Science.gov

Sample records for improved molecular technique

  1. Improved Molecular Technique for the Differentiation of Neotropical Anopheline Species

    PubMed Central

    Matson, Ryan; Rios, Carlos Tong; Chavez, Cesar Banda; Gilman, Robert H.; Florin, David; Sifuentes, Victor Lopez; Greffa, Roldan Cardenas; Yori, Pablo Peñataro; Fernandez, Roberto; Portocarrero, Daniel Velasquez; Vinetz, Joseph M.; Kosek, Margaret

    2008-01-01

    We evaluated a PCR-RFLP of the ribosomal internal transcribed spacer 2 region (ITS2) to distinguish species of Anopheles commonly reported in the Amazon and validated this method using reared F1 offspring. The following species of Anopheles were used for molecular analysis: An. (Nys.) benarrochi, An. (Nys.) darlingi, An. (Nys.) nuneztovari, An. (Nys.) konderi, An. (Nys.) rangeli, and An. (Nys.) triannulatus sensu lato (s.l.). In addition, three species of the subgenus Anopheles, An. (Ano.) forattini, An. (Ano.) mattogrossensis, and An. (Ano.) peryassui were included for testing. Each of the nine species tested yielded diagnostic banding patterns. The PCR-RFLP method was successful in identifying all life stages including exuviae with small fractions of the sample. The assay is rapid and can be applied as an unbiased confirmatory method for identification of morphologic variants, disputed samples, imperfectly preserved specimens, and life stages from which taxonomic keys do not allow for definitive species determination. PMID:18337348

  2. Australian endemic pest tephritids: genetic, molecular and microbial tools for improved Sterile Insect Technique.

    PubMed

    Raphael, Kathryn A; Shearman, Deborah C A; Gilchrist, A Stuart; Sved, John A; Morrow, Jennifer L; Sherwin, William B; Riegler, Markus; Frommer, Marianne

    2014-01-01

    Among Australian endemic tephritid fruit flies, the sibling species Bactrocera tryoni and Bactrocera neohumeralis have been serious horticultural pests since the introduction of horticulture in the nineteenth century. More recently, Bactrocera jarvisi has also been declared a pest in northern Australia. After several decades of genetic research there is now a range of classical and molecular genetic tools that can be used to develop improved Sterile Insect Technique (SIT) strains for control of these pests. Four-way crossing strategies have the potential to overcome the problem of inbreeding in mass-reared strains of B. tryoni. The ability to produce hybrids between B. tryoni and the other two species in the laboratory has proved useful for the development of genetically marked strains. The identification of Y-chromosome markers in B. jarvisi means that male and female embryos can be distinguished in any strain that carries a B. jarvisi Y chromosome. This has enabled the study of homologues of the sex-determination genes during development of B jarvisi and B. tryoni, which is necessary for the generation of genetic-sexing strains. Germ-line transformation has been established and a draft genome sequence for B. tryoni released. Transcriptomes from various species, tissues and developmental stages, to aid in identification of manipulation targets for improving SIT, have been assembled and are in the pipeline. Broad analyses of the microbiome have revealed a metagenome that is highly variable within and across species and defined by the environment. More specific analyses detected Wolbachia at low prevalence in the tropics but absent in temperate regions, suggesting a possible role for this endosymbiont in future control strategies.

  3. Australian endemic pest tephritids: genetic, molecular and microbial tools for improved Sterile Insect Technique

    PubMed Central

    2014-01-01

    Among Australian endemic tephritid fruit flies, the sibling species Bactrocera tryoni and Bactrocera neohumeralis have been serious horticultural pests since the introduction of horticulture in the nineteenth century. More recently, Bactrocera jarvisi has also been declared a pest in northern Australia. After several decades of genetic research there is now a range of classical and molecular genetic tools that can be used to develop improved Sterile Insect Technique (SIT) strains for control of these pests. Four-way crossing strategies have the potential to overcome the problem of inbreeding in mass-reared strains of B. tryoni. The ability to produce hybrids between B. tryoni and the other two species in the laboratory has proved useful for the development of genetically marked strains. The identification of Y-chromosome markers in B. jarvisi means that male and female embryos can be distinguished in any strain that carries a B. jarvisi Y chromosome. This has enabled the study of homologues of the sex-determination genes during development of B jarvisi and B. tryoni, which is necessary for the generation of genetic-sexing strains. Germ-line transformation has been established and a draft genome sequence for B. tryoni released. Transcriptomes from various species, tissues and developmental stages, to aid in identification of manipulation targets for improving SIT, have been assembled and are in the pipeline. Broad analyses of the microbiome have revealed a metagenome that is highly variable within and across species and defined by the environment. More specific analyses detected Wolbachia at low prevalence in the tropics but absent in temperate regions, suggesting a possible role for this endosymbiont in future control strategies. PMID:25470996

  4. Molecular technologies to improve the effectiveness of the sterile insect technique.

    PubMed

    Franz, Gerald; Robinson, Alan S

    2011-01-01

    The application of the Sterile Insect Technique (SIT) in area-wide integrated pest management (AW-IPM) programmes continues to increase. However, programme efficiency can still be considerably enhanced when certain components of the technology are improved, such as the development of improved strains for mass rearing and release. These include strains that (1) produce only male insects for sterilization and release and (2) carry easily identifiable markers to identify released sterile insects in the field. Using both classical and modern biotechnology techniques, key insect pests are targeted, where SIT programmes are being implemented. The pests include mosquitoes, the Mexican fruit fly, the codling moth, the oriental fruit fly and the pink bollworm. This special issue summarizes the results of research efforts aimed at the development and evaluation of new strains to a level where a decision can be made as to their suitability for use in large scale SIT programmes. Major beneficiaries will be operational AW-IPM programmes that apply the SIT against major insect pests.

  5. [Molecular techniques in mycology].

    PubMed

    Rodríguez-Tudela, Juan Luis; Cuesta, Isabel; Gómez-López, Alicia; Alastruey-Izquierdo, Ana; Bernal-Martínez, Leticia; Cuenca-Estrella, Manuel

    2008-11-01

    An increasing number of molecular techniques for the diagnosis of fungal infections have been developed in the last few years, due to the growing prevalence of mycoses and the length of time required for diagnosis when classical microbiological methods are used. These methods are designed to resolve the following aspects of mycological diagnosis: a) Identification of fungi to species level by means of sequencing relevant taxonomic targets; b) early clinical diagnosis of invasive fungal infections; c) detection of molecular mechanisms of resistance to antifungal agents; and d) molecular typing of fungi. Currently, these methods are restricted to highly developed laboratories. However, some of these techniques will probably be available in daily clinical practice in the near future.

  6. A new technique to improve the mechanical and biological performance of ultra high molecular weight polyethylene using a nylon coating.

    PubMed

    Firouzi, Dariush; Youssef, Aya; Amer, Momen; Srouji, Rami; Amleh, Asma; Foucher, Daniel A; Bougherara, Habiba

    2014-04-01

    A new patent pending technique is proposed in this study to improve the mechanical and biological performance of ultra high molecular weight polyethylene (UHMWPE), i.e., to uniformly coat nylon onto the UHMWPE fiber (Firouzi et al., 2012). Mechanical tests were performed on neat and new nylon coated UHMWPE fibers to examine the tensile strength and creep resistance of the samples at different temperatures. Cytotoxicity and osteolysis induced by wear debris of the materials were investigated using (MTT) assay, and RT-PCR for tumor necrosis factor alpha (TNFα) and interleukin 6 (IL-6) osteolysis markers. Mechanical test results showed substantial improvement in maximum creep time, maximum breaking force, and toughness values of Nylon 6,6 and Nylon 6,12 coated UHMWPE fibers between average 15% and 60% at 25, 50, and 70°C. Furthermore, cytotoxicity studies have demonstrated significant improvement in cell viability using the nylon coated UHMWPE over the neat one (72.4% vs 54.8%) for 48h and (80.7 vs 5%) for 72h (P<0.01). Osteolysis test results have shown that the expression levels of TNFα and IL-6 markers induced by the neat UHMWPE fiber were significantly higher than those induced by the Nylon 6,6 coated UHMWPE (2.5 fold increase for TNFα at 48h, and three fold increase for IL-6 at 72h (P<0.01)). This study suggests that UHMWPE coated with nylon could be used as a novel material in clinical applications with lower cytotoxicity, less wear debris-induced osteolysis, and superior mechanical properties compared to neat UHMWPE. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. Improved Search Techniques

    NASA Technical Reports Server (NTRS)

    Albornoz, Caleb Ronald

    2012-01-01

    Thousands of millions of documents are stored and updated daily in the World Wide Web. Most of the information is not efficiently organized to build knowledge from the stored data. Nowadays, search engines are mainly used by users who rely on their skills to look for the information needed. This paper presents different techniques search engine users can apply in Google Search to improve the relevancy of search results. According to the Pew Research Center, the average person spends eight hours a month searching for the right information. For instance, a company that employs 1000 employees wastes $2.5 million dollars on looking for nonexistent and/or not found information. The cost is very high because decisions are made based on the information that is readily available to use. Whenever the information necessary to formulate an argument is not available or found, poor decisions may be made and mistakes will be more likely to occur. Also, the survey indicates that only 56% of Google users feel confident with their current search skills. Moreover, just 76% of the information that is available on the Internet is accurate.

  8. Guide to molecular cloning techniques

    SciTech Connect

    Berger, S.L.; Kimmel, A.R.

    1987-01-01

    This book includes the following selections: requirements for a molecular biology laboratory; general methods for isolating and characterizing nucleic acids; enzymatic techniques and recombinant DNA technology; restriction enzymes; growth and maintenance of bacteria; genetic cloning, preparation and characterization of RNA; preparation of cDNA and the generation of cDNA libraries; selections of clones from libraries; and identification and characterization of specific clones.

  9. A liftoff technique for molecular nanopatterning.

    PubMed

    Hang, Qingling; Wang, Yuliang; Lieberman, Marya; Bernstein, Gary H

    2003-08-01

    For quantum-dot cellular automata molecular electronic devices, one of the fundamental tasks is to arrange the molecules on a surface in a controlled manner. In this report, we discuss a molecular lift off technique to form nanopatterns toward the development of molecular circuits. In our molecular lift off technique, we use electron beam lithography to form nano-trenches on a polymethylmethacrylate (PMMA) film on a SiO2 wafer. This wafer is soaked in a Creutz-Taube ion [(NH3)5Ru(pyrazine)Ru(NH3)5](o-toluenesulfonate)5 (CT5) aqueous solution. After residual PMMA removal, atomic force microscopy is used to investigate the resulting surface. Thirty-five nanometer CT5 lines are demonstrated on a SiO2 surface. Compared with other molecular nanopatterning techniques, ours is both economical and capable of high-resolution.

  10. Techniques for molecular imaging probe design.

    PubMed

    Reynolds, Fred; Kelly, Kimberly A

    2011-12-01

    Molecular imaging allows clinicians to visualize disease-specific molecules, thereby providing relevant information in the diagnosis and treatment of patients. With advances in genomics and proteomics and underlying mechanisms of disease pathology, the number of targets identified has significantly outpaced the number of developed molecular imaging probes. There has been a concerted effort to bridge this gap with multidisciplinary efforts in chemistry, proteomics, physics, material science, and biology--all essential to progress in molecular imaging probe development. In this review, we discuss target selection, screening techniques, and probe optimization with the aim of developing clinically relevant molecularly targeted imaging agents.

  11. Techniques for Molecular Imaging Probe Design

    PubMed Central

    Reynolds, Fred; Kelly, Kimberly A.

    2011-01-01

    Molecular imaging allows clinicians to visualize disease specific molecules, thereby providing relevant information in the diagnosis and treatment of patients. With advances in genomics and proteomics and underlying mechanisms of disease pathology, the number of targets identified has significantly outpaced the number of developed molecular imaging probes. There has been a concerted effort to bridge this gap with multidisciplinary efforts in chemistry, proteomics, physics, material science, and biology; all essential to progress in molecular imaging probe development. In this review, we will discuss target selection, screening techniques and probe optimization with the aim of developing clinically relevant molecularly targeted imaging agents. PMID:22201532

  12. Techniques for Investigating Molecular Toxicology of Nanomaterials.

    PubMed

    Wang, Yanli; Li, Chenchen; Yao, Chenjie; Ding, Lin; Lei, Zhendong; Wu, Minghong

    2016-06-01

    Nanotechnology has been a rapidly developing field in the past few decades, resulting in the more and more exposure of nanomaterials to human. The increased applications of nanomaterials for industrial, commercial and life purposes, such as fillers, catalysts, semiconductors, paints, cosmetic additives and drug carriers, have caused both obvious and potential impacts on human health and environment. Nanotoxicology is used to study the safety of nanomaterials and has grown at the historic moment. Molecular toxicology is a new subdiscipline to study the interactions and impacts of materials at the molecular level. To better understand the relationship between the molecular toxicology and nanomaterials, this review summarizes the typical techniques and methods in molecular toxicology which are applied when investigating the toxicology of nanomaterials and include six categories: namely; genetic mutation detection, gene expression analysis, DNA damage detection, chromosomal aberration analysis, proteomics, and metabolomics. Each category involves several experimental techniques and methods.

  13. Insect pathogens: molecular approaches and techniques

    USDA-ARS?s Scientific Manuscript database

    This book serves as a primer for molecular techniques in insect pathology and is tailored for a wide scientific audience. Contributing authors are internationally recognized experts. The book comprises four sections: 1) pathogen identification and diagnostics, 2) pathogen population genetics and p...

  14. Use of molecular techniques in bioremediation.

    PubMed

    Płaza, G; Ulfig, K; Hazen, T C; Brigmon, R L

    2001-01-01

    In a practical sense, biotechnology is concerned with the production of commercial products generated by biological processes. More formally, biotechnology may be defined as "the application of scientific and engineering principles to the processing of material by biological agents to provide goods and services" (Cantor, 2000). From a historical perspective, biotechnology dates back to the time when yeast was first used for beer or wine fermentation, and bacteria were used to make yogurt. In 1972, the birth of recombinant DNA technology moved biotechnology to new heights and led to the establishment of a new industry. Progress in biotechnology has been truly remarkable. Within four years of the discovery of recombinant DNA technology, genetically modified organisms (GMOs) were making human insulin, interferon, and human growth hormone. Now, recombinant DNA technology and its products--GMOs are widely used in environmental biotechnology (Glick and Pasternak, 1988; Cowan, 2000). Bioremediation is one of the most rapidly growing areas of environmental biotechnology. Use of bioremediation for environmental clean up is popular due to low costs and its public acceptability. Indeed, bioremediation stands to benefit greatly and advance even more rapidly with the adoption of molecular techniques developed originally for other areas of biotechnology. The 1990s was the decade of molecular microbial ecology (time of using molecular techniques in environmental biotechnology). Adoption of these molecular techniques made scientists realize that microbial populations in the natural environments are much more diverse than previously thought using traditional culture methods. Using molecular ecological methods, such as direct DNA isolation from environmental samples, denaturing gradient gel electrophoresis (DGGE), PCR methods, nucleic acid hybridization etc., we can now study microbial consortia relevant to pollutant degradation in the environment. These techniques promise to

  15. Techniques for Improving Spelling Performance.

    ERIC Educational Resources Information Center

    Saylor, Paul

    Improving spelling performance of college students is a question of insuring that the correct information is in long-term memory and readily retrievable. Any system of spelling instruction should recognize the capacity limits of the sensory register and short-term memory; provide for identification of and concentration on the distinctive features…

  16. Computational Improvements to Quantum Wave Packet ab Initio Molecular Dynamics Using a Potential-Adapted, Time-Dependent Deterministic Sampling Technique.

    PubMed

    Jakowski, Jacek; Sumner, Isaiah; Iyengar, Srinivasan S

    2006-09-01

    In a recent publication, we introduced a computational approach to treat the simultaneous dynamics of electrons and nuclei. The method is based on a synergy between quantum wave packet dynamics and ab initio molecular dynamics. Atom-centered density-matrix propagation or Born-Oppenheimer dynamics can be used to perform ab initio dynamics. In this paper, wave packet dynamics is conducted using a three-dimensional direct product implementation of the distributed approximating functional free-propagator. A fundamental computational difficulty in this approach is that the interaction potential between the two components of the methodology needs to be calculated frequently. Here, we overcome this problem through the use of a time-dependent deterministic sampling measure that predicts, at every step of the dynamics, regions of the potential which are important. The algorithm, when combined with an on-the-fly interpolation scheme, allows us to determine the quantum dynamical interaction potential and gradients at every dynamics step in an extremely efficient manner. Numerical demonstrations of our sampling algorithm are provided through several examples arranged in a cascading level of complexity. Starting from a simple one-dimensional quantum dynamical treatment of the shared proton in [Cl-H-Cl](-) and [CH3-H-Cl](-) along with simultaneous dynamical treatment of the electrons and classical nuclei, through a complete three-dimensional treatment of the shared proton in [Cl-H-Cl](-) as well as treatment of a hydrogen atom undergoing donor-acceptor transitions in the biological enzyme, soybean lipoxygenase-1 (SLO-1), we benchmark the algorithm thoroughly. Apart from computing various error estimates, we also compare vibrational density of states, inclusive of full quantum effects from the shared proton, using a novel unified velocity-velocity, flux-flux autocorrelation function. In all cases, the potential-adapted, time-dependent sampling procedure is seen to improve the

  17. Techniques for improving reliability of computers

    NASA Technical Reports Server (NTRS)

    Cater, W. C.; Mccarthy, C. E.; Jessep, D. C.; Wadia, A. B.; Milligan, F. G.; Bouricius, W. G.

    1972-01-01

    Modular design techniques improve methods of error detection, diagnosis, and recovery. Theoretical computer (MARCS (Modular Architecture for Reliable Computer Systems)) study deals with postulated and modeled technology indigenous to 1975-1980. Study developments are discussed.

  18. Automatic Molecular Design using Evolutionary Techniques

    NASA Technical Reports Server (NTRS)

    Globus, Al; Lawton, John; Wipke, Todd; Saini, Subhash (Technical Monitor)

    1998-01-01

    Molecular nanotechnology is the precise, three-dimensional control of materials and devices at the atomic scale. An important part of nanotechnology is the design of molecules for specific purposes. This paper describes early results using genetic software techniques to automatically design molecules under the control of a fitness function. The fitness function must be capable of determining which of two arbitrary molecules is better for a specific task. The software begins by generating a population of random molecules. The population is then evolved towards greater fitness by randomly combining parts of the better individuals to create new molecules. These new molecules then replace some of the worst molecules in the population. The unique aspect of our approach is that we apply genetic crossover to molecules represented by graphs, i.e., sets of atoms and the bonds that connect them. We present evidence suggesting that crossover alone, operating on graphs, can evolve any possible molecule given an appropriate fitness function and a population containing both rings and chains. Prior work evolved strings or trees that were subsequently processed to generate molecular graphs. In principle, genetic graph software should be able to evolve other graph representable systems such as circuits, transportation networks, metabolic pathways, computer networks, etc.

  19. Molecular detection of pathogens in water--the pros and cons of molecular techniques.

    PubMed

    Girones, Rosina; Ferrús, Maria Antonia; Alonso, José Luis; Rodriguez-Manzano, Jesus; Calgua, Byron; Corrêa, Adriana de Abreu; Hundesa, Ayalkibet; Carratala, Anna; Bofill-Mas, Sílvia

    2010-08-01

    Pollution of water by sewage and run-off from farms produces a serious public health problem in many countries. Viruses, along with bacteria and protozoa in the intestine or in urine are shed and transported through the sewer system. Even in highly industrialized countries, pathogens, including viruses, are prevalent throughout the environment. Molecular methods are used to monitor viral, bacterial, and protozoan pathogens, and to track pathogen- and source-specific markers in the environment. Molecular techniques, specifically polymerase chain reaction-based methods, provide sensitive, rapid, and quantitative analytical tools with which to study such pathogens, including new or emerging strains. These techniques are used to evaluate the microbiological quality of food and water, and to assess the efficiency of virus removal in drinking and wastewater treatment plants. The range of methods available for the application of molecular techniques has increased, and the costs involved have fallen. These developments have allowed the potential standardization and automation of certain techniques. In some cases they facilitate the identification, genotyping, enumeration, viability assessment, and source-tracking of human and animal contamination. Additionally, recent improvements in detection technologies have allowed the simultaneous detection of multiple targets in a single assay. However, the molecular techniques available today and those under development require further refinement in order to be standardized and applicable to a diversity of matrices. Water disinfection treatments may have an effect on the viability of pathogens and the numbers obtained by molecular techniques may overestimate the quantification of infectious microorganisms. The pros and cons of molecular techniques for the detection and quantification of pathogens in water are discussed. (c) 2010 Elsevier Ltd. All rights reserved.

  20. Molecular Technique to Understand Deep Microbial Diversity

    NASA Technical Reports Server (NTRS)

    Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.

    2012-01-01

    Current sequencing-based and DNA microarray techniques to study microbial diversity are based on an initial PCR (polymerase chain reaction) amplification step. However, a number of factors are known to bias PCR amplification and jeopardize the true representation of bacterial diversity. PCR amplification of the minor template appears to be suppressed by the exponential amplification of the more abundant template. It is widely acknowledged among environmental molecular microbiologists that genetic biosignatures identified from an environment only represent the most dominant populations. The technological bottleneck has overlooked the presence of the less abundant minority population, and underestimated their role in the ecosystem maintenance. To generate PCR amplicons for subsequent diversity analysis, bacterial l6S rRNA genes are amplified by PCR using universal primers. Two distinct PCR regimes are employed in parallel: one using normal and the other using biotinlabeled universal primers. PCR products obtained with biotin-labeled primers are mixed with streptavidin-labeled magnetic beads and selectively captured in the presence of a magnetic field. Less-abundant DNA templates that fail to amplify in this first round of PCR amplification are subjected to a second round of PCR using normal universal primers. These PCR products are then subjected to downstream diversity analyses such as conventional cloning and sequencing. A second round of PCR amplified the minority population and completed the deep diversity picture of the environmental sample.

  1. Supervision That Improves Teaching: Strategies and Techniques.

    ERIC Educational Resources Information Center

    Sullivan, Susan; Glanz, Jeffrey

    This book offers a plan for improved classroom practice through the supervisory process. It includes hands-on practices for developing a personalized supervision strategy, research-based and empirically tested strategies, field-tested tools and techniques for qualitative and quantitative observation, a comprehensive resource of traditional and…

  2. Techniques for improved surface discharge switch performance

    SciTech Connect

    Engel, T.G.; Kristiansen, M.; Stemprok, R.

    1995-12-31

    Several techniques have been developed to improve the performance of surface discharge switches (i.e., SDS). These improvements are reported in this investigation and are planned for the development of a prototype switch for the Atlas experimental facility at Los Alamos National Laboratory. One performance improvement technique consists of implanting graphite inserts in the insulator substrate to form capacitively-coupled field emission points with the underlying trigger electrode. These capacitively-coupled field emission points have reduced the trigger risetime normally required for efficient multi-channeling from 1,000 V/ns to 60 V/ns. The resulting discharge has many channels and appears nearly sheet-like in nature. The improved multi-channeling allows the electrodes, which normally rest directly on the insulator surface, to be raised off the insulator surface thereby extending the lifetime of the insulator. Lifetime tests for the improved SDS has been done for 5,000 commutations at 15 kV switch holdoff voltages, 750 kA peak currents, and 70 {micro}s wide pulses. The switch was in good condition at the end of this test and had recorded only 10 prefires during this test. To meet the switch performance requirements for the Atlas facility, further improvements in switch prefire and jitter performance can be accomplished.

  3. An improved infrared technique for sorting pecans

    NASA Astrophysics Data System (ADS)

    Graeve, Thorsten; Dereniak, Eustace L.; Lamonica, John A., Jr.

    1991-10-01

    This paper presents the results of a study of pecan spectral reflectances. It describes an experiment for measuring the contrast between several components of raw pecan product to be sorted. An analysis of the experimental data reveals high contrast ratios in the infrared spectrum, suggesting a potential improvement in sorting efficiency when separating pecan meat from shells. It is believed that this technique has the potential to dramatically improve the efficiency of current sorting machinery, and to reduce the cost of processing pecans for the consumer market.

  4. RF TECHNIQUES FOR IMPROVED LUMINOSITY IN RHIC.

    SciTech Connect

    BRENNAN,J.M.BLASKIEWICZ,J.BUTLER,J.DELONG,J.FISCHER,W.HAYES,T.

    2004-07-05

    The luminosity of the Relativistic Heavy Ion Collider has improved significantly [1] over the first three physics runs. A number of special rf techniques have been developed to facilitate higher luminosity. The techniques described herein include: an ultra low-noise rf source for the 197 MHz storage rf system, a frequency shift switch-on technique for transferring bunches from the acceleration to the storage system, synchronizing the rings during the energy ramp (including crossing the transition energy) to avoid incidental collisions, installation of dedicated 200 MHZ cavities to provide longitudinal Landau damping on the ramp, and the development of a bunch merging scheme in the Booster to increase the available bunch intensity from the injectors.

  5. A comparison of tetrahedral mesh improvement techniques

    SciTech Connect

    Freitag, L.A.; Ollivier-Gooch, C.

    1996-12-01

    Automatic mesh generation and adaptive refinement methods for complex three-dimensional domains have proven to be very successful tools for the efficient solution of complex applications problems. These methods can, however, produce poorly shaped elements that cause the numerical solution to be less accurate and more difficult to compute. Fortunately, the shape of the elements can be improved through several mechanisms, including face-swapping techniques that change local connectivity and optimization-based mesh smoothing methods that adjust grid point location. The authors consider several criteria for each of these two methods and compare the quality of several meshes obtained by using different combinations of swapping and smoothing. Computational experiments show that swapping is critical to the improvement of general mesh quality and that optimization-based smoothing is highly effective in eliminating very small and very large angles. The highest quality meshes are obtained by using a combination of swapping and smoothing techniques.

  6. [Application of molecular biological techniques in Taenia identification].

    PubMed

    Li, Yan; Liu, Hang; Yang, Yi-Mei

    2011-10-01

    The traditional identification of Taenia spp. based on morphological features of adult and cysticercus has difficulties in identifying the morphologically similar species. The recent development of molecular techniques provides more scientific ways for distinguishing Taenia species. This paper summarizes the application of molecular biological techniques in the identification of Taenia, such as analysis of DNA sequence, PCR-RFLP and LAMP.

  7. Improved Chromatographic Techniques for Sulfur Pollutants

    NASA Technical Reports Server (NTRS)

    Hartmann, C. H.

    1971-01-01

    This paper describes several improvements in instrumental techniques for the analysis of low ppb concentrations of sulfur gases using gas chromatography (G.C.). This work has focused on the analytical problem of ambient air monitoring of the two main sulfur gas pollutants, hydrogen sulfide and sulfur dioxide. The most significant technical improvement that will be reported here is the newly developed silica gel column for ppb concentrations of the light sulfur gases (COS, H2S, CS2, SO2, CH3SH). A simplified inlet system will be described which improves reliability of the GC system. The flame photometric detector is used as the means of selectively and sensitively detecting the low concentrations of sulfur gases. Improvements will be described which have yielded better performance than previously reported for this application of the detector. Also included in this paper will be a report of field monitoring using this improved GC system. Reliability and repeatability of performance at the low ppb concentrations of sulfur gases will be demonstrated.

  8. A Simple Lightning Assimilation Technique For Improving ...

    EPA Pesticide Factsheets

    Convective rainfall is often a large source of error in retrospective modeling applications. In particular, positive rainfall biases commonly exist during summer months due to overactive convective parameterizations. In this study, lightning assimilation was applied in the Kain-Fritsch (KF) convective scheme to improve retrospective simulations using the Weather Research and Forecasting (WRF) model. The assimilation method has a straightforward approach: Force KF deep convection where lightning is observed and, optionally, suppress deep convection where lightning is absent. WRF simulations were made with and without lightning assimilation over the continental United States for July 2012, July 2013, and January 2013. The simulations were evaluated against NCEP stage-IV precipitation data and MADIS near-surface meteorological observations. In general, the use of lightning assimilation considerably improves the simulation of summertime rainfall. For example, the July 2012 monthly-averaged bias of 6-h accumulated rainfall is reduced from 0.54 mm to 0.07 mm and the spatial correlation is increased from 0.21 to 0.43 when lightning assimilation is used. Statistical measures of near-surface meteorological variables also are improved. Consistent improvements also are seen for the July 2013 case. These results suggest that this lightning assimilation technique has the potential to substantially improve simulation of warm-season rainfall in retrospective WRF appli

  9. A simple lightning assimilation technique for improving ...

    EPA Pesticide Factsheets

    Convective rainfall is often a large source of error in retrospective modeling applications. In particular, positive rainfall biases commonly exist during summer months due to overactive convective parameterizations. In this study, lightning assimilation was applied in the Kain-Fritsch (KF) convective scheme to improve retrospective simulations using the Weather Research and Forecasting (WRF) model. The assimilation method has a straightforward approach: force KF deep convection where lightning is observed and, optionally, suppress deep convection where lightning is absent. WRF simulations were made with and without lightning assimilation over the continental United States for July 2012, July 2013, and January 2013. The simulations were evaluated against NCEP stage-IV precipitation data and MADIS near-surface meteorological observations. In general, the use of lightning assimilation considerably improves the simulation of summertime rainfall. For example, the July 2012 monthly averaged bias of 6 h accumulated rainfall is reduced from 0.54 to 0.07 mm and the spatial correlation is increased from 0.21 to 0.43 when lightning assimilation is used. Statistical measures of near-surface meteorological variables also are improved. Consistent improvements also are seen for the July 2013 case. These results suggest that this lightning assimilation technique has the potential to substantially improve simulation of warm-season rainfall in retrospective WRF applications. The

  10. Molecular biology techniques and applications for ocean sensing

    NASA Astrophysics Data System (ADS)

    Zehr, J. P.; Hewson, I.; Moisander, P.

    2009-05-01

    The study of marine microorganisms using molecular biological techniques is now widespread in the ocean sciences. These techniques target nucleic acids which record the evolutionary history of microbes, and encode for processes which are active in the ocean today. Molecular techniques can form the basis of remote instrumentation sensing technologies for marine microbial diversity and ecological function. Here we review some of the most commonly used molecular biological techniques. These techniques include the polymerase chain reaction (PCR) and reverse-transcriptase PCR, quantitative PCR, whole assemblage "fingerprinting" approaches (based on nucleic acid sequence or length heterogeneity), oligonucleotide microarrays, and high-throughput shotgun sequencing of whole genomes and gene transcripts, which can be used to answer biological, ecological, evolutionary and biogeochemical questions in the ocean sciences. Moreover, molecular biological approaches may be deployed on ocean sensor platforms and hold promise for tracking of organisms or processes of interest in near-real time.

  11. Airborne myxomycete spores: detection using molecular techniques.

    PubMed

    Kamono, Akiko; Kojima, Hisaya; Matsumoto, Jun; Kawamura, Kimitaka; Fukui, Manabu

    2009-01-01

    Myxomycetes are organisms characterized by a life cycle that includes a fruiting body stage. Myxomycete fruiting bodies contain spores, and wind dispersal of the spores is considered important for this organism to colonize new areas. In this study, the presence of airborne myxomycetes and the temporal changes in the myxomycete composition of atmospheric particles (aerosols) were investigated with a polymerase chain reaction (PCR)-based method for Didymiaceae and Physaraceae. Twenty-one aerosol samples were collected on the roof of a three-story building located in Sapporo, Hokkaido Island, northern Japan. PCR analysis of DNA extracts from the aerosol samples indicated the presence of airborne myxomycetes in all the samples, except for the one collected during the snowfall season. Denaturing gradient gel electrophoresis (DGGE) analysis of the PCR products showed seasonally varying banding patterns. The detected DGGE bands were subjected to sequence analyses, and four out of nine obtained sequences were identical to those of fruiting body samples collected in Hokkaido Island. It appears that the difference in the fruiting period of each species was correlated with the seasonal changes in the myxomycete composition of the aerosols. Molecular evidence shows that newly formed spores are released and dispersed in the air, suggesting that wind-driven dispersal of spores is an important process in the life history of myxomycetes. This study is the first to detect airborne myxomycetes with the use of molecular ecological analyses and to characterize their seasonal distribution.

  12. Airborne myxomycete spores: detection using molecular techniques

    NASA Astrophysics Data System (ADS)

    Kamono, Akiko; Kojima, Hisaya; Matsumoto, Jun; Kawamura, Kimitaka; Fukui, Manabu

    2009-01-01

    Myxomycetes are organisms characterized by a life cycle that includes a fruiting body stage. Myxomycete fruiting bodies contain spores, and wind dispersal of the spores is considered important for this organism to colonize new areas. In this study, the presence of airborne myxomycetes and the temporal changes in the myxomycete composition of atmospheric particles (aerosols) were investigated with a polymerase chain reaction (PCR)-based method for Didymiaceae and Physaraceae. Twenty-one aerosol samples were collected on the roof of a three-story building located in Sapporo, Hokkaido Island, northern Japan. PCR analysis of DNA extracts from the aerosol samples indicated the presence of airborne myxomycetes in all the samples, except for the one collected during the snowfall season. Denaturing gradient gel electrophoresis (DGGE) analysis of the PCR products showed seasonally varying banding patterns. The detected DGGE bands were subjected to sequence analyses, and four out of nine obtained sequences were identical to those of fruiting body samples collected in Hokkaido Island. It appears that the difference in the fruiting period of each species was correlated with the seasonal changes in the myxomycete composition of the aerosols. Molecular evidence shows that newly formed spores are released and dispersed in the air, suggesting that wind-driven dispersal of spores is an important process in the life history of myxomycetes. This study is the first to detect airborne myxomycetes with the use of molecular ecological analyses and to characterize their seasonal distribution.

  13. Hybrid opto-electric techniques for molecular diagnostics

    SciTech Connect

    Haque, Aeraj Ul

    2012-01-01

    Hybrid optoelectric techniques reflect a new paradigm in microfluidics. In essence, these are microfluidic techniques that employ a synergistic combination of optical and electrical forces to enable noninvasive manipulation of fluids and/or particle-type entities at the micro/nano-scale [1]. Synergy between optical and electrical forces bestows these techniques with several unique features that are promising to bring new opportunities in molecular diagnostics. Within the scope of molecular diagnostics, several aspects of optoelectric techniques promise to play a relevant role. These include, but are not limited to, sample preparation, sorting, purification, amplification and detection.

  14. Application of molecular techniques on heterotrophic hydrogen production research.

    PubMed

    Li, R Y; Zhang, T; Fang, H H P

    2011-09-01

    This paper reviews the application of molecular techniques in heterotrophic hydrogen production studies. Commonly used molecular techniques are introduced briefly first, including cloning-sequencing after polymerase chain reaction (PCR), denaturing gradient gel electrophoresis (DGGE), terminal-restriction fragment length polymorphism (T-RFLP), fluorescence in situ hybridization (FISH) and quantitative real-time PCR. Application of the molecular techniques in heterotrophic hydrogen production studies are discussed in details, focusing on identification of new isolates for hydrogen production, characterization of microbial compositions in bioreactors, monitoring microbial diversity variation, visualization of microbial distribution in hydrogen-producing granular sludge, and quantification of various microbial populations. Some significant findings in recent hydrogen production studies with the application of molecular techniques are discussed, followed by a research outlook of the heterotrophic biohydrogen field.

  15. Functional molecular markers for crop improvement.

    PubMed

    Kage, Udaykumar; Kumar, Arun; Dhokane, Dhananjay; Karre, Shailesh; Kushalappa, Ajjamada C

    2016-10-01

    A tremendous decline in cultivable land and resources and a huge increase in food demand calls for immediate attention to crop improvement. Though molecular plant breeding serves as a viable solution and is considered as "foundation for twenty-first century crop improvement", a major stumbling block for crop improvement is the availability of a limited functional gene pool for cereal crops. Advancement in the next generation sequencing (NGS) technologies integrated with tools like metabolomics, proteomics and association mapping studies have facilitated the identification of candidate genes, their allelic variants and opened new avenues to accelerate crop improvement through development and use of functional molecular markers (FMMs). The FMMs are developed from the sequence polymorphisms present within functional gene(s) which are associated with phenotypic trait variations. Since FMMs obviate the problems associated with random DNA markers, these are considered as "the holy grail" of plant breeders who employ targeted marker assisted selections (MAS) for crop improvement. This review article attempts to consider the current resources and novel methods such as metabolomics, proteomics and association studies for the identification of candidate genes and their validation through virus-induced gene silencing (VIGS) for the development of FMMs. A number of examples where the FMMs have been developed and used for the improvement of cereal crops for agronomic, food quality, disease resistance and abiotic stress tolerance traits have been considered.

  16. Teaching Molecular Biological Techniques in a Research Content

    ERIC Educational Resources Information Center

    Stiller, John W.; Coggins, T. Chad

    2006-01-01

    Molecular biological methods, such as the polymerase chain reaction (PCR) and gel electrophoresis, are now commonly taught to students in introductory biology courses at the college and even high school levels. This often includes hands-on experience with one or more molecular techniques as part of a general biology laboratory. To assure that most…

  17. Teaching Molecular Biological Techniques in a Research Content

    ERIC Educational Resources Information Center

    Stiller, John W.; Coggins, T. Chad

    2006-01-01

    Molecular biological methods, such as the polymerase chain reaction (PCR) and gel electrophoresis, are now commonly taught to students in introductory biology courses at the college and even high school levels. This often includes hands-on experience with one or more molecular techniques as part of a general biology laboratory. To assure that most…

  18. Optimizing correlation techniques for improved earthquake location

    USGS Publications Warehouse

    Schaff, D.P.; Bokelmann, G.H.R.; Ellsworth, W.L.; Zanzerkia, E.; Waldhauser, F.; Beroza, G.C.

    2004-01-01

    Earthquake location using relative arrival time measurements can lead to dramatically reduced location errors and a view of fault-zone processes with unprecedented detail. There are two principal reasons why this approach reduces location errors. The first is that the use of differenced arrival times to solve for the vector separation of earthquakes removes from the earthquake location problem much of the error due to unmodeled velocity structure. The second reason, on which we focus in this article, is that waveform cross correlation can substantially reduce measurement error. While cross correlation has long been used to determine relative arrival times with subsample precision, we extend correlation measurements to less similar waveforms, and we introduce a general quantitative means to assess when correlation data provide an improvement over catalog phase picks. We apply the technique to local earthquake data from the Calaveras Fault in northern California. Tests for an example streak of 243 earthquakes demonstrate that relative arrival times with normalized cross correlation coefficients as low as ???70%, interevent separation distances as large as to 2 km, and magnitudes up to 3.5 as recorded on the Northern California Seismic Network are more precise than relative arrival times determined from catalog phase data. Also discussed are improvements made to the correlation technique itself. We find that for large time offsets, our implementation of time-domain cross correlation is often more robust and that it recovers more observations than the cross spectral approach. Longer time windows give better results than shorter ones. Finally, we explain how thresholds and empirical weighting functions may be derived to optimize the location procedure for any given region of interest, taking advantage of the respective strengths of diverse correlation and catalog phase data on different length scales.

  19. Improved fabrication techniques for infrared bolometers

    NASA Astrophysics Data System (ADS)

    Lange, A. E.; Kreysa, E.; McBride, S. E.; Richards, P. L.; Haller, E. E.

    1983-09-01

    Techniques are described for producing improved infrared bolometers from doped germanium. Ion implantation and sputter metalization have been used to make ohmic electrical contacts to Ge:Ga chips. This method results in a high yield of small monolithic bolometers with very little lowfrequency noise. When one of these chips is used as the thermometric element of a composite bolometer, it must be bonded to a dielectric substrate. The thermal resistance of the conventional epoxy bond has been measured and found to be undesirably large. A procedure for soldering the chip to a metalized portion of the substrate is described which reduced this resistance. The contribution of the metal film absorber to the heat capacity of a composite bolometer has been measured. The heat capacity of a NiCr absorber at 1.3K can dominate the bolometer performance. A Bi absorber has significantly lower heat capacity. A low-temperature blackbody calibrator has been built to measure the optical responsivity of bolometers. A composite bolometer system with a throughput of ˜0.1 sr cm2 has been constructed using our new techniques. In negligible background, it has an optical NEP of3.6 \\cdot 10^{ - 15} W/sqrt {Hz} at 1.0K with a time constant of 20 ms. The noise in this bolometer is white above 2.5 Hz and is somewhat below the value predicted by thermodynamic equilibrium theory. It is in agreement with calculations based on a recent nonequilibrium theory.

  20. Improved fabrication techniques for infrared bolometers

    NASA Technical Reports Server (NTRS)

    Lange, A. E.; Kreysa, E.; Mcbride, S. E.; Richards, P. L.; Haller, E. E.

    1983-01-01

    Techniques are described for producing improved infrared bolometers from doped germanium. Ion implantation and sputter metalization have been used to make ohmic electrical contacts to Ge:Ga chips. This method results in a high yield of small monolithic bolometers with very little low-frequency noise. When one of these chips is used as the thermometric element of a composite bolometer, it must be bonded to a dielectric substrate. The thermal resistance of the conventional epoxy bond has been measured and found to be undesirably large. A procedure for soldering the chip to a metalized portion of the substrate is described which reduced this resistance. The contribution of the metal film absorber to the heat capacity of a composite bolometer has been measured. The heat capacity of a NiCr absorber at 1.3 K can dominate the bolometer performance. A Bi absorber has significantly lower heat capacity. A low temperature blackbody calibrator has been built to measure the optical responsivity of bolometers. A composite bolometer system with a throughput of approx. 0.1 sr sq cm was constructed using the new techniques. In negligible background it has an optical NEP of 3.6 10((exp -15) W/sq root of Hz at 1.0 K with a time constant of 20 ms. The noise in this bolometer is white above 2.5 Hz and is somewhat below the value predicted by thermodynamic equilibrium theory. It is in agreement with calculations based on a recent nonequilibrium theory.

  1. Molecular Imprinting Techniques Used for the Preparation of Biosensors

    PubMed Central

    Ertürk, Gizem; Mattiasson, Bo

    2017-01-01

    Molecular imprinting is the technology of creating artificial recognition sites in polymeric matrices which are complementary to the template in their size, shape and spatial arrangement of the functional groups. Molecularly imprinted polymers (MIPs) and their incorporation with various transducer platforms are among the most promising approaches for detection of several analytes. There are a variety of molecular imprinting techniques used for the preparation of biomimetic sensors including bulk imprinting, surface imprinting (soft lithography, template immobilization, grafting, emulsion polymerization) and epitope imprinting. This chapter presents an overview of all of these techniques with examples from particular publications. PMID:28165419

  2. Molecular Imprinting Techniques Used for the Preparation of Biosensors.

    PubMed

    Ertürk, Gizem; Mattiasson, Bo

    2017-02-04

    Molecular imprinting is the technology of creating artificial recognition sites in polymeric matrices which are complementary to the template in their size, shape and spatial arrangement of the functional groups. Molecularly imprinted polymers (MIPs) and their incorporation with various transducer platforms are among the most promising approaches for detection of several analytes. There are a variety of molecular imprinting techniques used for the preparation of biomimetic sensors including bulk imprinting, surface imprinting (soft lithography, template immobilization, grafting, emulsion polymerization) and epitope imprinting. This chapter presents an overview of all of these techniques with examples from particular publications.

  3. Improving feed slurry rheology by colloidal techniques

    SciTech Connect

    Heath, W.O.; Ternes, R.L.

    1984-06-01

    Pacific Northwest Laboratory (PSN) has investigated three colloidal techniques in the laboratory to improve the sedimentation and flowability of Hanford simulated (nonradioactive) current acid waste (CAW) melter feed slurry: polymer-induced bridging flocculation; manipulating glass former (raw SiO/sub 2/ or frit) particle size; and alteration of nitric acid content. All three methods proved successful in improving the rheology of the simulated CAW feed. This initially had exhibited nearly worst-case flow and clogging properties, but was transformed into a flowable, resuspendable (nonclogging) feed. While each has advantages and disadvantages, the following three specific alternatives proved successful: addition of a polyelectrolyte in 2000 ppM concentration to feed slurry; substitution of a 49 wt % SiO/sub 2/ colloidal suspension (approx. 10-micron particle size) for the -325 mesh (less than or equal to 44-micron particle size) raw-chemical SiO/sub 2/; and increase of nitric acid content from the reference 1.06 M to optimum 1.35 M. The first method, polymer-induced bridging flocculation, results in a high sediment volume, nonclogging CAW feed. The second method, involving the use of colloidal silica particles results in a nonsedimenting feed that when left unagitated forms a gel. The third method, increase in feed acidity, results in a highly resuspendable (nonclogging) melter feed. Further research is therefore required to determine which of the three alternatives is the preferred method of achieving rheological control of CAW melter feeds.

  4. Improved molecular tools for sugar cane biotechnology.

    PubMed

    Kinkema, Mark; Geijskes, Jason; Delucca, Paulo; Palupe, Anthony; Shand, Kylie; Coleman, Heather D; Brinin, Anthony; Williams, Brett; Sainz, Manuel; Dale, James L

    2014-03-01

    Sugar cane is a major source of food and fuel worldwide. Biotechnology has the potential to improve economically-important traits in sugar cane as well as diversify sugar cane beyond traditional applications such as sucrose production. High levels of transgene expression are key to the success of improving crops through biotechnology. Here we describe new molecular tools that both expand and improve gene expression capabilities in sugar cane. We have identified promoters that can be used to drive high levels of gene expression in the leaf and stem of transgenic sugar cane. One of these promoters, derived from the Cestrum yellow leaf curling virus, drives levels of constitutive transgene expression that are significantly higher than those achieved by the historical benchmark maize polyubiquitin-1 (Zm-Ubi1) promoter. A second promoter, the maize phosphonenolpyruvate carboxylate promoter, was found to be a strong, leaf-preferred promoter that enables levels of expression comparable to Zm-Ubi1 in this organ. Transgene expression was increased approximately 50-fold by gene modification, which included optimising the codon usage of the coding sequence to better suit sugar cane. We also describe a novel dual transcriptional enhancer that increased gene expression from different promoters, boosting expression from Zm-Ubi1 over eightfold. These molecular tools will be extremely valuable for the improvement of sugar cane through biotechnology.

  5. Improved modeling techniques for turbomachinery flow fields

    SciTech Connect

    Lakshminarayana, B.; Fagan, J.R. Jr.

    1995-10-01

    This program has the objective of developing an improved methodology for modeling turbomachinery flow fields, including the prediction of losses and efficiency. Specifically, the program addresses the treatment of the mixing stress tensor terms attributed to deterministic flow field mechanisms required in steady-state Computational Fluid Dynamic (CFD) models for turbo-machinery flow fields. These mixing stress tensors arise due to spatial and temporal fluctuations (in an absolute frame of reference) caused by rotor-stator interaction due to various blade rows and by blade-to-blade variation of flow properties. These tasks include the acquisition of previously unavailable experimental data in a high-speed turbomachinery environment, the use of advanced techniques to analyze the data, and the development of a methodology to treat the deterministic component of the mixing stress tensor. Penn State will lead the effort to make direct measurements of the momentum and thermal mixing stress tensors in high-speed multistage compressor flow field in the turbomachinery laboratory at Penn State. They will also process the data by both conventional and conditional spectrum analysis to derive momentum and thermal mixing stress tensors due to blade-to-blade periodic and aperiodic components, revolution periodic and aperiodic components arising from various blade rows and non-deterministic (which includes random components) correlations. The modeling results from this program will be publicly available and generally applicable to steady-state Navier-Stokes solvers used for turbomachinery component (compressor or turbine) flow field predictions. These models will lead to improved methodology, including loss and efficiency prediction, for the design of high-efficiency turbomachinery and drastically reduce the time required for the design and development cycle of turbomachinery.

  6. Improved techniques for monitoring the HF spectrum

    NASA Astrophysics Data System (ADS)

    Giesbrecht, James E.; Clarke, Russell; Abbott, Derek

    2004-03-01

    A critical review of contemporary papers on modulation recognition, signal separation, and Single Station Location (SSL) is described in the context of High-Frequency (HF) radio-communications. High-frequency communications is undergoing resurgence despite advances in long-range satellite communication systems. Defense agencies are using the HF spectrum for backup communications as well as for spectrum surveillance applications. Spectrum management organizations are monitoring the HF spectrum to control and enforce licensing. This type of activity usually requires a system that is able to determine the location of a source of transmissions, separate valid signals from interferers and noise, and characterize signals-of-interest (SOI). The immediate aim is to show that commercial-off-the-shelf (COTS) equipment can be used to locate HF transmission sources, enhance SOIs and reject interference, and recognize signal types. The described work on single-station-location (SSL), signal separation, and modulation recognition is contributing to these goals. This paper describes the overall objectives and some of the disadvantages and benefits of various schemes for single-station-location (SSL), signal separation, and modulation recognition. It also proposes new approaches that may relieve shortcomings of existing methods -- including selection of benchmarks or modulations for various transmission scenarios and propagation modes, and use of multiple digital receivers or compression techniques to improve modulation recognition, signal separation, and location of HF emitters.

  7. Improved data visualization techniques for analyzing macromolecule structural changes

    PubMed Central

    Kim, Jae Hyun; Iyer, Vidyashankara; Joshi, Sangeeta B; Volkin, David B; Middaugh, C Russell

    2012-01-01

    The empirical phase diagram (EPD) is a colored representation of overall structural integrity and conformational stability of macromolecules in response to various environmental perturbations. Numerous proteins and macromolecular complexes have been analyzed by EPDs to summarize results from large data sets from multiple biophysical techniques. The current EPD method suffers from a number of deficiencies including lack of a meaningful relationship between color and actual molecular features, difficulties in identifying contributions from individual techniques, and a limited ability to be interpreted by color-blind individuals. In this work, three improved data visualization approaches are proposed as techniques complementary to the EPD. The secondary, tertiary, and quaternary structural changes of multiple proteins as a function of environmental stress were first measured using circular dichroism, intrinsic fluorescence spectroscopy, and static light scattering, respectively. Data sets were then visualized as (1) RGB colors using three-index EPDs, (2) equiangular polygons using radar charts, and (3) human facial features using Chernoff face diagrams. Data as a function of temperature and pH for bovine serum albumin, aldolase, and chymotrypsin as well as candidate protein vaccine antigens including a serine threonine kinase protein (SP1732) and surface antigen A (SP1650) from S. pneumoniae and hemagglutinin from an H1N1 influenza virus are used to illustrate the advantages and disadvantages of each type of data visualization technique. PMID:22898970

  8. A Brief Review of Molecular Techniques to Assess Plant Diversity

    PubMed Central

    Arif, Ibrahim A.; Bakir, Mohammad A.; Khan, Haseeb A.; Al Farhan, Ahmad H.; Al Homaidan, Ali A.; Bahkali, Ali H.; Sadoon, Mohammad Al; Shobrak, Mohammad

    2010-01-01

    Massive loss of valuable plant species in the past centuries and its adverse impact on environmental and socioeconomic values has triggered the conservation of plant resources. Appropriate identification and characterization of plant materials is essential for the successful conservation of plant resources and to ensure their sustainable use. Molecular tools developed in the past few years provide easy, less laborious means for assigning known and unknown plant taxa. These techniques answer many new evolutionary and taxonomic questions, which were not previously possible with only phenotypic methods. Molecular techniques such as DNA barcoding, random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), microsatellites and single nucleotide polymorphisms (SNP) have recently been used for plant diversity studies. Each technique has its own advantages and limitations. These techniques differ in their resolving power to detect genetic differences, type of data they generate and their applicability to particular taxonomic levels. This review presents a basic description of different molecular techniques that can be utilized for DNA fingerprinting and molecular diversity analysis of plant species. PMID:20559503

  9. Improved extraction technique for biological fluids

    NASA Technical Reports Server (NTRS)

    Jahnsen, V. J.

    1975-01-01

    Liquid-liquid extraction technique speeds up separation of biological fluids into number of compounds. This eliminates agitation, emulsion formation, centrifugation, mechanical separation of phases, filtration, and other steps that have been used previously. Extraction efficiencies are equal or better than current manual liquid-liquid extraction techniques.

  10. Ion plating technique improves thin film deposition

    NASA Technical Reports Server (NTRS)

    Mattox, D. M.

    1968-01-01

    Ion plating technique keeps the substrate surface clean until the film is deposited, allows extensive diffusion and chemical reaction, and joins insoluble or incompatible materials. The technique involves the deposition of ions on the substrate surface while it is being bombarded with inert gas ions.

  11. A Improved Transmission System Harmonic Modeling Technique.

    NASA Astrophysics Data System (ADS)

    Akram, Muhammad Fayyaz

    1994-01-01

    The development of a comprehensive approach to the modeling of electric power transmission systems at harmonic frequencies is presented. For harmonic analysis it is not practically possible to model a large transmission system with its neighboring interconnected systems in detail due to computer time and memory limitations. A large number of components of a large system also makes switching studies a recognized problem with respect to the desired accuracy, and required engineering and computer time. Current methods depend on the trial and error approach or the individual analyst's knowledge of the system, which are imprecise and expensive to develop at harmonic frequencies. The approach to solve this problem involves the development of a formal method for dividing large-scale transmission systems into a main study system and a group of external systems. Then, using an efficient and appropriate method of adjoint network sensitivity analysis, the size of the system model is reduced, keeping the same frequency characteristics as that of the original system. This reduction in model size in turn accommodates larger transmission system size and increases the accuracy and computational efficiency. An efficient and accurate method is also presented that determines the relative importance of external system equivalents on the harmonic impedance of a transmission network. The bilinear theorem provides an economical method of determining the appropriate locations for simplification of external systems. Using this technique, the system model error bounds can be fixed and the high error range of the external system equivalent impedance can be reduced. For filter designs, the most important issue of computing harmonic impedance boundaries is improved by using an efficient adjoint network sensitivity analysis. Using this sensitivity analysis an order of critical components is developed. The number of outage contingencies to be analyzed is reduced by a large factor which

  12. LOCO with Constraints and Improved Fitting Technique

    SciTech Connect

    Huang, Xiaobiao; Safranek, James; Portmann, Greg; /LBL, Berkeley

    2009-06-18

    } reduction, i.e., small {chi}{sup 2} reduction with large changes of {Delta}K. Under effects of random noise, the fitting solution tends to crawl toward these patterns and ends up with unrealistically large {Delta}K. Such a solution is not very useful in optics correction because after the solution is dialed in, the quadrupoles will not respond as predicted by the lattice model due to magnet hysteresis. We will show that adding constraints to the fitting parameters is an effective way to combat this problem of LOCO. In fact, it improves optics calibration precision even for machines that don't show severe degeneracy behavior. LOCO fitting is essentially to solve a nonlinear least square problem with an iterative approach. The linear least square technique is applied in each iteration to move the solution toward the minimum. This approach is commonly referred to as the Gauss-Newton method. By using singular value decomposition (SVD) to invert the Jacobian matrix, this method has generally been very successful for LOCO. However, this method is based on a linear expansion of the residual vector over the fitting parameters which is valid only when the starting solution is sufficiently close to the real minimum. The fitting algorithm can have difficulties to converge when the initial guess is too far off. For example, it's possible for the {chi}{sup 2} merit function to increase after an iteration instead of decrease. This situation can be improved by using more robust nonlinear least square fitting algorithms, such as the Levenberg-Marquardt method. We will discuss the degeneracy problem in section 2 and then show how the constrained fitting can help in section 3. The application of Levenberg-Marquadt method to LOCO is shown in section 4. A summary is given in section 5.

  13. Improving Demonstration Using Better Interaction Techniques

    DTIC Science & Technology

    2007-11-02

    Programming by demonstration (PBD) can be used to create tools and methods that eliminate the need to learn difficult computer languages. Gamut is a...do this, Gamut uses advanced interaction techniques that make it easier for a software author to express all needed aspects of one’s program. These...techniques include a simplified way to demonstrate new examples, called nudges, and a way to highlight objects to show they are important. Also, Gamut

  14. Assessment of knowledge of participants on basic molecular biology techniques after 5-day intensive molecular biology training workshops in Nigeria.

    PubMed

    Yisau, J I; Adagbada, A O; Bamidele, T; Fowora, M; Brai, B I C; Adebesin, O; Bamidele, M; Fesobi, T; Nwaokorie, F O; Ajayi, A; Smith, S I

    2017-02-01

    The deployment of molecular biology techniques for diagnosis and research in Nigeria is faced with a number of challenges, including the cost of equipment and reagents coupled with the dearth of personnel skilled in the procedures and handling of equipment. Short molecular biology training workshops were conducted at the Nigerian Institute of Medical Research (NIMR), to improve the knowledge and skills of laboratory personnel and academics in health, research, and educational facilities. Five-day molecular biology workshops were conducted annually between 2011 and 2014, with participants drawn from health, research facilities, and the academia. The courses consisted of theoretical and practical sessions. The impact of the workshops on knowledge and skill acquisition was evaluated by pre- and post-tests which consisted of 25 multiple choice and other questions. Sixty-five participants took part in the workshops. The mean knowledge of molecular biology as evaluated by the pre- and post-test assessments were 8.4 (95% CI 7.6-9.1) and 13.0 (95 CI 11.9-14.1), respectively. The mean post-test score was significantly greater than the mean pre-test score (p < 0.0001). The five-day molecular biology workshop significantly increased the knowledge and skills of participants in molecular biology techniques. © 2017 by The International Union of Biochemistry and Molecular Biology, 2017.

  15. Improved Hanle effect measurement technique for fast ions.

    NASA Technical Reports Server (NTRS)

    Liu, C. H.; Gardiner, R. B.; Church, D. A.

    1973-01-01

    An improved averaging technique for use with foil-excited fast ions is applied to a Hanle-effect measurement of the mean life of some fast ions. With improved data analysis, the employed technique is expected to be more precise, as well as experimentally simpler than previously used techniques.

  16. Improving Maladaptive Behaviors Using Sensory Integration Techniques.

    ERIC Educational Resources Information Center

    Shuman, Theresa

    A study examined the use of sensory integration techniques to reduce the maladaptive behaviors that interfered with the learning of nine high school students with mental impairments attending a special school. Maladaptive behaviors identified included rocking, toe walking, echolalia, resistance to change, compulsive behaviors, aggression,…

  17. Does Retelling Technique Improve Speaking Fluency?

    ERIC Educational Resources Information Center

    Rachmawaty, Noor; Hermagustiana, Istanti

    2010-01-01

    This paper is based on a study on speaking fluency performed by six low level students using retelling technique. The aim of the study is to find out the effect of retelling on the students' speaking fluency and to know the strategies used by those students while retelling a story. The data were the speaking transcripts which were analyzed to see…

  18. Phase behaviors of polymer solutions using molecular simulation technique.

    PubMed

    Yang, Jung Ho; Bae, Young Chan

    2008-08-14

    Phase behaviors of polymer solutions are estimated using a combination of thermodynamic models and molecular simulation technique. In general, many parameters of binary systems are determined by fitting a thermodynamic model with experimental data. In this study, we obtained all parameters using molecular simulation. To take the specific interaction into account, we assume that it only occurs between a solvent molecule and a specific group. Our results show that the theoretical treatment accounting for the specific interaction gives more accurate predictions than those without consideration of specific interaction. Also, our approach describes the phase equilibria of various polymer solutions over the entire concentration remarkably well.

  19. Molecular dynamics techniques for modeling G protein-coupled receptors.

    PubMed

    McRobb, Fiona M; Negri, Ana; Beuming, Thijs; Sherman, Woody

    2016-10-01

    G protein-coupled receptors (GPCRs) constitute a major class of drug targets and modulating their signaling can produce a wide range of pharmacological outcomes. With the growing number of high-resolution GPCR crystal structures, we have the unprecedented opportunity to leverage structure-based drug design techniques. Here, we discuss a number of advanced molecular dynamics (MD) techniques that have been applied to GPCRs, including long time scale simulations, enhanced sampling techniques, water network analyses, and free energy approaches to determine relative binding free energies. On the basis of the many success stories, including those highlighted here, we expect that MD techniques will be increasingly applied to aid in structure-based drug design and lead optimization for GPCRs.

  20. Improved NDI techniques for aircraft inspections

    NASA Astrophysics Data System (ADS)

    Hagemaier, Donald J.; Wilson, Dwight

    1996-11-01

    Through the use of an 'integrated product team' approach and new inspection techniques incorporating the latest in imaging capabilities and automation, the costs of some man- power intensive tasks can now be drastically reduced. Also, through the use of advanced eddy current techniques, the detectable size of cracks under flush-head fasteners can be reduced while maintaining a reliable inspection. Early in this decade, the FAA Technical Center and NASA LaRC formulated an aging aircraft research plan. The unique aspect about the research is that it is driven by the aircraft manufacturers and airlines in order to center only on those areas in which help is needed and to keep it focused. Once developed, the manufacturer works with the FAA Validation Center at Sandia National Labs., the airline, and the researcher to transfer technology to the field. This article describes the evaluation and results obtained using eddy current technology to determine the minimum detectable crack size under installed flush-head fasteners. Secondly, it describes the integrated efforts of engineers at McDonnell Douglas Aerospace and Northwest Airlines in the successful application of MAUS eddy current C-scanning of the DC-10 circumferential and axial crown splices. The eddy current C-scanning greatly reduced the man-hour effort required for the existing radiographic inspection. Thirdly, it describes the use of a novel ultrasonic technique coupled to a scanner and graphics for the detection and quantification of corrosion thinning and stress corrosion cracking of the DC-9 lower wing tee cap. This successful effort resulted from a rather large integrated task team. It also results in a vast man-hour savings over the existing internal visual inspection.

  1. Improved dosimetry techniques for intravascular brachytherapy

    NASA Astrophysics Data System (ADS)

    Sehgal, Varun

    Coronary artery disease leads to the accumulation of atheromatous plaque leading to coronary stenosis. Coronary intervention techniques such as balloon angioplasty and atherectomy are used to address coronary stenosis and establish a stable lumen thus enhancing blood flow to the myocardium. Restenosis or re-blockage of the arteries is a major limitation of the above mentioned interventional techniques. Neointimal hyperplasia or proliferation of cells in response to the vascular injury as a result of coronary intervention is considered to be one of the major causes of restenosis. Recent studies indicated that irradiation of the coronary lesion site, with radiation doses ranging from 15 to 30 Gy, leads to diminishing neointimal hyperplasia with subsequent reduction in restenosis. The radiation dose is given by catheter-based radiation delivery systems using beta-emitters 90Sr/90Y, 32P and gamma-emitting 192Ir among others. However the dose schema used for dose prescription for these sources are relatively simplistic, and are based on calculations using uniform homogenous water or tissue media and simple cylinder geometry. Stenotic coronary vessels are invariably lined with atheromatous plaque of heterogeneous composition, the radiation dose distribution obtained from such dosimetry data can cause significant variations in the actual dose received by a given patient. Such discrepancies in dose calculation can introduce relatively large uncertainties in the limits of dose window for effective and safe application of intravascular brachytherapy, and consequently in the clinical evaluation of the efficacy of this modality. In this research study we investigated the effect of different geometrical and material heterogeneities, including residual plaque, catheter non-centering, lesion eccentricity and cardiac motion on the radiation dose delivered at the lesion site. Correction factors including dose perturbation factors and dose variation factors have been calculated

  2. Application of Molecular Genetics and Transformation to Barley Improvement

    USDA-ARS?s Scientific Manuscript database

    This chapter of the new barley monograph summarizes current applications of molecular genetics and transformation to barley improvement. The chapter describes recent applications of molecular markers including association genetics, QTL mapping and marker assisted selection in barley programs, and in...

  3. Molecular imaging of rheumatoid arthritis: emerging markers, tools, and techniques.

    PubMed

    Put, Stéphanie; Westhovens, René; Lahoutte, Tony; Matthys, Patrick

    2014-04-15

    Early diagnosis and effective monitoring of rheumatoid arthritis (RA) are important for a positive outcome. Instant treatment often results in faster reduction of inflammation and, as a consequence, less structural damage. Anatomical imaging techniques have been in use for a long time, facilitating diagnosis and monitoring of RA. However, mere imaging of anatomical structures provides little information on the processes preceding changes in synovial tissue, cartilage, and bone. Molecular imaging might facilitate more effective diagnosis and monitoring in addition to providing new information on the disease pathogenesis. A limiting factor in the development of new molecular imaging techniques is the availability of suitable probes. Here, we review which cells and molecules can be targeted in the RA joint and discuss the advances that have been made in imaging of arthritis with a focus on such molecular targets as folate receptor, F4/80, macrophage mannose receptor, E-selectin, intercellular adhesion molecule-1, phosphatidylserine, and matrix metalloproteinases. In addition, we discuss a new tool that is being introduced in the field, namely the use of nanobodies as tracers. Finally, we describe additional molecules displaying specific features in joint inflammation and propose these as potential new molecular imaging targets, more specifically receptor activator of nuclear factor κB and its ligand, chemokine receptors, vascular cell adhesion molecule-1, αVβ₃ integrin, P2X7 receptor, suppression of tumorigenicity 2, dendritic cell-specific transmembrane protein, and osteoclast-stimulatory transmembrane protein.

  4. Umbilical Connect Techniques Improvement-Technology Study

    NASA Technical Reports Server (NTRS)

    Valkema, Donald C.

    1972-01-01

    The objective of this study was to develop concepts, specifications, designs, techniques, and procedures capable of significantly reducing the time required to connect and verify umbilicals for ground services to the space shuttle. The desired goal was to reduce the current time requirement of several shifts for the Saturn 5/Apollo to an elapsed time of less than one hour to connect and verify all of the space shuttle ground service umbilicals. The study was conducted in four phases: (1) literature and hardware examination, (2) concept development, (3) concept evaluation and tradeoff analysis, and (4) selected concept design. The final product of this study was a detail design of a rise-off disconnect panel prototype test specimen for a LO2/LH2 booster (or an external oxygen/hydrogen tank for an orbiter), a detail design of a swing-arm mounted preflight umbilical carrier prototype test specimen, and a part 1 specification for the umbilical connect and verification design for the vehicles as defined in the space shuttle program.

  5. Improved fabrication techniques for infrared bolometers

    NASA Technical Reports Server (NTRS)

    Lange, A. E.; Mcbride, S. E.; Richards, P. L.; Haller, E. E.; Kreysa, E.

    1983-01-01

    Ion implantation and sputter metallization are used to produce ohmic electrical contacts to Ge:Ga chips. The method is shown to give a high yield of small monolithic bolometers with very little low-frequency noise. It is noted that when one of the chips is used as the thermometric element of a composite bolometer it must be bonded to a dielectric substrate. The thermal resistance of the conventional epoxy bond is measured and found to be undesirably large. A procedure for soldering the chip to a metallized portion of the substrate in such a way as to reduce this resistance is outlined. An evaluation is made of the contribution of the metal film absorber to the heat capacity of a composite bolometer. It is found that the heat capacity of a NiCr absorber at 1.3 K can dominate the bolometer performance. A Bi absorber possesses significantly lower heat capacity. A low-temperature blackbody calibrator is built to measure the optical responsivity of bolometers. A composite bolometer system with a throughput of approximately 0.1 sr sq cm is constructed using the new techniques. The noise in this bolometer is white above 2.5 Hz and is slightly below the value predicted by thermodynamic equilibrium theory.

  6. Improved fabrication techniques for infrared bolometers

    NASA Technical Reports Server (NTRS)

    Lange, A. E.; Mcbride, S. E.; Richards, P. L.; Haller, E. E.; Kreysa, E.

    1983-01-01

    Ion implantation and sputter metallization are used to produce ohmic electrical contacts to Ge:Ga chips. The method is shown to give a high yield of small monolithic bolometers with very little low-frequency noise. It is noted that when one of the chips is used as the thermometric element of a composite bolometer it must be bonded to a dielectric substrate. The thermal resistance of the conventional epoxy bond is measured and found to be undesirably large. A procedure for soldering the chip to a metallized portion of the substrate in such a way as to reduce this resistance is outlined. An evaluation is made of the contribution of the metal film absorber to the heat capacity of a composite bolometer. It is found that the heat capacity of a NiCr absorber at 1.3 K can dominate the bolometer performance. A Bi absorber possesses significantly lower heat capacity. A low-temperature blackbody calibrator is built to measure the optical responsivity of bolometers. A composite bolometer system with a throughput of approximately 0.1 sr sq cm is constructed using the new techniques. The noise in this bolometer is white above 2.5 Hz and is slightly below the value predicted by thermodynamic equilibrium theory.

  7. Improvement of Rocket Engine Plume Analysis Techniques

    NASA Technical Reports Server (NTRS)

    Smith, S. D.

    1982-01-01

    A nozzle plume flow field code was developed. The RAMP code which was chosen as the basic code is of modular construction and has the following capabilities: two phase with two phase transonic solution; a two phase, reacting gas (chemical equilibrium reaction kinetics), supersonic inviscid nozzle/plume solution; and is operational for inviscid solutions at both high and low altitudes. The following capabilities were added to the code: a direct interface with JANNAF SPF code; shock capturing finite difference numerical operator; two phase, equilibrium/frozen, boundary layer analysis; a variable oxidizer to fuel ratio transonic solution; an improved two phase transonic solution; and a two phase real gas semiempirical nozzle boundary layer expansion.

  8. Improved techniques for switching power amplifiers

    SciTech Connect

    Flinder, F.M.; Wolfs, P.J.; Kwong, K.C.

    1993-10-01

    The control system design of a dc to 10 kHz bandwidth 45 kVA current sourced power amplifier suitable for geophysical exploration applications is presented. A five-level modulation scheme has been implemented using a modified bridge topology with only four switches. This scheme give as an order of magnitude improvement in switching ripple and control performance over two-level modulation. Using this system, a 50 kHz switch frequency allows a 20 kHz, {minus}3dB bandwidth to be easily achieved. Simulation as well as tenth scale model test results are presented. The current output waveform reproduction is of high quality over the rated dc to 10 kHz frequency range. The THD is 0.3% at 1 kHz.

  9. Molecular Diode Studies Based on a Highly Sensitive Molecular Measurement Technique

    PubMed Central

    Iwane, Madoka; Fujii, Shintaro; Kiguchi, Manabu

    2017-01-01

    In 1974, molecular electronics pioneers Mark Ratner and Arieh Aviram predicted that a single molecule could act as a diode, in which electronic current can be rectified. The electronic rectification property of the diode is one of basic functions of electronic components and since then, the molecular diode has been investigated as a first single-molecule device that would have a practical application. In this review, we first describe the experimental fabrication and electronic characterization techniques of molecular diodes consisting of a small number of molecules or a single molecule. Then, two main mechanisms of the rectification property of the molecular diode are discussed. Finally, representative results for the molecular diode are reviewed and a brief outlook on crucial issues that need to be addressed in future research is discussed. PMID:28445393

  10. Molecular Diode Studies Based on a Highly Sensitive Molecular Measurement Technique.

    PubMed

    Iwane, Madoka; Fujii, Shintaro; Kiguchi, Manabu

    2017-04-26

    In 1974, molecular electronics pioneers Mark Ratner and Arieh Aviram predicted that a single molecule could act as a diode, in which electronic current can be rectified. The electronic rectification property of the diode is one of basic functions of electronic components and since then, the molecular diode has been investigated as a first single-molecule device that would have a practical application. In this review, we first describe the experimental fabrication and electronic characterization techniques of molecular diodes consisting of a small number of molecules or a single molecule. Then, two main mechanisms of the rectification property of the molecular diode are discussed. Finally, representative results for the molecular diode are reviewed and a brief outlook on crucial issues that need to be addressed in future research is discussed.

  11. Improved Techniques for Targeting Additional Observations to Improve Forecast Skill

    DTIC Science & Technology

    2016-06-07

    T oulouse F rance Grant Num ber: N00014{99{1{0755 LONG-TERM GOAL This project aims to improv e ensemble forecast and adaptive observ ation tec...be studied. It will be assessed whether the assimilation system can be geared to more readily accept adaptive observations made in currently data

  12. Performance improvement of BOTDR system using wavelength diversity technique

    NASA Astrophysics Data System (ADS)

    Lalam, Nageswara; Ng, Wai Pang; Dai, Xuewu; Wu, Qiang; Fu, Yong Qing

    2017-04-01

    In this paper, a novel technique was proposed to improve the sensing performance by employing wavelength diversity in Brillouin optical time domain reflectometry (BOTDR). This technique enables to maximize the launch pump power to achieve a higher measurement accuracy, without activating the nonlinear effects, which limit the conventional BOTDR performance. Experimentally, we have demonstrated the proposed technique, that provides measurement accuracy improvement of 3.6 times at far end of the sensing fibre compared to the conventional BOTDR system.

  13. Application of Molecular Diagnostic Techniques for Viral Testing

    PubMed Central

    Cobo, Fernando

    2012-01-01

    Nucleic acid amplification techniques are commonly used currently to diagnose viral diseases and manage patients with this kind of illnesses. These techniques have had a rapid but unconventional route of development during the last 30 years, with the discovery and introduction of several assays in clinical diagnosis. The increase in the number of commercially available methods has facilitated the use of this technology in the majority of laboratories worldwide. This technology has reduced the use of some other techniques such as viral culture based methods and serological assays in the clinical virology laboratory. Moreover, nucleic acid amplification techniques are now the methods of reference and also the most useful assays for the diagnosis in several diseases. The introduction of these techniques and their automation provides new opportunities for the clinical laboratory to affect patient care. The main objectives in performing nucleic acid tests in this field are to provide timely results useful for high-quality patient care at a reasonable cost, because rapid results are associated with improvements in patients care. The use of amplification techniques such as polymerase chain reaction, real-time polymerase chain reaction or nucleic acid sequence-based amplification for virus detection, genotyping and quantification have some advantages like high sensitivity and reproducibility, as well as a broad dynamic range. This review is an up-to-date of the main nucleic acid techniques and their clinical applications, and special challenges and opportunities that these techniques currently provide for the clinical virology laboratory. PMID:23248732

  14. Molecularly imprinted polymers for on-line extraction techniques.

    PubMed

    Moein, Mohammad M; Abdel-Rehim, Mohamed

    2015-01-01

    Recent years have seen an increasing interest in the use of molecularly imprinted polymers (MIPs) as a sorbent for different extraction methods and this is due to its high selectivity. The MIP is designed to show specificity for the analyte of interest. Moreover, MIPs show physical robustness, resistance to high temperatures and pressures, and stability in the presence of acids, bases and a wide range of organic solvents. In the present article, various novel sample preparation techniques which MIPs applied as sorbent and on-line connected with analytical instruments were highlighted and discussed. The future aspects of MIPs as well were described.

  15. Molecular Genetic Tools and Techniques in Fission Yeast.

    PubMed

    Murray, Johanne M; Watson, Adam T; Carr, Antony M

    2016-05-02

    The molecular genetic tools used in fission yeast have generally been adapted from methods and approaches developed for use in the budding yeast, Saccharomyces cerevisiae Initially, the molecular genetics of Schizosaccharomyces pombe was developed to aid gene identification, but it is now applied extensively to the analysis of gene function and the manipulation of noncoding sequences that affect chromosome dynamics. Much current research using fission yeast thus relies on the basic processes of introducing DNA into the organism and the extraction of DNA for subsequent analysis. Targeted integration into specific genomic loci is often used to create site-specific mutants or changes to noncoding regulatory elements for subsequent phenotypic analysis. It is also regularly used to introduce additional sequences that generate tagged proteins or to create strains in which the levels of wild-type protein can be manipulated through transcriptional regulation and/or protein degradation. Here, we draw together a collection of core molecular genetic techniques that underpin much of modern research using S. pombe We summarize the most useful methods that are routinely used and provide guidance, learned from experience, for the successful application of these methods.

  16. Hybrid molecular-continuum techniques for micro and nano flows

    NASA Astrophysics Data System (ADS)

    Reese, Jason; Ritos, Konstantinos; Borg, Matthew; Lockerby, Duncan

    2015-11-01

    Nano- and micro-confined fluid flows are often characterised by non-continuum effects that require special treatment beyond the scope of conventional continuum-fluid modelling. However, if the flow system has high-aspect-ratio components (e.g. long narrow channels) the computational cost of a fully molecular-based simulation can be prohibitive. In this talk we present some important elements of a heterogeneous molecular-continuum method that exploits the various degrees of scale separation in both time and space that are very often present in these types of flows. We demonstrate the ability of these techniques to predict the flow of water in aligned carbon nanotube (CNT) membranes: the tube diameters are 1-2 nm and the tube lengths (i.e. the membrane thicknesses) are 2-6 orders of magnitude larger. We compare our results with experimental data. We also find very good agreement with experimental results for a 1 mm thick membrane that has CNTs of diameter 1.59 nm. In this case, our hybrid multiscale simulation is orders of magnitude faster than a full molecular dynamics simulation.

  17. Studies of thermal transport properties using molecular dynamics simulation techniques

    NASA Astrophysics Data System (ADS)

    Ratanapisit, Juraivan

    The purpose of this research has been to investigate the transport properties of fluids using novel techniques in molecular dynamics simulations: symplectic integration algorithms for equations of motion, Baranyai's thermostatted fluid wall algorithm, and Rapaport's algorithm for hard chain fluids. In the symplectic integration study, an extensive series of equilibrium molecular dynamic simulations have been performed to investigate the accuracy, stability and efficiency of second order explicit symplectic integrators: position Verlet, velocity Verlet, and the McLauchlan-Atela algorithms. To our knowledge, previous studies of the symplectic integrators have only looked at the thermodynamic energy using a simple model fluid. Our work presents realistic but perhaps the simplest simulations possible to test the effect of the integrators on the three main transport properties. Our results suggest that if an algorithm fails to adequately conserve energy, it will also show significant uncertainties in transport property calculations. A large portion of the simulation study focused on a new algorithm for thermal conductivity based on Baranyai's fluid wall method. This algorithm is stable enough to perform simulations even using large time steps and provides reasonable values and uncertainties for the thermal conductivity. The investigation was conducted using two different thermostat algorithms: the Gaussian and Nosé-Hoover thermostats. The final part of this research focused on the viscosity of hard chain fluids. This study was initiated with an investigation of the equilibrium molecular dynamic simulations of pure hard-sphere molecules. The natural extension of that work was to hard chain fluids. (Abstract shortened by UMI.)

  18. An improved technique for repeated gavage administration to rat neonates.

    PubMed

    Watanabe, Chiaki; Kuwagata, Makiko; Yoshimura, Shinsuke; Azegami, Jiro; Kojima, Kouichi; Ono, Hiroshi; Nagao, Tetsuji

    2003-09-01

    The technique for gavage administration to rat nurslings was improved to allow determination of the direct effects of chemical substances in the nurslings. Rat neonates were treated with distilled water from postnatal day 1 through 20 using this technique. The viability of neonates during the administration period was comparable to that of untreated neonates. No adverse effects of this technique on the development of neonates were found, and no histological alterations of the esophagus or pharynx. Therefore, we conclude that use of our improved gavage administration method will contribute to ensuring successful neonatal development and thus allowing accurate assessment of the toxicological effects of test compounds on rat nurslings.

  19. Development of Improved Oil Field Waste Injection Disposal Techniques

    SciTech Connect

    Terralog Technologies

    2002-11-25

    The goals of this project have was to: (1) assemble and analyze a comprehensive database of past waste injection operations; (2) develop improved diagnostic techniques for monitoring fracture growth and formation changes; (3) develop operating guidelines to optimize daily operations and ultimate storage capacity of the target formation; and (4) to apply these improved models and guidelines in the field.

  20. Development of Improved Oil Field Waste Injection Disposal Techniques

    SciTech Connect

    Terralog Technologies USA Inc.

    2001-12-17

    The goals of this DOE sponsored project are to: (1) assemble and analyze a comprehensive database of past waste injection operations; (2) develop improved diagnostic techniques for monitoring fracture growth and formation changes; (3) develop operating guidelines to optimize daily operations and ultimate storage capacity of the target formation; and (4) to test these improved models and guidelines in the field.

  1. An improved switching converter model using discrete and average techniques

    NASA Technical Reports Server (NTRS)

    Shortt, D. J.; Lee, F. C.

    1982-01-01

    The nonlinear modeling and analysis of dc-dc converters has been done by averaging and discrete-sampling techniques. The averaging technique is simple, but inaccurate as the modulation frequencies approach the theoretical limit of one-half the switching frequency. The discrete technique is accurate even at high frequencies, but is very complex and cumbersome. An improved model is developed by combining the aforementioned techniques. This new model is easy to implement in circuit and state variable forms and is accurate to the theoretical limit.

  2. Diagnosis of Whipple's disease using molecular biology techniques.

    PubMed

    Cosme, Ángel; Ojeda, Evelia; Muñagorri, Ana I; Gaminde, Eduardo; Bujanda, Luis; Larzabal, Mikel; Gil, Inés

    2011-04-01

    The diagnosis of Whipple's disease (WD) is based on the existence of clinical signs and symptoms compatible with the disease and in the presence of PAS-positive diastase-resistant granules in the macrophages of the small intestine. If there is suspicion of the disease but no histological findings or only isolated extraintestinal manifestations, species-specific PCR using different sequences of the T. whippleii genome from different tissue types and biological fluids is recommended.This study reports two cases: the first patient had diarrhea and the disease was suspected after an endoscopic examination of the ileum, while the second patient had multi-systemic manifestations,particularly abdominal, thoracic, and peripheral lymphadenopathies. In both cases, the diagnosis was confirmed using molecular biology techniques to samples from the small intestine or from a retroperineal lymph node, respectively.

  3. Molecular genetic techniques for gene manipulation in Candida albicans

    PubMed Central

    Xu, Qiu-Rong; Yan, Lan; Lv, Quan-Zhen; Zhou, Mi; Sui, Xue; Cao, Yong-Bing; Jiang, Yuan-Ying

    2014-01-01

    Candida albicans is one of the most common fungal pathogen in humans due to its high frequency as an opportunistic and pathogenic fungus causing superficial as well as invasive infections in immunocompromised patients. An understanding of gene function in C. albicans is necessary to study the molecular basis of its pathogenesis, virulence and drug resistance. Several manipulation techniques have been used for investigation of gene function in C. albicans, including gene disruption, controlled gene expression, protein tagging, gene reintegration, and overexpression. In this review, the main cassettes containing selectable markers used for gene manipulation in C. albicans are summarized; the advantages and limitations of these cassettes are discussed concerning the influences on the target gene expression and the virulence of the mutant strains. PMID:24759671

  4. Modeling large RNAs and ribonucleoprotein particles using molecular mechanics techniques.

    PubMed Central

    Malhotra, A; Tan, R K; Harvey, S C

    1994-01-01

    There is a growing body of low-resolution structural data that can be utilized to devise structural models for large RNAs and ribonucleoproteins. These models are routinely built manually. We introduce an automated refinement protocol to utilize such data for building low-resolution three-dimensional models using the tools of molecular mechanics. In addition to specifying the positions of each nucleotide, the protocol provides quantitative estimates of the uncertainties in those positions, i.e., the resolution of the model. In typical applications, the resolution of the models is about 10-20 A. Our method uses reduced representations and allows us to refine three-dimensional structures of systems as big as the 16S and 23S ribosomal RNAs, which are about one to two orders of magnitude larger than nucleic acids that can be examined by traditional all-atom modeling methods. Nonatomic resolution structural data--secondary structure, chemical cross-links, chemical and enzymatic footprinting patterns, protein positions, solvent accessibility, and so on--are combined with known motifs in RNA structure to predict low-resolution models of large RNAs. These structural constraints are imposed on the RNA chain using molecular mechanics-type potential functions with parameters based on the quality of experimental data. Surface potential functions are used to incorporate shape and positional data from electron microscopy image reconstruction experiments into our models. The structures are optimized using techniques of energy refinement to get RNA folding patterns. In addition to providing a consensus model, the method finds the range of models consistent with the data, which allows quantitative evaluation of the resolution of the model. The method also identifies conflicts in the experimental data. Although our protocol is aimed at much larger RNAs, we illustrate these techniques using the tRNA structure as an example and test-bed. Images FIGURE 7 FIGURE 8 PMID:7521223

  5. Molecular Genetic Tools and Techniques for Marchantia polymorpha Research.

    PubMed

    Ishizaki, Kimitsune; Nishihama, Ryuichi; Yamato, Katsuyuki T; Kohchi, Takayuki

    2016-02-01

    Liverworts occupy a basal position in the evolution of land plants, and are a key group to address a wide variety of questions in plant biology. Marchantia polymorpha is a common, easily cultivated, dioecious liverwort species, and is emerging as an experimental model organism. The haploid gametophytic generation dominates the diploid sporophytic generation in its life cycle. Genetically homogeneous lines in the gametophyte generation can be established easily and propagated through asexual reproduction, which aids genetic and biochemical experiments. Owing to its dioecy, male and female sexual organs are formed in separate individuals, which enables crossing in a fully controlled manner. Reproductive growth can be induced at the desired times under laboratory conditions, which helps genetic analysis. The developmental process from a single-celled spore to a multicellular body can be observed directly in detail. As a model organism, molecular techniques for M. polymorpha are well developed; for example, simple and efficient protocols of Agrobacterium-mediated transformation have been established. Based on them, various strategies for molecular genetics, such as introduction of reporter constructs, overexpression, gene silencing and targeted gene modification, are available. Herein, we describe the technologies and resources for reverse and forward genetics in M. polymorpha, which offer an excellent experimental platform to study the evolution and diversity of regulatory systems in land plants.

  6. Quantitative management techniques in dietetics: improving practice through technology transfer.

    PubMed

    Brown, D M; Hoover, L W

    1988-12-01

    A content analysis of articles appearing chronologically in the Journal of The American Dietetic Association since its inception in 1925 reveals the breadth and depth of management practice in the dietetic profession. This historical review highlights the introduction, demonstration, and adoption of management tools and techniques in the profession, with particular emphasis on quantitative management science techniques. Seven classifications of management science techniques were used for the content analysis. Although applications of forecasting, simulation, linear programming, and queuing models have been reported in the Journal, a gap is evident between the demonstration of management science techniques and operational use of these techniques in dietetic practice. Dietetic researchers, practitioners, and educators have vital roles in facilitating the transfer of quantitative management science technology into operational dietetic practice. Assessment of the state-of-the-art of dietetic management practice relative to proven quantitative management science techniques reveals the need for improved technology transfer to enhance professional ability in both tactical and strategic decision making.

  7. Improved internal control for molecular diagnosis assays.

    PubMed

    Vinayagamoorthy, T; Maryanski, Danielle; Vinayagamoorthy, Dilanthi; Hay, Katie S L; Yo, Jacob; Carter, Mark; Wiegel, Joseph

    2015-01-01

    The two principal determining steps in molecular diagnosis are the amplification and the identification steps. Accuracy of DNA amplification is primarily determined by the annealing sequence of the PCR primer to the analyte DNA. Accuracy for identification is determined either by the annealing region of a labelled probe for the real time PCR analysis, or the annealing of a sequencing primer for DNA sequencing analysis, that binds to the respective analyte (amplicon). Presently, housekeeping genes (Beta globin, GAPDH) are used in molecular diagnosis to verify that the PCR conditions are optimum, and are thus known as amplification controls [1-4]. Although these genes have been useful as amplification controls, they lack the true definition of an internal control because the primers and annealing conditions are not identical to the analyte being assayed. This may result in a false negative report [5]. The IC-Code platform technology described here provides a true internal control where the internal control and analyte share identical PCR primers annealing sequences for the amplification step and identical sequencing primer annealing sequence for the identification step. •The analyte and internal control have the same PCR and sequencing annealing sequences.•This method assures for little or no false negatives and false positives due to the method's design of using identical annealing conditions for the internal control and analyte, and by using DNA sequencing analysis for the identification step of the analyte, respectively.•This method also allows for a set lower limit of detection to be used by varying the amount of internal control used in the assay.

  8. Improving "lab-on-a-chip" techniques using biomedical nanotechnology: a review.

    PubMed

    Gorjikhah, Fatemeh; Davaran, Soodabeh; Salehi, Roya; Bakhtiari, Mohsen; Hasanzadeh, Arash; Panahi, Yunes; Emamverdy, Masumeh; Akbarzadeh, Abolfazl

    2016-11-01

    Nanotechnology and its applications in biomedical sciences principally in molecular nanodiagnostics are known as nanomolecular diagnostics, which provides new options for clinical nanodiagnostic techniques. Molecular nanodiagnostics are a critical role in the development of personalized medicine, which features point-of care performance of diagnostic procedure. This can to check patients at point-of-care facilities or in remote or resource-poor locations, therefore reducing checking time from days to minutes. In this review, applications of nanotechnology suited to biomedicine are discussed in two main class: biomedical applications for use inside (such as drugs, diagnostic techniques, prostheses, and implants) and outside the body (such as "lab-on-a-chip" techniques). A lab-on-a-chip (LOC) is a tool that incorporates numerous laboratory tasks onto a small device, usually only millimeters or centimeters in size. Finally, are discussed the applications of biomedical nanotechnology in improving "lab-on-a-chip" techniques.

  9. Improved spatial resolution in PET scanners using sampling techniques

    PubMed Central

    Surti, Suleman; Scheuermann, Ryan; Werner, Matthew E.; Karp, Joel S.

    2009-01-01

    Increased focus towards improved detector spatial resolution in PET has led to the use of smaller crystals in some form of light sharing detector design. In this work we evaluate two sampling techniques that can be applied during calibrations for pixelated detector designs in order to improve the reconstructed spatial resolution. The inter-crystal positioning technique utilizes sub-sampling in the crystal flood map to better sample the Compton scatter events in the detector. The Compton scatter rejection technique, on the other hand, rejects those events that are located further from individual crystal centers in the flood map. We performed Monte Carlo simulations followed by measurements on two whole-body scanners for point source data. The simulations and measurements were performed for scanners using scintillators with Zeff ranging from 46.9 to 63 for LaBr3 and LYSO, respectively. Our results show that near the center of the scanner, inter-crystal positioning technique leads to a gain of about 0.5-mm in reconstructed spatial resolution (FWHM) for both scanner designs. In a small animal LYSO scanner the resolution improves from 1.9-mm to 1.6-mm with the inter-crystal technique. The Compton scatter rejection technique shows higher gains in spatial resolution but at the cost of reduction in scanner sensitivity. The inter-crystal positioning technique represents a modest acquisition software modification for an improvement in spatial resolution, but at a cost of potentially longer data correction and reconstruction times. The Compton scatter rejection technique, while also requiring a modest acquisition software change with no increased data correction and reconstruction times, will be useful in applications where the scanner sensitivity is very high and larger improvements in spatial resolution are desirable. PMID:19779586

  10. Molecular Techniques for Detection, Species Differentiation, and Phylogenetic Analysis of Microsporidia

    PubMed Central

    Franzen, Caspar; Müller, Andreas

    1999-01-01

    Microsporidia are obligate intracellular protozoan parasites that infect a broad range of vertebrates and invertebrates. These parasites are now recognized as one of the most common pathogens in human immunodeficiency virus-infected patients. For most patients with infectious diseases, microbiological isolation and identification techniques offer the most rapid and specific determination of the etiologic agent. This is not a suitable procedure for microsporidia, which are obligate intracellular parasites requiring cell culture systems for growth. Therefore, the diagnosis of microsporidiosis currently depends on morphological demonstration of the organisms themselves. Although the diagnosis of microsporidiosis and identification of microsporidia by light microscopy have greatly improved during the last few years, species differentiation by these techniques is usually impossible and transmission electron microscopy may be necessary. Immunfluorescent-staining techniques have been developed for species differentiation of microsporidia, but the antibodies used in these procedures are available only at research laboratories at present. During the last 10 years, the detection of infectious disease agents has begun to include the use of nucleic acid-based technologies. Diagnosis of infection caused by parasitic organisms is the last field of clinical microbiology to incorporate these techniques and molecular techniques (e.g., PCR and hybridization assays) have recently been developed for the detection, species differentiation, and phylogenetic analysis of microsporidia. In this paper we review human microsporidial infections and describe and discuss these newly developed molecular techniques. PMID:10194459

  11. Improved techniques for thermomechanical testing in support of deformation modeling

    NASA Technical Reports Server (NTRS)

    Castelli, Michael G.; Ellis, John R.

    1992-01-01

    The feasibility of generating precise thermomechanical deformation data to support constitutive model development was investigated. Here, the requirement is for experimental data that is free from anomalies caused by less than ideal equipment and procedures. A series of exploratory tests conducted on Hastelloy X showed that generally accepted techniques for strain controlled tests were lacking in at least three areas. Specifically, problems were encountered with specimen stability, thermal strain compensation, and temperature/mechanical strain phasing. The source of these difficulties was identified and improved thermomechanical testing techniques to correct them were developed. These goals were achieved by developing improved procedures for measuring and controlling thermal gradients and by designing a specimen specifically for thermomechanical testing. In addition, innovative control strategies were developed to correctly proportion and phase the thermal and mechanical components of strain. Subsequently, the improved techniques were used to generate deformation data for Hastelloy X over the temperature range, 200 to 1000 C.

  12. Comparison and improvement of color-based image retrieval techniques

    NASA Astrophysics Data System (ADS)

    Zhang, Yujin; Liu, Zhong W.; He, Yun

    1997-12-01

    With the increasing popularity of image manipulation with contents, many color-based image retrieval techniques have been proposed in the literature. A systematic and comparative study of 8 representative techniques is first presented in this paper, which uses a database of 200 images of flags and trademarks. These techniques are determined to cover the variations of the color models used, of the characteristic color features employed and of the distance measures calculated for judging the similarity of color images. The results of this comparative study are presented both by the list of retrieved images for subjective visual inspection and by the retrieving ratios computed for objective judgement. All of them show that the cumulative histogram based techniques using Euclidean distance measures in two perception related color spaces give best results among the 8 techniques under consideration. Started from the best performed techniques, works toward further improving their retrieving capability are then carried on and this has resulted 2 new techniques which use local cumulative histograms. The new techniques have been tested by using a database of 400 images of real flowers which are quite complicated in color contents. Some satisfactory results, compared to that obtained by using existing cumulative histogram based techniques are obtained and presented.

  13. Improved expanding ring technique for determining dynamic material properties.

    PubMed

    Liang, M Z; Li, X Y; Qin, J G; Lu, F Y

    2013-06-01

    An improved expanding ring experimental technique has been described to determine dynamic material properties under conditions approximating uniform one-dimensional tensile loading. There are mainly explosive expanding ring technique and electromagnetic expanding ring technique currently, for which exist many limitations in practical applications. The work reported herein is an attempt to overcome this difficulty by lateral efficiency loading produced by projectile, made of low-density material, impacting the same material filling. The lateral efficiency loading is a convenient and effective method, which allows materials to be in uniform uniaxial stress conditions at a high stress rate. The procedure is illustrated by experiments performed on 1100-0 aluminum rings.

  14. New implantation techniques for improved solar cell junctions

    NASA Technical Reports Server (NTRS)

    Spitzer, M. B.; Bunker, S. N.

    1982-01-01

    Ion implantation techniques offering improved cell performance and reduced cost have been studied. These techniques include non-mass-analyzed phosphorus implantation, argon implantation gettering, and low temperature boron annealing. It is found that cells produced by non-mass-analyzed implantation perform as well as mass-analyzed controls, and that the cell performance is largely independent of process parameters. A study of argon implantation gettering shows no improvement over non-gettered controls. Results of low temperature boron annealing experiments are presented.

  15. Improving word learning in children using an errorless technique.

    PubMed

    Warmington, Meesha; Hitch, Graham J; Gathercole, Susan E

    2013-03-01

    The current experiment examined the relative advantage of an errorless learning technique over an errorful one in the acquisition of novel names for unfamiliar objects in typically developing children aged between 7 and 9 years. Errorless learning led to significantly better learning than did errorful learning. Processing speed and vocabulary predicted unique significant variance in errorful learning but not errorless learning, suggesting a possible locus for the errorless advantage. Errorless methods may provide a suitable basis not only for improving language learning but also for improving classroom learning and identifying children who will benefit from this technique. Copyright © 2012 Elsevier Inc. All rights reserved.

  16. New implantation techniques for improved solar cell junctions

    NASA Technical Reports Server (NTRS)

    Spitzer, M. B.; Bunker, S. N.

    1982-01-01

    Ion implantation techniques offering improved cell performance and reduced cost have been studied. These techniques include non-mass-analyzed phosphorus implantation, argon implantation gettering, and low temperature boron annealing. It is found that cells produced by non-mass-analyzed implantation perform as well as mass-analyzed controls, and that the cell performance is largely independent of process parameters. A study of argon implantation gettering shows no improvement over non-gettered controls. Results of low temperature boron annealing experiments are presented.

  17. Improving molecular testing and personalized medicine in non-small-cell lung cancer in Ontario.

    PubMed

    Lim, C; Sekhon, H S; Cutz, J C; Hwang, D M; Kamel-Reid, S; Carter, R F; Santos, G da Cunha; Waddell, T; Binnie, M; Patel, M; Paul, N; Chung, T; Brade, A; El-Maraghi, R; Sit, C; Tsao, M S; Leighl, N B

    2017-04-01

    Although molecular testing has become standard in managing advanced nonsquamous non-small-cell lung cancer (nsclc), most patients undergo minimally invasive procedures, and the diagnostic tumour specimens available for testing are usually limited. A knowledge translation initiative to educate diagnostic specialists about sampling techniques and laboratory processes was undertaken to improve the uptake and application of molecular testing in advanced lung cancer. A multidisciplinary panel of physician experts including pathologists, respirologists, interventional thoracic radiologists, thoracic surgeons, medical oncologists, and radiation oncologists developed a specialty-specific education program, adapting international clinical guidelines to the local Ontario context. Expert recommendations from the program are reported here. Panel experts agreed that specialists procuring samples for lung cancer diagnosis should choose biopsy techniques that maximize tumour cellularity, and that conservation strategies to maximize tissue for molecular testing should be used in tissue processing. The timeliness of molecular reporting can be improved by pathologist-initiated reflex testing upon confirmation of nonsquamous nsclc and by prompt transportation of specimens to designated molecular diagnostic centres. To coordinate timely molecular testing and optimal treatment, collaboration and communication between all clinicians involved in diagnosing patients with advanced lung cancer are mandatory. Knowledge transfer to diagnostic lung cancer specialists could potentially improve molecular testing and treatment for advanced lung cancer patients.

  18. Improving molecular testing and personalized medicine in non-small-cell lung cancer in Ontario

    PubMed Central

    Lim, C.; Sekhon, H.S.; Cutz, J.C.; Hwang, D.M.; Kamel-Reid, S.; Carter, R.F.; Santos, G. da Cunha; Waddell, T.; Binnie, M.; Patel, M.; Paul, N.; Chung, T.; Brade, A.; El-Maraghi, R.; Sit, C.; Tsao, M.S.; Leighl, N.B.

    2017-01-01

    Background Although molecular testing has become standard in managing advanced nonsquamous non-small-cell lung cancer (nsclc), most patients undergo minimally invasive procedures, and the diagnostic tumour specimens available for testing are usually limited. A knowledge translation initiative to educate diagnostic specialists about sampling techniques and laboratory processes was undertaken to improve the uptake and application of molecular testing in advanced lung cancer. Methods A multidisciplinary panel of physician experts including pathologists, respirologists, interventional thoracic radiologists, thoracic surgeons, medical oncologists, and radiation oncologists developed a specialty-specific education program, adapting international clinical guidelines to the local Ontario context. Expert recommendations from the program are reported here. Results Panel experts agreed that specialists procuring samples for lung cancer diagnosis should choose biopsy techniques that maximize tumour cellularity, and that conservation strategies to maximize tissue for molecular testing should be used in tissue processing. The timeliness of molecular reporting can be improved by pathologist-initiated reflex testing upon confirmation of nonsquamous nsclc and by prompt transportation of specimens to designated molecular diagnostic centres. To coordinate timely molecular testing and optimal treatment, collaboration and communication between all clinicians involved in diagnosing patients with advanced lung cancer are mandatory. Conclusions Knowledge transfer to diagnostic lung cancer specialists could potentially improve molecular testing and treatment for advanced lung cancer patients. PMID:28490924

  19. New technologies and techniques to improve adenoma detection in colonoscopy

    PubMed Central

    Bond, Ashley; Sarkar, Sanchoy

    2015-01-01

    Adenoma detection rate (ADR) is a key component of colonoscopy quality assessment, with a direct link between itself and future mortality from colorectal cancer. There are a number of potential factors, both modifiable and non-modifiable that can impact upon ADR. As methods, understanding and technologies advance, so should our ability to improve ADRs, and thus, reduce colorectal cancer mortality. This article will review new technologies and techniques that improve ADR, both in terms of the endoscopes themselves and adjuncts to current systems. In particular it focuses on effective techniques and behaviours, developments in image enhancement, advancement in endoscope design and developments in accessories that may improve ADR. It also highlights the key role that continued medical education plays in improving the quality of colonoscopy and thus ADR. The review aims to present a balanced summary of the evidence currently available and does not propose to serve as a guideline. PMID:26265990

  20. Small fenestra stapedectomy technique: reducing risk and improving hearing.

    PubMed

    Bailey, H A; Pappas, J J; Graham, S S

    1983-10-01

    During the past 25 years many variations have emerged in stapedectomy, most of which centered around either a change in the prosthesis itself or in the type of oval window seal. The small fenestra stapedectomy technique (SFT) represents a change in surgical procedure rather than in prosthetic design. This technique offers the opportunity to improve hearing results while reducing risks in stapedectomy surgery. Four areas of significant improvement are seen in patients in whom the SFT was used: (1) improved hearing in the high frequencies of 2000, 4000, and 8000 Hz, (2) improved speech discrimination scores, (3) a significant reduction in the number of reported vestibular complaints, and (4) a reduction in the number of serious postoperative sensorineural hearing losses.

  1. How Students Learn: Improving Teaching Techniques for Business Discipline Courses

    ERIC Educational Resources Information Center

    Cluskey, Bob; Elbeck, Matt; Hill, Kathy L.; Strupeck, Dave

    2011-01-01

    The focus of this paper is to familiarize business discipline faculty with cognitive psychology theories of how students learn together with teaching techniques to assist and improve student learning. Student learning can be defined as the outcome from the retrieval (free recall) of desired information. Student learning occurs in two processes.…

  2. Quantitative analysis of genomic element interactions by molecular colony technique.

    PubMed

    Gavrilov, Alexey A; Chetverina, Helena V; Chermnykh, Elina S; Razin, Sergey V; Chetverin, Alexander B

    2014-03-01

    Distant genomic elements were found to interact within the folded eukaryotic genome. However, the used experimental approach (chromosome conformation capture, 3C) enables neither determination of the percentage of cells in which the interactions occur nor demonstration of simultaneous interaction of >2 genomic elements. Each of the above can be done using in-gel replication of interacting DNA segments, the technique reported here. Chromatin fragments released from formaldehyde-cross-linked cells by sodium dodecyl sulfate extraction and sonication are distributed in a polyacrylamide gel layer followed by amplification of selected test regions directly in the gel by multiplex polymerase chain reaction. The fragments that have been cross-linked and separate fragments give rise to multi- and monocomponent molecular colonies, respectively, which can be distinguished and counted. Using in-gel replication of interacting DNA segments, we demonstrate that in the material from mouse erythroid cells, the majority of fragments containing the promoters of active β-globin genes and their remote enhancers do not form complexes stable enough to survive sodium dodecyl sulfate extraction and sonication. This indicates that either these elements do not interact directly in the majority of cells at a given time moment, or the formed DNA-protein complex cannot be stabilized by formaldehyde cross-linking.

  3. Mechanical Properties of Nanostructured Materials Determined Through Molecular Modeling Techniques

    NASA Technical Reports Server (NTRS)

    Clancy, Thomas C.; Gates, Thomas S.

    2005-01-01

    The potential for gains in material properties over conventional materials has motivated an effort to develop novel nanostructured materials for aerospace applications. These novel materials typically consist of a polymer matrix reinforced with particles on the nanometer length scale. In this study, molecular modeling is used to construct fully atomistic models of a carbon nanotube embedded in an epoxy polymer matrix. Functionalization of the nanotube which consists of the introduction of direct chemical bonding between the polymer matrix and the nanotube, hence providing a load transfer mechanism, is systematically varied. The relative effectiveness of functionalization in a nanostructured material may depend on a variety of factors related to the details of the chemical bonding and the polymer structure at the nanotube-polymer interface. The objective of this modeling is to determine what influence the details of functionalization of the carbon nanotube with the polymer matrix has on the resulting mechanical properties. By considering a range of degree of functionalization, the structure-property relationships of these materials is examined and mechanical properties of these models are calculated using standard techniques.

  4. [Etiologic diagnosis in meningitis and encephalitis molecular biology techniques].

    PubMed

    Conca, Natalia; Santolaya, María Elena; Farfan, Mauricio J; Cofré, Fernanda; Vergara, Alejandra; Salazar, Liliana; Torres, Juan Pablo

    2016-01-01

    The aetiological study of infections of the central nervous system has traditionally been performed using bacterial cultures and, more recently, using polymerase chain reaction (PCR) for herpes simplex virus (HSV). Bacterial cultures may not have good performance, especially in the context of patients who have received antibiotics prior to sampling, and a request for HSV only by PCR reduces the information to only one aetiological agent. The aim of this study is to determine the infectious causes of meningitis and encephalitis, using traditional microbiology and molecular biology to improve the aetiological diagnosis of these diseases. A prospective study was conducted on 19 patients with suspected meningitis, admitted to the Luis Calvo Mackenna Hospital in Santiago, Chile, from March 1, 2011 to March 30, 2012. After obtaining informed consent, the CSF samples underwent cytochemical study, conventional culture, multiplex PCR for the major producing bacterial meningitis (N. meningitidis, S. pneumoniae, H. influenzae), real-time single PCR for HSV-1 and 2, VZV, EBV, CMV, HHV-6 and enterovirus. Clinical and epidemiological data were also collected from the clinical records. Of the 19 patients analysed, 2 were diagnosed by conventional methods and 7 by adding molecular biology (increase to 37%). Three patients had meningitis due to S. pneumoniae, one due to Enterobacter cloacae, 2 patients meningoencephalitis HSV-1, and one VZV meningitis. The addition of PCR to conventional diagnostic methods in CNS infections increases the probability of finding the causal agent. This allows a more adequate, timely and rational management of the disease. Copyright © 2014. Publicado por Elsevier España, S.L.U.

  5. Computer aid molecular design based on meta-heuristics techniques

    NASA Astrophysics Data System (ADS)

    Rusu, T.; Bulacovschi, V.

    One of the challenges in modern chemistry is the problem of designing new molecules with desired properties. The traditional approach to this problem are usually expensive and time-consuming iterative process with the scientist or engineer hypothesizing a compound, synthesizing the material, testing for desired properties, and redesigning the candidate if the desired properties are not met. In the last years, a lot of scientists have reached to the conclusion that the artificial intelligence methods can improve/facilitate the design of new macromolecules with desired properties. One of the challenges in computer aid macromolecular design is to avoid local minima. Our paper present the use of meta-heuristics techniques that can solve this problem.

  6. Improved Differential Evolution with Shrinking Space Technique for Constrained Optimization

    NASA Astrophysics Data System (ADS)

    Fu, Chunming; Xu, Yadong; Jiang, Chao; Han, Xu; Huang, Zhiliang

    2017-05-01

    Most of the current evolutionary algorithms for constrained optimization algorithm are low computational efficiency. In order to improve efficiency, an improved differential evolution with shrinking space technique and adaptive trade-off model, named ATMDE, is proposed to solve constrained optimization problems. The proposed ATMDE algorithm employs an improved differential evolution as the search optimizer to generate new offspring individuals into evolutionary population. For the constraints, the adaptive trade-off model as one of the most important constraint-handling techniques is employed to select better individuals to retain into the next population, which could effectively handle multiple constraints. Then the shrinking space technique is designed to shrink the search region according to feedback information in order to improve computational efficiency without losing accuracy. The improved DE algorithm introduces three different mutant strategies to generate different offspring into evolutionary population. Moreover, a new mutant strategy called "DE/rand/best/1" is constructed to generate new individuals according to the feasibility proportion of current population. Finally, the effectiveness of the proposed method is verified by a suite of benchmark functions and practical engineering problems. This research presents a constrained evolutionary algorithm with high efficiency and accuracy for constrained optimization problems.

  7. Interventions to improve inhaler technique for people with asthma.

    PubMed

    Normansell, Rebecca; Kew, Kayleigh M; Mathioudakis, Alexander G

    2017-03-13

    Asthma is a common chronic disease worldwide. Inhalers are often prescribed to help control asthma symptoms, improve quality of life and reduce the risk of exacerbations or flare-ups. However, evidence suggests that many people with asthma do not use their inhaler correctly. It is therefore important to evaluate whether interventions aimed specifically at improving technique are effective and safe, and whether use of these interventions translates into improved clinical outcomes. To assess the impact of interventions to improve inhaler technique on clinical outcomes and safety in adults and children with asthma. We searched the Cochrane Airways Trials Register, which contains records compiled from multiple electronic and handsearched resources. We also searched trial registries and reference lists of primary studies. We conducted the most recent search on 23 November 2016. We included studies comparing a group of adults or children with asthma receiving an inhaler technique intervention versus a group receiving a control or alternative intervention. We included parallel and cluster-randomised trials of any duration conducted in any setting, and planned to include only the first phase of any cross-over trials identified. We included studies reported as full-text articles, those published as abstracts only and unpublished data. Two review authors screened the search results for eligible studies. We extracted outcome data, assessed risk of bias in duplicate and resolved discrepancies by involving another review author. We grouped studies making similar comparisons by consensus (e.g. all those comparing enhanced inhaler technique education vs usual care) and conducted meta-analyses only if treatments, participants and the underlying clinical question were similar enough for pooling to make sense. We analysed dichotomous data as odds ratios, and continuous data as mean differences or standardised mean differences, all with random-effects models. We described skewed data

  8. Applications of process improvement techniques to improve workflow in abdominal imaging.

    PubMed

    Tamm, Eric Peter

    2016-03-01

    Major changes in the management and funding of healthcare are underway that will markedly change the way radiology studies will be reimbursed. The result will be the need to deliver radiology services in a highly efficient manner while maintaining quality. The science of process improvement provides a practical approach to improve the processes utilized in radiology. This article will address in a step-by-step manner how to implement process improvement techniques to improve workflow in abdominal imaging.

  9. An improved coding technique for image encryption and key management

    NASA Astrophysics Data System (ADS)

    Wu, Xu; Ma, Jie; Hu, Jiasheng

    2005-02-01

    An improved chaotic algorithm for image encryption on the basis of conventional chaotic encryption algorithm is proposed. Two keys are presented in our technique. One is called private key, which is fixed and protected in the system. The other is named assistant key, which is public and transferred with the encrypted image together. For different original image, different assistant key should be chosen so that one could get different encrypted key. The updated encryption algorithm not only can resist a known-plaintext attack, but also offers an effective solution for key management. The analyses and the computer simulations show that the security is improved greatly, and can be easily realized with hardware.

  10. Digital subtraction angiography: principles and pitfalls of image improvement techniques.

    PubMed

    Levin, D C; Schapiro, R M; Boxt, L M; Dunham, L; Harrington, D P; Ergun, D L

    1984-09-01

    The technology of imaging methods in digital subtraction angiography (DSA) is discussed in detail. Areas covered include function of the video camera in both interlaced and sequential scan modes, digitization by the analog-to-digital converter, logarithmic signal processing, dose rates, and acquisition of images using frame integration and pulsed-sequential techniques. Also discussed are various methods of improving image content and quality by both hardware and software modifications. These include the development of larger image intensifiers, larger matrices, video camera improvements, reregistration, hybrid subtraction, matched filtering, recursive filtering, DSA tomography, and edge enhancement.

  11. Improving range resolution with a frequency-hopping technique

    NASA Technical Reports Server (NTRS)

    Stitt, G. R.; Bowhill, S. A.

    1986-01-01

    Range resolution of a conventional pulsed Doppler radar is determined by the scattering volume defined by the transmitted pulse shape. To increase the resolution, the length of the pulse must be reduced. Reducing the pulse length also reduces the transmitted power and hense the signal to noise ratio unless the peak power capability of the transmitter is greatly increased. Improved range resolution may also be attained through the use of various pulse coding methods, but such methods are sometimes difficult to implement from a hardware standpoint. The frequency-hopping (F-H) technique described increases the range resolution of pulse Doppler MST (mesosphere stratosphere troposphere) radar without the need for extensive modifications to the radar transmitter. This technique consists of sending a repeated sequence of pulses, each pulse in the sequence being transmitted at a unique radio frequency that is under the control of a microcomputer. This technique is discussed along with other radar parameters.

  12. Improvement of modal scaling factors using mass additive technique

    NASA Technical Reports Server (NTRS)

    Zhang, Qiang; Allemang, Randall J.; Wei, Max L.; Brown, David L.

    1987-01-01

    A general investigation into the improvement of modal scaling factors of an experimental modal model using additive technique is discussed. Data base required by the proposed method consists of an experimental modal model (a set of complex eigenvalues and eigenvectors) of the original structure and a corresponding set of complex eigenvalues of the mass-added structure. Three analytical methods,i.e., first order and second order perturbation methods, and local eigenvalue modification technique, are proposed to predict the improved modal scaling factors. Difficulties encountered in scaling closely spaced modes are discussed. Methods to compute the necessary rotational modal vectors at the mass additive points are also proposed to increase the accuracy of the analytical prediction.

  13. New and Improved Techniques for the Study of Pathogenic Fungi.

    PubMed

    Cairns, Timothy C; Studholme, David J; Talbot, Nicholas J; Haynes, Ken

    2016-01-01

    Fungal pathogens pose serious threats to human, plant, and ecosystem health. Improved diagnostics and antifungal strategies are therefore urgently required. Here, we review recent developments in online bioinformatic tools and associated interactive data archives, which enable sophisticated comparative genomics and functional analysis of fungal pathogens in silico. Additionally, we highlight cutting-edge experimental techniques, including conditional expression systems, recyclable markers, RNA interference, genome editing, compound screens, infection models, and robotic automation, which are promising to revolutionize the study of both human and plant pathogenic fungi. These novel techniques will allow vital knowledge gaps to be addressed with regard to the evolution of virulence, host-pathogen interactions and antifungal drug therapies in both the clinic and agriculture. This, in turn, will enable delivery of improved diagnosis and durable disease-control strategies.

  14. Improvements to the enzyme-developed radial immunodiffusion technique.

    PubMed

    Vidal, José

    2002-12-15

    An enzyme-developed radial immunodiffusion technique, previously known as the diffusion-in-gel enzyme-linked immunosorbent assay (DIG-ELISA), has been improved in two ways: (a) antibody-containing spots have been made larger and more distinct by revealing them with a mixture of hydrogen peroxide, 3,3'-diaminobenzidine and nickel, and further intensification of the ensuing spots with silver; (b) the reliability of the method has been enhanced by chemically coupling the antigen to a layer of a polyamino acid (poly(lysine, phenylalanine)) adsorbed to the bottom of the polystyrene petri dish. The usefulness of the improved technique is illustrated by reference to the measurement of serum concentrations of IgM and IgG, and in the assessment of antibody levels against a particulate antigen (erythrocytes).

  15. Tumor functional and molecular imaging utilizing ultrasound and ultrasound-mediated optical techniques.

    PubMed

    Yuan, Baohong; Rychak, Joshua

    2013-02-01

    Tumor functional and molecular imaging has significantly contributed to cancer preclinical research and clinical applications. Among typical imaging modalities, ultrasonic and optical techniques are two commonly used methods; both share several common features such as cost efficiency, absence of ionizing radiation, relatively inexpensive contrast agents, and comparable maximum-imaging depth. Ultrasonic and optical techniques are also complementary in imaging resolution, molecular sensitivity, and imaging space (vascular and extravascular). The marriage between ultrasonic and optical techniques takes advantages of both techniques. This review introduces tumor functional and molecular imaging using microbubble-based ultrasound and ultrasound-mediated optical imaging techniques.

  16. Algorithmic improvements to an exact region-filling technique

    NASA Astrophysics Data System (ADS)

    Elias Fabris, Antonio; Ramos Batista, Valério

    2015-09-01

    We present many algorithmic improvements in our early region filling technique, which in a previous publication was already proved to be correct for all connected digital pictures. Ours is an integer-only method that also finds all interior points of any given digital picture by displaying and storing them in a locating matrix. Our filling/locating program is applicable both in computer graphics and image processing.

  17. Molecular Genetics Techniques to Develop New Treatments for Brain Cancers

    SciTech Connect

    Fox, Jacob; Fathallan-Shaykh, Hassan

    2006-09-22

    The objectives of this report are: (1) to devise novel molecular gene therapies for malignant brain tumors, (2) advance our understanding of the immune system in the central nervous system; and (3) apply genomics to find molecular probes to diagnose brain tumors, predict prognosis, biological behavior and their response to treatment.

  18. Somatic Embryogenesis: Still a Relevant Technique in Citrus Improvement.

    PubMed

    Omar, Ahmad A; Dutt, Manjul; Gmitter, Frederick G; Grosser, Jude W

    2016-01-01

    The genus Citrus contains numerous fresh and processed fruit cultivars that are economically important worldwide. New cultivars are needed to battle industry threatening diseases and to create new marketing opportunities. Citrus improvement by conventional methods alone has many limitations that can be overcome by applications of emerging biotechnologies, generally requiring cell to plant regeneration. Many citrus genotypes are amenable to somatic embryogenesis, which became a key regeneration pathway in many experimental approaches to cultivar improvement. This chapter provides a brief history of plant somatic embryogenesis with focus on citrus, followed by a discussion of proven applications in biotechnology-facilitated citrus improvement techniques, such as somatic hybridization, somatic cybridization, genetic transformation, and the exploitation of somaclonal variation. Finally, two important new protocols that feature plant regeneration via somatic embryogenesis are provided: protoplast transformation and Agrobacterium-mediated transformation of embryogenic cell suspension cultures.

  19. Mass spectrometric techniques for characterizing low-molecular-weight resins used as paint varnishes.

    PubMed

    Bonaduce, I; Colombini, M P; Degano, I; Di Girolamo, F; La Nasa, J; Modugno, F; Orsini, S

    2013-01-01

    The molecular structure of three low-molecular-weight resins used as paint varnishes has been characterized by use of an approach based on three different mass spectrometric techniques. We investigated the ketone resin MS2A, the aldehyde resin Laropal A81, and the hydrocarbon resin Regalrez 1094, now commonly used in restoration. To date, the molecular structures of these resins have not been completely elucidated. To improve current knowledge of the chemical composition of these materials, information obtained by gas chromatography-mass spectrometry (GC/MS), pyrolysis-gas chromatography-mass spectrometry (Py/GC/MS), and electrospray ionization mass spectrometry (ESI-Q-ToF) was combined. Analysis, in solution, of the whole polymeric fraction of the resins by flow-injection ESI-Q-ToF, and of the non-polymeric fraction by GC-MS, enabled us to identify previously unreported features of the polymer structures. In addition, the Py-GC/MS profiles that we obtained will help to enhance the databases currently available in the literature. The proposed approach can be extended to other low-molecular-weight resins used as varnishes in conservation.

  20. CELLULAR, BIOCHEMICAL, AND MOLECULAR TECHNIQUES IN DEVELOPMENTAL TOXICOLOGY

    EPA Science Inventory

    Cellular, molecular and biochemical approaches vastly expand the possibilities for revealing the underlying mechanisms of developmental toxicity. The increasing interest in embryonic development as a model system for the study of gene expression has resulted in a cornucopia of i...

  1. Effective colonoscopy training techniques: strategies to improve patient outcomes

    PubMed Central

    Papanikolaou, Ioannis S; Karatzas, Pantelis S; Varytimiadis, Lazaros T; Tsigaridas, Athanasios; Galanopoulos, Michail; Viazis, Nikos; Karamanolis, Dimitrios G

    2016-01-01

    Colonoscopy has substantially evolved during the last 20 years and many different training techniques have been developed in order to improve the performance of endoscopists. The most known are mechanical simulators, virtual reality simulators, computer-simulating endoscopy, magnetic endoscopic imaging, and composite and explanted animal organ simulators. Current literature generally indicates that the use of simulators improves performance of endoscopists and enhances safety of patients, especially during the initial phase of training. Moreover, newer endoscopes and imaging techniques such as high-definition colonoscopes, chromocolonoscopy with dyes spraying, and third-eye retroscope have been incorporated in everyday practice, offering better visualization of the colon and detection of polyps. Despite the abundance of these different technological features, training devices are not widely used and no official guideline or specified training algorithm or technique for lower gastrointestinal endoscopy has been evolved. In this review, we present the most important training methods currently available and evaluate these using existing literature. We also try to propose a training algorithm for novice endoscopists. PMID:27099542

  2. Effective colonoscopy training techniques: strategies to improve patient outcomes.

    PubMed

    Papanikolaou, Ioannis S; Karatzas, Pantelis S; Varytimiadis, Lazaros T; Tsigaridas, Athanasios; Galanopoulos, Michail; Viazis, Nikos; Karamanolis, Dimitrios G

    2016-01-01

    Colonoscopy has substantially evolved during the last 20 years and many different training techniques have been developed in order to improve the performance of endoscopists. The most known are mechanical simulators, virtual reality simulators, computer-simulating endoscopy, magnetic endoscopic imaging, and composite and explanted animal organ simulators. Current literature generally indicates that the use of simulators improves performance of endoscopists and enhances safety of patients, especially during the initial phase of training. Moreover, newer endoscopes and imaging techniques such as high-definition colonoscopes, chromocolonoscopy with dyes spraying, and third-eye retroscope have been incorporated in everyday practice, offering better visualization of the colon and detection of polyps. Despite the abundance of these different technological features, training devices are not widely used and no official guideline or specified training algorithm or technique for lower gastrointestinal endoscopy has been evolved. In this review, we present the most important training methods currently available and evaluate these using existing literature. We also try to propose a training algorithm for novice endoscopists.

  3. Improving the embryo implantation via novel molecular targets.

    PubMed

    Li, Jingjie; Liang, Xiaoyan; Chen, Zijiang

    2013-07-01

    With the development of modern assisted reproductive technology(ART), the treatment of infertility and the pregnant outcome by ART have been significantly improved. However, implantation failure, particularly the unexplained repeated implantation failure (RIF), is still the unsolved and principal problem to affect the outcome of ART. The completed embryo, the receptive uterus and a series of precisely controlled molecular events between the blastocyst and endometrium are all indispensable for the success of implantation. Thus, deep insight into the molecular mechanisms that impact the endometrial receptivity and embryo implantation is an effective way to improve the implantation rate. Here the novel molecular targets and biomarkers have been reviewed that are reported and proved during more recent years in the aspects of ion channels, aquaporins, long noncoding RNAs and microRNAs, kruppel like factors, metabolism related molecules and the endogenous retroviruses. Evaluation of implantation markers may help clinicians to predict pregnancy outcome and detect occult implantation deficiency. Moreover, these novel molecular targets are expected to apply to the clinical practice from bench to bedside and improve the implantation efficiency in ART and natural conception.

  4. A novel pretreatment method combining sealing technique with direct injection technique applied for improving biosafety.

    PubMed

    Wang, Xinyu; Gao, Jing-Lin; Du, Chaohui; An, Jing; Li, MengJiao; Ma, Haiyan; Zhang, Lina; Jiang, Ye

    2017-01-01

    People today have a stronger interest in the risk of biosafety in clinical bioanalysis. A safe, simple, effective method of preparation is needed urgently. To improve biosafety of clinical analysis, we used antiviral drugs of adefovir and tenofovir as model drugs and developed a safe pretreatment method combining sealing technique with direct injection technique. The inter- and intraday precision (RSD %) of the method were <4%, and the extraction recoveries ranged from 99.4 to 100.7%. Meanwhile, the results showed that standard solution could be used to prepare calibration curve instead of spiking plasma, acquiring more accuracy result. Compared with traditional methods, the novel method not only improved biosecurity of the pretreatment method significantly, but also achieved several advantages including higher precision, favorable sensitivity and satisfactory recovery. With these highly practical and desirable characteristics, the novel method may become a feasible platform in bioanalysis.

  5. Strain mapping accuracy improvement using super-resolution techniques.

    PubMed

    Bárcena-González, G; Guerrero-Lebrero, M P; Guerrero, E; Fernández-Reyes, D; González, D; Mayoral, A; Utrilla, A D; Ulloa, J M; Galindo, P L

    2016-04-01

    Super-resolution (SR) software-based techniques aim at generating a final image by combining several noisy frames with lower resolution from the same scene. A comparative study on high-resolution high-angle annular dark field images of InAs/GaAs QDs has been carried out in order to evaluate the performance of the SR technique. The obtained SR images present enhanced resolution and higher signal-to-noise (SNR) ratio and sharpness regarding the experimental images. In addition, SR is also applied in the field of strain analysis using digital image processing applications such as geometrical phase analysis and peak pairs analysis. The precision of the strain mappings can be improved when SR methodologies are applied to experimental images. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

  6. LEAN SIX SIGMA TECHNIQUES TO IMPROVE OPHTHALMOLOGY CLINIC EFFICIENCY.

    PubMed

    Ciulla, Thomas A; Tatikonda, Mohan V; ElMaraghi, Yehya A; Hussain, Rehan M; Hill, Amanda L; Clary, Julie M; Hattab, Eyas

    2017-07-18

    Ophthalmologists serve an increasing volume of a growing elderly population undergoing increasingly complex outpatient medical care, including extensive diagnostic testing and treatment. The resulting prolonged patient visit times ("patient flow times") limit quality, patient and employee satisfaction, and represent waste. Lean Six Sigma process improvement was used in a vitreoretinal practice to decrease patient flow time, demonstrating that this approach can yield significant improvement in health care. Process flow maps were created to determine the most common care pathways within clinic. Three months' visits from the electronic medical record system, which tracks patient task times at each process step in the office were collected. Care tasks and care pathways consuming the greatest time and variation were identified and modified. Follow-up analysis from 6 weeks' visits was conducted to assess improvement. Nearly all patients took one of five paths through the office. Patient flow was redesigned to reduce waiting room time by having staff members immediately start patients into one of those five paths; staffing was adjusted to address high demand tasks, and scheduling was optimized around derived predictors of patient flow times. Follow-up analysis revealed a statistically significant decline in mean patient flow time by 18% and inpatient flow time SD by 4.6%. Patient and employee satisfaction scores improved. Manufacturing industry techniques, such as Lean and Six Sigma, can be used to improve patient care, minimize waste, and enhance patient and staff satisfaction in outpatient clinics.

  7. Improved agarose gel electrophoresis method and molecular mass calculation for high molecular mass hyaluronan.

    PubMed

    Cowman, Mary K; Chen, Cherry C; Pandya, Monika; Yuan, Han; Ramkishun, Dianne; LoBello, Jaclyn; Bhilocha, Shardul; Russell-Puleri, Sparkle; Skendaj, Eraldi; Mijovic, Jovan; Jing, Wei

    2011-10-01

    The molecular mass of the polysaccharide hyaluronan (HA) is an important determinant of its biological activity and physicochemical properties. One method currently used for the analysis of the molecular mass distribution of an HA sample is gel electrophoresis. In the current work, an improved agarose gel electrophoresis method for analysis of high molecular mass HA is presented and validated. HA mobility in 0.5% agarose minigels was found to be linearly related to the logarithm of molecular mass in the range from approximately 200 to 6000 kDa. A sample load of 2.5 μg for polydisperse HA samples was employed. Densitometric scanning of stained gels allowed analysis of the range of molecular masses present in the sample as well as calculation of weight-average and number-average values. The method was validated for a polydisperse HA sample with a weight-average molecular mass of approximately 2000 kDa. Excellent agreement was found between the weight-average molecular mass determined by electrophoresis and that determined by rheological measurement of the solution viscosity. The revised method was then used to show that heating solutions of HA at 100°C, followed by various cooling procedures, had no effect on the HA molecular mass distribution.

  8. New metrology techniques improve the production of silicon diffractive optics

    NASA Astrophysics Data System (ADS)

    Brooks, Cynthia B.; Gully-Santiago, Michael; Grigas, Michelle; Jaffe, Daniel T.

    2014-07-01

    Silicon immersion gratings and grisms offer significant advantages in compactness and performance over frontsurface gratings and over grisms made from lower-index materials. At the same time, the high refractive index of Si (3.4) leads to very stringent constraints on the allowable groove position errors, typically rms < 20 nm over 100 mm and repetitive error of <5 nm amplitude. For both types of devices, we produce grooves in silicon using photolithography, plasma etching, and wet etching. To date, producers have used contact photolithography to pattern UV sensitive photoresist as the initial processing step, then transferred this pattern to a layer of silicon nitride that, in turn, serves as a hard mask during the wet etching of grooves into silicon. For each step of the groove production, we have used new and sensitive techniques to determine the contribution of that step to the phase non-uniformity. Armed with an understanding of the errors and their origins, we could then implement process controls for each step. The plasma uniformity was improved for the silicon nitride mask etch process and the phase contribution of the plasma etch step was measured. We then used grayscale lithography, a technique in which the photoresist is deliberately underexposed, to measure large-scale nonuniformities in the UV exposure system to an accuracy of 3-5%, allowing us to make corrections to the optical alignment. Additionally, we used a new multiple-exposure technique combined with laser interferometry to measure the relationship between UV exposure dose and line edge shift. From these data we predict the contribution of the etching and photolithographic steps to phase error of the grating surface. These measurements indicate that the errors introduced during the exposure step dominate the contributions of all the other processing steps. This paper presents the techniques used to quantify individual process contributions to phase errors and steps that were taken to improve

  9. Enhanced sampling techniques in molecular dynamics simulations of biological systems.

    PubMed

    Bernardi, Rafael C; Melo, Marcelo C R; Schulten, Klaus

    2015-05-01

    Molecular dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014 Elsevier B.V. All rights reserved.

  10. Improved Techniques for Endoscopic Mucosal Resection (EMR) in Colorectal Adenoma

    PubMed Central

    Sold, Moritz; Kähler, Georg

    2014-01-01

    Summary Background Endoscopic therapy of colorectal adenomas and early cancers is a standard method. Besides oncological criteria, the method is limited by polyp location, size, and texture. Method Based on the current literature, technical modifications and developments in endoscopic mucosal resection are described. Results Numerous approaches exist to improve the conditions of resection, including optimisation of mucosal elevation and modification of techniques, tools, and devices. Conclusion Endoscopic therapy of sessile and flat colorectal polyps remains a challenge. Some of the presented modifications can help to address this challenge. PMID:26286120

  11. Restricted environmental stimulation technique improves human performance: rifle marksmanship.

    PubMed

    Barabasz, A; Barabasz, M; Bauman, J

    1993-06-01

    This study controlled for relaxation and guided imagery confounds noted in much previous research on enhancement of human performance using the restricted environmental stimulation technique (REST). Dry flotation REST was used where subjects lay ("floated") on a salt-water-filled bladder in a sound-attenuated, light-free chamber. 9 men and 3 women in a rifle marksmanship training course, exposed to dry-flotation REST, showed significantly higher rifle marksmanship scores than the university students who as matched controls were exposed to relaxation (9 men and 3 women). Further, only the former showed a significant pre- to posttest improvement in scores, which suggests REST's positive effects on marksmanship go beyond the induction of relaxation by hypnosis. The results support hypotheses summarized in 1982 by Barabasz regarding potentiation by REST of internally generated imagery and subsequent improvement observed in a nonREST posttest environment.

  12. Molecular alignment and orientation with a hybrid Raman scattering technique

    NASA Astrophysics Data System (ADS)

    Bustard, Philip J.; Lausten, R.; Sussman, Benjamin J.

    2012-11-01

    We demonstrate a scheme for the preparation of molecular alignment and angular momentum orientation using a hybrid combination of two limits of Raman scattering. First a weak, impulsive pump pulse initializes the system via the nonresonant dynamic Stark effect. Then, having overcome the influence of the vacuum fluctuations, an amplification pulse selectively enhances the initial coherences by transient stimulated Raman scattering, generating alignment and angular momentum orientation of molecular hydrogen. The amplitude and phase of the resulting coherent dynamics are experimentally probed, indicating an amplification factor of 4.5. An analytic theory is developed to model the dynamics.

  13. Historical shoreline mapping (I): improving techniques and reducing positioning errors

    USGS Publications Warehouse

    Thieler, E. Robert; Danforth, William W.

    1994-01-01

    A critical need exists among coastal researchers and policy-makers for a precise method to obtain shoreline positions from historical maps and aerial photographs. A number of methods that vary widely in approach and accuracy have been developed to meet this need. None of the existing methods, however, address the entire range of cartographic and photogrammetric techniques required for accurate coastal mapping. Thus, their application to many typical shoreline mapping problems is limited. In addition, no shoreline mapping technique provides an adequate basis for quantifying the many errors inherent in shoreline mapping using maps and air photos. As a result, current assessments of errors in air photo mapping techniques generally (and falsely) assume that errors in shoreline positions are represented by the sum of a series of worst-case assumptions about digitizer operator resolution and ground control accuracy. These assessments also ignore altogether other errors that commonly approach ground distances of 10 m. This paper provides a conceptual and analytical framework for improved methods of extracting geographic data from maps and aerial photographs. We also present a new approach to shoreline mapping using air photos that revises and extends a number of photogrammetric techniques. These techniques include (1) developing spatially and temporally overlapping control networks for large groups of photos; (2) digitizing air photos for use in shoreline mapping; (3) preprocessing digitized photos to remove lens distortion and film deformation effects; (4) simultaneous aerotriangulation of large groups of spatially and temporally overlapping photos; and (5) using a single-ray intersection technique to determine geographic shoreline coordinates and express the horizontal and vertical error associated with a given digitized shoreline. As long as historical maps and air photos are used in studies of shoreline change, there will be a considerable amount of error (on the

  14. Enhanced Sampling Techniques in Molecular Dynamics Simulations of Biological Systems

    PubMed Central

    Bernardi, Rafael C.; Melo, Marcelo C. R.; Schulten, Klaus

    2014-01-01

    Background Molecular Dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. Scope of review In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. Major Conclusions Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. General Significance Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. PMID:25450171

  15. The Use of Molecular Techniques at Hazardous Waste Sites

    EPA Science Inventory

    It is clear that typical protocols used for soil analysis would certainly fail to adequately interrogate ground-water treatment systems unless they were substantially modified. The modifications found necessary to compensate for the low biomass include molecular tools and techniq...

  16. The Use of Molecular Techniques at Hazardous Waste Sites

    EPA Science Inventory

    It is clear that typical protocols used for soil analysis would certainly fail to adequately interrogate ground-water treatment systems unless they were substantially modified. The modifications found necessary to compensate for the low biomass include molecular tools and techniq...

  17. Lidar signal-to-noise ratio improvements: Considerations and techniques

    NASA Astrophysics Data System (ADS)

    Hassebo, Yasser Y.

    The primary objective of this study is to improve lidar signal-to-noise ratio (SNR) and hence extend attainable lidar ranges through reduction of the sky background noise (BGP), which dominates other sources of noise in daytime operations. This is particularly important for Raman lidar techniques where the Raman backscattered signal of interest is relatively weak compared with the elastic backscatter lidars. Two approaches for reduction of sky background noise are considered: (1) Improvements in lidar SNR by optimization of the design of the lidar receiver were examined by a series of simulations. This part of the research concentrated on biaxial lidar systems, where overlap between laser beam and receiver field of view (FOV) is an important aspect of noise considerations. The first optimized design evolved is a wedge shaped aperture. While this design has the virtue of greatly reducing background light, it is difficult to implement practically, requiring both changes in area and position with lidar range. A second more practical approach, which preserves some of the advantages of the wedge design, was also evolved. This uses a smaller area circular aperture optimally located in the image plane for desired ranges. Simulated numerical results for a biaxial lidar have shown that the best receiver parameters selection is one using a small circular aperture (field stop) with a small telescope focal length f, to ensure the minimum FOV that accepts all return signals over the entire lidar range while at the same time minimizing detected BGP and hence maximizing lidar SNR and attainable lidar ranges. The improvement in lidar SNR was up to 18%. (2) A polarization selection technique was implemented to reduce sky background signal for linearly polarized monostatic elastic backscatter lidar measurements. The technique takes advantage of naturally occurring polarization properties in scattered sky light, and then ensures that both the lidar transmitter and receiver track and

  18. Improving face image extraction by using deep learning technique

    NASA Astrophysics Data System (ADS)

    Xue, Zhiyun; Antani, Sameer; Long, L. R.; Demner-Fushman, Dina; Thoma, George R.

    2016-03-01

    The National Library of Medicine (NLM) has made a collection of over a 1.2 million research articles containing 3.2 million figure images searchable using the Open-iSM multimodal (text+image) search engine. Many images are visible light photographs, some of which are images containing faces ("face images"). Some of these face images are acquired in unconstrained settings, while others are studio photos. To extract the face regions in the images, we first applied one of the most widely-used face detectors, a pre-trained Viola-Jones detector implemented in Matlab and OpenCV. The Viola-Jones detector was trained for unconstrained face image detection, but the results for the NLM database included many false positives, which resulted in a very low precision. To improve this performance, we applied a deep learning technique, which reduced the number of false positives and as a result, the detection precision was improved significantly. (For example, the classification accuracy for identifying whether the face regions output by this Viola- Jones detector are true positives or not in a test set is about 96%.) By combining these two techniques (Viola-Jones and deep learning) we were able to increase the system precision considerably, while avoiding the need to manually construct a large training set by manual delineation of the face regions.

  19. Improved Infrastucture for Cdms and JPL Molecular Spectroscopy Catalogues

    NASA Astrophysics Data System (ADS)

    Endres, Christian; Schlemmer, Stephan; Drouin, Brian; Pearson, John; Müller, Holger S. P.; Schilke, P.; Stutzki, Jürgen

    2014-06-01

    Over the past years a new infrastructure for atomic and molecular databases has been developed within the framework of the Virtual Atomic and Molecular Data Centre (VAMDC). Standards for the representation of atomic and molecular data as well as a set of protocols have been established which allow now to retrieve data from various databases through one portal and to combine the data easily. Apart from spectroscopic databases such as the Cologne Database for Molecular Spectroscopy (CDMS), the Jet Propulsion Laboratory microwave, millimeter and submillimeter spectral line catalogue (JPL) and the HITRAN database, various databases on molecular collisions (BASECOL, KIDA) and reactions (UMIST) are connected. Together with other groups within the VAMDC consortium we are working on common user tools to simplify the access for new customers and to tailor data requests for users with specified needs. This comprises in particular tools to support the analysis of complex observational data obtained with the ALMA telescope. In this presentation requests to CDMS and JPL will be used to explain the basic concepts and the tools which are provided by VAMDC. In addition a new portal to CDMS will be presented which has a number of new features, in particular meaningful quantum numbers, references linked to data points, access to state energies and improved documentation. Fit files are accessible for download and queries to other databases are possible.

  20. Microfluidic derivatisation technique for determination of gaseous molecular iodine with GC-MS.

    PubMed

    Pang, Xiaobing; Carpenter, Lucy J; Lewis, Alastair C

    2015-05-01

    Gaseous molecular iodine (I2) is an important source of reactive iodine in the marine atmosphere, but the sources of I2 are not well understood due to the lack of an easily accessible, sensitive and robust technique for analysis. In this study a microfluidic derivatisation technique combined with GC-MS has been developed to measure gaseous I2. Good linearity in the range of 0.2-416 ppb and low detection limits varying from 6 to 25 ppt for different derivatisation reagents have been achieved, which is a substantial improvement in sensitivity compared with the spectrophotometric method (detection limit of 1.20 ppb) in our previous study [L.J. Carpenter, S.M. MacDonald, M.D. Shaw, R. Kumar, R.W. Saunders, R. Parthipan, J. Wilson, J.M.C. Plane, Nature Geoscience, 6 (2013) 108-111]. The microfluidic technique was employed to quantify I2 produced from the heterogeneous reactions of potassium iodide solution and ozone. Good agreement was observed between the results of the microfluidic technique and the simulation of a coupled surface water-air kinetic model in the amount of I2 produced on the ozonolysis of iodide solutions. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

  1. Improved LWR Cladding Performance by EPD Surface Modification Technique

    SciTech Connect

    Corradini, Michael; Sridharan, Kumar

    2012-11-26

    This project will utilize the electro-phoretic deposition technique (EPD) in conjunction with nanofluids to deposit oxide coatings on prototypic zirconium alloy cladding surfaces. After demonstrating that this surface modification is reproducible and robust, the team will subject the modified surface to boiling and corrosion tests to characterize the improved nucleate boiling behavior and superior corrosion performance. The scope of work consists of the following three tasks: The first task will employ the EPD surface modification technique to coat the surface of a prototypic set of zirconium alloy cladding tube materials (e.g. Zircaloy and advanced alloys such as M5) with a micron-thick layer of zirconium oxide nanoparticles. The team will characterize the modified surface for uniformity using optical microscopy and scanning-electron microscopy, and for robustness using standard hardness measurements. After zirconium alloy cladding samples have been prepared and characterized using the EPD technique, the team will begin a set of boiling experiments to measure the heat transfer coefficient and critical heat flux (CHF) limit for each prepared sample and its control sample. This work will provide a relative comparison of the heat transfer performance for each alloy and the surface modification technique employed. As the boiling heat transfer experiments begin, the team will also begin corrosion tests for these zirconium alloy samples using a water corrosion test loop that can mimic light water reactor (LWR) operational environments. They will perform extended corrosion tests on the surface-modified zirconium alloy samples and control samples to examine the robustness of the modified surface, as well as the effect on surface oxidation

  2. Improving human object recognition performance using video enhancement techniques

    NASA Astrophysics Data System (ADS)

    Whitman, Lucy S.; Lewis, Colin; Oakley, John P.

    2004-12-01

    Atmospheric scattering causes significant degradation in the quality of video images, particularly when imaging over long distances. The principle problem is the reduction in contrast due to scattered light. It is known that when the scattering particles are not too large compared with the imaging wavelength (i.e. Mie scattering) then high spatial resolution information may be contained within a low-contrast image. Unfortunately this information is not easily perceived by a human observer, particularly when using a standard video monitor. A secondary problem is the difficulty of achieving a sharp focus since automatic focus techniques tend to fail in such conditions. Recently several commercial colour video processing systems have become available. These systems use various techniques to improve image quality in low contrast conditions whilst retaining colour content. These systems produce improvements in subjective image quality in some situations, particularly in conditions of haze and light fog. There is also some evidence that video enhancement leads to improved ATR performance when used as a pre-processing stage. Psychological literature indicates that low contrast levels generally lead to a reduction in the performance of human observers in carrying out simple visual tasks. The aim of this paper is to present the results of an empirical study on object recognition in adverse viewing conditions. The chosen visual task was vehicle number plate recognition at long ranges (500 m and beyond). Two different commercial video enhancement systems are evaluated using the same protocol. The results show an increase in effective range with some differences between the different enhancement systems.

  3. Characterization of a Mycobacterium intracellulare Variant Strain by Molecular Techniques

    PubMed Central

    Menendez, M. C.; Palenque, E.; Navarro, M. C.; Nuñez, M. C.; Rebollo, M. J.; Garcia, M. J.

    2001-01-01

    This paper describes a Mycobacterium intracellulare variant strain causing an unusual infection. Several isolates obtained from an immunocompromised patient were identified as members of the Mycobacterium avium complex (MAC) by the commercial AccuProbe system and biochemical standard identification. Further molecular approaches were undertaken for a more accurate characterization of the bacteria. Up to seven different genomic sequences were analyzed, ranging from conserved mycobacterial genes such as 16S ribosomal DNA to MAC-specific genes such as mig (macrophage-induced gene). The results obtained identify the isolates as a variant of M. intracellulare, an example of the internal variability described for members of the MAC, particularly within that species. The application of other molecular approaches is recommended for more accurate identification of bacteria described as MAC members. PMID:11724827

  4. Characterization of a Mycobacterium intracellulare variant strain by molecular techniques.

    PubMed

    Menendez, M C; Palenque, E; Navarro, M C; Nuñez, M C; Rebollo, M J; Garcia, M J

    2001-12-01

    This paper describes a Mycobacterium intracellulare variant strain causing an unusual infection. Several isolates obtained from an immunocompromised patient were identified as members of the Mycobacterium avium complex (MAC) by the commercial AccuProbe system and biochemical standard identification. Further molecular approaches were undertaken for a more accurate characterization of the bacteria. Up to seven different genomic sequences were analyzed, ranging from conserved mycobacterial genes such as 16S ribosomal DNA to MAC-specific genes such as mig (macrophage-induced gene). The results obtained identify the isolates as a variant of M. intracellulare, an example of the internal variability described for members of the MAC, particularly within that species. The application of other molecular approaches is recommended for more accurate identification of bacteria described as MAC members.

  5. Phosphoproteomics and molecular cardiology: techniques, applications and challenges.

    PubMed

    Sun, Zeyu; Hamilton, Karyn L; Reardon, Kenneth F

    2012-09-01

    Protein phosphorylation has been widely documented as a key regulatory and signaling mechanism associated with many cardiac diseases. Recent advances in phosphoproteomic technologies such as phosphopeptide enrichment, novel mass spectrometry applications, and bioinformatic tools have resulted in high-throughput identification and quantitation of protein phosphorylation in a global manner. This review summarizes mainstream phosphoproteomic workflows and highlights the most recent applications of phosphoproteomics used in a range of molecular cardiology research.

  6. Molecular Probes in Marine Ecology: Concepts, Techniques and Applications.

    DTIC Science & Technology

    1991-08-16

    bacterial Woody Hastings: bioluminescence . 20 Wed. Paul Dunlap: The lux genes in bacteria : organization, structure, and expression. 21 Thurs. Chuck...probes for microbial identification. Ken Nealson: Taxonomy physiology and distribution of marine bioluminescent bacteria . 10 Tues. Ann Bucklin: Allozymic...cuponsored with the microbiology course, the first of these being on bioluminescence and symbiosis on July 7, and the second on molecular approaches to

  7. Protocols, practices, and the reproduction of technique in molecular biology.

    PubMed

    Lynch, Michael

    2002-06-01

    Protocols are one of the main organizational resources in molecular biology. They are written instructions that specify ingredients, equipment, and sequences of steps for making technical preparations. Some protocols are published in widely used manuals, while others are hand-written variants used by particular laboratories and individual technicians. It is widely understood, both in molecular biology and in social studies of science, that protocols do not describe exactly what practitioners do in the laboratory workplace. In social studies of science, the difference between protocols and the actual practices of doing them often is used to set up ironic contrasts between 'messy' laboratory practices and the appearance of technical order. Alternatively, in ethnomethodological studies of work, the difference is examined as a constitutive feature, both of the lived-work of doing technical projects, and of the administrative work of regulating and evaluating such projects. The present article takes its point of departure from ethnomethodology, and begins with a discussion of local problems with performing molecular biology protocols on specific occasions. The discussion then moves to particular cases in criminal law in which defense attorneys cross-examine forensic technicians and lab administrators. In these interrogations, the distinction between protocols and actual practices animates the dialogue and becomes consequential for judgments in the case at hand. The article concludes with a discussion of administrative science: the work of treating protocols and paper trails as proxies for actual 'scientific' practices.

  8. Biochemistry and Molecular Biology Techniques for Person Characterization

    ERIC Educational Resources Information Center

    Herrero, Salvador; Ivorra, Jose Luis; Garcia-Sogo, Magdalena; Martinez-Cortina, Carmen

    2008-01-01

    Using the traditional serological tests and the most novel techniques for DNA fingerprinting, forensic scientists scan different traits that vary from person to person and use the data to include or exclude suspects based on matching with the evidence obtained in a criminal case. Although the forensic application of these methods is well known,…

  9. Biochemistry and Molecular Biology Techniques for Person Characterization

    ERIC Educational Resources Information Center

    Herrero, Salvador; Ivorra, Jose Luis; Garcia-Sogo, Magdalena; Martinez-Cortina, Carmen

    2008-01-01

    Using the traditional serological tests and the most novel techniques for DNA fingerprinting, forensic scientists scan different traits that vary from person to person and use the data to include or exclude suspects based on matching with the evidence obtained in a criminal case. Although the forensic application of these methods is well known,…

  10. Thin-film growth and patterning techniques for small molecular organic compounds used in optoelectronic device applications.

    PubMed

    Biswas, Shaurjo; Shalev, Olga; Shtein, Max

    2013-01-01

    Rapid advances in research and development in organic electronics have resulted in many exciting discoveries and applications, including organic light-emitting devices for information display and illumination, solar cells, photodetectors, chemosensors, and logic. Organic optoelectronic materials are broadly classified as polymeric or small molecular. For the latter category, solvent-free deposition techniques are generally preferred to form well-defined interfaces and improve device performance. This article reviews several deposition and patterning methods for small molecular thin films and devices, including organic molecular beam deposition, vacuum thermal evaporation, organic vapor phase deposition, and organic vapor jet printing, and compares them to several other methods that have been proposed recently. We hope this review provides a compact but informative summary of the state of the art in organic device processing and addresses the various techniques' governing physical principles.

  11. Optimization techniques in molecular structure and function elucidation.

    PubMed

    Sahinidis, Nikolaos V

    2009-12-01

    This paper discusses recent optimization approaches to the protein side-chain prediction problem, protein structural alignment, and molecular structure determination from X-ray diffraction measurements. The machinery employed to solve these problems has included algorithms from linear programming, dynamic programming, combinatorial optimization, and mixed-integer nonlinear programming. Many of these problems are purely continuous in nature. Yet, to this date, they have been approached mostly via combinatorial optimization algorithms that are applied to discrete approximations. The main purpose of the paper is to offer an introduction and motivate further systems approaches to these problems.

  12. Chemical reactions on solid surfaces using molecular beam techniques

    NASA Astrophysics Data System (ADS)

    Palmer, R. L.

    1980-07-01

    Thermal energy molecular beams have been used to study chemical interactions with metal surfaces. Chemisorption of simple molecules such as H2, O2, CH4, C2Hx and CO was investigated on single and polycrystalline surfaces of Pt, Ni, Co, and Ag. Kinetic parameters and reaction mechanisms were determined for model catalytic reactions including CO and C2Hx oxidation and methanation from H2/CO mixtures. Chemical reactions of NOx with CO and D2 on Pt(111) and other surfaces have been surveyed and the kinetics of NO and O2 chemisorption have been measured. The theory of adsorption/desorption kinetics is reviewed and certain deficiencies identified.

  13. Evaluation of oesophageal transit velocity using the improved Demons technique.

    PubMed

    De Souza, Michele N; Xavier, Fernando E B; Secaf, Marie; Troncon, Luiz E A; de Oliveira, Ricardo B; Moraes, Eder R

    2016-01-01

    This paper presents a novel method to compute oesophageal transit velocity in a direct and automatized manner by the registration of scintigraphy images. A total of 36 images from nine healthy volunteers were processed. Four dynamic image series per volunteer were acquired after a minimum 8 h fast. Each acquisition was made following the ingestion of 5 ml saline labelled with about 26 MBq (700 µCi) technetium-99m phytate in a single swallow. Between the acquisitions, another two swallows of 5 ml saline were performed to clear the oesophagus. The composite acquired files were made of 240 frames of anterior and posterior views. Each frame is the accumulate count for 250 ms.At the end of acquisitions, the images were corrected for radioactive decay, the geometric mean was computed between the anterior and posterior views and the registration of a set of subsequent images was performed. Utilizing the improved Demons technique, we obtained from the deformation field the regional resultant velocity, which is directly related to the oesophagus transit velocity. The mean regional resulting velocities decreases progressively from the proximal to the distal oesophageal portions and, at the proximal portion, is virtually identical to the primary peristaltic pump typical velocity. Comparison between this parameter and 'time-activity' curves reveals consistency in velocities obtained using both methods, for the proximal portion. Application of the improved Demons technique, as an easy and automated method to evaluate velocities of oesophageal bolus transit, is feasible and seems to yield consistent data, particularly for the proximal oesophagus.

  14. X-ray Constrained Extremely Localized Molecular Orbitals: Theory and Critical Assessment of the New Technique.

    PubMed

    Genoni, Alessandro

    2013-07-09

    Following the X-ray constrained wave function approach proposed by Jayatilaka, we have devised a new technique that allows to extract molecular orbitals strictly localized on small molecular fragments from sets of experimental X-ray structure factors amplitudes. Since the novel strategy enables to obtain electron distributions that have quantum mechanical features and that can be easily interpreted in terms of traditional chemical concepts, the method can be also considered as a new useful tool for the determination and the analysis of charge densities from high-resolution X-ray experiments. In this paper, we describe in detail the theory of the new technique, which, in comparison to our preliminary work, has been improved both treating the effects of isotropic secondary extinctions and introducing a new protocol to halt the fitting procedure against the experimental X-ray scattering data. The performances of the novel strategy have been studied both in function of the basis-sets flexibility and in function of the quality of the considered crystallographic data. The tests performed on four different systems (α-glycine, l-cysteine, (aminomethyl)phosphonic acid and N-(trifluoromethyl)formamide) have shown that the achievement of good statistical agreements with the experimental measures mainly depends on the quality of the crystal structures (i.e., geometry positions and thermal parameters) used in the X-ray constrained calculations. Finally, given the reliable transferability of the obtained Extremely Localized Molecular Orbitals (ELMOs), we envisage to exploit the novel approach to construct new ELMOs databases suited to the development of linear-scaling methods for the refinement of macromolecular crystal structures.

  15. Molecular imaging with optics: primer and case for near-infrared fluorescence techniques in personalized medicine.

    PubMed

    Sevick-Muraca, Eva M; Rasmussen, John C

    2008-01-01

    We compare and contrast the development of optical molecular imaging techniques with nuclear medicine with a didactic emphasis for initiating readers into the field of molecular imaging. The nuclear imaging techniques of gamma scintigraphy, single-photon emission computed tomography, and positron emission tomography are first briefly reviewed. The molecular optical imaging techniques of bioluminescence and fluorescence using gene reporter/probes and gene reporters are described prior to introducing the governing factors of autofluorescence and excitation light leakage. The use of dual-labeled, near-infrared excitable and radio-labeled agents are described with comparative measurements between planar fluorescence and nuclear molecular imaging. The concept of time-independent and -dependent measurements is described with emphasis on integrating time-dependent measurements made in the frequency domain for 3-D tomography. Finally, we comment on the challenges and progress for translating near-infrared (NIR) molecular imaging agents for personalized medicine.

  16. Novel techniques and future directions in molecular diagnosis of malaria in resource-limited settings.

    PubMed

    Oriero, Eniyou Cheryll; Van Geertruyden, Jean-Pierre; Nwakanma, Davis C; D'Alessandro, Umberto; Jacobs, Jan

    2015-01-01

    Despite being preventable and treatable, malaria remains a global health concern with approximately 1.2 billion people at high risk of being infected, 90% of whom are in the resource-limited settings of sub-Saharan Africa. The continued decline in malaria cases globally has rekindled the possibility of elimination in certain regions. As humans constitute the main reservoir of malaria, prompt and accurate diagnosis by microscopy or rapid diagnostic tests is part not only of effective disease management but also of control measures. However, for malaria elimination, more sensitive diagnostic tools are needed to detect asymptomatic and sub-microscopic infections that contribute to transmission. Molecular techniques, which involve amplification of nucleic acids, are being developed and modified to suit this purpose. This report provides a summary of the nucleic acid amplification tests that are currently available for diagnosis of malaria, with current improvements and adaptations for use in resource-limited settings.

  17. Laboratory techniques in plant molecular biology taught with UniformMu insertion alleles of maize

    USDA-ARS?s Scientific Manuscript database

    An undergraduate course - Laboratory Techniques in Plant Molecular Biology - was organized around our research application of UniformMu insertion alleles to investigate mitochondrial functions in plant reproduction. The course objectives were to develop students’ laboratory, record keeping, bioinfor...

  18. An improved astrometric calibration technique for space debris observation

    NASA Astrophysics Data System (ADS)

    Sun, Rong-Yu; Zhao, Chang-Yin; Lu, Yao

    2016-02-01

    An optical survey is the main technique for detecting space debris. Due to the specific characteristics of observation, the pointing errors and tracking errors of the telescope as well as image degradation may be significant, which make it difficult for astrometric calibration. Here we present an improved method that corrects the pointing and tracking errors, and measures the image position precisely. The pipeline is tested on a number of CCD images obtained from a 1-m telescope administered by Xinjiang Astronomical Observatory while observing a GPS satellite. The results show that the position measurement error of the background stars is around 0.1 pixel, while the time cost for a single frame is about 7.5 s; hence the reliability and accuracy of our method are demonstrated. In addition, our method shows a versatile and feasible way to perform space debris observation utilizing non-dedicated telescopes, which means more sensors could be involved and the ability to perform surveys could be improved.

  19. Visualization techniques for improved orientation in three-dimensional echocardiography

    NASA Astrophysics Data System (ADS)

    Wolf, Ivo; de Simone, Raffaele; Hastenteufel, Mark; Mottl-Link, Sibylle; Meinzer, Hans-Peter

    2002-05-01

    Repair of a defect heart valve is of great advantage for the patient in comparison to replacement with a prosthesis. The applicability and the success of heart valve repair can be improved by an exact diagnosis of the valve's pathological modification. The best way for imaging heart valve insufficiencies is echocardiography, since it is fast, relatively cheap, can be used intraoperatively and provides information about morphology as well as blood flow. Three-dimensional echocardiography has been proven to be superior to conventional echocardiographic techniques. Although the overall structures are much better displayed by three-dimensional visualization methods, it is sometimes difficult to comprehend the orientation of the scene, since anatomical landmarks like the aortic outflow tract may be hidden by other structures. Also, such anatomical landmarks often are only partly contained in the acquired data set so that they are clearly visible in a few slices only, making them difficult to find in a three-dimensional visualization. The knowledge of the absolute orientation is of essential value for the surgeon to mentally transfer the preoperatively acquired data to the intraoperative situs. Therefore, it is desirable to have additional hints for orientation in the three-dimensional scene. We present methods that enable better and easier orientation and therefore improve the usability of three-dimensional echocardiography.

  20. Selective extraction of lamivudine in human serum and urine using molecularly imprinted polymer technique.

    PubMed

    Shekarchi, Maryam; Pourfarzib, Mojgan; Akbari-Adergani, Behrouz; Mehramizi, Ali; Javanbakht, Mehran; Dinarvand, Rassoul

    2013-07-15

    In this work, a novel technique is described for determination of lamivudine in biological fluids by molecularly imprinted polymers (MIPs) as the sample clean-up method joint with high performance liquid chromatography (HPLC). MIPs were prepared using methacrylic acid as functional monomer, ethylene glycol dimethacrylate as crosslinker, acetonitrile and tetrahydrofuran as porogen and lamivudine as the template molecule. The new imprinted polymer was used as a molecular sorbent for the separation of lamivudine from human serum and urine. Molecular recognition properties, binding capacity and selectivity of the MIPs were evaluated and the results showed that the obtained MIPs have a high affinity for lamivudine in aqueous medium. HPLC analyses showed that the extraction of lamivudine from serum and urine by MIPs had a linear calibration curve in the range of 60-700μg/L with excellent precisions of 2.73% for serum and 2.60% for urine. The limit of detection and quantization of lamivudine was 19.34 and 58.6μg/L in serum and 7.95 and 24.05μg/L in urine respectively. MIP extraction provided about 10 fold LOQ improvement in serum and 5 fold LOQ improvement in urine samples. The recoveries of lamivudine in serum and urine samples were found to be 84.2-93.5% and 82.5-90.8% respectively. Due to the high precision and accuracy, this method may be the UV-HPLC choice with MIP extraction for bioequivalence analysis of lamivudine in serum and urine.

  1. Molecular techniques in the diagnosis of deep and systemic mycosis.

    PubMed

    Springer, Jan; Einsele, Hermann; Loeffler, Juergen

    2012-01-01

    Making an early and sensitive diagnosis of invasive fungal infections in high-risk patients is mandatory, because it has major consequences on the effectiveness of antifungal therapy. Molecular assays have the potential to become the cornerstone of diagnosis, allowing for rapid, reliable detection of minute amounts of fungal DNA in various specimens at a low cost. PCR is gaining popularity as the platforms become more automated and commercially available; however, further studies are needed to explore the diagnostic value in patient subgroups (ie, children) and to define whether the underlying disease or the use of antifungal prophylaxis may influence assay results. Individualized management of high-risk patients would be desirable to integrate preemptive therapy strategies, and individual host and genetic factors. Pharmacological and epidemiological considerations should also be evaluated.

  2. Advanced techniques for constrained internal coordinate molecular dynamics.

    PubMed

    Wagner, Jeffrey R; Balaraman, Gouthaman S; Niesen, Michiel J M; Larsen, Adrien B; Jain, Abhinandan; Vaidehi, Nagarajan

    2013-04-30

    Internal coordinate molecular dynamics (ICMD) methods provide a more natural description of a protein by using bond, angle, and torsional coordinates instead of a Cartesian coordinate representation. Freezing high-frequency bonds and angles in the ICMD model gives rise to constrained ICMD (CICMD) models. There are several theoretical aspects that need to be developed to make the CICMD method robust and widely usable. In this article, we have designed a new framework for (1) initializing velocities for nonindependent CICMD coordinates, (2) efficient computation of center of mass velocity during CICMD simulations, (3) using advanced integrators such as Runge-Kutta, Lobatto, and adaptive CVODE for CICMD simulations, and (4) cancelling out the "flying ice cube effect" that sometimes arises in Nosé-Hoover dynamics. The Generalized Newton-Euler Inverse Mass Operator (GNEIMO) method is an implementation of a CICMD method that we have developed to study protein dynamics. GNEIMO allows for a hierarchy of coarse-grained simulation models based on the ability to rigidly constrain any group of atoms. In this article, we perform tests on the Lobatto and Runge-Kutta integrators to determine optimal simulation parameters. We also implement an adaptive coarse-graining tool using the GNEIMO Python interface. This tool enables the secondary structure-guided "freezing and thawing" of degrees of freedom in the molecule on the fly during molecular dynamics simulations and is shown to fold four proteins to their native topologies. With these advancements, we envision the use of the GNEIMO method in protein structure prediction, structure refinement, and in studying domain motion. Copyright © 2013 Wiley Periodicals, Inc.

  3. Applying data mining techniques to improve diagnosis in neonatal jaundice.

    PubMed

    Ferreira, Duarte; Oliveira, Abílio; Freitas, Alberto

    2012-12-07

    Hyperbilirubinemia is emerging as an increasingly common problem in newborns due to a decreasing hospital length of stay after birth. Jaundice is the most common disease of the newborn and although being benign in most cases it can lead to severe neurological consequences if poorly evaluated. In different areas of medicine, data mining has contributed to improve the results obtained with other methodologies.Hence, the aim of this study was to improve the diagnosis of neonatal jaundice with the application of data mining techniques. This study followed the different phases of the Cross Industry Standard Process for Data Mining model as its methodology.This observational study was performed at the Obstetrics Department of a central hospital (Centro Hospitalar Tâmega e Sousa--EPE), from February to March of 2011. A total of 227 healthy newborn infants with 35 or more weeks of gestation were enrolled in the study. Over 70 variables were collected and analyzed. Also, transcutaneous bilirubin levels were measured from birth to hospital discharge with maximum time intervals of 8 hours between measurements, using a noninvasive bilirubinometer.Different attribute subsets were used to train and test classification models using algorithms included in Weka data mining software, such as decision trees (J48) and neural networks (multilayer perceptron). The accuracy results were compared with the traditional methods for prediction of hyperbilirubinemia. The application of different classification algorithms to the collected data allowed predicting subsequent hyperbilirubinemia with high accuracy. In particular, at 24 hours of life of newborns, the accuracy for the prediction of hyperbilirubinemia was 89%. The best results were obtained using the following algorithms: naive Bayes, multilayer perceptron and simple logistic. The findings of our study sustain that, new approaches, such as data mining, may support medical decision, contributing to improve diagnosis in neonatal

  4. Applying data mining techniques to improve diagnosis in neonatal jaundice

    PubMed Central

    2012-01-01

    Background Hyperbilirubinemia is emerging as an increasingly common problem in newborns due to a decreasing hospital length of stay after birth. Jaundice is the most common disease of the newborn and although being benign in most cases it can lead to severe neurological consequences if poorly evaluated. In different areas of medicine, data mining has contributed to improve the results obtained with other methodologies. Hence, the aim of this study was to improve the diagnosis of neonatal jaundice with the application of data mining techniques. Methods This study followed the different phases of the Cross Industry Standard Process for Data Mining model as its methodology. This observational study was performed at the Obstetrics Department of a central hospital (Centro Hospitalar Tâmega e Sousa – EPE), from February to March of 2011. A total of 227 healthy newborn infants with 35 or more weeks of gestation were enrolled in the study. Over 70 variables were collected and analyzed. Also, transcutaneous bilirubin levels were measured from birth to hospital discharge with maximum time intervals of 8 hours between measurements, using a noninvasive bilirubinometer. Different attribute subsets were used to train and test classification models using algorithms included in Weka data mining software, such as decision trees (J48) and neural networks (multilayer perceptron). The accuracy results were compared with the traditional methods for prediction of hyperbilirubinemia. Results The application of different classification algorithms to the collected data allowed predicting subsequent hyperbilirubinemia with high accuracy. In particular, at 24 hours of life of newborns, the accuracy for the prediction of hyperbilirubinemia was 89%. The best results were obtained using the following algorithms: naive Bayes, multilayer perceptron and simple logistic. Conclusions The findings of our study sustain that, new approaches, such as data mining, may support medical decision

  5. Improved mesh based photon sampling techniques for neutron activation analysis

    SciTech Connect

    Relson, E.; Wilson, P. P. H.; Biondo, E. D.

    2013-07-01

    The design of fusion power systems requires analysis of neutron activation of large, complex volumes, and the resulting particles emitted from these volumes. Structured mesh-based discretization of these problems allows for improved modeling in these activation analysis problems. Finer discretization of these problems results in large computational costs, which drives the investigation of more efficient methods. Within an ad hoc subroutine of the Monte Carlo transport code MCNP, we implement sampling of voxels and photon energies for volumetric sources using the alias method. The alias method enables efficient sampling of a discrete probability distribution, and operates in 0(1) time, whereas the simpler direct discrete method requires 0(log(n)) time. By using the alias method, voxel sampling becomes a viable alternative to sampling space with the 0(1) approach of uniformly sampling the problem volume. Additionally, with voxel sampling it is straightforward to introduce biasing of volumetric sources, and we implement this biasing of voxels as an additional variance reduction technique that can be applied. We verify our implementation and compare the alias method, with and without biasing, to direct discrete sampling of voxels, and to uniform sampling. We study the behavior of source biasing in a second set of tests and find trends between improvements and source shape, material, and material density. Overall, however, the magnitude of improvements from source biasing appears to be limited. Future work will benefit from the implementation of efficient voxel sampling - particularly with conformal unstructured meshes where the uniform sampling approach cannot be applied. (authors)

  6. Using "Pseudomonas Putida xylE" Gene to Teach Molecular Cloning Techniques for Undergraduates

    ERIC Educational Resources Information Center

    Dong, Xu; Xin, Yi; Ye, Li; Ma, Yufang

    2009-01-01

    We have developed and implemented a serial experiment in molecular cloning laboratory course for undergraduate students majored in biotechnology. "Pseudomonas putida xylE" gene, encoding catechol 2, 3-dioxygenase, was manipulated to learn molecular biology techniques. The integration of cloning, expression, and enzyme assay gave students…

  7. Using "Pseudomonas Putida xylE" Gene to Teach Molecular Cloning Techniques for Undergraduates

    ERIC Educational Resources Information Center

    Dong, Xu; Xin, Yi; Ye, Li; Ma, Yufang

    2009-01-01

    We have developed and implemented a serial experiment in molecular cloning laboratory course for undergraduate students majored in biotechnology. "Pseudomonas putida xylE" gene, encoding catechol 2, 3-dioxygenase, was manipulated to learn molecular biology techniques. The integration of cloning, expression, and enzyme assay gave students…

  8. Techniques for studying protein trafficking and molecular motors in neurons

    PubMed Central

    Feng, Shanxi; Arnold, Don B.

    2016-01-01

    This review focuses on techniques that facilitate the visualization of protein trafficking. In the mid-1990’s the cloning of GFP allowed fluorescently tagged proteins to be expressed in cells and then visualized in real time. This advance allowed a glimpse, for the first time, of the complex system within cells for distributing proteins. It quickly became apparent, however, that time-lapse sequences of exogenously expressed GFP-labeled proteins can be difficult to interpret. Reasons for this include the relatively low signal that comes from moving proteins and high background rates from stationary proteins and other sources, as well as the difficulty of identifying the origins and destinations of specific vesicular carriers. In this review we will examine a range of techniques that have overcome these issues to varying degrees and discuss the insights into protein trafficking that they have enabled. We will concentrate on neurons, as they are highly polarized and, thus, their trafficking systems tend to be accessible for study. PMID:26800506

  9. Detecting Molecular Properties by Various Laser-Based Techniques

    SciTech Connect

    Hsin, Tse-Ming

    2007-01-01

    Four different laser-based techniques were applied to study physical and chemical characteristics of biomolecules and dye molecules. These techniques are liole burning spectroscopy, single molecule spectroscopy, time-resolved coherent anti-Stokes Raman spectroscopy and laser-induced fluorescence microscopy. Results from hole burning and single molecule spectroscopy suggested that two antenna states (C708 & C714) of photosystem I from cyanobacterium Synechocystis PCC 6803 are connected by effective energy transfer and the corresponding energy transfer time is ~6 ps. In addition, results from hole burning spectroscopy indicated that the chlorophyll dimer of the C714 state has a large distribution of the dimer geometry. Direct observation of vibrational peaks and evolution of coumarin 153 in the electronic excited state was demonstrated by using the fs/ps CARS, a variation of time-resolved coherent anti-Stokes Raman spectroscopy. In three different solvents, methanol, acetonitrile, and butanol, a vibration peak related to the stretch of the carbonyl group exhibits different relaxation dynamics. Laser-induced fluorescence microscopy, along with the biomimetic containers-liposomes, allows the measurement of the enzymatic activity of individual alkaline phosphatase from bovine intestinal mucosa without potential interferences from glass surfaces. The result showed a wide distribution of the enzyme reactivity. Protein structural variation is one of the major reasons that are responsible for this highly heterogeneous behavior.

  10. [Enhanced molecular techniques for the diagnosis of human papillomavirus infections].

    PubMed

    Ursu, Ramona Gabriela; Onofriescu, M; Nemescu, D; Iancu, Luminiţa Smaranda

    2009-01-01

    optimisation of Real Time PCR technique for quantifying oncogenic types 16 and 18 of Human Papilloma Viruses, genotyped through classic PCR, followed by hybridisation. DNA/ HPV was purified with High Pure PCR Template Preparation kit (ROCHE DIAGNOSTICS), genotyping was performed with Linear Array HPV Genotyping (ROCHE DIAGNOSTICS) and PCR reaction was realized with ABI 9700 Gold Plate System. Absolute quantification of HPV 16 and 18 was performed with Path-HPV16/18 Real-time PCR detection kit for Human Papillomavirus, 2 x Precision Mastermix kits (PrimerDesign), and the instrument used was MX3000P STRATAGENE. I. HPV genotyping was optimised through testing of 12 cervical samples, collected from patients who have signed the informed consent approved by the local Bioethical Committee. Among the tested samples, 5 were negative for any HPV type, 3 patients had unique infections with oncogenic HPV type, and 2 patients had multiple infections, with oncogenic and non-oncogenic HPV types. Negative and positive controls were validated, identical as the internal control - beta globin gene. II. Absolute quantification for HPV 16 and 18 were performed on two samples tested by the previous method. The number of viral copies was determined using the standard curves procedure, whose parameters values were between the accepted limits. We fulfilled the quality criteria for both techniques: genotyping assay and viral load quantification by Real Time PCR. This allows us to start the study for monitoring persistent infections with HPV 16 and HPV 18.

  11. Bioluminescence: a versatile technique for imaging cellular and molecular features

    PubMed Central

    Paley, Miranda A.

    2016-01-01

    Bioluminescence is a ubiquitous imaging modality for visualizing biological processes in vivo. This technique employs visible light and interfaces readily with most cell and tissue types, making it a versatile technology for preclinical studies. Here we review basic bioluminescence imaging principles, along with applications of the technology that are relevant to the medicinal chemistry community. These include noninvasive cell tracking experiments, analyses of protein function, and methods to visualize small molecule metabolites. In each section, we also discuss how bioluminescent tools have revealed insights into experimental therapies and aided drug discovery. Last, we highlight the development of new bioluminescent tools that will enable more sensitive and multi-component imaging experiments and, thus, expand our broader understanding of living systems. PMID:27594981

  12. Improving structure-based function prediction using molecular dynamics

    PubMed Central

    Glazer, Dariya S.; Radmer, Randall J.; Altman, Russ B.

    2009-01-01

    Summary The number of molecules with solved three-dimensional structure but unknown function is increasing rapidly. Particularly problematic are novel folds with little detectable similarity to molecules of known function. Experimental assays can determine the functions of such molecules, but are time-consuming and expensive. Computational approaches can identify potential functional sites; however, these approaches generally rely on single static structures and do not use information about dynamics. In fact, structural dynamics can enhance function prediction: we coupled molecular dynamics simulations with structure-based function prediction algorithms that identify Ca2+ binding sites. When applied to 11 challenging proteins, both methods showed substantial improvement in performance, revealing 22 more sites in one case and 12 more in the other, with a modest increase in apparent false positives. Thus, we show that treating molecules as dynamic entities improves the performance of structure-based function prediction methods. PMID:19604472

  13. Improved Space Surveillance Network (SSN) Scheduling using Artificial Intelligence Techniques

    NASA Astrophysics Data System (ADS)

    Stottler, D.

    There are close to 20,000 cataloged manmade objects in space, the large majority of which are not active, functioning satellites. These are tracked by phased array and mechanical radars and ground and space-based optical telescopes, collectively known as the Space Surveillance Network (SSN). A better SSN schedule of observations could, using exactly the same legacy sensor resources, improve space catalog accuracy through more complementary tracking, provide better responsiveness to real-time changes, better track small debris in low earth orbit (LEO) through efficient use of applicable sensors, efficiently track deep space (DS) frequent revisit objects, handle increased numbers of objects and new types of sensors, and take advantage of future improved communication and control to globally optimize the SSN schedule. We have developed a scheduling algorithm that takes as input the space catalog and the associated covariance matrices and produces a globally optimized schedule for each sensor site as to what objects to observe and when. This algorithm is able to schedule more observations with the same sensor resources and have those observations be more complementary, in terms of the precision with which each orbit metric is known, to produce a satellite observation schedule that, when executed, minimizes the covariances across the entire space object catalog. If used operationally, the results would be significantly increased accuracy of the space catalog with fewer lost objects with the same set of sensor resources. This approach inherently can also trade-off fewer high priority tasks against more lower-priority tasks, when there is benefit in doing so. Currently the project has completed a prototyping and feasibility study, using open source data on the SSN's sensors, that showed significant reduction in orbit metric covariances. The algorithm techniques and results will be discussed along with future directions for the research.

  14. Advanced radiation measurement techniques in diagnostic radiology and molecular imaging.

    PubMed

    Del Guerra, Alberto; Belcari, Nicola; Llacer, Gabriela Llosa; Marcatili, Sara; Moehrs, Sascha; Panetta, Daniele

    2008-01-01

    This paper reports some technological advances recently achieved in the fields of micro-CT and small animal PET instrumentation. It highlights a balance between image-quality improvement and dose reduction. Most of the recent accomplishments in these fields are due to the use of novel imaging sensors such as CMOS-based X-ray detectors and silicon photomultipliers (SiPM). Some of the research projects carried out at the University of Pisa for the development of such advanced radiation imaging technology are also described.

  15. Advanced Techniques for Constrained Internal Coordinate Molecular Dynamics

    PubMed Central

    Wagner, Jeffrey R.; Balaraman, Gouthaman S.; Niesen, Michiel J. M.; Larsen, Adrien B.; Jain, Abhinandan; Vaidehi, Nagarajan

    2013-01-01

    Internal coordinate molecular dynamics (ICMD) methods provide a more natural description of a protein by using bond, angle and torsional coordinates instead of a Cartesian coordinate representation. Freezing high frequency bonds and angles in the ICMD model gives rise to constrained ICMD (CICMD) models. There are several theoretical aspects that need to be developed in order to make the CICMD method robust and widely usable. In this paper we have designed a new framework for 1) initializing velocities for non-independent CICMD coordinates, 2) efficient computation of center of mass velocity during CICMD simulations, 3) using advanced integrators such as Runge-Kutta, Lobatto and adaptive CVODE for CICMD simulations, and 4) cancelling out the “flying ice cube effect” that sometimes arises in Nosé-Hoover dynamics. The Generalized Newton-Euler Inverse Mass Operator (GNEIMO) method is an implementation of a CICMD method that we have developed to study protein dynamics. GNEIMO allows for a hierarchy of coarse-grained simulation models based on the ability to rigidly constrain any group of atoms. In this paper, we perform tests on the Lobatto and Runge-Kutta integrators to determine optimal simulation parameters. We also implement an adaptive coarse graining tool using the GNEIMO Python interface. This tool enables the secondary structure-guided “freezing and thawing” of degrees of freedom in the molecule on the fly during MD simulations, and is shown to fold four proteins to their native topologies. With these advancements we envision the use of the GNEIMO method in protein structure prediction, structure refinement, and in studying domain motion. PMID:23345138

  16. Usefulness of molecular techniques to identify ongoing tuberculosis transmission in Saudi Arabia.

    PubMed

    Al-Hajoj, Sahal A; Mohammed, Viqaruddin K; Al-Hokail, Abdullah A

    2007-02-01

    This study represents the first time that molecular tracing techniques have been used to identify patterns of tuberculosis TB infection in Saudi Arabia. The 2 strains were isolated from a socio-economically advantage family who share a number of common facilities including a car and a driver. There are several factors that may play vital roles in on-going transmission of TB in Saudi Arabia including a high number of expatriates, the Hajj pilgrimage, and the social habits of Saudi citizens. Our sibling case series is believed to be a frequent pattern of disease transmission in this country. Control measures such as health education, active case finding, and prompt and supervised medical treatment are needed. More studies using molecular techniques are recommended to find the incidence of cross infection in Saudi Arabia. In addition, molecular techniques have to be established in all reference laboratories to help the detection of ongoing active transmission, molecular epidemiology and detect sources of infection.

  17. An Improved Fungal Mounting Technique for Nomarski Microscopy.

    ERIC Educational Resources Information Center

    Fairclough, Andrew; And Others

    1985-01-01

    Conventional sellotape techniques for fungal mounting produce interference patterns when using Normarsky microscopy. A technique is described which overcomes this problem and produces a permanent mount with a completely clear background. (Author/JN)

  18. Exploring JLA supernova data with improved flux-averaging technique

    NASA Astrophysics Data System (ADS)

    Wang, Shuang; Wen, Sixiang; Li, Miao

    2017-03-01

    In this work, we explore the cosmological consequences of the ``Joint Light-curve Analysis'' (JLA) supernova (SN) data by using an improved flux-averaging (FA) technique, in which only the type Ia supernovae (SNe Ia) at high redshift are flux-averaged. Adopting the criterion of figure of Merit (FoM) and considering six dark energy (DE) parameterizations, we search the best FA recipe that gives the tightest DE constraints in the (zcut, Δ z) plane, where zcut and Δ z are redshift cut-off and redshift interval of FA, respectively. Then, based on the best FA recipe obtained, we discuss the impacts of varying zcut and varying Δ z, revisit the evolution of SN color luminosity parameter β, and study the effects of adopting different FA recipe on parameter estimation. We find that: (1) The best FA recipe is (zcut = 0.6, Δ z=0.06), which is insensitive to a specific DE parameterization. (2) Flux-averaging JLA samples at zcut >= 0.4 will yield tighter DE constraints than the case without using FA. (3) Using FA can significantly reduce the redshift-evolution of β. (4) The best FA recipe favors a larger fractional matter density Ωm. In summary, we present an alternative method of dealing with JLA data, which can reduce the systematic uncertainties of SNe Ia and give the tighter DE constraints at the same time. Our method will be useful in the use of SNe Ia data for precision cosmology.

  19. Improved Detection Technique for Solvent Rinse Cleanliness Verification

    NASA Technical Reports Server (NTRS)

    Hornung, S. D.; Beeson, H. D.

    2001-01-01

    The NASA White Sands Test Facility (WSTF) has an ongoing effort to reduce or eliminate usage of cleaning solvents such as CFC-113 and its replacements. These solvents are used in the final clean and cleanliness verification processes for flight and ground support hardware, especially for oxygen systems where organic contaminants can pose an ignition hazard. For the final cleanliness verification in the standard process, the equivalent of one square foot of surface area of parts is rinsed with the solvent, and the final 100 mL of the rinse is captured. The amount of nonvolatile residue (NVR) in the solvent is determined by weight after the evaporation of the solvent. An improved process of sampling this rinse, developed at WSTF, requires evaporation of less than 2 mL of the solvent to make the cleanliness verification. Small amounts of the solvent are evaporated in a clean stainless steel cup, and the cleanliness of the stainless steel cup is measured using a commercially available surface quality monitor. The effectiveness of this new cleanliness verification technique was compared to the accepted NVR sampling procedures. Testing with known contaminants in solution, such as hydraulic fluid, fluorinated lubricants, and cutting and lubricating oils, was performed to establish a correlation between amount in solution and the process response. This report presents the approach and results and discusses the issues in establishing the surface quality monitor-based cleanliness verification.

  20. Improving default risk prediction using Bayesian model uncertainty techniques.

    PubMed

    Kazemi, Reza; Mosleh, Ali

    2012-11-01

    Credit risk is the potential exposure of a creditor to an obligor's failure or refusal to repay the debt in principal or interest. The potential of exposure is measured in terms of probability of default. Many models have been developed to estimate credit risk, with rating agencies dating back to the 19th century. They provide their assessment of probability of default and transition probabilities of various firms in their annual reports. Regulatory capital requirements for credit risk outlined by the Basel Committee on Banking Supervision have made it essential for banks and financial institutions to develop sophisticated models in an attempt to measure credit risk with higher accuracy. The Bayesian framework proposed in this article uses the techniques developed in physical sciences and engineering for dealing with model uncertainty and expert accuracy to obtain improved estimates of credit risk and associated uncertainties. The approach uses estimates from one or more rating agencies and incorporates their historical accuracy (past performance data) in estimating future default risk and transition probabilities. Several examples demonstrate that the proposed methodology can assess default probability with accuracy exceeding the estimations of all the individual models. Moreover, the methodology accounts for potentially significant departures from "nominal predictions" due to "upsetting events" such as the 2008 global banking crisis. © 2012 Society for Risk Analysis.

  1. Temperature and leakage aware techniques to improve cache reliability

    NASA Astrophysics Data System (ADS)

    Akaaboune, Adil

    Decreasing power consumption in small devices such as handhelds, cell phones and high-performance processors is now one of the most critical design concerns. On-chip cache memories dominate the chip area in microprocessors and thus arises the need for power efficient cache memories. Cache is the simplest cost effective method to attain high speed memory hierarchy and, its performance is extremely critical for high speed computers. Cache is used by the microprocessor for channeling the performance gap between processor and main memory (RAM) hence the memory bandwidth is frequently a bottleneck which can affect the peak throughput significantly. In the design of any cache system, the tradeoffs of area/cost, performance, power consumption, and thermal management must be taken into consideration. Previous work has mainly concentrated on performance and area/cost constraints. More recent works have focused on low power design especially for portable devices and media-processing systems, however fewer research has been done on the relationship between heat management, Leakage power and cost per die. Lately, the focus of power dissipation in the new generations of microprocessors has shifted from dynamic power to idle power, a previously underestimated form of power loss that causes battery charge to drain and shutdown too early due the waste of energy. The problem has been aggravated by the aggressive scaling of process; device level method used originally by designers to enhance performance, conserve dissipation and reduces the sizes of digital circuits that are increasingly condensed. This dissertation studies the impact of hotspots, in the cache memory, on leakage consumption and microprocessor reliability and durability. The work will first prove that by eliminating hotspots in the cache memory, leakage power will be reduced and therefore, the reliability will be improved. The second technique studied is data quality management that improves the quality of the data

  2. Molecular techniques for studying gene expression in carcinogenesis.

    PubMed

    Ahmed, Farid E

    2002-11-01

    Many genes and signaling pathways controlling cell proliferation, death, differentiation, and genomic integrity are involved in cancer development. Various methods are available for detection and quantification of messenger RNA. Older methods such as Northern blots, nuclease protection, plaque hybridization, and slot blots suffer from being inherently serial, measure a single mRNA at a time, or being difficult to automate. New techniques for analysis of gene expression include: (a) comprehensive open systems such as serial analysis of gene expression (SAGE), differential display (DD) analysis, RNA arbitrarily primer (RAP)-PCR, restriction endonucleolytic analysis of differentially expressed sequences (READS), amplified restriction fragment-length polymorphism (AFLP), total gene expression analysis (TOGA), and use of internal standard competitive template primers (CTs) in a quantitative multiplex RT-PCR method [StaRT-(PCR)], and (b) focused closed systems such as: high density cDNA filter hybridization (HDFCA) analysis, suppression subtractive hybridization (SSH), differential screening (DS), several forms of high-density cDNA arrays, or oligonucleotide chips, and tissue microarrays. Sometimes, a combination of these systems is used to enhance the sensitivity and specificity of the assays. While closed systems are excellent for the initial screening of large number of sequences, the value of the information generated is generally limited to an often arbitrarily chosen known sequence. On the other hand, only the open system platform has the potential to evaluate the expression patterns of tens of thousands of genes that have not yet been cloned or partially sequenced in a quantitative manner. A cost analysis of the most commonly used expression technologies is provided. A method for purifying tumors from surrounding stroma and normal tissue employing laser microdissection, and subsequent RNA isolation/amplification from few cells employing sensitive kits are also

  3. High molecular weight insulating polymers can improve the performance of molecular solar cells

    NASA Astrophysics Data System (ADS)

    Huang, Ye; Wen, Wen; Kramer, Edward; Bazan, Guillermo

    2014-03-01

    Solution-processed molecular semiconductors for the fabrication of solar cells have emerged as a competitive alternative to their conjugated polymer counterparts, primarily because such materials systems exhibit no batch-to-batch variability, can be purified to a greater extent and offer precisely defined chemical structures. Highest power conversion efficiencies (PCEs) have been achieved through a combination of molecular design and the application of processing methods that optimize the bulk heterojunction (BHJ) morphology. However, one finds that the methods used for controlling structural order, for example the use of high boiling point solvent additives, have been inspired by examination of the conjugated polymer literature. It stands to reason that a different class of morphology modifiers should be sought that address challenges unique to molecular films, including difficulties in obtaining thicker films and avoiding the dewetting of active photovoltaic layers. Here we show that the addition of small quantities of high molecular weight polystyrene (PS) is a very simple to use and economically viable additive that improves PCE. Remarkably, the PS spontaneously accumulates away from the electrodes as separate domains that do not interfere with charge extraction and collection or with the arrangement of the donor and acceptor domains in the BHJ blend.

  4. Nanotechnology versus other techniques in improving drug dissolution.

    PubMed

    Kwok, Philip Chi Lip; Chan, Hak-Kim

    2014-01-01

    Many newly discovered drug molecules have low aqueous solubility, which results in low bioavailability. One way to improve their dissolution is to formulate them as nanoparticles, which have high specific surface areas, consequently increasing the dissolution rate and solubility. Nanoparticles can be produced via top-down or bottom-up methods. Top-down techniques such as wet milling and high pressure homogenisation involve reducing large particles to nano-sizes. Some pharmaceutical products made by these processes have been marketed. Bottom-up methods such as precipitation and controlled droplet evaporation form nanoparticles from molecules in solution. To minimise aggregation upon drying and promote redispersion of the nanoparticles upon reconstitution or administration, hydrophilic matrix formers are added to the formulation. However, the nanoparticles will eventually agglomerate together after dispersing in the liquid and hinders dissolution. Currently there is no pharmacopoeial method specified for nanoparticles. Amongst the current dissolution apparatus available for powders, the flow-through cell has been shown to be the most suitable. Regulatory and pharmacopoeial standards should be established in the future to standardise the dissolution testing of nanoparticles. More nanoparticle formulations of new hydrophobic drugs are expected to be developed in the future with the advancement of nanotechnology. However, the agglomeration problem is inherent and difficult to overcome. Thus the benefit of dissolution enhancement often cannot be fully realised. On the other hand, chemical strategies such as modifying the parent drug molecule to form a more soluble salt form, prodrug, or cyclodextrin complexation are well established and have been shown to be effective in enhancing dissolution. Thus the value of nanoformulations needs to be interpreted in the light of their limitations. Chemical approaches should also be considered in new product development.

  5. Improved Experimental Techniques for Analyzing Nucleic Acid Transport Through Protein Nanopores in Planar Lipid Bilayers

    NASA Astrophysics Data System (ADS)

    Costa, Justin A.

    The translocation of nucleic acid polymers across cell membranes is a fundamental requirement for complex life and has greatly contributed to genomic molecular evolution. The diversity of pathways that have evolved to transport DNA and RNA across membranes include protein receptors, active and passive transporters, endocytic and pinocytic processes, and various types of nucleic acid conducting channels known as nanopores. We have developed a series of experimental techniques, collectively known as "Wicking", that greatly improves the biophysical analysis of nucleic acid transport through protein nanopores in planar lipid bilayers. We have verified the Wicking method using numerous types of classical ion channels including the well-studied chloride selective channel, CLIC1. We used the Wicking technique to reconstitute α-hemolysin and found that DNA translocation events of types A and B could be routinely observed using this method. Furthermore, measurable differences were observed in the duration of blockade events as DNA length and composition was varied, consistent with previous reports. Finally, we tested the ability of the Wicking technology to reconstitute the dsRNA transporter Sid-1. Exposure to dsRNAs of increasing length and complexity showed measurable differences in the current transitions suggesting that the charge carrier was dsRNA. However, the translocation events occurred so infrequently that a meaningful electrophysiological analysis was not possible. Alterations in the lipid composition of the bilayer had a minor effect on the frequency of translocation events but not to such a degree as to permit rigorous statistical analysis. We conclude that in many instances the Wicking method is a significant improvement to the lipid bilayer technique, but is not an optimal method for analyzing transport through Sid-1. Further refinements to the Wicking method might have future applications in high throughput DNA sequencing, DNA computation, and

  6. Functional characterisation of metal(loid) processes in planta through the integration of synchrotron techniques and plant molecular biology

    PubMed Central

    Donner, Erica; Punshon, Tracy; Guerinot, Mary Lou; Lombi, Enzo

    2013-01-01

    Functional characterisation of the genes regulating metal(loid) homeostasis in plants is a major focus of crop biofortification, phytoremediation, and food security research. This paper focuses on the potential for advancing plant metal(loid) research by combining molecular biology and synchrotron-based techniques. Recent advances in x-ray focussing optics and fluorescence detection have greatly improved the potential of synchrotron techniques for plant science research, allowing metal(loids) to be imaged in vivo in hydrated plant tissues at sub-micron resolution. Laterally resolved metal(loid) speciation can also be determined. By using molecular techniques to probe the location of gene expression and protein localisation and combining it with this synchrotron-derived data, functional information can be effectively and efficiently assigned to specific genes. This paper provides a review of the state of the art in this field, and provides examples as to how synchrotron-based methods can be combined with molecular techniques to facilitate functional characterisation of genes in planta. PMID:22200921

  7. COLD-PCR: improving the sensitivity of molecular diagnostics assays

    PubMed Central

    Milbury, Coren A; Li, Jin; Liu, Pingfang; Makrigiorgos, G Mike

    2011-01-01

    The detection of low-abundance DNA variants or mutations is of particular interest to medical diagnostics, individualized patient treatment and cancer prognosis; however, detection sensitivity for low-abundance variants is a pronounced limitation of most currently available molecular assays. We have recently developed coamplification at lower denaturation temperature-PCR (COLD-PCR) to resolve this limitation. This novel form of PCR selectively amplifies low-abundance DNA variants from mixtures of wild-type and mutant-containing (or variant-containing) sequences, irrespective of the mutation type or position on the amplicon, by using a critical denaturation temperature. The use of a lower denaturation temperature in COLD-PCR results in selective denaturation of amplicons with mutation-containing molecules within wild-type mutant heteroduplexes or with a lower melting temperature. COLD-PCR can be used in lieu of conventional PCR in several molecular applications, thus enriching the mutant fraction and improving the sensitivity of downstream mutation detection by up to 100-fold. PMID:21405967

  8. Exponential repulsion improves structural predictability of molecular docking.

    PubMed

    Bazgier, Václav; Berka, Karel; Otyepka, Michal; Banáš, Pavel

    2016-10-30

    Molecular docking is a powerful tool for theoretical prediction of the preferred conformation and orientation of small molecules within protein active sites. The obtained poses can be used for estimation of binding energies, which indicate the inhibition effect of designed inhibitors, and therefore might be used for in silico drug design. However, the evaluation of ligand binding affinity critically depends on successful prediction of the native binding mode. Contemporary docking methods are often based on scoring functions derived from molecular mechanical potentials. In such potentials, nonbonded interactions are typically represented by electrostatic interactions between atom-centered partial charges and standard 6-12 Lennard-Jones potential. Here, we present implementation and testing of a scoring function based on more physically justified exponential repulsion instead of the standard Lennard-Jones potential. We found that this scoring function significantly improved prediction of the native binding modes in proteins bearing narrow active sites such as serine proteases and kinases. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  9. Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock

    PubMed Central

    Soares, Pedro; Ermini, Luca; Thomson, Noel; Mormina, Maru; Rito, Teresa; Röhl, Arne; Salas, Antonio; Oppenheimer, Stephen; Macaulay, Vincent; Richards, Martin B.

    2009-01-01

    There is currently no calibration available for the whole human mtDNA genome, incorporating both coding and control regions. Furthermore, as several authors have pointed out recently, linear molecular clocks that incorporate selectable characters are in any case problematic. We here confirm a modest effect of purifying selection on the mtDNA coding region and propose an improved molecular clock for dating human mtDNA, based on a worldwide phylogeny of > 2000 complete mtDNA genomes and calibrating against recent evidence for the divergence time of humans and chimpanzees. We focus on a time-dependent mutation rate based on the entire mtDNA genome and supported by a neutral clock based on synonymous mutations alone. We show that the corrected rate is further corroborated by archaeological dating for the settlement of the Canary Islands and Remote Oceania and also, given certain phylogeographic assumptions, by the timing of the first modern human settlement of Europe and resettlement after the Last Glacial Maximum. The corrected rate yields an age of modern human expansion in the Americas at ∼15 kya that—unlike the uncorrected clock—matches the archaeological evidence, but continues to indicate an out-of-Africa dispersal at around 55–70 kya, 5–20 ky before any clear archaeological record, suggesting the need for archaeological research efforts focusing on this time window. We also present improved rates for the mtDNA control region, and the first comprehensive estimates of positional mutation rates for human mtDNA, which are essential for defining mutation models in phylogenetic analyses. PMID:19500773

  10. Improving molecular tools for global surveillance of measles virus.

    PubMed

    Bankamp, Bettina; Byrd-Leotis, Lauren A; Lopareva, Elena N; Woo, Gibson K S; Liu, Chunyu; Jee, Youngmee; Ahmed, Hinda; Lim, Wilina W; Ramamurty, Nalini; Mulders, Mick N; Featherstone, David; Bellini, William J; Rota, Paul A

    2013-09-01

    The genetic characterization of wild-type measles viruses plays an important role in the description of viral transmission pathways and the verification of measles elimination. The 450 nucleotides that encode the carboxyl-terminus of the nucleoprotein (N-450) are routinely sequenced for genotype analysis. The objectives of this study were to develop improved primers and controls for RT-PCR reactions used for genotyping of measles samples and to develop a method to provide a convenient, safe, and inexpensive means to distribute measles RNA for RT-PCR assays and practice panels. A newly designed, genetically defined synthetic RNA and RNA isolated from cells infected with currently circulating genotypes were used to compare the sensitivity of primer pairs in RT-PCR and nested PCR. FTA® cards loaded with lysates of measles infected cells were tested for their ability to preserve viral RNA and destroy virus infectivity. A new primer pair, MeV216/MeV214, was able to amplify N-450 from viruses representing 10 currently circulating genotypes and a genotype A vaccine strain and demonstrated 100-fold increased sensitivity compared to the previously used primer set. A nested PCR assay further increased the sensitivity of detection from patient samples. A synthetic positive control RNA was developed that produced PCR products that are distinguishable by size from PCR products amplified from clinical samples. FTA® cards completely inactivated measles virus and stabilized RNA for at least six months. These improved molecular tools will advance molecular characterization of circulating measles viruses globally and provide enhanced quality control measures. Published by Elsevier B.V.

  11. Low-mass molecular dynamics simulation: A simple and generic technique to enhance configurational sampling

    SciTech Connect

    Pang, Yuan-Ping

    2014-09-26

    Highlights: • Reducing atomic masses by 10-fold vastly improves sampling in MD simulations. • CLN025 folded in 4 of 10 × 0.5-μs MD simulations when masses were reduced by 10-fold. • CLN025 folded as early as 96.2 ns in 1 of the 4 simulations that captured folding. • CLN025 did not fold in 10 × 0.5-μs MD simulations when standard masses were used. • Low-mass MD simulation is a simple and generic sampling enhancement technique. - Abstract: CLN025 is one of the smallest fast-folding proteins. Until now it has not been reported that CLN025 can autonomously fold to its native conformation in a classical, all-atom, and isothermal–isobaric molecular dynamics (MD) simulation. This article reports the autonomous and repeated folding of CLN025 from a fully extended backbone conformation to its native conformation in explicit solvent in multiple 500-ns MD simulations at 277 K and 1 atm with the first folding event occurring as early as 66.1 ns. These simulations were accomplished by using AMBER forcefield derivatives with atomic masses reduced by 10-fold on Apple Mac Pros. By contrast, no folding event was observed when the simulations were repeated using the original AMBER forcefields of FF12SB and FF14SB. The results demonstrate that low-mass MD simulation is a simple and generic technique to enhance configurational sampling. This technique may propel autonomous folding of a wide range of miniature proteins in classical, all-atom, and isothermal–isobaric MD simulations performed on commodity computers—an important step forward in quantitative biology.

  12. Improved technique for CT-guided celiac ganglia block

    SciTech Connect

    Haaga, J.R.; Kori, S.H.; Eastwood, D.W.; Borowski, G.P.

    1984-06-01

    Celiac nerve blocks have been performed without radiologic guidance, but recently several groups have reported computed tomography (CT)-guided techniques. The authors present a new technique of CT-guided celiac nerve block using an 18 gauge Teflon catheter, which permits a test block dose and permanent alcohol block with one procedure. The results of this new technique were very encouraging. Of nine cancer patients who had the test block, seven had good pain relief; these same patients had good pain control with the permanent block. Of six patients with pancreatitis, six had good pain relief from the test block, and three had some long-term relief from the permanent block.

  13. Is liquid-based cytology the magic bullet for performing molecular techniques?

    PubMed

    Abedi-Ardekani, Behnoush; Vielh, Philippe

    2014-01-01

    The role of pathology has evolved from the first microscopic definitions of diseases by Virchow to the new concept of molecular cytopathology. The management of diseases is now a multidisciplinary approach with the translation of morphological, imagery and molecular findings to therapeutic protocols. Obtaining the most reliable diagnostic material is the essential part of the medical management of patients. Here, we try to gain a concise insight into the available data regarding the role of cytology in the application of molecular techniques, focusing on cancer cytopathology. Obtaining cytological material is now feasible by different methods, and in some cases it is the only possible approach to a lesion which is not easily accessible for tissue sampling. The methods of obtaining cytological material have evolved in recent years in parallel with rapid advances in high-throughput molecular techniques, opening new windows for the diagnosis and management of diseases. Different kinds of cytological material are reliable for the application of molecular techniques. Cytological material obtained in a liquid base has advantages such as the better preservation of cytomorphological features and the use of the remaining liquid for nucleic acid extraction even after long storage and the application of molecular methods.

  14. Molecular ultrastructure of the urothelial surface: insights from a combination of various microscopic techniques.

    PubMed

    Zupančič, Daša; Romih, Rok; Robenek, Horst; Žužek Rožman, Kristina; Samardžija, Zoran; Kostanjšek, Rok; Kreft, Mateja Erdani

    2014-11-01

    The urothelium forms the blood-urine barrier, which depends on the complex organization of transmembrane proteins, uroplakins, in the apical plasma membrane of umbrella cells. Uroplakins compose 16 nm intramembrane particles, which are assembled into urothelial plaques. Here we present an integrated survey on the molecular ultrastructure of urothelial plaques in normal umbrella cells with advanced microscopic techniques. We analyzed the ultrastructure and performed measurements of urothelial plaques in the normal mouse urothelium. We used field emission scanning electron microscopy (FESEM), atomic force microscopy (AFM), transmission electron microscopy (TEM) on immunolabeled ultrathin sections (immuno-TEM), and freeze-fracture replicas (FRIL). We performed immunolabeling of uroplakins for scanning electron microscopy (immuno-FESEM). All microscopic techniques revealed a variability of urothelial plaque diameters ranging from 332 to 1179 nm. All immunolabeling techniques confirmed the presence of uroplakins in urothelial plaques. FRIL showed the association of uroplakins with 16 nm intramembrane particles and their organization into plaques. Using different microscopic techniques and applied qualitative and quantitative evaluation, new insights into the urothelial apical surface molecular ultrastructure have emerged and may hopefully provide a timely impulse for many ongoing studies. The combination of various microscopic techniques used in this study shows how these techniques complement one another. The described advantages and disadvantages of each technique should be considered for future studies of molecular and structural membrane specializations in other cells and tissues. © 2014 Wiley Periodicals, Inc.

  15. Contemporary nucleic acid-based molecular techniques for detection, identification, and characterization of Bifidobacterium.

    PubMed

    Mianzhi, Yao; Shah, Nagendra P

    2017-03-24

    Bifidobacteria are one of the most important bacterial groups found in the gastrointestinal tract of humans. Medical and food industry researchers have focused on bifidobacteria because of their health-promoting properties. Researchers have historically relied on classic phenotypic approaches (culture and biochemical tests) for detection and identification of bifidobacteria. Those approaches still have values for the identification and detection of some bifidobacterial species, but they are often labor-intensive and time-consuming and can be problematic in differentiating closely related species. Rapid, accurate, and reliable methods for detection, identification, and characterization of bifidobacteria in a mixed bacterial population have become a major challenge. The advent of nucleic acid-based molecular techniques has significantly advanced isolation and detection of bifidobacteria. Diverse nucleic acid-based molecular techniques have been employed, including hybridization, target amplification, and fingerprinting. Certain techniques enable the detection, characterization, and identification at genus-, species-, and strains-levels, whereas others allow typing of species or strains of bifidobacteria. In this review, an overview of methodological principle, technique complexity, and application of various nucleic acid-based molecular techniques for detection, identification, and characterization of bifidobacteria is presented. Advantages and limitations of each technique are discussed, and significant findings based on particular techniques are also highlighted.

  16. New insight into biodegradation of polylactide (PLA)/clay nanocomposites using molecular ecological techniques.

    PubMed

    Sangwan, Parveen; Way, Cameron; Wu, Dong-Yang

    2009-07-07

    Novel molecular ecological techniques were used to study changes in microbial community structure and population during degradation of polylactide (PLA)/organically modified layered silicates (OMLS) nanocomposites. Cloned gene sequences belonging to members of the phyla Actinobacteria and Ascomycota comprized the most dominant groups of microorganisms during biodegradation of PLA/OMLS nanocomposites. Due to their numerical abundance, members of these microbial groups are likely to play an important role during biodegradation process. This paper presents new insights into the biodegradability of PLA/OMLS nanocomposites and highlights the importance of using novel molecular ecological techniques for in situ identification of new microorganisms involved in biodegradation of polymeric materials.

  17. Improvement of ultrasound speckle image velocimetry using image enhancement techniques.

    PubMed

    Yeom, Eunseop; Nam, Kweon-Ho; Paeng, Dong-Guk; Lee, Sang Joon

    2014-01-01

    Ultrasound-based techniques have been developed and widely used in noninvasive measurement of blood velocity. Speckle image velocimetry (SIV), which applies a cross-correlation algorithm to consecutive B-mode images of blood flow has often been employed owing to its better spatial resolution compared with conventional Doppler-based measurement techniques. The SIV technique utilizes speckles backscattered from red blood cell (RBC) aggregates as flow tracers. Hence, the intensity and size of such speckles are highly dependent on hemodynamic conditions. The grayscale intensity of speckle images varies along the radial direction of blood vessels because of the shear rate dependence of RBC aggregation. This inhomogeneous distribution of echo speckles decreases the signal-to-noise ratio (SNR) of a cross-correlation analysis and produces spurious results. In the present study, image-enhancement techniques such as contrast-limited adaptive histogram equalization (CLAHE), min/max technique, and subtraction of background image (SB) method were applied to speckle images to achieve a more accurate SIV measurement. A mechanical sector ultrasound scanner was used to obtain ultrasound speckle images from rat blood under steady and pulsatile flows. The effects of the image-enhancement techniques on SIV analysis were evaluated by comparing image intensities, velocities, and cross-correlation maps. The velocity profiles and wall shear rate (WSR) obtained from RBC suspension images were compared with the analytical solution for validation. In addition, the image-enhancement techniques were applied to in vivo measurement of blood flow in human vein. The experimental results of both in vitro and in vivo SIV measurements show that the intensity gradient in heterogeneous speckles has substantial influence on the cross-correlation analysis. The image-enhancement techniques used in this study can minimize errors encountered in ultrasound SIV measurement in which RBCs are used as flow

  18. Integrating fossils with molecular phylogenies improves inference of trait evolution.

    PubMed

    Slater, Graham J; Harmon, Luke J; Alfaro, Michael E

    2012-12-01

    Comparative biologists often attempt to draw inferences about tempo and mode in evolution by comparing the fit of evolutionary models to phylogenetic comparative data consisting of a molecular phylogeny with branch lengths and trait measurements from extant taxa. These kinds of approaches ignore historical evidence for evolutionary pattern and process contained in the fossil record. In this article, we show through simulation that incorporation of fossil information dramatically improves our ability to distinguish among models of quantitative trait evolution using comparative data. We further suggest a novel Bayesian approach that allows fossil information to be integrated even when explicit phylogenetic hypotheses are lacking for extinct representatives of extant clades. By applying this approach to a comparative dataset comprising body sizes for caniform carnivorans, we show that incorporation of fossil information not only improves ancestral state estimates relative to those derived from extant taxa alone, but also results in preference of a model of evolution with trend toward large body size over alternative models such as Brownian motion or Ornstein-Uhlenbeck processes. Our approach highlights the importance of considering fossil information when making macroevolutionary inference, and provides a way to integrate the kind of sparse fossil information that is available to most evolutionary biologists.

  19. Improving the capacity of molecular communication using enzymatic reaction cycles.

    PubMed

    Awan, Hamdan; Chou, Chun Tung

    2017-09-18

    This paper considers the capacity of a diffusion-based molecular communication link assuming the receiver uses chemical reactions. The key contribution is we show that enzymatic reaction cycles, which is a class of chemical reactions commonly found in cells consisting of a forward and a backward enzymatic reaction, can improve the capacity of the communication link. The technical difficulty in analysing enzymatic reaction cycles is that their reaction rates are nonlinear. We deal with this by assuming that the amount of certain chemicals in the enzymatic reaction cycle is large. In order to simplify the problem further, we use singular perturbation to study a particular operating regime of the enzymatic reaction cycles. This allows us to derive a closed-form expression of the channel gain. This expression suggests that we can improve the channel gain by increasing the total amount of substrate in the enzymatic reaction cycle. By using numerical calculations, we show that the effect of the enzymatic reaction cycle is to increase the channel gain and to reduce the noise, which results in a better signal-to-noise ratio and in turn a higher communication capacity. Furthermore, we show that we can increase the capacity by increasing the total amount of substrate in the enzymatic reaction cycle.

  20. Quality Improvement of Liver Ultrasound Images Using Fuzzy Techniques

    PubMed Central

    Bayani, Azadeh; Langarizadeh, Mostafa; Radmard, Amir Reza; Nejad, Ahmadreza Farzaneh

    2016-01-01

    Background: Liver ultrasound images are so common and are applied so often to diagnose diffuse liver diseases like fatty liver. However, the low quality of such images makes it difficult to analyze them and diagnose diseases. The purpose of this study, therefore, is to improve the contrast and quality of liver ultrasound images. Methods: In this study, a number of image contrast enhancement algorithms which are based on fuzzy logic were applied to liver ultrasound images - in which the view of kidney is observable - using Matlab2013b to improve the image contrast and quality which has a fuzzy definition; just like image contrast improvement algorithms using a fuzzy intensification operator, contrast improvement algorithms applying fuzzy image histogram hyperbolization, and contrast improvement algorithms by fuzzy IF-THEN rules. Results: With the measurement of Mean Squared Error and Peak Signal to Noise Ratio obtained from different images, fuzzy methods provided better results, and their implementation - compared with histogram equalization method - led both to the improvement of contrast and visual quality of images and to the improvement of liver segmentation algorithms results in images. Conclusion: Comparison of the four algorithms revealed the power of fuzzy logic in improving image contrast compared with traditional image processing algorithms. Moreover, contrast improvement algorithm based on a fuzzy intensification operator was selected as the strongest algorithm considering the measured indicators. This method can also be used in future studies on other ultrasound images for quality improvement and other image processing and analysis applications. PMID:28077898

  1. Quality Improvement of Liver Ultrasound Images Using Fuzzy Techniques.

    PubMed

    Bayani, Azadeh; Langarizadeh, Mostafa; Radmard, Amir Reza; Nejad, Ahmadreza Farzaneh

    2016-12-01

    Liver ultrasound images are so common and are applied so often to diagnose diffuse liver diseases like fatty liver. However, the low quality of such images makes it difficult to analyze them and diagnose diseases. The purpose of this study, therefore, is to improve the contrast and quality of liver ultrasound images. In this study, a number of image contrast enhancement algorithms which are based on fuzzy logic were applied to liver ultrasound images - in which the view of kidney is observable - using Matlab2013b to improve the image contrast and quality which has a fuzzy definition; just like image contrast improvement algorithms using a fuzzy intensification operator, contrast improvement algorithms applying fuzzy image histogram hyperbolization, and contrast improvement algorithms by fuzzy IF-THEN rules. With the measurement of Mean Squared Error and Peak Signal to Noise Ratio obtained from different images, fuzzy methods provided better results, and their implementation - compared with histogram equalization method - led both to the improvement of contrast and visual quality of images and to the improvement of liver segmentation algorithms results in images. Comparison of the four algorithms revealed the power of fuzzy logic in improving image contrast compared with traditional image processing algorithms. Moreover, contrast improvement algorithm based on a fuzzy intensification operator was selected as the strongest algorithm considering the measured indicators. This method can also be used in future studies on other ultrasound images for quality improvement and other image processing and analysis applications.

  2. [Molecular techniques for cyanobacteria detection at Riogrande II and La Fe water reservoirs, Colombia].

    PubMed

    Hurtado-Alarcón, Julio César; Polanía-Vorenberg, Jaime

    2014-03-01

    In lentic water bodies as reservoirs occur eutrophication processes, originated mainly from human activities (i.e. agriculture, animal exploitation). This influx of nutrients in aquatic ecosystems could promote blooms of potentially toxic cyanobacteria. The purpose of this work is to detect the presence of cyanobacteria strains in water samples, using molecular techniques to help in preventive management of reservoirs dedicated to water purification. We used two molecular techniques to detect genes implied with the synthesis of hepatotoxic microcystins from potentially toxic cyanobacteria strains, and to evaluate the molecular diversity of cyanobacteria in water samples from two high-mountain reservoirs used for purification of drinking water for the metropolitan area of Medellin, Colombia. Between 2010-2011 collections of 12 water samples were taken and DNA extraction together with PCR and DGGE analyses where carried out. We amplified 22 sequences between 250-300bp of the genes mcyA and mcyE, and these sequences were related with several strains and cyanobacteria genera accessions from NCBI-GenBank databases. Moreover, sequence amplifications of the 16S small ribosomal RNA subunit - 16S rRNA- between 400-800bp were also performed in order to use them for the DGGE technique. The amplification products of DGGE were set in polyacrilamide gel with posterior denaturing electrophoresis, and the scanned images of the gel bands were analysed with the software GelCompar II. For Riogrande II and La Fe reservoirs we found 35 and 30 different DGGE bands, respectively, as a measurement of molecular diversity in these artificial ecosystems. Here, we demonstrated the utility of two molecular techniques for the detection of genes associated with toxicity and molecular diversity of cyanobacteria in reservoirs destined for drinking water in urban centers. We recommend strongly following with periodically molecular biology studies in these ecosystems combined with limnological and

  3. Improved estimates of coordinate error for molecular replacement

    SciTech Connect

    Oeffner, Robert D.; Bunkóczi, Gábor; McCoy, Airlie J.; Read, Randy J.

    2013-11-01

    A function for estimating the effective root-mean-square deviation in coordinates between two proteins has been developed that depends on both the sequence identity and the size of the protein and is optimized for use with molecular replacement in Phaser. A top peak translation-function Z-score of over 8 is found to be a reliable metric of when molecular replacement has succeeded. The estimate of the root-mean-square deviation (r.m.s.d.) in coordinates between the model and the target is an essential parameter for calibrating likelihood functions for molecular replacement (MR). Good estimates of the r.m.s.d. lead to good estimates of the variance term in the likelihood functions, which increases signal to noise and hence success rates in the MR search. Phaser has hitherto used an estimate of the r.m.s.d. that only depends on the sequence identity between the model and target and which was not optimized for the MR likelihood functions. Variance-refinement functionality was added to Phaser to enable determination of the effective r.m.s.d. that optimized the log-likelihood gain (LLG) for a correct MR solution. Variance refinement was subsequently performed on a database of over 21 000 MR problems that sampled a range of sequence identities, protein sizes and protein fold classes. Success was monitored using the translation-function Z-score (TFZ), where a TFZ of 8 or over for the top peak was found to be a reliable indicator that MR had succeeded for these cases with one molecule in the asymmetric unit. Good estimates of the r.m.s.d. are correlated with the sequence identity and the protein size. A new estimate of the r.m.s.d. that uses these two parameters in a function optimized to fit the mean of the refined variance is implemented in Phaser and improves MR outcomes. Perturbing the initial estimate of the r.m.s.d. from the mean of the distribution in steps of standard deviations of the distribution further increases MR success rates.

  4. Improved molecular collision models for nonequilibrium rarefied gases

    NASA Astrophysics Data System (ADS)

    Parsons, Neal

    The Direct Simulation Monte Carlo (DSMC) method typically used to model thermochemical nonequilibrium rarefied gases requires accurate total collision cross sections, reaction probabilities, and molecular internal energy exchange models. However, the baseline total cross sections are often determined from extrapolations of relatively low-temperature viscosity data, reaction probabilities are defined such that experimentally determined equilibrium reaction rates are replicated, and internal energy relaxation models are phenomenological in nature. Therefore, these models have questionable validity in modeling strongly nonequilibrium gases with temperatures greater than those possible in experimental test facilities. To rectify this deficiency, the Molecular Dynamics/Quasi-Classical Trajectories (MD/QCT) method can be used to accurately compute total collision cross sections, reaction probabilities, and internal energy exchange models based on first principles for hypervelocity collision conditions. In this thesis, MD/QCT-based models were used to improve simulations of two unique nonequilibrium rarefied gas systems: the Ionian atmosphere and hypersonic shocks in Earth's atmosphere. The Jovian plasma torus flows over Io at ≈ 57 km/s, inducing high-speed collisions between atmospheric SO2 and the hypervelocity plasma's O atoms and ions. The DSMC method is well-suited to model the rarefied atmosphere, so MD/QCT studies are therefore conducted to improve DSMC collision models of the critical SO2-O collision pair. The MD/QCT trajectory simulations employed a new potential energy surface that was developed using a ReaxFF fit to a set of ab initio calculations. Compared to the MD/QCT results, the baseline DSMC models are found to significantly under-predict total cross sections, use reaction probabilities that are unrealistically high, and give unphysical internal energies above the dissociation energy for non-reacting inelastic collisions and under-predicts post

  5. Improving Examination Performance through the Clenched Fist Technique.

    ERIC Educational Resources Information Center

    Stanton, Harry E.

    1988-01-01

    The literature on the use of hypnosis in an educational setting is briefly reviewed, and a hypnotic approach involving the use of the clenched fist as a conditioned trigger to improve examination performance is described. A study of 60 high school students indicates that the approach can improve test outcomes. (TJH)

  6. Improving Examination Performance through the Clenched Fist Technique.

    ERIC Educational Resources Information Center

    Stanton, Harry E.

    1988-01-01

    The literature on the use of hypnosis in an educational setting is briefly reviewed, and a hypnotic approach involving the use of the clenched fist as a conditioned trigger to improve examination performance is described. A study of 60 high school students indicates that the approach can improve test outcomes. (TJH)

  7. Improved Cancer Therapy and Molecular Imaging with Multivalent, Multispecific Antibodies

    PubMed Central

    Rossi, Edmund A.; Chang, Chien-Hsing; Goldenberg, David M.

    2010-01-01

    Summation Antibodies are highly versatile proteins with the ability to be used to target diverse compounds, such as radionuclides for imaging and therapy, or drugs and toxins for therapy, but also can be used unconjugated to elicit therapeutically beneficial responses, usually with minimal toxicity. This update describes a new procedure for forming multivalent and/or multispecific proteins, known as the dock-and-lock (DNL) technique. Developed as a procedure for preparing bispecific antibodies capable of binding divalently to a tumor antigen and monovalently to a radiolabeled hapten-peptide for pretargeted imaging and therapy, this methodology has the flexibility to create a number of other biologic agents of therapeutic interest. A variety of constructs, based on anti-CD20 and CD22 antibodies, have been made, with results showing that multispecific antibodies have very different properties from the respective parental monospecific antibodies. The technique is not restricted to antibody combination, but other biologics, such as interferon-α2b, have been prepared. These types of constructs not only allow small biologics to be sustained in the blood longer, but also to be selectively targeted. Thus, DNL technology is a highly flexible platform that can be used to prepare many different types of agents that could further improve cancer detection and therapy. PMID:20187791

  8. Improved cancer therapy and molecular imaging with multivalent, multispecific antibodies.

    PubMed

    Sharkey, Robert M; Rossi, Edmund A; Chang, Chien-Hsing; Goldenberg, David M

    2010-02-01

    Antibodies are highly versatile proteins with the ability to be used to target diverse compounds, such as radionuclides for imaging and therapy, or drugs and toxins for therapy, but also can be used unconjugated to elicit therapeutically beneficial responses, usually with minimal toxicity. This update describes a new procedure for forming multivalent and/or multispecific proteins, known as the dock-and-lock (DNL) technique. Developed as a procedure for preparing bispecific antibodies capable of binding divalently to a tumor antigen and monovalently to a radiolabeled hapten-peptide for pretargeted imaging and therapy, this methodology has the flexibility to create a number of other biologic agents of therapeutic interest. A variety of constructs, based on anti-CD20 and CD22 antibodies, have been made, with results showing that multispecific antibodies have very different properties from the respective parental monospecific antibodies. The technique is not restricted to antibody combination, but other biologics, such as interferon-alpha2b, have been prepared. These types of constructs not only allow small biologics to be sustained in the blood longer, but also to be selectively targeted. Thus, DNL technology is a highly flexible platform that can be used to prepare many different types of agents that could further improve cancer detection and therapy.

  9. Millimeter-wave Velocity Modulation Spectroscopy as a Technique to Selectively Detect Molecular Ions

    NASA Astrophysics Data System (ADS)

    Halfen, Dewayne; Ziurys, Lucy

    2009-05-01

    Molecular ions are usually very unstable and reactive species. As a result, their spectroscopic features can be difficult to identify and distinguish from those of neutral species, which tend to be more stable and thus have stronger signals. The technique of velocity modulation allows this disadvantage to be removed. This method uses the alternating plus and minus polarity of an electric field created by an AC discharge, which also produces the molecular ions, to selectively detect the molecular ions, while eliminating the neutral features. This technique has been applied at infrared and optical wavelengths for many years with much success. Recently, we designed and built a millimeter-wave velocity modulation spectrometer, the first ever constructed. This instrument has been used to create and study multiple molecular ions, including metal-bearing molecular ions. The rotational spectrum of these species, such as TiCl^+, VCl^+, TiF^+, FeO^+, FeCO^+, and SiCl^+, has been investigated with this new machine in our laboratory. Results of these studies along with a description of the velocity modulation technique and instrument will be presented.

  10. Improved Techniques for Automatic Chord Recognition from Music Audio Signals

    ERIC Educational Resources Information Center

    Cho, Taemin

    2014-01-01

    This thesis is concerned with the development of techniques that facilitate the effective implementation of capable automatic chord transcription from music audio signals. Since chord transcriptions can capture many important aspects of music, they are useful for a wide variety of music applications and also useful for people who learn and perform…

  11. Integrative Teaching Techniques and Improvement of German Speaking Learning Skills

    ERIC Educational Resources Information Center

    Litualy, Samuel Jusuf

    2016-01-01

    This research ist a Quasi-Experimental research which only applied to one group without comparison group. It aims to prove whether the implementation of integrative teaching technique has influenced the speaking skill of the students in German Education Study Program of FKIP, Pattimura University. The research was held in the German Education…

  12. Improving Word Learning in Children Using an Errorless Technique

    ERIC Educational Resources Information Center

    Warmington, Meesha; Hitch, Graham J.; Gathercole, Susan E.

    2013-01-01

    The current experiment examined the relative advantage of an errorless learning technique over an errorful one in the acquisition of novel names for unfamiliar objects in typically developing children aged between 7 and 9 years. Errorless learning led to significantly better learning than did errorful learning. Processing speed and vocabulary…

  13. Improved wax mold technique forms complex passages in solid structures

    NASA Technical Reports Server (NTRS)

    Hellbaum, R. F.; Page, A. D.; Phillips, A. R.

    1971-01-01

    Low-cost fabricating technique produces minute, complex air passages in fluidic devices. Air jet interactions in these function as electronic and electromechanical control systems. Wax cores are fabricated without distortion by two-wax process using nonsoluble pattern-wax and water-soluble wax. Significant steps in fabrication process are discussed.

  14. Improving Exam Performance with the Clenched Fist Technique.

    ERIC Educational Resources Information Center

    Stanton, Harry E.

    1988-01-01

    The use of one specific ego-enhancing hypnotic approach, a technique that employs a conditioned "trigger," the clenched fist, to facilitate the changing of troublesome emotional states, is described. Forty first-year university students were the subjects of the study. (MLW)

  15. Do Classroom Assessment Techniques (CATs) Improve Student Learning?

    ERIC Educational Resources Information Center

    Cottell, Philip; Harwood, Elaine

    1998-01-01

    In a study of effectiveness of classroom assessment techniques (CATs) on student learning, two college accounting teachers each taught two classes, one using CATs and one not using them. Course results did not suggest greater learning in CATs classes, better student participation, or more positive attitudes. Further research is recommended on the…

  16. Improving Exam Performance with the Clenched Fist Technique.

    ERIC Educational Resources Information Center

    Stanton, Harry E.

    1988-01-01

    The use of one specific ego-enhancing hypnotic approach, a technique that employs a conditioned "trigger," the clenched fist, to facilitate the changing of troublesome emotional states, is described. Forty first-year university students were the subjects of the study. (MLW)

  17. Improved Techniques for Automatic Chord Recognition from Music Audio Signals

    ERIC Educational Resources Information Center

    Cho, Taemin

    2014-01-01

    This thesis is concerned with the development of techniques that facilitate the effective implementation of capable automatic chord transcription from music audio signals. Since chord transcriptions can capture many important aspects of music, they are useful for a wide variety of music applications and also useful for people who learn and perform…

  18. Intelligent Techniques Using Molecular Data Analysis in Leukaemia: An Opportunity for Personalized Medicine Support System.

    PubMed

    Banjar, Haneen; Adelson, David; Brown, Fred; Chaudhri, Naeem

    2017-01-01

    The use of intelligent techniques in medicine has brought a ray of hope in terms of treating leukaemia patients. Personalized treatment uses patient's genetic profile to select a mode of treatment. This process makes use of molecular technology and machine learning, to determine the most suitable approach to treating a leukaemia patient. Until now, no reviews have been published from a computational perspective concerning the development of personalized medicine intelligent techniques for leukaemia patients using molecular data analysis. This review studies the published empirical research on personalized medicine in leukaemia and synthesizes findings across studies related to intelligence techniques in leukaemia, with specific attention to particular categories of these studies to help identify opportunities for further research into personalized medicine support systems in chronic myeloid leukaemia. A systematic search was carried out to identify studies using intelligence techniques in leukaemia and to categorize these studies based on leukaemia type and also the task, data source, and purpose of the studies. Most studies used molecular data analysis for personalized medicine, but future advancement for leukaemia patients requires molecular models that use advanced machine-learning methods to automate decision-making in treatment management to deliver supportive medical information to the patient in clinical practice.

  19. The GenTechnique Project: Developing an Open Environment for Learning Molecular Genetics.

    ERIC Educational Resources Information Center

    Calza, R. E.; Meade, J. T.

    1998-01-01

    The GenTechnique project at Washington State University uses a networked learning environment for molecular genetics learning. The project is developing courseware featuring animation, hyper-link controls, and interactive self-assessment exercises focusing on fundamental concepts. The first pilot course featured a Web-based module on DNA…

  20. Molecular techniques in the biotechnological fight against halogenated compounds in anoxic environments

    PubMed Central

    Ding, Chang; He, Jianzhong

    2012-01-01

    Summary Microbial treatment of environmental contamination by anthropogenic halogenated organic compounds has become popular in recent decades, especially in the subsurface environments. Molecular techniques such as polymerase chain reaction‐based fingerprinting methods have been extensively used to closely monitor the presence and activities of dehalogenating microbes, which also lead to the discovery of new dehalogenating bacteria and novel functional genes. Nowadays, traditional molecular techniques are being further developed and optimized for higher sensitivity, specificity, and accuracy to better fit the contexts of dehalogenation. On the other hand, newly developed high throughput techniques, such as microarray and next‐generation sequencing, provide unsurpassed detection ability, which has enabled large‐scale comparative genomic and whole‐genome transcriptomic analysis. The aim of this review is to summarize applications of various molecular tools in the field of microbially mediated dehalogenation of various halogenated organic compounds. It is expected that traditional molecular techniques and nucleic‐acid‐based biomarkers will still be favoured in the foreseeable future because of relative low costs and high flexibility. Collective analyses of metagenomic sequencing data are still in need of information from individual dehalogenating strains and functional reductive dehalogenase genes in order to draw reliable conclusions. PMID:22070763

  1. Discriminating coastal rangeland production and improvements with computer aided techniques

    NASA Technical Reports Server (NTRS)

    Reeves, C. A.; Faulkner, D. P.

    1975-01-01

    The feasibility and utility of using satellite data and computer-aided remote sensing analysis techniques to conduct range inventories were tested. This pilot study was focused over a 250,000 acre site in Galveston and Brazoria Counties along the Texas Gulf Coast. Rectified enlarged aircraft color infrared photographs of this site were used as the ground truth base. The different land categories were identified, delineated, and measured. Multispectral scanner (MSS) bulk data from LANDSAT-1 was received and analyzed with the Image 100 pattern recognition system. Features of interest were delineated on the image console giving the number of picture elements classified; the picture elements were converted to acreages and the accuracy of the technique was evaluated by comparison with data base results for three test sites. The accuracies for computer aided classification of coastal marshes ranged from 89% to 96%.

  2. Improved esthetic results with fine-tip Dermabond application technique.

    PubMed

    Santibanez-Gallerani, Alberto; Armstrong, Milton B; Thaller, Seth R

    2004-09-01

    Tissue glues and adhesives have achieved increasing popularity as alternatives to small wound closure. When applying these substances, it is often difficult to avoid contact with the surrounding skin and foreign objects such as surgical gloves. A technique for the application of Dermabond is described in this report. Twenty wounds less than 10 cm in length were reapproximated using a fine-tip tuberculin syringe applicator. The wounds were evaluated immediately after the application, and 2, 4, and 6 weeks after surgery. Use of the tuberculin fine-tip technique allowed reapproximation of the wound edges with no clinical evidence of surrounding tissue damage. There were no apparent decreases in wound strength or associated discoloration or fuzziness onto the skin. Esthetic results were considered good to excellent by patients. Dermabond can be accurately applied with a tuberculin syringe, avoiding the surrounding tissue damage and foreign object adhesion reported in the literature.

  3. Improved technique for Young's modulus determination by flexural resonance

    NASA Astrophysics Data System (ADS)

    Scafe, E.; Fabbri, L.; Grillo, G.; di Rese, L.

    1992-10-01

    Elastic properties in structural ceramics are widely studied with different experimental techniques in order to obtain engineering and diagnostic data about the processed materials. A new set-up for measuring flexural resonance is presented. The apparatus is based on electrostatic excitation where sample vibrations are detected by a laser modulation technique. Due to the high sensitivity and accuracy of this experimental set-up, it was possible to measure Young's modulus of samples with relatively high thickness/length ratios, thus allowing elastic properties determination directly on bending-strength test bars. The measurements were performed according to ASTM procedure. The high frequency resolution allowed the evaluation of internal friction variation due to processing, by nonlinear least square analysis of resonance curves.

  4. Laboratory technique for coloring titanium abutments to improve esthetics.

    PubMed

    Wadhwani, Chandur P K; O'Brien, Richard; Kattadiyil, Mathew T; Chung, Kwok-Hung

    2016-04-01

    Titanium alloys are used for implant abutments onto which prostheses are attached. One major disadvantage of titanium abutments is their esthetics; the metallic gray color may show through the restorative material or through surrounding tissues. A laboratory technique using readily available household items is described that can alter the abutment color by anodization. Copyright © 2016 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.

  5. An improved technique for isolating codominant compound microsatellite markers.

    PubMed

    Lian, Chunlan L; Abdul Wadud, Md; Geng, Qifang; Shimatani, Kenichiro; Hogetsu, Taizo

    2006-07-01

    An approach for developing codominant polymorphic markers (compound microsatellite (SSR) markers), with substantial time and cost savings, is introduced in this paper. In this technique, fragments flanked by a compound SSR sequence at one end were amplified from the constructed DNA library using compound SSR primer (AC)6(AG)5 or (TC)6(AC)5 and an adaptor primer for the suppression-PCR. A locus-specific primer was designed from the sequence flanking the compound SSR. The primer pairs of the locus-specific and compound SSR primers were used as a compound SSR marker. Because only one locus-specific primer was needed for design of each marker and only a common compound SSR primer was needed as the fluorescence-labeled primer for analyzing all the compound SSR markers, this approach substantially reduced the cost of developing codominant markers and analyzing their polymorphism. We have demonstrated this technique for Dendropanax trifidus and easily developed 11 codominant markers with high polymorphism for D. trifidus. Use of the technique for successful isolation of codominant compound SSR markers for several other plant species is currently in progress.

  6. Molecular approaches for genetic improvement of seed quality and characterization of genetic diversity in soybean: a critical review.

    PubMed

    Tripathi, Niraj; Khare, Dhirendra

    2016-10-01

    Soybean is an economically important leguminous crop. Genetic improvements of soybeans have focused on enhancement of seed and oil yield, development of varieties suited to different cropping systems, and breeding resistant/tolerant varieties for various biotic and abiotic stresses. Plant breeders have used conventional breeding techniques for the improvement of these traits in soybean. The conventional breeding process can be greatly accelerated through the application of molecular and genomic approaches. Molecular markers have proved to be a new tool in soybean breeding by enhancing selection efficiency in a rapid and time-bound manner. An overview of molecular approaches for the genetic improvement of soybean seed quality parameters, considering recent applications of marker-assisted selection and 'omics' research, is provided in this article.

  7. Traditional and Molecular Techniques for the Study of Emerging Bacterial Diseases: One Laboratory’s Perspective

    PubMed Central

    Houpikian, Pierre

    2002-01-01

    Identification of emerging bacterial pathogens generally results from a chain of events involving microscopy, serology, molecular tools, and culture. Because of the spectacular molecular techniques developed in the last decades, some authors think that these techniques will shortly supplant culture. The key steps that led to the discovery of emerging bacteria have been reviewed to determine the real contribution of each technique. Historically, microscopy has played a major role. Serology provided indirect evidence for causality. Isolation and culture were crucial, as all emerging bacteria have been grown on artificial media or cell lines or at least propagated in animals. With the use of broad-range polymerase chain reaction, some bacteria have been identified or detected in new clinical syndromes. Culture has irreplaceable advantages for studying emerging bacterial diseases, as it allows antigenic studies, antibiotic susceptibility testing, experimental models, and genetic studies to be carried out, and remains the ultimate goal of pathogen identification. PMID:11897062

  8. Development of Improved Crosslinking Monomers for Molecularly Imprinted Materials

    DTIC Science & Technology

    2002-04-05

    Molecular imprinting involves the self-assembled complexation of a substrate to functional monomers to form a pre- polymer complex which is "locked-in" to...on the design of crosslinking monomers for molecular imprinting , we have developed new classes of crosslinked polymers to optimize the performance of...of the design, synthesis, polymerization and performance of these new crosslinking monomers for molecularly imprinted polymers will be reported

  9. Development and validation of techniques for improving software dependability

    NASA Technical Reports Server (NTRS)

    Knight, John C.

    1992-01-01

    A collection of document abstracts are presented on the topic of improving software dependability through NASA grant NAG-1-1123. Specific topics include: modeling of error detection; software inspection; test cases; Magnetic Stereotaxis System safety specifications and fault trees; and injection of synthetic faults into software.

  10. Improving Attendance of Kindergarten Students through Behavior Modification Techniques.

    ERIC Educational Resources Information Center

    Schofield, Betty D.

    A behavior modification program was implemented to improve attendance and punctuality patterns of kindergarten students attending a small, rural elementary school. Also incorporated into the intervention were self-esteem and parent involvement components. Motivational strategies used were: a token economy; group-oriented behavior management…

  11. Improving Attendance of Kindergarten Students through Behavior Modification Techniques.

    ERIC Educational Resources Information Center

    Schofield, Betty D.

    A behavior modification program was implemented to improve attendance and punctuality patterns of kindergarten students attending a small, rural elementary school. Also incorporated into the intervention were self-esteem and parent involvement components. Motivational strategies used were: a token economy; group-oriented behavior management…

  12. The Integration of Nanoscale Techniques for an Improved Battery Technology

    DTIC Science & Technology

    2012-06-08

    interface (lithium metal batteries), in electrolyte performance and in cell geometry and cathode structure are needed for lithium batteries...PaperReceived PARAMESWAR HARI, MICHAL BYRCZEK, DALE TEETERS, PRAVIN UTEKAR. INVESTIGATIONS ON THE ELECTRICAL PROPERTIES OF ZnO NANORODS AND...power system. Specifically, improvements in the stabilization of the electrode/electrolyte interface (lithium metal batteries), in electrolyte

  13. Improving coarse woody debris measurements: a taper-based technique

    Treesearch

    Christopher W. Woodall; James A. Westfall

    2007-01-01

    Coarse woody debris (CWD) are dead and down trees of a certain minimum size that are an important forest ecosystem component (e.g., wildlife habitat, carbon stocks, and fuels). Accurately measuring the dimensions of CWD is important for ensuring the quality of CWD estimates and hence for accurately assessing forest ecosystem attributes. To improve the quality of CWD...

  14. [Techniques to Improve the Educational Climate in Your School].

    ERIC Educational Resources Information Center

    Braukmann, William T.

    This presentation was based on the assumption that developing the art of making teachers and students feel good about themselves is of paramount importance in helping youngsters to learn. The author offers and elaborates on 12 tips to help principals improve school climate: (1) Be aware that the principal's most important function is getting…

  15. Improved Tandem Measurement Techniques for Aerosol Particle Analysis

    NASA Astrophysics Data System (ADS)

    Rawat, Vivek Kumar

    Non-spherical, chemically inhomogeneous (complex) nanoparticles are encountered in a number of natural and engineered environments, including combustion systems (which produces highly non-spherical aggregates), reactors used in gas-phase materials synthesis of doped or multicomponent materials, and in ambient air. These nanoparticles are often highly diverse in size, composition and shape, and hence require determination of property distribution functions for accurate characterization. This thesis focuses on development of tandem mobility-mass measurement techniques coupled with appropriate data inversion routines to facilitate measurement of two dimensional size-mass distribution functions while correcting for the non-idealities of the instruments. Chapter 1 provides the detailed background and motivation for the studies performed in this thesis. In chapter 2, the development of an inversion routine is described which is employed to determine two dimensional size-mass distribution functions from Differential Mobility Analyzer-Aerosol Particle Mass analyzer tandem measurements. Chapter 3 demonstrates the application of the two dimensional distribution function to compute cumulative mass distribution function and also evaluates the validity of this technique by comparing the calculated total mass concentrations to measured values for a variety of aerosols. In Chapter 4, this tandem measurement technique with the inversion routine is employed to analyze colloidal suspensions. Chapter 5 focuses on application of a transverse modulation ion mobility spectrometer coupled with a mass spectrometer to study the effect of vapor dopants on the mobility shifts of sub 2 nm peptide ion clusters. These mobility shifts are then compared to models based on vapor uptake theories. Finally, in Chapter 6, a conclusion of all the studies performed in this thesis is provided and future avenues of research are discussed.

  16. Using simulation-optimization techniques to improve multiphase aquifer remediation

    SciTech Connect

    Finsterle, S.; Pruess, K.

    1995-03-01

    The T2VOC computer model for simulating the transport of organic chemical contaminants in non-isothermal multiphase systems has been coupled to the ITOUGH2 code which solves parameter optimization problems. This allows one to use linear programming and simulated annealing techniques to solve groundwater management problems, i.e. the optimization of operations for multiphase aquifer remediation. A cost function has to be defined, containing the actual and hypothetical expenses of a cleanup operation which depend - directly or indirectly - on the state variables calculated by T2VOC. Subsequently, the code iteratively determines a remediation strategy (e.g. pumping schedule) which minimizes, for instance, pumping and energy costs, the time for cleanup, and residual contamination. We discuss an illustrative sample problem to discuss potential applications of the code. The study shows that the techniques developed for estimating model parameters can be successfully applied to the solution of remediation management problems. The resulting optimum pumping scheme depends, however, on the formulation of the remediation goals and the relative weighting between individual terms of the cost function.

  17. Improved analysis techniques for cylindrical and spherical double probes

    SciTech Connect

    Beal, Brian; Brown, Daniel; Bromaghim, Daron; Johnson, Lee; Blakely, Joseph

    2012-07-15

    A versatile double Langmuir probe technique has been developed by incorporating analytical fits to Laframboise's numerical results for ion current collection by biased electrodes of various sizes relative to the local electron Debye length. Application of these fits to the double probe circuit has produced a set of coupled equations that express the potential of each electrode relative to the plasma potential as well as the resulting probe current as a function of applied probe voltage. These equations can be readily solved via standard numerical techniques in order to determine electron temperature and plasma density from probe current and voltage measurements. Because this method self-consistently accounts for the effects of sheath expansion, it can be readily applied to plasmas with a wide range of densities and low ion temperature (T{sub i}/T{sub e} Much-Less-Than 1) without requiring probe dimensions to be asymptotically large or small with respect to the electron Debye length. The presented approach has been successfully applied to experimental measurements obtained in the plume of a low-power Hall thruster, which produced a quasineutral, flowing xenon plasma during operation at 200 W on xenon. The measured plasma densities and electron temperatures were in the range of 1 Multiplication-Sign 10{sup 12}-1 Multiplication-Sign 10{sup 17} m{sup -3} and 0.5-5.0 eV, respectively. The estimated measurement uncertainty is +6%/-34% in density and +/-30% in electron temperature.

  18. Using ICT techniques for improving mechatronic systems' dependability

    NASA Astrophysics Data System (ADS)

    Miron, Emanuel; Silva, João P. M. A.; Machado, José; Olaru, Dumitru; Prisacaru, Gheorghe

    2013-10-01

    The use of analysis techniques for industrial controller's analysis, such as Simulation and Formal Verification, is complex on industrial context. This complexity is due to the fact that such techniques require sometimes high investment in specific skilled human resources that have sufficient theoretical knowledge in those domains. This paper aims, mainly, to show that it is possible to obtain a timed automata model for formal verification purposes, considering the CAD model of a mechanical component. This systematic approach can be used, by companies, for the analysis of industrial controllers programs. For this purpose, it is discussed, in the paper, the best way to systematize these procedures, and this paper describes, only, the first step of a complex process and promotes a discussion of the main difficulties that can be found and a possibility for handle those difficulties. A library for formal verification purposes is obtained from original 3D CAD models using Software as a Service platform (SaaS) that, nowadays, has become a common deliverable model for many applications, because SaaS is typically accessed by users via internet access.

  19. Closing the diarrhoea diagnostic gap in Indian children by the application of molecular techniques.

    PubMed

    Ajjampur, S S R; Rajendran, P; Ramani, S; Banerjee, I; Monica, B; Sankaran, P; Rosario, V; Arumugam, R; Sarkar, R; Ward, H; Kang, G

    2008-11-01

    A large proportion of diarrhoeal illnesses in children in developing countries are ascribed to an unknown aetiology because the only available methods, such as microscopy and culture, have low sensitivity. This study was aimed at decreasing the diagnostic gap in diarrhoeal disease by the application of molecular techniques. Faecal samples from 158 children with and 99 children without diarrhoea in a hospital in South India were tested for enteric pathogens using conventional diagnostic methods (culture, microscopy and enzyme immunoassays) and molecular methods (six PCR-based assays). The additional use of molecular techniques increased identification to at least one aetiological agent in 76.5 % of diarrhoeal specimens, compared with 40.5 % using conventional methods. Rotavirus (43.3 %), enteropathogenic Escherichia coli (15.8 %), norovirus (15.8 %) and Cryptosporidium spp. (15.2 %) are currently the most common causes of diarrhoea in hospitalized children in Vellore, in contrast to a study conducted two decades earlier in the same hospital, where bacterial pathogens such as Shigella spp., Campylobacter spp. and enterotoxigenic E. coli were more prevalent. Molecular techniques significantly increased the detection rates of pathogens in children with diarrhoea, but a more intensive study, testing for a wider range of infectious agents and including more information on non-infectious causes of diarrhoea, is required to close the diagnostic gap in diarrhoeal disease.

  20. DNA-binding study of anticancer drug cytarabine by spectroscopic and molecular docking techniques.

    PubMed

    Shahabadi, Nahid; Falsafi, Monireh; Maghsudi, Maryam

    2017-01-02

    The interaction of anticancer drug cytarabine with calf thymus DNA (CT-DNA) was investigated in vitro under simulated physiological conditions by multispectroscopic techniques and molecular modeling study. The fluorescence spectroscopy and UV absorption spectroscopy indicated drug interacted with CT-DNA in a groove-binding mode, while the binding constant of UV-vis and the number of binding sites were 4.0 ± 0.2 × 10(4) L mol(-1) and 1.39, respectively. The fluorimetric studies showed that the reaction between the drugs with CT-DNA is exothermic. Circular dichroism spectroscopy was employed to measure the conformational change of DNA in the presence of cytarabine. Furthermore, the drug induces detectable changes in its viscosity for DNA interaction. The molecular modeling results illustrated that cytarabine strongly binds to groove of DNA by relative binding energy of docked structure -20.61 KJ mol(-1). This combination of multiple spectroscopic techniques and molecular modeling methods can be widely used in the investigation on the interaction of small molecular pollutants and drugs with biomacromolecules for clarifying the molecular mechanism of toxicity or side effect in vivo.

  1. RNAi screening comes of age: improved techniques and complementary approaches

    PubMed Central

    Mohr, Stephanie E.; Smith, Jennifer A.; Shamu, Caroline E.; Neumüller, Ralph A.; Perrimon, Norbert

    2014-01-01

    Gene silencing through sequence-specific targeting of mRNAs by RNAi has enabled genome-wide functional screens in cultured cells and in vivo in model organisms. These screens have resulted in the identification of new cellular pathways and potential drug targets. Considerable progress has been made to improve the quality of RNAi screen data through the development of new experimental and bioinformatics approaches. The recent availability of genome-editing strategies, such as the CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 system, when combined with RNAi, could lead to further improvements in screen data quality and follow-up experiments, thus promoting our understanding of gene function and gene regulatory networks. PMID:25145850

  2. Online Learning Techniques for Improving Robot Navigation in Unfamiliar Domains

    DTIC Science & Technology

    2010-12-01

    segmentation output and impact on performance . . . . . . . . . 63 5.5 Effects of varying smoothness parameter λ. . . . . . . . . . . . . . . . . . . . . 64...restrictions on the recency of overhead data, our algorithm further increases its impact on improving robot navigation. Far-Range Sensor Data Features. Ladar...FROLL, and MOLL . . . . . 36 4.7 Additional path comparisions for baseline system, FROLL, and MOLL . . . . . 37 4.8 Effect of FROLL performance at Ft

  3. Improved numerical techniques for processing Monte Carlo thermal scattering data

    SciTech Connect

    Schmidt, E; Rose, P

    1980-01-01

    As part of a Thermal Benchmark Validation Program sponsored by the Electric Power Research Institute (EPRI), the National Nuclear Data Center has been calculating thermal reactor lattices using the SAM-F Monte Carlo Computer Code. As part of this program a significant improvement has been made in the adequacy of the numerical procedures used to process the thermal differential scattering cross sections for hydrogen bound in H/sub 2/O.

  4. Improved ceramic slip casting technique. [application to aircraft model fabrication

    NASA Technical Reports Server (NTRS)

    Buck, Gregory M. (Inventor); Vasquez, Peter (Inventor)

    1993-01-01

    A primary concern in modern fluid dynamics research is the experimental verification of computational aerothermodynamic codes. This research requires high precision and detail in the test model employed. Ceramic materials are used for these models because of their low heat conductivity and their survivability at high temperatures. To fabricate such models, slip casting techniques were developed to provide net-form, precision casting capability for high-purity ceramic materials in aqueous solutions. In previous slip casting techniques, block, or flask molds made of plaster-of-paris were used to draw liquid from the slip material. Upon setting, parts were removed from the flask mold and cured in a kiln at high temperatures. Casting detail was usually limited with this technique -- detailed parts were frequently damaged upon separation from the flask mold, as the molded parts are extremely delicate in the uncured state, and the flask mold is inflexible. Ceramic surfaces were also marred by 'parting lines' caused by mold separation. This adversely affected the aerodynamic surface quality of the model as well. (Parting lines are invariably necessary on or near the leading edges of wings, nosetips, and fins for mold separation. These areas are also critical for flow boundary layer control.) Parting agents used in the casting process also affected surface quality. These agents eventually soaked into the mold, the model, or flaked off when releasing the case model. Different materials were tried, such as oils, paraffin, and even an algae. The algae released best, but some of it remained on the model and imparted an uneven texture and discoloration on the model surface when cured. According to the present invention, a wax pattern for a shell mold is provided, and an aqueous mixture of a calcium sulfate-bonded investment material is applied as a coating to the wax pattern. The coated wax pattern is then dried, followed by curing to vaporize the wax pattern and leave a shell

  5. Characterization of a seeded pulsed molecular beam using the velocity map imaging technique

    NASA Astrophysics Data System (ADS)

    Lietard, Aude; Poisson, Lionel; Mestdagh, Jean-Michel; Gaveau, Marc-André

    2016-11-01

    An experimental study has been performed to characterize the density and the velocity distribution in a pulsed molecular beam generated by a source associating a pulsed valve and an oven placed just downstream. In its operating mode, the flow is alternatively in a supersonic and effusive regime. The Velocity Map Imaging (VMI) technique associated with laser ionization allows measuring the velocity distribution and the density of molecules as a function of time during the expansion. It gives us a very precise insight into the structure of the molecule bunch, and therefore into the nature of the expansion from which the molecular beam is extracted.

  6. Techniques for achieving thermal equilibrium in molecular dynamics calculations for solids

    NASA Astrophysics Data System (ADS)

    Wu, Ernest Yue; Friauf, Robert J.

    1990-06-01

    We develop techniques for achieving thermal equilibrium in molecular dynamics calculations for solids. Atoms in a Lennard-Jones solid are initially given random velocities and displacements from their equilibrium positions with suitably scaled Maxwellian distributions. A quantitative criterion for thermal equilibrium of the solid is established by using the equipartition of energy theorem. At high temperatures, thermal expansion is studied, and we introduce a method for adjusting the lattice parameter to ensure zero external pressure. The results of molecular dynamics simulations show agreement with experimental data for rare gas and ionic crystals.

  7. Improved memory loading techniques for the TSRV display system

    NASA Technical Reports Server (NTRS)

    Easley, W. C.; Lynn, W. A.; Mcluer, D. G.

    1986-01-01

    A recent upgrade of the TSRV research flight system at NASA Langley Research Center retained the original monochrome display system. However, the display memory loading equipment was replaced requiring design and development of new methods of performing this task. This paper describes the new techniques developed to load memory in the display system. An outdated paper tape method for loading the BOOTSTRAP control program was replaced by EPROM storage of the characters contained on the tape. Rather than move a tape past an optical reader, a counter was implemented which steps sequentially through EPROM addresses and presents the same data to the loader circuitry. A cumbersome cassette tape method for loading the applications software was replaced with a floppy disk method using a microprocessor terminal installed as part of the upgrade. The cassette memory image was transferred to disk and a specific software loader was written for the terminal which duplicates the function of the cassette loader.

  8. Multidetector CT and dentascan software: dosimetric evaluation and technique improvement.

    PubMed

    Fanucci, E; Leporace, M; Di Costanzo, G; Fiaschetti, V; Simonetti, G

    2006-02-01

    The development of new operative techniques in oral and maxillofacial surgery within the last few years has led to an increasing demand for Dentascan examination, also in paediatric patients. It is necessary to modify acquisition parameters to reduce the absorbed dose. The aim of this study was to define a Dentascan protocol in which a reduced X-ray dose could be used. Dosimeters were applied to the eyes, mouth, parotid glands, thyroid and back of the neck of an anthropomorphic Plexiglas phantom that underwent multidetector computed tomography (MDCT) Dentascan examinations. Both 120kV and 80 kV were used to study the mandibular and maxillary arches. Examinations obtained with the 80 kV protocol showed a ten-fold reduction in the absorbed dose, without affecting image quality. We suggest a Dentascan protocol that reduces the X-ray dose administered to the patient while ensuring the same high diagnostic accuracy.

  9. Improved techniques for sampling complex pedigrees with the Gibbs sampler

    PubMed Central

    Abraham, K Joseph; Totir, Liviu R; Fernando, Rohan L

    2007-01-01

    Markov chain Monte Carlo (MCMC) methods have been widely used to overcome computational problems in linkage and segregation analyses. Many variants of this approach exist and are practiced; among the most popular is the Gibbs sampler. The Gibbs sampler is simple to implement but has (in its simplest form) mixing and reducibility problems; furthermore in order to initiate a Gibbs sampling chain we need a starting genotypic or allelic configuration which is consistent with the marker data in the pedigree and which has suitable weight in the joint distribution. We outline a procedure for finding such a configuration in pedigrees which have too many loci to allow for exact peeling. We also explain how this technique could be used to implement a blocking Gibbs sampler. PMID:17212946

  10. Improved technique for blood flow velocity measurement using Doppler effect

    NASA Astrophysics Data System (ADS)

    Valadares Oliveira, Eduardo J.; Nantes Button, Vera L. d. S.; Maia, Joaquim M.; Costa, Eduardo T.

    2002-04-01

    The Doppler velocimeter developed allows to determine the angle between the ultrasonic beam and the velocity vector of the flow, and to calculate the precise blood flow in a vessel. Four piezoelectric transducers constitute the Doppler velocimeter. Three of these transducers are positioned to form an equilateral triangle (base of a pyramid). When these transducers move simultaneously, backward or forward from the initial position, the emitted ultrasonic beams focalize on a position (peak of the pyramid) closer or farther from the transducers faces, according to the depth of the vessel where we intend to measure de flow. The angle between the transducers allows adjusting the height of this pyramid and the position of the focus (where the three beams meet). A forth transducer is used to determine the diameter of the vessel and monitor the position of the Doppler velocimeter relative to the vessel. Simulation results showed that with this technique is possible to accomplish precise measurement of blood flow.

  11. Improvements to the compressed-sample (CS) technique for MALDI-TOF mass spectrometry.

    PubMed

    Hyzak, Lukas; Giese, Susanne; Kling, Hans-Willi; Wulf, Volker; Melchior, David; Köhler, Michael; Schmitz, Oliver J

    2013-02-01

    A recently developed solvent-free compressed-sample technique for matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) analysis allows the reproducible analysis of synthetic polymers and peptides up to 3,500 Da. In this work, we present an improvement in resolution, an increase in intensity and a decrease of the variation coefficient, as illustrated by the analysis of PEG 2000 and MALDI imaging experiments. These advantages were achieved by homogenization of the electrical field, which was disturbed by the drills in the original MALDI target. In order to homogenize the electrical field, a new target with smaller drills was developed, metal powder was added to the matrix/analyte mixture and a round laser raster was used. Furthermore, a ball mill was implemented for the sample preparation to replace the extremely user-dependent grinding in a mortar. The new conditions were successfully applied to the quantification of several peptides of higher molecular weight and gave higher precision than had previously been achieved with the compressed-sample technique.

  12. Improvements in Cesarean Section Techniques: Arad's Obstetrics Department Experience on Adapting the Vejnovic Cesarean Section Technique.

    PubMed

    Furau, Cristian; Furau, Gheorghe; Dascau, Voicu; Ciobanu, Gheorghe; Onel, Cristina; Stanescu, Casiana

    2013-09-01

    Cesarean section has become recently the first choice for delivery in many clinics in Romania and worldwide. The purpose of our study is to assess the benefits of introducing the adapted Vejnovic uterine suture technique into daily practice. A total of 1703 out of the 1776 cesarean section performed in the period January, 2012 - March, 2013 in the Obstetric Department of the Emergency Clinical County Hospital of Arad were retrospectively analyzed based on the cesarean section registries, birth registries and patient's personal medical records. We compared results between the group of patients undergoing adapted Vejnovic cesarean section technique and the group of patients operated in a classic manner. The cesarean section rate in the studied period was 56.48%. Adapted Vejnovic cesarean section technique was performed in 548 cases (30.86% of the cases), furthermore in the last 3 months studied it reached 57.27%. Mean APGAR score was better in the adapted Vejnovic cesarean section group (8.43) compared with the reference group (8.34). No significant differences were seen between the two groups regarding maternal age, gestation, weeks of gestation, newborn weight, anesthesia and indications for cesarean section. Exteriorizing the uterus helped the incidental diagnosis of 35 uterine myoma, 22 adnexal masses and 13 uterine malformations. In a society with a constant growth of cesarean rate, the adapted Vejnovic cesarean section technique is becoming popular amongst clinicians for its advantages, but further studies need to be developed for its standardization.

  13. An improved version of the Green's function molecular dynamics method

    NASA Astrophysics Data System (ADS)

    Kong, Ling Ti; Denniston, Colin; Müser, Martin H.

    2011-02-01

    This work presents an improved version of the Green's function molecular dynamics method (Kong et al., 2009; Campañá and Müser, 2004 [1,2]), which enables one to study the elastic response of a three-dimensional solid to an external stress field by taking into consideration only atoms near the surface. In the previous implementation, the effective elastic coefficients measured at the Γ-point were altered to reduce finite size effects: their eigenvalues corresponding to the acoustic modes were set to zero. This scheme was found to work well for simple Bravais lattices as long as only atoms within the last layer were treated as Green's function atoms. However, it failed to function as expected in all other cases. It turns out that a violation of the acoustic sum rule for the effective elastic coefficients at Γ (Kong, 2010 [3]) was responsible for this behavior. In the new version, the acoustic sum rule is enforced by adopting an iterative procedure, which is found to be physically more meaningful than the previous one. In addition, the new algorithm allows one to treat lattices with bases and the Green's function slab is no longer confined to one layer. New version program summaryProgram title: FixGFC/FixGFMD v1.12 Catalogue identifier: AECW_v1_1 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECW_v1_1.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 206 436 No. of bytes in distributed program, including test data, etc.: 4 314 850 Distribution format: tar.gz Programming language: C++ Computer: All Operating system: Linux Has the code been vectorized or parallelized?: Yes. Code has been parallelized using MPI directives. RAM: Depends on the problem Classification: 7.7 External routines: LAMMPS ( http://lammps.sandia.gov/), MPI ( http

  14. Advanced Measurement and Modeling Techniques for Improved SOFC Cathodes

    SciTech Connect

    Stuart Adler; L. Dunyushkina; S. Huff; Y. Lu; J. Wilson

    2006-12-31

    The goal of this project was to develop an improved understanding of factors governing performance and degradation of mixed-conducting SOFC cathodes. Two new diagnostic tools were developed to help achieve this goal: (1) microelectrode half-cells for improved isolation of cathode impedance on thin electrolytes, and (2) nonlinear electrochemical impedance spectroscopy (NLEIS), a variant of traditional impedance that allows workers to probe nonlinear rates as a function of frequency. After reporting on the development and efficacy of these tools, this document reports on the use of these and other tools to better understand performance and degradation of cathodes based on the mixed conductor La{sub 1-x}Sr{sub x}CoO{sub 3-{delta}} (LSC) on gadolinia or samaria-doped ceria (GDC or SDC). We describe the use of NLEIS to measure O{sub 2} exchange on thin-film LSC electrodes, and show that O{sub 2} exchange is most likely governed by dissociative adsorption. We also describe parametric studies of porous LSC electrodes using impedance and NLEIS. Our results suggest that O{sub 2} exchange and ion transport co-limit performance under most relevant conditions, but it is O{sub 2} exchange that is most sensitive to processing, and subject to the greatest degradation and sample-to-sample variation. We recommend further work that focuses on electrodes of well-defined or characterized geometry, and probes the details of surface structure, composition, and impurities. Parallel work on primarily electronic conductors (LSM) would also be of benefit to developers, and to improved understanding of surface vs. bulk diffusion.

  15. Techniques for improving transients in learning control systems

    NASA Technical Reports Server (NTRS)

    Chang, C.-K.; Longman, Richard W.; Phan, Minh

    1992-01-01

    A discrete modern control formulation is used to study the nature of the transient behavior of the learning process during repetitions. Several alternative learning control schemes are developed to improve the transient performance. These include a new method using an alternating sign on the learning gain, which is very effective in limiting peak transients and also very useful in multiple-input, multiple-output systems. Other methods include learning at an increasing number of points progressing with time, or an increasing number of points of increasing density.

  16. Applying program comprehension techniques to improve software inspections

    NASA Technical Reports Server (NTRS)

    Rifkin, Stan; Deimel, Lionel

    1994-01-01

    Software inspections are widely regarded as a cost-effective mechanism for removing defects in software, though performing them does not always reduce the number of customer-discovered defects. We present a case study in which an attempt was made to reduce such defects through inspection training that introduced program comprehension ideas. The training was designed to address the problem of understanding the artifact being reviewed, as well as other perceived deficiencies of the inspection process itself. Measures, both formal and informal, suggest that explicit training in program understanding may improve inspection effectiveness.

  17. A technique for improved blood sampling during sleep studies.

    PubMed

    Ona, E; Dimsdale, J E; Ancoli-Israel, S; Dillon, E; Watkins, L; Coy, T V; Clausen, J

    1994-11-01

    Research protocols often require that blood samples be drawn during sleep. This study compares the efficacy of obtaining nocturnal blood samples using a standard heparinized intravenous setup versus the same intravenous setup used in conjunction with a small chemical heating pad. The chemical heating pad significantly improved the number of blood samples obtained and the maintenance of intravenous patency. The use of a chemical heating pad is an economical way to resolve the frustration of lost blood samples while maintaining a reasonable environment to monitor sleep.

  18. Binding of ibuprofen to human hemoglobin: Elucidation of their molecular recognition by spectroscopy, calorimetry and molecular modeling techniques.

    PubMed

    Seal, Paromita; Sikdar, Jyotirmoy; Roy, Amartya; Haldar, Rajen

    2017-09-22

    Ibuprofen, used for the treatment of acute and chronic pain, osteoarthritis, rheumatoid arthritis, and related conditions has ample affinity to globular proteins. Here we have explored this fundamental study pertaining to the interaction of ibuprofen with human hemoglobin (HHb), using multispectroscopic, calorimetric, and molecular modeling techniques to gain insights into molecular aspects of binding mechanism. Ibuprofen-induced graded decrease in absorption spectra indicates protein disruption along with sedimentation of HHb particle. Red shifting of absorption peak at 195 nm indicates alteration in the secondary structure of HHb upon interaction with ibuprofen. Flouremetric and isothermal titration calorimetric (ITC) studies suggested one binding site in HHb for ibuprofen at 298.15 K. However, with increase in temperature, ITC revealed increasing number of binding sites. The negative values of Gibbs energy change (ΔG(0)) and enthalpy change (ΔH(0)) along with positive value of entropy change (ΔS(0)) strongly suggest that it is entropy-driven spontaneous exothermic reaction. Moreover, hydrophobic interaction, hydrogen bonding and π-π interaction play major role in this binding process as evidenced from ANS (8-anilino-1-napthalenesulphonic acid), sucrose binding, and molecular modeling studies. The interaction impacts on structural integrity and functional aspects of HHb as confirmed by CD spectroscopy, increased free iron release, increased rate of co-oxidation and decreased rate of esterase activity. These findings suggest us to conclude that ibuprofen upon interaction perturbs both structural and functional aspects of HHb.

  19. Systematic infrared image quality improvement using deep learning based techniques

    NASA Astrophysics Data System (ADS)

    Zhang, Huaizhong; Casaseca-de-la-Higuera, Pablo; Luo, Chunbo; Wang, Qi; Kitchin, Matthew; Parmley, Andrew; Monge-Alvarez, Jesus

    2016-10-01

    Infrared thermography (IRT, or thermal video) uses thermographic cameras to detect and record radiation in the longwavelength infrared range of the electromagnetic spectrum. It allows sensing environments beyond the visual perception limitations, and thus has been widely used in many civilian and military applications. Even though current thermal cameras are able to provide high resolution and bit-depth images, there are significant challenges to be addressed in specific applications such as poor contrast, low target signature resolution, etc. This paper addresses quality improvement in IRT images for object recognition. A systematic approach based on image bias correction and deep learning is proposed to increase target signature resolution and optimise the baseline quality of inputs for object recognition. Our main objective is to maximise the useful information on the object to be detected even when the number of pixels on target is adversely small. The experimental results show that our approach can significantly improve target resolution and thus helps making object recognition more efficient in automatic target detection/recognition systems (ATD/R).

  20. Improvements in analysis techniques for segmented mirror arrays

    NASA Astrophysics Data System (ADS)

    Michels, Gregory J.; Genberg, Victor L.; Bisson, Gary R.

    2016-08-01

    The employment of actively controlled segmented mirror architectures has become increasingly common in the development of current astronomical telescopes. Optomechanical analysis of such hardware presents unique issues compared to that of monolithic mirror designs. The work presented here is a review of current capabilities and improvements in the methodology of the analysis of mechanically induced surface deformation of such systems. The recent improvements include capability to differentiate surface deformation at the array and segment level. This differentiation allowing surface deformation analysis at each individual segment level offers useful insight into the mechanical behavior of the segments that is unavailable by analysis solely at the parent array level. In addition, capability to characterize the full displacement vector deformation of collections of points allows analysis of mechanical disturbance predictions of assembly interfaces relative to other assembly interfaces. This capability, called racking analysis, allows engineers to develop designs for segment-to-segment phasing performance in assembly integration, 0g release, and thermal stability of operation. The performance predicted by racking has the advantage of being comparable to the measurements used in assembly of hardware. Approaches to all of the above issues are presented and demonstrated by example with SigFit, a commercially available tool integrating mechanical analysis with optical analysis.

  1. Action Research to Improve the Learning Space for Diagnostic Techniques.

    PubMed

    Ariel, Ellen; Owens, Leigh

    2015-12-01

    The module described and evaluated here was created in response to perceived learning difficulties in diagnostic test design and interpretation for students in third-year Clinical Microbiology. Previously, the activities in lectures and laboratory classes in the module fell into the lower cognitive operations of "knowledge" and "understanding." The new approach was to exchange part of the traditional activities with elements of interactive learning, where students had the opportunity to engage in deep learning using a variety of learning styles. The effectiveness of the new curriculum was assessed by means of on-course student assessment throughout the module, a final exam, an anonymous questionnaire on student evaluation of the different activities and a focus group of volunteers. Although the new curriculum enabled a major part of the student cohort to achieve higher pass grades (p < 0.001), it did not meet the requirements of the weaker students, and the proportion of the students failing the module remained at 34%. The action research applied here provided a number of valuable suggestions from students on how to improve future curricula from their perspective. Most importantly, an interactive online program that facilitated flexibility in the learning space for the different reagents and their interaction in diagnostic tests was proposed. The methods applied to improve and assess a curriculum refresh by involving students as partners in the process, as well as the outcomes, are discussed. Journal of Microbiology & Biology Education.

  2. Improving pyroelectric energy harvesting using a sandblast etching technique.

    PubMed

    Hsiao, Chun-Ching; Siao, An-Shen

    2013-09-10

    Large amounts of low-grade heat are emitted by various industries and exhausted into the environment. This heat energy can be used as a free source for pyroelectric power generation. A three-dimensional pattern helps to improve the temperature variation rates in pyroelectric elements by means of lateral temperature gradients induced on the sidewalls of the responsive elements. A novel method using sandblast etching is successfully applied in fabricating the complex pattern of a vortex-like electrode. Both experiment and simulation show that the proposed design of the vortex-like electrode improved the electrical output of the pyroelectric cells and enhanced the efficiency of pyroelectric harvesting converters. A three-dimensional finite element model is generated by commercial software for solving the transient temperature fields and exploring the temperature variation rate in the PZT pyroelectric cells with various designs. The vortex-like type has a larger temperature variation rate than the fully covered type, by about 53.9%.The measured electrical output of the vortex-like electrode exhibits an obvious increase in the generated charge and the measured current, as compared to the fully covered electrode, by of about 47.1% and 53.1%, respectively.

  3. Improving Pyroelectric Energy Harvesting Using a Sandblast Etching Technique

    PubMed Central

    Hsiao, Chun-Ching; Siao, An-Shen

    2013-01-01

    Large amounts of low-grade heat are emitted by various industries and exhausted into the environment. This heat energy can be used as a free source for pyroelectric power generation. A three-dimensional pattern helps to improve the temperature variation rates in pyroelectric elements by means of lateral temperature gradients induced on the sidewalls of the responsive elements. A novel method using sandblast etching is successfully applied in fabricating the complex pattern of a vortex-like electrode. Both experiment and simulation show that the proposed design of the vortex-like electrode improved the electrical output of the pyroelectric cells and enhanced the efficiency of pyroelectric harvesting converters. A three-dimensional finite element model is generated by commercial software for solving the transient temperature fields and exploring the temperature variation rate in the PZT pyroelectric cells with various designs. The vortex-like type has a larger temperature variation rate than the fully covered type, by about 53.9%.The measured electrical output of the vortex-like electrode exhibits an obvious increase in the generated charge and the measured current, as compared to the fully covered electrode, by of about 47.1% and 53.1%, respectively. PMID:24025557

  4. Improving the treatment of musculoskeletal infections with molecular diagnostics.

    PubMed

    Tarkin, Ivan S; Dunman, Paul M; Garvin, Kevin L

    2005-08-01

    Molecular diagnostic strategies have been implemented to enhance the treatment of musculoskeletal infections. Once primarily a research tool, molecular-based assays, have become accepted clinical tests for the genomic detection of certain pathogens involved in bone and joint infections. Currently, culture remains the gold standard for identifying most organisms causing infection. However, molecular assays are beneficial in clinical cases in which standard culture-based tests are unreliable or untimely. We will review current clinical utility of this emerging technology and roles for assays in the future.

  5. Improved Battery State Estimation Using Novel Sensing Techniques

    NASA Astrophysics Data System (ADS)

    Abdul Samad, Nassim

    Lithium-ion batteries have been considered a great complement or substitute for gasoline engines due to their high energy and power density capabilities among other advantages. However, these types of energy storage devices are still yet not widespread, mainly because of their relatively high cost and safety issues, especially at elevated temperatures. This thesis extends existing methods of estimating critical battery states using model-based techniques augmented by real-time measurements from novel temperature and force sensors. Typically, temperature sensors are located near the edge of the battery, and away from the hottest core cell regions, which leads to slower response times and increased errors in the prediction of core temperatures. New sensor technology allows for flexible sensor placement at the cell surface between cells in a pack. This raises questions about the optimal locations of these sensors for best observability and temperature estimation. Using a validated model, which is developed and verified using experiments in laboratory fixtures that replicate vehicle pack conditions, it is shown that optimal sensor placement can lead to better and faster temperature estimation. Another equally important state is the state of health or the capacity fading of the cell. This thesis introduces a novel method of using force measurements for capacity fade estimation. Monitoring capacity is important for defining the range of electric vehicles (EVs) and plug-in hybrid electric vehicles (PHEVs). Current capacity estimation techniques require a full discharge to monitor capacity. The proposed method can complement or replace current methods because it only requires a shallow discharge, which is especially useful in EVs and PHEVs. Using the accurate state estimation accomplished earlier, a method for downsizing a battery pack is shown to effectively reduce the number of cells in a pack without compromising safety. The influence on the battery performance (e

  6. Quality improving techniques for free-viewpoint DIBR

    NASA Astrophysics Data System (ADS)

    Do, Luat; Zinger, Sveta; de With, Peter H. N.

    2010-02-01

    Interactive free-viewpoint selection applied to a 3D multi-view signal is a possible attractive feature of the rapidly developing 3D TV media. This paper explores a new rendering algorithm that computes a free-viewpoint based on depth image warping between two reference views from existing cameras. We have developed three quality enhancing techniques that specifically aim at solving the major artifacts. First, resampling artifacts are filled in by a combination of median filtering and inverse warping. Second, contour artifacts are processed while omitting warping of edges at high discontinuities. Third, we employ a depth signal for more accurate disocclusion inpainting. We obtain an average PSNR gain of 3 dB and 4.5 dB for the 'Breakdancers' and 'Ballet' sequences, respectively, compared to recently published results. While experimenting with synthetic data, we observe that the rendering quality is highly dependent on the complexity of the scene. Moreover, experiments are performed using compressed video from surrounding cameras. The overall system quality is dominated by the rendering quality and not by coding.

  7. Beneficent Persuasion: Techniques and Ethical Guidelines to Improve Patients’ Decisions

    PubMed Central

    Swindell, J. S.; McGuire, Amy L.; Halpern, Scott D.

    2010-01-01

    Physicians frequently encounter patients who make decisions that contravene their long-term goals. Behavioral economists have shown that irrationalities and self-thwarting tendencies pervade human decision making, and they have identified a number of specific heuristics (rules of thumb) and biases that help explain why patients sometimes make such counterproductive decisions. In this essay, we use clinical examples to describe the many ways in which these heuristics and biases influence patients’ decisions. We argue that physicians should develop their understanding of these potentially counterproductive decisional biases and, in many cases, use this knowledge to rebias their patients in ways that promote patients’ health or other values. Using knowledge of decision-making psychology to persuade patients to engage in healthy behaviors or to make treatment decisions that foster their long-term goals is ethically justified by physicians’ duties to promote their patients’ interests and will often enhance, rather than limit, their patients’ autonomy. We describe techniques that physicians may use to frame health decisions to patients in ways that are more likely to motivate patients to make choices that are less biased and more conducive to their long-term goals. Marketers have been using these methods for decades to get patients to engage in unhealthy behaviors; employers and policy makers are beginning to consider the use of similar approaches to influence healthy choices. It is time for clinicians also to make use of behavioral psychology in their interactions with patients. PMID:20458111

  8. Beneficent persuasion: techniques and ethical guidelines to improve patients' decisions.

    PubMed

    Swindell, J S; McGuire, Amy L; Halpern, Scott D

    2010-01-01

    Physicians frequently encounter patients who make decisions that contravene their long-term goals. Behavioral economists have shown that irrationalities and self-thwarting tendencies pervade human decision making, and they have identified a number of specific heuristics (rules of thumb) and biases that help explain why patients sometimes make such counterproductive decisions. In this essay, we use clinical examples to describe the many ways in which these heuristics and biases influence patients' decisions. We argue that physicians should develop their understanding of these potentially counterproductive decisional biases and, in many cases, use this knowledge to rebias their patients in ways that promote patients' health or other values. Using knowledge of decision-making psychology to persuade patients to engage in healthy behaviors or to make treatment decisions that foster their long-term goals is ethically justified by physicians' duties to promote their patients' interests and will often enhance, rather than limit, their patients' autonomy. We describe techniques that physicians may use to frame health decisions to patients in ways that are more likely to motivate patients to make choices that are less biased and more conducive to their long-term goals. Marketers have been using these methods for decades to get patients to engage in unhealthy behaviors; employers and policy makers are beginning to consider the use of similar approaches to influence healthy choices. It is time for clinicians also to make use of behavioral psychology in their interactions with patients.

  9. Improving Alzheimer's disease diagnosis with machine learning techniques.

    PubMed

    Trambaiolli, Lucas R; Lorena, Ana C; Fraga, Francisco J; Kanda, Paulo A M; Anghinah, Renato; Nitrini, Ricardo

    2011-07-01

    There is not a specific test to diagnose Alzheimer's disease (AD). Its diagnosis should be based upon clinical history, neuropsychological and laboratory tests, neuroimaging and electroencephalography (EEG). Therefore, new approaches are necessary to enable earlier and more accurate diagnosis and to follow treatment results. In this study we used a Machine Learning (ML) technique, named Support Vector Machine (SVM), to search patterns in EEG epochs to differentiate AD patients from controls. As a result, we developed a quantitative EEG (qEEG) processing method for automatic differentiation of patients with AD from normal individuals, as a complement to the diagnosis of probable dementia. We studied EEGs from 19 normal subjects (14 females/5 males, mean age 71.6 years) and 16 probable mild to moderate symptoms AD patients (14 females/2 males, mean age 73.4 years. The results obtained from analysis of EEG epochs were accuracy 79.9% and sensitivity 83.2%. The analysis considering the diagnosis of each individual patient reached 87.0% accuracy and 91.7% sensitivity.

  10. Recent improvements in PDS technique for low-absorption measurements

    NASA Astrophysics Data System (ADS)

    Montecchi, Marco; Masetti, Enrico; Emiliani, Gabriele

    1990-08-01

    Photothermal Deflection Spectroscopy (PDS) is a recently developed technique that is finding a useful application in the measurement of low optical absorptance of thin films. Among the noise sources affecting the PDS measurement, probe beam pointing instability and mechanical vibration play a considerable role. In this work an optoelectronic system for the reduction of their influence is described. Moreover, PDS measurements are typically performed keeping the sample immersed in a deflecting liquid; thus measured values of absorptance must be corrected when other surrounding media, as air, are considered. This correction is an easy task for single film coatings. Here the general case of an unknown multiplayer coating is analysed; a range of values containing the true absorptance in air is obtained by theoretical analysis and a practical method to evaluate the absorptance in air is discussed. Finally, deflecting liquids alternative to the commonly used CCI4 have been examined. Useful optical range, thermal diffusivity and "relative deflecting power" of CCI4, CS2, Iso-octane and Aceton are reported.

  11. IMPROVED TECHNIQUES FOR THE PREPARATION OF ULTRATHIN FROZEN SECTIONS

    PubMed Central

    Bernhard, W.; Viron, Annie

    1971-01-01

    Ultrathin frozen sections of biological tissues for electron microscopy provide certain advantages in cytochemical studies in which the penetration of cells by large molecules is necessary and in morphological studies of cellular constituents which are dissolved by the reagents employed in routine plastic embedding. The recent introduction of several types of commercially available cryo-ultramicrotomes makes it possible for many laboratories to employ this valuable tool. This paper summarizes recent improvements in the methods developed in this laboratory for preparing ultrathin frozen sections and reviews some of the inherent problems involved in their use. These procedures may serve as a baseline for other investigators who can then modify or adapt them for their specific purposes. PMID:4103954

  12. Applying total quality management techniques to improve software development.

    PubMed

    Mezher, T; Assem Abdul Malak, M; el-Medawar, H

    1998-01-01

    Total Quality Management (TQM) is a new management philosophy and a set of guiding principles that represent the basis of a continuously improving organization. This paper sheds light on the application of TQM concepts for software development. A fieldwork study was conducted on a Lebanese software development firm and its customers to determine the major problems affecting the organization's operation and to assess the level of adoption of TQM concepts. Detailed questionnaires were prepared and handed out to the firm's managers, programmers, and customers. The results of the study indicate many deficiencies in applying TQM concepts, especially in the areas of planning, defining customer requirements, teamwork, relationship with suppliers, and adopting standards and performance measures. One of the major consequences of these deficiencies is considerably increased programming errors and delays in delivery. Recommendations on achieving quality are discussed.

  13. Techniques to improve the economics of limestone FGDS

    SciTech Connect

    Bresowar, G.E.; Klingspor, J.

    1995-12-31

    Many utilities have evaluated the cost of scrubbing versus fuel switching in various plans and scenarios to determine the most economical means for meeting the requirements of the new law. Presently, the future cost of removing a ton of SO{sub 2} is based on fuel switching, and the market values are in the range of $150 - $250 per ton. The perceived cost of FGDS retrofits is $250 - $400 per ton for eastern medium to high sulfur coal. ABB has studied the overall costs of FGDS and has developed a series of cost reducing improvements. and innovations. The improvements are manifested in ABBs new limestone FGDS technology known by the code phrase {open_quote}Stealth FGDS{close_quotes}. Stealth promises low capital and operating cost, high removal efficiencies for SO{sub 2} and other pollutants, little or positive environmental and economic impact on the local community, salable or non-hazardous by-products, ease of retrofit, and exceptionally short installation schedules. The concepts are being demonstrated in one system at the Miles Generating Station of Ohio Edison Company. Bearing the name {open_quote}LS-2 Advanced SO, Scrubbing{close_quotes}, the Stealth scrubber at Niles is a 110 MWe turnkey, retrofit unit to be completed 20 months after the release of engineering. It will remove 20,000 or more tons per year of SO{sub 2} from the flue gases generated by both Unit 1 and Unit 2 boilers, producing wallboard-grade gypsum. Upon completion of a four month test program, the plant will be operated by Ohio Edison for a four to five year reliability demonstration period. The performance and economic projections for LS-2 scrubbers show the technology to be quite attractive relative to projections for fuel switching when installed in a manner similar to the installation plan for Niles. The description and basis for these economic projections are described in this paper.

  14. [Molecular repair mechanisms using the Intratissue Percutaneous Electrolysis technique in patellar tendonitis].

    PubMed

    Abat, F; Valles, S L; Gelber, P E; Polidori, F; Stitik, T P; García-Herreros, S; Monllau, J C; Sanchez-Ibánez, J M

    2014-01-01

    To investigate the molecular mechanisms of tissue response after treatment with the Intratissue Percutaneous Electrolysis (EPI(®)) technique in collagenase-induced tendinopathy in Sprague-Dawley rats. Tendinopathy was induced by injecting 50 μg of type i collagenase into the patellar tendon of 24 Sprague Dawley rats of 7 months of age and weighting 300 g. The sample was divided into 4 groups: the control group, collagenase group, and two EPI(®) technique treatment groups of 3 and 6 mA, respectively. An EPI(®) treatment session was applied, and after 3 days, the tendons were analysed using immunoblotting and electrophoresis techniques. An analysis was also made of cytochrome C protein, Smac/Diablo, vascular endothelial growth factor and its receptor 2, as well as the nuclear transcription factor peroxisome proliferator-activated receptor gamma. A statistically significant increase, compared to the control group, was observed in the expression of cytochrome C, Smac/Diablo, vascular endothelial growth factor, its receptor 2 and peroxisome proliferator-activated receptor gamma in the groups in which the EPI(®) technique was applied. EPI(®) technique produces an increase in anti-inflammatory and angiogenic molecular mechanisms in collagenase-induced tendon injury in rats. Copyright © 2013 SECOT. Published by Elsevier Espana. All rights reserved.

  15. Optical birefringence and molecular orientation of crazed fibres utilizing the phase shifting interferometric technique

    NASA Astrophysics Data System (ADS)

    Sokkar, T. Z. N.; El-Farahaty, K. A.; El-Bakary, M. A.; Omar, E. Z.; Hamza, A. A.

    2017-09-01

    In this article, the features of the phase shifting interferometric technique were utilized to investigate the effect of the presence of crazes in both outer and inner layers on optical birefringence and molecular orientation of polypropylene fibres. The Pluta polarizing interference microscope was used as a phase shifting technique. This method includes adding a stepper motor with a control unit to the micrometer screw of the Pluta microscope. This optical system was calibrated to be used as a phase shifting interferometric technique. The advantage of this technique is that it can detect the crazes in both inner and outer layers of the sample under test. Via this method, the relation between the presence of the crazes (in both inner and outer layers) and the optical molecular orientation of polypropylene (PP) fibres was demonstrated. To clarify the role of this method, the spatial carrier frequency technique was used to show the effect of the presence of the crazes only in the outer layers on the phase distribution values and hence the structural properties of PP fibres.

  16. Control genes in quantitative molecular biological techniques: the variability of invariance.

    PubMed

    Stürzenbaum, S R; Kille, P

    2001-10-01

    The measurement of transcript levels constitutes the foundation of today's molecular genetics. Independent of the techniques used, quantifications are generally normalised using invariant control genes to account for sample handling, loading and experimental variation. All of the widely used control genes are evaluated, dissecting different methodological approaches and issues regarding the experimental context (e.g. development and tissue type). Furthermore, the major sources of error are highlighted when applying these techniques. Finally, different approaches undertaken to assess the invariance of control genes are critically analysed to generate a procedure that will help to discern the best control for novel experiments.

  17. Nonlinear Raman Techniques in Femtosecond Time Resolved Spectroscopy for the Analysis and Control of Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Materny, Arnulf; Konradi, Jakow; Namboodiri, Vinu; Namboodiri, Mahesh; Scaria, Abraham

    2008-11-01

    The use of four-wave mixing techniques in femtosecond time-resolved spectroscopy has considerable advantages. Due to the many degrees of freedom offered e.g. by coherent anti-Stokes Raman scattering (CARS), the dynamics even of complex systems can be analyzed in detail. Using pulse shaping techniques in combination with a self-learning loop approach, molecular mode excitation can be controlled very efficiently in a multi-photon excitation process. Results obtained from the optimal control of CARS on β-carotene are discussed.

  18. Nonlinear Raman Techniques in Femtosecond Time Resolved Spectroscopy for the Analysis and Control of Molecular Dynamics

    SciTech Connect

    Materny, Arnulf; Konradi, Jakow; Namboodiri, Vinu; Namboodiri, Mahesh; Scaria, Abraham

    2008-11-14

    The use of four-wave mixing techniques in femtosecond time-resolved spectroscopy has considerable advantages. Due to the many degrees of freedom offered e.g. by coherent anti-Stokes Raman scattering (CARS), the dynamics even of complex systems can be analyzed in detail. Using pulse shaping techniques in combination with a self-learning loop approach, molecular mode excitation can be controlled very efficiently in a multi-photon excitation process. Results obtained from the optimal control of CARS on {beta}-carotene are discussed.

  19. External ventricular drain infection: improved technique can reduce infection rates.

    PubMed

    Kitchen, William J; Singh, Navneet; Hulme, Sharon; Galea, James; Patel, Hiren C; King, Andrew T

    2011-10-01

    The placement of external ventricular drain (EVD) is a common neurosurgical procedure to drain cerebrospinal fluid (CSF) in many acute neurosurgical conditions that disrupt the normal CSF absorption pathway. Infection is the primary complication with infection rates ranging between 0% and 45%, and this is associated with significant morbidity and mortality, prolonged hospital stay and increased hospital costs.This article compares and discusses the differences in rates of EVD CSF infection between clinical neurosurgical practice and the infection rates in a group of research patients where EVDs were sampled frequently as part of the study. Patients who had EVD placed were identified by review of theatre logs from 2005-2008. A retrospective case-note review was performed with the primary end point being those patients treated with intrathecal antibiotics. Patients within the research group were identified from established data and the same primary endpoint was used. A standard silicone catheter was the EVD used in both cohorts. Patients were excluded if the EVD was placed for diagnoses other than hydrocephalus associated with aneurysmal subarachnoid haemorrhage (SAH). Ninety-four patients had 156 EVDs placed within the clinical group, 49 patients were treated giving an infection rate within this group of 52.1% per patient and 31.4% per EVD. Thirty-nine patients had 39 EVDs placed within the research group, four patients were treated, the infection rate within this group was 10.3% per EVD, p = 0.0001. Sampling or irrigating ventricular drainage systems does not increase the risk of CNS infection providing the operator has appropriate experience and has used theatre standard aseptic technique.

  20. Machine learning for molecular scattering dynamics: Gaussian Process models for improved predictions of molecular collision observables

    NASA Astrophysics Data System (ADS)

    Krems, Roman; Cui, Jie; Li, Zhiying

    2016-05-01

    We show how statistical learning techniques based on kriging (Gaussian Process regression) can be used for improving the predictions of classical and/or quantum scattering theory. In particular, we show how Gaussian Process models can be used for: (i) efficient non-parametric fitting of multi-dimensional potential energy surfaces without the need to fit ab initio data with analytical functions; (ii) obtaining scattering observables as functions of individual PES parameters; (iii) using classical trajectories to interpolate quantum results; (iv) extrapolation of scattering observables from one molecule to another; (v) obtaining scattering observables with error bars reflecting the inherent inaccuracy of the underlying potential energy surfaces. We argue that the application of Gaussian Process models to quantum scattering calculations may potentially elevate the theoretical predictions to the same level of certainty as the experimental measurements and can be used to identify the role of individual atoms in determining the outcome of collisions of complex molecules. We will show examples and discuss the applications of Gaussian Process models to improving the predictions of scattering theory relevant for the cold molecules research field. Work supported by NSERC of Canada.

  1. [Differential diagnosis of imported filariasis by molecular techniques (2006-2009)].

    PubMed

    Jiménez, Maribel; González, Luis Miguel; Bailo, Begoña; Blanco, Alejandra; García, Luz; Pérez-González, Francisco; Fuentes, Isabel; Gárate, Teresa

    2011-11-01

    The last few years has seen an increase in the number of immigrants and travellers from endemic areas where filariasis are mainly caused by Loa loa (L. loa), Mansonella perstans (M. perstans) and Wuchereria bancrofti (W. bancrofti) species. These demographic changes has led to the need for better filariae species-specific molecular diagnostic tests to solve problems, as alternatives to the more time consuming classic parasitology methods. Thus, the objective of the present work was the implementation of optimised molecular protocols (nested-PCR and ITS1-RFLP) developed in our laboratory, for the differential diagnosis of filarial parasites. The results obtained were compared with those obtained using the conventional parasitological methods. A total of 523 samples (517 peripheral blood, 5 adult worms and one vitreous body) were sent to Parasitology Department of the National Microbiology Centre, Carlos II Research Institute (ISCIII), from 47 Health Centres in the Autonomous Regions of Spain, from 2006 to 2009. The samples were studied by the Knott technique, nested-PCR and ITS1-RFLP. The molecular techniques applied on blood samples showed to be more sensitive that Knott's concentration technique in the diagnosis of both L. loa (n=12 versus n=4) and M. perstans (n=57 versus n=25) infections. The nested-PCR and ITS1-RFLP are potential diagnostic tools for daily routine laboratory species-specific and sensitive detection of L. loa and M. perstans filarial species in immigrant population and travellers from endemic areas where these filarial species are co-endemic. Knott's concentration technique was less sensitive than molecular methods and should be carried out as a complementary diagnostic assay. Copyright © 2010 Elsevier España, S.L. All rights reserved.

  2. Fiber optic profenofos sensor based on surface plasmon resonance technique and molecular imprinting.

    PubMed

    Shrivastav, Anand M; Usha, Sruthi P; Gupta, Banshi D

    2016-05-15

    A successful approach for the fabrication and characterization of an optical fiber sensor for the detection of profenofos based on surface plasmon resonance (SPR) and molecular imprinting is introduced. Molecular imprinting technology is used for the creation of three dimensional binding sites having complementary shape and size of the specific template molecule over a polymer for the recognition of the same. Binding of template molecule with molecularly imprinted polymer (MIP) layer results in the change in the dielectric nature of the sensing surface (polymer) and is identified by SPR technique. Spectral interrogation method is used for the characterization of the sensing probe. The operating profenofos concentration range of the sensor is from 10(-4) to 10(-1)µg/L. A red shift of 18.7 nm in resonance wavelength is recorded for this profenofos concentration range. The maximum sensitivity of the sensor is 12.7 nm/log (µg/L) at 10(-4)µg/L profenofos concentration. Limit of detection (LOD) of the sensor is found to be 2.5×10(-6)µg/L. Selectivity measurements predict the probe highly selective for the profenofos molecule. Besides high sensitivity due to SPR technique and selectivity due to molecular imprinting, proposed sensor has numerous other advantages like immunity to electromagnetic interference, fast response, low cost and capability of online monitoring and remote sensing of analyte due to the fabrication of the probe on optical fiber. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. A novel system identification technique for improved wearable hemodynamics assessment.

    PubMed

    Wiens, Andrew D; Inan, Omer T

    2015-05-01

    Recent advances have led to renewed interest in ballistocardiography (BCG), a noninvasive measure of the small movements of the body due to cardiovascular events. A broad range of platforms have been developed and verified for BCG measurement including beds, chairs, and weighing scales: while the body is coupled to such a platform, the cardiogenic movements are measured. Wearable BCG, measured with an accelerometer affixed to the body, may enable continuous, or more regular, monitoring during the day; however, the signals from such wearable BCGs represent local or distal accelerations of skin and tissue rather than the whole body. In this paper, we propose a novel method to reconstruct the BCG measured with a weighing scale (WS BCG) from a wearable sensor via a training step to remove these local effects. Preliminary validation of this method was performed with 15 subjects: the wearable sensor was placed at three locations on the surface of the body while WS BCG measurements were recorded simultaneously. A regularized system identification approach was used to reconstruct the WS BCG from the wearable BCG. Preliminary results suggest that the relationship between local and central disturbances is highly dependent on both the individual and the location where the accelerometer is placed on the body and that these differences can be resolved via calibration to accurately measure changes in cardiac output and contractility from a wearable sensor. Such measurements could be highly effective, for example, for improved monitoring of heart failure patients at home.

  4. Improved vapor-phase deposition technique for antistiction monolayers

    NASA Astrophysics Data System (ADS)

    Ashurst, Robert W.; Carraro, Carlo; Chinn, Jeff D.; Fuentes, Victor; Kobrin, Boris; Maboudian, Roya; Nowak, Romuald; Yi, Richard

    2004-01-01

    We have developed an improved vapor-phase deposition method and an apparatus for the wafer-scale coating of monolayer films typically used in anti-stiction applications. The method consists of a surface preparation step using an O2 plasma followed by the tunable deposition of a monolayer film in the same reactor. This process has been successfully applied to MEMS test structures and has demonstrated superior anti-stiction performance. The deposition process allows tuning of the film properties by the precise metering of the precursor and a catalyst as part of the process control scheme. The anti-stiction monolayer film deposited from dimethyldichlorosilane (DDMS), tridecafluoro-1,1,2,2-tetrahydrooctyltrichlorosilane (FOTS), and heptadecafluoro-1,1,2,2-tetrahydrodecyltrichlorosilane (FDTS) were characterized using contact angle analysis, atomic force microscopy (AFM), and X-ray photoelectron spectroscopy (XPS). The coefficient of static friction was measured using a sidewall test device and the work of adhesion using a cantilever beam array. The results showed that excellent quality, uniformity, and reproducibility could be achieved across a whole wafer using this method and equipment.

  5. Geocoding coronial data: tools and techniques to improve data quality.

    PubMed

    Freestone, Darren; Williamson, Dianne; Wollersheim, Dennis

    2012-01-01

    Clinical, administrative and demographic health information is fundamental to understanding the nature of health and evaluating the effectiveness of efforts to reduce morbidity and mortality of the population. The demographic data item 'location' is an integral part of any injury surveillance tool or injury prevention strategy. The true value of location data can only be realised once these data have been appropriately classified and quality assured. Geocoding as a means of classifying location is increasingly used in various health fields to enable spatial analysis of data. This article reports on research carried out in Australia at the National Coroners Information System (NCIS). Trends in the use of NCIS location-based data by researchers were identified. The research also aimed to establish the factors that impacted on the quality of geocoded data and the extent of this impact. A systematic analysis of the geocoding process identified source documentation, data cleaning, and software settings as key factors impacting on data quality. Understanding and application of these processes can improve data quality and therefore inform the analysis and interpretation of these data by researchers.

  6. Improved techniques for fluid diversion in oil recovery. Final report

    SciTech Connect

    Seright, R.

    1996-01-01

    This three-year project had two technical objectives. The first objective was to compare the effectiveness of gels in fluid diversion (water shutoff) with those of other types of processes. Several different types of fluid-diversion processes were compared, including those using gels, foams, emulsions, particulates, and microorganisms. The ultimate goals of these comparisons were to (1) establish which of these processes are most effective in a given application and (2) determine whether aspects of one process can be combined with those of other processes to improve performance. Analyses and experiments were performed to verify which materials are the most effective in entering and blocking high-permeability zones. The second objective of the project was to identify the mechanisms by which materials (particularly gels) selectively reduce permeability to water more than to oil. A capacity to reduce water permeability much more than oil or gas permeability is critical to the success of gel treatments in production wells if zones cannot be isolated during gel placement. Topics covered in this report include (1) determination of gel properties in fractures, (2) investigation of schemes to optimize gel placement in fractured systems, (3) an investigation of why some polymers and gels can reduce water permeability more than oil permeability, (4) consideration of whether microorganisms and particulates can exhibit placement properties that are superior to those of gels, and (5) examination of when foams may show placement properties that are superior to those of gels.

  7. Force detection technique for molecular experiments in living cells using gradient optical traps

    NASA Astrophysics Data System (ADS)

    Farre, Arnau; Lopez-Quesada, Carol; Mas, Josep; Martin-Badosa, Estela; Montes-Usategui, Mario

    2009-05-01

    The powerful results in the molecular and cellular domain that are currently obtained using optical tweezers are leading to an increasing interest in this biophysical tool. This technique uses a highly focused laser beam to noninvasively trap and manipulate microscopic particles. Moreover, once calibrated, it can be used to accurately measure the forces and positions involved in many different molecular processes. Our research interest revolves around the study of the mechanics of cytoplasmic streaming in tobacco cells. Unfortunately, standard force detection techniques are not suitable for experiments in living cells. Golgi apparatuses that need to be used as handles to interact with motor proteins propelling them along the cytoskeletal filaments are not spherical, and the cytoplasm is an optically nonhomogeneous medium. In that case, the experiment does not meet the requirements for current force calibration methods, so forces cannot be accurately measured. Here, we show a new force detection technique for gradient optical traps based on the measurement of the change in momentum of the photons of a trapping beam. This method allows the study of molecular processes in living samples, and the use of beams and particles with arbitrary shapes.

  8. The Use of Gene Modification and Advanced Molecular Structure Analyses towards Improving Alfalfa Forage

    PubMed Central

    Lei, Yaogeng; Hannoufa, Abdelali; Yu, Peiqiang

    2017-01-01

    Alfalfa is one of the most important legume forage crops in the world. In spite of its agronomic and nutritive advantages, alfalfa has some limitations in the usage of pasture forage and hay supplement. High rapid degradation of protein in alfalfa poses a risk of rumen bloat to ruminants which could cause huge economic losses for farmers. Coupled with the relatively high lignin content, which impedes the degradation of carbohydrate in rumen, alfalfa has unbalanced and asynchronous degradation ratio of nitrogen to carbohydrate (N/CHO) in rumen. Genetic engineering approaches have been used to manipulate the expression of genes involved in important metabolic pathways for the purpose of improving the nutritive value, forage yield, and the ability to resist abiotic stress. Such gene modification could bring molecular structural changes in alfalfa that are detectable by advanced structural analytical techniques. These structural analyses have been employed in assessing alfalfa forage characteristics, allowing for rapid, convenient and cost-effective analysis of alfalfa forage quality. In this article, we review two major obstacles facing alfalfa utilization, namely poor protein utilization and relatively high lignin content, and highlight genetic studies that were performed to overcome these drawbacks, as well as to introduce other improvements to alfalfa quality. We also review the use of advanced molecular structural analysis in the assessment of alfalfa forage for its potential usage in quality selection in alfalfa breeding. PMID:28146083

  9. ENHANCEMENT OF ENVIRONMENTAL SAMPLING THROUGH AN IMPROVED AIR MONITORING TECHNIQUE

    SciTech Connect

    Hanks, D

    2010-06-07

    Environmental sampling (ES) is a key component of International Atomic Energy Agency (IAEA) safeguarding approaches throughout the world. Performance of ES (e.g. air, water, vegetation, sediments, soil and biota) supports the IAEAs mission of drawing conclusions concerning the absence of undeclared nuclear material or nuclear activities in a State and has been available since the introduction of safeguards strengthening measures approved by the IAEA Board of Governors (1992-1997). A recent step-change improvement in the gathering and analysis of air samples at uranium/plutonium bulk handling facilities is an important addition to the international nuclear safeguards inspector's toolkit. Utilizing commonly used equipment throughout the IAEA network of analytical laboratories for particle analysis, researchers are developing the next generation of ES equipment for air grab and constant samples. Isotopic analysis of collected particles from an Aerosol Contaminant Extractor (ACE) silicon substrate has been performed with excellent results in determining attribute and isotopic composition of chemical elements present in an actual test-bed sample. The new collection equipment will allow IAEA nuclear safeguards inspectors to develop enhanced safeguarding approaches for complicated facilities. This paper will explore the use of air monitoring to establish a baseline environmental signature of a particular facility that could be used for comparison of consistencies in declared operations. The implementation of air monitoring will be contrasted against the use of smear ES when used during unannounced inspections, design information verification, limited frequency unannounced access, and complementary access visits at bulk handling facilities. Technical aspects of the air monitoring device and the analysis of its environmental samples will demonstrate the essential parameters required for successful application of the system.

  10. A Novel System Identification Technique for Improved Wearable Hemodynamics Assessment

    PubMed Central

    Wiens, Andrew D.; Inan, Omer T.

    2015-01-01

    Recent advances have led to renewed interest in ballistocardiography (BCG), a non-invasive measure of the small reaction forces on the body from cardiovascular events. A broad range of platforms have been developed and verified for BCG measurement including beds, chairs, and weighing scales: while the body is coupled to such a platform, the cardiogenic movements of the center-of-mass (COM) are measured. Wearable BCG, measured with an accelerometer affixed to the body, may enable continuous, or more regular, monitoring during the day; however, the signals from such wearable BCGs represent local or distal accelerations of skin and tissue rather than the displacement of the body's COM. In this paper we propose a novel method to reconstruct the COM BCG from a wearable sensor via a training step to remove these local effects. Preliminary validation of this method was performed with fifteen subjects: the wearable sensor was placed at three locations on the surface of the body while COM BCG measurements were recorded simultaneously with a modified weighing scale. A regularized system identification approach was used to reconstruct the COM BCG from the wearable signal. Preliminary results suggest that the relationship between local and central forces is highly dependent on both the individual and the location where the wearable sensor is placed on the body and that these differences can be resolved via calibration to accurately measure changes in cardiac output and contractility from a wearable sensor. Such measurements could be highly effective, for example, for improved monitoring of heart failure patients at home. PMID:25561589

  11. Techniques for Improving the Performance of Future EVA Maneuvering Systems

    NASA Technical Reports Server (NTRS)

    Williams, Trevor W.

    1995-01-01

    The Simplified Aid for EVA Rescue (SAFER) is a small propulsive backpack that was developed as an in-house effort at Johnson Space Center; it is a lightweight system which attaches to the underside of the Primary Life Support Subsystem (PLSS) backpack of the Extravehicular Mobility Unit (EMU). SAFER provides full six-axis control, as well as Automatic Attitude Hold (AAH), by means of a set of cold-gas nitrogen thrusters and a rate sensor-based control system. For compactness, a single hand controller is used, together with mode switching, to command all six axes. SAFER was successfully test-flown on the STS-64 mission in September 1994 as a Development Test Objective (DTO); development of an operational version is now proceeding. This version will be available for EVA self-rescue on the International Space Station and Mir, starting with the STS-86/Mir-7 mission in September 1997. The DTO SAFER was heavily instrumented, and produced in-flight data that was stored in a 12 MB computer memory on-board. This has allowed post-flight analysis to yield good estimates for the actual mass properties (moments and products of inertia and center of mass location) encountered on-orbit. By contrast, Manned Maneuvering Unit (MMU) post-flight results were generated mainly from analysis of video images, and so were not very accurate. The main goal of the research reported here was to use the detailed SAFER on-orbit mass properties data to optimize the design of future EVA maneuvering systems, with the aim being to improve flying qualities and/or reduce propellant consumption. The Automation, Robotics and Simulation Division Virtual Reality (VR) Laboratory proved to be a valuable research tool for such studies. A second objective of the grant was to generate an accurate dynamics model in support of the reflight of the DTO SAFER on STS-76/Mir-3. One complicating factor was the fact that a hand controller stowage box was added to the underside of SAFER on this flight; the position of

  12. The emergence of molecular profiling and omics techniques in seagrass biology; furthering our understanding of seagrasses.

    PubMed

    Davey, Peter A; Pernice, Mathieu; Sablok, Gaurav; Larkum, Anthony; Lee, Huey Tyng; Golicz, Agnieszka; Edwards, David; Dolferus, Rudy; Ralph, Peter

    2016-09-01

    Seagrass meadows are disappearing at alarming rates as a result of increasing coastal development and climate change. The emergence of omics and molecular profiling techniques in seagrass research is timely, providing a new opportunity to address such global issues. Whilst these applications have transformed terrestrial plant research, they have only emerged in seagrass research within the past decade; In this time frame we have observed a significant increase in the number of publications in this nascent field, and as of this year the first genome of a seagrass species has been sequenced. In this review, we focus on the development of omics and molecular profiling and the utilization of molecular markers in the field of seagrass biology. We highlight the advances, merits and pitfalls associated with such technology, and importantly we identify and address the knowledge gaps, which to this day prevent us from understanding seagrasses in a holistic manner. By utilizing the powers of omics and molecular profiling technologies in integrated strategies, we will gain a better understanding of how these unique plants function at the molecular level and how they respond to on-going disturbance and climate change events.

  13. Charge transport in molecular junctions: From tunneling to hopping with the probe technique

    SciTech Connect

    Kilgour, Michael; Segal, Dvira

    2015-07-14

    We demonstrate that a simple phenomenological approach can be used to simulate electronic conduction in molecular wires under thermal effects induced by the surrounding environment. This “Landauer-Büttiker’s probe technique” can properly replicate different transport mechanisms, phase coherent nonresonant tunneling, ballistic behavior, and hopping conduction. Specifically, our simulations with the probe method recover the following central characteristics of charge transfer in molecular wires: (i) the electrical conductance of short wires falls off exponentially with molecular length, a manifestation of the tunneling (superexchange) mechanism. Hopping dynamics overtakes superexchange in long wires demonstrating an ohmic-like behavior. (ii) In off-resonance situations, weak dephasing effects facilitate charge transfer, but under large dephasing, the electrical conductance is suppressed. (iii) At high enough temperatures, k{sub B}T/ϵ{sub B} > 1/25, with ϵ{sub B} as the molecular-barrier height, the current is enhanced by a thermal activation (Arrhenius) factor. However, this enhancement takes place for both coherent and incoherent electrons and it does not readily indicate on the underlying mechanism. (iv) At finite-bias, dephasing effects may impede conduction in resonant situations. We further show that memory (non-Markovian) effects can be implemented within the Landauer-Büttiker’s probe technique to model the interaction of electrons with a structured environment. Finally, we examine experimental results of electron transfer in conjugated molecular wires and show that our computational approach can reasonably reproduce reported values to provide mechanistic information.

  14. Bio-functions and molecular carbohydrate structure association study in forage with different source origins revealed using non-destructive vibrational molecular spectroscopy techniques.

    PubMed

    Ji, Cuiying; Zhang, Xuewei; Yan, Xiaogang; Mostafizar Rahman, M; Prates, Luciana L; Yu, Peiqiang

    2017-08-05

    The objectives of this study were to: 1) investigate forage carbohydrate molecular structure profiles; 2) bio-functions in terms of CHO rumen degradation characteristics and hourly effective degradation ratio of N to OM (HEDN/OM), and 3) quantify interactive association between molecular structures, bio-functions and nutrient availability. The vibrational molecular spectroscopy was applied to investigate the structure feature on a molecular basis. Two sourced-origin alfalfa forages were used as modeled forages. The results showed that the carbohydrate molecular structure profiles were highly linked to the bio-functions in terms of rumen degradation characteristics and hourly effective degradation ratio. The molecular spectroscopic technique can be used to detect forage carbohydrate structure features on a molecular basis and can be used to study interactive association between forage molecular structure and bio-functions. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Bio-functions and molecular carbohydrate structure association study in forage with different source origins revealed using non-destructive vibrational molecular spectroscopy techniques

    NASA Astrophysics Data System (ADS)

    Ji, Cuiying; Zhang, Xuewei; Yan, Xiaogang; Mostafizar Rahman, M.; Prates, Luciana L.; Yu, Peiqiang

    2017-08-01

    The objectives of this study were to: 1) investigate forage carbohydrate molecular structure profiles; 2) bio-functions in terms of CHO rumen degradation characteristics and hourly effective degradation ratio of N to OM (HEDN/OM), and 3) quantify interactive association between molecular structures, bio-functions and nutrient availability. The vibrational molecular spectroscopy was applied to investigate the structure feature on a molecular basis. Two sourced-origin alfalfa forages were used as modeled forages. The results showed that the carbohydrate molecular structure profiles were highly linked to the bio-functions in terms of rumen degradation characteristics and hourly effective degradation ratio. The molecular spectroscopic technique can be used to detect forage carbohydrate structure features on a molecular basis and can be used to study interactive association between forage molecular structure and bio-functions.

  16. Molecular Rayleigh Scattering Techniques Developed for Measuring Gas Flow Velocity, Density, Temperature, and Turbulence

    NASA Technical Reports Server (NTRS)

    Mielke, Amy F.; Seasholtz, Richard G.; Elam, Kristie A.; Panda, Jayanta

    2005-01-01

    Nonintrusive optical point-wise measurement techniques utilizing the principles of molecular Rayleigh scattering have been developed at the NASA Glenn Research Center to obtain time-averaged information about gas velocity, density, temperature, and turbulence, or dynamic information about gas velocity and density in unseeded flows. These techniques enable measurements that are necessary for validating computational fluid dynamics (CFD) and computational aeroacoustic (CAA) codes. Dynamic measurements allow the calculation of power spectra for the various flow properties. This type of information is currently being used in jet noise studies, correlating sound pressure fluctuations with velocity and density fluctuations to determine noise sources in jets. These nonintrusive techniques are particularly useful in supersonic flows, where seeding the flow with particles is not an option, and where the environment is too harsh for hot-wire measurements.

  17. Molecular Dynamics and Monte Carlo simulations in the microcanonical ensemble: Quantitative comparison and reweighting techniques.

    PubMed

    Schierz, Philipp; Zierenberg, Johannes; Janke, Wolfhard

    2015-10-07

    Molecular Dynamics (MD) and Monte Carlo (MC) simulations are the most popular simulation techniques for many-particle systems. Although they are often applied to similar systems, it is unclear to which extent one has to expect quantitative agreement of the two simulation techniques. In this work, we present a quantitative comparison of MD and MC simulations in the microcanonical ensemble. For three test examples, we study first- and second-order phase transitions with a focus on liquid-gas like transitions. We present MD analysis techniques to compensate for conservation law effects due to linear and angular momentum conservation. Additionally, we apply the weighted histogram analysis method to microcanonical histograms reweighted from MD simulations. By this means, we are able to estimate the density of states from many microcanonical simulations at various total energies. This further allows us to compute estimates of canonical expectation values.

  18. Kinetic and Diagnostic Studies of Molecular Plasmas Using Laser Absorption Techniques

    NASA Astrophysics Data System (ADS)

    Welzel, S.; Rousseau, A.; Davies, P. B.; Röpcke, J.

    2007-10-01

    Within the last decade mid infrared absorption spectroscopy between 3 and 20 μm, known as Infrared Laser Absorption Spectroscopy (IRLAS) and based on tuneable semiconductor lasers, namely lead salt diode lasers, often called tuneable diode lasers (TDL), and quantum cascade lasers (QCL) has progressed considerably as a powerful diagnostic technique for in situ studies of the fundamental physics and chemistry of molecular plasmas. The increasing interest in processing plasmas containing hydrocarbons, fluorocarbons, organo-silicon and boron compounds has lead to further applications of IRLAS because most of these compounds and their decomposition products are infrared active. IRLAS provides a means of determining the absolute concentrations of the ground states of stable and transient molecular species, which is of particular importance for the investigation of reaction kinetics. Information about gas temperature and population densities can also be derived from IRLAS measurements. A variety of free radicals and molecular ions have been detected, especially using TDLs. Since plasmas with molecular feed gases are used in many applications such as thin film deposition, semiconductor processing, surface activation and cleaning, and materials and waste treatment, this has stimulated the adaptation of infrared spectroscopic techniques to industrial requirements. The recent development of QCLs offers an attractive new option for the monitoring and control of industrial plasma processes as well as for highly time-resolved studies on the kinetics of plasma processes. The aim of the present article is threefold: (i) to review recent achievements in our understanding of molecular phenomena in plasmas, (ii) to report on selected studies of the spectroscopic properties and kinetic behaviour of radicals, and (iii) to describe the current status of advanced instrumentation for TDLAS in the mid infrared.

  19. Kinetic and Diagnostic Studies of Molecular Plasmas Using Laser Absorption Techniques

    NASA Astrophysics Data System (ADS)

    Röpcke, Jürgen; Engeln, Richard; Schram, Daan; Rousseau, Antoine; Davies, Paul B.

    Within the last decade, mid-infrared absorption spectroscopy between 3 and 20 μm - known as infrared laser absorption spectroscopy (IRLAS) and based on tunable semiconductor lasers, namely lead salt diode lasers, often called tunable diode lasers (TDLs), and quantum cascade lasers (QCLs) - has progressed considerably as a powerful diagnostic technique for in situ studies of the fundamental physics and chemistry of molecular plasmas. The increasing interest in processing plasmas containing hydrocarbons, fluorocarbons, and organosilicon compounds has led to further applications of IRLAS because most of these compounds and their decomposition products are infrared active. IRLAS provides a means of determining the absolute concentrations of the ground states of stable and transient molecular species, which is of particular importance for the investigation of reaction kinetics. Information about gas temperature and population densities can also be derived from IRLAS measurements. A variety of free radicals and molecular ions have been detected, especially using TDLs. Since plasmas with molecular feed gases are used in many applications such as thin film deposition, semiconductor processing, surface activation and cleaning, and materials and waste treatment, this has stimulated the adaptation of infrared spectroscopic techniques to industrial requirements. The recent development of QCLs offers an attractive new option for the monitoring and control of industrial plasma processes as well as for highly time-resolved studies on the kinetics of plasma processes. The aim of the present contribution is threefold (1) to review recent achievements in our understanding of molecular phenomena in plasmas including interactions with solid surfaces, (2) to report on selected studies of the spectroscopic properties and kinetic behavior of radicals, and (3) to review new applications of QCLs and to describe the current status of advanced instrumentation for QCLAS in the midinfrared.

  20. Molecular bases and improvement of heat tolerance in crop plants

    USDA-ARS?s Scientific Manuscript database

    High temperature is a major constraint to crop productivity, causing substantial reductions in yield and quality, and expected to become a more devastating factor due to global warming. A better understanding of molecular mechanisms of tolerance to high temperatures is necessary for designing and de...

  1. Probing the molecular interaction of triazole fungicides with human serum albumin by multispectroscopic techniques and molecular modeling.

    PubMed

    Zhang, Jing; Zhuang, Shulin; Tong, Changlun; Liu, Weiping

    2013-07-31

    Triazole fungicides, one category of broad-spectrum fungicides, are widely applied in agriculture and medicine. The extensive use leads to many residues and casts potential detrimental effects on aquatic ecosystems and human health. After exposure of the human body, triazole fungicides may penetrate into the bloodstream and interact with plasma proteins. Whether they could have an impact on the structure and function of proteins is still poorly understood. By using multispectroscopic techniques and molecular modeling, the interaction of several typical triazole fungicides with human serum albumin (HSA), the major plasma protein, was investigated. The steady-state and time-resolved fluorescence spectra manifested that static type, due to complex formation, was the dominant mechanism for fluorescence quenching. Structurally related binding modes speculated by thermodynamic parameters agreed with the prediction of molecular modeling. For triadimefon, hydrogen bonding with Arg-218 and Arg-222 played an important role, whereas for imazalil, myclobutanil, and penconazole, the binding process was mainly contributed by hydrophobic and electrostatic interactions. Via alterations in three-dimensional fluorescence and circular dichroism spectral properties, it was concluded that triazoles could induce slight conformational and some microenvironmental changes of HSA. It is anticipated that these data can provide some information for possible toxicity risk of triazole fungicides to human health and be helpful in reinforcing the supervision of food safety.

  2. Molecular Phenotyping Combines Molecular Information, Biological Relevance, and Patient Data to Improve Productivity of Early Drug Discovery.

    PubMed

    Drawnel, Faye Marie; Zhang, Jitao David; Küng, Erich; Aoyama, Natsuyo; Benmansour, Fethallah; Araujo Del Rosario, Andrea; Jensen Zoffmann, Sannah; Delobel, Frédéric; Prummer, Michael; Weibel, Franziska; Carlson, Coby; Anson, Blake; Iacone, Roberto; Certa, Ulrich; Singer, Thomas; Ebeling, Martin; Prunotto, Marco

    2017-05-18

    Today, novel therapeutics are identified in an environment which is intrinsically different from the clinical context in which they are ultimately evaluated. Using molecular phenotyping and an in vitro model of diabetic cardiomyopathy, we show that by quantifying pathway reporter gene expression, molecular phenotyping can cluster compounds based on pathway profiles and dissect associations between pathway activities and disease phenotypes simultaneously. Molecular phenotyping was applicable to compounds with a range of binding specificities and triaged false positives derived from high-content screening assays. The technique identified a class of calcium-signaling modulators that can reverse disease-regulated pathways and phenotypes, which was validated by structurally distinct compounds of relevant classes. Our results advocate for application of molecular phenotyping in early drug discovery, promoting biological relevance as a key selection criterion early in the drug development cascade. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Diagnostic procedures in tularaemia with special focus on molecular and immunological techniques.

    PubMed

    Splettstoesser, W D; Tomaso, H; Al Dahouk, S; Neubauer, H; Schuff-Werner, P

    2005-08-01

    Tularaemia is a severe bacterial zoonosis caused by the highly infectious agent Francisella tularensis. It is endemic in countries of the northern hemisphere ranging from North America to Europe, Asia and Japan. Very recently, Francisella-like strains causing disease in humans were described from tropical northern Australia. In the last decade, efforts have been made to develop sensitive and specific immunological and molecular techniques for the laboratory diagnosis of tularaemia and also for the definite identification of members of the species F. tularensis and its four subspecies. Screening for the keyword 'Francisella' a Medline search over the last decade was performed and articles describing diagnostic methods for tularaemia and its causative agent were selected. Besides classical microbiological techniques (cultivation, biochemical profiling, susceptibility testing) several new immunological and molecular approaches to identify F. tularensis have been introduced employing highly specific antibodies and various polymerase chain reaction (PCR)-based methods. Whereas direct antigen detection by enzyme-linked immunosorbent assay (ELISA) or immunofluorescence might allow early presumptive diagnosis of tularaemia, these methods--like all PCR techniques--still await further evaluation. Therefore, diagnosis of tularaemia still relies mainly on the demonstration of specific antibodies in the host. ELISA and immunoblot methods started to replace the standard tube or micro-agglutination assays. However, the diagnostic value of antibody detection in the very early clinical phase of tularaemia is limited. Francisella tularensis is regarded as a 'highest priority' biological agent (category 'A' according to the CDC, Atlanta, GA, USA), thus rapid and reliable diagnosis of tularaemia is required not only for a timely onset of therapy, the handling of outbreak investigations but also for the surveillance of endemic foci. Only very recently, evaluated test kits for

  4. Synchrotron-Based Microspectroscopic Analysis of Molecular and Biopolymer Structures Using Multivariate Techniques and Advanced Multi-Components Modeling

    SciTech Connect

    Yu, P.

    2008-01-01

    More recently, advanced synchrotron radiation-based bioanalytical technique (SRFTIRM) has been applied as a novel non-invasive analysis tool to study molecular, functional group and biopolymer chemistry, nutrient make-up and structural conformation in biomaterials. This novel synchrotron technique, taking advantage of bright synchrotron light (which is million times brighter than sunlight), is capable of exploring the biomaterials at molecular and cellular levels. However, with the synchrotron RFTIRM technique, a large number of molecular spectral data are usually collected. The objective of this article was to illustrate how to use two multivariate statistical techniques: (1) agglomerative hierarchical cluster analysis (AHCA) and (2) principal component analysis (PCA) and two advanced multicomponent modeling methods: (1) Gaussian and (2) Lorentzian multi-component peak modeling for molecular spectrum analysis of bio-tissues. The studies indicated that the two multivariate analyses (AHCA, PCA) are able to create molecular spectral corrections by including not just one intensity or frequency point of a molecular spectrum, but by utilizing the entire spectral information. Gaussian and Lorentzian modeling techniques are able to quantify spectral omponent peaks of molecular structure, functional group and biopolymer. By application of these four statistical methods of the multivariate techniques and Gaussian and Lorentzian modeling, inherent molecular structures, functional group and biopolymer onformation between and among biological samples can be quantified, discriminated and classified with great efficiency.

  5. Molecular-Based Optical Measurement Techniques for Transition and Turbulence in High-Speed Flow

    NASA Technical Reports Server (NTRS)

    Bathel, Brett F.; Danehy, Paul M.; Cutler, Andrew D.

    2013-01-01

    High-speed laminar-to-turbulent transition and turbulence affect the control of flight vehicles, the heat transfer rate to a flight vehicle's surface, the material selected to protect such vehicles from high heating loads, the ultimate weight of a flight vehicle due to the presence of thermal protection systems, the efficiency of fuel-air mixing processes in high-speed combustion applications, etc. Gaining a fundamental understanding of the physical mechanisms involved in the transition process will lead to the development of predictive capabilities that can identify transition location and its impact on parameters like surface heating. Currently, there is no general theory that can completely describe the transition-to-turbulence process. However, transition research has led to the identification of the predominant pathways by which this process occurs. For a truly physics-based model of transition to be developed, the individual stages in the paths leading to the onset of fully turbulent flow must be well understood. This requires that each pathway be computationally modeled and experimentally characterized and validated. This may also lead to the discovery of new physical pathways. This document is intended to describe molecular based measurement techniques that have been developed, addressing the needs of the high-speed transition-to-turbulence and high-speed turbulence research fields. In particular, we focus on techniques that have either been used to study high speed transition and turbulence or techniques that show promise for studying these flows. This review is not exhaustive. In addition to the probe-based techniques described in the previous paragraph, several other classes of measurement techniques that are, or could be, used to study high speed transition and turbulence are excluded from this manuscript. For example, surface measurement techniques such as pressure and temperature paint, phosphor thermography, skin friction measurements and

  6. [Application of molecular diagnostic techniques in precision medicine of personalized treatment for colorectal cancer].

    PubMed

    Fu, Ji; Lin, Guole

    2016-01-01

    Precision medicine is to customize the treatment options for individual patient based on the personal genome information. Colorectal cancer (CRC) is one of the most common cancer worldwide. Molecular heterogeneity of CRC, which includes the MSI phenotype, hypermutation phenotype, and their relationship with clinical preferences, is believed to be one of the main factors responsible for the considerable variability in treatment response. The development of powerful next-generation sequencing (NGS) technologies allows us to further understand the biological behavior of colorectal cancer, and to analyze the prognosis and chemotherapeutic drug reactions by molecular diagnostic techniques, which can guide the clinical treatment. This paper will introduce the new findings in this field. Meanwhile we integrate the new progress of key pathways including EGFR, RAS, PI3K/AKT and VEGF, and the experience in selective patients through associated molecular diagnostic screening who gain better efficacy after target therapy. The technique for detecting circulating tumor DNA (ctDNA) is introduced here as well, which can identify patients with high risk for recurrence, and demonstrate the risk of chemotherapy resistance. Mechanism of tumor drug resistance may be revealed by dynamic observation of gene alteration during treatment.

  7. Integrating Nanostructured Artificial Receptors with Whispering Gallery Mode Optical Microresonators via Inorganic Molecular Imprinting Techniques

    PubMed Central

    Hammond, G. Denise; Vojta, Adam L.; Grant, Sheila A.; Hunt, Heather K.

    2016-01-01

    The creation of label-free biosensors capable of accurately detecting trace contaminants, particularly small organic molecules, is of significant interest for applications in environmental monitoring. This is achieved by pairing a high-sensitivity signal transducer with a biorecognition element that imparts selectivity towards the compound of interest. However, many environmental pollutants do not have corresponding biorecognition elements. Fortunately, biomimetic chemistries, such as molecular imprinting, allow for the design of artificial receptors with very high selectivity for the target. Here, we perform a proof-of-concept study to show how artificial receptors may be created from inorganic silanes using the molecular imprinting technique and paired with high-sensitivity transducers without loss of device performance. Silica microsphere Whispering Gallery Mode optical microresonators are coated with a silica thin film templated by a small fluorescent dye, fluorescein isothiocyanate, which serves as our model target. Oxygen plasma degradation and solvent extraction of the template are compared. Extracted optical devices are interacted with the template molecule to confirm successful sorption of the template. Surface characterization is accomplished via fluorescence and optical microscopy, ellipsometry, optical profilometry, and contact angle measurements. The quality factors of the devices are measured to evaluate the impact of the coating on device sensitivity. The resulting devices show uniform surface coating with no microstructural damage with Q factors above 106. This is the first report demonstrating the integration of these devices with molecular imprinting techniques, and could lead to new routes to biosensor creation for environmental monitoring. PMID:27314397

  8. Integrating Nanostructured Artificial Receptors with Whispering Gallery Mode Optical Microresonators via Inorganic Molecular Imprinting Techniques.

    PubMed

    Hammond, G Denise; Vojta, Adam L; Grant, Sheila A; Hunt, Heather K

    2016-06-15

    The creation of label-free biosensors capable of accurately detecting trace contaminants, particularly small organic molecules, is of significant interest for applications in environmental monitoring. This is achieved by pairing a high-sensitivity signal transducer with a biorecognition element that imparts selectivity towards the compound of interest. However, many environmental pollutants do not have corresponding biorecognition elements. Fortunately, biomimetic chemistries, such as molecular imprinting, allow for the design of artificial receptors with very high selectivity for the target. Here, we perform a proof-of-concept study to show how artificial receptors may be created from inorganic silanes using the molecular imprinting technique and paired with high-sensitivity transducers without loss of device performance. Silica microsphere Whispering Gallery Mode optical microresonators are coated with a silica thin film templated by a small fluorescent dye, fluorescein isothiocyanate, which serves as our model target. Oxygen plasma degradation and solvent extraction of the template are compared. Extracted optical devices are interacted with the template molecule to confirm successful sorption of the template. Surface characterization is accomplished via fluorescence and optical microscopy, ellipsometry, optical profilometry, and contact angle measurements. The quality factors of the devices are measured to evaluate the impact of the coating on device sensitivity. The resulting devices show uniform surface coating with no microstructural damage with Q factors above 10⁶. This is the first report demonstrating the integration of these devices with molecular imprinting techniques, and could lead to new routes to biosensor creation for environmental monitoring.

  9. Tracking down sulphate-reducing microorganisms by molecular and isotope-labelling techniques

    NASA Astrophysics Data System (ADS)

    Loy, Alexander

    2010-05-01

    Sulphate-reducing microorganisms (SRM) are of great ecological importance for carbon compound degradation and sulphur cycling in many anoxic ecosystems, including marine sediments, peatlands, and oil reservoirs. However, the activity of SRM can result in oil souring and pipeline corrosion and thus is also an economic burden for the oil industry. Molecular diversity surveys based on rRNA genes and dsrAB, genes that encode major subunits of the dissimilatory sulfite reductase, indicate that our view of the natural diversity of SRM (as we know it from cultivation) is far from being complete. This enormous phylogenetic diversity complicates unbiased identification and quantification of SRM by molecular methods such as fluorescence in situ hybridization, real-time PCR or DNA microarrays. Combining these 16S rRNA and dsrAB-based molecular methods with substrate-mediated isotope labelling techniques is a potential solution for identification and functional characterization of yet uncultivated SRM. Using SRM in peatlands as an example, the problems and opportunities of these techniques for diagnosing and monitoring SRM in the environment will be discussed in this talk.

  10. Concentration measurements in molecular gas mixtures with a two-pump pulse femtosecond polarization spectroscopy technique

    NASA Astrophysics Data System (ADS)

    Hertz, E.; Chaux, R.; Faucher, O.; Lavorel, B.

    2001-08-01

    Recently, we have demonstrated the ability of the Raman-induced polarization spectroscopy (RIPS) technique to accurately determine concentration or polarizability anisotropy ratio in low-pressure binary molecular mixtures [E. Hertz, B. Lavorel, O. Faucher, and R. Chaux, J. Chem. Phys. 113, 6629 (2000)]. It has been also pointed out that macroscopic interference, occurring when two revivals associated to different molecules time overlap, can be used to achieve measurements with picosecond time resolution. The applicability of the technique is intrinsically limited to a concentration range where the signals of both molecules are of the same magnitude. In this paper, a two-pump pulse sequence with different intensities is used to overcome this limitation. The relative molecular responses are weighted by the relative laser pump intensities to give comparable signals. Furthermore, by tuning the time delay between the two-pump pulses, macroscopic interference can be produced regardless of the accidental coincidences between the two molecular temporal responses. The study is performed in a CO2-N2O gas mixture and the concentration is measured with and without macroscopic interference. Applications of the method in the field of noninvasive diagnostics of combustion media are envisaged.

  11. Control of molecular weight of polystyrene using the reverse iodine transfer polymerization (RITP)-emulsion technique.

    PubMed

    Oh, Hyeong Geun; Shin, Hongcheol; Jung, Hyejun; Lee, Byung Hyung; Choe, Soonja

    2011-01-15

    The RITP-emulsion polymerization of styrene in the presence of molecular iodine has been successfully performed using potassium persulfate (KPS) as an initiator and 1-hexadecanesulfonate as an emulsifier under argon atmosphere at 80°C for 7 hrs in the absence of light. The effects of the iodine concentration, molar ratio between KPS and iodine, and solid contents on the molecular weight of polystyrene (PS) were studied. As the iodine concentration increased from 0.05 to 0.504 mmol under the fixed [KPS]/[I(2)] ratio at 4.5, the weight-average molecular weight of PS substantially decreased from 126,120 to 35,690 g/mol, the conversion increased from 85.0% to 95.2%, and the weight-average particle diameter decreased from 159 to 103 nm. In addition, as the ratio of [KPS]/[I(2)] increased from 0.5 to 6.0 at the fixed [I(2)] of 0.504 mmol, the weight-average molecular weight of PS decreased from 72,170 to 30,640 g/mol with high conversion between 81.7% and 96.5%. Moreover, when the styrene solid content increased from 10 to 40 wt.% at the fixed [KPS]/[I(2)] ratio of 4.5, the weight-average molecular weight of PS varied between 33,500 and 37,200 g/mol, the conversion varied between 94.9% and 89.7% and the weight-average diameter varied from 122 to 205 nm. Thus, the control of molecular weight of PS less than 100,000g/mol with high conversion (95%) and particle stability of up to 40 wt.% solid content were easily achieved through the usage of iodine with suitable ratio of [KPS]/[I(2)] in the RITP-emulsion polymerization technique, which is of great industrial importance.

  12. Comparison of molecular techniques for the typing of Mycoplasma hyopneumoniae isolates.

    PubMed

    Stakenborg, Tim; Vicca, Jo; Maes, Dominiek; Peeters, Johan; de Kruif, Aart; Haesebrouck, Freddy; Butaye, Patrick

    2006-08-01

    In this study, we compared the potential of amplified fragment length polymorphism (AFLP), random amplified polymorphic DNA (RAPD) analysis, restriction fragment length polymorphism (RFLP) of the gene encoding lipoprotein P146, and the variable number of tandem repeats (VNTR) of the P97 encoding gene, as possible methods for typing an international collection of Mycoplasma hyopneumoniae isolates. All techniques showed a typeability of 100% and high intraspecific diversity. However, the discriminatory power of the different techniques varied considerably. AFLP (>0.99) and PCR-RFLP of the P146 encoding gene (>0.98) were more discriminatory than RAPD (0.95) and estimation of the VNTR of P97 (<0.92). Other, preferentially well spread, tandem repeat regions should be included in order for this latter technique to become valuable for typing purposes. RAPD was also found to be a less interesting typing technique because of its low reproducibility between different runs. Nevertheless, all molecular techniques showed overall more resemblance between strains isolated from different pigs from the same herd. On the other hand, none of the techniques was able to show a clear relationship between the country of origin and the fingerprints obtained. We conclude that AFLP and an earlier described PFGE technique are highly reliable and discriminatory typing techniques for outlining the genomic diversity of M. hyopneumoniae isolates. Our data also show that RFLP of a highly variable gene encoding P146 may be an equally useful alternative for demonstrating intraspecific variability, although the generation of sequence variability of the gene remains unclear and must be further examined.

  13. A Partnership Training Program in Breast Cancer Research Using Molecular Imaging Techniques

    DTIC Science & Technology

    2008-07-01

    can be coated and stabilized with this multi-dentate block copolymer in water . It is expected that the novel multi-dentate ligand can improve the...detectable immediately after heat treatment . This decrease was related to the duration of heating at 43oC. Relative to the gold standard of...early stage and providing information on treatment selection and its outcome. Molecular imaging provides opportunities to fulfill the clinical needs.1

  14. Using circumacenes to improve organic electronics and molecular electronics: design clues.

    PubMed

    Pérez-Jiménez, Angel J; Sancho-García, Juan C

    2009-11-25

    Theoretical modeling is used here to ascertain the potential use of circumacenes to improve the transport parameters of pi-conjugated materials acting as: (i) the layered molecular constituent for organic electronic devices; and (ii) the molecular component of gold-molecule-gold nanobridges for molecular electronic device use. It is concluded that, to a first approximation, the molecular length or, alternatively, the HOMO-LUMO gap (HOMO: highest occupied molecular orbital; LUMO: lowest unoccupied molecular orbital) can be used to relate the two transport regimes usually found in these two fields, thus serving as a key design parameter for guaranteeing good performance of circumanthracene for both regimes. It is also clearly established that going beyond this simple relationship requires knowledge of the detailed molecule-contact geometry of the molecular nanobridge, and how its tremendous impact on the binding strength and the conductance prevents blind extrapolation of results obtained for molecular nanobridges built by means of different experimental set-ups.

  15. TMSmesh: A Robust Method for Molecular Surface Mesh Generation Using a Trace Technique.

    PubMed

    Chen, Minxin; Lu, Benzhuo

    2011-01-11

    Qualified, stable, and efficient molecular surface meshing appears to be necessitated by recent developments for realistic mathematical modeling and numerical simulation of biomolecules, especially in implicit solvent modeling (e.g., see a review in B. Z. Lu et al. Commun. Comput. Phys. 2008, 3, 973-1009). In this paper, we present a new method: tracing molecular surface for meshing (TMSmesh) the Gaussian surface of biomolecules. The method computes the surface points by solving a nonlinear equation directly, polygonizes by connecting surface points through a trace technique, and finally outputs a triangulated mesh. TMSmesh has a linear complexity with respect to the number of atoms and is shown to be capable of handling molecules consisting of more than one million atoms, which is usually difficult for the existing methods for surface generation used in molecular visualization and geometry analysis. Moreover, the meshes generated by TMSmesh are successfully tested in boundary element solutions of the Poisson-Boltzmann equation, which directly gives rise to a route to simulate electrostatic solvation of large-scale molecular systems. The binary version of TMSmesh and a set of representative PQR benchmark molecules are downloadable at our Web page http://lsec.cc.ac.cn/∼lubz/Meshing.html .

  16. Comparison of mass spectrometric techniques for generating molecular weight information on a class of ethoxylated oligomers.

    PubMed

    Parees, D M; Hanton, S D; Clark, P A; Willcox, D A

    1998-04-01

    The results of fast atom bombardment (FAB), time-of-flight secondary ion mass spectrometry (ToF-SIMS), matrix-assisted laser desorption/ionization (MALD/I), electrospray ionization (ESI), and field desorption (FD) analyses of ethoxylated oligomers of 2,4,7,9-tetramethyl-5-decyne-4,7-diol (Surfynol(®) 104) were compared.Each of these desorption mass spectrometry (MS) techniques can produce spectra of unfragmented cationized oligomers. From the observed ion series we calculate average molecular weight information. We have compared the results of mass spectrometric analyses of a series of ethoxylated Surfynol surfactants. Our data indicate that FAB, ToF-SIMS, MALDI/I, and ESI produce similar results for the lower molecular weight species, but that as the average molecular weight increases FAB and SIMS produce slightly lower results than MALD/I and FD. This could be due to increased fragmentation. ESI produced a result similar to FAB and SIMS for the highest average molecular weight material. Further experiments compare the mass spectral results with gas chromatographic quantitative data. Although gas chromatography is not expected to accurately analyze the higher mass oligomers, we observe significant differences in intensities of the short-chain oligomers (especially the 0- and 1-mers) when compared to the desorption mass spectrometer results. These differences may reflect poor cationization efficiency for very short oligomer chains in the mass spectrometric analyses.

  17. Advanced Molecular Diagnostic Techniques for Detection of Food-borne Pathogens; Current Applications and Future Challenges.

    PubMed

    Umesha, S; Manukumar, H M

    2016-01-08

    The elimination of disease-causing microbes from the food supply is a primary goal and this review deals with the overall techniques availavle for detection of food-borne pathogens. Now-a-days conventional methods are replaced by advanced methods like Biosensors, Nucleic Acid-based Tests (NAT) and different PCR based techniques used in molecular biology to identify specific pathogens. Bacillus cereus, Staphylococcus aureus, Proteus vulgaris, Escherichia coli, Campylobacter, Listeria monocytogenes, Salmonella spp, Aspergillus spp. Fusarium spp. Penicillium spp., and pathogens are detected in contaminated food items which cause always diseases in human in any one or the other way. Identification of food-borne pathogens in a short period of time is still a challenge to the scientific field in general and food technology in particular. The low level of food contamination by major pathogens requires specific sensitive detection platforms and the present area of hot research looking forward to new nanomolecular techniques for nanomaterials, make them suitable for the development of assays with high sensitivity, response time and portability. With the sound of these we attemet to highlight a comprehensive overview about food-borne pathogen detection by rapid, sensitive, accurate and cost affordable in situ analytical methods from conventional methods to recent molecular approaches for advanced food and microbiology research.

  18. Shedding light on the puzzle of drug-membrane interactions: Experimental techniques and molecular dynamics simulations.

    PubMed

    Lopes, Daniela; Jakobtorweihen, Sven; Nunes, Cláudia; Sarmento, Bruno; Reis, Salette

    2017-01-01

    Lipid membranes work as barriers, which leads to inevitable drug-membrane interactions in vivo. These interactions affect the pharmacokinetic properties of drugs, such as their diffusion, transport, distribution, and accumulation inside the membrane. Furthermore, these interactions also affect their pharmacodynamic properties with respect to both therapeutic and toxic effects. Experimental membrane models have been used to perform in vitro assessment of the effects of drugs on the biophysical properties of membranes by employing different experimental techniques. In in silico studies, molecular dynamics simulations have been used to provide new insights at an atomistic level, which enables the study of properties that are difficult or even impossible to measure experimentally. Each model and technique has its advantages and disadvantages. Hence, combining different models and techniques is necessary for a more reliable study. In this review, the theoretical backgrounds of these (in vitro and in silico) approaches are presented, followed by a discussion of the pharmacokinetic and pharmacodynamic properties of drugs that are related to their interactions with membranes. All approaches are discussed in parallel to present for a better connection between experimental and simulation studies. Finally, an overview of the molecular dynamics simulation studies used for drug-membrane interactions is provided. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Nanotools and molecular techniques to rapidly identify and fight bacterial infections.

    PubMed

    Dinarelli, S; Girasole, M; Kasas, S; Longo, G

    2016-01-20

    Reducing the emergence and spread of antibiotic-resistant bacteria is one of the major healthcare issues of our century. In addition to the increased mortality, infections caused by multi-resistant bacteria drastically enhance the healthcare costs, mainly because of the longer duration of illness and treatment. While in the last 20years, bacterial identification has been revolutionized by the introduction of new molecular techniques, the current phenotypic techniques to determine the susceptibilities of common Gram-positive and Gram-negative bacteria require at least two days from collection of clinical samples. Therefore, there is an urgent need for the development of new technologies to determine rapidly drug susceptibility in bacteria and to achieve faster diagnoses. These techniques would also lead to a better understanding of the mechanisms that lead to the insurgence of the resistance, greatly helping the quest for new antibacterial systems and drugs. In this review, we describe some of the tools most currently used in clinical and microbiological research to study bacteria and to address the challenge of infections. We discuss the most interesting advancements in the molecular susceptibility testing systems, with a particular focus on the many applications of the MALDI-TOF MS system. In the field of the phenotypic characterization protocols, we detail some of the most promising semi-automated commercial systems and we focus on some emerging developments in the field of nanomechanical sensors, which constitute a step towards the development of rapid and affordable point-of-care testing devices and techniques. While there is still no innovative technique that is capable of completely substituting for the conventional protocols and clinical practices, many exciting new experimental setups and tools could constitute the basis of the standard testing package of future microbiological tests.

  20. Pressurised metered dose inhaler-spacer technique in young children improves with video instruction.

    PubMed

    Shaw, Nicole; Le Souëf, Peter; Turkovic, Lidija; McCahon, Lucy; Kicic, Anthony; Sly, Peter D; Devadason, Sunalene; Schultz, André

    2016-07-01

    The importance of good device technique to maximise delivery of aerosolised medications is widely recognised. Pressurised metered dose inhaler (pMDI)-spacer technique was investigated in 122 children, aged 2-7 years, with asthma. Eight individual steps of device technique were evaluated before and after viewing an instructional video for correct device technique. Video measurements were repeated every three months for nine months. Device technique improved directly after video instruction at the baseline study visit (p < 0.001) but had no immediate effect at subsequent visits. Additionally, pMDI-spacer technique improved with successive visits over one year for the group overall as evidenced by increases in the proportion of children scoring maximal (p = 0.02) and near-maximal (p = 0.04) scores. Repeated video instruction over time improves inhaler technique in young children. • Correct device technique is considered essential for sufficient delivery of inhaled medication. • Poor inhaler use is common in young asthmatic children using pressurised metered dose inhalers and spacers. What is New: • Video instruction could be used as a strategy to improve device technique in young children.

  1. Future Directions in Pain Management: Integrating Anatomically Selective Delivery Techniques With Novel Molecularly Selective Agents.

    PubMed

    Pleticha, Josef; Maus, Timothy P; Beutler, Andreas S

    2016-04-01

    Treatment for chronic, locoregional pain ranks among the most prevalent unmet medical needs. The failure of systemic analgesic drugs, such as opioids, is often due to their off-target toxicity, development of tolerance, and abuse potential. Interventional pain procedures provide target specificity but lack pharmacologically selective agents with long-term efficacy. Gene therapy vectors are a new tool for the development of molecularly selective pain therapies, which have already been proved to provide durable analgesia in preclinical models. Taken together, advances in image-guided delivery and gene therapy may lead to a new class of dual selective analgesic treatments integrating the molecular selectivity of analgesic genes with the anatomic selectivity of interventional delivery techniques.

  2. A technique for mass spectrometer measurements of atomic and molecular oxygen in the lower thermosphere

    NASA Technical Reports Server (NTRS)

    Kayser, D. C.; Potter, W. E.

    1978-01-01

    A neutral mass spectrometer with a quasi-open ion source was flown on each of the Atmosphere Explorer (AE) C, D, and E satellites. The three instruments provided an opportunity to study the effects of different source insert materials on the source surface chemistry. It was found that, after a period of conditioning in space, the recombination coefficient of atomic oxygen on gold appears to be substantially lower than it is on Nichrome V. The lower recombination coefficient on gold allows the spectrometer to directly measure a significant fraction of the incident atomic oxygen, making it possible to distinguish between ambient O and O2. Equations are developed to calculate the atomic and molecular oxygen densities. Preliminary measurements of molecular oxygen densities obtained by this technique agree well with measurements taken in the fly-through mode of operation.

  3. Measuring molecular biomarkers in epidemiologic studies: laboratory techniques and biospecimen considerations.

    PubMed

    Erickson, Heidi S

    2012-09-28

    The future of personalized medicine depends on the ability to efficiently and rapidly elucidate a reliable set of disease-specific molecular biomarkers. High-throughput molecular biomarker analysis methods have been developed to identify disease risk, diagnostic, prognostic, and therapeutic targets in human clinical samples. Currently, high throughput screening allows us to analyze thousands of markers from one sample or one marker from thousands of samples and will eventually allow us to analyze thousands of markers from thousands of samples. Unfortunately, the inherent nature of current high throughput methodologies, clinical specimens, and cost of analysis is often prohibitive for extensive high throughput biomarker analysis. This review summarizes the current state of high throughput biomarker screening of clinical specimens applicable to genetic epidemiology and longitudinal population-based studies with a focus on considerations related to biospecimens, laboratory techniques, and sample pooling. Copyright © 2012 John Wiley & Sons, Ltd.

  4. Novel cytogenetic and molecular techniques in the diagnosis of congenital anomalies in newborns.

    PubMed

    Szczałuba, Krzysztof; Śmigiel, Robert

    2015-01-01

    Knowledge of what causes developmental disorders, including congenital structural defects/anomalies, in the newborn population, facilitates the choice of further investigations, therapy and rehabilitation, allows the use of appropriate prophylaxis against comorbidities, makes it possible to specify prognosis, as well as provide reliable family counselling (both pre- and postnatal). Attempting to formulate a clinical diagnosis of a specific congenital anomaly syndrome, with or without dysmorphic features, based on history and detailed physical examination, remains crucial for the selection of the right genetic testing. Modern methods of molecular cytogenetics and molecular biology are targeted in nature (microdeletion MLPA, single gene sequencing) or are capable of analyzing the genome as a whole (array CGH, newgeneration sequencing). Especially the latter techniques are now causing a rapid increase of diagnostic efficacy across different age groups, including newborns.

  5. A new crossed molecular beam apparatus using time-sliced ion velocity imaging technique

    SciTech Connect

    Wu Guorong; Zhang Weiqing; Pan Huilin; Shuai Quan; Jiang Bo; Dai Dongxu; Yang Xueming

    2008-09-15

    A new crossed molecular beam apparatus has been constructed for investigating polyatomic chemical reactions using the time-sliced ion velocity map imaging technique. A unique design is adopted for one of the two beam sources and allows us to set up the molecular beam source either horizontally or vertically. This can be conveniently used to produce versatile atomic or radical beams from photodissociation and as well as electric discharge. Intensive H-atom beam source with high speed ratio was produced by photodissociation of the HI molecule and was reacted with the CD{sub 4} molecule. Vibrational-state resolved HD product distribution was measured by detecting the CD{sub 3} product. Preliminary results were also reported on the F+SiH{sub 4} reaction using the discharged F atom beam. These results demonstrate that this new instrument is a powerful tool for investigating chemical dynamics of polyatomic reactions.

  6. Improvement in Empirical Potential Functions for Increasing the Utility of Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Yamashita, Takefumi

    Accurate modeling of potential functions is critical for realistic molecular dynamics (MD) simulations. In this study, improvement in potential functions is discussed by revisiting the multistate empirical valence bond (MS-EVB) method and the FUJI force field. The MS-EVB method enables simulation of dynamic chemical reactions in various situations. In this study, excess protons in water under shear were investigated by combining the MS-EVB method with the non-equilibrium MD technique. It was found that the orientation of the hydronium-like moiety is considerably more anisotropic under shear than that of the water molecule. Separately, the FUJI force field includes main-chain torsional parameters carefully derived on the basis of high-level ab initio calculations. To further demonstrate that the use of the FUJI force field improves the accuracy of MD results beyond previously reported examples, the conformational distribution of the Ala dipeptide was investigated. The results obtained using the FUJI force field agreed more closely with the experimental results than those obtained using other standard force fields. Interestingly, the MD trajectories with the FUJI force field undergo the Y conformation more frequently than those with other popular force fields. Furthermore, it was found that the choice of force field affects the structures of an antigen-antibody complex obtained using MD simulations. These improvements in the force fields essentially extend the range of applications for the MD simulation method.

  7. Applied Protein and Molecular Techniques for Characterization of B Cell Neoplasms in Horses

    PubMed Central

    Badial, Peres R.; Tallmadge, Rebecca L.; Miller, Steven; Stokol, Tracy; Richards, Kristy; Borges, Alexandre S.

    2015-01-01

    Mature B cell neoplasms cover a spectrum of diseases involving lymphoid tissues (lymphoma) or blood (leukemia), with an overlap between these two presentations. Previous studies describing equine lymphoid neoplasias have not included analyses of clonality using molecular techniques. The objective of this study was to use molecular techniques to advance the classification of B cell lymphoproliferative diseases in five adult equine patients with a rare condition of monoclonal gammopathy, B cell leukemia, and concurrent lymphadenopathy (lymphoma/leukemia). The B cell neoplasms were phenotypically characterized by gene and cell surface molecule expression, secreted immunoglobulin (Ig) isotype concentrations, Ig heavy-chain variable (IGHV) region domain sequencing, and spectratyping. All five patients had hyperglobulinemia due to IgG1 or IgG4/7 monoclonal gammopathy. Peripheral blood leukocyte immunophenotyping revealed high proportions of IgG1- or IgG4/7-positive cells and relative T cell lymphopenia. Most leukemic cells lacked the surface B cell markers CD19 and CD21. IGHG1 or IGHG4/7 gene expression was consistent with surface protein expression, and secreted isotype and Ig spectratyping revealed one dominant monoclonal peak. The mRNA expression of the B cell-associated developmental genes EBF1, PAX5, and CD19 was high compared to that of the plasma cell-associated marker CD38. Sequence analysis of the IGHV domain of leukemic cells revealed mutated Igs. In conclusion, the protein and molecular techniques used in this study identified neoplastic cells compatible with a developmental transition between B cell and plasma cell stages, and they can be used for the classification of equine B cell lymphoproliferative disease. PMID:26311245

  8. A Survey of Techniques for Modeling and Improving Reliability of Computing Systems

    SciTech Connect

    Mittal, Sparsh; Vetter, Jeffrey S.

    2015-04-24

    Recent trends of aggressive technology scaling have greatly exacerbated the occurrences and impact of faults in computing systems. This has made `reliability' a first-order design constraint. To address the challenges of reliability, several techniques have been proposed. In this study, we provide a survey of architectural techniques for improving resilience of computing systems. We especially focus on techniques proposed for microarchitectural components, such as processor registers, functional units, cache and main memory etc. In addition, we discuss techniques proposed for non-volatile memory, GPUs and 3D-stacked processors. To underscore the similarities and differences of the techniques, we classify them based on their key characteristics. We also review the metrics proposed to quantify vulnerability of processor structures. Finally, we believe that this survey will help researchers, system-architects and processor designers in gaining insights into the techniques for improving reliability of computing systems.

  9. A Survey of Techniques for Modeling and Improving Reliability of Computing Systems

    DOE PAGES

    Mittal, Sparsh; Vetter, Jeffrey S.

    2015-04-24

    Recent trends of aggressive technology scaling have greatly exacerbated the occurrences and impact of faults in computing systems. This has made `reliability' a first-order design constraint. To address the challenges of reliability, several techniques have been proposed. In this study, we provide a survey of architectural techniques for improving resilience of computing systems. We especially focus on techniques proposed for microarchitectural components, such as processor registers, functional units, cache and main memory etc. In addition, we discuss techniques proposed for non-volatile memory, GPUs and 3D-stacked processors. To underscore the similarities and differences of the techniques, we classify them based onmore » their key characteristics. We also review the metrics proposed to quantify vulnerability of processor structures. Finally, we believe that this survey will help researchers, system-architects and processor designers in gaining insights into the techniques for improving reliability of computing systems.« less

  10. Robotic Spent Fuel Monitoring – It is time to improve old approaches and old techniques!

    SciTech Connect

    Tobin, Stephen Joseph; Dasari, Venkateswara Rao; Trellue, Holly Renee

    2016-12-13

    This report describes various approaches and techniques associated with robotic spent fuel monitoring. The purpose of this description is to improve the quality of measured signatures, reduce the inspection burden on the IAEA, and to provide frequent verification.

  11. Gender identification of Grasshopper Sparrows comparing behavioral, morphological, and molecular techniques

    USGS Publications Warehouse

    Ammer, F.K.; Wood, P.B.; McPherson, R.J.

    2008-01-01

    Correct gender identification in monomorphic species is often difficult especially if males and females do not display obvious behavioral and breeding differences. We compared gender specific morphology and behavior with recently developed DNA techniques for gender identification in the monomorphic Grasshopper Sparrow (Ammodramus savannarum). Gender was ascertained with DNA in 213 individuals using the 2550F/2718R primer set and 3% agarose gel electrophoresis. Field observations using behavior and breeding characteristics to identify gender matched DNA analyses with 100% accuracy for adult males and females. Gender was identified with DNA for all captured juveniles that did not display gender specific traits or behaviors in the field. The molecular techniques used offered a high level of accuracy and may be useful in studies of dispersal mechanisms and winter assemblage composition in monomorphic species.

  12. A modified staining technique for arbuscular mycorrhiza compatible with molecular probes.

    PubMed

    Pitet, M; Camprubí, A; Calvet, C; Estaún, V

    2009-02-01

    The effects of the different steps of the root staining on the arbuscular mycorrhizal (AM) fungal rDNA extraction and amplification have been assessed. The results obtained using molecular techniques are compared with those obtained from fresh, non-stained leek roots. A modified staining procedure that eliminates heating, the use of hydrochloric acid and trypan blue, has been proved to be the most adequate to observe the AM colonisation in different plant species with/without lignified roots allowing at the same time the subsequent rDNA extraction and amplification from the stained roots. The staining technique decreased the sensitivity of the process and a higher number of roots had to be used to obtain enough material for a positive amplification. The extraction and amplification process was reliable up to 3 days after staining. A week after staining, the amplification was not dependable and after 2 weeks there was no amplification from stained material.

  13. Improving virus production through quasispecies genomic selection and molecular breeding.

    PubMed

    Pérez-Rodríguez, Francisco J; D'Andrea, Lucía; de Castellarnau, Montserrat; Costafreda, Maria Isabel; Guix, Susana; Ribes, Enric; Quer, Josep; Gregori, Josep; Bosch, Albert; Pintó, Rosa M

    2016-11-03

    Virus production still is a challenging issue in antigen manufacture, particularly with slow-growing viruses. Deep-sequencing of genomic regions indicative of efficient replication may be used to identify high-fitness minority individuals suppressed by the ensemble of mutants in a virus quasispecies. Molecular breeding of quasispecies containing colonizer individuals, under regimes allowing more than one replicative cycle, is a strategy to select the fittest competitors among the colonizers. A slow-growing cell culture-adapted hepatitis A virus strain was employed as a model for this strategy. Using genomic selection in two regions predictive of efficient translation, the internal ribosome entry site and the VP1-coding region, high-fitness minority colonizer individuals were identified in a population adapted to conditions of artificially-induced cellular transcription shut-off. Molecular breeding of this population with a second one, also adapted to transcription shut-off and showing an overall colonizer phenotype, allowed the selection of a fast-growing population of great biotechnological potential.

  14. Improving virus production through quasispecies genomic selection and molecular breeding

    PubMed Central

    Pérez-Rodríguez, Francisco J.; D’Andrea, Lucía; de Castellarnau, Montserrat; Costafreda, Maria Isabel; Guix, Susana; Ribes, Enric; Quer, Josep; Gregori, Josep; Bosch, Albert; Pintó, Rosa M.

    2016-01-01

    Virus production still is a challenging issue in antigen manufacture, particularly with slow-growing viruses. Deep-sequencing of genomic regions indicative of efficient replication may be used to identify high-fitness minority individuals suppressed by the ensemble of mutants in a virus quasispecies. Molecular breeding of quasispecies containing colonizer individuals, under regimes allowing more than one replicative cycle, is a strategy to select the fittest competitors among the colonizers. A slow-growing cell culture-adapted hepatitis A virus strain was employed as a model for this strategy. Using genomic selection in two regions predictive of efficient translation, the internal ribosome entry site and the VP1-coding region, high-fitness minority colonizer individuals were identified in a population adapted to conditions of artificially-induced cellular transcription shut-off. Molecular breeding of this population with a second one, also adapted to transcription shut-off and showing an overall colonizer phenotype, allowed the selection of a fast-growing population of great biotechnological potential. PMID:27808108

  15. Nanoparticle Enhanced Laser Induced Breakdown Spectroscopy for Improving the Detection of Molecular Bands

    NASA Astrophysics Data System (ADS)

    Koral, Can; De Giacomo, Alessandro; Mao, Xianglei; Zorba, Vassilia; Russo, Richard E.

    2016-11-01

    Enhancement of molecular band emission in laser-induced plasmas is important for improving sensitivity and limits of detection in molecular sensing and molecular isotope analysis. In this work we introduce the use of Nanoparticle Enhanced Laser Induced Breakdown (NELIBS) for the enhancement of molecular band emission in laser-induced plasmas, and study the underlying mechanisms responsible for the observed enhancement. The use of Ag nanoparticles leads to an order of magnitude enhancement for AlO (B2Σ+ → Χ+ Σ+) system emission from an Al-based alloy. We demonstrate that the mechanism responsible for the enhancement of molecular bands differs from that of atomic emission, and can be traced down to the increased number of atomic species in NELIBS which lead to AlO molecular formation. These findings showcase the potential of NELIBS as a simple and viable technology for enhancing molecular band emission in laser-induced plasmas.

  16. An efficient and accurate molecular alignment and docking technique using ab initio quality scoring

    PubMed Central

    Füsti-Molnár, László; Merz, Kenneth M.

    2008-01-01

    An accurate and efficient molecular alignment technique is presented based on first principle electronic structure calculations. This new scheme maximizes quantum similarity matrices in the relative orientation of the molecules and uses Fourier transform techniques for two purposes. First, building up the numerical representation of true ab initio electronic densities and their Coulomb potentials is accelerated by the previously described Fourier transform Coulomb method. Second, the Fourier convolution technique is applied for accelerating optimizations in the translational coordinates. In order to avoid any interpolation error, the necessary analytical formulas are derived for the transformation of the ab initio wavefunctions in rotational coordinates. The results of our first implementation for a small test set are analyzed in detail and compared with published results of the literature. A new way of refinement of existing shape based alignments is also proposed by using Fourier convolutions of ab initio or other approximate electron densities. This new alignment technique is generally applicable for overlap, Coulomb, kinetic energy, etc., quantum similarity measures and can be extended to a genuine docking solution with ab initio scoring. PMID:18624561

  17. Advanced techniques in molecular genetics and its implications on genetic testing and screening in the Arabian Peninsula.

    PubMed

    Abu-Amero, Khaled K; Kondkar, Altaf A

    2013-10-01

    Molecular diagnosis of human disorders is referred to as the detection of the various pathogenic mutations in DNA and/or RNA samples in order to facilitate detection, diagnosis, sub-classification, prognosis, and monitoring response to therapy. The use of molecular biology techniques to expand scientific knowledge of the natural history of diseases, identify people who are at risk for acquiring specific diseases, and diagnose human diseases at the nucleic acid level. Molecular diagnostics combines laboratory medicine with the knowledge and technology of molecular genetics and has been enormously revolutionized over the last decades, benefiting from the discoveries in the field of molecular biology. This review will discuss in details the recent advances in molecular diagnostics and how the Arabian Peninsula can benefit from those techniques knowing for a fact the high percentages of consanguineous marriages and the tribal nature of marriages which resulted in high incidence of genetic diseases.

  18. Improving Health Promotion Using Quality Improvement Techniques in Australian Indigenous Primary Health Care

    PubMed Central

    Percival, Nikki; O’Donoghue, Lynette; Lin, Vivian; Tsey, Komla; Bailie, Ross Stewart

    2016-01-01

    Although some areas of clinical health care are becoming adept at implementing continuous quality improvement (CQI) projects, there has been limited experimentation of CQI in health promotion. In this study, we examined the impact of a CQI intervention on health promotion in four Australian Indigenous primary health care centers. Our study objectives were to (a) describe the scope and quality of health promotion activities, (b) describe the status of health center system support for health promotion activities, and (c) introduce a CQI intervention and examine the impact on health promotion activities and health centers systems over 2 years. Baseline assessments showed suboptimal health center systems support for health promotion and significant evidence-practice gaps. After two annual CQI cycles, there were improvements in staff understanding of health promotion and systems for planning and documenting health promotion activities had been introduced. Actions to improve best practice health promotion, such as community engagement and intersectoral partnerships, were inhibited by the way health center systems were organized, predominately to support clinical and curative services. These findings suggest that CQI can improve the delivery of evidence-based health promotion by engaging front line health practitioners in decision-making processes about the design/redesign of health center systems to support the delivery of best practice health promotion. However, further and sustained improvements in health promotion will require broader engagement of management, senior staff, and members of the local community to address organizational and policy level barriers. PMID:27066470

  19. Improving Health Promotion Using Quality Improvement Techniques in Australian Indigenous Primary Health Care.

    PubMed

    Percival, Nikki; O'Donoghue, Lynette; Lin, Vivian; Tsey, Komla; Bailie, Ross Stewart

    2016-01-01

    Although some areas of clinical health care are becoming adept at implementing continuous quality improvement (CQI) projects, there has been limited experimentation of CQI in health promotion. In this study, we examined the impact of a CQI intervention on health promotion in four Australian Indigenous primary health care centers. Our study objectives were to (a) describe the scope and quality of health promotion activities, (b) describe the status of health center system support for health promotion activities, and (c) introduce a CQI intervention and examine the impact on health promotion activities and health centers systems over 2 years. Baseline assessments showed suboptimal health center systems support for health promotion and significant evidence-practice gaps. After two annual CQI cycles, there were improvements in staff understanding of health promotion and systems for planning and documenting health promotion activities had been introduced. Actions to improve best practice health promotion, such as community engagement and intersectoral partnerships, were inhibited by the way health center systems were organized, predominately to support clinical and curative services. These findings suggest that CQI can improve the delivery of evidence-based health promotion by engaging front line health practitioners in decision-making processes about the design/redesign of health center systems to support the delivery of best practice health promotion. However, further and sustained improvements in health promotion will require broader engagement of management, senior staff, and members of the local community to address organizational and policy level barriers.

  20. Molecular Weight Determination by an Improved Temperature-Monitored Vapor-Density Method.

    ERIC Educational Resources Information Center

    Grider, Douglas J.; And Others

    1988-01-01

    Recommends determining molecular weights of liquids by use of a thermocouple. Utilizing a mathematical gas equation, the molecular weight can be determined from the measurement of the vapor temperature upon complete evaporation. Lists benefits as reduced time and cost, and improved safety factors. (ML)

  1. Molecular Weight Determination by an Improved Temperature-Monitored Vapor-Density Method.

    ERIC Educational Resources Information Center

    Grider, Douglas J.; And Others

    1988-01-01

    Recommends determining molecular weights of liquids by use of a thermocouple. Utilizing a mathematical gas equation, the molecular weight can be determined from the measurement of the vapor temperature upon complete evaporation. Lists benefits as reduced time and cost, and improved safety factors. (ML)

  2. A top-down approach to prepare silicoaluminophosphate molecular sieve nanocrystals with improved catalytic activity.

    PubMed

    Yang, Miao; Tian, Peng; Wang, Chan; Yuan, Yangyang; Yang, Yue; Xu, Shutao; He, Yanli; Liu, Zhongmin

    2014-02-21

    Silicoaluminophosphate SAPO-34 molecular sieve nanocrystals have been prepared by a post-synthesis milling and recrystallization method, which is further proven to be universally applicable to other SAPO molecular sieves. The obtained SAPO-34 with reduced Si enrichment on the external surface shows considerably improved catalytic performance in the MTO reaction.

  3. Evaluation of genetically modified sugarcane lines carrying Cry 1AC gene using molecular marker techniques.

    PubMed

    Ismail, Roba M

    2013-01-01

    Five genetically modified insect resistant sugarcane lines harboring the Bt Cry 1AC gene to produce insecticidal proteins were compared with non-transgenic control by using three types of molecular marker techniques namely, RAPD, ISSR and AFLP. These techniques were applied on transgenic and non-transgenic plants to investigate the genetic variations, which may appear in sugarcane clones. This variation might demonstrate the genomic changes associated with the transformation process, which could change important molecular basis of various biological phenomena. Genetic variations were screened using 22 different RAPD primers, 10 ISSR primers and 13 AFLP primer combinations. Analysis of RAPD and ISSR banding patterns gave no exclusive evidence for genetic variations. Meanwhile, the percentage of polymorphic bands was 0.45% in each of RAPD and ISSR, while the polymorphism generated by AFLP analysis was 1.8%. The maximum percentage of polymorphic bands was 1.4%, 1.1% and 5.5% in RAPD, ISSR and AFLP, respectively. These results demonstrate that most transgenic lines showed genomic homogeneity and verified minor genomic changes. Dendrograms revealing the relationships among the transgenic and control plants were developed from the data of each of the three marker types.

  4. Molecular characterization of the plant biopolyester cutin by AFM and spectroscopic techniques.

    PubMed

    Benítez, José J; Matas, Antonio J; Heredia, Antonio

    2004-08-01

    Atomic force microscopy, FT-IR spectroscopy, and solid-state nuclear magnetic resonance have been used to improve our current knowledge on the molecular characteristics of the biopolyester cutin, the main component of the plant cuticle. After comparison of samples of cutin isolated from young and mature tomato fruit cuticles has been possible to establish different degrees of cross-linking in the biopolymer and that the polymer is mainly formed after esterification of secondary hydroxyl groups of the monomers that form this type of cutin. Atomic force microscopy gave useful structural information on the molecular topography of the outer surface of the isolated samples. The texture of these samples is a consequence of the cross-linking degree or chemical status of the polymer. Thus, the more dense and cross-linked cutin from ripe or mature tomato fruit is characterized by a flatter and more globular texture in addition to the development of elongated and orientated superstructures.

  5. Recent applications of boxed molecular dynamics: a simple multiscale technique for atomistic simulations

    PubMed Central

    Booth, Jonathan; Vazquez, Saulo; Martinez-Nunez, Emilio; Marks, Alison; Rodgers, Jeff; Glowacki, David R.; Shalashilin, Dmitrii V.

    2014-01-01

    In this paper, we briefly review the boxed molecular dynamics (BXD) method which allows analysis of thermodynamics and kinetics in complicated molecular systems. BXD is a multiscale technique, in which thermodynamics and long-time dynamics are recovered from a set of short-time simulations. In this paper, we review previous applications of BXD to peptide cyclization, solution phase organic reaction dynamics and desorption of ions from self-assembled monolayers (SAMs). We also report preliminary results of simulations of diamond etching mechanisms and protein unfolding in atomic force microscopy experiments. The latter demonstrate a correlation between the protein's structural motifs and its potential of mean force. Simulations of these processes by standard molecular dynamics (MD) is typically not possible, because the experimental time scales are very long. However, BXD yields well-converged and physically meaningful results. Compared with other methods of accelerated MD, our BXD approach is very simple; it is easy to implement, and it provides an integrated approach for simultaneously obtaining both thermodynamics and kinetics. It also provides a strategy for obtaining statistically meaningful dynamical results in regions of configuration space that standard MD approaches would visit only very rarely. PMID:24982247

  6. Recent applications of boxed molecular dynamics: a simple multiscale technique for atomistic simulations.

    PubMed

    Booth, Jonathan; Vazquez, Saulo; Martinez-Nunez, Emilio; Marks, Alison; Rodgers, Jeff; Glowacki, David R; Shalashilin, Dmitrii V

    2014-08-06

    In this paper, we briefly review the boxed molecular dynamics (BXD) method which allows analysis of thermodynamics and kinetics in complicated molecular systems. BXD is a multiscale technique, in which thermodynamics and long-time dynamics are recovered from a set of short-time simulations. In this paper, we review previous applications of BXD to peptide cyclization, solution phase organic reaction dynamics and desorption of ions from self-assembled monolayers (SAMs). We also report preliminary results of simulations of diamond etching mechanisms and protein unfolding in atomic force microscopy experiments. The latter demonstrate a correlation between the protein's structural motifs and its potential of mean force. Simulations of these processes by standard molecular dynamics (MD) is typically not possible, because the experimental time scales are very long. However, BXD yields well-converged and physically meaningful results. Compared with other methods of accelerated MD, our BXD approach is very simple; it is easy to implement, and it provides an integrated approach for simultaneously obtaining both thermodynamics and kinetics. It also provides a strategy for obtaining statistically meaningful dynamical results in regions of configuration space that standard MD approaches would visit only very rarely.

  7. Molecular Breeding Strategy and Challenges Towards Improvement of Blast Disease Resistance in Rice Crop.

    PubMed

    Ashkani, Sadegh; Rafii, Mohd Y; Shabanimofrad, Mahmoodreza; Miah, Gous; Sahebi, Mahbod; Azizi, Parisa; Tanweer, Fatah A; Akhtar, Mohd Sayeed; Nasehi, Abbas

    2015-01-01

    Rice is a staple and most important security food crop consumed by almost half of the world's population. More rice production is needed due to the rapid population growth in the world. Rice blast caused by the fungus, Magnaporthe oryzae is one of the most destructive diseases of this crop in different part of the world. Breakdown of blast resistance is the major cause of yield instability in several rice growing areas. There is a need to develop strategies providing long-lasting disease resistance against a broad spectrum of pathogens, giving protection for a long time over a broad geographic area, promising for sustainable rice production in the future. So far, molecular breeding approaches involving DNA markers, such as QTL mapping, marker-aided selection, gene pyramiding, allele mining and genetic transformation have been used to develop new resistant rice cultivars. Such techniques now are used as a low-cost, high-throughput alternative to conventional methods allowing rapid introgression of disease resistance genes into susceptible varieties as well as the incorporation of multiple genes into individual lines for more durable blast resistance. The paper briefly reviewed the progress of studies on this aspect to provide the interest information for rice disease resistance breeding. This review includes examples of how advanced molecular method have been used in breeding programs for improving blast resistance. New information and knowledge gained from previous research on the recent strategy and challenges towards improvement of blast disease such as pyramiding disease resistance gene for creating new rice varieties with high resistance against multiple diseases will undoubtedly provide new insights into the rice disease control.

  8. Molecular Breeding Strategy and Challenges Towards Improvement of Blast Disease Resistance in Rice Crop

    PubMed Central

    Ashkani, Sadegh; Rafii, Mohd Y.; Shabanimofrad, Mahmoodreza; Miah, Gous; Sahebi, Mahbod; Azizi, Parisa; Tanweer, Fatah A.; Akhtar, Mohd Sayeed; Nasehi, Abbas

    2015-01-01

    Rice is a staple and most important security food crop consumed by almost half of the world’s population. More rice production is needed due to the rapid population growth in the world. Rice blast caused by the fungus, Magnaporthe oryzae is one of the most destructive diseases of this crop in different part of the world. Breakdown of blast resistance is the major cause of yield instability in several rice growing areas. There is a need to develop strategies providing long-lasting disease resistance against a broad spectrum of pathogens, giving protection for a long time over a broad geographic area, promising for sustainable rice production in the future. So far, molecular breeding approaches involving DNA markers, such as QTL mapping, marker-aided selection, gene pyramiding, allele mining and genetic transformation have been used to develop new resistant rice cultivars. Such techniques now are used as a low-cost, high-throughput alternative to conventional methods allowing rapid introgression of disease resistance genes into susceptible varieties as well as the incorporation of multiple genes into individual lines for more durable blast resistance. The paper briefly reviewed the progress of studies on this aspect to provide the interest information for rice disease resistance breeding. This review includes examples of how advanced molecular method have been used in breeding programs for improving blast resistance. New information and knowledge gained from previous research on the recent strategy and challenges towards improvement of blast disease such as pyramiding disease resistance gene for creating new rice varieties with high resistance against multiple diseases will undoubtedly provide new insights into the rice disease control. PMID:26635817

  9. Molecular investigation on the interaction of spermine with proteinase K by multispectroscopic techniques and molecular simulation studies.

    PubMed

    Hosseini-Koupaei, Mansoore; Shareghi, Behzad; Saboury, Ali Akbar; Davar, Fateme

    2017-01-01

    The alteration in structure, function and stability of proteinase K in the presence of spermine was investigated using spectroscopic methods and simulation techniques. The stability and enzyme activity of proteinase K-spermine complex were significantly enhanced as compared to that of the pure enzyme. The increase in the value of Vmax and the catalytic efficiency of Proteinase K in presence of spermine confirmed that the polyamine could bring the enzyme hyperactivation. UV-vis spectroscopy, intrinsic fluorescence and circular dichroism methods demonstrated that the binding of spermine changed the microenvironment and structure of proteinase K. The fluorescence studies, showing that spermine quenched the intensity of proteinase K with static mechanism. Thermodynamic parameters analysis suggested that hydrogen bond and van der Waals forces play a key role in complex stability which is in agreement with modeling studies. The CD spectra represented the secondary structure alteration of proteinase K with an increase in α-helicity and a decrease in β-sheet of proteinase K upon spermine conjugation. The molecular simulation results proposed that spermine could interact with proteinase K spontaneously at single binding site, which is in agreement with spectroscopic results. This agreement between experimental and theoretical results may be a worth method for protein-ligand complex studies.

  10. Triage quality control is missing tools-a new observation technique for ED quality improvement.

    PubMed

    Malmström, Tomi; Harjola, Veli-Pekka; Torkki, Paulus; Kumpulainen, Salla; Malmström, Raija

    2017-04-01

    Correct assessment of patient urgency is critical to ensuring patient safety in emergency departments (EDs). Although significant time and effort have been devoted to developing triage systems, less attention has been paid to the development of quality control. The aim of this study is to introduce and test observation technique, which enables identifying of patient groups at risk of erroneous assessment in triage. The introduced technique is aimed to be less laborious to use than existing triage quality control methods. The study developed an observation technique for identifying patients with possible erroneous assessments in triage. Data sample for the observation technique is carried out with survey form filled in by nurse. Hospital ED with ~74 000 patient visits annually. Consecutive adult patients in an ED for baseline study period of 14 days (1774 patients) in 2010 and control study period of 4 days (541 patients) in 2012. Triage observation technique for continuous improvement of triage performance. Primary measures of triage improvement were triage accuracy and nurses' ability to predict patient admissions. With the observation technique the ED staff was able to identify patient groups at risk for erroneous triage. Under-triage related mostly to patients with chest pain, shortness of breath, collapse, stomach pain and infections. Instead injures and muscular skeletal symptoms were seldom undertriaged even though they are common. EDs can control triage quality with simple observation technique. The usability of observation technique and triage quality improvement process were good.

  11. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques.

    PubMed Central

    Katchalski-Katzir, E; Shariv, I; Eisenstein, M; Friesem, A A; Aflalo, C; Vakser, I A

    1992-01-01

    A geometric recognition algorithm was developed to identify molecular surface complementarity. It is based on a purely geometric approach and takes advantage of techniques applied in the field of pattern recognition. The algorithm involves an automated procedure including (i) a digital representation of the molecules (derived from atomic coordinates) by three-dimensional discrete functions that distinguishes between the surface and the interior; (ii) the calculation, using Fourier transformation, of a correlation function that assesses the degree of molecular surface overlap and penetration upon relative shifts of the molecules in three dimensions; and (iii) a scan of the relative orientations of the molecules in three dimensions. The algorithm provides a list of correlation values indicating the extent of geometric match between the surfaces of the molecules; each of these values is associated with six numbers describing the relative position (translation and rotation) of the molecules. The procedure is thus equivalent to a six-dimensional search but much faster by design, and the computation time is only moderately dependent on molecular size. The procedure was tested and validated by using five known complexes for which the correct relative position of the molecules in the respective adducts was successfully predicted. The molecular pairs were deoxyhemoglobin and methemoglobin, tRNA synthetase-tyrosinyl adenylate, aspartic proteinase-peptide inhibitor, and trypsin-trypsin inhibitor. A more realistic test was performed with the last two pairs by using the structures of uncomplexed aspartic proteinase and trypsin inhibitor, respectively. The results are indicative of the extent of conformational changes in the molecules tolerated by the algorithm. Images PMID:1549581

  12. Imaging patterns predict patient survival and molecular subtype in glioblastoma via machine learning techniques.

    PubMed

    Macyszyn, Luke; Akbari, Hamed; Pisapia, Jared M; Da, Xiao; Attiah, Mark; Pigrish, Vadim; Bi, Yingtao; Pal, Sharmistha; Davuluri, Ramana V; Roccograndi, Laura; Dahmane, Nadia; Martinez-Lage, Maria; Biros, George; Wolf, Ronald L; Bilello, Michel; O'Rourke, Donald M; Davatzikos, Christos

    2016-03-01

    MRI characteristics of brain gliomas have been used to predict clinical outcome and molecular tumor characteristics. However, previously reported imaging biomarkers have not been sufficiently accurate or reproducible to enter routine clinical practice and often rely on relatively simple MRI measures. The current study leverages advanced image analysis and machine learning algorithms to identify complex and reproducible imaging patterns predictive of overall survival and molecular subtype in glioblastoma (GB). One hundred five patients with GB were first used to extract approximately 60 diverse features from preoperative multiparametric MRIs. These imaging features were used by a machine learning algorithm to derive imaging predictors of patient survival and molecular subtype. Cross-validation ensured generalizability of these predictors to new patients. Subsequently, the predictors were evaluated in a prospective cohort of 29 new patients. Survival curves yielded a hazard ratio of 10.64 for predicted long versus short survivors. The overall, 3-way (long/medium/short survival) accuracy in the prospective cohort approached 80%. Classification of patients into the 4 molecular subtypes of GB achieved 76% accuracy. By employing machine learning techniques, we were able to demonstrate that imaging patterns are highly predictive of patient survival. Additionally, we found that GB subtypes have distinctive imaging phenotypes. These results reveal that when imaging markers related to infiltration, cell density, microvascularity, and blood-brain barrier compromise are integrated via advanced pattern analysis methods, they form very accurate predictive biomarkers. These predictive markers used solely preoperative images, hence they can significantly augment diagnosis and treatment of GB patients. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Neuro-Oncology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  13. Imaging patterns predict patient survival and molecular subtype in glioblastoma via machine learning techniques

    PubMed Central

    Macyszyn, Luke; Akbari, Hamed; Pisapia, Jared M.; Da, Xiao; Attiah, Mark; Pigrish, Vadim; Bi, Yingtao; Pal, Sharmistha; Davuluri, Ramana V.; Roccograndi, Laura; Dahmane, Nadia; Martinez-Lage, Maria; Biros, George; Wolf, Ronald L.; Bilello, Michel; O'Rourke, Donald M.; Davatzikos, Christos

    2016-01-01

    Background MRI characteristics of brain gliomas have been used to predict clinical outcome and molecular tumor characteristics. However, previously reported imaging biomarkers have not been sufficiently accurate or reproducible to enter routine clinical practice and often rely on relatively simple MRI measures. The current study leverages advanced image analysis and machine learning algorithms to identify complex and reproducible imaging patterns predictive of overall survival and molecular subtype in glioblastoma (GB). Methods One hundred five patients with GB were first used to extract approximately 60 diverse features from preoperative multiparametric MRIs. These imaging features were used by a machine learning algorithm to derive imaging predictors of patient survival and molecular subtype. Cross-validation ensured generalizability of these predictors to new patients. Subsequently, the predictors were evaluated in a prospective cohort of 29 new patients. Results Survival curves yielded a hazard ratio of 10.64 for predicted long versus short survivors. The overall, 3-way (long/medium/short survival) accuracy in the prospective cohort approached 80%. Classification of patients into the 4 molecular subtypes of GB achieved 76% accuracy. Conclusions By employing machine learning techniques, we were able to demonstrate that imaging patterns are highly predictive of patient survival. Additionally, we found that GB subtypes have distinctive imaging phenotypes. These results reveal that when imaging markers related to infiltration, cell density, microvascularity, and blood–brain barrier compromise are integrated via advanced pattern analysis methods, they form very accurate predictive biomarkers. These predictive markers used solely preoperative images, hence they can significantly augment diagnosis and treatment of GB patients. PMID:26188015

  14. New Molecular Techniques to Study the Skin Microbiota of Diabetic Foot Ulcers

    PubMed Central

    Lavigne, Jean-Philippe; Sotto, Albert; Dunyach-Remy, Catherine; Lipsky, Benjamin A.

    2015-01-01

    Significance: Diabetic foot ulcers (DFU) are a major and growing public health problem. They pose difficulties in clinical practice in both diagnosis and management. Bacterial interactions on the skin surface are important in the pathophysiology of DFU and may contribute to a delay in healing. Fully identifying bacteria present in these wounds is difficult with traditional culture methods. New molecular tools, however, have greatly contributed to our understanding of the role of the cutaneous microbiota in DFU. Recent Advances: Molecular technologies revealed new information concerning how bacteria are organized in DFU. This has led to the concept of “functionally equivalent pathogroups,” meaning that certain bacterial species which are usually nonpathogenic (or at least incapable of maintaining a chronic infection on their own) may coaggregate symbiotically in a pathogenic biofilm and act synergistically to cause a chronic infection. The distribution of pathogens in multispecies biofilms is nonrandom. The high bacterial diversity is probably related to the development of a microbial biofilm that is irreversibly attached to the wound matrix. Critical Issues: Using molecular techniques requires a financial outlay for high-cost equipment. They are still too time-consuming to perform and reporting is too delayed for them to be used in routine practice. Finally, they do not differentiate live from dead or pathogenic from nonpathogenic microorganisms. Future Directions: Molecular tools have better documented the composition and organization of the skin flora. Further advances are required to elucidate which among the many bacteria in the DFU flora are likely to be pathogens, rather than colonizers. PMID:25566413

  15. Implementing and Improving Automated Electronic Tumor Molecular Profiling

    PubMed Central

    Staggs, David B.; Hackett, Lauren; Haberman, Erich; Tod, Mike; Levy, Mia; Warner, Jeremy

    2016-01-01

    Oncology practice increasingly requires the use of molecular profiling of tumors to inform the use of targeted therapeutics. However, many oncologists use third-party laboratories to perform tumor genomic testing, and these laboratories may not have electronic interfaces with the provider’s electronic medical record (EMR) system. The resultant reporting mechanisms, such as plain-paper faxing, can reduce report fidelity, slow down reporting procedures for a physician’s practice, and make reports less accessible. Vanderbilt University Medical Center and its genomic laboratory testing partner have collaborated to create an automated electronic reporting system that incorporates genetic testing results directly into the clinical EMR. This system was iteratively tested, and causes of failure were discovered and addressed. Most errors were attributable to data entry or typographical errors that made reports unable to be linked to the correct patient in the EMR. By providing direct feedback to providers, we were able to significantly decrease the rate of transmission errors (from 6.29% to 3.84%; P < .001). The results and lessons of 1 year of using the system and transmitting 832 tumor genomic testing reports are reported. PMID:26813927

  16. Genomics, Physiology, and Molecular Breeding Approaches for Improving Salt Tolerance.

    PubMed

    Ismail, Abdelbagi M; Horie, Tomoaki

    2017-02-22

    Salt stress reduces land and water productivity and contributes to poverty and food insecurity. Increased salinization caused by human practices and climate change is progressively reducing agriculture productivity despite escalating calls for more food. Plant responses to salt stress are fairly well understood, involving numerous critical processes that are each controlled by multiple genes. Knowledge of the critical mechanisms controlling salt uptake and exclusion from functioning tissues, signaling of salt stress, and the arsenal of protective metabolites is advancing. However, little progress has been made in developing salt-tolerant varieties of crop species using standard (but slow) breeding approaches. The genetic diversity available within cultivated crops and their wild relatives provides rich sources for trait and gene discovery that has yet to be sufficiently utilized. Transforming this knowledge into modern approaches using genomics and molecular tools for precision breeding will accelerate the development of tolerant cultivars and help sustain food production. Expected final online publication date for the Annual Review of Plant Biology Volume 68 is April 29, 2017. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

  17. Using mental imagery to deliver self-regulation techniques to improve sleep behaviors.

    PubMed

    Loft, Marisa H; Cameron, Linda D

    2013-12-01

    Poor sleep habits and insufficient sleep represent significant workplace health issues. Applying self-regulation theory, we conducted a randomized, controlled trial testing the efficacy of mental imagery techniques promoting arousal reduction and implementation intentions to improve sleep behavior. We randomly assigned 104 business employees to four imagery-based interventions: arousal reduction, implementation intentions, combined arousal reduction and implementation intentions, or control imagery. Participants practiced their techniques daily for 21 days. They completed online measures of sleep quality, behaviors, and self-efficacy at baseline and Day 21; and daily measures of sleep behaviors. Participants using implementation intention imagery exhibited greater improvements in self-efficacy, sleep behaviors, sleep quality, and time to sleep relative to participants using arousal reduction and control imagery. Implementation intention imagery can improve sleep behavior for daytime employees. Use of arousal reduction imagery was unsupported. Self-regulation imagery techniques show promise for improving sleep behaviors.

  18. [The use of molecular biology techniques in the articles published in Revista Médica de Chile].

    PubMed

    Herskovic, V; Jacard, M; Reyes, H

    2000-04-01

    Molecular biology is a new branch of biological sciences, with novel laboratory techniques that are being progressively applied into biomedical and clinical research and, furthermore, into medical practice. To evaluate the use of molecular biology techniques in Chilean biomedical and clinical research and its evolution in the recent decade. All papers published as research articles, clinical experiences or case reports, in Revista Médica de Chile, during two time periods: 1987-1989 and 1997-1999, were reviewed to find out whether molecular biology techniques had been used or not. This journal publishes roughly 40% of papers generated in Chile, in biomedical or clinical topics, while another 15% appears in foreign journals. Among 341 papers published in 1987-1989, 57 (16.7%) had used one or more molecular biology techniques; in contrast, among 318 papers published in 1997-1999, 91 (28.8%) had used them (p < 0.001). Most papers using molecular biology techniques were research articles. Immunology, genetics, endocrinology, hematology, hepatology and rheumatology were the specialties providing a greater number and proportion of papers using molecular biology techniques. Chilean universities were the main institutions sponsoring these articles and FONDECYT (the Chilean Government Research Granting Office) was the main source of funding. The University of Chile (State-owned) provided most centers where these publications had been generated, followed by the Pontifical Catholic University of Chile. Molecular biology techniques have been rapidly and progressively incorporated as research tools in biomedicine and clinical medicine, in Chile. At the present time, these techniques are predominantly used in research conducted in University settings and funded by Governmental research grants.

  19. Role of Artificial Intelligence Techniques (Automatic Classifiers) in Molecular Imaging Modalities in Neurodegenerative Diseases.

    PubMed

    Cascianelli, Silvia; Scialpi, Michele; Amici, Serena; Forini, Nevio; Minestrini, Matteo; Fravolini, Mario Luca; Sinzinger, Helmut; Schillaci, Orazio; Palumbo, Barbara

    2017-01-01

    Artificial Intelligence (AI) is a very active Computer Science research field aiming to develop systems that mimic human intelligence and is helpful in many human activities, including Medicine. In this review we presented some examples of the exploiting of AI techniques, in particular automatic classifiers such as Artificial Neural Network (ANN), Support Vector Machine (SVM), Classification Tree (ClT) and ensemble methods like Random Forest (RF), able to analyze findings obtained by positron emission tomography (PET) or single-photon emission tomography (SPECT) scans of patients with Neurodegenerative Diseases, in particular Alzheimer's Disease. We also focused our attention on techniques applied in order to preprocess data and reduce their dimensionality via feature selection or projection in a more representative domain (Principal Component Analysis - PCA - or Partial Least Squares - PLS - are examples of such methods); this is a crucial step while dealing with medical data, since it is necessary to compress patient information and retain only the most useful in order to discriminate subjects into normal and pathological classes. Main literature papers on the application of these techniques to classify patients with neurodegenerative disease extracting data from molecular imaging modalities are reported, showing that the increasing development of computer aided diagnosis systems is very promising to contribute to the diagnostic process.

  20. [Attaching importance to molecular imaging techniques and promoting precision diagnosis in burns].

    PubMed

    Yu, Y M; Peng, X

    2017-08-20

    The explosive growth and advancement of computer science in recent decades have prompted the rapid development and wide applications of imaging techniques in life science, which have brought about revolutionary changes in modern medicine. Nowadays, it is possible to visualize multiple physiological and disease processes, precisely and non-invasively, in a living human body. Modern medicine has even started"reading the mind", to diagnose psychology, behavior and degenerative disorders of human brain. The border between the organic and inorganic diseases in old dogma is disappearing because imaging techniques have"visualized"the neurological and tissue changes of inorganic disorders. Severe burn injury is associated with very complicated pathological processes, which are always at the borderline between life and death. Complete recovery of patients with severe burn injury, if possible, may take years of time. Hence, a real-time monitoring of the disease process is of pivotal importance in early recognition and prevention of life-threatening complications and in assessing the therapeutic efficacy for a less-eventful recovery. Here we review and introduce some potential applications of modern imaging techniques in burn care and research, which may benefit burn patients. Some techniques are still in their early or pre-clinical stage and some are mature techniques in other fields of medicine, which are potentially applicable in burn diagnosis and treatment through our research. We intend to bring your interest to this field which may eventually lead to new revenues improving our clinical work on burn victims.

  1. Ultra-filtration of human serum for improved quantitative analysis of low molecular weight biomarkers using ATR-IR spectroscopy.

    PubMed

    Bonnier, Franck; Blasco, Hélène; Wasselet, Clément; Brachet, Guillaume; Respaud, Renaud; Carvalho, Luis Felipe C S; Bertrand, Dominique; Baker, Matthew J; Byrne, Hugh J; Chourpa, Igor

    2017-01-09

    Infrared spectroscopy is a reliable, rapid and cost effective characterisation technique, delivering a molecular finger print of the sample. It is expected that its sensitivity would enable detection of small chemical variations in biological samples associated with disease. ATR-IR is particularly suitable for liquid sample analysis and, although air drying is commonly performed before data collection, just a drop of human serum is enough for screening and early diagnosis. However, the dynamic range of constituent biochemical concentrations in the serum composition remains a limiting factor to the reliability of the technique. Using glucose as a model spike in human serum, it has been demonstrated in the present study that fractionating the serum prior to spectroscopic analysis can considerably improve the precision and accuracy of quantitative models based on the partial least squares regression algorithm. By depleting the abundant high molecular weight proteins, which otherwise dominate the spectral signatures collected, the ability to monitor changes in the concentrations of the low molecular weight constituents is enhanced. The Root Mean Square Error for the Validation set (RMSEV) has been improved by a factor of 5 following human serum processing with an average relative error in the predictive values below 1% being achieved. Moreover, the approach is easily transferable to different bodily fluids, which would support the development of more efficient and suitable clinical protocols for exploration of vibrational spectroscopy based ex vivo diagnostic tools.

  2. Improved hand hygiene technique and compliance in healthcare workers using gaming technology.

    PubMed

    Higgins, A; Hannan, M M

    2013-05-01

    In 2009, the World Health Organization recommended the use of a 'multi-faceted, multi-modal hand hygiene strategy' (Five Moments for Hand Hygiene) to improve hand hygiene compliance among healthcare workers. As part of this initiative, a training programme was implemented using an automated gaming technology training and audit tool to educate staff on hand hygiene technique in an acute healthcare setting. To determine whether using this automated training programme and audit tool as part of a multi-modal strategy would improve hand hygiene compliance and technique in an acute healthcare setting. A time-series quasi-experimental design was chosen to measure compliance with the Five Moments for Hand Hygiene and handwashing technique. The study was performed from November 2009 to April 2012. An adenosine triphosphate monitoring system was used to measure handwashing technique, and SureWash (Glanta Ltd, Dublin, Ireland), an automated auditing and training unit, was used to provide assistance with staff training and education. Hand hygiene technique and compliance improved significantly over the study period (P < 0.0001). Incorporation of new automated teaching technology into a hand hygiene programme can encourage staff participation in learning, and ultimately improve hand hygiene compliance and technique in the acute healthcare setting. Copyright © 2013 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

  3. A Research Project-Based and Self-Determined Teaching System of Molecular Biology Techniques for Undergraduates

    ERIC Educational Resources Information Center

    Zhang, Shuping

    2008-01-01

    Molecular biology techniques play a very important role in understanding the biological activity. Students who major in biology should know not only how to perform experiments, but also the reasons for performing them. Having the concept of conducting research by integrating various techniques is especially important. This paper introduces a…

  4. A Research Project-Based and Self-Determined Teaching System of Molecular Biology Techniques for Undergraduates

    ERIC Educational Resources Information Center

    Zhang, Shuping

    2008-01-01

    Molecular biology techniques play a very important role in understanding the biological activity. Students who major in biology should know not only how to perform experiments, but also the reasons for performing them. Having the concept of conducting research by integrating various techniques is especially important. This paper introduces a…

  5. An improved molecular diagnostic assay for canine and feline dermatophytosis.

    PubMed

    Cafarchia, Claudia; Gasser, Robin B; Figueredo, Luciana A; Weigl, Stefania; Danesi, Patrizia; Capelli, Gioia; Otranto, Domenico

    2013-02-01

    The few studies attempting to specifically characterize dermatophytes from hair samples of dogs and cats using PCR-based methodology relied on sequence-based analysis of selected genetic markers. The aim of the present investigation was to establish and evaluate a PCR-based approach employing genetic markers of nuclear DNA for the specific detection of dermatophytes on such specimens. Using 183 hair samples, we directly compared the test results of our one-step and nested-PCR assays with those based on conventional microscopy and in vitro culture techniques (using the latter as the reference method). The one step-PCR was highly accurate (AUC > 90) for the testing of samples from dogs, but only moderately accurate (AUC = 78.6) for cats. A nested-PCR was accurate (AUC = 93.6) for samples from cats, and achieved higher specificity (94.1 and 94.4%) and sensitivity (100 and 94.9%) for samples from dogs and cats, respectively. In addition, the nested-PCR allowed the differentiation of Microsporum canis from Trichophyton interdigitale (zoophilic) and geophilic dermatophytes (i.e., Microsporum gypseum or Trichophyton terrestre), which was not possible using the one step-assay. The PCRs evaluated here provide practical tools for diagnostic applications to support clinicians in initiating prompt and targeted chemotherapy of dermatophytoses.

  6. Chemical intermediate detection following corona discharge on volatile organic compounds: general method using molecular beam techniques

    NASA Astrophysics Data System (ADS)

    He, Luning; Sulkes, Mark

    2011-07-01

    Nonthermal plasma (NTP)-based treatments of volatile organic compounds (VOCs) have potential for effective environmental remediation. Theory and experiment that consider the basic science pertaining to discharge events have helped improve NTP remediation outcomes. If direct information on early post-discharge chemical intermediates were also available, it would likely lead to additional improvement in NTP remediation outcomes. To this point, however, experiments yielding direct information on post-NTP VOC intermediates have been limited. An approach using supersonic expansion molecular beam methods offers general promise for detection of post-discharge VOC intermediates. To illustrate the potential utility of these methods, we present mass spectra showing the growth of early products formed when pulsed corona discharges were carried out on toluene in He and then in He with added O2. Good general detection of neutral post-discharge species was obtained using 800 nm 150 fs photoionization pulses.

  7. Molecular approaches for improved clotting factors for hemophilia

    PubMed Central

    Powell, Jerry S.

    2013-01-01

    Hemophilia is caused by a functional deficiency of one of the coagulation proteins. Therapy for no other group of genetic diseases has seen the progress that has been made for hemophilia over the past 40 years, from a life expectancy in 1970 of ∼20 years for a boy born with severe hemophilia to essentially a normal life expectancy in 2013 with current prophylaxis therapy. However, these therapies are expensive and require IV infusions 3 to 4 times each week. These are exciting times for hemophilia because several new technologies that promise extended half-lives for factor products, with potential for improvements in quality of life for persons with hemophilia, are in late-phase clinical development. PMID:24065241

  8. An improved technique for the 2H/1H analysis of urines from diabetic volunteers

    USGS Publications Warehouse

    Coplen, T.B.; Harper, I.T.

    1994-01-01

    The H2-H2O ambient-temperature equilibration technique for the determination of 2H/1H ratios in urinary waters from diabetic subjects provides improved accuracy over the conventional Zn reduction technique. The standard deviation, ~ 1-2???, is at least a factor of three better than that of the Zn reduction technique on urinary waters from diabetic volunteers. Experiments with pure water and solutions containing glucose, urea and albumen indicate that there is no measurable bias in the hydrogen equilibration technique.The H2-H2O ambient-temperature equilibration technique for the determination of 2H/1H ratios in urinary waters from diabetic subjects provides improved accuracy over the conventional Zn reduction technique. The standard deviation, approximately 1-2%, is at least a factor of three better than that of the Zn reduction technique on urinary waters from diabetic volunteers. Experiments with pure water and solutions containing glucose, urea and albumen indicate that there is no measurable bias in the hydrogen equilibration technique.

  9. Power Doppler myocardial contrast echocardiography using an improved multiple frame triggered Harmonic Angio technique.

    PubMed

    Murthy, T H; Locricchio, E; Kuersten, B; Li, P; Baisch, C; Vannan, M A

    2001-04-01

    Although B-mode harmonic, intermittent-triggered myocardial contrast echocardiography (MCE) is a well-established technique, a variety of MCE techniques have been introduced recently to improve myocardial opacification. One such technique uses a power Doppler method in conjunction with multiple frame triggering (MFT), but has been limited by nonuniform microbubble destruction and blooming as well as motion artifacts. Utilizing two different contrast agents, Definity and Optison, we tested the feasibility of an improved version of Harmonic Angio MFT that utilizes a lower transmit frequency, reduced packet size, and more stringent wall filter in normal volunteers and in patients with known perfusion defects. The results showed that Harmonic Angio MFT produced fill frames with readily visible opacification and destruction frames with little visible opacification. The patterns of opacification also correlated with the expected perfusion patterns in both groups of subjects. Thus, Harmonic Angio MFT appears to be a promising new MCE technique.

  10. Use of molecular epidemiological techniques in a pilot study on workers exposed to chromium.

    PubMed Central

    Gao, M; Levy, L S; Faux, S P; Aw, T C; Braithwaite, R A; Brown, S S

    1994-01-01

    OBJECTIVES--Molecular epidemiological techniques, capable of detecting damage to DNA, were used to see if such damage occurred in the lymphocytes of a group of workers exposed to chromium. The two aims of this pilot study were to see if these new techniques might make useful biological monitoring tools for workers exposed to chromium and also, to help assess whether the current occupational exposure limit for chromium (VI) was sufficiently protective in this specific working situation. METHODS--Volunteer groups of 10 workers exposed to chromium and 10 non-exposed workers provided urine and blood samples towards the end of the working week. Chromium concentrations were measured in whole blood, plasma, lymphocytes, and urine. Lymphocytes were used to examine two forms of DNA damage in the two groups; these were the level of DNA strand breakage and, the production of 8-hydroxydeoxyguanosine. RESULTS--Chromium concentration in whole blood, plasma, and urine of workers exposed to chromium was significantly raised (P < 0.01) compared with non-exposed controls, but in isolated lymphocytes, there was only a modest but significant (P < 0.05) increase in chromium in the group exposed to chromium. There was no difference in the levels of DNA strand breaks or 8-hydroxydeoxyguanosine between the groups. Air monitoring for chromium was not undertaken but current levels for the group exposed to chromium were reported to be around 0.01 mg/m3, which is 20% of the current United Kingdom occupational exposure limit. CONCLUSIONS--We were unable to detect any damage in lymphocytic DNA due to exposure to chromium. This may have been due to the low chromium exposure (< 20% of the United Kingdom occupational exposure limit), the ability of plasma to detoxify chromium (VI) to chromium (III) before it reached the lymphocytes, or perhaps the insensitivity of the molecular techniques used. It is now important to test these and other such techniques on groups exposed to levels closer to the

  11. Vibrio parahaemolyticus: a review on the pathogenesis, prevalence, and advance molecular identification techniques

    PubMed Central

    Letchumanan, Vengadesh; Chan, Kok-Gan; Lee, Learn-Han

    2014-01-01

    Vibrio parahaemolyticus is a Gram-negative halophilic bacterium that is found in estuarine, marine and coastal environments. V. parahaemolyticus is the leading causal agent of human acute gastroenteritis following the consumption of raw, undercooked, or mishandled marine products. In rare cases, V. parahaemolyticus causes wound infection, ear infection or septicaemia in individuals with pre-existing medical conditions. V. parahaemolyticus has two hemolysins virulence factors that are thermostable direct hemolysin (tdh)-a pore-forming protein that contributes to the invasiveness of the bacterium in humans, and TDH-related hemolysin (trh), which plays a similar role as tdh in the disease pathogenesis. In addition, the bacterium is also encodes for adhesions and type III secretion systems (T3SS1 and T3SS2) to ensure its survival in the environment. This review aims at discussing the V. parahaemolyticus growth and characteristics, pathogenesis, prevalence and advances in molecular identification techniques. PMID:25566219

  12. Electrical characterization of ensemble of GaN nanowires grown by the molecular beam epitaxy technique

    NASA Astrophysics Data System (ADS)

    Kolkovsky, Vl.; Zytkiewicz, Z. R.; Sobanska, M.; Klosek, K.

    2013-08-01

    High quality Schottky contacts are formed on GaN nanowires (NWs) structures grown by the molecular beam epitaxy technique on Si(111) substrate. The current-voltage characteristics show the rectification ratio of about 103 and the leakage current of about 10-4 A/cm2 at room temperature. From the capacitance-voltage measurements the free carrier concentration in GaN NWs is determined as about 1016 cm-3. Two deep levels (H200 and E280) are found in the structures containing GaN NWs. H200 is attributed to an extended defect located at the interface between the substrate and SiNx or near the sidewalls at the bottom of the NWs whereas E280 is tentatively assigned to a gallium-vacancy- or nitrogen interstitials-related defect.

  13. Development of molecular based optical techniques for thermometry and velocimetry for fluorocarbon media

    NASA Astrophysics Data System (ADS)

    Pouya, Shahram; Blanchard, Gary; Koochesfahani, Manoochehr

    2016-11-01

    Fluorocarbon solvents are very stable inert fluids with unique physical properties that make them attractive compounds as refrigerant and several medical applications such as contrast enhanced ultrasound imaging. Since they do not mix with typical organic solvents or water, most luminescent (fluorescent or phosphorescent) probes cannot be used as tracers for optical diagnostic techniques. Perfluoropentane, a compound from this family, is used as a simulant fluid by NASA for two-phase heat transfer/mixing experiments under micro-gravity condition due to its low boiling temperature. Here we study the feasibility of employing non-intrusive optical methods for measurements of temperature and/or velocity within Perfluoropentane as the working fluid. Preliminary results of temperature and velocity measurement using Laser Induced Fluorescence and Molecular Tagging Velocimetry are presented. This work was supported by NASA Grant Number NNX16AD52A.

  14. Synthesis and Bioconjugation of Gold Nanoparticles as Potential Molecular Probes for Light-Based Imaging Techniques

    PubMed Central

    Rayavarapu, Raja Gopal; Petersen, Wilma; Ungureanu, Constantin; Post, Janine N.; van Leeuwen, Ton G.; Manohar, Srirang

    2007-01-01

    We have synthesized and characterized gold nanoparticles (spheres and rods) with optical extinction bands within the “optical imaging window.” The intense plasmon resonant driven absorption and scattering peaks of these nanoparticles make them suitable as contrast agents for optical imaging techniques. Further, we have conjugated these gold nanoparticles to a mouse monoclonal antibody specific to HER2 overexpressing SKBR3 breast carcinoma cells. The bioconjugation protocol uses noncovalent modes of binding based on a combination of electrostatic and hydrophobic interactions of the antibody and the gold surface. We discuss various aspects of the synthesis and bioconjugation protocols and the characterization results of the functionalized nanoparticles. Some proposed applications of these potential molecular probes in the field of biomedical imaging are also discussed. PMID:18354723

  15. Vibrio parahaemolyticus: a review on the pathogenesis, prevalence, and advance molecular identification techniques.

    PubMed

    Letchumanan, Vengadesh; Chan, Kok-Gan; Lee, Learn-Han

    2014-01-01

    Vibrio parahaemolyticus is a Gram-negative halophilic bacterium that is found in estuarine, marine and coastal environments. V. parahaemolyticus is the leading causal agent of human acute gastroenteritis following the consumption of raw, undercooked, or mishandled marine products. In rare cases, V. parahaemolyticus causes wound infection, ear infection or septicaemia in individuals with pre-existing medical conditions. V. parahaemolyticus has two hemolysins virulence factors that are thermostable direct hemolysin (tdh)-a pore-forming protein that contributes to the invasiveness of the bacterium in humans, and TDH-related hemolysin (trh), which plays a similar role as tdh in the disease pathogenesis. In addition, the bacterium is also encodes for adhesions and type III secretion systems (T3SS1 and T3SS2) to ensure its survival in the environment. This review aims at discussing the V. parahaemolyticus growth and characteristics, pathogenesis, prevalence and advances in molecular identification techniques.

  16. Developing an efficient technique for satellite image denoising and resolution enhancement for improving classification accuracy

    NASA Astrophysics Data System (ADS)

    Thangaswamy, Sree Sharmila; Kadarkarai, Ramar; Thangaswamy, Sree Renga Raja

    2013-01-01

    Satellite images are corrupted by noise during image acquisition and transmission. The removal of noise from the image by attenuating the high-frequency image components removes important details as well. In order to retain the useful information, improve the visual appearance, and accurately classify an image, an effective denoising technique is required. We discuss three important steps such as image denoising, resolution enhancement, and classification for improving accuracy in a noisy image. An effective denoising technique, hybrid directional lifting, is proposed to retain the important details of the images and improve visual appearance. The discrete wavelet transform based interpolation is developed for enhancing the resolution of the denoised image. The image is then classified using a support vector machine, which is superior to other neural network classifiers. The quantitative performance measures such as peak signal to noise ratio and classification accuracy show the significance of the proposed techniques.

  17. Improving SVDD classification performance on hyperspectral images via correlation based ensemble technique

    NASA Astrophysics Data System (ADS)

    Uslu, Faruk Sukru; Binol, Hamidullah; Ilarslan, Mustafa; Bal, Abdullah

    2017-02-01

    Support Vector Data Description (SVDD) is a nonparametric and powerful method for target detection and classification. The SVDD constructs a minimum hypersphere enclosing the target objects as much as possible. It has advantages of sparsity, good generalization and using kernel machines. In many studies, different methods have been offered in order to improve the performance of the SVDD. In this paper, we have presented ensemble methods to improve classification performance of the SVDD in remotely sensed hyperspectral imagery (HSI) data. Among various ensemble approaches we have selected bagging technique for training data set with different combinations. As a novel technique for weighting we have proposed a correlation based weight coefficients assignment. In this technique, correlation between each bagged classifier is calculated to give coefficients to weighted combinators. To verify the improvement performance, two hyperspectral images are processed for classification purpose. The obtained results show that the ensemble SVDD has been found to be significantly better than conventional SVDD in terms of classification accuracy.

  18. Techniques and Procedures to Improve 25mm Gunnery of the Bradley Fighting Vehicle

    DTIC Science & Technology

    1988-10-01

    Gunnery of the Bradley Fighting Vehicle DTIC Mike S. Perkins F I-ECTE Litton Computer Services Division SEP 07 1989 Litton Systems, Inc. October 1988...Classification, Techniques and Procedures to Improve 25mm Gunnery of the Bradley Fighting Vehicle 12. PERSONAL AUTHOR(S) Perkins, Mike S. (Litton Computer...Research has been conducted to develop and evaluate procedures and techniques to im- prove 25mm gunnery of the Bradley Fighting Vehicle OB1RV)P. The

  19. A comparative study of conventional and molecular techniques in diagnosis of campylobacter gastroenteritis in children.

    PubMed

    Ghosh, Roumi; Uppal, Beena; Aggarwal, Prabhav; Chakravarti, Anita; Jha, Arun Kumar; Dubey, A P

    2014-01-01

    Campylobacter species are a significant cause of gastroenteritis among children worldwide. Conventional methods for detection of Campylobacter spp. based on cultural isolation and biochemical tests are cumbersome and time consuming. Because of their superior sensitivity and cost effectiveness, molecular methods are often used for identification of the pathogens. To evaluate different diagnostic methods for identification of Campylobacter. Faecal samples were collected from 585 children (age ≤ 12 years) with acute diarrhoea admitted in a tertiary-care hospital, excluding children already on antimicrobial therapy. All samples were examined by four methods: Grams' staining, culture methods, Enzyme-Immuno Assay, and Polymerase Chain Reaction (PCR). After Grams' staining, samples were inoculated on modified charcoal cefoperazone deoxycholate agar. ProSpecT™ Microplate Assay® and PCR assay using cadF gene was done for detection of Campylobacter specific antigen and DNA, respectively, in faecal samples. McNemar's test was used to compare the results wherever applicable. 197 cases (33.67%) were found to be positive for Campylobacter by at least one method. But only 121 (20.78%) out of the 585 stool specimens tested fulfilled the positivity criteria, i.e., positive either by culture or by any two tests among other three. Culture had very low sensitivity (37.19%), whereas PCR had the highest (96.69%) sensitivity but lowest positive predictive value (86.03%). Rapid Grams' staining technique (sensitivity 63.64%) was found to be better than culture. Detection by PCR and ELISA was significantly better than by culture on selective media and Grams' staining (p<0.0001). Molecular techniques significantly increased detection rates of Campylobacter in children with diarrhoea. However, enzyme-immuno assay with high accuracy has the advantage of applicability in resource-poor settings.

  20. An effusive molecular beam technique for studies of polyatomic gas-surface reactivity and energy transfer.

    PubMed

    Cushing, G W; Navin, J K; Valadez, L; Johánek, V; Harrison, I

    2011-04-01

    An effusive molecular beam technique is described to measure alkane dissociative sticking coefficients, S(T(g), T(s); ϑ), on metal surfaces for which the impinging gas temperature, T(g), and surface temperature, T(s), can be independently varied, along with the angle of incidence, ϑ, of the impinging gas. Effusive beam experiments with T(g) = T(s) = T allow for determination of angle-resolved dissociative sticking coefficients, S(T; ϑ), which when averaged over the cos (ϑ)/π angular distribution appropriate to the impinging flux from a thermal ambient gas yield the thermal dissociative sticking coefficient, S(T). Nonequilibrium S(T(g), T(s); ϑ) measurements for which T(g) ≠ T(s) provide additional opportunities to characterize the transition state and gas-surface energy transfer at reactive energies. A resistively heated effusive molecular beam doser controls the T(g) of the impinging gas striking the surface. The flux of molecules striking the surface from the effusive beam is determined from knowledge of the dosing geometry, chamber pressure, and pumping speed. Separate experiments with a calibrated leak serve to fix the chamber pumping speed. Postdosing Auger electron spectroscopy is used to measure the carbon of the alkyl radical reaction product that is deposited on the surface as a result of alkane dissociative sticking. As implemented in a typical ultrahigh vacuum chamber for surface analysis, the technique has provided access to a dynamic range of roughly 6 orders of magnitude in the initial dissociative sticking coefficient for small alkanes on Pt(111).

  1. Sex determination of Pohnpei Micronesian kingfishers using morphological and molecular genetic techniques

    USGS Publications Warehouse

    Kesler, Dylan C.; Lopes, I.F.; Haig, Susan M.

    2006-01-01

    Conservation-oriented studies of Micronesian Kingfishers (Todiramphus cinnamominus) have been hindered by a lack of basic natural history information, despite the status of the Guam subspecies (T. c. cinnamominus) as one of the most endangered species in the world. We used tissue samples and morphometric measures from museum specimens and wild-captured Pohnpei Micronesian Kingfishers (T. c. reichenbachii) to develop methods for sex determination. We present a modified molecular protocol and a discriminant function that yields the probability that a particular individual is male or female. Our results revealed that females were significantly larger than males, and the discriminant function correctly predicted sex in 73% (30/41) of the individuals. The sex of 86% (18/21) of individuals was correctly assigned when a moderate reliability threshold was set. Sex determination using molecular genetic techniques was more reliable than methods based on morphology. Our results will facilitate recovery efforts for the critically endangered Guam Micronesian Kingfisher and provide a basis for sex determination in the 11 other endangered congeners in the Pacific Basin.

  2. Inquiry-Based Learning: Inflammation as a Model to Teach Molecular Techniques for Assessing Gene Expression†

    PubMed Central

    Gunn, Kathryn E.; McCauslin, Christine Seitz; Staiger, Jennifer; Pirone, Dana M.

    2013-01-01

    This laboratory module simulates the process used by working scientists to ask and answer a question of biological interest. Instructors facilitate acquisition of knowledge using a comprehensive, inquiry-based approach in which students learn theory, hypothesis development, experimental design, and data interpretation and presentation. Using inflammation in macrophages as a model system, students perform a series of molecular biology techniques to address the biological question: “Does stimulus ‘X’ induce inflammation?” To ask this question, macrophage cells are treated with putative inflammatory mediators and then assayed for evidence of inflammatory response. Students become familiar with their assigned mediator and the relationship between their mediator and inflammation by conducting literature searches, then using this information to generate hypotheses which address the effect of their mediator on induction of inflammation. The cellular and molecular approaches used to test their hypotheses include transfection and luciferase reporter assay, immunoblot, fluorescence microscopy, enzyme-linked immunosorbent assay, and quantitative PCR. Quantitative and qualitative reasoning skills are developed through data analysis and demonstrated by successful completion of post-lab worksheets and the generation and oral presentation of a scientific poster. Learning objective assessment relies on four instruments: pre-lab quizzes, post-lab worksheets, poster presentation, and posttest. Within three cohorts (n = 85) more than 95% of our students successfully achieved the learning objectives. PMID:24358382

  3. Application of molecular techniques for the assessment of microorganism diversity on cultural heritage objects.

    PubMed

    Otlewska, Anna; Adamiak, Justyna; Gutarowska, Beata

    2014-01-01

    As a result of their unpredictable ability to adapt to varying environmental conditions, microorganisms inhabit different types of biological niches on Earth. Owing to the key role of microorganisms in many biogeochemical processes, trends in modern microbiology emphasize the need to know and understand the structure and function of complex microbial communities. This is particularly important if the strategy relates to microbial communities that cause biodeterioration of materials that constitute our cultural heritage. Until recently, the detection and identification of microorganisms inhabiting objects of cultural value was based only on cultivation-dependent methods. In spite of many advantages, these methods provide limited information because they identify only viable organisms capable of growth under standard laboratory conditions. However, in order to carry out proper conservation and renovation, it is necessary to know the complete composition of microbial communities and their activity. This paper presents and characterizes modern techniques such as genetic fingerprinting and clone library construction for the assessment of microbial diversity based on molecular biology. Molecular methods represent a favourable alternative to culture-dependent methods and make it possible to assess the biodiversity of microorganisms inhabiting technical materials and cultural heritage objects.

  4. The persistence of bifidobacteria populations in a river measured by molecular and culture techniques.

    PubMed

    Bonjoch, X; Lucena, F; Blanch, A R

    2009-10-01

    To determine relative to faecal coliforms (FC) and sulfite-reducing clostridia (SRC), the environmental persistence of natural populations of Bifidobacterium spp. enumerated by culturing and quantitative polymerase chain reaction (q-PCR). Dialysis tubing containing river supplemented with overnight cultures of Bifidobacterium adolescentis (BA) and Bifidobacterium dentium (BD) or urban wastewater were suspended in a river for up to 10 days. At intervals, the contents of each dialysis tube were assayed using q-PCR assays for BA and BD, and selective culture media for FC, SRC, total bifidobacteria (TB), sorbitol-fermenting bifidobacteria (SFB) and cultivable BA. Mean summer T(90) values were 251 h for SRC, 92 h for FC, 48 h for BA and BD by q-PCR, and 9 h for TB. Bifidobacterium spp. was the population with the lowest persistence, showing seasonal differences in T(90) when measured by culture techniques or by q-PCR. This difference in relative persistence is because of a longer persistence of molecular targets than cultivable cells. The persistence of a viable bifidobacteria cells is shorter, but the longest persistence of molecular targets. This factor could be used for origin the faecal pollution in water for the development of microbial source tracking (MST).

  5. Molecular techniques for detection of Tribolium confusum infestations in stored products.

    PubMed

    Nowaczyk, K; Obrepalska-Steplowska, A; Gawlak, M; Throne, J E; Olejarski, P; Nawrot, J

    2009-08-01

    The confused flour beetle, Tribolium confusum Jacquelin du Val (Coleoptera: Tenebrionidae) is a stored-product pest that contaminates a wide range of food products, from flour and cereals to spices. The insect reduces food quality and is responsible for large economic losses every year. Although several methods for detection of stored-product pests are common and widely used, they are time-consuming and expensive. Therefore, establishing molecular methods of detection of stored-product pests could provide a useful alternative method. We have undertaken attempts to establish methods of detection of T. confusum based on molecular biology techniques of standard and real-time polymerase chain reaction (PCR). Total DNA of T. confusum and red flour beetle, Tribolium castaneum (Herbst) (Coleoptera: Tenebrionidae), used as a negative control, was isolated from insects and used as a template in standard and real-time PCR reactions. Specific primers have been designed on the basis of sequences of internal transcribed spacer (ITS) fragment of rDNA and subunit I of mitochondrial cytochrome oxidase of T. confusum available in the GenBank database. Standard PCR reactions with primers specific to the ITS fragment proved to be reliable and sensitive. Real-time PCR reactions with primers specific for mitochondrial DNA are considered to serve as a supplemental detection method for quantitative assessment of the infestation level.

  6. Development of Pressure Sensitive Molecular Film as a Measurement Technique for Micro-Flows

    NASA Astrophysics Data System (ADS)

    Matsuda, Y.; Mori, H.; Sakazaki, Y.; Uchida, T.; Suzuki, S.; Yamaguchi, H.; Niimi, T.

    2008-12-01

    The pressure-sensitive paint (PSP) has potential as a diagnostic tool for pressure measurement in the high Knudsen number regime because it works as a so-called "molecular sensor." However, there are few reports concerning application of the PSP to micro devices, because the conventional PSP is too thick owing to the use of polymer binder. In our previous work, we have adopted Langmuir-Blodgett (LB) technique to fabricate pressure sensitive molecular films (PSMFs) using Pd(II) Mesoporphyrin IX (PdMP). The PSMF based on PdMP has pressure sensitivity only at low pressure range (below 3 kPa). In this study, we have constructed PSMF composed of Pt(II) Mesoporphyrin IX (PtMP) to be applied to pressure measurement near atmospheric pressure. The pressure sensitivity of PSMF based on PtMP has been tested, and it is clarified that the PSMF of PtMP has equivalent pressure sensitivity of polymer PSP. Moreover, we have applied PSMF to measurement of pressure distribution of micro-channel gas flow, showing its usefulness.

  7. Full symmetry implementation in condensed matter and molecular physics-Modified group projector technique

    NASA Astrophysics Data System (ADS)

    Damnjanović, Milan; Milošević, Ivanka

    2015-06-01

    Symmetry is well established as one of the fundamental concepts in physics, accurately extracting relevant characteristics of the studied object, giving deep and transparent insight to its properties. In the solid state and molecular physics the most abundant application is reduction of the dimension of the eigenproblem of the Hamiltonian, with the resulting eigenvectors labeled by good quantum numbers, forming the so called symmetry adapted basis. Such a basis is the starting point for subsequent analysis of the physical properties of the system, performed usually by applying adequate perturbation technique. Standard procedure for finding a symmetry adapted basis involves Wigner operators, which are sums of the operators acting in the quantum state space (Hilbert space, most usually) over all elements of the symmetry group of the systems. However, both the dimension of the state space and the number of the symmetry transformations are infinite even in the simplest approximate models in crystal physics making obstacles for direct application of the standard Wigner projector technique, and its numerical implementation. On the other hand, there is a minimal part of the system, the full symmetry elementary cell (symcell), from which the whole system can be built by action of the full symmetry group elements on it. A clear heuristic idea, that symcell and full symmetry group, determine the properties of the entire system, is fully realized within modified group projector technique. Namely, when applying this technique, the full symmetry of the system is used to provide reduction of calculations to the symcell only, singling out its state space (of a finite dimension!) as the effective state space to be worked in. Physical observables, expressed through their irreducible tensor components, obtain their counterparts in this finite-dimensional space of a symcell. It remains to consider only the symmetry transformations which leave the symcell invariant. This is absolutely

  8. Limitations and improvements upon the two-level approximation for molecular nonlinear optics

    NASA Astrophysics Data System (ADS)

    Andrews, David L.; Bradshaw, David S.; Coles, Matt M.

    2011-03-01

    When parametric nonlinear processes are employed in the cause of efficient optical frequency conversion, the media involved are generally subjected to substantially off-resonant input radiation. As such, it is usually only electronic ground states of the conversion material that are significantly populated; higher levels are engaged only in the capacity of virtual states, and it is frequently assumed that just one such state dominates in determining the response. Calculating the nonlinear optical susceptibilities of molecules on this basis, excluding all but the ground and one excited state in a sum-over-states formulation, signifies the adoption of a two-level model, a technique that is widely deployed in the calculation and analysis of nonlinear optical properties. The two-level model offers tractable and physically simple representations of molecular response, including wavelength dependence; it is also the origin of the widely applied 'push-pull' approach to designing optically nonlinear chromophores. By contrast, direct ab initio calculations of optical susceptibility are commonly frustrated by a complete failure to determine such dispersion features. However, caution is required; the two-level model can deliver potentially misleading results if it is applied without regard to the criteria for its validity, especially when molecular excited states are significantly populated. On the basis of a precise, quantum electrodynamical basis for the theory, we explore in detail why there are grounds for questioning the general validity of two-level calculations in nonlinear optics; we assess the criteria for high frequency conversion efficiency and provide a new graphical method to assist in determining the applicability of a two-level model for hyperpolarizability calculations. Lastly, this paper also explores the applicability and detailed conditions for the two-level model for electronically excited molecules, identifying problematic results and providing tractable

  9. Improvement technique of sensitized HAZ by GTAW cladding applied to a BWR power plant

    SciTech Connect

    Tujimura, Hiroshi; Tamai, Yasumasa; Furukawa, Hideyasu; Kurosawa, Kouichi; Chiba, Isao; Nomura, Keiichi

    1995-12-31

    A SCC(Stress Corrosion Cracking)-resistant technique, in which the sleeve installed by expansion is melted by GTAW process without filler metal with outside water cooling, was developed. The technique was applied to ICM (In-Core Monitor) housings of a BWR power plant in 1993. The ICM housings of which materials are type 304 Stainless Steels are sensitized with high tensile residual stresses by welding to the RPV (Reactor Pressure Vessel). As the result, ICM housings have potential of SCC initiation. Therefore, the improvement technique resistant to SCC was needed. The technique can improve chemical composition of the housing inside and residual stresses of the housing outside at the same time. Sensitization of the housing inner surface area is eliminated by replacing low-carbon with proper-ferrite microstructure clad. High tensile residual stresses of housing outside surface area is improved into compressive side. Compressive stresses of outside surface are induced by thermal stresses which are caused by inside cladding with outside water cooling. The clad is required to be low-carbon metal with proper ferrite and not to have the new sensitized HAZ (Heat Affected Zone) on the surface by cladding. The effect of the technique was qualified by SCC test, chemical composition check, ferrite content measurement and residual stresses measurement etc. All equipment for remote application were developed and qualified, too. The technique was successfully applied to a BWR plant after sufficient training.

  10. An improved visualization-based force-measurement technique for short-duration hypersonic facilities

    NASA Astrophysics Data System (ADS)

    Laurence, Stuart J.; Karl, Sebastian

    2010-06-01

    This article is concerned with describing and exploring the limitations of an improved version of a recently proposed visualization-based technique for the measurement of forces and moments in short-duration hypersonic wind tunnels. The technique is based on tracking the motion of a free-flying body over a sequence of high-speed visualizations; while this idea is not new in itself, the use of high-speed digital cinematography combined with a highly accurate least-squares tracking algorithm allows improved results over what have been previously possible with such techniques. The technique precision is estimated through the analysis of artificially constructed and experimental test images, and the resulting error in acceleration measurements is characterized. For wind-tunnel scale models, position measurements to within a few microns are shown to be readily attainable. Image data from two previous experimental studies in the T5 hypervelocity shock tunnel are then reanalyzed with the improved technique: the uncertainty in the mean drag acceleration is shown to be reduced to the order of the flow unsteadiness, 2-3%, and time-resolved acceleration measurements are also shown to be possible. The response time of the technique for the configurations studied is estimated to be ˜0.5 ms. Comparisons with computations using the DLR TAU code also yield agreement to within the overall experimental uncertainty. Measurement of the pitching moment for blunt geometries still appears challenging, however.

  11. Diphtheria in the Republic of Georgia: Use of Molecular Typing Techniques for Characterization of Corynebacterium diphtheriae Strains

    PubMed Central

    Sulakvelidze, Alexander; Kekelidze, Merab; Gomelauri, Tsaro; Deng, Yingkang; Khetsuriani, Nino; Kobaidze, Ketino; De Zoysa, Aruni; Efstratiou, Androulla; Morris, J. Glenn; Imnadze, Paata

    1999-01-01

    Sixty-six Corynebacterium diphtheriae strains (62 of the gravis biotype and 4 of the mitis biotype) isolated during the Georgian diphtheria epidemic of 1993 to 1998 and 13 non-Georgian C. diphtheriae strains (10 Russian and 3 reference isolates) were characterized by (i) biotyping, (ii) toxigenicity testing with the Elek assay and PCR, (iii) the randomly amplified polymorphic DNA (RAPD) technique, and (iv) pulsed-field gel electrophoresis (PFGE). Fifteen selected strains were ribotyped. Six RAPD types and 15 PFGE patterns were identified among all strains examined, and 12 ribotypes were found among the 15 strains that were ribotyped. The Georgian epidemic apparently was caused by one major clonal group of C. diphtheriae (PFGE type A, ribotype R1), which was identical to the predominant epidemic strain(s) isolated during the concurrent diphtheria epidemic in Russia. A dendrogram based on the PFGE patterns revealed profound differences between the minor (nonpredominant) epidemic strains found in Georgia and Russia. The methodologies for RAPD typing, ribotyping, and PFGE typing of C. diphtheriae strains were improved to enable rapid and convenient molecular typing of the strains. The RAPD technique was adequate for biotype differentiation; however, PFGE and ribotyping were better (and equal to each other) at discriminating between epidemiologically related and unrelated isolates. PMID:10488190

  12. Improvement of the technique in treatment of internal hemorrhoids with Nd:YAG laser

    NASA Astrophysics Data System (ADS)

    Bao, Xiao-qing; Zhu, Jing; Shi, Hong-Min

    2005-07-01

    Objective: To observe and study the improvement of the technique in treatment of internal hemorrhoids with Nd:YAG laser and evaluate the effective rate. Methods: 60 patients of internal hemorrhoids were treated with Nd:YAG laser (10-15mw) irradiating on the mucosa of the lesions. Results: Among 60 patients, 57 patients were primarily cured with one treatment, 3 patients were primarily cured with two treatments. The effective rate was 95% with one treatment, and it reached to 100% with two treatments. Conclusions: the improvement of the technique in treatment of internal hemorrhoids with Nd:YAG laser is effective and easy to operate.

  13. Video-assisted structured teaching to improve aseptic technique during neuraxial block.

    PubMed

    Friedman, Z; Siddiqui, N; Mahmoud, S; Davies, S

    2013-09-01

    Teaching epidural catheter insertion tends to focus on developing manual dexterity rather than improving aseptic technique which usually remains poor despite increasing experience. The aim of this study was to compare epidural aseptic technique performance, by novice operators after a targeted teaching intervention, with operators taught aseptic technique before the intervention was initiated. Starting July 2008, two groups of second-year anaesthesia residents (pre- and post-teaching intervention) performing their 4-month obstetric anaesthesia rotation in a university affiliated centre were videotaped three to four times while performing epidural procedures. Trained blinded independent examiners reviewed the procedures. The primary outcome was a comparison of aseptic technique performance scores (0-30 points) graded on a scale task-specific checklist. A total of 86 sessions by 29 residents were included in the study analysis. The intraclass correlation coefficient for inter-rater reliability for the aseptic technique was 0.90. The median aseptic technique scores for the rotation period were significantly higher in the post-intervention group [27.58, inter-quartile range (IQR) 22.33-29.50 vs 16.56, IQR 13.33-22.00]. Similar results were demonstrated when scores were analysed for low, moderate, and high levels of experience throughout the rotation. Procedure-specific aseptic technique teaching, aided by video assessment and video demonstration, helped significantly improve aseptic practice by novice trainees. Future studies should consider looking at retention over longer periods of time in more senior residents.

  14. Evaluation of growth conditions and DNA extraction techniques used in the molecular analysis of dermatophytes.

    PubMed

    Gnat, S; Nowakiewicz, A; Ziółkowska, G; Trościańczyk, A; Majer-Dziedzic, B; Zięba, P

    2017-05-01

    Recent molecular methods for diagnosis of superficial mycoses have determined the need for a rapid and easy method of extracting DNA. The aim of study was to determine growth conditions and techniques of DNA extraction for Microsporum canis, Trichophyton mentagrophytes and T. verrucosum. Samples were prepared of each of the DNA extraction methods (phenol-chloroform, CTAB and four different kits) for all of the incubation periods (4, 7 and 10 days) of the cultures on the solid and in the liquid medium. The highest DNA concentrations were obtained using the phenol-chloroform method. The concentration of DNA extracted with the CTAB method accounted for 62·21%, for kits it corresponded from 35·53 to 15·41%. The analysis of the DNA weight yield revealed the highest isolation efficiency of the phenol-chloroform method, 1 mg of mycelium yielded 223·8 μg DNA. Lower DNA yield (by 39·32%) was obtained with the CTAB method; in the case of kits by 68·46-85·32%. In most of the techniques, the DNA yield on the solid medium was higher. In summary, the highest DNA yield was noted in the 7-day cultures and extraction with the phenol-chloroform method. Importantly, the type of culture was not relevant for the diagnostic result. Most mycoses are caused by fungi that reside in nature. The severity of the infection depends on the pathogenic attributes, socioeconomic factors and local environmental conditions. Recent diagnosis increasingly relies on not only the clinical features. Molecular identifications have determined the need for a rapid and easy method of extracting DNA. Usually two factors have to be considered: maximize the DNA yield and ensure that the extracted DNA is susceptible to enzymatic reactions. These data suggest that phenol-chloroform methods and a 7-day culture period may be useful for validation and constitute the first step of molecular diagnosis of dermatophytes. © 2017 The Society for Applied Microbiology.

  15. Improving patient safety and optimizing nursing teamwork using crew resource management techniques.

    PubMed

    West, Priscilla; Sculli, Gary; Fore, Amanda; Okam, Nwoha; Dunlap, Cleveland; Neily, Julia; Mills, Peter

    2012-01-01

    This project describes the application of the "sterile cockpit rule," a crew resource management (CRM) technique, targeted to improve efficacy and safety for nursing assistants in the performance of patient care duties. Crew resource management techniques have been successfully implemented in the aviation industry to improve flight safety. Application of these techniques can improve patient safety in medical settings. The Veterans Affairs (VA) National Center for Patient Safety conducted a CRM training program in select VA nursing units. One unit developed a novel application of the sterile cockpit rule to create protected time for certified nursing assistants (CNAs) while they collected vital signs and blood glucose data at the beginning of each shift. The typical nursing authority structure was reversed, with senior nurses protecting CNAs from distractions. This process led to improvements in efficiency and communication among nurses, with the added benefit of increased staff morale. Crew resource management techniques can be used to improve efficiency, morale, and patient safety in the healthcare setting.

  16. The use of molecular imaging combined with genomic techniques to understand the heterogeneity in cancer metastasis

    PubMed Central

    Chowdhury, R; Ganeshan, B; Irshad, S; Lawler, K; Eisenblätter, M; Milewicz, H; Rodriguez-Justo, M; Miles, K; Ellis, P; Groves, A; Punwani, S

    2014-01-01

    Tumour heterogeneity has, in recent times, come to play a vital role in how we understand and treat cancers; however, the clinical translation of this has lagged behind advances in research. Although significant advancements in oncological management have been made, personalized care remains an elusive goal. Inter- and intratumour heterogeneity, particularly in the clinical setting, has been difficult to quantify and therefore to treat. The histological quantification of heterogeneity of tumours can be a logistical and clinical challenge. The ability to examine not just the whole tumour but also all the molecular variations of metastatic disease in a patient is obviously difficult with current histological techniques. Advances in imaging techniques and novel applications, alongside our understanding of tumour heterogeneity, have opened up a plethora of non-invasive biomarker potential to examine tumours, their heterogeneity and the clinical translation. This review will focus on how various imaging methods that allow for quantification of metastatic tumour heterogeneity, along with the potential of developing imaging, integrated with other in vitro diagnostic approaches such as genomics and exosome analyses, have the potential role as a non-invasive biomarker for guiding the treatment algorithm. PMID:24597512

  17. The use of molecular imaging combined with genomic techniques to understand the heterogeneity in cancer metastasis.

    PubMed

    Chowdhury, R; Ganeshan, B; Irshad, S; Lawler, K; Eisenblätter, M; Milewicz, H; Rodriguez-Justo, M; Miles, K; Ellis, P; Groves, A; Punwani, S; Ng, T

    2014-06-01

    Tumour heterogeneity has, in recent times, come to play a vital role in how we understand and treat cancers; however, the clinical translation of this has lagged behind advances in research. Although significant advancements in oncological management have been made, personalized care remains an elusive goal. Inter- and intratumour heterogeneity, particularly in the clinical setting, has been difficult to quantify and therefore to treat. The histological quantification of heterogeneity of tumours can be a logistical and clinical challenge. The ability to examine not just the whole tumour but also all the molecular variations of metastatic disease in a patient is obviously difficult with current histological techniques. Advances in imaging techniques and novel applications, alongside our understanding of tumour heterogeneity, have opened up a plethora of non-invasive biomarker potential to examine tumours, their heterogeneity and the clinical translation. This review will focus on how various imaging methods that allow for quantification of metastatic tumour heterogeneity, along with the potential of developing imaging, integrated with other in vitro diagnostic approaches such as genomics and exosome analyses, have the potential role as a non-invasive biomarker for guiding the treatment algorithm.

  18. Identification of Viable Helicobacter pylori in Drinking Water Supplies by Cultural and Molecular Techniques.

    PubMed

    Santiago, Paula; Moreno, Yolanda; Ferrús, M Antonía

    2015-08-01

    Helicobacter pylori is one of the most common causes of chronic bacterial infection in humans, directly related to peptic ulcer and gastric cancer. It has been suggested that H. pylori can be acquired through different transmission routes, including water. In this study, culture and qPCR were used to detect and identify the presence of H. pylori in drinking water. Furthermore, the combined techniques PMA-qPCR and DVC-FISH were applied for detection of viable cells of H. pylori. Among 24 drinking water samples, 16 samples were positive for the presence of H. pylori, but viable cells were only detected in six samples. Characteristic colonies, covered by a mass of bacterial unspecific growth, were observed on selective agar plates from an only sample, after enrichment. The mixed culture was submitted to DVC-FISH and qPCR analysis, followed by sequencing of the amplicons. Molecular techniques confirmed the growth of H. pylori on the agar plate. Our results demonstrate for the first time that H. pylori can survive and be potentially infective in drinking water, showing that water distribution systems could be a potential route for H. pylori transmission. © 2015 John Wiley & Sons Ltd.

  19. Development of Ultra-High Molecular Weight Polyethylene (UHMWPE) Coating by Cold Spray Technique

    NASA Astrophysics Data System (ADS)

    Ravi, Kesavan; Ichikawa, Yuji; Deplancke, Tiana; Ogawa, Kazuhiro; Lame, Olivier; Cavaille, Jean-Yves

    2015-08-01

    Ultra-high molecular weight polyethylene or UHMWPE is an extremely difficult material to coat with, as it is rubbery and chemically very inert. The Cold Spray process appears to be a promising alternative processing technique but polymers are in general difficult to deposit using this method. So, attempts to develop UHMWPE coatings were made using a downstream injection cold spray technique incorporating a few modifications. A conventional cold spray machine yielded only a few deposited particles of UHMWPE on the substrate surface, but with some modifications in the nozzle geometry (especially the length and inner geometry) a thin coating of 45 μm on Al substrate was obtained. Moreover, experiments with the addition of fumed nano-alumina to the feedstock yielded a coating of 1-4 mm thickness on Al and polypropylene substrates. UHMWPE was seen to be melt crystallized during the coating formation, as can be seen from the differential calorimetry curves. Influence of nano-ceramic particles was explained by observing the creation of a bridge bond between UHMWPE particles.

  20. Nanomechanical testing technique for millimeter-sized and smaller molecular crystals.

    PubMed

    Maughan, Michael R; Carvajal, M Teresa; Bahr, David F

    2015-01-01

    Large crystals are used as a control for the development of a mounting and nanoindentation testing technique for millimeter-sized and smaller molecular crystals. Indentation techniques causing either only elastic or elastic-plastic deformation produce similar results in assessing elastic modulus, however, the elastic indents are susceptible to surface angle and roughness effects necessitating larger sample sizes for similar confidence bounds. Elastic-plastic indentations give the most accurate results and could be used to determine the different elastic constants for anisotropic materials by indenting different crystal faces, but not by rotating the indenter about its axis and indenting the same face in a different location. The hardness of small and large crystals is similar, suggesting that defect content probed in this study is similar, and that small crystals can be compared directly to larger ones. The Young's modulus and hardness of the model test material, griseofulvin, are given for the first time to be 11.5GPa and 0.4GPa respectively. Copyright © 2015 Elsevier B.V. All rights reserved.

  1. Low-mass molecular dynamics simulation: a simple and generic technique to enhance configurational sampling.

    PubMed

    Pang, Yuan-Ping

    2014-09-26

    CLN025 is one of the smallest fast-folding proteins. Until now it has not been reported that CLN025 can autonomously fold to its native conformation in a classical, all-atom, and isothermal-isobaric molecular dynamics (MD) simulation. This article reports the autonomous and repeated folding of CLN025 from a fully extended backbone conformation to its native conformation in explicit solvent in multiple 500-ns MD simulations at 277K and 1atm with the first folding event occurring as early as 66.1ns. These simulations were accomplished by using AMBER forcefield derivatives with atomic masses reduced by 10-fold on Apple Mac Pros. By contrast, no folding event was observed when the simulations were repeated using the original AMBER forcefields of FF12SB and FF14SB. The results demonstrate that low-mass MD simulation is a simple and generic technique to enhance configurational sampling. This technique may propel autonomous folding of a wide range of miniature proteins in classical, all-atom, and isothermal-isobaric MD simulations performed on commodity computers-an important step forward in quantitative biology. Copyright © 2014 The Author. Published by Elsevier Inc. All rights reserved.

  2. Intelligibility improvement of analog communication systems using an amplitude control technique.

    NASA Technical Reports Server (NTRS)

    Wishna, S.

    1973-01-01

    An amplitude control technique has been employed for use with analog voice communication systems, which improves low-level phoneme reception and eliminates the received noise between words and syllables. Tests were conducted on a narrow-band frequency-modulation simplex voice communication channel employing the amplitude control technique. Presented for both the modified rhyme word tests and the phonetically balanced word tests are a series of graphical plots of the tests' score distribution, mean, and standard deviation as a function of received carrier-to-noise power density ratio. At low received carrier-to-noise power density ratios, a significant improvement in the intelligibility was obtained. A voice intelligibility improvement of more than 2 dB was obtained for the modified rhyme test words, and a voice intelligibility improvement in excess of 4 dB was obtained for the phonetically balanced word tests.

  3. Intelligibility improvement of analog communication systems using an amplitude control technique.

    NASA Technical Reports Server (NTRS)

    Wishna, S.

    1973-01-01

    An amplitude control technique has been employed for use with analog voice communication systems, which improves low-level phoneme reception and eliminates the received noise between words and syllables. Tests were conducted on a narrow-band frequency-modulation simplex voice communication channel employing the amplitude control technique. Presented for both the modified rhyme word tests and the phonetically balanced word tests are a series of graphical plots of the tests' score distribution, mean, and standard deviation as a function of received carrier-to-noise power density ratio. At low received carrier-to-noise power density ratios, a significant improvement in the intelligibility was obtained. A voice intelligibility improvement of more than 2 dB was obtained for the modified rhyme test words, and a voice intelligibility improvement in excess of 4 dB was obtained for the phonetically balanced word tests.

  4. New AFM Techniques for Investigating Molecular Growth Mechanisms of Protein Crystals

    NASA Technical Reports Server (NTRS)

    Li, Huayu; Nadarajah, Arunan; Konnert, John H.; Pusey, Marc L.

    1998-01-01

    Atomic Force Microscopy (AFM) has emerged as a powerful technique for investigating protein crystal growth. Earlier AFM studies were among the first to demonstrate that these crystals grew by dislocation and 2D nucleation growth mechanisms [1]. These investigations were restricted to the micron range where only surface features, such as dislocation hillocks and 2D islands are visible. Most AFM instruments can scan at higher resolutions and have the potential to resolve individual protein molecules at nanometer ranges. Such scans are essential for determining the molecular packing arrangements on crystal faces and for probing the growth process at the molecular level. However, at this resolution the AFM tip influences the image produced, with the resulting image being a convolution of the tip shape and the surface morphology [2]. In most studies this problem is resolved by deconvoluting the image to obtain the true surface morphology. Although deconvolution routines work reasonably well for simple one- dimensional shapes, for complex surfaces this approach does not produce accurate results. In this study we devised a new approach which takes advantage of the precise molecular order of crystal surfaces, combined with the knowledge of individual molecular shapes from the crystallographic data of the protein and the AFM tip shape. This information is used to construct expected theoretical AFM images by convoluting the tip shape with the constructed crystal surface shape for a given surface packing arrangement. By comparing the images from actual AFM scans with the constructed ones for different possible surface packing arrangements, the correct packing arrangement can be conclusively determined. This approach was used in this study to determine the correct one from two possible packing arrangements on (I 10) faces of tetragonal lysozyme crystals. Another novel AFM technique was also devised to measure the dimension of individual growth units of the crystal faces

  5. Improved hidden Markov models for molecular motors, part 2: extensions and application to experimental data.

    PubMed

    Syed, Sheyum; Müllner, Fiona E; Selvin, Paul R; Sigworth, Fred J

    2010-12-01

    Unbiased interpretation of noisy single molecular motor recordings remains a challenging task. To address this issue, we have developed robust algorithms based on hidden Markov models (HMMs) of motor proteins. The basic algorithm, called variable-stepsize HMM (VS-HMM), was introduced in the previous article. It improves on currently available Markov-model based techniques by allowing for arbitrary distributions of step sizes, and shows excellent convergence properties for the characterization of staircase motor timecourses in the presence of large measurement noise. In this article, we extend the VS-HMM framework for better performance with experimental data. The extended algorithm, variable-stepsize integrating-detector HMM (VSI-HMM) better models the data-acquisition process, and accounts for random baseline drifts. Further, as an extension, maximum a posteriori estimation is provided. When used as a blind step detector, the VSI-HMM outperforms conventional step detectors. The fidelity of the VSI-HMM is tested with simulations and is applied to in vitro myosin V data where a small 10 nm population of steps is identified. It is also applied to an in vivo recording of melanosome motion, where strong evidence is found for repeated, bidirectional steps smaller than 8 nm in size, implying that multiple motors simultaneously carry the cargo.

  6. Rapid evolution of hyaluronan synthase to improve hyaluronan production and molecular mass in Bacillus subtilis.

    PubMed

    Zhang, Linpei; Huang, Hao; Wang, Hao; Chen, Jian; Du, Guocheng; Kang, Zhen

    2016-12-01

    To improve the production and molecular mass of the glycosaminoglycan hyaluronan (HA) in Bacillus subtilis by engineering hyaluronan synthase (HAS) from Streptococcus zooepidemicus. By mutating regions within HAS intracellular domains, five positive variants exhibiting higher HA production (from 1.22 to 2.24 g l(-1)) and molecular mass values (from 1.20 to 1.36 × 10(6) Da) were constructed and characterized. Overexpression of the V5 variant and the genes tuaD and glmU increased HA production and molecular mass to 2.8 g l(-1) and 2.4 × 10(6) Da, respectively. This study provides a novel strategy for improving HA production and its molecular mass.

  7. Improving Metered Dose Inhaler Technique in the Emergency Department: A Prospective Study

    PubMed Central

    Richards, John R.; Luskin, Michael J.; Krivoshto, Irina N.; Derlet, Robert W.

    2004-01-01

    Objective: To determine if improvement in patients’ metered dose inhaler (MDI) technique could be achieved in the emergency department (ED) with the use of a simple illustrated instruction sheet. Methods: Prospective evaluation of a convenience sample of patients with asthma or COPD. Patients were first subjectively and objectively evaluated on their usual MDI technique, then were given an illustrated instruction sheet to study for 5 minutes. There was no verbal coaching prior to the post-test. A post-test evaluation was then performed. Results were compared using paired Student t test. Results: A total of 115 patients were enrolled. Mean age was 34.9±13.1 years, and mean years using MDI was 5.7±3.8. Subjective improvement in technique was reported by 110 patients (96%) with a mean pre-test score of 7.4±1.5 and post-test score of 9.2±1.1 (p<0.0001, 10 point scale). Objective improvement was achieved in 113 patients (98%) with a mean pre-test score of 3.9±1.3 and post-test score of 5.8±1.0 (p<0.0001, 7 point scale), corresponding to a 30% improvement in technique (95% CI: 22,39). Forty-four patients (38%) reported never having been shown proper MDI technique by a health care professional, and 112 patients (97%) found the instruction sheet helpful. Conclusions: Rapid objective and subjective improvement of MDI technique from both patients’ and physicians’ perspective is possible in the ED with the use of an illustrated instruction sheet, and requires minimal effort from the treating emergency physician. PMID:20847849

  8. Genetic Optimization of Training Sets for Improved Machine Learning Models of Molecular Properties.

    PubMed

    Browning, Nicholas J; Ramakrishnan, Raghunathan; von Lilienfeld, O Anatole; Roethlisberger, Ursula

    2017-04-06

    The training of molecular models of quantum mechanical properties based on statistical machine learning requires large data sets which exemplify the map from chemical structure to molecular property. Intelligent a priori selection of training examples is often difficult or impossible to achieve, as prior knowledge may be unavailable. Ordinarily representative selection of training molecules from such data sets is achieved through random sampling. We use genetic algorithms for the optimization of training set composition consisting of tens of thousands of small organic molecules. The resulting machine learning models are considerably more accurate: in the limit of small training sets, mean absolute errors for out-of-sample predictions are reduced by up to ∼75%. We discuss and present optimized training sets consisting of 10 molecular classes for all molecular properties studied. We show that these classes can be used to design improved training sets for the generation of machine learning models of the same properties in similar but unrelated molecular sets.

  9. Peptide dynamics by molecular dynamics simulation and diffusion theory method with improved basis sets

    NASA Astrophysics Data System (ADS)

    Hsu, Po Jen; Lai, S. K.; Rapallo, Arnaldo

    2014-03-01

    Improved basis sets for the study of polymer dynamics by means of the diffusion theory, and tests on a melt of cis-1,4-polyisoprene decamers, and a toluene solution of a 71-mer syndiotactic trans-1,2-polypentadiene were presented recently [R. Gaspari and A. Rapallo, J. Chem. Phys. 128, 244109 (2008)]. The proposed hybrid basis approach (HBA) combined two techniques, the long time sorting procedure and the maximum correlation approximation. The HBA takes advantage of the strength of these two techniques, and its basis sets proved to be very effective and computationally convenient in describing both local and global dynamics in cases of flexible synthetic polymers where the repeating unit is a unique type of monomer. The question then arises if the same efficacy continues when the HBA is applied to polymers of different monomers, variable local stiffness along the chain and with longer persistence length, which have different local and global dynamical properties against the above-mentioned systems. Important examples of this kind of molecular chains are the proteins, so that a fragment of the protein transthyretin is chosen as the system of the present study. This peptide corresponds to a sequence that is structured in β-sheets of the protein and is located on the surface of the channel with thyroxin. The protein transthyretin forms amyloid fibrils in vivo, whereas the peptide fragment has been shown [C. P. Jaroniec, C. E. MacPhee, N. S. Astrof, C. M. Dobson, and R. G. Griffin, Proc. Natl. Acad. Sci. U.S.A. 99, 16748 (2002)] to form amyloid fibrils in vitro in extended β-sheet conformations. For these reasons the latter is given considerable attention in the literature and studied also as an isolated fragment in water solution where both experimental and theoretical efforts have indicated the propensity of the system to form β turns or α helices, but is otherwise predominantly unstructured. Differing from previous computational studies that employed implicit

  10. Peptide dynamics by molecular dynamics simulation and diffusion theory method with improved basis sets

    SciTech Connect

    Hsu, Po Jen; Lai, S. K.; Rapallo, Arnaldo

    2014-03-14

    Improved basis sets for the study of polymer dynamics by means of the diffusion theory, and tests on a melt of cis-1,4-polyisoprene decamers, and a toluene solution of a 71-mer syndiotactic trans-1,2-polypentadiene were presented recently [R. Gaspari and A. Rapallo, J. Chem. Phys. 128, 244109 (2008)]. The proposed hybrid basis approach (HBA) combined two techniques, the long time sorting procedure and the maximum correlation approximation. The HBA takes advantage of the strength of these two techniques, and its basis sets proved to be very effective and computationally convenient in describing both local and global dynamics in cases of flexible synthetic polymers where the repeating unit is a unique type of monomer. The question then arises if the same efficacy continues when the HBA is applied to polymers of different monomers, variable local stiffness along the chain and with longer persistence length, which have different local and global dynamical properties against the above-mentioned systems. Important examples of this kind of molecular chains are the proteins, so that a fragment of the protein transthyretin is chosen as the system of the present study. This peptide corresponds to a sequence that is structured in β-sheets of the protein and is located on the surface of the channel with thyroxin. The protein transthyretin forms amyloid fibrils in vivo, whereas the peptide fragment has been shown [C. P. Jaroniec, C. E. MacPhee, N. S. Astrof, C. M. Dobson, and R. G. Griffin, Proc. Natl. Acad. Sci. U.S.A. 99, 16748 (2002)] to form amyloid fibrils in vitro in extended β-sheet conformations. For these reasons the latter is given considerable attention in the literature and studied also as an isolated fragment in water solution where both experimental and theoretical efforts have indicated the propensity of the system to form β turns or α helices, but is otherwise predominantly unstructured. Differing from previous computational studies that employed implicit

  11. Application of traditional clinical pathology quality control techniques to molecular pathology.

    PubMed

    Liang, Shu-Ling; Lin, Ming-Tseh; Hafez, Michael J; Gocke, Christopher D; Murphy, Kathleen M; Sokoll, Lori J; Eshleman, James R

    2008-03-01

    Many molecular diagnostic laboratories have evolved from research laboratories, initially performing low numbers of homebrew assays, but many laboratories now perform more kit-based assays, with ever increasing test volumes. One such assay is assessment of bone marrow transplantation engraftment. Allogeneic bone marrow transplantation is performed primarily in the treatment of hematological malignancies. Monitoring of engraftment was traditionally evaluated using minisatellites (variable number tandem repeats) and Southern blotting, but most laboratories now use Food and Drug Administration-cleared microsatellite (short tandem repeats) kits to assess the extent of engraftment. With the increase in equipment reliability, the use of kit-based assays, and the desire to provide the highest quality clinical data, we began applying traditional clinical pathology quality control tools to the molecular diagnostics laboratory. In this study, we demonstrate this approach using a microsatellite-based bone marrow engraftment assay. We analyzed control samples (pure and mixed) for two different microsatellites to establish quality control parameters and constructed Levey-Jennings charts to monitor both the precision and accuracy of this assay. By incorporating these tools into an overall quality assurance program, a laboratory can identify systematic errors and perform corrective actions before actual assay failure, thereby improving the quality of patient care.

  12. Improving human forensics through advances in genetics, genomics and molecular biology.

    PubMed

    Kayser, Manfred; de Knijff, Peter

    2011-03-01

    Forensic DNA profiling currently allows the identification of persons already known to investigating authorities. Recent advances have produced new types of genetic markers with the potential to overcome some important limitations of current DNA profiling methods. Moreover, other developments are enabling completely new kinds of forensically relevant information to be extracted from biological samples. These include new molecular approaches for finding individuals previously unknown to investigators, and new molecular methods to support links between forensic sample donors and criminal acts. Such advances in genetics, genomics and molecular biology are likely to improve human forensic case work in the near future.

  13. Using biomechanics to improve the surgical technique for internal fixation of intracapsular femoral neck fractures.

    PubMed

    Wu, Chi-Chuan

    2010-01-01

    Despite advances in science and technology, the success rate for the treatment of displaced intracapsular femoral neck fractures in high-energy injuries remains disappointing. The blood supply system in the femoral head of humans does not favor recovery from these fractures. Once these fractures occur, osteonecrosis and nonunion rates may be as high as 30%, even if the newest technique is used. There are some surgical techniques used to supplement internal fixation to reestablish the blood supply in the femoral head, but none have been evidently successful. After analysis of related studies, the author concludes that immediate surgical treatment using improved techniques incorporating the principles of biomechanics can improve the success rate of treatment of these fractures. Using these principles, the fracture site can achieve sufficient stability. Consequently, the blood supply in the femoral head and neck can be reestablished earlier and loss of reduction of fragments during treatment can be minimized. Thus, the chance of full recovery from these complicated fractures can be maximized. In this study, the biomechanical characteristics of these fractures and the principles associated with the surgical techniques used for treating them are reviewed and clarified. Finally, a surgical technique which is ideal from the author's viewpoint is presented. The author believes that the recommended surgical technique may become the best method for treating these complicated fractures.

  14. Incentive device improves spacer technique but not clinical outcome in preschool children with asthma.

    PubMed

    Schultz, André; Sly, Peter D; Zhang, Guicheng; Venter, André; Le Souëf, Peter N; Devadason, Sunalene G

    2012-01-01

    To investigate the influence of an incentive device, the Funhaler, on spacer technique and symptom control in young children with asthma and recurrent wheeze. Randomised controlled trial where 132 2-6 year old asthmatic children received regular inhaled fluticasone through Aerochamber Plus, or Funhaler. The setting was a research clinic at Princess Margaret Hospital for Children, Perth, Australia. Subjects were followed up for a year. The main outcome measure was asthma symptoms. Proficiency in spacer technique was measured as salbutamol inhaled from spacer onto filter. Quality of life was measured every three months. Groups were compared in terms of spacer technique, symptoms and quality of life. The relationship between spacer technique and clinical outcome was examined. There was no difference between Funhaler and Aerochamber groups in wheeze free days, cough free days, bronchodilator free days or quality of life (P = 0.90, 0.87, 0.74 and 0.11 respectively). Spacer technique was better in the Funhaler group (P = 0.05), particularly in subjects younger than 4 years of age (P = 0.002). Drug dose on filter (as the mean of five 100 mg doses) ranged from zero to 136 mg. Use of Funhaler incentive device does not improve clinical outcome, but improves spacer technique in children younger than 4 years. Variability in drug delivery is large in young children using pressurised metered dose inhalers and spacers. © 2011 The Authors. Journal of Paediatrics and Child Health © 2011 Paediatrics and Child Health Division (Royal Australasian College of Physicians).

  15. Turning Continuous Quality Improvement into Institutional Practice: The Tools and Techniques.

    ERIC Educational Resources Information Center

    Cornesky, Robert A.

    This manual is intended to assist managers of support units at institutions of higher education in the implementation of Continuous Quality Improvement (CQI). The purpose is to describe a cooperative model for CQI which will permit managers to evaluate the quality of their units and institution, and by using the described tools and techniques, to…

  16. After-School Toolkit: Tips, Techniques and Templates for Improving Program Quality

    ERIC Educational Resources Information Center

    Gutierrez, Nora; Bradshaw, Molly; Furano, Kathryn

    2008-01-01

    This toolkit offers program managers a hands-on guide for implementing quality programming in the after-school hours. The kit includes tools and techniques that increased the quality of literacy programming and helped improve student reading gains in the Communities Organizing Resources to Advance Learning (CORAL) initiative of The James Irvine…

  17. Methods and Techniques for Improving the Educational Aspirational Level of Senior High School Students.

    ERIC Educational Resources Information Center

    Summers, Ruby

    This paper presents methods and techniques for improving the educational aspirational level of disadvantaged senior high school students. The objectives of the program are listed, followed by a list of ten activity areas within which the substance of the motivational thrusts of the project are to be implemented. The activity areas are discussed.…

  18. After-School Toolkit: Tips, Techniques and Templates for Improving Program Quality

    ERIC Educational Resources Information Center

    Gutierrez, Nora; Bradshaw, Molly; Furano, Kathryn

    2008-01-01

    This toolkit offers program managers a hands-on guide for implementing quality programming in the after-school hours. The kit includes tools and techniques that increased the quality of literacy programming and helped improve student reading gains in the Communities Organizing Resources to Advance Learning (CORAL) initiative of The James Irvine…

  19. The Ticket to Retention: A Classroom Assessment Technique Designed to Improve Student Learning

    ERIC Educational Resources Information Center

    Divoll, Kent A.; Browning, Sandra T.; Vesey, Winona M.

    2012-01-01

    Classroom assessment techniques (CATs) or other closure activities are widely promoted for use in college classrooms. However, research on whether CATs improve student learning are mixed. The authors posit that the results are mixed because CATs were designed to "help teachers find out what students are learning in the classroom and how well…

  20. Radiation Oncology In Vitro: Trends to Improve Radiotherapy through Molecular Targets

    PubMed Central

    Feofanova, Natália; Geraldo, Jony Marques; de Andrade, Lídia Maria

    2014-01-01

    Much has been investigated to improve the beneficial effects of radiotherapy especially in that case where radioresistant behavior is observed. Beyond simple identification of resistant phenotype the discovery and development of specific molecular targets have demonstrated therapeutic potential in cancer treatment including radiotherapy. Alterations on transduction signaling pathway related with MAPK cascade are the main axis in cancer cellular proliferation even as cell migration and invasiveness in irradiated tumor cell lines; then, for that reason, more studies are in course focusing on, among others, DNA damage enhancement, apoptosis stimulation, and growth factors receptor blockages, showing promising in vitro results highlighting molecular targets associated with ionizing radiation as a new radiotherapy strategy to improve clinical outcome. In this review we discuss some of the main molecular targets related with tumor cell proliferation and migration as well as their potential contributions to radiation oncology improvements. PMID:25302298

  1. Radiation oncology in vitro: trends to improve radiotherapy through molecular targets.

    PubMed

    Feofanova, Natália; Geraldo, Jony Marques; de Andrade, Lídia Maria

    2014-01-01

    Much has been investigated to improve the beneficial effects of radiotherapy especially in that case where radioresistant behavior is observed. Beyond simple identification of resistant phenotype the discovery and development of specific molecular targets have demonstrated therapeutic potential in cancer treatment including radiotherapy. Alterations on transduction signaling pathway related with MAPK cascade are the main axis in cancer cellular proliferation even as cell migration and invasiveness in irradiated tumor cell lines; then, for that reason, more studies are in course focusing on, among others, DNA damage enhancement, apoptosis stimulation, and growth factors receptor blockages, showing promising in vitro results highlighting molecular targets associated with ionizing radiation as a new radiotherapy strategy to improve clinical outcome. In this review we discuss some of the main molecular targets related with tumor cell proliferation and migration as well as their potential contributions to radiation oncology improvements.

  2. An original and effective technique to improve exposure in open surgery.

    PubMed

    Nohuz, E; Chêne, G

    2017-01-01

    Exposure, especially when the organs are enlarged, remains one of the most important issue in open surgery. Considering this constraint appears critical in the progress of the surgical procedure. We highlight our technique which affords optimal exposure and improves manipulation and extraction of enlarged organs. This original and effective technique is derived from an obstetrical device used to perform an assisted vaginal delivery. It improves exposure, reduces tissue manipulation, and enhances removal of the surgical specimen during hysterectomies and myomectomies. It can be similarly helpful sometimes to grasp and remove (by mini laparotomy) enlarged adnexa during laparoscopic procedures. Moreover, this trick appears particularly suited in case of obese patients. This new technique procures a real benefit for both the patient and the surgeon in terms of ergonomics and safety.

  3. Brachial plexus surgery: the role of the surgical technique for improvement of the functional outcome.

    PubMed

    Flores, Leandro Pretto

    2011-08-01

    The study aims to demonstrate the techniques employed in surgery of the brachial plexus that are associated to evidence-based improvement of the functional outcome of these patients. A retrospective study of one hundred cases of traumatic brachial plexus injuries. Comparison between the postoperative outcomes associated to some different surgical techniques was demonstrated. The technique of proximal nerve roots grafting was associated to good results in about 70% of the cases. Significantly better outcomes were associated to the Oberlin's procedure and the Sansak's procedure, while the improvement of outcomes associated to phrenic to musculocutaneous nerve and the accessory to suprascapular nerve transfer did not reach statistical significance. Reinnervation of the hand was observed in less than 30% of the cases. Brachial plexus surgery renders satisfactory results for reinnervation of the proximal musculature of the upper limb, however the same good outcomes are not usually associated to the reinnervation of the hand.

  4. Utility of magnetic cell separation as a molecular sperm preparation technique.

    PubMed

    Said, Tamer M; Agarwal, Ashok; Zborowski, Maciej; Grunewald, Sonja; Glander, Hans-Juergen; Paasch, Uwe

    2008-01-01

    Assisted reproductive techniques (ARTs) have become the treatment of choice in many cases of infertility; however, the current success rates of these procedures remain suboptimal. Programmed cell death (apoptosis) most likely contributes to failed ART and to the decrease in sperm quality after cryopreservation. There is a likelihood that some sperm selected for ART will display features of apoptosis despite their normal appearance, which may be partially responsible for the low fertilization and implantation rates seen with ART. One of the features of apoptosis is the externalization of phosphatidylserine (PS) residues, which are normally present on the inner leaflet of the sperm plasma membrane. Colloidal superparamagnetic microbeads ( approximately 50 nm in diameter) conjugated with annexin V bind to PS and are used to separate dead and apoptotic spermatozoa by magnetic-activated cell sorting (MACS). Cells with externalized PS will bind to these microbeads, whereas nonapoptotic cells with intact membranes do not bind and could be used during ARTs. We have conducted a series of experiments to investigate whether the MACS technology could be used to improve ART outcomes. Our results clearly indicate that integrating MACS as a part of sperm preparation techniques will improve semen quality and cryosurvival rates by eliminating apoptotic sperm. Nonapoptotic spermatozoa prepared by MACS display higher quality in terms of routine sperm parameters and apoptosis markers. The higher sperm quality is represented by an increased oocyte penetration potential and cryosurvival rates. Thus, the selection of nonapoptotic spermatozoa by MACS should be considered to enhance ART success rates.

  5. TWT efficiency improvement by a low-cost technique for deposition of carbon on MDC electrodes

    NASA Technical Reports Server (NTRS)

    Ebihara, Ben T.; Ramins, Peter; Peet, Shelly

    1987-01-01

    A simple method of improving the TWT and multistage depressed collector (MDC) efficiency has been demonstrated. The efficiency improvement was produced by the application of a thin layer of carbon to the copper electrodes of the MDC by means of a rapid low-cost technique involving the pyrolysis of hydrocarbon oil in electric arc discharges. Experimental results with a representative TWT and MDC showed an 11 percent improvement in both the TWT and MDC efficiencies as compared to those of the same TWT and MDC with machined copper electrode surfaces. An extended test with a 550-W CW TWT indicated good durability of the carbon-coated electrode surfaces.

  6. Novel Augmentation Technique for Patellar Tendon Repair Improves Strength and Decreases Gap Formation: A Cadaveric Study.

    PubMed

    Black, James C; Ricci, William M; Gardner, Michael J; McAndrew, Christopher M; Agarwalla, Avinesh; Wojahn, Robert D; Abar, Orchid; Tang, Simon Y

    2016-12-01

    Patellar tendon ruptures commonly are repaired using transosseous patellar drill tunnels with modified-Krackow sutures in the patellar tendon. This simple suture technique has been associated with failure rates and poor clinical outcomes in a modest proportion of patients. Failure of this repair technique can result from gap formation during loading or a single catastrophic event. Several augmentation techniques have been described to improve the integrity of the repair, but standardized biomechanical evaluation of repair strength among different techniques is lacking. The purpose of this study was to describe a novel figure-of-eight suture technique to augment traditional fixation and evaluate its biomechanical performance. We hypothesized that the augmentation technique would (1) reduce gap formation during cyclic loading and (2) increase the maximum load to failure. Ten pairs (two male, eight female) of fresh-frozen cadaveric knees free of overt disorders or patellar tendon damage were used (average donor age, 76 years; range, 65-87 years). For each pair, one specimen underwent the standard transosseous tunnel suture repair with a modified-Krackow suture technique and the second underwent the standard repair with our experimental augmentation method. Nine pairs were suitable for testing. Each specimen underwent cyclic loading while continuously measuring gap formation across the repair. At the completion of cyclic loading, load to failure testing was performed. A difference in gap formation and mean load to failure was seen in favor of the augmentation technique. At 250 cycles, a 68% increase in gap formation was seen for the control group (control: 5.96 ± 0.86 mm [95% CI, 5.30-6.62 mm]; augmentation: 3.55 ± 0.56 mm [95% CI, 3.12-3.98 mm]; p = 0.02). The mean load to failure was 13% greater in the augmentation group (control: 899.57 ± 96.94 N [95% CI, 825.06-974.09 N]; augmentation: 1030.70 ± 122.41 N [95% CI, 936.61-1124.79 N]; p = 0.01). This biomechanical

  7. An efficient technique for nuclei segmentation based on ellipse descriptor analysis and improved seed detection algorithm.

    PubMed

    Xu, Hongming; Lu, Cheng; Mandal, Mrinal

    2014-09-01

    In this paper, we propose an efficient method for segmenting cell nuclei in the skin histopathological images. The proposed technique consists of four modules. First, it separates the nuclei regions from the background with an adaptive threshold technique. Next, an elliptical descriptor is used to detect the isolated nuclei with elliptical shapes. This descriptor classifies the nuclei regions based on two ellipticity parameters. Nuclei clumps and nuclei with irregular shapes are then localized by an improved seed detection technique based on voting in the eroded nuclei regions. Finally, undivided nuclei regions are segmented by a marked watershed algorithm. Experimental results on 114 different image patches indicate that the proposed technique provides a superior performance in nuclei detection and segmentation.

  8. Improved importance sampling technique for efficient simulation of digital communication systems

    NASA Technical Reports Server (NTRS)

    Lu, Dingqing; Yao, Kung

    1988-01-01

    A new, improved importance sampling (IIS) approach to simulation is considered. Some basic concepts of IS are introduced, and detailed evolutions of simulation estimation variances for Monte Carlo (MC) and IS simulations are given. The general results obtained from these evolutions are applied to the specific previously known conventional importance sampling (CIS) technique and the new IIS technique. The derivation for a linear system with no signal random memory is considered in some detail. For the CIS technique, the optimum input scaling parameter is found, while for the IIS technique, the optimum translation parameter is found. The results are generalized to a linear system with memory and signals. Specific numerical and simulation results are given which show the advantages of CIS over MC and IIS over CIS for simulations of digital communications systems.

  9. Improved importance sampling technique for efficient simulation of digital communication systems

    NASA Technical Reports Server (NTRS)

    Lu, Dingqing; Yao, Kung

    1988-01-01

    A new, improved importance sampling (IIS) approach to simulation is considered. Some basic concepts of IS are introduced, and detailed evolutions of simulation estimation variances for Monte Carlo (MC) and IS simulations are given. The general results obtained from these evolutions are applied to the specific previously known conventional importance sampling (CIS) technique and the new IIS technique. The derivation for a linear system with no signal random memory is considered in some detail. For the CIS technique, the optimum input scaling parameter is found, while for the IIS technique, the optimum translation parameter is found. The results are generalized to a linear system with memory and signals. Specific numerical and simulation results are given which show the advantages of CIS over MC and IIS over CIS for simulations of digital communications systems.

  10. An improved sample loading technique for cellular metabolic response monitoring under pressure

    NASA Astrophysics Data System (ADS)

    Gikunda, Millicent Nkirote

    To monitor cellular metabolism under pressure, a pressure chamber designed around a simple-to-construct capillary-based spectroscopic chamber coupled to a microliter-flow perfusion system is used in the laboratory. Although cyanide-induced metabolic responses from Saccharomyces cerevisiae (baker's yeast) could be controllably induced and monitored under pressure, previously used sample loading technique was not well controlled. An improved cell-loading technique which is based on use of a secondary inner capillary into which the sample is loaded then inserted into the capillary pressure chamber, has been developed. As validation, we demonstrate the ability to measure the chemically-induced metabolic responses at pressures of up to 500 bars. This technique is shown to be less prone to sample loss due to perfusive flow than the previous techniques used.

  11. Landing Technique Improvements After an Aquatic-Based Neuromuscular Training Program in Physically Active Women.

    PubMed

    Scarneo, Samantha E; Root, Hayley J; Martinez, Jessica C; Denegar, Craig; Casa, Douglas J; Mazerolle, Stephanie M; Dann, Catie L; Aerni, Giselle A; DiStefano, Lindsay J

    2017-01-01

    Neuromuscular training programs (NTPs) improve landing technique and decrease vertical ground-reaction forces (VGRFs), resulting in injury-risk reduction. NTPs in an aquatic environment may elicit the same improvements as land-based programs with reduced joint stress. To examine the effects of an aquatic NTP on landing technique as measured by the Landing Error Scoring System (LESS) and VGRFs, immediately and 4 mo after the intervention. Repeated measures, pool and laboratory. Fifteen healthy, recreationally active women (age 21 ± 2 y, mass 62.02 ± 8.18 kg, height 164.74 ± 5.97 cm) who demonstrated poor landing technique (LESS-Real Time > 4). All participants completed an aquatic NTP 3 times/wk for 6 wk. Participants' landing technique was evaluated using a jump-landing task immediately before (PRE), immediately after (POST), and 4 mo after (RET) the intervention period. A single rater, blinded to time point, graded all videos using the LESS, which is a valid and reliable movement-screening tool. Peak VGRFs were measured during the stance phase of the jump-landing test. Repeated-measure analyses of variance with planned comparisons were performed to explore differences between time points. LESS scores were lower at POST (4.46 ± 1.69 errors) and at RET (4.2 ± 1.72 errors) than at PRE (6.30 ± 1.78 errors) (P < .01). No significant differences were observed between POST and RET (P > .05). Participants also landed with significantly lower peak VGRFs (P < .01) from PRE (2.69 ± .72 N) to POST (2.23 ± .66 N). The findings introduce evidence that an aquatic NTP improves landing technique and suggest that improvements are retained over time. These results show promise of using an aquatic NTP when there is a desire to reduce joint loading, such as early stages of rehabilitation, to improve biomechanics and reduce injury risk.

  12. Electrochemical microfluidic chip based on molecular imprinting technique applied for therapeutic drug monitoring.

    PubMed

    Liu, Jiang; Zhang, Yu; Jiang, Min; Tian, Liping; Sun, Shiguo; Zhao, Na; Zhao, Feilang; Li, Yingchun

    2017-05-15

    In this work, a novel electrochemical detection platform was established by integrating molecularly imprinting technique with microfluidic chip and applied for trace measurement of three therapeutic drugs. The chip foundation is acrylic panel with designed grooves. In the detection cell of the chip, a Pt wire is used as the counter electrode and reference electrode, and a Au-Ag alloy microwire (NPAMW) with 3D nanoporous surface modified with electro-polymerized molecularly imprinted polymer (MIP) film as the working electrode. Detailed characterization of the chip and the working electrode was performed, and the properties were explored by cyclic voltammetry and electrochemical impedance spectroscopy. Two methods, respectively based on electrochemical catalysis and MIP/gate effect were employed for detecting warfarin sodium by using the prepared chip. The linearity of electrochemical catalysis method was in the range of 5×10(-6)-4×10(-4)M, which fails to meet clinical testing demand. By contrast, the linearity of gate effect was 2×10(-11)-4×10(-9)M with remarkably low detection limit of 8×10(-12)M (S/N=3), which is able to satisfy clinical assay. Then the system was applied for 24-h monitoring of drug concentration in plasma after administration of warfarin sodium in rabbit, and the corresponding pharmacokinetic parameters were obtained. In addition, the microfluidic chip was successfully adopted to analyze cyclophosphamide and carbamazepine, implying its good versatile ability. It is expected that this novel electrochemical microfluidic chip can act as a promising format for point-of-care testing via monitoring different analytes sensitively and conveniently. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Molecular Imaging of Tumors Using a Quantitative T1 Mapping Technique via Magnetic Resonance Imaging

    PubMed Central

    Herrmann, Kelsey; Johansen, Mette L.; Craig, Sonya E.; Vincent, Jason; Howell, Michael; Gao, Ying; Lu, Lan; Erokwu, Bernadette; Agnes, Richard S.; Lu, Zheng-Rong; Pokorski, Jonathan K.; Basilion, James; Gulani, Vikas; Griswold, Mark; Flask, Chris; Brady-Kalnay, Susann M.

    2015-01-01

    Magnetic resonance imaging (MRI) of glioblastoma multiforme (GBM) with molecular imaging agents would allow for the specific localization of brain tumors. Prior studies using T1-weighted MR imaging demonstrated that the SBK2-Tris-(Gd-DOTA)3 molecular imaging agent labeled heterotopic xenograft models of brain tumors more intensely than non-specific contrast agents using conventional T1-weighted imaging techniques. In this study, we used a dynamic quantitative T1 mapping strategy to more objectively compare intra-tumoral retention of the SBK2-Tris-(Gd-DOTA)3 agent over time in comparison to non-targeted control agents. Our results demonstrate that the targeted SBK2-Tris-(Gd-DOTA)3 agent, a scrambled-Tris-(Gd-DOTA)3 control agent, and the non-specific clinical contrast agent Optimark™ all enhanced flank tumors of human glioma cells with similar maximal changes on T1 mapping. However, the retention of the agents differs. The non-specific agents show significant recovery within 20 min by an increase in T1 while the specific agent SBK2-Tris-(Gd-DOTA)3 is retained in the tumors and shows little recovery over 60 min. The retention effect is demonstrated by percent change in T1 values and slope calculations as well as by calculations of gadolinium concentration in tumor compared to muscle. Quantitative T1 mapping demonstrates the superior binding and retention in tumors of the SBK2-Tris-(Gd-DOTA)3 agent over time compared to the non-specific contrast agent currently in clinical use. PMID:26435847

  14. Head up and head mounted display performance improvements through advanced techniques in the manipulation of light

    NASA Astrophysics Data System (ADS)

    Wisely, Paul L.

    2009-05-01

    Since their introduction a number of years ago, head up and helmet mounted displays have undergone continuous and intensive development in aerospace applications. To date, the designs have been performed using geometric optic design techniques and have progressed to the point where very little further improvement in their characteristics is possible. This paper describes a display realised by the use of new optical design techniques based on wave-guiding principles that have enabled substantial further significant improvements to be made. These improvements are not only in respect of size, weight and volume for a given optical performance, but also in the optical characteristics that currently limit the usability of such displays in many applications. Displays that have been realised and tested through these methods are described and their performance in laboratory and flight trials discussed, together with considerations for further progress in their development.

  15. A Novel Technique to Improve the Processing of Minute Ureteroscopic Biopsies.

    PubMed

    Golan, Shay; Gerber, Glenn; Margel, David; Rath-Wolfson, Lea; Ehrlich, Yaron; Koren, Rumelia; Lifshitz, David

    2017-04-03

    To examine the ability of a new specimen handling technique to improve histopathological yield of ureteroscopic biopsies, performed in patients with suspected upper tract urothelial carcinoma (UTUC). In a bi-center retrospective study we compared the results of the new tissue handling technique (group 1) with the standard technique (group 2). In the new technique, to achieve maximal tissue preservation, the specimen is mounted on filter paper prior to embedding in paraffin. Multivariate analysis was performed to determine which factors are associated with optimal histological results. We further compared the biopsies with the final specimen in a subgroup of patients who underwent nephroureterectomy (NU). Of 55 ureteroscopic biopsies, 1 biopsy from group 1 (new technique) and 3 biopsies from group 2 (standard technique) were inadequate for pathological examination. 51 UTUC specimens were analyzed. Tumor grade and stage were determined in 85% and 63% of the patients in group 1 and in 83% and 25% of group 2 (p=0.85 and p=0.007). Orientation was preserved in 82% of group 1 and 42% of group 2 (p=0.003). On multivariate analysis biopsy technique and biopsy diameter were found to predict stage determination (p=0.01 and p=0.007) and tissue orientation (p=0.005 and p=0.04). Among patients who underwent NU, stage concordance between the biopsy and final pathology was observed in 56% and 27% of the patients in group 1 and 2, respectively. The new processing technique for small UTUC forceps biopsies decreases the rate of biopsies with insufficient material and improves biopsy interpretation.

  16. Video instruction is more effective than written instruction in improving inhaler technique.

    PubMed

    Shah, Romil F; Gupta, Rakesh M

    2017-10-01

    Many patients with asthma use inhalers incorrectly. Better inhaler technique is associated with better asthma control. We tested the effectiveness of a computer-based video training solution versus traditional written instructions, both which may be used in a resource-limited setting, for teaching inhaler technique. We hypothesized that computer based training will provide a higher quality of instruction which will improve technique more effectively than written training. 50 asthma patients were recruited from pulmonary clinic at the Junta De Beneficencia Hospital, Ecuador (average age 48.2 years, 58% female). Inhaler technique was taught using written instructions in 20 and video in 30 patients. Inhaler technique was analyzed by video recording pre and post training inhaler use. Inhaler technique score was calculated for each video recording. Baseline performance was equivalent in each group, achieving an average of around 5 of 11 of the inhaler steps. Video training was significantly more effective than written instructions (change of 3.6 points vs. change of 0.4 points, p < 0.001), and improved inhaler technique by 70% (8.6 vs 5.03, p < 0.001); written training did not result in a significant increase in inhaler competency (5.9 vs. 5.5, p = 0.11). We conclude that written instruction appears to be inadequate to achieve safe and effective administration of inhaled medicine. In contrast, video-based education can effectively create adequate inhaler technique without additional provider time. REGISTRATION NUMBER (CLINICALTRIALS.GOV IDENTIFIER): NCT02660879. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. An improved DNA marker technique for genetic characterization using RAMP-PCR with high-GC primers.

    PubMed

    Wei, C L; Cheng, J L; Khan, M A; Yang, L Q; Imani, S; Chen, H C; Fu, J J

    2016-09-16

    Random amplified polymorphic DNA (RAPD) is a widely used molecular marker technique. As traditional RAPD has poor reproducibility and productivity, we previously developed an improved RAPD method (termed RAMP-PCR), which increased the reproducibility, number of bands, and efficiency of studies on polymorphism. To further develop the efficiency of this method, we used high-GC content primers for improved RAMP-PCR with DNA samples from Lonicera japonica. Comparison of amplification profiles obtained by standard RAPD primers with those obtained by regular PCR and RAMP-PCR, and high-GC primers with regular PCR and RAMP-PCR showed that the average number of bands and polymorphisms per primer gradually and significantly increased (from 6.4 to 15.0 and from 4.6 to 10.2, respectively). Cluster dendrograms showed similar results, indicating that this new method is consistent and reproducible. A total of 22 samples from different species, including plants, animals, and humans, were used for RAMP-PCR with high-GC primers. Multiple bands were successfully amplified from all samples, demonstrating that this method is a reliable technique with consistent results and may be of general interest in studies on different genera and species. We developed highly effective DNA markers, which can provide a more effective and potentially valuable approach than traditional RAPD for the genetic identification of various organisms, particularly of medicinal plants.

  18. Improving the diagnosis and management of neuroendocrine tumors: utilizing new advances in biomarker and molecular imaging science.

    PubMed

    Giandomenico, Valeria; Modlin, Irvin M; Pontén, Fredrik; Nilsson, Mats; Landegren, Ulf; Bergqvist, Jonas; Khan, Mohid S; Millar, Robert P; Långström, Bengt; Borlak, Jürgen; Eriksson, Barbro; Nielsen, Bengt; Baltzer, Lars; Waterton, John C; Ahlström, Håkan; Öberg, Kjell

    2013-01-01

    Neuroendocrine tumors (NET) are malignant solid tumors that arise in hormone-secreting tissue of the diffuse neuroendocrine system or endocrine glands. Although traditionally understood to be a rare disease, the incidence and prevalence of NET have increased greatly in the past 3 decades. However, during this time, progress in diagnosis and outcome of NET has generally been modest. In order to achieve improved outcome in NET, a better understanding of NET biology combined with more reliable serum markers and better techniques to identify tumor localization and small lesions are needed. Although some NET biomarkers exist, sensitive and specific markers that predict tumor growth and behavior are generally lacking. In addition, the integration of new molecular imaging technologies in patient diagnosis and follow-up has the potential to enhance care. To discuss developments and issues required to improve diagnostics and management of NET patients, with specific focus on the latest advances in molecular imaging and biomarker science, 17 global leaders in the fields of NET, molecular imaging and biomarker technology gathered to participate in a 2-day meeting hosted by Prof. Kjell Öberg at the University of Uppsala in Sweden. During this time, findings were presented regarding methods with potential prognostic and treatment applications in NET or other types of cancers. This paper describes the symposium presentations and resulting discussions.

  19. A Tablet-Based Multimedia Education Tool Improves Provider and Subject Knowledge of Inhaler Use Techniques.

    PubMed

    Mulhall, Aaron M; Zafar, Muhammad A; Record, Samantha; Channell, Herman; Panos, Ralph J

    2017-02-01

    Although inhaled medications are effective therapies for COPD, many patients and providers use them incorrectly. We recruited providers who prescribe inhalers or teach inhaler technique and assessed their use of metered-dose inhalers (MDIs), various dry powder inhalers (DPIs), and Respimat using predefined checklists. Then they watched tablet-based multimedia educational videos that demonstrated correct inhaler technique by a clinical pharmacist with teach-back from a patient and were re-evaluated. We also recruited patients with COPD and assessed their use of their prescribed inhalers and then retested them after 3-6 months. Baseline and follow-up respiratory symptoms were measured by the COPD Assessment Test. Fifty-eight providers and 50 subjects participated. For all providers, correct inhaler technique (reported as percentage correct steps) increased after the videos: MDI without a spacer (72% vs 97%) MDI with a spacer (72% vs 96%), formoterol DPI (50% vs 94%), mometasone DPI (43% vs 95%), tiotropium DPI (73% vs 99%), and Respimat (32% vs 93%) (before vs after, P < .001 for all comparisons). Subjects also improved their inhaler use technique after viewing the educational videos: MDI without a spacer (69% vs 92%), MDI with a spacer (73% vs 95%), and tiotropium DPI (83% vs 96%) (before vs after, P < .001 for all comparisons). The beneficial effect of this educational intervention declined slightly for subjects but was durably improved after several months. COPD Assessment Test scores did not demonstrate any change in respiratory symptoms. A tablet-based inhaler education tool improved inhaler technique for both providers and subjects. Although this intervention did show durable efficacy for improving inhaler use by patients, it did not reduce their respiratory symptoms. Copyright © 2017 by Daedalus Enterprises.

  20. Probing the interaction of anthraquinone with DNA by spectroscopy, molecular modeling and cancer cell imaging technique.

    PubMed

    Yang, Lei; Fu, Zheng; Niu, Xiaoqing; Zhang, Guisheng; Cui, Fengling; Zhou, Chunwu

    2015-05-25

    A new anthraquinone derivative, (E)-2-(1-(4,5-dihydroxy-6-(hydroxymethyl)-tetrahydro-2H-pyran-2-yloxyimino)ethyl)-1,4-dihydroxyanthracene-9,10-dione (AODGlc), was synthesized and its binding properties towards DNA were explored under physiological conditions by fluorescence spectroscopy, DNA melting as well as docking techniques. The experimental results revealed that AODGlc could bind to calf thymus DNA (ctDNA) through intercalation between DNA base pairs. The values of thermodynamic parameters at different temperatures including ΔG, ΔH, and ΔS and the molecular modeling study implied that hydrophobic interactions and hydrogen bonds were the main interactions in the AODGlc-ctDNA system. Cervical cancer cells (HepG2 cells) were used in cell viability assay and cell imaging experiment. AODGlc could interact with HepG2 cells and kill HepG2 cells under high concentration with nice curative effect, indicating its potential bioapplication in the future. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  1. Quantum and Molecular Mechanical (QM/MM) Monte Carlo Techniques for Modeling Condensed-Phase Reactions

    PubMed Central

    Jorgensen, Wiliiam L.

    2014-01-01

    A recent review (Acc. Chem. Res. 2010, 43:142–151) examined our use and development of a combined quantum and molecular mechanical (QM/MM) technique for modelling organic and enzymatic reactions. Advances included the PDDG/PM3 semiempirical QM (SQM) method, computation of multi-dimensional potentials of mean force (PMF), incorporation of on-the-fly QM in Monte Carlo simulations, and a polynomial quadrature method for rapidly treating proton-transfer reactions. The current article serves as a follow up on our progress. Highlights include new reactions, alternative SQM methods, a polarizable OPLS force field, and novel solvent environments, e.g., “on water” and room temperature ionic liquids. The methodology is strikingly accurate across a wide range of condensed-phase and antibody-catalyzed reactions including substitution, decarboxylation, elimination, isomerization, and pericyclic classes. Comparisons are made to systems treated with continuum-based solvents and ab initio or density functional theory (DFT) methods. Overall, the QM/MM methodology provides detailed characterization of reaction paths, proper configurational sampling, several advantages over implicit solvent models, and a reasonable computational cost. PMID:25431625

  2. Comparison of the utility of barley retrotransposon families for genetic analysis by molecular marker techniques.

    PubMed

    Leigh, F; Kalendar, R; Lea, V; Lee, D; Donini, P; Schulman, A H

    2003-07-01

    The Sequence-Specific Amplification Polymorphism (S-SAP) method, and the related molecular marker techniques IRAP (inter-retrotransposon amplified polymorphism) and REMAP (retrotransposon-microsatellite amplified polymorphism), are based on retrotransposon activity, and are increasingly widely used. However, there have been no systematic analyses of the parameters of these methods or of the utility of different retrotransposon families in producing polymorphic, scorable fingerprints. We have generated S-SAP, IRAP, and REMAP data for three barley (Hordeum vulgare L.) varieties using primers based on sequences from six retrotransposon families (BARE-1, BAGY-1, BAGY-2, Sabrina, Nikita and Sukkula). The effect of the number of selective bases on the S-SAP profiles has been examined and the profiles obtained with eight MseI+3 selective primers compared for all the elements. Polymorphisms detected in the insertion pattern of all the families show that each can be used for S-SAP. The uniqueness of each transposition event and differences in the historic activity of each family suggest that the use of multiple retrotransposon families for genetic analysis will find applications in mapping, fingerprinting, and marker-assisted selection and evolutionary studies, not only in barley and other Hordeum species and related taxa, but also more generally.

  3. Species identification of Mycobacterium avium complex isolates by a variety of molecular techniques.

    PubMed

    Beggs, M L; Stevanova, R; Eisenach, K D

    2000-02-01

    Organisms in the Mycobacterium avium complex (MAC; M. avium, M. intracellulare, and "nonspecific or X" MAC) are emerging pathogens among individual organisms of which significant genetic variability is displayed. The objective of the present study was to evaluate various molecular methods for the rapid and definitive identification of MAC species. Isolates were obtained from both human immunodeficiency virus (HIV)-positive patients and HIV-negative patients with and without known predisposing conditions. The isolates were initially hybridized with nucleic acid probes complementary to the rRNA of the respective mycobacterial species (AccuProbe Culture Confirmation kits for M. avium, M. intracellulare, and MAC species; Gen-Probe). Isolates were also examined by PCR and in some cases by Southern blot hybridization for the insertion element IS1245. Two other techniques included a PCR assay that amplifies the mig gene, a putative virulence factor for MAC, and hsp65 gene amplification and sequencing. This study led to the following observations. Eighty-five percent of the isolates from HIV-positive patients were M. avium and 86% of the isolates from HIV-negative patients were M. intracellulare. Fifteen of the M. avium isolates did not contain IS1245 and 7% of the M. intracellulare isolates were found to carry IS1245. All of the M. avium strains were mig positive, and all of the M. intracellulare strains were mig negative.

  4. New understanding of rhizosphere processes enabled by advances in molecular and spatially resolved techniques

    DOE PAGES

    Hess, Nancy J.; Pasa-Tolic, Ljiljana; Bailey, Vanessa L.; ...

    2017-04-12

    Understanding the role played by microorganisms within soil systems is challenged by the unique intersection of physics, chemistry, mineralogy and biology in fostering habitat for soil microbial communities. To address these challenges will require observations across multiple spatial and temporal scales to capture the dynamics and emergent behavior from complex and interdependent processes. The heterogeneity and complexity of the rhizosphere require advanced techniques that press the simultaneous frontiers of spatial resolution, analyte sensitivity and specificity, reproducibility, large dynamic range, and high throughput. Fortunately many exciting technical advancements are now available to inform and guide the development of new hypotheses. Themore » aim of this Special issue is to provide a holistic view of the rhizosphere in the perspective of modern molecular biology methodologies that enabled a highly-focused, detailed view on the processes in the rhizosphere, including numerous, strong and complex interactions between plant roots, soil constituents and microorganisms. We discuss the current rhizosphere research challenges and knowledge gaps, as well as perspectives and approaches using newly available state-of-the-art toolboxes. These new approaches and methodologies allow the study of rhizosphere processes and properties, and rhizosphere as a central component of ecosystems and biogeochemical cycles.« less

  5. [Review of two Japanese cases with tinea faciei identified by molecular biological techniques as Arthroderma vanbreuseghemii].

    PubMed

    Noguchi, Hiromitsu; Sakae, Hitoko; Hattori, Mariko; Hiruma, Masataro

    2010-01-01

    A 26-year-old female (Case 1) presented with scaly erythema on the left cheek. Positive direct microscopic examination results indicated a diagnosis of tinea faciei. Colonies were isolated after incubation on Mycosel agar medium. Trichophyton mentagrophytes was morphologically identified based on giant colony formation and slide culture. Furthermore, nucleotide sequence analysis of the internal transcribed spacer 1 (ITS1) region of the rDNA gene identified Arthroderma vanbreuseghemii. The patient had 9 cats in her home, and similar colonies were isolated from 2 of these 9 cats by the hairbrush culture method. The isolated organism was identified as A. vanbreuseghemii , suggesting the cats to be the source of infection. An 11-year-old boy (Case 2) had palm-sized erythematous plaques from the nasal base to the area around the left eye and on the left cheek. Positive direct microscopic examination results indicated a diagnosis of tinea faciei. The patient had been treated with topical steroids for 6 weeks before the onset of these manifestations. The isolated organism was identified as A. vanbreuseghemii . His dog and two cats were tested but did not appear to be the source of infection. Since 2000, there have been 25 cases of tinea in Japan, identified as A. vanbreuseghemii by molecular biological techniques. Twelve cases had tinea on the face, and 11 had used topical steroids. A. vanbreuseghemii was found to be one of the important pathogens in tinea faciei.

  6. Application of molecular techniques to the elucidation of the microbial community structure of antique paintings.

    PubMed

    Santos, Antonio; Cerrada, Alejandro; García, Silvia; San Andrés, Margarita; Abrusci, Concepción; Marquina, Domingo

    2009-11-01

    This paper uses molecular techniques to describe the microstructure and microbiological communities of sixteenth century artwork and their relationships. The microbiological populations, analysed by denaturing gradient gel electrophoresis (DGGE), were highly influenced by the chemical composition of the pictorial layers detected by energy-dispersive X-ray analysis. DGGE revealed that the diversity of microbial communities was lower in pictorial layers composed of pigments with metals, such as Pb, Cu and Hg, than in those found in pictorial layers without such compounds. The number of cultivable microorganisms, mainly fungi and bacteria, was very low in comparison to those found by DGGE, revealing the presence of both cultivable and as-yet-uncultivated (or not viable) species in the samples analysed. Both fungi and bacteria were present in a non-random spatial distribution. Environmental scanning electron microscopy and fluorescent in situ hybridisation analyses revealed that bacterial populations were usually found in close contact with the surface of the pictorial layers, and fungal populations were located on the bacterial biofilm. This work shows, for the first time, the correlation between the diversity of the microbial populations and the chemical composition of the pictorial layers of an artwork.

  7. Investigation of Nalidixic Acid Resistance Mechanism in Salmonella enterica Using Molecular Simulation Techniques.

    PubMed

    Preethi, B; Shanthi, V; Ramanathan, K

    2015-09-01

    The emergence of nalidixic acid-resistant strains of Salmonella typhimurium remains to be a major public health problem. In particular, the substitution of Asn in place of Asp at the 87 loci in the GyrA of S. typhimurium was experimentally stated for nalidixic acid resistance. However, the data on the possible mechanism of nalidixic acid resistance are limited. In this study, I-Mutant2.0 and DUET program were employed to explore the impact of mutation on the stability of GyrA protein. Subsequently, molecular simulation techniques were employed to provide detailed information on the nalidixic acid-resistant associates with the D87N mutation in the GyrA of S. typhimurium. The binding free energy data depicts that nalidixic acid forms stable complex only with native-type GyrA than mutant (D87N) type GyrA protein. Moreover, our results theoretically suggest that hydrogen bonding formed by the Arg91 is certainly responsible for the GyrA of S. typhimurium drug selectivity. It is hoped that these evidences are immensely important for the development of new antibiotic and to overcome the nalidixic acid resistance in the near future.

  8. Cautionary observations on preparing and interpreting brain images using molecular biology-based staining techniques.

    PubMed

    Ito, Kei; Okada, Ryuichi; Tanaka, Nobuaki K; Awasaki, Takeshi

    2003-10-01

    Though molecular biology-based visualization techniques such as antibody staining, in situ hybridization, and induction of reporter gene expression have become routine procedures for analyzing the structures of the brain, precautions to prevent misinterpretation have not always been taken when preparing and interpreting images. For example, sigmoidal development of the chemical processes in staining might exaggerate the specificity of a label. Or, adjustment of exposure for bright fluorescent signals might result in overlooking weak signals. Furthermore, documentation of a staining pattern is affected easily by recognized organized features in the image while other parts interpreted as "disorganized" may be ignored or discounted. Also, a higher intensity of a label per cell can often be confused with a higher percentage of labeled cells among a population. The quality, and hence interpretability, of the three-dimensional reconstruction with confocal microscopy can be affected by the attenuation of fluorescence during the scan, the refraction between the immersion and mounting media, and the choice of the reconstruction algorithm. Additionally, visualization of neurons with the induced expression of reporter genes can suffer because of the low specificity and low ubiquity of the expression drivers. The morphology and even the number of labeled cells can differ considerably depending on the reporters and antibodies used for detection. These aspects might affect the reliability of the experiments that involves induced expression of effector genes to perturb cellular functions. Examples of these potential pitfalls are discussed here using staining of Drosophila brain. Copyright 2003 Wiley-Liss, Inc.

  9. Tympano-cartilago-stapediopexy: a method to improve hearing in open technique tympanoplasty.

    PubMed

    Moustafa, H M; Khalifa, M A

    1990-12-01

    Canal wall-down technique tympanoplasty was indicated in about 41 per cent of our cases with chronic suppurative otitis media. In this series done during the last four years, of 576 tympanoplasties, 240 cases needed type III tympanoplasty. In 145 cases, myringostapediopexy was carried out using temporalis fascia grafting over the head of the stapes. Tympano-cartilago-stapediopexy was performed in the other 95 cases by using tragal cartilage and perichondrium over the stapes. A comparison between the results of both methods of grafting is discussed. Improvement in hearing was achieved after tympano-cartilago-stapediopexy. This method proved to be suitable for those cases which need open technique tympanoplasty.

  10. Signal Amplification Technique (SAT): an approach for improving resolution and reducing image noise in computed tomography

    SciTech Connect

    Phelps, M.E.; Huang, S.C.; Hoffman, E.J.; Plummer, D.; Carson, R.

    1981-01-01

    Spatial resolution improvements in computed tomography (CT) have been limited by the large and unique error propagation properties of this technique. The desire to provide maximum image resolution has resulted in the use of reconstruction filter functions designed to produce tomographic images with resolution as close as possible to the intrinsic detector resolution. Thus, many CT systems produce images with excessive noise with the system resolution determined by the detector resolution rather than the reconstruction algorithm. CT is a rigorous mathematical technique which applies an increasing amplification to increasing spatial frequencies in the measured data. This mathematical approach to spatial frequency amplification cannot distinguish between signal and noise and therefore both are amplified equally. We report here a method in which tomographic resolution is improved by using very small detectors to selectively amplify the signal and not noise. Thus, this approach is referred to as the signal amplification technique (SAT). SAT can provide dramatic improvements in image resolution without increases in statistical noise or dose because increases in the cutoff frequency of the reconstruction algorithm are not required to improve image resolution. Alternatively, in cases where image counts are low, such as in rapid dynamic or receptor studies, statistical noise can be reduced by lowering the cutoff frequency while still maintaining the best possible image resolution. A possible system design for a positron CT system with SAT is described.

  11. INCENTIVE DEVICE IMPROVES SPACER TECHNIQUE BUT NOT CLINICAL OUTCOME IN PRESCHOOL CHILDREN WITH ASTHMA

    PubMed Central

    Schultz, André; Sly, Peter D; Zhang, Guicheng; Venter, André; le Souëf, Peter N; Devadason, Sunalene G

    2011-01-01

    Background Inhaled corticosteroid use reduces respiratory symptoms in young children with recurrent wheeze. Delivery of steroids with pressurised metered dose inhalers and spacers is influenced by children’s proficiency/technique in using delivery devices. Objectives To investigate the influence of an incentive device, the Funhaler®, on spacer technique and symptom control in young children with asthma and recurrent wheeze. Methods Randomised controlled trial where 132 2–6 year old asthmatic children received regular inhaled fluticasone through Aerochamber Plus®, or Funhaler®. The setting was a research clinic at Princess Margaret Hospital for Children, Perth, Australia. Subjects were followed up for a year. The main outcome measure was asthma symptoms. Proficiency in spacer technique was measured as salbutamol inhaled from spacer onto filter. Quality of life was measured three-monthly. Groups were compared in terms of spacer technique, symptoms and quality of life. The relationship between spacer technique and clinical outcome was examined. Results There was no difference between Funhaler and Aerochamber groups in wheeze free days, cough free days, bronchodilator free days or quality of life (p = 0.90, 0.87, 0.74 and 0.11 respectively). Spacer technique was better in the Funhaler group (p = 0.05), particularly in subjects younger than 4 years of age (p = 0.002). Drug dose on filter (as the mean of five 100μg doses) ranged from zero to 136μg. Conclusion Use of Funhaler® incentive device does not improve clinical outcome, but improves spacer technique in children younger than 4 years. Variability in drug delivery is large in young children using pMDI-spacers. PMID:22040259

  12. Characterization of Microstructure and Molecular Dynamics with High Frequency Oscillatory Techniques

    NASA Astrophysics Data System (ADS)

    Remmler, Torsten; Amin, Samiul; Ferrante, Andrea; Pechhold, Wolfgang

    2009-07-01

    To characterize the rheological behaviour of complex viscoelastic fluids, polymer melts and other soft materials, motor-drive controlled rheometers are mainly used, either at constant stress or strain rate, or in the oscillatory mode. The latter has proved advantageous to discover the viscoelastic functions G*, η*, J* as fingerprints of the material under investigation, it's composition, molecular modelling and applicability. A conclusive analysis of such a viscoelastic spectrum can only be achieved if the amplitudes chosen guarantee linearity and if the frequency range covers more than 6 decades to reach the low kHz-domain. Investigations of many materials with motor-drive controlled rheometers are limited at higher frequencies and reach the above mentioned goal by applying the time-temperature superposition principle, i.e. the mastercurve technique. Since this method is restricted to rheologically simple materials (e.g. some polymer melts), but exclude those of small activation energies and others with temperature-sensitive chemical/physical structures including phase transitions, oscillating rheometry should be extended into higher real-frequency ranges, to establish useful linear viscoelastic spectroscopy. Since complex fluids can have structural arrangement over a wide range of lengthscales and their relaxation mechanisms can impact the dynamics over a wide range of timescales, multiple techniques need to be employed in order to accurately and fully establish the links between rheology, microstructure & dynamics. This is also critical information, required for fully validating developed theory and models. In this talk, advantages and limits of classical oscillatory rheometry will be covered, handling and principle of operation of two high frequency options are introduced and typical examples for real frequency spectra on soft matter, such as polymer melts, polymer solutions and weak gels will be shown. A xanthum gum based system has been investigated not only

  13. Clinical and molecular analyses of Beckwith-Wiedemann syndrome: Comparison between spontaneous conception and assisted reproduction techniques.

    PubMed

    Tenorio, Jair; Romanelli, Valeria; Martin-Trujillo, Alex; Fernández, García-Moya; Segovia, Mabel; Perandones, Claudia; Pérez Jurado, Luis A; Esteller, Manel; Fraga, Mario; Arias, Pedro; Gordo, Gema; Dapía, Irene; Mena, Rocío; Palomares, María; Pérez de Nanclares, Guiomar; Nevado, Julián; García-Miñaur, Sixto; Santos-Simarro, Fernando; Martinez-Glez, Víctor; Vallespín, Elena; Monk, David; Lapunzina, Pablo

    2016-10-01

    Beckwith-Wiedemann syndrome (BWS) is an overgrowth syndrome characterized by an excessive prenatal and postnatal growth, macrosomia, macroglossia, and hemihyperplasia. The molecular basis of this syndrome is complex and heterogeneous, involving genes located at 11p15.5. BWS is correlated with assisted reproductive techniques. BWS in individuals born following assisted reproductive techniques has been found to occur four to nine times higher compared to children with to BWS born after spontaneous conception. Here, we report a series of 187 patients with to BWS born either after assisted reproductive techniques or conceived naturally. Eighty-eight percent of BWS patients born via assisted reproductive techniques had hypomethylation of KCNQ1OT1:TSS-DMR in comparison with 49% for patients with BWS conceived naturally. None of the patients with BWS born via assisted reproductive techniques had hypermethylation of H19/IGF2:IG-DMR, neither CDKN1 C mutations nor patUPD11. We did not find differences in the frequency of multi-locus imprinting disturbances between groups. Patients with BWS born via assisted reproductive techniques had an increased frequency of advanced bone age, congenital heart disease, and decreased frequency of earlobe anomalies but these differences may be explained by the different molecular background compared to those with BWS and spontaneous fertilization. We conclude there is a correlation of the molecular etiology of BWS with the type of conception. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  14. Preliminary physiological characteristics of thermotolerant Saccharomyces cerevisiae clinical isolates identified by molecular biology techniques.

    PubMed

    Siedlarz, P; Sroka, M; Dyląg, M; Nawrot, U; Gonchar, M; Kus-Liśkiewicz, M

    2016-03-01

    The aim of the study was a molecular identification and physiological characteristic of the five Saccharomyces cerevisiae strains isolated from patients. The tested isolates were compared with control strains (which are of laboratory or commercial origin). The relation of the isolates to baker's yeast S. cerevisiae was studied using species-specific primers in PCR analysis of the ITS-26S region of DNA. Five isolates were genetically identified as the yeast belonging to the genus S. cerevisiae. The effects of temperature and carbon sources on the growth of the yeast strains were analysed. A quantitative characterization of growth kinetics approve that some tested isolates are thermotolerant and are able to grow at range 37-39°C. Among them, one representative is characterized by the highest specific growth rate (0·637 h(-1) ). In conclusions, some strains are defined as potential candidates to use in the biotechnology due to a higher growth rate at elevated temperatures. Screening for further evaluation of biotechnological significance of the tested isolates will be done (e.g. ethanol and trehalose production at higher temperatures). The physiological characterization and confirmation of species identification by molecular methods for yeasts important in the context of biotechnology industry were demonstrated. Thermotolerant microbial strains are required in various industrial applications, for improving productivity and for decreasing the risk of undesirable contaminations when higher temperatures are used. It is important to search for such strains in extreme environments or exotic niches. In this paper, new thermotolerant strains were identified belonging to the Saccharomyces cerevisiae, but differed from typical bakers' yeast, essentially by their growth rate at higher temperature. The described yeast strains are promising for using in biotechnological industry, especially, for production of ethanol and other products at higher temperatures. © 2015 The

  15. Acanthamoeba keratitis: improving the Scottish diagnostic service for the rapid molecular detection of Acanthamoeba species.

    PubMed

    Alexander, Claire Low; Coyne, Michael; Jones, Brian; Anijeet, Deepa

    2015-07-01

    Acanthamoeba species are responsible for causing the potentially sight-threatening condition, Acanthamoeba keratitis, which is commonly associated with contact lens use. In this report, we highlight the challenges faced using conventional laboratory identification methods to identify this often under-reported pathogen, and discuss the reasons for introducing the first national service in Scotland for the rapid and sensitive molecular identification of Acanthamoeba species. By comparing culture and molecular testing data from a total of 63 patients (n = 80 samples) throughout Scotland presenting with ocular eye disease, we describe the improvement in detection rates where an additional four positive cases were identified using a molecular assay versus culture. The testing of a further ten patients by confocal imaging is also presented. This report emphasizes the importance of continuing to improve clinical laboratory services to ensure a prompt, correct diagnosis and better prognosis, in addition to raising awareness of this potentially debilitating opportunistic pathogen.

  16. Improving Students' Learning With Effective Learning Techniques: Promising Directions From Cognitive and Educational Psychology.

    PubMed

    Dunlosky, John; Rawson, Katherine A; Marsh, Elizabeth J; Nathan, Mitchell J; Willingham, Daniel T

    2013-01-01

    Many students are being left behind by an educational system that some people believe is in crisis. Improving educational outcomes will require efforts on many fronts, but a central premise of this monograph is that one part of a solution involves helping students to better regulate their learning through the use of effective learning techniques. Fortunately, cognitive and educational psychologists have been developing and evaluating easy-to-use learning techniques that could help students achieve their learning goals. In this monograph, we discuss 10 learning techniques in detail and offer recommendations about their relative utility. We selected techniques that were expected to be relatively easy to use and hence could be adopted by many students. Also, some techniques (e.g., highlighting and rereading) were selected because students report relying heavily on them, which makes it especially important to examine how well they work. The techniques include elaborative interrogation, self-explanation, summarization, highlighting (or underlining), the keyword mnemonic, imagery use for text learning, rereading, practice testing, distributed practice, and interleaved practice. To offer recommendations about the relative utility of these techniques, we evaluated whether their benefits generalize across four categories of variables: learning conditions, student characteristics, materials, and criterion tasks. Learning conditions include aspects of the learning environment in which the technique is implemented, such as whether a student studies alone or with a group. Student characteristics include variables such as age, ability, and level of prior knowledge. Materials vary from simple concepts to mathematical problems to complicated science texts. Criterion tasks include different outcome measures that are relevant to student achievement, such as those tapping memory, problem solving, and comprehension. We attempted to provide thorough reviews for each technique, so this

  17. A multiscale simulation technique for molecular electronics: design of a directed self-assembled molecular n-bit shift register memory device.

    PubMed

    Lambropoulos, Nicholas A; Reimers, Jeffrey R; Crossley, Maxwell J; Hush, Noel S; Silverbrook, Kia

    2013-12-20

    A general method useful in molecular electronics design is developed that integrates modelling on the nano-scale (using quantum-chemical software) and on the micro-scale (using finite-element methods). It is applied to the design of an n-bit shift register memory that could conceivably be built using accessible technologies. To achieve this, the entire complex structure of the device would be built to atomic precision using feedback-controlled lithography to provide atomic-level control of silicon devices, controlled wet-chemical synthesis of molecular insulating pillars above the silicon, and controlled wet-chemical self-assembly of modular molecular devices to these pillars that connect to external metal electrodes (leads). The shift register consists of n connected cells that read data from an input electrode, pass it sequentially between the cells under the control of two external clock electrodes, and deliver it finally to an output device. The proposed cells are trimeric oligoporphyrin units whose internal states are manipulated to provide functionality, covalently connected to other cells via dipeptide linkages. Signals from the clock electrodes are conveyed by oligoporphyrin molecular wires, and μ-oxo porphyrin insulating columns are used as the supporting pillars. The developed multiscale modelling technique is applied to determine the characteristics of this molecular device, with in particular utilization of the inverted region for molecular electron-transfer processes shown to facilitate latching and control using exceptionally low energy costs per logic operation compared to standard CMOS shift register technology.

  18. Evaluation of Advanced Signal Processing Techniques to Improve Detection and Identification of Embedded Defects

    SciTech Connect

    Clayton, Dwight A.; Santos-Villalobos, Hector J.; Baba, Justin S.

    2016-09-01

    By the end of 1996, 109 Nuclear Power Plants were operating in the United States, producing 22% of the Nation’s electricity [1]. At present, more than two thirds of these power plants are more than 40 years old. The purpose of the U.S. Department of Energy Office of Nuclear Energy’s Light Water Reactor Sustainability (LWRS) Program is to develop technologies and other solutions that can improve the reliability, sustain the safety, and extend the operating lifetimes of nuclear power plants (NPPs) beyond 60 years [2]. The most important safety structures in an NPP are constructed of concrete. The structures generally do not allow for destructive evaluation and access is limited to one side of the concrete element. Therefore, there is a need for techniques and technologies that can assess the internal health of complex, reinforced concrete structures nondestructively. Previously, we documented the challenges associated with Non-Destructive Evaluation (NDE) of thick, reinforced concrete sections and prioritized conceptual designs of specimens that could be fabricated to represent NPP concrete structures [3]. Consequently, a 7 feet tall, by 7 feet wide, by 3 feet and 4-inch-thick concrete specimen was constructed with 2.257-inch-and 1-inch-diameter rebar every 6 to 12 inches. In addition, defects were embedded the specimen to assess the performance of existing and future NDE techniques. The defects were designed to give a mix of realistic and controlled defects for assessment of the necessary measures needed to overcome the challenges with more heavily reinforced concrete structures. Information on the embedded defects is documented in [4]. We also documented the superiority of Frequency Banded Decomposition (FBD) Synthetic Aperture Focusing Technique (SAFT) over conventional SAFT when probing defects under deep concrete cover. Improvements include seeing an intensity corresponding to a defect that is either not visible at all in regular, full frequency content SAFT

  19. Assessment of the quality of dna extracted by two techniques from Mycobacterium tuberculosis for fast molecular identification and genotyping

    PubMed Central

    Miyata, Marcelo; Santos, Adolfo Carlos Barreto; Mendes, Natália Helena; Cunha, Eunice Atsuko; de Melo, Fernando Augusto Fiúza; Leite, Clarice Queico Fujimura

    2011-01-01

    We report a comparative study of two DNA extraction techniques, thermolysis and chemical lysis (CTAB), for molecular identification and genotyping of M. tuberculosis. Forty DNA samples were subjected to PCR and the results demonstrated that with thermolysis it is possible to obtain useful data that enables fast identification and genotyping. PMID:24031692

  20. Improvement in Automatic Postural Coordination Following Alexander Technique Lessons in a Person With Low Back Pain

    PubMed Central

    Cacciatore, Timothy W; Horak, Fay B; Henry, Sharon M

    2006-01-01

    Background and Purpose The relationship between abnormal postural coordination and back pain is unclear. The Alexander Technique (AT) aims to improve postural coordination by using conscious processes to alter automatic postural coordination and ongoing muscular activity, and it has been reported to reduce low back pain. This case report describes the use of the AT with a client with low back pain and the observed changes in automatic postural responses and back pain. Case Description The client was a 49-year-old woman with a 25-year history of left-sided, idiopathic, lumbrosacral back pain. Automatic postural coordination was measured using a force plate during horizontal platform translations and one-legged standing. Outcomes The client was tested monthly for 4 months before AT lessons and for 3 months after lessons. Before lessons, she consistently had laterally asymmetric automatic postural responses to translations. After AT lessons, the magnitude and asymmetry of her responses and balance improved and her low back pain decreased. Discussion Further research is warranted to study whether AT lessons improve low back pain–associated abnormalities in automatic postural coordination and whether improving automatic postural coordination helps to reduce low back pain. [Cacciatore TW, Horak FB, Henry SM. Improvement in automatic postural coordination following Alexander Technique lessons in a person with low back pain. PMID:15921477

  1. A knowledge-based approach to improving optimization techniques in system planning

    NASA Technical Reports Server (NTRS)

    Momoh, J. A.; Zhang, Z. Z.

    1990-01-01

    A knowledge-based (KB) approach to improve mathematical programming techniques used in the system planning environment is presented. The KB system assists in selecting appropriate optimization algorithms, objective functions, constraints and parameters. The scheme is implemented by integrating symbolic computation of rules derived from operator and planner's experience and is used for generalized optimization packages. The KB optimization software package is capable of improving the overall planning process which includes correction of given violations. The method was demonstrated on a large scale power system discussed in the paper.

  2. Improved Signal Processing Technique Leads to More Robust Self Diagnostic Accelerometer System

    NASA Technical Reports Server (NTRS)

    Tokars, Roger; Lekki, John; Jaros, Dave; Riggs, Terrence; Evans, Kenneth P.

    2010-01-01

    The self diagnostic accelerometer (SDA) is a sensor system designed to actively monitor the health of an accelerometer. In this case an accelerometer is considered healthy if it can be determined that it is operating correctly and its measurements may be relied upon. The SDA system accomplishes this by actively monitoring the accelerometer for a variety of failure conditions including accelerometer structural damage, an electrical open circuit, and most importantly accelerometer detachment. In recent testing of the SDA system in emulated engine operating conditions it has been found that a more robust signal processing technique was necessary. An improved accelerometer diagnostic technique and test results of the SDA system utilizing this technique are presented here. Furthermore, the real time, autonomous capability of the SDA system to concurrently compensate for effects from real operating conditions such as temperature changes and mechanical noise, while monitoring the condition of the accelerometer health and attachment, will be demonstrated.

  3. Improvement of synthetic aperture techniques by means of the coarray analysis

    NASA Astrophysics Data System (ADS)

    Martín-Arguedas, C. J.; Martínez-Graullera, O.; Romero-Laorden, D.; Pérez-López, M.; Gómez-Ullate, L.

    2012-05-01

    In the field of ultrasonic imaging, the synthetic aperture techniques are well known due to their ability for obtain images using fewer resources. Initially, these techniques were developed to reduce the cost and complexity of phased array instrumentation. Although these drawbacks have already been overcome, the interest on the synthetic aperture systems has not decayed. The reasons of that are the high image quality achieved with these techniques (images dynamically focused both in emission and reception), and the fact that they are an excellent solution for the design of new high performance instrumentation with a low volume and power consumption, easily integrable in autonomous and embedded systems. Using the coarray as a model of the pulse-echo systems, the present work analyzes experimentally the main synthetic aperture strategies appeared until now, introducing two new proposals (2R-SAFT and nR-SAFT) that allow to improve the quality of the images without increase the hardware complexity of the system.

  4. A simple technique to improve centration during trephination of the donor lenticula in DSAEK.

    PubMed

    Koenig, Steven B

    2010-01-01

    The author describes a technique to improve centration of the trephination of the donor corneal lenticula during Descemet's stripping and automated endothelial keratoplasty. Following resection of the anterior corneal lamella with the microkeratome, a 10-mm trephine stained with gentian-violet dye is used to mark the perimeter of the resection bed. The remaining donor cornea is centered on the Barron-Hessburg punching block endothelial side up using the easily seen annular mark as a guide. Using this technique, the author has successfully avoided eccentrically trephined donor lenticulae in cases. This simple technique allows the surgeon performing Descemet's stripping and automated endothelial keratoplasty to consistently punch the donor lenticula within the margins of the anterior lamellar resection.

  5. Improvements in sparse matrix/vector technique applications for on-line load flow calculation

    SciTech Connect

    Ristanovic, P.; Bjelogrlic, M.; Babic, B.S.

    1989-02-01

    Sparsity technique is applied to a wide range of problems in power systems analysis. In this paper the authors propose several analytical and computational improvements in sparsity applications. The new partial matrix refactorization method and ordering algorithm are presented. The proposed method is very efficient when applied to various kinds of programs, such as: on-line load flow, optimal power flow and steady-state security analysis. The proposed methodology is applied in a fast decoupled load flow program which include the treatment of tap violations on under-load tap changing (ULTC) transformers and reactive power generation on PV buses. Effects of proposed improvements are well tested and documented on the three networks: 118 bus IEEE test network and two utility networks with 209 and 519 buses, respectively. Keywords: sparsity technique, load flow analysis, security analysis.

  6. [Discoveries and techniques that have contributed to improving the treatment of pancreatic diseases].

    PubMed

    Navarro, Salvador

    2015-05-01

    Due to its retroperitoneal location, the pancreas has historically been a mysterious organ that is difficult to examine and which complicates treatment. The discovery of anesthesia and asepsis in the mid-19th century allowed laparotomic diagnosis, which was previously only possible at autopsy. The expectations of surgery were improved by the detection of blood groups, vitamin K synthesis, and the development of intensive care units. In addition, high levels of presurgical diagnosis and an unquestionable improvement of its results were enabled by advances in laboratory methods (serum quantification of amylase and lipase, tumoral markers, genetics, and techniques for measuring exocrine pancreatic function), imaging and endoscopic modalities, and fine tuning of surgical techniques. In this article, we review the history of the main milestones that have allowed progress in all these aspects. Copyright © 2014 Elsevier España, S.L.U. and AEEH y AEG. All rights reserved.

  7. Improvement of dynamic range of filter-less fluorescence sensor with body-biasing technique

    NASA Astrophysics Data System (ADS)

    Moriwaki, Yu; Takahashi, Kazuhiro; Akita, Ippei; Ishida, Makoto; Sawada, Kazuaki

    2015-04-01

    Although fluorescence microscopy is an important technique in biomedical fields, the bulky equipment is disadvantageous in some situations. We have previously proposed a filter-less fluorescence sensor whose operation is based on the light absorption coefficient, which depends on the wavelength in a silicon substrate. In this sensor, the ratio of the excitation light intensity to the fluorescence intensity is as high as 400:1 upon optimizing the impurity concentration and the depth of the p-well region. To improve the dynamic range, herein we use a body-biasing technique to optimize the potential distribution of the sensing area to acquire sufficient photocurrent. Consequently, the dynamic range of the filter-less fluorescence sensor is improved to 800:1 with an 8 V substrate voltage.

  8. An improved leakage current compensation technique for a 4πγ ionization chamber system

    NASA Astrophysics Data System (ADS)

    Hino, Y.; Kawada, Y.; Nazaroh

    1996-02-01

    A current integration method using a small capacitor is most commonly employed for precise measurements of small currents from 4πγ ionization chambers for the secondary standardization of radionuclides. An improved technique has been developed for eliminating the possible effect due to the electrical leakage and/or current loss across the feedback capacitor used in the integration of the ionization current. This method is based upon charge integration from a fixed negative level of potential to nearly the same level of positive potential via the zero point. The validity of this method is demonstrated for some typical applications of 4πγ ionization chamber systems. This technique can contribute to the improvement of accuracy and to the extension of the intensity range of radioactive source in 4πγ ionization measurement.

  9. Detection of Occult Lymph Node Metastases in Esophageal Cancer by Minimally Invasive Staging Combined with Molecular Diagnostic Techniques

    PubMed Central

    Kassis, Edmund S.; Nguyen, Ninh; Shriver, Sharon P.; Siegfried, Jill M.; Schauer, Philip R.

    1998-01-01

    Background and Objectives: Lymph node metastases are the most important prognostic factor in patients with esophageal cancer. Histologic examination misses micrometastases in up to 20% of lymph nodes evaluated. In addition, non-invasive imaging modalities are not sensitive enough to detect small lymph nodes metastases. The objective of this study was to investigate the use of reverse transcriptase-polymerase chain reaction (RT-PCR) of messenger RNA (mRNA) for carcinoembryonic antigen (CEA) to increase the detection of micrometastases in lymph nodes from patients with esophageal cancer. Methods: RT-PCR of CEA mRNA was performed in lymph nodes from patients with malignant and benign esophageal disease. Each specimen was examined histopathologically and by RT-PCR and the results were compared. Results: Metastases were present in 29 of 60 (48%) lymph nodes sample by minimally invasive staging from 13 patients with esophageal cancer when examined histopathologically. RT-PCR identified nodal metastases in 46 of these 60 (77%) samples. RT-PCR detected CEA mRNA in all 29 histologically positive samples and in 17 histologically negative lymph nodes. All lymph nodes from patients with benign disease (n=15) were negative both histopathologically and by RT-PCR. The stage of two patients was reclassified based on the RT-PCR results, which identified lymph node spread undetected histopathologically. Both of these patients developed recurrent disease after resection of the primary tumor. Conclusions: RT-PCR is more sensitive than histologic examination in the detection of lymph node metastases in esophageal cancer and can lead to diagnosis of a more advanced stage in some patients. The combination of minimally invasive surgical techniques in combination with new molecular diagnostic techniques may improve our ability to stage cancer patients. PMID:10036123

  10. Low-molecular-weight polyethylene glycol improves survival in experimental sepsis.

    PubMed

    Ackland, Gareth L; Gutierrez Del Arroyo, Ana; Yao, Song T; Stephens, Robert C; Dyson, Alexander; Klein, Nigel J; Singer, Mervyn; Gourine, Alexander V

    2010-02-01

    For several chronic inflammatory disease states, therapy is enhanced by improving the pharmacokinetic properties of anti-inflammatory drugs through conjugation with polyethylene glycol. We hypothesized that part of the beneficial action of PEGylated drugs may be derived from the anti-inflammatory properties of polyethylene glycol (PEG) itself. Randomized, double-blinded, controlled ex vivo and in vivo laboratory studies. University research laboratories. Human neutrophils and mononuclear cells, macrophage cell line, and adult rats and mice. The effect of PEG (either low-molecular-weight [200-400] or high-molecular-weight [>4000]) was assessed on survival after systemic inflammation induced by lipopolysaccharide or zymosan. The effects of PEG on zymosan, lipopolysaccharide, or streptolysin-induced inflammatory and bioenergetic responses of immune cells were also assessed. Low-molecular-weight PEG reduced inflammatory cytokine expression, pyrexia, and mortality by >50% in both lipopolysaccharide and zymosan models of sepsis. Low-molecular-weight PEG reduced cytokine expression both in vivo and in vitro, and attenuated activation of human neutrophils in response to lipopolysaccharide or zymosan. By contrast, high-molecular-weight PEG conferred less significant survival effects after lipopolysaccharide and zymosan, and it did not exhibit such profound anti-inflammatory effects. Low-molecular-weight PEG attenuated lipopolysaccharide-induced activation of pro-apoptotic pathways (lysophosphatidic acid receptor and caspase-domain signaling) in the livers of endotoxemic rats. Streptolysin-induced necrosis of human neutrophils was reduced by low-molecular-weight PEG, indicating a mechanism that involves coating and/or stabilizing the cellular membrane. Low-molecular-weight PEG preserved human neutrophil responses to septic serum and bioenergetic function in macrophages and neutrophils. PEG is a commonly used, safe, nonimmunogenic molecule possessing hitherto unappreciated

  11. Improvement in cardioplegic perfusion technique in single aortic clamping - initial results

    PubMed Central

    Sobral, Marcelo Luiz Peixoto; dos Santos Júnior, Sérgio Francisco; de Sá, Juliano Cavalcante; Terrazas, Anderson da Silva; Trompieri, Daniel Francisco de Mendonça; de Sousa, Thierry Araújo Nunes; dos Santos, Gilmar Geraldo; Stolf, Noedir Antonio Groppo

    2014-01-01

    Introduction The most common method used for myocardial protection is administering cardioplegic solution in the coronary circulation. Nevertheless, protection may be achieved by intermittent perfusion of the coronary system with patient's own blood. The intermittent perfusion may be performed by multiple sequences of clamping and opening of the aortic clamp or due single clamping and accessory cannulation of the aortic root as in the improved technique proposed in this study, reperfusion without the need for multiple clamping of the aorta. Objective To evaluate the clinical outcome and the occurrence of neurological events in in-hospital patients submitted to myocardial revascularization surgery with the "improved technique" of intermittent perfusion of the aortic root with single clamping. Methods This is a prospective, cross-sectional, observational study that describes a myocardial management technique that consists of intermittent perfusion of the aortic root with single clamping in which 50 patients (mean age 58.5±7.19 years old) have been submitted to the myocardial revasculrization surgery under the proposed technique. Clinical and laboratory variables, pre- and post-surgery, have been assessed. Results The mean peak level of post-surgery CKMB was 51.64±27.10 U/L in the second post-surgery and of troponin I was 3.35±4.39 ng/ml in the fourth post-surgery, within normal limits. No deaths have occurred and one patient presented mild neurological disorder. Hemodynamic monitoring has not indicated any changes. Conclusion The myocardial revascularization surgery by perfusion with the improved technique with intermittent aortic root with single clamping proved to be safe, enabling satisfactory clinical results. PMID:25140473

  12. Fabrication of a novel biosensor for macromolecules detection through molecular imprinting technique

    NASA Astrophysics Data System (ADS)

    Yu, Yingjie

    There is an increasing need for precise molecular detection as a diagnostic tool for early identification of diseases, pathogens, and abnormal protein levels in the body. Typical chemical analytical methods are generally costly, unstable, and time-consuming. Molecular imprinting (MI) technique, based on the "lock and key model", could be a simple method to overcome those shortcomings. In this study, a self-assembled monolayer (SAM) was employed as a platform to fabricate MI biosensor for detection of macromolecules. I demonstrated that, when the monolayer was formed on a rough surface, this method was in fact templating molecules in three dimensions, and hence was not limited by the height of the monolayer, but rather by the height of the roughness. This hypothesis was tested on biomolecules of multiple length scales. The SAM is assembled on the walls of the niche, forming a 3D pattern of the analyte uniquely molded to its contour. The surfaces with multi-scale roughness were prepared by evaporation of gold onto electropolished (smooth) and unpolished (rough) Si wafers, where the native roughness was found to have a normal distribution centered around 5 and 90 nm respectively. Our studies, using molecules, such as proteins, i.e., hemoglobin, ranging from a few nanometers, to viruses (i.e. polio, adenovirus), ranging from several tens of nanometers, and protein complexes ranging from several hundred nanometers, showed that when the size of the analyte matched the roughness of the gold surface, this method was very effective and could detect even small changes in the configuration, such as those induced by changes in the pH of the system. The detection method was further quantified by applying it to the detection of CEA in pancreatic cyst fluid obtained from 18 patients under IRB 95867-6. The results of the MI biosensor were directly compared with those obtained using ELISA in the hospital pathology laboratory with excellent agreement, except that the MI biosensor

  13. The use of artificial intelligence techniques to improve the multiple payload integration process

    NASA Technical Reports Server (NTRS)

    Cutts, Dannie E.; Widgren, Brian K.

    1992-01-01

    A maximum return of science and products with a minimum expenditure of time and resources is a major goal of mission payload integration. A critical component then, in successful mission payload integration is the acquisition and analysis of experiment requirements from the principal investigator and payload element developer teams. One effort to use artificial intelligence techniques to improve the acquisition and analysis of experiment requirements within the payload integration process is described.

  14. Novel fabrication technique for improving the figure-of-merit of thermoelectric materials

    NASA Technical Reports Server (NTRS)

    Beaty, J. S.; Masters, R.; Vandersande, J. W.; Wood, C.

    1989-01-01

    Reduction of the thermal conductivity of thermoelectric materials in order to improve the figure of merit and, hence, the conversion efficiency is discussed. A novel fabrication technique that reduces the thermal conductivity without too adverse an effect on the electrical properties is reported. This is achieved by producing an oxygen-free, very-fine-grain SiGe alloy with very small (on the order of 50 A) precipitates.

  15. An improved technique of expanding metal ring experiment under high explosive loading

    NASA Astrophysics Data System (ADS)

    Tang, Tiegang; Ren, Guowu; Guo, Zhaoliang; Li, Qingzhong

    2013-04-01

    An experimental technique for metal expanding ring subjected to high explosive loading is conducted to significantly improve the loading stability compared with the traditional setup of two-end detonator initiation. Aspects of the circuit design, experimental arrangement, and initiation principle are illustrated in great detail. In terms of this experimental platform, we examine the velocity response of an individual ring, which demonstrates the experimental reproducibility. Moreover, fragmentation of multiple rings stacked on a metal driver is discussed.

  16. Techniques for Improving the Performance of Sparse Matrix Factorization on Multiprocessor Workstations

    DTIC Science & Technology

    1990-06-01

    DATES COVERED 4. TITLE AND SUBTITLE S. FUNDING NUMBERS Techniques for Improving the Performance of Sparse Matrix 87-K-0828 Factorization on...ABSTRACT (Maximum 200 words) Abstract - this paper vk Ioo6at the problem of factoring large sparse systems of equations on high-performance multiprocessor... factorization codes achieve only a small fraction of this potential. A major limiting factor is the cost of memory accesses performed during the factorization

  17. Stable adaptive PI control for permanent magnet synchronous motor drive based on improved JITL technique.

    PubMed

    Zheng, Shiqi; Tang, Xiaoqi; Song, Bao; Lu, Shaowu; Ye, Bosheng

    2013-07-01

    In this paper, a stable adaptive PI control strategy based on the improved just-in-time learning (IJITL) technique is proposed for permanent magnet synchronous motor (PMSM) drive. Firstly, the traditional JITL technique is improved. The new IJITL technique has less computational burden and is more suitable for online identification of the PMSM drive system which is highly real-time compared to traditional JITL. In this way, the PMSM drive system is identified by IJITL technique, which provides information to an adaptive PI controller. Secondly, the adaptive PI controller is designed in discrete time domain which is composed of a PI controller and a supervisory controller. The PI controller is capable of automatically online tuning the control gains based on the gradient descent method and the supervisory controller is developed to eliminate the effect of the approximation error introduced by the PI controller upon the system stability in the Lyapunov sense. Finally, experimental results on the PMSM drive system show accurate identification and favorable tracking performance.

  18. A Kalman Filter Technique for Improving Medium-Term Predictions of the Sunspot Number

    NASA Astrophysics Data System (ADS)

    Podladchikova, T.; van der Linden, R.

    2012-04-01

    In this work we describe a technique developed to improve medium-term prediction methods of monthly smoothed sunspot numbers. Each month, the predictions are updated using the last available observations (see the monthly output in real time at http://sidc.oma.be/products/kalfil). The improvement of the predictions is provided by applying an adaptive Kalman filter to the medium-term predictions obtained by any other method, using the six-monthly mean values of sunspot numbers covering the six months between the last available value of the 13-month running mean (the starting point for the predictions) and the "current time" ( i.e. now). Our technique provides an effective estimate of the sunspot index at the current time. This estimate becomes the new starting point for the updated prediction that is shifted six months ahead in comparison with the last available 13-month running mean, and it provides an increase of prediction accuracy. Our technique has been tested on three medium-term prediction methods that are currently in real-time operation: The McNish-Lincoln method (NGDC), the standard method (SIDC), and the combined method (SIDC). With our technique, the prediction accuracy for the McNish-Lincoln method is increased by 17 - 30%, for the standard method by 5 - 21% and for the combined method by 6 - 57%.

  19. [New abdominal wall reconstruction technique with a plastic-rehabilitative intent (back pain improvement)].

    PubMed

    Palmieri, Beniamino; Grappolini, Simone; Blandini, Daniele; De-Anna, Dino; Savio, Stefano; Ferrari, Paolo; Ferrari, Giovanni; William, Pillosu; Campanini, Isabella; Guido, Vezzosi; Tenchini, Paolo; Benuzzi, Giorgia; Palmieri, Lucia

    2004-01-01

    Many abdominal wall reconstruction techniques have generally failed to pay attention to a number of anatomical considerations concerning the continuity of the thoraco-lumboabdominal fascia that envelops the dorsal and ventral muscles. We have introduced a new surgical technique (round mesh) developed to improve the abdominal wall weakness or pathology (hernia, laparocele) with the aim of restoring the muscular synergy between the anterior and posterior trunk compartments, thus improving sacroiliac stability, posture, and standing effort endurance. One hundred patients of both sexes were enrolled in this investigation. All were affected by abdominal wall impairment, frank hernia or laparocele, and had been complaining of lumbar and sciatic pain for long periods without any definite intervertebral disk pathology. They underwent pre- and postoperative subjective and objective evaluation and insertion of a prefascial polypropylene mesh with a posterior martingale that passes across the spine and paravertebral muscles, ending in two wider rectangles that are criss-crossed ventrally and finally sutured to the iliopubic brim. All the patients improved either subjectively or objectively with the round mesh procedure. This new technique is particularly useful in cases of reduction or impairment of the recti abdominis, transverse and oblique muscles, because simple suture and plication of these muscles is no guarantee of long-term functional restoration.

  20. Increased Oil Production and Reserves from Improved Completion Techniques in the Bluebell Field, Uinta Basin, Utah

    SciTech Connect

    Deo, M.D.; Morgan, C.D.

    1999-04-28

    The objective of the project is to increase oil production and reserves by the use of improved reservoir characterization and completion techniques in the Uinta Basin, Utah. To accomplish this objective, a two-year geologic and engineering characterization of the Bluebell field was conducted. The study evaluated surface and subsurface data, currently used completion techniques, and common production problems. It was determined that advanced case- and open-hole logs could be effective in determining productive beds and that stage-interval (about 500 ft [150 m] per stage) and bed-scale isolation completion techniques could result in improved well performance. In the first demonstration well (Michelle Ute well discussed in the previous technical report), dipole shear anisotropy (anisotropy) and dual-burst thermal decay time (TDT) logs were run before and isotope tracer log was run after the treatment. The logs were very helpful in characterizing the remaining hydrocarbon potential in the well. But, mechanical failure resulted in a poor recompletion and did not result in a significant improvement in the oil production from the well.

  1. Functional results in airflow improvement using a "flip-flap" alar technique: our experience.

    PubMed

    Di Stadio, Arianna; Macro, Carlo

    2017-02-21

    Pinched nasal point can be arising as congenital malformation or as results of unsuccessfully surgery. The nasal valve alteration due to this problem is not only an esthetic problem but also a functional one because can modify the nasal airflow. Several surgical techniques were proposed in literature, we proposed our. The purpose of the study is the evaluation of nose airway flow using our flip-flap technique for correction of pinched nasal tip. This is a retrospective study conducted on twelve patients. Tip cartilages were remodeled by means of autologous alar cartilage grafting. The patients underwent a rhinomanometry pre and post-surgery to evaluate the results, and they performed a self-survey to evaluate their degree of satisfaction in term of airflow sensation improvement. Rhinomanometry showed improved nasal air flow (range from 25% to 75%) in all patients. No significant differences were showed between unilateral and bilateral alar malformation (p=0.49). Patient's satisfaction reached the 87.5%. Our analysis on the combined results (rhinomanometry and surveys) showed that this technique leads to improvement of nasal flow in patients affected by pinched nasal tip in all cases. Copyright © 2017 Associação Brasileira de Otorrinolaringologia e Cirurgia Cérvico-Facial. Published by Elsevier Editora Ltda. All rights reserved.

  2. Fundamentals of quality assessment of molecular amplification methods in clinical diagnostics. International Federation of Clinical Chemistry Scientific Division Committee on Molecular Biology Techniques.

    PubMed

    Neumaier, M; Braun, A; Wagener, C

    1998-01-01

    The increasing interest in molecular biology diagnostics is a result of the tremendous gain of scientific knowledge in genetics, made possible especially since the introduction of amplification techniques. High expectations have been placed on genetic testing, and the number of laboratories now using the relevant technology is rapidly increasing--resulting in an obvious need for standardization and definition of laboratory organization. This communication is an effort towards that end. We address aspects that should be considered when structuring a new molecular diagnostic laboratory, and we discuss individual preanalytical and analytical procedures, from sampling to evaluation of assay results. In addition, different means of controlling contamination are discussed. Because the methodology is in constant change, no general standards can be defined. Accordingly, this publication is intended to serve as a recommendation for good laboratory practice and internal quality control and as a guide to troubleshooting, primarily in amplification techniques.

  3. microDuMIP: target-enrichment technique for microarray-based duplex molecular inversion probes

    PubMed Central

    Yoon, Jung-Ki; Ahn, Jinwoo; Kim, Han Sang; Han, Soo Min; Jang, Hoon; Lee, Min Goo; Lee, Ji Hyun; Bang, Duhee

    2015-01-01

    Molecular inversion probe (MIP)-based capture is a scalable and effective target-enrichment technology that can use synthetic single-stranded oligonucleotides as probes. Unlike the straightforward use of synthetic oligonucleotides for low-throughput target capture, high-throughput MIP capture has required laborious protocols to generate thousands of single-stranded probes from DNA microarray because of multiple enzymatic steps, gel purifications and extensive PCR amplifications. Here, we developed a simple and efficient microarray-based MIP preparation protocol using only one enzyme with double-stranded probes and improved target capture yields by designing probes with overlapping targets and unique barcodes. To test our strategy, we produced 11 510 microarray-based duplex MIPs (microDuMIPs) and captured 3554 exons of 228 genes in a HapMap genomic DNA sample (NA12878). Under our protocol, capture performance and precision of calling were compatible to conventional MIP capture methods, yet overlapping targets and unique barcodes allowed us to precisely genotype with as little as 50 ng of input genomic DNA without library preparation. microDuMIP method is simpler and cheaper, allowing broader applications and accurate target sequencing with a scalable number of targets. PMID:25414325

  4. The Henry Ford Production System: LEAN Process Redesign Improves Service in the Molecular Diagnostic Laboratory

    PubMed Central

    Cankovic, Milena; Varney, Ruan C.; Whiteley, Lisa; Brown, Ron; D'Angelo, Rita; Chitale, Dhananjay; Zarbo, Richard J.

    2009-01-01

    Accurate and timely molecular test results play an important role in patient management; consequently, there is a customer expectation of short testing turnaround times. Baseline data analysis revealed that the greatest challenge to timely result generation occurred in the preanalytic phase of specimen collection and transport. Here, we describe our efforts to improve molecular testing turnaround times by focusing primarily on redesign of preanalytic processes using the principles of LEAN production. Our goal was to complete greater than 90% of the molecular tests in less than 3 days. The project required cooperation from different laboratory disciplines as well as individuals outside of the laboratory. The redesigned processes involved defining and standardizing the protocols and approaching blood and tissue specimens as analytes for molecular testing. The LEAN process resulted in fewer steps, approaching the ideal of a one-piece flow for specimens through collection/retrieval, transport, and different aspects of the testing process. The outcome of introducing the LEAN process has been a 44% reduction in molecular test turnaround time for tissue specimens, from an average of 2.7 to 1.5 days. In addition, extending LEAN work principles to the clinician suppliers has resulted in a markedly increased number of properly collected and shipped blood specimens (from 50 to 87%). These continuous quality improvements were accomplished by empowered workers in a blame-free environment and are now being sustained with minimal management involvement. PMID:19661386

  5. Inhaler device technique can be improved in older adults through tailored education: findings from a randomised controlled trial

    PubMed Central

    Crane, Melanie A; Jenkins, Christine R; Goeman, Dianne P; Douglass, Jo A

    2014-01-01

    Aim: To investigate the effects of inhaler device technique education on improving inhaler technique in older people with asthma. Methods: In a randomised controlled trial, device technique education was provided to a sample of 123 adults aged >55 years who had a doctor diagnosis of asthma. The active education group received one-on-one technique coaching, including observation, verbal instruction and physical demonstration at baseline. The passive group received a device-specific instruction pamphlet only. Inhaler technique, including the critical steps for each device type, was assessed and scored according to Australian National Asthma Council (NAC) guidelines. Device technique was scored objectively at baseline and again at 3 and 12 months post education. Results: The majority of participants demonstrated poor technique at baseline. Only 11 (21%) of the active intervention group and 7 (16%) of the passive group demonstrated 100% correct technique. By 3 months 26 (48%) of the active group achieved adequate technique. Improvement in technique was observed in the active group at 3 months (P<0.001) and remained significant at 12 months (P<0.001). No statistically significant improvement was observed in the passive group. Conclusion: The provision of active device technique education improves device technique in older adults. Passive education alone fails to achieve any improvement in device technique. PMID:25188403

  6. The Utility of Droplet Elimination by Thermal Annealing Technique for Fabrication of GaN/AlGaN Terahertz Quantum Cascade Structure by Radio Frequency Molecular Beam Epitaxy

    NASA Astrophysics Data System (ADS)

    Terashima, Wataru; Hirayama, Hideki

    2010-12-01

    We investigated the utility of a droplet elimination by thermal annealing (DETA) technique during the radio-frequency molecular beam epitaxy growth of a quantum cascade laser (QCL) structure. DETA is a method in which droplets deposited on the surface are eliminated by temporarily increasing the substrate temperature. DETA is a useful method which makes it possible not only to increase the number of periods in the QC structure, but also to improve the surface and structural properties of the QC structure. We could successfully increase the radiant intensity from a QCL sample by increasing the number of periods in the stacked QC structure with the DETA method.

  7. Molecular Technique to Reduce PCR Bias for Deeper Understanding of Microbial Diversity

    NASA Technical Reports Server (NTRS)

    Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.

    2012-01-01

    Current planetary protection policies require that spacecraft targeted to sensitive solar system bodies be assembled and readied for launch in controlled cleanroom environments. A better understanding of the distribution and frequency at which high-risk contaminant microbes are encountered on spacecraft surfaces would significantly aid in assessing the threat of forward contamination. However, despite a growing understanding of the diverse microbial populations present in cleanrooms, less abundant microbial populations are probably not adequately taken into account due to technological limitations. This novel approach encompasses a wide spectrum of microbial species and will represent the true picture of spacecraft cleanroom-associated microbial diversity. All of the current microbial diversity assessment techniques are based on an initial PCR amplification step. However, a number of factors are known to bias PCR amplification and jeopardize the true representation of bacterial diversity. PCR amplification of a minor template appears to be suppressed by the amplification of a more abundant template. It is widely acknowledged among environmental molecular microbiologists that genetic biosignatures identified from an environment only represent the most dominant populations. The technological bottleneck overlooks the presence of the less abundant minority population and may underestimate their role in the ecosystem maintenance. DNA intercalating agents such as propidium monoazide (PMA) covalently bind with DNA molecules upon photolysis using visible light, and make it unavailable for DNA polymerase enzyme during polymerase chain reaction (PCR). Environmental DNA samples will be treated with suboptimum PMA concentration, enough to intercalate with 90 99% of the total DNA. The probability of PMA binding with DNA from abundant bacterial species will be much higher than binding with DNA from less abundant species. This will increase the relative DNA concentration of

  8. Weighted Least Squares Techniques for Improved Received Signal Strength Based Localization

    PubMed Central

    Tarrío, Paula; Bernardos, Ana M.; Casar, José R.

    2011-01-01

    The practical deployment of wireless positioning systems requires minimizing the calibration procedures while improving the location estimation accuracy. Received Signal Strength localization techniques using propagation channel models are the simplest alternative, but they are usually designed under the assumption that the radio propagation model is to be perfectly characterized a priori. In practice, this assumption does not hold and the localization results are affected by the inaccuracies of the theoretical, roughly calibrated or just imperfect channel models used to compute location. In this paper, we propose the use of weighted multilateration techniques to gain robustness with respect to these inaccuracies, reducing the dependency of having an optimal channel model. In particular, we propose two weighted least squares techniques based on the standard hyperbolic and circular positioning algorithms that specifically consider the accuracies of the different measurements to obtain a better estimation of the position. These techniques are compared to the standard hyperbolic and circular positioning techniques through both numerical simulations and an exhaustive set of real experiments on different types of wireless networks (a wireless sensor network, a WiFi network and a Bluetooth network). The algorithms not only produce better localization results with a very limited overhead in terms of computational cost but also achieve a greater robustness to inaccuracies in channel modeling. PMID:22164092

  9. Weighted least squares techniques for improved received signal strength based localization.

    PubMed

    Tarrío, Paula; Bernardos, Ana M; Casar, José R

    2011-01-01

    The practical deployment of wireless positioning systems requires minimizing the calibration procedures while improving the location estimation accuracy. Received Signal Strength localization techniques using propagation channel models are the simplest alternative, but they are usually designed under the assumption that the radio propagation model is to be perfectly characterized a priori. In practice, this assumption does not hold and the localization results are affected by the inaccuracies of the theoretical, roughly calibrated or just imperfect channel models used to compute location. In this paper, we propose the use of weighted multilateration techniques to gain robustness with respect to these inaccuracies, reducing the dependency of having an optimal channel model. In particular, we propose two weighted least squares techniques based on the standard hyperbolic and circular positioning algorithms that specifically consider the accuracies of the different measurements to obtain a better estimation of the position. These techniques are compared to the standard hyperbolic and circular positioning techniques through both numerical simulations and an exhaustive set of real experiments on different types of wireless networks (a wireless sensor network, a WiFi network and a Bluetooth network). The algorithms not only produce better localization results with a very limited overhead in terms of computational cost but also achieve a greater robustness to inaccuracies in channel modeling.

  10. Improving image classification in a complex wetland ecosystem through image fusion techniques

    NASA Astrophysics Data System (ADS)

    Kumar, Lalit; Sinha, Priyakant; Taylor, Subhashni

    2014-01-01

    The aim of this study was to evaluate the impact of image fusion techniques on vegetation classification accuracies in a complex wetland system. Fusion of panchromatic (PAN) and multispectral (MS) Quickbird satellite imagery was undertaken using four image fusion techniques: Brovey, hue-saturation-value (HSV), principal components (PC), and Gram-Schmidt (GS) spectral sharpening. These four fusion techniques were compared in terms of their mapping accuracy to a normal MS image using maximum-likelihood classification (MLC) and support vector machine (SVM) methods. Gram-Schmidt fusion technique yielded the highest overall accuracy and kappa value with both MLC (67.5% and 0.63, respectively) and SVM methods (73.3% and 0.68, respectively). This compared favorably with the accuracies achieved using the MS image. Overall, improvements of 4.1%, 3.6%, 5.8%, 5.4%, and 7.2% in overall accuracies were obtained in case of SVM over MLC for Brovey, HSV, GS, PC, and MS images, respectively. Visual and statistical analyses of the fused images showed that the Gram-Schmidt spectral sharpening technique preserved spectral quality much better than the principal component, Brovey, and HSV fused images. Other factors, such as the growth stage of species and the presence of extensive background water in many parts of the study area, had an impact on classification accuracies.

  11. Experimental verification of pulse-probing technique for improving phase coherence grating lobe suppression.

    PubMed

    Torbatian, Zahra; Adamson, Rob; Brown, Jeremy A

    2013-07-01

    Fabrication of high-frequency phased-array ultrasound transducers is challenging because of the small element- to-element pitch required to avoid large grating lobes appearing in the field-of-view. Phase coherence imaging (PCI) was recently proposed as a highly effective technique to suppress grating lobes in large-pitch arrays for synthetic aperture beamforming. Our previous work proposed and theoretically validated a technique called pulse probing for improving grating lobe suppression when transmit beamforming is used with PCI. The present work reports the experimental verification of the proposed technique, in which the data was collected using a high-frequency ultrasound system and the processing was done offline. The data was collected with a 50-MHz, 256-element, 1.26 λ-pitch linear array, for which only the central 64-elements were used as the full aperture while the beam was steered to various angles. By sending a defocused pulse, the PCI weighting factors could be calculated, and were subsequently applied to the conventional transmit-receive beamforming. The experimental two-way radiation patterns showed that the grating lobe level was suppressed approximately 40 dB using the proposed technique, consistent with the theory. The suppression of overlapping grating lobes in reconstructed phased array images from multiple wire-phantoms in a water bath and tissue phantoms further validated the effectiveness of the proposed technique. The application of pulse probing along with PCI should simplify the fabrication of large-pitch phased arrays at high frequencies.

  12. Improving gemcitabine-mediated radiosensitization using molecularly targeted therapy: A review

    PubMed Central

    Morgan, Meredith A.; Parsels, Leslie A.; Maybaum, Jonathan; Lawrence, Theodore S.

    2009-01-01

    In the last three decades gemcitabine has progressed from the status of a laboratory cytotoxic drug to a standard clinical chemotherapeutic agent and a potent radiation sensitizer. In an effort to improve the efficacy of gemcitabine, additional chemotherapeutic agents have been combined with gemcitabine (both with and without radiation) but with toxicity proving to be a major limitation. Therefore, the integration of molecularly targeted agents, which potentially produce less toxicity than standard chemotherapy, with gemcitabine-radiation is a promising strategy for improving chemoradiation. Two of the most promising targets, described in this review, for improving the efficacy of gemcitabine-radiation are EGFR and Chk1. PMID:18980967

  13. How enhanced molecular ions in Cold EI improve compound identification by the NIST library.

    PubMed

    Alon, Tal; Amirav, Aviv

    2015-12-15

    Library-based compound identification with electron ionization (EI) mass spectrometry (MS) is a well-established identification method which provides the names and structures of sample compounds up to the isomer level. The library (such as NIST) search algorithm compares different EI mass spectra in the library's database with the measured EI mass spectrum, assigning each of them a similarity score called 'Match' and an overall identification probability. Cold EI, electron ionization of vibrationally cold molecules in supersonic molecular beams, provides mass spectra with all the standard EI fragment ions combined with enhanced Molecular Ions and high-mass fragments. As a result, Cold EI mass spectra differ from those provided by standard EI and tend to yield lower matching scores. However, in most cases, library identification actually improves with Cold EI, as library identification probabilities for the correct library mass spectra increase, despite the lower matching factors. This research examined the way that enhanced molecular ion abundances affect library identification probability and the way that Cold EI mass spectra, which include enhanced molecular ions and high-mass fragment ions, typically improve library identification results. It involved several computer simulations, which incrementally modified the relative abundances of the various ions and analyzed the resulting mass spectra. The simulation results support previous measurements, showing that while enhanced molecular ion and high-mass fragment ions lower the matching factor of the correct library compound, the matching factors of the incorrect library candidates are lowered even more, resulting in a rise in the identification probability for the correct compound. This behavior which was previously observed by analyzing Cold EI mass spectra can be explained by the fact that high-mass ions, and especially the molecular ion, characterize a compound more than low-mass ions and therefore carries more

  14. Fast molecular beacon hybridization in organic solvents with improved target specificity.

    PubMed

    Dave, Neeshma; Liu, Juewen

    2010-12-02

    DNA hybridization is of tremendous importance in biology, bionanotechnology, and biophysics. Molecular beacons are engineered DNA hairpins with a fluorophore and a quencher labeled on each of the two ends. A target DNA can open the hairpin to give an increased fluorescence signal. To date, the majority of molecular beacon detections have been performed only in aqueous buffers. We describe herein DNA detection in nine different organic solvents, methanol, ethanol, isopropanol, acetonitrile, formamide, dimethylformamide (DMF), dimethyl sulfoxide (DMSO), ethylene glycol, and glycerol, varying each up to 75% (v/v). In comparison with detection in water, the detection in organic solvents showed several important features. First, the molecular beacon hybridizes to its target DNA in the presence of all nine solvents up to a certain percentage. Second, the rate of this hybridization was significantly faster in most organic solvents compared with water. For example, in 56% ethanol, the beacon showed a 70-fold rate enhancement. Third, the ability of the molecular beacon to discriminate single-base mismatch is still maintained. Lastly, the DNA melting temperature in the organic solvents showed a solvent concentration-dependent decrease. This study suggests that molecular beacons can be used for applications where organic solvents must be involved or organic solvents can be intentionally added to improve the molecular beacon performance.

  15. A Biochemistry and Molecular Biology Experiment and Evaluation System for Biotechnology Specialty Students: An Effective Evaluation System to Improve the Biochemistry and Molecular Biology Experiment Teaching

    ERIC Educational Resources Information Center

    Li, Suxia; Wu, Haizhen; Zhao, Jian; Ou, Ling; Zhang, Yuanxing

    2010-01-01

    In an effort to achieve high success in knowledge and technique acquisition as a whole, a biochemistry and molecular biology experiment was established for high-grade biotechnology specialty students after they had studied essential theory and received proper technique training. The experiment was based on cloning and expression of alkaline…

  16. A Biochemistry and Molecular Biology Experiment and Evaluation System for Biotechnology Specialty Students: An Effective Evaluation System to Improve the Biochemistry and Molecular Biology Experiment Teaching

    ERIC Educational Resources Information Center

    Li, Suxia; Wu, Haizhen; Zhao, Jian; Ou, Ling; Zhang, Yuanxing

    2010-01-01

    In an effort to achieve high success in knowledge and technique acquisition as a whole, a biochemistry and molecular biology experiment was established for high-grade biotechnology specialty students after they had studied essential theory and received proper technique training. The experiment was based on cloning and expression of alkaline…

  17. Understanding the interaction between valsartan and detergents by NMR techniques and molecular dynamics simulation.

    PubMed

    Cao, Chenyu; Mao, Jiezhen; Li, Fang; Yang, Minghui; He, Hongqing; Jiang, Ling; Liu, Maili

    2012-06-28

    Valsartan (VST) is one of the Angiotensin II receptor antagonists, which is widely used in clinical hypertension treatment. It is believed that VST incorporates into biological membranes before it binds to AT(1) receptor. Herein the interactions between VST and detergents, mimicking the membrane environment, were investigated by using nuclear magnetic resonance (NMR) techniques and molecular dynamics (MD) simulation. We observed that VST has two conformers (trans and cis) exchanging slowly in DPC (dodecyl-phosphocholine) micelles, a widely used detergent. The changes of chemical shifts, relaxation rates, and self-diffusion coefficients of VST protons indicate that both conformers have strong interactions with DPC. NOE cross peaks and MD simulation reveal that DPC interacts with VST not only through the hydrophobic lipid chain, but also the hydrophilic headgroup, locating VST at the charged headgroup and upper part of the micelles. Our results are in good agreement with the Raman spectroscopic studies of VST in the DPPC (dipalmitoyl-phosphatidylcholine) bilayers by Potamitis et al. (Biochim. Biophys. Acta. 2011). The concentration ratio of trans over cis conformers is 0.94, showing that two conformers have the same affinities with the detergent, which is significantly smaller than our previous results obtained in SDS (sodium dodecyl sulfate) micelles. MD simulation suggested that the cis conformer has slightly lower binding free energy than the trans conformer when interacting with DPC. The conformational change of VST was further investigated in two detergents, CTAB (hexadecyltrimethylammonium bromide) and Tween-20 (polysorbate 20). Ratios of conformer A and B in the presence of detergents are in the order of DPC, CTAB < Tween-20 < SDS, which is correlated with the charge characters of their head groups. NMR investigations and MD simulations indicate that the electrostatic interaction plays an essential role in the binding process of VST with detergents, and the

  18. Desulfovibrionales-related bacteria in a paper mill environment as detected with molecular techniques and culture.

    PubMed

    Maukonen, Johanna; Saarela, Maria; Raaska, Laura

    2006-01-01

    The aim of the present study was to evaluate the suitability of a nested PCR-DGGE (denaturing gradient gel electrophoresis) method for the detection of Desulfovibrionales-related sulfate-reducing bacteria (SRB) from paper mill samples. The samples were also analyzed with culturing. SRB cause/enhance industrial problems, namely creation of foul-smelling gases (hydrogen sulfide) and biological corrosion, and so far there has not been a simple method to study these bacteria in paper mill laboratories. In our study, culturing was able to detect Desulfovibrionales-related bacteria from two different white waters, two different brokes, pulp, clay, and slime. Out of the isolated Desulfovibrionales, 23 enrichment cultures were further characterized with Desulfovibrionales-selective PCR-DGGE. An identical Desulfovibrio species sequence was found from paper machine I (broke I, slime, and pulp) and from paper machine II (broke II and white water II), suggesting an in-house contamination with the same strain. Desulfovibrionales-selective PCR-DGGE was also performed from DNA templates extracted directly from the paper mill samples. The DGGE profiles derived from the samples without prior enrichment were more diverse and the sequenced amplicons proved to belong to the Desulfovibrionales order. Moreover, molecular techniques were able to detect Desulfovibrionales-related bacteria from calcium carbonate samples whereas culture did not. Altogether, the nested PCR-DGGE method used in this study was suitable for the detection of Desulfovibrionales-related SRB directly from different paper mill samples and it could be used for the rapid identification of SRB-contaminated industrial sites and, when combined with sequencing, for tracing of the contamination routes.

  19. [Evaluation of discriminatory power of molecular epidemiology techniques in Mycobacterium tuberculosis Venezuelan isolates].

    PubMed

    Méndez, Marìa Victoria; León, Cristy; Escalona, Arnelly; Abadia, Edgar; Da Mata, Omaira; de Waard, Jacobus; Takiff, Howard Eugene

    2016-03-01

    The techniques of spoligotyping and mycobacterial interspersed repetitive unit and variable-number tandem repeat typing with 24 loci (MIRU-VNTR-24), have been