

  12. Development and Application of a New Microarray- Based Method for High-Throughput Screening of Carbohydrate Active Enzymes

    DEFF Research Database (Denmark)

    Vidal Melgosa, Silvia

    biological roles in plants and in addition to biofuel production they are extensively used in other industrial processes including in detergents, textiles, paper and the food industry. A vast repertoire of CAZymes exists in nature but there is a growing disparity between our ability to putatively identify...... new CAZymes and our ability to empirically characterise their activities. This is a serious hindrance for the optimal exploitation of their diversity and there is therefore a pressing need for the development of new high-throughput technology for CAZyme screening. Here we describe the development of a...... new method for assessing CAZyme activities that is based on combining the multiplexing capacity of carbohydrate microarrays with the specificity of monoclonal antibodies and carbohydrate binding modules. The results presented in this thesis demonstrate that this new high-throughput semi...

  13. Small-angle X-ray scattering investigations of biomolecular confinement, loading, and release from liquid-crystalline nanochannel assemblies

    Czech Academy of Sciences Publication Activity Database

    Angelova, A.; Angelov, Borislav; Garamus, V. M.; Couvreur, P.; Lesieur, S.

    2012-01-01

    Roč. 3, č. 3 (2012), s. 445-457. ISSN 1948-7185 Institutional research plan: CEZ:AV0Z40500505 Keywords : nanochannels * biomolecular nanostructures * SAXS Subject RIV: CD - Macromolecular Chemistry Impact factor: 6.585, year: 2012

  14. Investigation of the Human Disease Osteogenesis Imperfecta: A Research-Based Introduction to Concepts and Skills in Biomolecular Analysis

    Science.gov (United States)

    Mate, Karen; Sim, Alistair; Weidenhofer, Judith; Milward, Liz; Scott, Judith

    2013-01-01

    A blended approach encompassing problem-based learning (PBL) and structured inquiry was used in this laboratory exercise based on the congenital disease Osteogenesis imperfecta (OI), to introduce commonly used techniques in biomolecular analysis within a clinical context. During a series of PBL sessions students were presented with several…

  15. Screen printing of a capacitive cantilever-based motion sensor on fabric using a novel sacrificial layer process for smart fabric applications

    International Nuclear Information System (INIS)

    Free-standing cantilevers have been fabricated by screen printing sacrificial and structural layers onto a standard polyester cotton fabric. By printing additional conductive layers, a complete capacitive motion sensor on fabric using only screen printing has been fabricated. This type of free-standing structure cannot currently be fabricated using conventional fabric manufacturing processes. In addition, compared to conventional smart fabric fabrication processes (e.g. weaving and knitting), screen printing offers the advantages of geometric design flexibility and the ability to simultaneously print multiple devices of the same or different designs. Furthermore, a range of active inks exists from the printed electronics industry which can potentially be applied to create many types of smart fabric. Four cantilevers with different lengths have been printed on fabric using a five-layer structure with a sacrificial material underneath the cantilever. The sacrificial layer is subsequently removed at 160 °C for 30 min to achieve a freestanding cantilever above the fabric. Two silver electrodes, one on top of the cantilever and the other on top of the fabric, are used to capacitively detect the movement of the cantilever. In this way, an entirely printed motion sensor is produced on a standard fabric. The motion sensor was initially tested on an electromechanical shaker rig at a low frequency range to examine the linearity and the sensitivity of each design. Then, these sensors were individually attached to a moving human forearm to evaluate more representative results. A commercial accelerometer (Microstrain G-link) was mounted alongside for comparison. The printed sensors have a similar motion response to the commercial accelerometer, demonstrating the potential of a printed smart fabric motion sensor for use in intelligent clothing applications. (paper)

  16. 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)

  17. Topics on distance correlation, feature screening and lifetime expectancy with application to Beaver Dam eye study data

    Science.gov (United States)

    Kong, Jing

    This thesis includes 4 pieces of work. In Chapter 1, we present the work with a method for examining mortality as it is seen to run in families, and lifestyle factors that are also seen to run in families, in a subpopulation of the Beaver Dam Eye Study that has died by 2011. We find significant distance correlations between death ages, lifestyle factors, and family relationships. Considering only sib pairs compared to unrelated persons, distance correlation between siblings and mortality is, not surprisingly, stronger than that between more distantly related family members and mortality. Chapter 2 introduces a feature screening procedure with the use of distance correlation and covariance. We demonstrate a property for distance covariance, which is incorporated in a novel feature screening procedure based on distance correlation as a stopping criterion. The approach is further implemented to two real examples, namely the famous small round blue cell tumors data and the Cancer Genome Atlas ovarian cancer data Chapter 3 pays attention to the right censored human longevity data and the estimation of lifetime expectancy. We propose a general framework of backward multiple imputation for estimating the conditional lifetime expectancy function and the variance of the estimator in the right censoring setting and prove the properties of the estimator. In addition, we apply the method to the Beaver Dam eye study data to study human longevity, where the expected human lifetime are modeled with smoothing spline ANOVA based on the covariates including baseline age, gender, lifestyle factors and disease variables. Chapter 4 compares two imputation methods for right censored data, namely the famous Buckley-James estimator and the backward imputation method proposed in Chapter 3 and shows that backward imputation method is less biased and more robust with heterogeneity.

  18. Polarizable atomic multipole X-ray refinement: application to peptide crystals

    OpenAIRE

    Schnieders, Michael J.; Fenn, Timothy D.; Pande, Vijay S.; Brunger, Axel T.

    2009-01-01

    Recent advances in computational chemistry have produced force fields based on a polarizable atomic multipole description of biomolecular electrostatics. In this work, the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field is applied to restrained refinement of molecular models against X-ray diffraction data from peptide crystals. A new formalism is also developed to compute anisotropic and aspherical structure factors using fast Fourier transformation (F...

  19. Improved silicon nanowire field-effect transistors for fast protein-protein interaction screening.

    Science.gov (United States)

    Lin, Ti-Yu; Li, Bor-Ran; Tsai, Sheng-Ta; Chen, Chien-Wei; Chen, Chung-Hsuan; Chen, Yit-Tsong; Pan, Chien-Yuan

    2013-02-21

    Understanding how proteins interact with each other is the basis for studying the biological mechanisms behind various physiological activities. Silicon nanowire field-effect transistors (SiNW-FETs) are sensitive sensors used to detect biomolecular interactions in real-time. However, the majority of the applications that use SiNW-FETs are for known interactions between different molecules. To explore the capability of SiNW-FETs as fast screening devices to identify unknown interacting molecules, we applied mass spectrometry (MS) to analyze molecules reversibly bound to the SiNW-FETs. Calmodulin (CaM) is a Ca(2+)-sensing protein that is ubiquitously expressed in cells and its interaction with target molecules is Ca(2+)-dependent. By modifying the SiNW-FET surface with glutathione, glutathione S-transferase (GST)-tagged CaM binds reversibly to the SiNW-FET. We first verified the Ca(2+)-dependent interaction between GST-CaM and purified troponin I, which is involved in muscle contraction, through the conductance changes of the SiNW-FET. Furthermore, the cell lysate containing overexpressed Ca(2+)/CaM-dependent protein kinase IIα induced a conductance change in the GST-CaM-modified SiNW-FET. The bound proteins were eluted and subsequently identified by MS as CaM and kinase. In another example, candidate proteins from neuronal cell lysates interacting with calneuron I (CalnI), a CaM-like protein, were captured with a GST-CalnI-modified SiNW-FET. The proteins that interacted with CalnI were eluted and verified by MS. The Ca(2+)-dependent interaction between GST-CalnI and one of the candidates, heat shock protein 70, was re-confirmed via the SiNW-FET measurement. Our results demonstrate the effectiveness of combining MS with SiNW-FETs to quickly screen interacting molecules from cell lysates. PMID:23235921

  20. 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 ...

  1. 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 ...

  2. 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- ...

  3. 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)

  4. Development of an energy spectrum measurement system using screen monitor and its application to study on the longitudinal wakefield in an electron linac

    International Nuclear Information System (INIS)

    We are developing a measurement system of energy spectra for the high intensity electron beam for L-band linac of the Institute of Scientific and Industrial Research, Osaka University. It consists of a thin fluorescence screen, a 12-bit CCD camera with the gate and an image control system in a PCI board. It is possible to measure the energy spectrum of a single electron pulse at a time with this device. To demonstrate performance of the system, energy spectra of the single bunch beam have been measure at different accelerating phases. As an application of the energy spectra measurement, the bunch induced voltage and the longitudinal bunch shape have been derived using energy spectra measured at two different linac rf phases. (author)

  5. 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.

  6. 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.

  7. 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.

  8. Biomolecular Electrostatics Simulation by an FMM-based BEM on 512 GPUs

    CERN Document Server

    Yokota, Rio; Bardhan, Jaydeep P; Knepley, Matthew G; Barba, L A

    2010-01-01

    We present simulations of biomolecular electrostatics at a scale not reached before, thanks to both algorithmic and hardware acceleration. The algorithmic acceleration is achieved with the fast multipole method (FMM) in conjunction with a boundary element method (BEM) formulation of the continuum electrostatic model. The hardware acceleration is achieved through graphics processors, GPUs. We demonstrate the power of our algorithms and software for the calculation of the electrostatic interactions between biological molecules in solution. Computational experiments are presented simulating the electrostatics of protein--drug binding and several multi-million atom systems consisting of hundreds to thousands of copies of the problems, which models over 20 million atoms and has more than six billion unknowns, one iteration step requires only a few minutes on 512 GPU nodes. We achieved a sustained performance of 34.6TFlops for the entire BEM calculation. We are currently adapting our solver to model the linearized ...

  9. 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 (BCA...... solution. Adsorbed masses of BSM onto hydrophobic surface, as probe by BCA, showed a continuously increasing trend up to 2mg/mL. But, the signals from EIA and ELLA, which probe the concentration of available unglycosylatedC-terminals and the central glycosylated regions, respectively, showed complicated......),enzyme-linkedimmunosorbentassay(EIA),andenzyme linkedlectinassay(ELLA).Theconformationand hydrodynamic diameter of highly purified BSM molecules, as characterized by circular dichroism (CD) spectroscopy and dynamic light scattering (DLS), respectively, showed a slight, yet gradual coiling and compaction in response to the increase in BSM concentration in bulk...

  10. Piezoelectric tuning fork biosensors for the quantitative measurement of biomolecular interactions

    Science.gov (United States)

    Gonzalez, Laura; Rodrigues, Mafalda; Benito, Angel Maria; Pérez-García, Lluïsa; Puig-Vidal, Manel; Otero, Jorge

    2015-12-01

    The quantitative measurement of biomolecular interactions is of great interest in molecular biology. Atomic force microscopy (AFM) has proved its capacity to act as a biosensor and determine the affinity between biomolecules of interest. Nevertheless, the detection scheme presents certain limitations when it comes to developing a compact biosensor. Recently, piezoelectric quartz tuning forks (QTFs) have been used as laser-free detection sensors for AFM. However, only a few studies along these lines have considered soft biological samples, and even fewer constitute quantified molecular recognition experiments. Here, we demonstrate the capacity of QTF probes to perform specific interaction measurements between biotin-streptavidin complexes in buffer solution. We propose in this paper a variant of dynamic force spectroscopy based on representing adhesion energies E (aJ) against pulling rates v (nm s-1). Our results are compared with conventional AFM measurements and show the great potential of these sensors in molecular interaction studies.

  11. Amplified vibrational circular dichroism as a probe of local biomolecular structure.

    Science.gov (United States)

    Domingos, Sérgio R; Huerta-Viga, Adriana; Baij, Lambert; Amirjalayer, Saeed; Dunnebier, Dorien A E; Walters, Annemarie J C; Finger, Markus; Nafie, Laurence A; de Bruin, Bas; Buma, Wybren Jan; Woutersen, Sander

    2014-03-01

    We show that the VCD signal intensities of amino acids and oligopeptides can be enhanced by up to 2 orders of magnitude by coupling them to a paramagnetic metal ion. If the redox state of the metal ion is changed from paramagnetic to diamagnetic the VCD amplification vanishes completely. From this observation and from complementary quantum-chemical calculations we conclude that the observed VCD amplification finds its origin in vibronic coupling with low-lying electronic states. We find that the enhancement factor is strongly mode dependent and that it is determined by the distance between the oscillator and the paramagnetic metal ion. This localized character of the VCD amplification provides a unique tool to specifically probe the local structure surrounding a paramagnetic ion and to zoom in on such local structure within larger biomolecular systems. PMID:24506134

  12. Biomolecular self-defense and futility of high-specificity therapeutic targeting.

    Science.gov (United States)

    Rosenfeld, Simon

    2011-01-01

    Robustness has been long recognized to be a distinctive property of living entities. While a reasonably wide consensus has been achieved regarding the conceptual meaning of robustness, the biomolecular mechanisms underlying this systemic property are still open to many unresolved questions. The goal of this paper is to provide an overview of existing approaches to characterization of robustness in mathematically sound terms. The concept of robustness is discussed in various contexts including network vulnerability, nonlinear dynamic stability, and self-organization. The second goal is to discuss the implications of biological robustness for individual-target therapeutics and possible strategies for outsmarting drug resistance arising from it. Special attention is paid to the concept of swarm intelligence, a well studied mechanism of self-organization in natural, societal and artificial systems. It is hypothesized that swarm intelligence is the key to understanding the emergent property of chemoresistance. PMID:22272063

  13. 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...

  14. 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.

  15. 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.

  16. Development and Application of a Gel-Based Immunoassay for the Rapid Screening of Salbutamol and Ractopamine Residues in Pork.

    Science.gov (United States)

    Li, Chenglong; Li, Jingya; Jiang, Wenxiao; Zhang, Suxia; Shen, Jianzhong; Wen, Kai; Wang, Zhanhui

    2015-12-01

    Salbutamol (SAL) and ractopamine (RAC) have been illegally used to promote protein synthesis and to increase the feed conversion rate in livestock. However, the residues of SAL and RAC could cause potential hazards for human health. The Ministry of Agriculture of China banned the use of SAL and RAC as growth promoters. In this paper, we provide detailed information on developing a rapid and sensitive gel-based immunoassay for on-site screening of SAL and RAC residues in pork. The detection time was shortened to 20 min. The limits of detection were 0.5 μg/kg for both SAL and RAC by visual detection, whereas the quantitative gel-based immunoassay enabled the detection of SAL (0.051 μg/kg) and RAC (0.020 μg/kg) in spiked pork samples. The gel-based immunoassay showed promise as a multiplexed immunoassay for on-site surveilling of SAL and RAC residues in pork. PMID:26595169

  17. 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

  18. 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.

  19. 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

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. 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

  6. 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...

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. Expression and Purification of PI3 Kinase {alpha} and Development of an ATP Depletion and an AlphaScreen PI3 Kinase Activity Assay

    DEFF Research Database (Denmark)

    Boldyreff, Brigitte; Rasmussen, Tine L; Jensen, Hans H; Cloutier, Alexandre; Beaudet, Lucille; Roby, Philippe; Issinger, Olaf-Georg

    2008-01-01

    Phosphoinositide-3-kinases are important targets for drug development because many proteins in the PI3 kinase signaling pathway are mutated, hyperactivated, or overexpressed in human cancers. Here, the authors coexpressed the human class Ia PI3 kinase p110alpha catalytic domain with an N-terminal....... In parallel, a second assay format using the AlphaScreen technology was optimized to measure PI3 kinase activity. Both assay formats used should be suitable for high-throughput screening for the identification of PI3 kinase inhibitors. (Journal of Biomolecular Screening XXXX:xx-xx)....

  12. 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.

  13. 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

  14. 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

  15. 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.

  16. 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

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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 ...

  4. 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 ...

  5. Development of Polarizable Models for Molecular Mechanical Calculations III: 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

    2012-01-01

    As an integrated step towards 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. PMID:22712654

  6. 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. PMID:22712654

  7. Screening neonatal

    OpenAIRE

    Urbón Artero, Alfonso; Reig del Moral, Celia

    2006-01-01

    Los autores de este artículo revisan el screening neonatal, desde la descripción por Wilson y Jungner en 1968 de los criterios que hansido aplicados en la detección precoz de enfermedades enel recién nacido, hasta los avances actuales en la medicina genómica que han modificado sustancialmente estas bases. Se comentan los métodos diagnósticos prenatales más utilizados como los analíticos y ultrasonografia prenatal. Se describen los procedimientos que se aplican en la actualidad y se describen ...

  8. 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...

  9. 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

  10. 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

  11. 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.

  12. 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.

  13. 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

  14. 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)

  15. 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...

  16. 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.

  17. 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.

  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. 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

  20. 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

  1. 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.

  2. Chemical and biomolecular characterization of Artemisia umbelliformis Lam., an important ingredient of the alpine liqueur "Genepi".

    Science.gov (United States)

    Rubiolo, Patrizia; Matteodo, Maura; Bicchi, Carlo; Appendino, Giovanni; Gnavi, Giorgio; Bertea, Cinzia; Maffei, Massimo

    2009-05-13

    Artemisia umbelliformis Lam., an important alpine plant used for the preparation of flavored beverages, showed a remarkable intraspecific variability, at both genomic and gene product (secondary metabolites) levels. The variability of A. umbelliformis Lam. currently cultivated in Piedmont (Italy, Au1) and in Switzerland (Au2) was investigated by combining the chemical analysis of essential oil and sesquiterpene lactones and the molecular characterization of the 5S-rRNA-NTS gene by PCR and PCR-RFLP. Marked differences were observed between the two plants. Au1 essential oil contained alpha- and beta-thujones as the main components, whereas Au2 contained 1,8-cineole, borneol, and beta-pinene. Au1 sesquiterpene lactone fractions contained cis-8-eudesmanolide derivatives and Au2 the trans-6-germacranolide costunolide. Specific A. umbelliformis Au1 and Au2 primers were designed on the sequence of the 5S-rRNA gene spacer region. Furthermore, a PCR-restriction fragment length polymorphism (PCR-RFLP) method was applied using RsaI and TaqI restriction enzymes. Chemical and biomolecular data contributed to the characterization of A. umbeliformis chemotypes. PMID:19326948

  3. 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

  4. 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

  5. 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

  6. Review of Transducer Principles for Label-Free Biomolecular Interaction Analysis

    Directory of Open Access Journals (Sweden)

    Janos Vörös

    2011-07-01

    Full Text Available Label-free biomolecular interaction analysis is an important technique to study the chemical binding between e.g., protein and protein or protein and small molecule in real-time. The parameters obtained with this technique, such as the affinity, are important for drug development. While the surface plasmon resonance (SPR instruments are most widely used, new types of sensors are emerging. These developments are generally driven by the need for higher throughput, lower sample consumption or by the need of complimentary information to the SPR data. This review aims to give an overview about a wide range of sensor transducers, the working principles and the peculiarities of each technology, e.g., concerning the set-up, sensitivity, sensor size or required sample volume. Starting from optical technologies like the SPR and waveguide based sensors, acoustic sensors like the quartz crystal microbalance (QCM and the film bulk acoustic resonator (FBAR, calorimetric and electrochemical sensors are covered. Technologies long established in the market are presented together with those newly commercially available and with technologies in the early development stage. Finally, the commercially available instruments are summarized together with their sensitivity and the number of sensors usable in parallel and an outlook for potential future developments is given.

  7. PARENT: A Parallel Software Suite for the Calculation of Configurational Entropy in Biomolecular Systems.

    Science.gov (United States)

    Fleck, Markus; Polyansky, Anton A; Zagrovic, Bojan

    2016-04-12

    Accurate estimation of configurational entropy from the in silico-generated biomolecular ensembles, e.g., from molecular dynamics (MD) trajectories, is dependent strongly on exhaustive sampling for physical reasons. This, however, creates a major computational problem for the subsequent estimation of configurational entropy using the Maximum Information Spanning Tree (MIST) or Mutual Information Expansion (MIE) approaches for internal molecular coordinates. In particular, the available software for such estimation exhibits serious limitations when it comes to molecules with hundreds or thousands of atoms, because of its reliance on a serial program architecture. To overcome this problem, we have developed a parallel, hybrid MPI/openMP C++ implementation of MIST and MIE, called PARENT, which is particularly optimized for high-performance computing and provides efficient estimation of configurational entropy in different biological processes (e.g., protein-protein interactions). In addition, PARENT also allows for a detailed mapping of intramolecular allosteric networks. Here, we benchmark the program on a set of 1-μs-long MD trajectories of 10 different protein complexes and their components, demonstrating robustness and good scalability. A direct comparison between MIST and MIE on the same dataset demonstrates a superior convergence behavior for the former approach, when it comes to total simulation length and configurational-space binning. PMID:26989950

  8. 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.

  9. 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.

  10. 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 ...

  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. 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

  13. 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

  14. The Effect of Biomolecular Gradients on Mesenchymal Stem Cell Chondrogenesis under Shear Stress

    Directory of Open Access Journals (Sweden)

    Alexander L. Rivera

    2015-03-01

    Full Text Available Tissue engineering is viewed as a promising option for long-term repair of cartilage lesions, but current engineered cartilage constructs fail to match the mechanical properties of native tissue. The extracellular matrix of adult human articular cartilage contains highly organized collagen fibrils that enhance the mechanical properties of the tissue. Unlike articular cartilage, mesenchymal stem cell (MSC based tissue engineered cartilage constructs lack this oriented microstructure and therefore display much lower mechanical strength. The goal of this study was to investigate the effect of biomolecular gradients and shear stress on MSCs undergoing chondrogenesis within a microfluidic device. Via poly(dimethyl siloxane soft-lithography, microfluidic devices containing a gradient generator were created. Human MSCs were seeded within these chambers and exposed to flow-based transforming growth factor β1 (TGF-β1 gradients. When the MSCs were both confluent and exposed to shear stress, the cells aligned along the flow direction. Exposure to TGF-β1 gradients led to chondrogenesis of MSCs, indicated by positive type II collagen staining. These results, together with a previous study that showed that aligned MSCs produce aligned collagen, suggest that oriented cartilage tissue structures with superior mechanical properties can be obtained by aligning MSCs along the flow direction and exposing MSCs to chondrogenic gradients.

  15. A computational study of the interaction of graphene structures with biomolecular units.

    Science.gov (United States)

    Carballeira, Diego López; Ramos-Berdullas, Nicolás; Pérez-Juste, Ignacio; Fajín, José Luis Cagide; Cordeiro, M Natália D S; Mandado, Marcos

    2016-06-01

    Due to the great interest that biochemical sensors constructed from graphene nanostructures have raised recently, in this work we analyse in detail the electronic factors responsible for the large affinity of biomolecular units for graphene surfaces using ab initio quantum chemical tools based on density functional theory. Both finite and periodic graphene structures have been employed in our study. Whereas the former allows the analysis of the different energy components contributing to the interaction energy separately, the periodic structure provides a more realistic calculation of the total adsorption energy in an extended graphene surface and serves to validate the results obtained using the finite model. In addition, qualitative relations between interaction energy and electron polarization upon adsorption have been established using the finite model. In this work, we have analysed thermodynamically stable adsorption complexes formed by glycine, melamine, pyronin cation, porphine, tetrabenzoporphine and phthalocyanine with a 2D structure of ninety six carbons and periodic structures formed by cells of fifty and seventy two carbons. Differences in the electrostatic, Pauli repulsion, induction and dispersion energies among aromatic and non-aromatic molecules, charged and non-charged molecules and H-π and stacking interactions have been thoroughly analysed in this work. PMID:27210053

  16. New quantitative total protein S-assay system for diagnosing protein S type II deficiency: clinical application of the screening system for protein S type II deficiency.

    Science.gov (United States)

    Tsuda, Tomohide; Jin, Xiuri; Tsuda, Hiroko; Ieko, Masahiro; Morishita, Eriko; Adachi, Tomoko; Hamasaki, Naotaka

    2012-01-01

    Venous thromboembolism (VTE) incidence is rising rapidly in Japan with lifestyle westernization and aging. Deficiency of protein S, an important blood coagulation regulator, is a risk factor for VTE. Protein S deficiency prevalence in Asians is approximately 10 times that in Caucasians and that of protein S type II deficiency, associated with the protein S Tokushima mutation (K155E), is quite high in Japan. However, currently available methods for measuring protein S are not precise enough for detection of this deficiency. We developed a novel assay system for precise simultaneous determinations of total protein S activity and total protein S antigen level, using a general-purpose automated analyzer, allowing protein S-specific activity (ratio of total protein S activity to total protein S antigen level) to be calculated. Mean specific activity was 0.99 for samples from healthy individuals but 0.69 or less (mean-3SD) in protein S type II-deficient and warfarin-treated samples, but was 1.0 in an estrogen-treated sample with significantly decreased protein S antigen. Protein S gene analyses in healthy individuals with specific activity 0.69 or less revealed the K155E mutation in all three. These results show our new assay system to be an effective screening tool for protein S type II deficiency. This system can also be used in an automated analyzer, facilitating numerous sample measurements, and is, thus, applicable to regular medical checkups and diagnosing VTE. Such applications would potentially contribute to early detection of protein S type II deficiency, and, thereby, to thrombosis prevention. PMID:22157257

  17. 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.

  18. 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.

  19. 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

  20. Ultrasound-mediated method for rapid delivery of nano-particles into cells for intracellular surface-enhanced Raman spectroscopy and cancer cell screening

    International Nuclear Information System (INIS)

    Surface-enhanced Raman spectroscopy (SERS) is a powerful technology for providing finger-printing information of cells. A big challenge has been the long time duration and inefficient uptake of metal nano-particles into living cells as substrate for SERS analysis. Herein, a simple method (based on ultrasound) for the rapid transfer of silver nanoparticles (NPs) into living cells for intracellular SERS spectroscopy was presented. In this study, the ultrasound-mediated method for NP delivery overcame the shortcoming of ‘passive uptake’, and achieved quick acquisition of reproducible SERS spectra from living human nasopharyngeal carcinoma cell lines (C666 and CNE1) and normal nasopharyngeal cell line (NP69). Tentative assignment of the Raman bands in the measured SERS spectra showed cancer cell specific biomolecular differences, including significantly lower DNA concentrations and higher protein concentrations in cancerous nasopharyngeal cells as compared to those of normal cells. Combined with PCA–LDA multivariate analysis, ultrasound-mediated cell SERS spectroscopy differentiated the cancerous cells from the normal nasopharyngeal cells with high diagnostic accuracy (98.7%), demonstrating great potential for high-throughput cancer cell screening applications. (paper)

  1. Neonatal screening.

    Science.gov (United States)

    Pàmpols, Teresa

    2003-01-01

    Neonatal screening (NS) is a medical act in the context of preventive medicine aimed at the early identification of infants affected by certain conditions that threaten their life and long-term health, for which a timely intervention can lead to a significant reduction of morbidity, mortality and associated disabilities. It emerged three decades ago in the context of prevention of mental retardation. Since then, around 600 inborn metabolic disorders have been described and technological progress has been impressive; nevertheless only around 5% of the disorders have been the object of NS. The most frequently cited reasons for the limitation are low prevalence and the lack of treatment. The tandem mass spectrometry has come in place in recent years across the globe, expanding NS to include several disorders of intermediary metabolism. This has shown, in addition to a prevalence much higher than previously thought, the benefits of early detection. The present work is a review of NS, not only from the point of view of technological/medical achievements, but also considering other factors which will affect specific disease selection, according to the social and organizational infrastructure that may expand the borders of NS. PMID:12921292

  2. Kinetic comparison of tissue non-specific and placental human alkaline phosphatases expressed in baculovirus infected cells: application to screening for Down's syndrome

    Directory of Open Access Journals (Sweden)

    Grozdea Jean J

    2002-01-01

    Full Text Available Abstract Background In humans, there are four alkaline phosphatases, and each form exibits a characteristic pattern of tissue distribution. The availability of an easy method to reveal their activity has resulted in large amount of data reporting correlations between variations in activity and illnesses. For example, alkaline phosphatase from neutrophils of mothers pregnent with a trisomy 21 fetus (Down's syndrome displays significant differences both in its biochemical and immunological properties, and in its affinity for some specific inhibitors. Results To analyse these differences, the biochemical characteristics of two isozymes (non specific and placental alkaline phosphatases were expressed in baculovirus infected cells. Comparative analysis of the two proteins allowed us to estimate the kinetic constants of denaturation and sensitivity to two inhibitors (L-p-bromotetramisole and thiophosphate, allowing better discrimination between the two enzymes. These parameters were then used to estimate the ratio of the two isoenzymes in neutrophils of pregnant mothers with or without a trisomy 21 fetus. It appeared that the placental isozyme represented 13% of the total activity of neutrophils of non pregnant women. This proportion did not significantly increase with normal pregnancy. By contrast, in pregnancies with trisomy 21 fetus, the proportion reached 60–80% of activity. Conclusion Over-expression of the placental isozyme compared with the tissue-nonspecific form in neutrophils of mother with a trisomy 21 fetus may explain why the characteristics of the alkaline phosphatase in these cells is different from normal. Application of this knowledge could improve the potential of using alkaline phosphatase measurements to screen for Down's syndrome.

  3. 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

  4. 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.

  5. 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

  6. 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.

  7. 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}.

  8. 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

  9. A synergic simulation-optimization approach for analyzing biomolecular dynamics in living organisms.

    Science.gov (United States)

    Sadegh Zadeh, Kouroush

    2011-01-01

    A synergic duo simulation-optimization approach was developed and implemented to study protein-substrate dynamics and binding kinetics in living organisms. The forward problem is a system of several coupled nonlinear partial differential equations which, with a given set of kinetics and diffusion parameters, can provide not only the commonly used bleached area-averaged time series in fluorescence microscopy experiments but more informative full biomolecular/drug space-time series and can be successfully used to study dynamics of both Dirac and Gaussian fluorescence-labeled biomacromolecules in vivo. The incomplete Cholesky preconditioner was coupled with the finite difference discretization scheme and an adaptive time-stepping strategy to solve the forward problem. The proposed approach was validated with analytical as well as reference solutions and used to simulate dynamics of GFP-tagged glucocorticoid receptor (GFP-GR) in mouse cancer cell during a fluorescence recovery after photobleaching experiment. Model analysis indicates that the commonly practiced bleach spot-averaged time series is not an efficient approach to extract physiological information from the fluorescence microscopy protocols. It was recommended that experimental biophysicists should use full space-time series, resulting from experimental protocols, to study dynamics of biomacromolecules and drugs in living organisms. It was also concluded that in parameterization of biological mass transfer processes, setting the norm of the gradient of the penalty function at the solution to zero is not an efficient stopping rule to end the inverse algorithm. Theoreticians should use multi-criteria stopping rules to quantify model parameters by optimization. PMID:21106190

  10. 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.

  11. Evolução biomolecular homoquiral: a origem e a amplificação da quiralidade nas moléculas da vida Homochiral biomolecular evolution: the origin and the amplification of chirality in life molecules

    Directory of Open Access Journals (Sweden)

    José Augusto R. Rodrigues

    2010-01-01

    Full Text Available The fact that biologically relevant molecules exist only as one of the two enantiomers is a fascinating example of complete symmetry breaking of chirality and has long intrigued our curiosity. The origin of this selective chirality has remained a fundamental enigma with regard to the origin of life since the time of Pasteur, 160 years ago. The symmetry breaking processes, which include autocatalytic crystallization, asymmetric autocatalysis, spontaneous crystallization, adsorption and polymerization of amino acids on mineral surfaces, provide new insights into the origin of biomolecular homochirality.

  12. Screen time and children

    Science.gov (United States)

    "Screen time" is a term used for activities done in front of a screen, such as watching TV, working on a computer, or playing video games. Screen time is sedentary activity, meaning you are being physically ...

  13. 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 ...

  14. 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 " ...

  15. 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 ...

  16. 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

  17. A Study of the Abrasion of Squeegees Used in Screen Printing and Its Effect on Performance with Application in Printed Electronics

    OpenAIRE

    Christopher O. Phillips; David G. Beynon; Simon M. Hamblyn; Glyn R. Davies; Gethin, David T.; Timothy C. Claypole

    2014-01-01

    This article presents a novel method for accelerated wear of squeegees used in screen printing and describes the development of mechanical tests which allow more in-depth measurement of squeegee properties. In this study, squeegees were abraded on the screen press so that they could be used for subsequent print tests to evaluate the effect of wear on the printed product. Squeegee wear was found to vary between different squeegee types and caused increases in ink transfer and wider printed fe...

  18. Four Principles to Consider Before Advising Women on Screening Mammography

    DEFF Research Database (Denmark)

    Keen, John D; Juhl Jørgensen, Karsten

    2015-01-01

    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...... might extend a woman's life is narrow, as many tumors that can form metastases will already have done so. Instead of encouraging screening mammography, physicians should help women make an informed decision as with any medical intervention....

  19. 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...

  20. 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...