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Sample records for advanced molecular techniques

  1. 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

  2. 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. PMID:18757466

  3. Recent advances in molecular medicine techniques for the diagnosis, prevention, and control of infectious diseases.

    PubMed

    França, R F O; da Silva, C C; De Paula, S O

    2013-06-01

    In recent years we have observed great advances in our ability to combat infectious diseases. Through the development of novel genetic methodologies, including a better understanding of pathogen biology, pathogenic mechanisms, advances in vaccine development, designing new therapeutic drugs, and optimization of diagnostic tools, significant infectious diseases are now better controlled. Here, we briefly describe recent reports in the literature concentrating on infectious disease control. The focus of this review is to describe the molecular methods widely used in the diagnosis, prevention, and control of infectious diseases with regard to the innovation of molecular techniques. Since the list of pathogenic microorganisms is extensive, we emphasize some of the major human infectious diseases (AIDS, tuberculosis, malaria, rotavirus, herpes virus, viral hepatitis, and dengue fever). As a consequence of these developments, infectious diseases will be more accurately and effectively treated; safe and effective vaccines are being developed and rapid detection of infectious agents now permits countermeasures to avoid potential outbreaks and epidemics. But, despite considerable progress, infectious diseases remain a strong challenge to human survival. PMID:23339016

  4. 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

  5. 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. PMID:25566219

  6. 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.

  7. Teletherapy: advanced techniques.

    PubMed

    Stockham, Abigail; Balagamwala, Ehsan H; Singh, Arun D; Macklis, Roger

    2013-01-01

    Radiotherapy has been utilized as a treatment for ophthalmologic processes for more than one hundred years. Over this century, the field of ophthalmologic oncology has been revolutionized through medical discoveries, development of novel surgical interventions, and innovation of advanced radiotherapy techniques. In this chapter, novel radiotherapy techniques are considered. Material presented will build on basic radiation therapy principles, techniques, and treatment parameters established in the previous chapter through consideration of intensity modulated radiotherapy, stereotactic radiotherapy, and heavy ion therapy. Deliberation of matters common across advanced radiotherapy techniques including target delineation, treatment planning, and requisites for ensuring accurate, precise treatment delivery will precede discussion of advanced radiotherapy techniques as applied to the management ophthalmologic malignancies. PMID:23989124

  8. [Advances in Molecular Cloning].

    PubMed

    Ashwini, M; Murugan, S B; Balamurugan, S; Sathishkumar, R

    2016-01-01

    "Molecular cloning" meaning creation of recombinant DNA molecules has impelled advancement throughout life sciences. DNA manipulation has become easy due to powerful tools showing exponential growth in applications and sophistication of recombinant DNA technology. Cloning genes has become simple what led to an explosion in the understanding of gene function by seamlessly stitching together multiple DNA fragments or by the use of swappable gene cassettes, maximizing swiftness and litheness. A novel archetype might materialize in the near future with synthetic biology techniques that will facilitate quicker assembly and iteration of DNA clones, accelerating the progress of gene therapy vectors, recombinant protein production processes and new vaccines by in vitro chemical synthesis of any in silico-specified DNA construct. The advent of innovative cloning techniques has opened the door to more refined applications such as identification and mapping of epigenetic modifications and high-throughput assembly of combinatorial libraries. In this review, we will examine the major breakthroughs in cloning techniques and their applications in various areas of biological research that have evolved mainly due to easy construction of novel expression systems. PMID:27028806

  9. Recent Advances in Nanobiotechnology and High-Throughput Molecular Techniques for Systems Biomedicine

    PubMed Central

    Kim, Eung-Sam; Ahn, Eun Hyun; Chung, Euiheon; Kim, Deok-Ho

    2013-01-01

    Nanotechnology-based tools are beginning to emerge as promising platforms for quantitative high-throughput analysis of live cells and tissues. Despite unprecedented progress made over the last decade, a challenge still lies in integrating emerging nanotechnology-based tools into macroscopic biomedical apparatuses for practical purposes in biomedical sciences. In this review, we discuss the recent advances and limitations in the analysis and control of mechanical, biochemical, fluidic, and optical interactions in the interface areas of nanotechnology-based materials and living cells in both in vitro and in vivo settings. PMID:24258011

  10. Advanced Communication Processing Techniques

    NASA Astrophysics Data System (ADS)

    Scholtz, Robert A.

    This document contains the proceedings of the workshop Advanced Communication Processing Techniques, held May 14 to 17, 1989, near Ruidoso, New Mexico. Sponsored by the Army Research Office (under Contract DAAL03-89-G-0016) and organized by the Communication Sciences Institute of the University of Southern California, the workshop had as its objective to determine those applications of intelligent/adaptive communication signal processing that have been realized and to define areas of future research. We at the Communication Sciences Institute believe that there are two emerging areas which deserve considerably more study in the near future: (1) Modulation characterization, i.e., the automation of modulation format recognition so that a receiver can reliably demodulate a signal without using a priori information concerning the signal's structure, and (2) the incorporation of adaptive coding into communication links and networks. (Encoders and decoders which can operate with a wide variety of codes exist, but the way to utilize and control them in links and networks is an issue). To support these two new interest areas, one must have both a knowledge of (3) the kinds of channels and environments in which the systems must operate, and of (4) the latest adaptive equalization techniques which might be employed in these efforts.

  11. Advanced Coating Removal Techniques

    NASA Technical Reports Server (NTRS)

    Seibert, Jon

    2006-01-01

    An important step in the repair and protection against corrosion damage is the safe removal of the oxidation and protective coatings without further damaging the integrity of the substrate. Two such methods that are proving to be safe and effective in this task are liquid nitrogen and laser removal operations. Laser technology used for the removal of protective coatings is currently being researched and implemented in various areas of the aerospace industry. Delivering thousands of focused energy pulses, the laser ablates the coating surface by heating and dissolving the material applied to the substrate. The metal substrate will reflect the laser and redirect the energy to any remaining protective coating, thus preventing any collateral damage the substrate may suffer throughout the process. Liquid nitrogen jets are comparable to blasting with an ultra high-pressure water jet but without the residual liquid that requires collection and removal .As the liquid nitrogen reaches the surface it is transformed into gaseous nitrogen and reenters the atmosphere without any contamination to surrounding hardware. These innovative technologies simplify corrosion repair by eliminating hazardous chemicals and repetitive manual labor from the coating removal process. One very significant advantage is the reduction of particulate contamination exposure to personnel. With the removal of coatings adjacent to sensitive flight hardware, a benefit of each technique for the space program is that no contamination such as beads, water, or sanding residue is left behind when the job is finished. One primary concern is the safe removal of coatings from thin aluminum honeycomb face sheet. NASA recently conducted thermal testing on liquid nitrogen systems and found that no damage occurred on 1/6", aluminum substrates. Wright Patterson Air Force Base in conjunction with Boeing and NASA is currently testing the laser remOval technique for process qualification. Other applications of liquid nitrogen operations include cutting of both soft and hard materials. While the laser will not cut materials, it can be used to roughen surfaces and to remove other materials from the substrate including oil, grease, and mold. The space program can benefit from several of these applications with the need for precise removal of coatings and other organic compounds in areas adjacent to sensitive space flight hardware. Significant advantages are evident when comparing liquid nitrogen and laser removal operations over current techniques of media blasting and sanding.

  12. Advanced qualification techniques

    SciTech Connect

    Winokur, P.S; Shaneyfelt, M.R.; Meisenheimer, T.L.; Fleetwood, D.M.

    1993-12-01

    This paper demonstrates use of the Qualified Manufacturers List (QML) methodology to qualify commercial and military microelectronics for use in space applications. QML ``builds in`` the hardness of product through statistical process control (SPC) of technology parameters relevant to the radiation response, test structure to integrated circuit (IC) correlations, and techniques for extrapolating laboratory test results to low-dose-rate space scenarios. Each of these elements is demonstrated and shown to be a cost-effective alternative to expensive end-of-line IC testing. Several examples of test structured-IC correlations are provided and recent work on complications arising from transistor scaling and geometry is discussed. The use of a 10-keV x-ray wafer-level test system to support SPC and establish ``process capability`` is illustrated and a comparison of 10-keV x-ray and Co{sup 60} gamma irradiations is provided for a wide range of CMOS technologies. The x-ray tester is shown to be cost-effective and its use in lot acceptance/qualification is recommended. Finally, a comparison is provided between MIL-STD-883D, Test Method 1019.4, which governs the testing of packaged semiconductor microcircuits in the DoD, and ESA/SSC Basic Specification No. 22900, Europe`s Total Dose Steady-State Irradiation Test Method. Test Method 1019.4 focuses on conservative estimates of MOS hardness for space and tactical applications, while Basic Specification 22900 focuses on improved simulation of low-dose-rate space environments.

  13. Techniques in Advanced Language Teaching.

    ERIC Educational Resources Information Center

    Ager, D. E.

    1967-01-01

    For ease of presentation, advanced grammar teaching techniques are briefly considered under the headings of structuralism (belief in the effectiveness of presenting grammar rules) and contextualism (belief in the maximum use by students of what they know in the target language). The structuralist's problem of establishing a syllabus is discussed…

  14. Molecular weight characterization of advanced thermoplastic resins

    NASA Technical Reports Server (NTRS)

    Young, Philip R.; Davis, Judith R.; Chang, Alice C.

    1989-01-01

    Analytical techniques including low angle laser light scattering photometry (LALLS), differential viscometry (DV), gel permeation chromatography (GPC), GPC-LALLS and GPC-DV, were used to characterize the molecular weight and molecular weight distribution of several advanced thermoplastics. A discussion is presented of various molecular-weight-related parameters obtained by these techniques on an experimental polyimide and poly(arylene ether ketone) and a commercially available polysulfone. Where possible, these parameters are correlated with processability and selected mechanical properties. The molecular weight was found to vary during the thermal conversion of poly(amic acid) to polyimide. However, no change in composition of the polysulfone was noted in response to various processing procedures.

  15. Advanced reproductive techniques in goats.

    PubMed

    Bretzlaff, K N; Romano, J E

    2001-07-01

    The use of ultrasonography for pregnancy diagnosis and reproductive tract evaluation in the goat has become more common in the past decade. Pregnancy-specific hormone assays are commercially available for pregnancy determination in goats. Hormonal methods of synchronization of estrus for artificial insemination have been refined, but a number of factors still make pregnancy results variable. Caprine embryo transfer is widely used commercially. More advanced reproductive techniques such as in-vitro production of embryos and cloning have been accomplished in goats; success rates with these techniques will likely rapidly improve. PMID:11515409

  16. Advanced techniques in placental biology -- workshop report.

    PubMed

    Nelson, D M; Sadovsky, Y; Robinson, J M; Croy, B A; Rice, G; Kniss, D A

    2006-04-01

    Major advances in placental biology have been realized as new technologies have been developed and existing methods have been refined in many areas of biological research. Classical anatomy and whole-organ physiology tools once used to analyze placental structure and function have been supplanted by more sophisticated techniques adapted from molecular biology, proteomics, and computational biology and bioinformatics. In addition, significant refinements in morphological study of the placenta and its constituent cell types have improved our ability to assess form and function in highly integrated manner. To offer an overview of modern technologies used by investigators to study the placenta, this workshop: Advanced techniques in placental biology, assembled experts who discussed fundamental principles and real time examples of four separate methodologies. Y. Sadovsky presented the principles of microRNA function as an endogenous mechanism of gene regulation. J. Robinson demonstrated the utility of correlative microscopy in which light-level and transmission electron microscopy are combined to provide cellular and subcellular views of placental cells. A. Croy provided a lecture on the use of microdissection techniques which are invaluable for isolating very small subsets of cell types for molecular analysis. Finally, G. Rice presented an overview methods on profiling of complex protein mixtures within tissue and/or fluid samples that, when refined, will offer databases that will underpin a systems approach to modern trophoblast biology. PMID:16546252

  17. Advances in Procedural Techniques - Antegrade

    PubMed Central

    Wilson, William; Spratt, James C.

    2014-01-01

    There have been many technological advances in antegrade CTO PCI, but perhaps most importantly has been the evolution of the “hybrid’ approach where ideally there exists a seamless interplay of antegrade wiring, antegrade dissection re-entry and retrograde approaches as dictated by procedural factors. Antegrade wire escalation with intimal tracking remains the preferred initial strategy in short CTOs without proximal cap ambiguity. More complex CTOs, however, usually require either a retrograde or an antegrade dissection re-entry approach, or both. Antegrade dissection re-entry is well suited to long occlusions where there is a healthy distal vessel and limited “interventional” collaterals. Early use of a dissection re-entry strategy will increase success rates, reduce complications, and minimise radiation exposure, contrast use as well as procedural times. Antegrade dissection can be achieved with a knuckle wire technique or the CrossBoss catheter whilst re-entry will be achieved in the most reproducible and reliable fashion by the Stingray balloon/wire. It should be avoided where there is potential for loss of large side branches. It remains to be seen whether use of newer dissection re-entry strategies will be associated with lower restenosis rates compared with the more uncontrolled subintimal tracking strategies such as STAR and whether stent insertion in the subintimal space is associated with higher rates of late stent malapposition and stent thrombosis. It is to be hoped that the algorithms, which have been developed to guide CTO operators, allow for a better transfer of knowledge and skills to increase uptake and acceptance of CTO PCI as a whole. PMID:24694104

  18. 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 provide a better understanding and better control of environmental biotechnology processes, thus enabling more cost effective and efficient bioremediation of our toxic waste and contaminated environments. PMID:11930989

  19. Advanced techniques of laser telemetry

    NASA Astrophysics Data System (ADS)

    Donati, S.; Gilardini, A.

    The relationships which govern a laser telemeter; noise sources; and measurement accuracy with pulsed and sinusoidal intensity modulation techniques are discussed. Developments in telemetry instrumention and optical detection are considered. Meteorological interferometers, geodimeters, and military telemeters are described. Propagation attenuation and signal to noise ratios are treated. It is shown that accuracy depends on the product of measurement time and received power. The frequency scanning technique of CW and long pulse telemetry; multifrequency techniques; pulse compression; and vernier technique are outlined.

  20. Signature molecular descriptor : advanced applications.

    SciTech Connect

    Visco, Donald Patrick, Jr.

    2010-04-01

    In this work we report on the development of the Signature Molecular Descriptor (or Signature) for use in the solution of inverse design problems as well as in highthroughput screening applications. The ultimate goal of using Signature is to identify novel and non-intuitive chemical structures with optimal predicted properties for a given application. We demonstrate this in three studies: green solvent design, glucocorticoid receptor ligand design and the design of inhibitors for Factor XIa. In many areas of engineering, compounds are designed and/or modified in incremental ways which rely upon heuristics or institutional knowledge. Often multiple experiments are performed and the optimal compound is identified in this brute-force fashion. Perhaps a traditional chemical scaffold is identified and movement of a substituent group around a ring constitutes the whole of the design process. Also notably, a chemical being evaluated in one area might demonstrate properties very attractive in another area and serendipity was the mechanism for solution. In contrast to such approaches, computer-aided molecular design (CAMD) looks to encompass both experimental and heuristic-based knowledge into a strategy that will design a molecule on a computer to meet a given target. Depending on the algorithm employed, the molecule which is designed might be quite novel (re: no CAS registration number) and/or non-intuitive relative to what is known about the problem at hand. While CAMD is a fairly recent strategy (dating to the early 1980s), it contains a variety of bottlenecks and limitations which have prevented the technique from garnering more attention in the academic, governmental and industrial institutions. A main reason for this is how the molecules are described in the computer. This step can control how models are developed for the properties of interest on a given problem as well as how to go from an output of the algorithm to an actual chemical structure. This report provides details on a technique to describe molecules on a computer, called Signature, as well as the computer-aided molecule design algorithm built around Signature. Two applications are provided of the CAMD algorithm with Signature. The first describes the design of green solvents based on data in the GlaxoSmithKline (GSK) Solvent Selection Guide. The second provides novel non-steroidal glucocorticoid receptor ligands with some optimally predicted properties. In addition to using the CAMD algorithm with Signature, it is demonstrated how to employ Signature in a high-throughput screening study. Here, after classifying both active and inactive inhibitors for the protein Factor XIa using Signature, the model developed is used to screen a large, publicly-available database called PubChem for the most active compounds.

  1. Advanced molecular cytogenetics in human and mouse

    PubMed Central

    Dorritie, Kathleen; Montagna, Cristina; Difilippantonio, Michael J.; Ried, Thomas

    2016-01-01

    Fluorescence in situ hybridization, spectral karyotyping, multiplex fluorescence in situ hybridization, comparative genomic hybridization, and more recently array comparative genomic hybridization, represent advancements in the field of molecular cytogenetics. The application of these techniques for the analysis of specimens from humans, or mouse models of human diseases, enables one to reliably identify and characterize complex chromosomal rearrangements resulting in alterations of the genome. As each of these techniques has advantages and limitations, a comprehensive analysis of cytogenetic aberrations can be accomplished through the utilization of a combination approach. As such, analyses of specific tumor types have proven invaluable in the identification of new tumor-specific chromosomal aberrations and imbalances (aneuploidy), as well as regions containing tumor-specific gene targets. Application of these techniques has already improved the classification of tumors into distinct categories, with the hope that this will lead to more tailored treatment strategies. These techniques, in particular the application of tumor-specific fluorescence in situ hybridization probes to interphase nuclei, are also powerful tools for the early identification of premalignant lesions. PMID:15347260

  2. Advances in enteral nutrition techniques.

    PubMed

    Baskin, W N

    1992-11-01

    The increasing use of enteral nutrition in hospitals has led to an expanded role for the gastroenterologist and surgeon in providing enteral access. New concepts in immunonutrition and gut support in critically ill patients have popularized early postoperative feeding. There is an ongoing need to update physicians on the diverse enteral access techniques now available. In addition to standard percutaneous endoscopic gastrostomy (PEG) and percutaneous endoscopic jejunostomy (PEJ) techniques, this review focuses on reflux prevention through double-lumen feeding-suction tubes, and describes the use of steerable catheters for rapid insertion of nasojejunal and PEJ tubes without endoscopy. Low-profile "button"-type devices, one-step button placement, replacement gastrostomy devices, and special enteral techniques for patients with cancer are also reviewed. PMID:1442672

  3. Stitching Techniques Advance Optics Manufacturing

    NASA Technical Reports Server (NTRS)

    2010-01-01

    Because NASA depends on the fabrication and testing of large, high-quality aspheric (nonspherical) optics for applications like the James Webb Space Telescope, it sought an improved method for measuring large aspheres. Through Small Business Innovation Research (SBIR) awards from Goddard Space Flight Center, QED Technologies, of Rochester, New York, upgraded and enhanced its stitching technology for aspheres. QED developed the SSI-A, which earned the company an R&D 100 award, and also developed a breakthrough machine tool called the aspheric stitching interferometer. The equipment is applied to advanced optics in telescopes, microscopes, cameras, medical scopes, binoculars, and photolithography."

  4. Advanced Spectroscopy Technique for Biomedicine

    NASA Astrophysics Data System (ADS)

    Zhao, Jianhua; Zeng, Haishan

    This chapter presents an overview of the applications of optical spectroscopy in biomedicine. We focus on the optical design aspects of advanced biomedical spectroscopy systems, Raman spectroscopy system in particular. Detailed components and system integration are provided. As examples, two real-time in vivo Raman spectroscopy systems, one for skin cancer detection and the other for endoscopic lung cancer detection, and an in vivo confocal Raman spectroscopy system for skin assessment are presented. The applications of Raman spectroscopy in cancer diagnosis of the skin, lung, colon, oral cavity, gastrointestinal tract, breast, and cervix are summarized.

  5. Advanced Intellect-Augmentation Techniques.

    ERIC Educational Resources Information Center

    Engelbart, D. C.

    This progress report covers a two-year project which is part of a program that is exploring the value of computer aids in augmenting human intellectual capability. The background and nature of the program, its resources, and the activities it has undertaken are outlined. User experience in applying augmentation tools and techniques to various…

  6. Advanced measurement techniques, part 1

    NASA Technical Reports Server (NTRS)

    Holmes, Bruce J.; Carraway, Debra L.; Manuel, Gregory S.; Croom, Cynthia C.

    1987-01-01

    In modern laminar flow flight and wind tunnel research, it is important to understand the specific cause(s) of laminar to turbulent boundary layer transition. Such information is crucial to the exploration of the limits of practical application of laminar flow for drag reduction on aircraft. The process of transition involves both the possible modes of disturbance growth, and the environmental conditioning of the instabilities by freestream or surface conditions. The possible modes of disturbance growth include viscous, inviscid, and modes which may bypass these natural ones. Theory provides information on the possible modes of disturbance amplification, but experimentation must be relied upon to determine which of those modes actually dominates the transition process in a given environment. The results to date of research on advanced devices and methods used for the study of transition phenomena in the subsonic and transonic flight and wind tunnel environments are presented.

  7. Advanced techniques in abdominal surgery.

    PubMed Central

    Monson, J R

    1993-01-01

    Almost every abdominal organ is now amenable to laparoscopic surgery. Laparoscopic appendicectomy is a routine procedure which also permits identification of other conditions initially confused with an inflamed appendix. However, assessment of appendiceal inflammation is more difficult. Almost all colonic procedures can be performed laparoscopically, at least partly, though resection for colonic cancer is still controversial. For simple patch repair of perforated duodenal ulcers laparoscopy is ideal, and inguinal groin hernia can be repaired satisfactorily with a patch of synthetic mesh. Many upper abdominal procedures, however, still take more time than the open operations. These techniques reduce postoperative pain and the incidence of wound infections and allow a much earlier return to normal activity compared with open surgery. They have also brought new disciplines: surgeons must learn different hand-eye coordination, meticulous haemostasis is needed to maintain picture quality, and delivery of specimens may be problematic. The widespread introduction of laparoscopic techniques has emphasised the need for adequate training (operations that were straight-forward open procedures may require considerable laparoscopic expertise) and has raised questions about trainee surgeons acquiring adequate experience of open procedures. Images FIG 9 p1347-a p1347-b p1349-a p1350-a p1350-b PMID:8257893

  8. Nuclear material investigations by advanced analytical techniques

    NASA Astrophysics Data System (ADS)

    Degueldre, C.; Kuri, G.; Martin, M.; Froideval, A.; Cammelli, S.; Orlov, A.; Bertsch, J.; Pouchon, M. A.

    2010-10-01

    Advanced analytical techniques have been used to characterize nuclear materials at the Paul Scherrer Institute during the last decade. The analysed materials ranged from reactor pressure vessel (RPV) steels, Zircaloy claddings to fuel samples. The processes studied included copper cluster build up in RPV steels, corrosion, mechanical and irradiation damage behaviour of PWR and BWR cladding materials as well as fuel defect development. The used advanced techniques included muon spin resonance spectroscopy for zirconium alloy defect characterization while fuel element materials were analysed by techniques derived from neutron and X-ray scattering and absorption spectroscopy.

  9. Advanced TMAH and TMAAc thermochemolysis-pyrolysis techniques for molecular characterization of size-separated fractions from aquatic dissolved organic matter.

    PubMed

    Peuravuori, Juhani; Pihlaja, Kalevi

    2007-09-01

    The structural similarities and differences between the original DOM and the eight size fractions separated were studied in detail with the pyrolysis technique in combination with gas chromatography and mass spectrometry (Py-GC-MS) using two alkylating reagents: TMAH (tetramethylammonium hydroxide), to find both esterified and free carboxylic acids; and TMAAc (tetramethylammonium acetate), to specify only free carboxylic acids. A statistical analysis of the original multidimensional TMAH and TMAAc pyrograms disclosed that the overall structural compositions of the five most important size fractions, accounting for 84% of the original DOM, greatly resembled each other. The remaining three minor size fractions were not classified as homogeneous associations, but they also contained the same total, covalently bound and free carboxylic acid species as the other size fractions and the original DOM mixture, thus representing some kind of intermediate forms. This fundamental outcome strongly supports the opinion that the native dissolved humic-like macromolecules resemble supramolecular associations of smaller molecular size moieties with similar structural functionalities. The concentrations of free aliphatic and aromatic dicarboxylic acids in the DOM solution were so low that their effects on the potential formation of multiply charged ions in electrospray ionization-MS (ESI-MS) studies are likely insignificant. PMID:17639357

  10. Hybrid mesh generation using advancing reduction technique

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study presents an extension of the application of the advancing reduction technique to the hybrid mesh generation. The proposed algorithm is based on a pre-generated rectangle mesh (RM) with a certain orientation. The intersection points between the two sets of perpendicular mesh lines in RM an...

  11. Advanced techniques using contrast media in neuroimaging.

    PubMed

    Ferré, Jean-Christophe; Shiroishi, Mark S; Law, Meng

    2012-11-01

    This article presents an overview of advanced magnetic resonance (MR) imaging techniques using contrast media in neuroimaging, focusing on T2*-weighted dynamic susceptibility contrast MR imaging and T1-weighted dynamic contrast-enhanced MR imaging. Image acquisition and data processing methods and their clinical application in brain tumors, stroke, dementia, and multiple sclerosis are discussed. PMID:23088946

  12. Advanced molecular surveillance of hepatitis C virus.

    PubMed

    Rossi, Livia Maria Gonçalves; Escobar-Gutierrez, Alejandro; Rahal, Paula

    2015-03-01

    Hepatitis C virus (HCV) infection is an important public health problem worldwide. HCV exploits complex molecular mechanisms, which result in a high degree of intrahost genetic heterogeneity. This high degree of variability represents a challenge for the accurate establishment of genetic relatedness between cases and complicates the identification of sources of infection. Tracking HCV infections is crucial for the elucidation of routes of transmission in a variety of settings. Therefore, implementation of HCV advanced molecular surveillance (AMS) is essential for disease control. Accounting for virulence is also important for HCV AMS and both viral and host factors contribute to the disease outcome. Therefore, HCV AMS requires the incorporation of host factors as an integral component of the algorithms used to monitor disease occurrence. Importantly, implementation of comprehensive global databases and data mining are also needed for the proper study of the mechanisms responsible for HCV transmission. Here, we review molecular aspects associated with HCV transmission, as well as the most recent technological advances used for virus and host characterization. Additionally, the cornerstone discoveries that have defined the pathway for viral characterization are presented and the importance of implementing advanced HCV molecular surveillance is highlighted. PMID:25781918

  13. Advanced Molecular Surveillance of Hepatitis C Virus

    PubMed Central

    Gonçalves Rossi, Livia Maria; Escobar-Gutierrez, Alejandro; Rahal, Paula

    2015-01-01

    Hepatitis C virus (HCV) infection is an important public health problem worldwide. HCV exploits complex molecular mechanisms, which result in a high degree of intrahost genetic heterogeneity. This high degree of variability represents a challenge for the accurate establishment of genetic relatedness between cases and complicates the identification of sources of infection. Tracking HCV infections is crucial for the elucidation of routes of transmission in a variety of settings. Therefore, implementation of HCV advanced molecular surveillance (AMS) is essential for disease control. Accounting for virulence is also important for HCV AMS and both viral and host factors contribute to the disease outcome. Therefore, HCV AMS requires the incorporation of host factors as an integral component of the algorithms used to monitor disease occurrence. Importantly, implementation of comprehensive global databases and data mining are also needed for the proper study of the mechanisms responsible for HCV transmission. Here, we review molecular aspects associated with HCV transmission, as well as the most recent technological advances used for virus and host characterization. Additionally, the cornerstone discoveries that have defined the pathway for viral characterization are presented and the importance of implementing advanced HCV molecular surveillance is highlighted. PMID:25781918

  14. Molecular dynamics simulations: advances and applications

    PubMed Central

    Hospital, Adam; Goñi, Josep Ramon; Orozco, Modesto; Gelpí, Josep L

    2015-01-01

    Molecular dynamics simulations have evolved into a mature technique that can be used effectively to understand macromolecular structure-to-function relationships. Present simulation times are close to biologically relevant ones. Information gathered about the dynamic properties of macromolecules is rich enough to shift the usual paradigm of structural bioinformatics from studying single structures to analyze conformational ensembles. Here, we describe the foundations of molecular dynamics and the improvements made in the direction of getting such ensemble. Specific application of the technique to three main issues (allosteric regulation, docking, and structure refinement) is discussed. PMID:26604800

  15. Recent advances in clinical/molecular andrology.

    PubMed

    Hafez, B

    1998-01-01

    During the last decade there were extensive investigations in clinical and molecular andrology with emphasis on assisted reproduction, micromanipulation techniques of gametes, sperm/egg interaction, male contraception, diabetes mellitus, varicocele, andropause versus menopause, sexual dysfunction, associated hypertension/stress, prostatic carcinoma and molecular parameters of male reproduction. Sperm hyperactivation is a required step in capacitation sequence. Sperm motility is measured by videotape to evaluate the Straight Line Velocity (microm/s) (VSLI). Fertilization/embryonic development results from single sperm transfer (S-MIST) and multiple sperm transfer. Fertilization/embryo development is achieved by injection of immotile sperm into the perivitelline space. To assess sperm viability, a supravital stain suitable for use in combination with immunofluorescent assay, Hoeschst 33258, is used. The dye fluoresces with an intense blue when bound to DNA. To assess sperm plasma membrane integrity, a hypo-osmotic swelling test (HOST) is performed, using fluoresceinated D-mannose enriched albumin (FITC-DMA). The ability of sperm to swell under hypo-osmotic conditions indicates an intact membrane. A human protein, C-peptide, thought to be a useless byproduct of insulin may protect against devastating heart and nerve damage that diabetes causes. Human diabetics may benefit from the substance. Over 15 million Americans have diabetes, in which blood sugar levels rise out of control. There are two types of diabetics: Type I diabetics produce no insulin, the hormone that regulates blood sugar. Type II diabetics are unable to use their insulin properly. Diabetics are at great risk of heart disease and nerve damage, as arteries throughout the body leak and nerve-cell impulses fail. C-peptide is a byproduct of insulin production; it can be produced by the body or synthetically. Production of this protein is not induced by insulin, so diabetics who take insulin do not get C-peptide with it. Varicocele occurs unilaterally on the left side in 78% to 93% of men. Typically the presence of a varicocele is associated with an abnormal semen analysis (sperm density and morphology) and a decreased testicular volume on the affected side. Impaired sperm motility occurs in 89.5% of all varicocele patients. Varicocele ligation improves semen parameters in two thirds of patients. A few studies on andropause included sexual dysfunction, hormonal changes, medical/psychological correlates of impotence, ostenopenia/osteoporosis and bone loss; indices of bone remodeling, testosterone supplementation, androgen, negative feedback and hypothalamo-pituitary-testicular axis. Prostatic cancer is the second leading cause of cancer death for men between the ages of 60 and 80. Early detection involves a simple blood test for prostate specific antigen (PSA). Regular screening and early detection are essential. This is an important test because a high antigen count can be the only symptom. Since no screening is 100% accurate, physicians recommend both a PSA blood test and a physical examination. Although heredity plays a major role in whether a man will develop prostate cancer, men who lead healthy lives can dramatically reduce their chances of cancer: low-fat diet, eating plenty of fruits and vegetables and not smoking. Recent advances in molecular andrology include peptide hormone binding proteins; gonadotropin-releasing hormone (GnRH) agonists/antagonists analog; gonadotropins/their receptors; growth factors/reproduction; peptides as intratesticular regulators; molecular cloning of reproductive proteins/peptides. Gene cloning is applied for characterization/expression of genes coding. The interaction of gp120 with CD4 receptor plays a role in syncytium formation, apoptosis and CD4 cell deletion in human immunodeficiency virus (HIV) infection. The recombinant V3 peptide of fragment 307-330 of HIV-1 can induce sperm head agglutination. The generation process of react PMID:9583357

  16. Advanced Tools and Techniques for Formal Techniques in Aerospace Systems

    NASA Technical Reports Server (NTRS)

    Knight, John C.

    2005-01-01

    This is the final technical report for grant number NAG-1-02101. The title of this grant was "Advanced Tools and Techniques for Formal Techniques In Aerospace Systems". The principal investigator on this grant was Dr. John C. Knight of the Computer Science Department, University of Virginia, Charlottesville, Virginia 22904-4740. This report summarizes activities under the grant during the period 7/01/2002 to 9/30/2004. This report is organized as follows. In section 2, the technical background of the grant is summarized. Section 3 lists accomplishments and section 4 lists students funded under the grant. In section 5, we present a list of presentations given at various academic and research institutions about the research conducted. Finally, a list of publications generated under this grant is included in section 6.

  17. Advanced flat panel display backlighting techniques

    NASA Astrophysics Data System (ADS)

    Smith-Gillespie, Robert

    2008-04-01

    Defense and security applications of flat panel displays can benefit from advances in backlighting techniques and technologies to achieve improved contrast and brightness, enhanced chromaticity, lighter weight, thinner form factor, and overall power dissipation. Capturing these benefits requires consideration of multiple engineering and manufacturing trade-offs and can seem overwhelming for display-head designers. This study focuses on how to determine which trade-offs are important in particular applications, how to evaluate trade-off opportunities for cost and performance while maintaining conformance with applications requirements, and how to create and maintain an effective supply chain while adapting to constantly shifting COTS component availability.

  18. Extremity amputations: principles, techniques, and recent advances.

    PubMed

    Morris, Carol D; Potter, Benjamin K; Athanasian, Edward A; Lewis, Valerae O

    2015-01-01

    It is estimated that approximately 1.7 million Americans are living with the loss of a limb, and this number is expected to nearly double by 2050. The most common reasons for amputation include vascular compromise, trauma, cancer, and congenital deformities. Orthopaedic surgeons are often called on to manage patients requiring an amputation or those with amputation-related conditions. It is helpful to review the principles and techniques for performing lower and upper limb amputations, with a focus on common complications and how to avoid them and to be familiar with recent advances in prosthetic design and management of a residual limb. PMID:25745899

  19. Advanced Imaging Techniques for the Pathologist.

    PubMed

    Fine, Jeffrey L

    2016-03-01

    Advanced imaging refers to direct microscopic imaging of tissue, without the need for traditional hematoxylin-eosin (H&E) microscopy, including microscope slides or whole-slide images. A detailed example is presented of optical coherence tomography (OCT), an imaging technique based on reflected light. Experience and example images are discussed in the larger context of the evolving relationship of surgical pathology to clinical patient care providers. Although these techniques are diagnostically promising, it is unlikely that they will directly supplant H&E histopathology. It is likely that OCT and related technologies will provide narrow, targeted diagnosis in a variety of in vivo (patient) and ex vivo (specimen) applications. PMID:26851667

  20. Insect pathogens: molecular approaches and techniques

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  1. Molecular wires and devices: advances and issues.

    PubMed

    Lindsay, Stuart

    2006-01-01

    Substantial advances have been made in (a) our experimental and theoretical understanding of simple tunnel junctions based on molecules, (b) the role of contacts tunneling and (c) experimental studies of redox-state gated transport. In addition, a new thermally-activated transport process has been discovered in a non-redox active system. Substantial challenges remain. The engineering of molecular contacts to technologically important electronic materials will stretch the ingenuity of synthetic chemists. The theory community must rise to the challenge of describing redox-mediated transport using first-principles, parameter free approaches. These advances will enable a new generation of devices that span the silicon (electronic) and carbon (bio-organic) worlds. PMID:16512386

  2. Advanced AE Techniques in Composite Materials Research

    NASA Technical Reports Server (NTRS)

    Prosser, William H.

    1996-01-01

    Advanced, waveform based acoustic emission (AE) techniques have been successfully used to evaluate damage mechanisms in laboratory testing of composite coupons. An example is presented in which the initiation of transverse matrix cracking was monitored. In these tests, broad band, high fidelity acoustic sensors were used to detect signals which were then digitized and stored for analysis. Analysis techniques were based on plate mode wave propagation characteristics. This approach, more recently referred to as Modal AE, provides an enhanced capability to discriminate and eliminate noise signals from those generated by damage mechanisms. This technique also allows much more precise source location than conventional, threshold crossing arrival time determination techniques. To apply Modal AE concepts to the interpretation of AE on larger composite specimens or structures, the effects of modal wave propagation over larger distances and through structural complexities must be well characterized and understood. To demonstrate these effects, measurements of the far field, peak amplitude attenuation of the extensional and flexural plate mode components of broad band simulated AE signals in large composite panels are discussed. These measurements demonstrated that the flexural mode attenuation is dominated by dispersion effects. Thus, it is significantly affected by the thickness of the composite plate. Furthermore, the flexural mode attenuation can be significantly larger than that of the extensional mode even though its peak amplitude consists of much lower frequency components.

  3. Advanced Bode Plot Techniques for Ultrasonic Transducers

    NASA Astrophysics Data System (ADS)

    DeAngelis, D. A.; Schulze, G. W.

    The Bode plot, displayed as either impedance or admittance versus frequency, is the most basic test used by ultrasonic transducer designers. With simplicity and ease-of-use, Bode plots are ideal for baseline comparisons such as spacing of parasitic modes or impedance, but quite often the subtleties that manifest as poor process control are hard to interpret or are nonexistence. In-process testing of transducers is time consuming for quantifying statistical aberrations, and assessments made indirectly via the workpiece are difficult. This research investigates the use of advanced Bode plot techniques to compare ultrasonic transducers with known "good" and known "bad" process performance, with the goal of a-priori process assessment. These advanced techniques expand from the basic constant voltage versus frequency sweep to include constant current and constant velocity interrogated locally on transducer or tool; they also include up and down directional frequency sweeps to quantify hysteresis effects like jumping and dropping phenomena. The investigation focuses solely on the common PZT8 piezoelectric material used with welding transducers for semiconductor wire bonding. Several metrics are investigated such as impedance, displacement/current gain, velocity/current gain, displacement/voltage gain and velocity/voltage gain. The experimental and theoretical research methods include Bode plots, admittance loops, laser vibrometry and coupled-field finite element analysis.

  4. Current developments in human molecular cytogenetic techniques.

    PubMed

    Liehr, Thomas; Claussen, Uwe

    2002-05-01

    In the last decade a variety of fluorescence in situ hybridization (FISH) assays have been developed. In this paper we present an overview on the currently available methods in molecular cytogenetics, highlighting their advantages and limitations, as well as their applications. Even though one has to be impressed by the total number of new techniques introduced in molecular cytogenetics, one has to be aware of the fact that it is not the brilliance of a technique that is important but the scientific question that can be addressed by it. In this review special emphasis has given in describing possible strategies for the characterization of marker and derivative chromosomes in tumor- and clinical cytogenetics. PMID:12041731

  5. Advances in nanodiagnostic techniques for microbial agents.

    PubMed

    Syed, Muhammad Ali

    2014-01-15

    Infectious diseases account for millions of sufferings and deaths in both developing as well as developed countries with a substantial economic loss. Massive increase in world population and international travel has facilitated their spread from one part of the world to other areas, making them one of the most significant global health risks. Furthermore, detection of bioterrorism agents in water, food and environmental samples as well traveler's baggage is a great challenge of the time for security purpose. Prevention strategies against infectious agents demand rapid and accurate detection and identification of the causative agents with highest sensitivity which should be equally available in different parts of the globe. Similarly, rapid and early diagnosis of infectious diseases has always been indispensable for their prompt cure and management, which has stimulated scientists to develop highly sophisticated techniques over centuries and the efforts continue unabated. Conventional diagnostic techniques are time consuming, tedious, expensive, less sensitive, and unsuitable for field situations. Nanodiagnostic assays have been promising for early, sensitive, point-of-care and cost-effective detection of microbial agents. There has been an explosive research in this area of science in last two decades yielding highly fascinating results. This review highlights some of the advancements made in the field of nanotechnology based assays for microbial detection since 2005 along with providing the basic understanding. PMID:24012709

  6. Advanced techniques in current signature analysis

    SciTech Connect

    Smith, S.F.; Castleberry, K.N.

    1992-03-01

    In general, both ac and dc motors can be characterized as weakly nonlinear systems, in which both linear and nonlinear effects occur simultaneously. Fortunately, the nonlinearities are generally well behaved and understood and an be handled via several standard mathematical techniques already well developed in the systems modeling area; examples are piecewise linear approximations and Volterra series representations. Field measurements of numerous motors and motor-driven systems confirm the rather complex nature of motor current spectra and illustrate both linear and nonlinear effects (including line harmonics and modulation components). Although previous current signature analysis (CSA) work at Oak Ridge and other sites has principally focused on the modulation mechanisms and detection methods (AM, PM, and FM), more recent studies have been conducted on linear spectral components (those appearing in the electric current at their actual frequencies and not as modulation sidebands). For example, large axial-flow compressors ({approximately}3300 hp) in the US gaseous diffusion uranium enrichment plants exhibit running-speed ({approximately}20 Hz) and high-frequency vibrational information (>1 kHz) in their motor current spectra. Several signal-processing techniques developed to facilitate analysis of these components, including specialized filtering schemes, are presented. Finally, concepts for the designs of advanced digitally based CSA units are offered, which should serve to foster the development of much more computationally capable ``smart`` CSA instrumentation in the next several years. 3 refs.

  7. Inverse lithography technique for advanced CMOS nodes

    NASA Astrophysics Data System (ADS)

    Villaret, Alexandre; Tritchkov, Alexander; Entradas, Jorge; Yesilada, Emek

    2013-04-01

    Resolution Enhancement Techniques have continuously improved over the last decade, driven by the ever growing constraints of lithography process. Despite the large number of RET applied, some hotspot configurations remain challenging for advanced nodes due to aggressive design rules. Inverse Lithography Technique (ILT) is evaluated here as a substitute to the dense OPC baseline. Indeed ILT has been known for several years for its near-to-ideal mask quality, while also being potentially more time consuming in terms of OPC run and mask processing. We chose to evaluate Mentor Graphics' ILT engine "pxOPCTM" on both lines and via hotspot configurations. These hotspots were extracted from real 28nm test cases where the dense OPC solution is not satisfactory. For both layer types, the reference OPC consists of a dense OPC engine coupled to rule-based and/or model-based assist generation method. The same CM1 model is used for the reference and the ILT OPC. ILT quality improvement is presented through Optical Rule Check (ORC) results with various adequate detectors. Several mask manufacturing rule constraints (MRC) are considered for the ILT solution and their impact on process ability is checked after mask processing. A hybrid OPC approach allowing localized ILT usage is presented in order to optimize both quality and runtime. A real mask is prepared and fabricated with this method. Finally, results analyzed on silicon are presented to compare localized ILT to reference dense OPC.

  8. Influenza A virus molecular virology techniques.

    PubMed

    Zhou, Bin; Wentworth, David E

    2012-01-01

    Molecular biological techniques for genomic analysis and for creation of recombinant viruses are critical tools in our efforts to understand and combat influenza A viruses. These molecular virology approaches are used in diagnostics, basic research, molecular epidemiology, bioinformatics, and vaccine development. The majority of the techniques used to study this segmented negative-sense RNA virus begin by purifying RNA from the virus, or infected cells, and converting it to cDNA, then to dsDNA, and amplifying that dsDNA using reverse transcription in combination with the polymerase chain reaction (RTPCR). The RTPCR amplicons can be probed, sequenced, or cloned into a variety of vectors for further analysis and to create recombinant influenza A viruses by plasmid-based reverse genetics. To accelerate the amplification and cloning process, we developed multi-segment-RTPCR (M-RTPCR) techniques that efficiently amplify the eight genomic viral RNA segments (vRNAs) of influenza A virus in a single reaction, irrespective of the virus strain. The M-RTPCR amplicons are ideal for nucleotide sequence analysis and cloning full-length vRNAs into plasmids or other vectors designed for protein expression or reverse genetics. Therefore, we also developed modified reverse-genetics plasmids that are designed to rapidly clone M-RTPCR products, or other full-length vRNA amplicons, using recombination-based techniques. The combination of M-RTPCR and recombination-based cloning confers sensitivity, speed, fidelity, and flexibility to the analysis and rescue of any strain/subtype of influenza A virus, without the need for in vitro propagation. The specific topics described in this chapter include purification of high-quality viral RNA, genomic amplification using two different M-RTPCR schemes, sequencing vRNA amplicons, and cloning vRNA amplicons into our modified reverse-genetics plasmids, or commercially available plasmids. PMID:22528160

  9. Advances in procedural techniques--antegrade.

    PubMed

    Wilson, William; Spratt, James C

    2014-05-01

    There have been many technological advances in antegrade CTO PCI, but perhaps most importantly has been the evolution of the "hybrid' approach where ideally there exists a seamless interplay of antegrade wiring, antegrade dissection re-entry and retrograde approaches as dictated by procedural factors. Antegrade wire escalation with intimal tracking remains the preferred initial strategy in short CTOs without proximal cap ambiguity. More complex CTOs, however, usually require either a retrograde or an antegrade dissection re-entry approach, or both. Antegrade dissection re-entry is well suited to long occlusions where there is a healthy distal vessel and limited "interventional" collaterals. Early use of a dissection re-entry strategy will increase success rates, reduce complications, and minimise radiation exposure, contrast use as well as procedural times. Antegrade dissection can be achieved with a knuckle wire technique or the CrossBoss catheter whilst re-entry will be achieved in the most reproducible and reliable fashion by the Stingray balloon/wire. It should be avoided where there is potential for loss of large side branches. It remains to be seen whether use of newer dissection re-entry strategies will be associated with lower restenosis rates compared with the more uncontrolled subintimal tracking strategies such as STAR and whether stent insertion in the subintimal space is associated with higher rates of late stent malapposition and stent thrombosis. It is to be hoped that the algorithms, which have been developed to guide CTO operators, allow for a better transfer of knowledge and skills to increase uptake and acceptance of CTO PCI as a whole. PMID:24694104

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

    PubMed Central

    2014-01-01

    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. PMID:25099015

  11. ADVANCES IN MOLECULAR IMAGING OF PANCREATIC BETA CELLS

    PubMed Central

    Lin, Mai; Lubag, Angelo; McGuire, Michael J.; Seliounine, Serguei Y.; Tsyganov, Edward N.; Antich, Peter P.; Sherry, A. Dean; Brown, Kathlynn C.; Sun, Xiankai

    2009-01-01

    The development of non-invasive imaging methods for early diagnosis of the beta cell associated metabolic diseases, including type 1 and type 2 diabetes (T1D and T2D), has recently drawn considerable interest from the molecular imaging community as well as clinical investigators. Due to the challenges imposed by the location of the pancreas, the sparsely dispersed beta cell population within the pancreas, and the poor understanding of the pathogenesis of the diseases, clinical diagnosis of beta cell abnormalities is still limited. Current diagnostic methods are invasive, often inaccurate, and usually performed post-onset of the disease. Advances in imaging techniques for probing beta cell mass and function are needed to address this critical health care problem. A variety of currently available imaging techniques have been tested for the assessment of the pancreatic beta cell islets. Here we discuss the current advances in magnetic resonance imaging (MRI), bioluminescence imaging (BLI), and nuclear imaging for the study of beta cell diseases. Spurred by early successes in nuclear imaging techniques for beta cells, especially positron emission tomography (PET), the need for beta cell specific ligands has expanded. Progress in the field for obtaining such ligands is presented. Additionally, we report our preliminary efforts of developing such a peptidic ligand for PET imaging of the pancreatic beta cells. PMID:18508529

  12. Bringing Advanced Computational Techniques to Energy Research

    SciTech Connect

    Mitchell, Julie C

    2012-11-17

    Please find attached our final technical report for the BACTER Institute award. BACTER was created as a graduate and postdoctoral training program for the advancement of computational biology applied to questions of relevance to bioenergy research.

  13. 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.

  14. Recent Advances in Molecular Magnetic Resonance Imaging of Liver Fibrosis

    PubMed Central

    Li, Zhiming; Sun, Jihong; Yang, Xiaoming

    2015-01-01

    Liver fibrosis is a life-threatening disease with high morbidity and mortality owing to its diverse causes. Liver biopsy, as the current gold standard for diagnosing and staging liver fibrosis, has a number of limitations, including sample variability, relatively high cost, an invasive nature, and the potential of complications. Most importantly, in clinical practice, patients often reject additional liver biopsies after initiating treatment despite their being necessary for long-term follow-up. To resolve these problems, a number of different noninvasive imaging-based methods have been developed for accurate diagnosis of liver fibrosis. However, these techniques only reflect morphological or perfusion-related alterations in the liver, and thus they are generally only useful for the diagnosis of late-stage liver fibrosis (liver cirrhosis), which is already characterized by “irreversible” anatomic and hemodynamic changes. Thus, it is essential that new approaches are developed for accurately diagnosing early-stage liver fibrosis as at this stage the disease may be “reversed” by active treatment. The development of molecular MR imaging technology has potential in this regard, as it facilitates noninvasive, target-specific imaging of liver fibrosis. We provide an overview of recent advances in molecular MR imaging for the diagnosis and staging of liver fibrosis and we compare novel technologies with conventional MR imaging techniques. PMID:25874221

  15. Advanced gradientlike methods for rigid-body molecular dynamics

    NASA Astrophysics Data System (ADS)

    Omelyan, Igor P.

    2007-07-01

    A novel approach is developed to integrate the equations of motion in many-body systems of interacting rigid polyatomic molecules. It is based on an advanced gradientlike decomposition technique in the presence of translational and orientational degrees of freedom. As a result, a new class of reversible phase-space volume preserving fourth-order algorithms for rotational motion is introduced. Contrary to standard nongradient decomposition integrators, the algorithms derived take into account additional analytically integrable terms in the exponential propagators, while the arising gradients are expressed in terms of forces and torques. This allows one to increase significantly the precision of the integration and, at the same time, reduce the increased computational costs. The optimized second-order integrator is also presented. The gradientlike and optimized algorithms are tested in molecular dynamics simulations of water versus well-established integrators known previously. It is shown that the new algorithms lead to the best efficiency in the rigid-body integration.

  16. Recent Advances in Sensing Using Atropoisomeric Molecular Receptors.

    PubMed

    Pasini, Dario; Nitti, Andrea

    2016-02-01

    We describe recent advances in chiroptical chemical sensors, in which the design and implementation is based upon the introduction of atropoisomerically chiral moiety within the molecular skeleton. This report include examples of acyclic, macrocyclic, and polymeric receptors that contain this motif. Although the main applications are in the enantioselective sensing of analytes, we report here some cases where the chiral receptors can in fact be used to senseachiral species. Using circular dichroism (CD) spectroscopy as the technique to detect a receptor-analyte interaction, we can distinguish two main sensor categories: that in which the CD signal of a stereolabile, CD-silent probe is activated upon binding, and that in which the signal of a CD-active probe is modulated upon binding. Particular emphasis will be given to cases in which CD spectroscopy is used orthogonally to other means of detection. Chirality 28:116-123, 2016. © 2015 Wiley Periodicals, Inc. PMID:26800253

  17. 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.

  18. Rapid identification of pathogens using molecular techniques.

    PubMed

    Sloots, Theo P; Nissen, Michael D; Ginn, Andrew N; Iredell, Jonathan R

    2015-04-01

    Real-time PCR is the traditional face of nucleic acid detection in the diagnostic microbiology laboratory and is now generally regarded as robust enough to be widely adopted. Methods based on nucleic acid detection of this type are bringing increased accuracy to diagnosis in areas where culture is difficult and/or expensive, and these methods are often effective partners to other rapid molecular diagnostic tools such as matrix-assisted laser desorption ionisation-time of flight mass spectrometry (MALDI-TOF MS). This change in practice has particularly affected the recognition of viruses and fastidious or antibiotic-exposed bacteria, but has been also shown to be effective in the recognition of troublesome or specialised phenotypes such as antiviral resistance and transmissible antibiotic resistance in the Enterobacteriaceae. Quantitation and high-intensity sequencing (of multiple whole genomes) has brought new opportunities as well as new challenges to the microbiology community. Diagnostic microbiologists currently training might be expected to deal less with the culture-based techniques of the last half-century than with the high-volume data and complex analyses of the next. PMID:25714588

  19. Advances in laparoscopic urologic surgery techniques

    PubMed Central

    Abdul-Muhsin, Haidar M.; Humphreys, Mitchell R.

    2016-01-01

    The last two decades witnessed the inception and exponential implementation of key technological advancements in laparoscopic urology. While some of these technologies thrived and became part of daily practice, others are still hindered by major challenges. This review was conducted through a comprehensive literature search in order to highlight some of the most promising technologies in laparoscopic visualization, augmented reality, and insufflation. Additionally, this review will provide an update regarding the current status of single-site and natural orifice surgery in urology. PMID:27134743

  20. Advances in laparoscopic urologic surgery techniques.

    PubMed

    Abdul-Muhsin, Haidar M; Humphreys, Mitchell R

    2016-01-01

    The last two decades witnessed the inception and exponential implementation of key technological advancements in laparoscopic urology. While some of these technologies thrived and became part of daily practice, others are still hindered by major challenges. This review was conducted through a comprehensive literature search in order to highlight some of the most promising technologies in laparoscopic visualization, augmented reality, and insufflation. Additionally, this review will provide an update regarding the current status of single-site and natural orifice surgery in urology. PMID:27134743

  1. Technological advances in extraction techniques and outpatient oral surgery.

    PubMed

    Weiss, Adam; Stern, Avichai; Dym, Harry

    2011-07-01

    There have been several exciting technological advances in extraction techniques and outpatient oral surgery within the last decade. A variety of new instruments and techniques are revolutionizing the fields of oral and maxillofacial surgery and dentistry. This article reviews the newer innovations in dentistry including the powered periotome, piezosurgery, the Physics Forceps, laser therapy, orthodontic techniques, and use of polyurethane foam. PMID:21726686

  2. Advances in molecular breeding of flowering dogwood (Cornus florida L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although the production and sales of ornamental crops represent significant contributions to the global economy, breeding and selection of ornamental plants using molecular markers lags far behind that used for agronomic crops. However, with the recent advances in molecular technologies including r...

  3. Advanced Interferometry Techniques for Burning Plasmas

    SciTech Connect

    Brower, D. L.; Ding, W. X.; Mirnov, V. V.; Van Zeeland, M. A.; Carlstrom, T. N.

    2008-03-12

    For future burning plasma experiments, all diagnostics must be re-evaluated in terms of their measurement capabilities and robustness to the new environment. This is certainly true for interferometry measurements where conventional approaches may not be ideal and interpretation may require modification due to high plasma temperatures. Optimizing these systems to provide maximum information will be crucial to understanding burning plasma dynamics. This paper will explore a variety of phase measurement techniques for the main body and divertor regions that can be utilized on burning plasma experiments like ITER and beyond.

  4. Advanced molecular self-assemblies facilitated by simple molecules.

    PubMed

    Wu, Zheng; Yan, Yun; Huang, Jianbin

    2014-12-01

    Advanced materials are often based on smart molecular self-assemblies that either respond to external stimuli or have hierarchical structures. Approaches to this goal usually stem from complicated molecular design and difficult organic synthesis. In this invited feature article, we demonstrate that desired molecular self-assemblies can be made conveniently by introducing simple functional molecules into amphiphilic systems. We show that upon introducing specific small molecules which serve as responders, modulators, or even building blocks, smart supramolecular architectures can be achieved which avoid complicated organic synthesis. We expect that this could be a general and economical way to produce advanced materials in the near future. PMID:24870151

  5. Advanced characterization techniques for high power VCSELs

    NASA Astrophysics Data System (ADS)

    Moench, Holger; Baier, Johannes; Gronenborn, Stephan; Kolb, Johanna; Miller, Michael; Pekarski, Pavel; Schemmann, Marcel; Valster, Adriaan

    2010-02-01

    The performance of high power VCSELs in a specific application depends on the geometrical and thermal design as well as on the quality of the epitaxially grown material. Due to the relatively high heat load in densely packed high power arrays the temperature in the active zone and the DBR mirrors changes significantly with the applied current and the traditional characterization methods become less meaningful than for low power devices. This paper presents a method to measure temperature independent power curves with the help of short pulse techniques and data mapping at different heat sink temperatures. In addition the internal quantum efficiency, the transparency current and the gain coefficient are measured by a novel method which operates the VCSEL material as an edge emitter and applies a cut-back technique. The optical losses in the DBR mirrors are determined using external feedback. In summary all relevant parameters which determine the quality of an epitaxial design are measured independently and can be directly compared with modeling and help to optimize the high power VCSEL performance.

  6. Advanced analysis techniques for uranium assay

    SciTech Connect

    Geist, W. H.; Ensslin, Norbert; Carrillo, L. A.; Beard, C. A.

    2001-01-01

    Uranium has a negligible passive neutron emission rate making its assay practicable only with an active interrogation method. The active interrogation uses external neutron sources to induce fission events in the uranium in order to determine the mass. This technique requires careful calibration with standards that are representative of the items to be assayed. The samples to be measured are not always well represented by the available standards which often leads to large biases. A technique of active multiplicity counting is being developed to reduce some of these assay difficulties. Active multiplicity counting uses the measured doubles and triples count rates to determine the neutron multiplication (f4) and the product of the source-sample coupling ( C ) and the 235U mass (m). Since the 35U mass always appears in the multiplicity equations as the product of Cm, the coupling needs to be determined before the mass can be known. A relationship has been developed that relates the coupling to the neutron multiplication. The relationship is based on both an analytical derivation and also on empirical observations. To determine a scaling constant present in this relationship, known standards must be used. Evaluation of experimental data revealed an improvement over the traditional calibration curve analysis method of fitting the doubles count rate to the 235Um ass. Active multiplicity assay appears to relax the requirement that the calibration standards and unknown items have the same chemical form and geometry.

  7. Recent advances in DNA sequencing techniques

    NASA Astrophysics Data System (ADS)

    Singh, Rama Shankar

    2013-06-01

    Successful mapping of the draft human genome in 2001 and more recent mapping of the human microbiome genome in 2012 have relied heavily on the parallel processing of the second generation/Next Generation Sequencing (NGS) DNA machines at a cost of several millions dollars and long computer processing times. These have been mainly biochemical approaches. Here a system analysis approach is used to review these techniques by identifying the requirements, specifications, test methods, error estimates, repeatability, reliability and trends in the cost reduction. The first generation, NGS and the Third Generation Single Molecule Real Time (SMART) detection sequencing methods are reviewed. Based on the National Human Genome Research Institute (NHGRI) data, the achieved cost reduction of 1.5 times per yr. from Sep. 2001 to July 2007; 7 times per yr., from Oct. 2007 to Apr. 2010; and 2.5 times per yr. from July 2010 to Jan 2012 are discussed.

  8. Advanced cooling techniques for FASTBUS electronics

    SciTech Connect

    Chato, J.C.; Golliher, E.L.; Downing, R.W.

    1986-02-01

    A multi-phase research and development effort has been conducted to explore improved cooling techniques for the FASTBUS system. The research was supported by the Fermi National Accelerator Laboratory. Some of the relevant, major requirements and limits of this system are: 1. The cooling system should not significantly interfere with the rapid handling of the cards; 2. The die temperatures of the integrated circuits should not exceed 85/sup 0/C; 3. The temperature differential between the dies of emitter coupled logic (ECL) circuits that connect directly to each other should not exceed 30/sup 0/C; 4. The temperature differential of the cooling air between any two points in the module should not exceed 20/sup 0/C; 5. In air cooled modules, the air temperature should not exceed 60/sup 0/C anywhere; and 6. The noise emanating from the computer should be at a tolerable level. The first requirement, together with some related considerations, virtually excludes any direct liquid cooling schemes. Thus heat removal from the chips themselves can be achieved either by convection to air or by a heat conducting structure which transfers the heat to the coolant used. The second through fourth requirements are generally rigorous. However, the fifth is for plastic encased microchips (CA3083 16-pin, high current transistor, dual in-line package) and can be relaxed for other types with lower internal thermal resistances. Our work can be divided into three parts. The first dealt with the development of an air cooled system based on the state-of-the-art of commercially available technology. The second explored various air cooling techniques and the third, examined methods where the heat from the chips was conducted to water cooled plates located parallel to the chip carrying cards.

  9. Advances of Molecular Imaging in Epilepsy.

    PubMed

    Galovic, Marian; Koepp, Matthias

    2016-06-01

    Positron emission tomography (PET) is a neuroimaging method that offers insights into the molecular functioning of a human brain. It has been widely used to study metabolic and neurotransmitter abnormalities in people with epilepsy. This article reviews the development of several PET radioligands and their application in studying the molecular mechanisms of epilepsy. Over the last decade, tracers binding to serotonin and γ-aminobutyric acid (GABA) receptors have been used to delineate the location of the epileptic focus. PET studies have examined the role of opioids, cannabinoids, acetylcholine, and dopamine in modulating neuronal hyperexcitability and seizure termination. In vivo analyses of drug transporters, e.g., P-glycoprotein, have increased our understanding of pharmacoresistance that could inform new therapeutic strategies. Finally, PET experiments targeting neuroinflammation and glutamate receptors might guide the development of novel biomarkers of epileptogenesis. PMID:27113252

  10. Diagnostics of nonlocal plasmas: advanced techniques

    NASA Astrophysics Data System (ADS)

    Mustafaev, Alexander; Grabovskiy, Artiom; Strakhova, Anastasiya; Soukhomlinov, Vladimir

    2014-10-01

    This talk generalizes our recent results, obtained in different directions of plasma diagnostics. First-method of flat single-sided probe, based on expansion of the electron velocity distribution function (EVDF) in series of Legendre polynomials. It will be demonstrated, that flat probe, oriented under different angles with respect to the discharge axis, allow to determine full EVDF in nonlocal plasmas. It is also shown, that cylindrical probe is unable to determine full EVDF. We propose the solution of this problem by combined using the kinetic Boltzmann equation and experimental probe data. Second-magnetic diagnostics. This method is implemented in knudsen diode with surface ionization of atoms (KDSI) and based on measurements of the magnetic characteristics of the KDSI in presence of transverse magnetic field. Using magnetic diagnostics we can investigate the wide range of plasma processes: from scattering cross-sections of electrons to plasma-surface interactions. Third-noncontact diagnostics method for direct measurements of EVDF in remote plasma objects by combination of the flat single-sided probe technique and magnetic polarization Hanley method.

  11. Innovative Tools Advance Revolutionary Weld Technique

    NASA Technical Reports Server (NTRS)

    2009-01-01

    The iconic, orange external tank of the space shuttle launch system not only contains the fuel used by the shuttle s main engines during liftoff but also comprises the shuttle s backbone, supporting the space shuttle orbiter and solid rocket boosters. Given the tank s structural importance and the extreme forces (7.8 million pounds of thrust load) and temperatures it encounters during launch, the welds used to construct the tank must be highly reliable. Variable polarity plasma arc welding, developed for manufacturing the external tank and later employed for building the International Space Station, was until 1994 the best process for joining the aluminum alloys used during construction. That year, Marshall Space Flight Center engineers began experimenting with a relatively new welding technique called friction stir welding (FSW), developed in 1991 by The Welding Institute, of Cambridge, England. FSW differs from traditional fusion welding in that it is a solid-state welding technique, using frictional heat and motion to join structural components without actually melting any of the material. The weld is created by a shouldered pin tool that is plunged into the seam of the materials to be joined. The tool traverses the line while rotating at high speeds, generating friction that heats and softens but does not melt the metal. (The heat produced approaches about 80 percent of the metal s melting temperature.) The pin tool s rotation crushes and stirs the plasticized metal, extruding it along the seam as the tool moves forward. The material cools and consolidates, resulting in a weld with superior mechanical properties as compared to those weld properties of fusion welds. The innovative FSW technology promises a number of attractive benefits. Because the welded materials are not melted, many of the undesirables associated with fusion welding porosity, cracking, shrinkage, and distortion of the weld are minimized or avoided. The process is more energy efficient, safe (no toxic smoke or shielding gas, liquid metal splatter, arcing, dangerous voltage, or radiation), and environmentally sound (no consumables, fumes, or noise) than fusion welding. Under computer control, an automated FSW machine can create welds with high reproducibility, improving efficiency and overall quality of manufactured materials. The process also allows for welding dissimilar metals as well as those metals considered to be "unweldable" such as the 7xxx series aluminum alloys. Its effectiveness and versatility makes FSW useful for aerospace, rail, automotive, marine, and military applications. A downside to FSW, however, is the keyhole opening left in the weld when the FSW pin tool exits the weld joint. This is a significant problem when using the FSW process to join circumferential structures such as pipes and storage containers. Furthermore, weld joints that taper in material thickness also present problems when using the conventional FSW pin tool, because the threaded pin rotating within the weld joint material is a fixed length. There must be capability for the rotating pin to both increase and decrease in length in real time while welding the tapered material. (Both circumferential and tapered thickness weldments are found in the space shuttle external tank.) Marshall engineers addressed both the keyhole and tapered material thickness problems by developing the auto-adjustable pin tool. This unique piece of equipment automatically withdraws the pin into the tool s shoulder for keyhole closeout. In addition, the auto-adjustable pin tool retracts, or shortens, the rotating pin while welding a weld joint that tapers from one thickness to a thinner thickness. This year, the impact of the Marshall innovation was recognized with an "Excellence in Technology Transfer Award" from the Federal Laboratory Consortium.

  12. 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.

  13. Evaluation of Advanced Retrieval Techniques in an Experimental Online Catalog.

    ERIC Educational Resources Information Center

    Larson, Ray R.

    1992-01-01

    Discusses subject searching problems in online library catalogs; explains advanced information retrieval (IR) techniques; and describes experiments conducted on a test collection database, CHESHIRE (California Hybrid Extended SMART for Hypertext and Information Retrieval Experimentation), which was created to evaluate IR techniques in online…

  14. The advance of liner technique in solid rocket engine

    NASA Astrophysics Data System (ADS)

    Feng, Ting; Tai, Yawsong

    1992-08-01

    The latest advances in liner techniques are summarized. Two methods for investigating liner composition and techniques to improve adhesive performance are introduced. It is shown that adhesion strength between propellent and case or insulator can be greatly increased using a linear containing dimer isocyanate or terminal blocking agent.

  15. Rhabdomyosarcoma: Advances in Molecular and Cellular Biology

    PubMed Central

    Sun, Xin; Guo, Wei; Shen, Jacson K.; Mankin, Henry J.; Hornicek, Francis J.; Duan, Zhenfeng

    2015-01-01

    Rhabdomyosarcoma (RMS) is the most common soft tissue malignancy in childhood and adolescence. The two major histological subtypes of RMS are alveolar RMS, driven by the fusion protein PAX3-FKHR or PAX7-FKHR, and embryonic RMS, which is usually genetically heterogeneous. The prognosis of RMS has improved in the past several decades due to multidisciplinary care. However, in recent years, the treatment of patients with metastatic or refractory RMS has reached a plateau. Thus, to improve the survival rate of RMS patients and their overall well-being, further understanding of the molecular and cellular biology of RMS and identification of novel therapeutic targets are imperative. In this review, we describe the most recent discoveries in the molecular and cellular biology of RMS, including alterations in oncogenic pathways, miRNA (miR), in vivo models, stem cells, and important signal transduction cascades implicated in the development and progression of RMS. Furthermore, we discuss novel potential targeted therapies that may improve the current treatment of RMS. PMID:26420980

  16. Molecular pathogenesis of hepatocellular carcinoma and impact of therapeutic advances

    PubMed Central

    Dhanasekaran, Renumathy; Bandoh, Salome; Roberts, Lewis R.

    2016-01-01

    Hepatocellular carcinoma (HCC) is a leading cause of cancer mortality and has an increasing incidence worldwide. HCC can be induced by multiple etiologies, is influenced by many risk factors, and has a complex pathogenesis. Furthermore, HCCs exhibit substantial heterogeneity, which compounds the difficulties in developing effective therapies against this highly lethal cancer. With advances in cancer biology and molecular and genetic profiling, a number of different mechanisms involved in the development and progression of HCC have been identified. Despite the advances in this area, the molecular pathogenesis of hepatocellular carcinoma is still not completely understood. This review aims to elaborate our current understanding of the most relevant genetic alterations and molecular pathways involved in the development and progression of HCC, and anticipate the potential impact of future advances on therapeutic drug development.

  17. Predicting Malignancy in Thyroid Nodules: Molecular Advances

    PubMed Central

    Melck, Adrienne L.; Yip, Linwah

    2016-01-01

    Over the last several years, a clearer understanding of the genetic alterations underlying thyroid carcinogenesis has developed. This knowledge can be utilized to tackle one of the greatest challenges facing thyroidologists: management of the indeterminate thyroid nodule. Despite the accuracy of fine needle aspiration cytology, many patients undergo invasive surgery in order to determine if a follicular or Hurthle cell neoplasm is malignant, and better diagnostic tools are required. A number of biomarkers have recently been studied and show promise in this setting. In particular, BRAF, RAS, PAX8-PPARγ, microRNAs and loss of heterozygosity have each been demonstrated as useful molecular tools for predicting malignancy and can thereby guide decisions regarding surgical management of nodular thyroid disease. This review summarizes the current literature surrounding each of these markers and highlights our institution’s prospective analysis of these markers and their subsequent incorporation into our management algorithms for thyroid nodules. PMID:21818817

  18. Advances in gamma titanium aluminides and their manufacturing techniques

    NASA Astrophysics Data System (ADS)

    Kothari, Kunal; Radhakrishnan, Ramachandran; Wereley, Norman M.

    2012-11-01

    Gamma titanium aluminides display attractive properties for high temperature applications. For over a decade in the 1990s, the attractive properties of titanium aluminides were outweighed by difficulties encountered in processing and machining at room temperature. But advances in manufacturing technologies, deeper understanding of titanium aluminides microstructure, deformation mechanisms, and advances in micro-alloying, has led to the production of gamma titanium aluminide sheets. An in-depth review of key advances in gamma titanium aluminides is presented, including microstructure, deformation mechanisms, and alloy development. Traditional manufacturing techniques such as ingot metallurgy and investment casting are reviewed and advances via powder metallurgy based manufacturing techniques are discussed. Finally, manufacturing challenges facing gamma titanium aluminides, as well as avenues to overcome them, are discussed.

  19. Pathology and Molecular Genetics of Meningioma: Recent Advances

    PubMed Central

    SHIBUYA, Makoto

    2015-01-01

    Meningiomas are the most common intracranial primary neoplasm in adults. Although the spectrum of clinical and molecular genetic issues regarding meningiomas remains undefined, novel genetic alterations that are associated with tumor morphology, malignancy, or location have recently been discovered. This review focuses on recent advances in understanding of the heterogenous pathology of meningiomas, particularly on associations between the clinical, histological, etiological, epidemiological, and molecular genetical aspects of the neoplasm. PMID:25744347

  20. Molecular techniques to interrogate and edit the Chlamydomonas nuclear genome.

    PubMed

    Jinkerson, Robert E; Jonikas, Martin C

    2015-05-01

    The success of the green alga Chlamydomonas reinhardtii as a model organism is to a large extent due to the wide range of molecular techniques that are available for its characterization. Here, we review some of the techniques currently used to modify and interrogate the C. reinhardtii nuclear genome and explore several technologies under development. Nuclear mutants can be generated with ultraviolet (UV) light and chemical mutagens, or by insertional mutagenesis. Nuclear transformation methods include biolistic delivery, agitation with glass beads, and electroporation. Transforming DNA integrates into the genome at random sites, and multiple strategies exist for mapping insertion sites. A limited number of studies have demonstrated targeted modification of the nuclear genome by approaches such as zinc-finger nucleases and homologous recombination. RNA interference is widely used to knock down expression levels of nuclear genes. A wide assortment of transgenes has been successfully expressed in the Chlamydomonas nuclear genome, including transformation markers, fluorescent proteins, reporter genes, epitope tagged proteins, and even therapeutic proteins. Optimized expression constructs and strains help transgene expression. Emerging technologies such as the CRISPR/Cas9 system, high-throughput mutant identification, and a whole-genome knockout library are being developed for this organism. We discuss how these advances will propel future investigations. PMID:25704665

  1. [Advanced online search techniques and dedicated search engines for physicians].

    PubMed

    Nahum, Yoav

    2008-02-01

    In recent years search engines have become an essential tool in the work of physicians. This article will review advanced search techniques from the world of information specialists, as well as some advanced search engine operators that may help physicians improve their online search capabilities, and maximize the yield of their searches. This article also reviews popular dedicated scientific and biomedical literature search engines. PMID:18357673

  2. Advanced liner-cooling techniques for gas turbine combustors

    NASA Technical Reports Server (NTRS)

    Norgren, C. T.; Riddlebaugh, S. M.

    1985-01-01

    Component research for advanced small gas turbine engines is currently underway at the NASA Lewis Research Center. As part of this program, a basic reverse-flow combustor geometry was being maintained while different advanced liner wall cooling techniques were investigated. Performance and liner cooling effectiveness of the experimental combustor configuration featuring counter-flow film-cooled panels is presented and compared with two previously reported combustors featuring: splash film-cooled liner walls; and transpiration cooled liner walls (Lamilloy).

  3. Advanced regenerative-cooling techniques for future space transportation systems

    NASA Technical Reports Server (NTRS)

    Wagner, W. R.; Shoji, J. M.

    1975-01-01

    A review of regenerative-cooling techniques applicable to advanced planned engine designs for space booster and orbit transportation systems has developed the status of the key elements of this cooling mode. This work is presented in terms of gas side, coolant side, wall conduction heat transfer, and chamber life fatigue margin considerations. Described are preliminary heat transfer and trade analyses performed using developed techniques combining channel wall construction with advanced, high-strength, high-thermal-conductivity materials (NARloy-Z or Zr-Cu alloys) in high heat flux regions, combined with lightweight steel tubular nozzle wall construction. Advanced cooling techniques such as oxygen cooling and dual-mode hydrocarbon/hydrogen fuel operation and their limitations are indicated for the regenerative cooling approach.

  4. 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.

  5. 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.

  6. Coal and char studies by advanced EMR techniques

    SciTech Connect

    Belford, R.L.; Clarkson, R.B.; Odintsov, B.M.

    1999-03-31

    Advanced magnetic resonance (EMR) methods are used to examine properties of coals, chars, and molecular species related to constituents of coal. During this grant period, further progress was made on proton NMR and low-frequency dynamic nuclear polarization (DNP) to examine the interaction between fluids such as water and the surface of suspended char particles. Effects of char particle size and type on water nuclear spin relaxation, T2, were measured and modeled.

  7. Coal and Coal Constituent Studies by Advanced EMR Techniques.

    SciTech Connect

    Belford, R.L.; Clarkson, R.B.; Odintsov, B.; Ceroke, P.J.

    1997-09-30

    Advanced electronic magnetic resonance (EMR) methods are used to examine properties of coals, chars, and molecular species related to constituents of coal. During this grant period, progress was made on a high frequency EMR system particularly appropriate for such studies and on low-frequency dynamic nuclear polarization (DNP) to examine the interaction between fluids such as water and the surface of suspended char particles.

  8. Coal and char studies by advanced EMR techniques

    SciTech Connect

    Belford, R.L.; Clarkson, R.B.; Odintsov, B.M.

    1998-09-30

    Advanced magnetic resonance (EMR) methods are used to examine properties of coals, chars, and molecular species related to constituents of coal. During this grant period, further progress was made on proton NMR and low-frequency dynamic nuclear polarization (DNP) to examine the interaction between fluids such as water and the surface of suspended char particles. Effects of char particle size on water nuclear spin relaxation, T2, were measured.

  9. 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

  10. 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…

  11. Advanced alloy design technique: High temperature cobalt base superalloy

    NASA Technical Reports Server (NTRS)

    Dreshfield, R. L.; Freche, J. C.; Sandrock, G. D.

    1972-01-01

    Advanced alloy design technique was developed for treating alloys that will have extended life in service at high temperature and intermediate temperatures. Process stabilizes microstructure of the alloy by designing it so that compound identified with embrittlement is eliminated or minimized. Design process is being used to develop both nickel and cobalt-base superalloys.

  12. Responses of Cell Renewal Systems to Long-term Low-Level Radiation Exposure: A Feasibility Study Applying Advanced Molecular Biology Techniques on Available Histological and Cytological Material of Exposed Animals and Men

    SciTech Connect

    Fliedner Theodor M.; Feinendegen Ludwig E.; Meineke Viktor; Fritz Thomas E.

    2005-02-28

    First results of this feasibility study showed that evaluation of the stored material of the chronically irradiated dogs with modern molecular biological techniques proved to be successful and extremely promising. Therefore an in deep analysis of at least part of the huge amount of remaining material is of outmost interest. The methods applied in this feasibility study were pathological evaluation with different staining methods, protein analysis by means of immunohistochemistry, strand break analysis with the TdT-assay, DNA- and RNA-analysis as well as genomic examination by gene array. Overall more than 50% of the investigated material could be used. In particular the results of an increased stimulation of the immune system within the dogs of the 3mSv group as both compared to the control and higher dose groups gives implications for the in depth study of the cellular events occurring in context with low dose radiation. Based on the findings of this study a further evaluation and statistically analysis of more material can help to identify promising biomarkers for low dose radiation. A systematic evaluation of a correlation of dose rates and strand breaks within the dog tissue might moreover help to explain mechanisms of tolerance to IR. One central problem is that most sequences for dog specific primers are not known yet. The discovery of the dog genome is still under progress. In this study the isolation of RNA within the dog tissue was successful. But up to now there are no gene arrays or gene chips commercially available, tested and adapted for canine tissue. The uncritical use of untested genomic test systems for canine tissue seems to be ineffective at the moment, time consuming and ineffective. Next steps in the investigation of genomic changes after IR within the stored dog tissue should be limited to quantitative RT-PCR of tested primer sequences for the dog. A collaboration with institutions working in the field of the discovery of the dog genome could have synergistic effects.

  13. Molecular rotors and motors: recent advances and future challenges.

    PubMed

    Michl, Josef; Sykes, E Charles H

    2009-05-26

    At the "Molecular Rotors and Motors" symposium of the Spring 2009 ACS National Meeting in Salt Lake City (March 22-26), a diverse mix of talks addressed many current issues in the field. Speakers described topics that varied from single-molecule rotors and nanomachines to exquisite synthetic approaches toward building functional materials and mathematical and computational methods aimed at uncovering design opportunities and highlighting the fundamental limitations of molecular motors. While the realization of building useful nanomachines remains far off, a general consensus abounded that investigating biological systems and understanding the implications of the laws of thermodynamics and quantum mechanics for the behavior of nanostructures will help drive important advances in the quest for molecular machinery. Molecular rotors were demonstrated to have practical applications as probes for microviscosity, and many speakers presented experimental studies that indicated that highly directed translation and rotation of individual molecules, as well as interacting dipolar arrays, are just around the corner. While this Nano Focus is not intended to be a comprehensive review of the subject, it will focus on several key advances that were presented at the ACS meeting and highlight future challenges for the field of molecular rotors and motors. PMID:19845364

  14. Advanced Packaging Materials and Techniques for High Power TR Module: Standard Flight vs. Advanced Packaging

    NASA Technical Reports Server (NTRS)

    Hoffman, James Patrick; Del Castillo, Linda; Miller, Jennifer; Jenabi, Masud; Hunter, Donald; Birur, Gajanana

    2011-01-01

    The higher output power densities required of modern radar architectures, such as the proposed DESDynI [Deformation, Ecosystem Structure, and Dynamics of Ice] SAR [Synthetic Aperture Radar] Instrument (or DSI) require increasingly dense high power electronics. To enable these higher power densities, while maintaining or even improving hardware reliability, requires advances in integrating advanced thermal packaging technologies into radar transmit/receive (TR) modules. New materials and techniques have been studied and compared to standard technologies.

  15. Recent Advances in Molecular, Multimodal and Theranostic Ultrasound Imaging

    PubMed Central

    Kiessling, Fabian; Fokong, Stanley; Bzyl, Jessica; Lederle, Wiltrud; Palmowski, Moritz; Lammers, Twan

    2014-01-01

    Ultrasound (US) imaging is an exquisite tool for the non-invasive and real-time diagnosis of many different diseases. In this context, US contrast agents can improve lesion delineation, characterization and therapy response evaluation. US contrast agents are usually micrometer-sized gas bubbles, stabilized with soft or hard shells. By conjugating antibodies to the microbubble (MB) surface, and by incorporating diagnostic agents, drugs or nucleic acids into or onto the MB shell, molecular, multimodal and theranostic MB can be generated. We here summarize recent advances in molecular, multimodal and theranostic US imaging, and introduce concepts how such advanced MB can be generated, applied and imaged. Examples are given for their use to image and treat oncological, cardiovascular and neurological diseases. Furthermore, we discuss for which therapeutic entities incorporation into (or conjugation to) MB is meaningful, and how US-mediated MB destruction can increase their extravasation, penetration, internalization and efficacy. PMID:24316070

  16. An Advanced Time Averaging Modelling Technique for Power Electronic Circuits

    NASA Astrophysics Data System (ADS)

    Jankuloski, Goce

    For stable and efficient performance of power converters, a good mathematical model is needed. This thesis presents a new modelling technique for DC/DC and DC/AC Pulse Width Modulated (PWM) converters. The new model is more accurate than the existing modelling techniques such as State Space Averaging (SSA) and Discrete Time Modelling. Unlike the SSA model, the new modelling technique, the Advanced Time Averaging Model (ATAM) includes the averaging dynamics of the converter's output. In addition to offering enhanced model accuracy, application of linearization techniques to the ATAM enables the use of conventional linear control design tools. A controller design application demonstrates that a controller designed based on the ATAM outperforms one designed using the ubiquitous SSA model. Unlike the SSA model, ATAM for DC/AC augments the system's dynamics with the dynamics needed for subcycle fundamental contribution (SFC) calculation. This allows for controller design that is based on an exact model.

  17. Technology development of fabrication techniques for advanced solar dynamic concentrators

    NASA Technical Reports Server (NTRS)

    Richter, Scott W.

    1991-01-01

    The objective of the advanced concentrator program is to develop the technology that will lead to lightweight, highly reflective, accurate, scaleable, and long lived space solar dynamic concentrators. The advanced concentrator program encompasses new and innovative concepts, fabrication techniques, materials selection, and simulated space environmental testing. Fabrication techniques include methods of fabricating the substrates and coating substrate surfaces to produce high quality optical surfaces, acceptable for further coating with vapor deposited optical films. The selected materials to obtain a high quality optical surface include microsheet glass and Eccocoat EP-3 epoxy, with DC-93-500 selected as a candidate silicone adhesive and levelizing layer. The following procedures are defined: cutting, cleaning, forming, and bonding microsheet glass. Procedures are also defined for surface cleaning, and EP-3 epoxy application. The results and analyses from atomic oxygen and thermal cycling tests are used to determine the effects of orbital conditions in a space environment.

  18. Technology development of fabrication techniques for advanced solar dynamic concentrators

    NASA Technical Reports Server (NTRS)

    Richter, Scott W.

    1991-01-01

    The objective of the advanced concentrator program is to develop the technology that will lead to lightweight, highly reflective, accurate, scaleable, and long lived space solar dynamic concentrators. The advanced concentrator program encompasses new and innovative concepts, fabrication techniques, materials selection, and simulated space environmental testing. Fabrication techniques include methods of fabricating the substrates and coating substrate surfaces to produce high-quality optical surfaces, acceptable for further coating with vapor deposited optical films. The selected materials to obtain a high quality optical surface include microsheet glass and Eccocoat EP-3 epoxy, with DC-93-500 selected as a candidate silicone adhesive and levelizing layer. The following procedures are defined: cutting, cleaning, forming, and bonding microsheet glass. Procedures are also defined for surface cleaning, and EP-3 epoxy application. The results and analyses from atomic oxygen and thermal cycling tests are used to determine the effects of orbital conditions in a space environment.

  19. Advanced Morphological and Functional Magnetic Resonance Techniques in Glaucoma

    PubMed Central

    Mastropasqua, Rodolfo; Agnifili, Luca; Mattei, Peter A.; Caulo, Massimo; Fasanella, Vincenzo; Navarra, Riccardo; Mastropasqua, Leonardo; Marchini, Giorgio

    2015-01-01

    Glaucoma is a multifactorial disease that is the leading cause of irreversible blindness. Recent data documented that glaucoma is not limited to the retinal ganglion cells but that it also extends to the posterior visual pathway. The diagnosis is based on the presence of signs of glaucomatous optic neuropathy and consistent functional visual field alterations. Unfortunately these functional alterations often become evident when a significant amount of the nerve fibers that compose the optic nerve has been irreversibly lost. Advanced morphological and functional magnetic resonance (MR) techniques (morphometry, diffusion tensor imaging, arterial spin labeling, and functional connectivity) may provide a means for observing modifications induced by this fiber loss, within the optic nerve and the visual cortex, in an earlier stage. The aim of this systematic review was to determine if the use of these advanced MR techniques could offer the possibility of diagnosing glaucoma at an earlier stage than that currently possible. PMID:26167474

  20. Data Compression Techniques for Advanced Space Transportation Systems

    NASA Technical Reports Server (NTRS)

    Bradley, William G.

    1998-01-01

    Advanced space transportation systems, including vehicle state of health systems, will produce large amounts of data which must be stored on board the vehicle and or transmitted to the ground and stored. The cost of storage or transmission of the data could be reduced if the number of bits required to represent the data is reduced by the use of data compression techniques. Most of the work done in this study was rather generic and could apply to many data compression systems, but the first application area to be considered was launch vehicle state of health telemetry systems. Both lossless and lossy compression techniques were considered in this study.

  1. The Advanced Space Plant Culture Device with Live Imaging Technique

    NASA Astrophysics Data System (ADS)

    Zheng, Weibo; Zhang, Tao; Tong, Guanghui

    The live imaging techniques, including the color and fluorescent imags, are very important and useful for space life science. The advanced space plant culture Device (ASPCD) with live imaging Technique, developed for Chinese Spacecraft, would be introduced in this paper. The ASPCD had two plant experimental chambers. Three cameras (two color cameras and one fluorescent camera) were installed in the two chambers. The fluorescent camera could observe flowering genes, which were labeled by GFP. The lighting, nutrient, temperature controling and water recycling were all independent in each chamber. The ASPCD would beed applied to investigate for the growth and development of the high plant under microgravity conditions on board the Chinese Spacecraft.

  2. Three-dimensional hybrid grid generation using advancing front techniques

    NASA Technical Reports Server (NTRS)

    Steinbrenner, John P.; Noack, Ralph W.

    1995-01-01

    A new 3-dimensional hybrid grid generation technique has been developed, based on ideas of advancing fronts for both structured and unstructured grids. In this approach, structured grids are first generate independently around individual components of the geometry. Fronts are initialized on these structure grids, and advanced outward so that new cells are extracted directly from the structured grids. Employing typical advancing front techniques, cells are rejected if they intersect the existing front or fail other criteria When no more viable structured cells exist further cells are advanced in an unstructured manner to close off the overall domain, resulting in a grid of 'hybrid' form. There are two primary advantages to the hybrid formulation. First, generating blocks with limited regard to topology eliminates the bottleneck encountered when a multiple block system is used to fully encapsulate a domain. Individual blocks may be generated free of external constraints, which will significantly reduce the generation time. Secondly, grid points near the body (presumably with high aspect ratio) will still maintain a structured (non-triangular or tetrahedral) character, thereby maximizing grid quality and solution accuracy near the surface.

  3. Advances in Computational Techniques to Study GPCR-Ligand Recognition.

    PubMed

    Ciancetta, Antonella; Sabbadin, Davide; Federico, Stephanie; Spalluto, Giampiero; Moro, Stefano

    2015-12-01

    G-protein-coupled receptors (GPCRs) are among the most intensely investigated drug targets. The recent revolutions in protein engineering and molecular modeling algorithms have overturned the research paradigm in the GPCR field. While the numerous ligand-bound X-ray structures determined have provided invaluable insights into GPCR structure and function, the development of algorithms exploiting graphics processing units (GPUs) has made the simulation of GPCRs in explicit lipid-water environments feasible within reasonable computation times. In this review we present a survey of the recent advances in structure-based drug design approaches with a particular emphasis on the elucidation of the ligand recognition process in class A GPCRs by means of membrane molecular dynamics (MD) simulations. PMID:26538318

  4. Characterization techniques for semiconductors and nanostructures: a review of recent advances

    NASA Astrophysics Data System (ADS)

    Acher, Olivier

    2015-01-01

    Optical spectroscopy techniques are widely used for the characterization of semiconductors and nanostructures. Confocal Raman microscopy is useful to retrieve chemical and molecular information at the ultimate submicrometer resolution of optical microscopy. Fast imaging capabilities, 3D confocal ability, and multiple excitation wavelengths, have increased the power of the technique while making it simpler to use for material scientists. Recently, the development of the Tip Enhanced Raman Spectroscopy (TERS) has opened the way to the use of Raman information at nanoscale, by combining the resolution of scanning probe microscopy and chemical selectivity of Raman spectroscopy. Significant advances have been reported in the field of profiling the atomic composition of multilayers, using the Glow Discharge Optical Emission Spectroscopy technique, including real-time determination of etched depth by interferometry. This allows the construction of precise atomic profiles of sophisticated multilayers with a few nm resolution. Ellipsometry is another widely used technique to determine the profile of multilayers, and recent development have provided enhanced spatial resolution useful for the investigation of patterned materials. In addition to the advances of the different characterization techniques, the capability to observe the same regions at micrometer scale at different stages of material elaboration, or with different instrument, is becoming a critical issue. Several advances have been made to allow precise re-localization and co-localization of observation with different complementary characterization techniques.

  5. Recent Advances in the Molecular Characterization of Circulating Tumor Cells

    PubMed Central

    Lowes, Lori E.; Allan, Alison L.

    2014-01-01

    Although circulating tumor cells (CTCs) were first observed over a century ago, lack of sensitive methodology precluded detailed study of these cells until recently. However, technological advances have now facilitated the identification, enumeration, and characterization of CTCs using a variety of methods. The majority of evidence supporting the use of CTCs in clinical decision-making has been related to enumeration using the CellSearch system and correlation with prognosis. Growing evidence also suggests that CTC monitoring can provide an early indication of patient treatment response based on comparison of CTC levels before and after therapy. However, perhaps the greatest potential that CTCs hold for oncology lies at the level of molecular characterization. Clinical treatment decisions may be more effective if they are based on molecular characteristics of metastatic cells rather than on those of the primary tumor alone. Molecular characterization of CTCs (which can be repeatedly isolated in a minimally invasive fashion) provides the opportunity for a real-time liquid biopsy that allows assessment of genetic drift, investigation of molecular disease evolution, and identification of actionable genomic characteristics. This review focuses on recent advances in this area, including approaches involving immunophenotyping, fluorescence in situ hybridization (FISH), multiplex RT-PCR, microarray, and genomic sequencing. PMID:24633084

  6. Advances in multimodality molecular imaging of bone structure and function

    PubMed Central

    Lambers, Floor M; Kuhn, Gisela; Müller, Ralph

    2012-01-01

    The skeleton is important to the body as a source of minerals and blood cells and provides a structural framework for strength, mobility and the protection of organs. Bone diseases and disorders can have deteriorating effects on the skeleton, but the biological processes underlying anatomical changes in bone diseases occurring in vivo are not well understood, mostly due to the lack of appropriate analysis techniques. Therefore, there is ongoing research in the development of novel in vivo imaging techniques and molecular markers that might help to gain more knowledge of these pathological pathways in animal models and patients. This perspective provides an overview of the latest developments in molecular imaging applied to bone. It emphasizes that multimodality imaging, the combination of multiple imaging techniques encompassing different image modalities, enhances the interpretability of data, and is imperative for the understanding of the biological processes and the associated changes in bone structure and function relationships in vivo. PMID:27127622

  7. Full Endoscopic Spinal Surgery Techniques: Advancements, Indications, and Outcomes

    PubMed Central

    Yue, James J.; Long, William

    2015-01-01

    Advancements in both surgical instrumentation and full endoscopic spine techniques have resulted in positive clinical outcomes in the treatment of cervical, thoracic, and lumbar spine pathologies. Endoscopic techniques impart minimal approach related disruption of non-pathologic spinal anatomy and function while concurrently maximizing functional visualization and correction of pathological tissues. An advanced understanding of the applicable functional neuroanatomy, in particular the neuroforamen, is essential for successful outcomes. Additionally, an understanding of the varying types of disc prolapse pathology in relation to the neuroforamen will result in more optimal surgical outcomes. Indications for lumbar endoscopic spine surgery include disc herniations, spinal stenosis, infections, medial branch rhizotomy, and interbody fusion. Limitations are based on both non spine and spine related findings. A high riding iliac wing, a more posteriorly located retroperitoneal cavity, an overly distal or proximally migrated herniated disc are all relative contra-indications to lumbar endoscopic spinal surgery techniques. Modifications in scope size and visual field of view angulation have enabled both anterior and posterior cervical decompression. Endoscopic burrs, electrocautery, and focused laser technology allow for the least invasive spinal surgical techniques in all age groups and across varying body habitus. Complications include among others, dural tears, dysesthsia, nerve injury, and infection. PMID:26114086

  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. Advances in Dendrobium molecular research: Applications in genetic variation, identification and breeding.

    PubMed

    Teixeira da Silva, Jaime A; Jin, Xiaohua; Dobránszki, Judit; Lu, Jiangjie; Wang, Huizhong; Zotz, Gerhard; Cardoso, Jean Carlos; Zeng, Songjun

    2016-02-01

    Orchids of the genus Dendrobium are of great economic importance in global horticultural trade and in Asian traditional medicine. For both areas, research yielding solid information on taxonomy, phylogeny, and breeding of this genus are essential. Traditional morphological and cytological characterization are used in combination with molecular results in classification and identification. Markers may be useful when used alone but are not always reliable in identification. The number of species studied and identified by molecular markers is small at present. Conventional breeding methods are time-consuming and laborious. In the past two decades, promising advances have been made in taxonomy, phylogeny and breeding of Dendrobium species due to the intensive use of molecular markers. In this review, we focus on the main molecular techniques used in 121 published studies and discuss their importance and possibilities in speeding up the breeding of new cultivars and hybrids. PMID:26493228

  10. Advanced aeroservoelastic stabilization techniques for hypersonic flight vehicles

    NASA Technical Reports Server (NTRS)

    Chan, Samuel Y.; Cheng, Peter Y.; Myers, Thomas T.; Klyde, David H.; Magdaleno, Raymond E.; Mcruer, Duane T.

    1992-01-01

    Advanced high performance vehicles, including Single-Stage-To-Orbit (SSTO) hypersonic flight vehicles, that are statically unstable, require higher bandwidth flight control systems to compensate for the instability resulting in interactions between the flight control system, the engine/propulsion dynamics, and the low frequency structural modes. Military specifications, such as MIL-F-9490D and MIL-F-87242, tend to limit treatment of structural modes to conventional gain stabilization techniques. The conventional gain stabilization techniques, however, introduce low frequency effective time delays which can be troublesome from a flying qualities standpoint. These time delays can be alleviated by appropriate blending of gain and phase stabilization techniques (referred to as Hybrid Phase Stabilization or HPS) for the low frequency structural modes. The potential of using HPS for compensating structural mode interaction was previously explored. It was shown that effective time delay was significantly reduced with the use of HPS; however, the HPS design was seen to have greater residual response than a conventional gain stablized design. Additional work performed to advance and refine the HPS design procedure, to further develop residual response metrics as a basis for alternative structural stability specifications, and to develop strategies for validating HPS design and specification concepts in manned simulation is presented. Stabilization design sensitivity to structural uncertainties and aircraft-centered requirements are also assessed.

  11. Advances in the surface modification techniques of bone-related implants for last 10 years

    PubMed Central

    Qiu, Zhi-Ye; Chen, Cen; Wang, Xiu-Mei; Lee, In-Seop

    2014-01-01

    At the time of implanting bone-related implants into human body, a variety of biological responses to the material surface occur with respect to surface chemistry and physical state. The commonly used biomaterials (e.g. titanium and its alloy, Co–Cr alloy, stainless steel, polyetheretherketone, ultra-high molecular weight polyethylene and various calcium phosphates) have many drawbacks such as lack of biocompatibility and improper mechanical properties. As surface modification is very promising technology to overcome such problems, a variety of surface modification techniques have been being investigated. This review paper covers recent advances in surface modification techniques of bone-related materials including physicochemical coating, radiation grafting, plasma surface engineering, ion beam processing and surface patterning techniques. The contents are organized with different types of techniques to applicable materials, and typical examples are also described. PMID:26816626

  12. MOLECULAR OPTICAL SPECTROSCOPIC TECHNIQUES FOR HAZARDOUS WASTE SITE SCREENING

    EPA Science Inventory

    The U.S. Environmental Protection Agency is interested in field screening hazardous waste sites for contaminants in the soil and surface and ground water. his study is an initial technical overview of the principal molecular spectroscopic techniques and instrumentation currently ...

  13. Testing aspects of advanced coherent electron cooling technique

    SciTech Connect

    Litvinenko, V.; Jing, Y.; Pinayev, I.; Wang, G.; Samulyak, R.; Ratner, D.

    2015-05-03

    An advanced version of the Coherent-electron Cooling (CeC) based on the micro-bunching instability was proposed. This approach promises significant increase in the bandwidth of the CeC system and, therefore, significant shortening of cooling time in high-energy hadron colliders. In this paper we present our plans of simulating and testing the key aspects of this proposed technique using the set-up of the coherent-electron-cooling proof-of-principle experiment at BNL.

  14. Advances in Molecular Characterization and Targeted Therapy in Dermatofibrosarcoma Protuberans

    PubMed Central

    Rutkowski, Piotr; Wozniak, Agnieszka; Switaj, Tomasz

    2011-01-01

    The molecular pathogenesis of dermatofibrosarcoma protuberans (DFSP) involves distinctive rearrangement of chromosomes 17 and 22 leading to formation of the COL1A1-PDGFB fusion gene. The knowledge of molecular events underlying development of DFSP resulted in the implementation of targeted therapy with imatinib—a tyrosine kinase inhibitor (TKI), to the clinical practice. The striking efficacy of imatinib in advanced cases of DFSP has been demonstrated in a few clinical trials. Thus, imatinib is currently considered the gold standard in the treatment of inoperable and/or metastatic and/or recurrent cases of DFSP. Therapy with imatinib may potentially facilitate resection or decrease possible disfigurement related to radical surgical procedure. Following partial response on imatinib significant percentage of patients may be rendered free of the disease by surgery of the residual tumor. PMID:21559214

  15. The molecular basis of social behavior: models, methods and advances.

    PubMed

    LeBoeuf, Adria C; Benton, Richard; Keller, Laurent

    2013-02-01

    Elucidating the molecular and neural basis of complex social behaviors such as communal living, division of labor and warfare requires model organisms that exhibit these multi-faceted behavioral phenotypes. Social insects, such as ants, bees, wasps and termites, are attractive models to address this problem, with rich ecological and ethological foundations. However, their atypical systems of reproduction have hindered application of classical genetic approaches. In this review, we discuss how recent advances in social insect genomics, transcriptomics, and functional manipulations have enhanced our ability to observe and perturb gene expression, physiology and behavior in these species. Such developments begin to provide an integrated view of the molecular and cellular underpinnings of complex social behavior. PMID:22995551

  16. Recent Advances of Radionuclide-based Molecular Imaging of Atherosclerosis

    PubMed Central

    Kazuma, Soraya M.; Sultan, Deborah; Zhao, Yongfeng; Detering, Lisa; You, Meng; Luehmann, Hannah P.; Abdalla, Dulcineia S.P.; Liu, Yongjian

    2015-01-01

    Atherosclerosis is a systemic disease characterized by the development of multifocal plaque lesions within vessel walls and extending into the vascular lumen. The disease takes decades to develop symptomatic lesions, affording opportunities for accurate detection of plaque progression, analysis of risk factors responsible for clinical events, and planning personalized treatment. Of the available molecular imaging modalities, radionuclide-based imaging strategies have been favored due to their sensitivity, quantitative detection and pathways for translational research. This review summarizes recent advances of radiolabeled small molecules, peptides, antibodies and nanoparticles for atherosclerotic plaque imaging during disease progression. PMID:26369676

  17. Recent Molecular Advances on Downstream Plant Responses to Abiotic Stress

    PubMed Central

    dos Reis, Sávio Pinho; Lima, Aline Medeiros; de Souza, Cláudia Regina Batista

    2012-01-01

    Abiotic stresses such as extremes of temperature and pH, high salinity and drought, comprise some of the major factors causing extensive losses to crop production worldwide. Understanding how plants respond and adapt at cellular and molecular levels to continuous environmental changes is a pre-requisite for the generation of resistant or tolerant plants to abiotic stresses. In this review we aimed to present the recent advances on mechanisms of downstream plant responses to abiotic stresses and the use of stress-related genes in the development of genetically engineered crops. PMID:22942725

  18. Recent advances in UHV techniques for particle accelerators

    SciTech Connect

    M. G. Rao

    1995-01-01

    The ultrahigh vacuum (UHV) requirements for storage rings and accelerators, and the development of the science and technology of UHV for particle accelerators and magnetic fusion devices have been recently reviewed by N.B. Mistry and H.F. Dylla respectively. In this paper, the latest developments in the advancement of UHV techniques for the vacuum integrity of Continuous Electron Beam Accelerator Facility (CEBAF) and for successfully dealing with the synchrotron radiation related beam line vacuum problem encountered in the design of the SSC are reviewed: the review includes developments in extreme sensitivity He leak detection technique based on the dynamic adsorption and desorption of He, operation of ionization gauges at Lhe temperatures, metal sponges for the effective cryopumping of H{sup 2} and He to pressures better than 10{sup -14} torr, and low cost and high He sensitivity RGA's. The details of a new extreme sensitivity He leak detector system are also discussed here.

  19. Advanced load-testing techniques for a science archive

    NASA Astrophysics Data System (ADS)

    Legassie, Mark; Bennett, Lee; Comeau, Susan; Dodd, Suzanne

    2008-07-01

    Performance goals for data archive systems need to be established early in the design process to ensure stability and acceptable response throughput. Load testing is one technique used to measure the progress towards these performance goals. Providing resources for load-test planning is critical, and this planning must include feasibility studies, tool analyses, and generation of an overall load-test strategy. This strategy is much different for science data archives than other systems, including commercial websites and high-volume data centers. This paper will provide an overview of the load testing performed on the Spitzer Space Telescope's science archive, which is part of Science Operations System at the Spitzer Science Center (SSC). Methods used for planning and conducting SSC load tests will be presented, and advanced load-testing techniques will be provided to address runtime issues and enhance verification results. This work was performed at the California Institute of Technology under contract to the National Aeronautics and Space Administration.

  20. Round cell tumors of bone: an update on recent molecular genetic advances.

    PubMed

    Wei, Shi; Siegal, Gene P

    2014-09-01

    Round cell tumors of bone are a divergent group of neoplasms that largely constitute Ewing sarcoma/primitive neuroectodermal tumor, small cell osteosarcoma, Langerhans cell histiocytosis, mensenchymal chondrosarcoma, and hematopoietic malignancies including lymphoma and plasmacytoma/myeloma, along with metastatic round cell tumors including neuroblastoma, rhabdomyosarcoma, and small cell carcinoma. These lesions share many histomorphologic similarities and often demonstrate overlapping clinical and radiologic characteristics, but typically have a diverse clinical outcome, thus warranting differing therapeutic modalities/regimens. Recent advances in molecular and cytogenetic techniques have identified a number of additional novel entities, including round cell sarcomas harboring CIC-DUX4 and BCOR-CCNB3 fusions, respectively. These novel findings have not only enhanced our understanding of the pathogenesis of round cell tumors, but also allowed us to reclassify some entities with potential therapeutic and prognostic significance. This article provides an overview focusing on recent molecular genetic advances in primary, nonhematologic round cell tumors of bone. PMID:25105937

  1. Recent advances in the molecular diagnostics of gastric cancer

    PubMed Central

    Kanda, Mitsuro; Kodera, Yasuhiro

    2015-01-01

    Gastric cancer (GC) is the third most common cause of cancer-related death in the world, representing a major global health issue. Although the incidence of GC is declining, the outcomes for GC patients remain dismal because of the lack of effective biomarkers to detect early GC and predict both recurrence and chemosensitivity. Current tumor markers for GC, including serum carcinoembryonic antigen and carbohydrate antigen 19-9, are not ideal due to their relatively low sensitivity and specificity. Recent improvements in molecular techniques are better able to identify aberrant expression of GC-related molecules, including oncogenes, tumor suppressor genes, microRNAs and long non-coding RNAs, and DNA methylation, as novel molecular markers, although the molecular pathogenesis of GC is complicated by tumor heterogeneity. Detection of genetic and epigenetic alterations from gastric tissue or blood samples has diagnostic value in the management of GC. There are high expectations for molecular markers that can be used as new screening tools for early detection of GC as well as for patient stratification towards personalized treatment of GC through prediction of prognosis and drug-sensitivity. In this review, the studies of potential molecular biomarkers for GC that have been reported in the publicly available literature between 2012 and 2015 are reviewed and summarized, and certain highlighted papers are examined. PMID:26379391

  2. Recent Advances in Techniques for Hyperspectral Image Processing

    NASA Technical Reports Server (NTRS)

    Plaza, Antonio; Benediktsson, Jon Atli; Boardman, Joseph W.; Brazile, Jason; Bruzzone, Lorenzo; Camps-Valls, Gustavo; Chanussot, Jocelyn; Fauvel, Mathieu; Gamba, Paolo; Gualtieri, Anthony; Marconcini, Mattia; Tilton, James C.; Trianni, Giovanna

    2009-01-01

    Imaging spectroscopy, also known as hyperspectral imaging, has been transformed in less than 30 years from being a sparse research tool into a commodity product available to a broad user community. Currently, there is a need for standardized data processing techniques able to take into account the special properties of hyperspectral data. In this paper, we provide a seminal view on recent advances in techniques for hyperspectral image processing. Our main focus is on the design of techniques able to deal with the highdimensional nature of the data, and to integrate the spatial and spectral information. Performance of the discussed techniques is evaluated in different analysis scenarios. To satisfy time-critical constraints in specific applications, we also develop efficient parallel implementations of some of the discussed algorithms. Combined, these parts provide an excellent snapshot of the state-of-the-art in those areas, and offer a thoughtful perspective on future potentials and emerging challenges in the design of robust hyperspectral imaging algorithms

  3. Surgical techniques for advanced stage pelvic organ prolapse.

    PubMed

    Brown, Douglas N; Strauchon, Christopher; Gonzalez, Hector; Gruber, Daniel

    2016-02-01

    Pelvic organ prolapse is an extremely common condition, with approximately 12% of women requiring surgical correction over their lifetime. This manuscript reviews the most recent literature regarding the comparative efficacy of various surgical repair techniques in the treatment of advanced stage pelvic organ prolapse. Uterosacral ligament suspension has similar anatomic and subjective outcomes when compared to sacrospinous ligament fixation at 12 months and is considered to be equally effective. The use of transvaginal mesh has been shown to be superior to native tissue vaginal repairs with respect to anatomic outcomes but at the cost of a higher complication rate. Minimally invasive sacrocolpopexy appears to be equivalent to abdominal sacrocolpopexy (ASC). Robot-assisted sacrocolpopexy (RSC) and laparoscopic sacrocolpopexy (LSC) appear as effective as abdominal sacrocolpopexy, however, prospective studies of comparing long-term outcomes of ASC, LSC, and RSC in relation to health care costs is paramount in the near future. Surgical correction of advanced pelvic organ prolapse can be accomplished via a variety of proven techniques. Selection of the correct surgical approach is a complex decision process and involves a multitude of factors. When deciding on the most suitable surgical intervention, the chosen route must be individualized for each patient taking into account the specific risks and benefits of each procedure. PMID:26448444

  4. Advanced IMCW Lidar Techniques for ASCENDS CO2 Column Measurements

    NASA Astrophysics Data System (ADS)

    Campbell, Joel; lin, bing; nehrir, amin; harrison, fenton; obland, michael

    2015-04-01

    Global atmospheric carbon dioxide (CO2) measurements for the NASA Active Sensing of CO2 Emissions over Nights, Days, and Seasons (ASCENDS) space mission are critical for improving our understanding of global CO2 sources and sinks. Advanced Intensity-Modulated Continuous-Wave (IM-CW) lidar techniques are investigated as a means of facilitating CO2 measurements from space to meet the ASCENDS measurement requirements. In recent numerical, laboratory and flight experiments we have successfully used the Binary Phase Shift Keying (BPSK) modulation technique to uniquely discriminate surface lidar returns from intermediate aerosol and cloud contamination. We demonstrate the utility of BPSK to eliminate sidelobes in the range profile as a means of making Integrated Path Differential Absorption (IPDA) column CO2 measurements in the presence of optically thin clouds, thereby eliminating the need to correct for sidelobe bias errors caused by the clouds. Furthermore, high accuracy and precision ranging to the surface as well as to the top of intermediate cloud layers, which is a requirement for the inversion of column CO2 number density measurements to column CO2 mixing ratios, has been demonstrated using new hyperfine interpolation techniques that takes advantage of the periodicity of the modulation waveforms. This approach works well for both BPSK and linear swept-frequency modulation techniques. The BPSK technique under investigation has excellent auto-correlation properties while possessing a finite bandwidth. A comparison of BPSK and linear swept-frequency is also discussed in this paper. These results are extended to include Richardson-Lucy deconvolution techniques to extend the resolution of the lidar beyond that implied by limit of the bandwidth of the modulation.

  5. Measuring the microbiome: perspectives on advances in DNA-based techniques for exploring microbial life

    PubMed Central

    Bunge, John; Gilbert, Jack A.; Moore, Jason H.

    2012-01-01

    This article reviews recent advances in ‘microbiome studies’: molecular, statistical and graphical techniques to explore and quantify how microbial organisms affect our environments and ourselves given recent increases in sequencing technology. Microbiome studies are moving beyond mere inventories of specific ecosystems to quantifications of community diversity and descriptions of their ecological function. We review the last 24 months of progress in this sort of research, and anticipate where the next 2 years will take us. We hope that bioinformaticians will find this a helpful springboard for new collaborations with microbiologists. PMID:22308073

  6. CD52 is a molecular target in advanced systemic mastocytosis.

    TOXLINE Toxicology Bibliographic Information

    Hoermann G; Blatt K; Greiner G; Putz EM; Berger A; Herrmann H; Cerny-Reiterer S; Gleixner KV; Walz C; Hoetzenecker K; Müllauer L; Reiter A; Sotlar K; Sexl V; Valent P; Mayerhofer M

    2014-08-01

    Advanced systemic mastocytosis (SM) is an aggressive hematopoietic neoplasm with poor prognosis and short survival times. So far, no curative therapy is available for affected patients. We have identified the cell surface antigen CD52 (CAMPATH-1) as a molecular target expressed abundantly on the surface of primary neoplastic mast cells (MCs) in patients with advanced SM. In contrast, neoplastic MCs of patients with indolent SM and normal MCs expressed only low levels or did not express CD52. To study the mechanisms of CD52 expression and the value of this antigen as a potential therapeutic target, we generated a human MC cell line, designated MCPV-1, by lentiviral immortalization of cord blood-derived MC progenitor cells. Functional studies revealed that activated RAS profoundly promotes surface expression of CD52. The CD52-targeting antibody alemtuzumab induced cell death in CD52(+) primary neoplastic MCs obtained from patients with SM as well as in MCPV-1 cells. NSG mice xenotransplanted with MCPV-1 cells survived significantly longer after treatment with alemtuzumab (median survival: 31 d untreated vs. 46 d treated; P=0.0012). We conclude that CD52 is a novel marker and potential therapeutic target in neoplastic MCs in patients with advanced SM.

  7. CD52 is a molecular target in advanced systemic mastocytosis.

    PubMed

    Hoermann, Gregor; Blatt, Katharina; Greiner, Georg; Putz, Eva Maria; Berger, Angelika; Herrmann, Harald; Cerny-Reiterer, Sabine; Gleixner, Karoline V; Walz, Christoph; Hoetzenecker, Konrad; Müllauer, Leonhard; Reiter, Andreas; Sotlar, Karl; Sexl, Veronika; Valent, Peter; Mayerhofer, Matthias

    2014-08-01

    Advanced systemic mastocytosis (SM) is an aggressive hematopoietic neoplasm with poor prognosis and short survival times. So far, no curative therapy is available for affected patients. We have identified the cell surface antigen CD52 (CAMPATH-1) as a molecular target expressed abundantly on the surface of primary neoplastic mast cells (MCs) in patients with advanced SM. In contrast, neoplastic MCs of patients with indolent SM and normal MCs expressed only low levels or did not express CD52. To study the mechanisms of CD52 expression and the value of this antigen as a potential therapeutic target, we generated a human MC cell line, designated MCPV-1, by lentiviral immortalization of cord blood-derived MC progenitor cells. Functional studies revealed that activated RAS profoundly promotes surface expression of CD52. The CD52-targeting antibody alemtuzumab induced cell death in CD52(+) primary neoplastic MCs obtained from patients with SM as well as in MCPV-1 cells. NSG mice xenotransplanted with MCPV-1 cells survived significantly longer after treatment with alemtuzumab (median survival: 31 d untreated vs. 46 d treated; P=0.0012). We conclude that CD52 is a novel marker and potential therapeutic target in neoplastic MCs in patients with advanced SM. PMID:24760752

  8. Nonculture molecular techniques for diagnosis of bacterial disease in animals: a diagnostic laboratory perspective.

    PubMed

    Cai, H Y; Caswell, J L; Prescott, J F

    2014-03-01

    The past decade has seen remarkable technical advances in infectious disease diagnosis, and the pace of innovation is likely to continue. Many of these techniques are well suited to pathogen identification directly from pathologic or clinical samples, which is the focus of this review. Polymerase chain reaction (PCR) and gene sequencing are now routinely performed on frozen or fixed tissues for diagnosis of bacterial infections of animals. These assays are most useful for pathogens that are difficult to culture or identify phenotypically, when propagation poses a biosafety hazard, or when suitable fresh tissue is not available. Multiplex PCR assays, DNA microarrays, in situ hybridization, massive parallel DNA sequencing, microbiome profiling, molecular typing of pathogens, identification of antimicrobial resistance genes, and mass spectrometry are additional emerging technologies for the diagnosis of bacterial infections from pathologic and clinical samples in animals. These technical advances come, however, with 2 caveats. First, in the age of molecular diagnosis, quality control has become more important than ever to identify and control for the presence of inhibitors, cross-contamination, inadequate templates from diagnostic specimens, and other causes of erroneous microbial identifications. Second, the attraction of these technologic advances can obscure the reality that medical diagnoses cannot be made on the basis of molecular testing alone but instead through integrated consideration of clinical, pathologic, and laboratory findings. Proper validation of the method is required. It is critical that veterinary diagnosticians understand not only the value but also the limitations of these technical advances for routine diagnosis of infectious disease. PMID:24569613

  9. Recent advances in molecular diagnostics of hepatitis B virus

    PubMed Central

    Datta, Sibnarayan; Chatterjee, Soumya; Veer, Vijay

    2014-01-01

    Hepatitis B virus (HBV) is one of the important global health problems today. Infection with HBV can lead to a variety of clinical manifestations including severe hepatic complications like liver cirrhosis and hepatocellular carcinoma. Presently, routine HBV screening and diagnosis is primarily based on the immuno-detection of HBV surface antigen (HBsAg). However, identification of HBV DNA positive cases, who do not have detectable HBsAg has greatly encouraged the use of nucleic acid amplification based assays, that are highly sensitive, specific and are to some extent tolerant to sequence variation. In the last few years, the field of HBV molecular diagnostics has evolved rapidly with advancements in the molecular biology tools, such as polymerase chain reaction (PCR) and real-time PCR. Recently, apart of PCR based amplification methods, a number of isothermal amplification assays, such as loop mediated isothermal amplification, transcription mediated amplification, ligase chain reaction, and rolling circle amplification have been utilized for HBV diagnosis. These assays also offer options for real time detection and integration into biosensing devices. In this manuscript, we review the molecular technologies that are presently available for HBV diagnostics, with special emphasis on isothermal amplification based technologies. We have also included the recent trends in the development of biosensors and use of next generation sequencing technologies for HBV. PMID:25356025

  10. Advanced Techniques for Removal of Retrievable Inferior Vena Cava Filters

    SciTech Connect

    Iliescu, Bogdan; Haskal, Ziv J.

    2012-08-15

    Inferior vena cava (IVC) filters have proven valuable for the prevention of primary or recurrent pulmonary embolism in selected patients with or at high risk for venous thromboembolic disease. Their use has become commonplace, and the numbers implanted increase annually. During the last 3 years, in the United States, the percentage of annually placed optional filters, i.e., filters than can remain as permanent filters or potentially be retrieved, has consistently exceeded that of permanent filters. In parallel, the complications of long- or short-term filtration have become increasingly evident to physicians, regulatory agencies, and the public. Most filter removals are uneventful, with a high degree of success. When routine filter-retrieval techniques prove unsuccessful, progressively more advanced tools and skill sets must be used to enhance filter-retrieval success. These techniques should be used with caution to avoid damage to the filter or cava during IVC retrieval. This review describes the complex techniques for filter retrieval, including use of additional snares, guidewires, angioplasty balloons, and mechanical and thermal approaches as well as illustrates their specific application.

  11. Advances in Time Estimation Methods for Molecular Data.

    PubMed

    Kumar, Sudhir; Hedges, S Blair

    2016-04-01

    Molecular dating has become central to placing a temporal dimension on the tree of life. Methods for estimating divergence times have been developed for over 50 years, beginning with the proposal of molecular clock in 1962. We categorize the chronological development of these methods into four generations based on the timing of their origin. In the first generation approaches (1960s-1980s), a strict molecular clock was assumed to date divergences. In the second generation approaches (1990s), the equality of evolutionary rates between species was first tested and then a strict molecular clock applied to estimate divergence times. The third generation approaches (since ∼2000) account for differences in evolutionary rates across the tree by using a statistical model, obviating the need to assume a clock or to test the equality of evolutionary rates among species. Bayesian methods in the third generation require a specific or uniform prior on the speciation-process and enable the inclusion of uncertainty in clock calibrations. The fourth generation approaches (since 2012) allow rates to vary from branch to branch, but do not need prior selection of a statistical model to describe the rate variation or the specification of speciation model. With high accuracy, comparable to Bayesian approaches, and speeds that are orders of magnitude faster, fourth generation methods are able to produce reliable timetrees of thousands of species using genome scale data. We found that early time estimates from second generation studies are similar to those of third and fourth generation studies, indicating that methodological advances have not fundamentally altered the timetree of life, but rather have facilitated time estimation by enabling the inclusion of more species. Nonetheless, we feel an urgent need for testing the accuracy and precision of third and fourth generation methods, including their robustness to misspecification of priors in the analysis of large phylogenies and data sets. PMID:26882983

  12. Advanced Fibre Bragg Grating and Microfibre Bragg Grating Fabrication Techniques

    NASA Astrophysics Data System (ADS)

    Chung, Kit Man

    Fibre Bragg gratings (FBGs) have become a very important technology for communication systems and fibre optic sensing. Typically, FBGs are less than 10-mm long and are fabricated using fused silica uniform phase masks which become more expensive for longer length or non-uniform pitch. Generally, interference UV laser beams are employed to make long or complex FBGs, and this technique introduces critical precision and control issues. In this work, we demonstrate an advanced FBG fabrication system that enables the writing of long and complex gratings in optical fibres with virtually any apodisation profile, local phase and Bragg wavelength using a novel optical design in which the incident angles of two UV beams onto an optical fibre can be adjusted simultaneously by moving just one optical component, instead of two optics employed in earlier configurations, to vary the grating pitch. The key advantage of the grating fabrication system is that complex gratings can be fabricated by controlling the linear movements of two translation stages. In addition to the study of advanced grating fabrication technique, we also focus on the inscription of FBGs written in optical fibres with a cladding diameter of several ten's of microns. Fabrication of microfibres was investigated using a sophisticated tapering method. We also proposed a simple but practical technique to filter out the higher order modes reflected from the FBG written in microfibres via a linear taper region while the fundamental mode re-couples to the core. By using this technique, reflection from the microfibre Bragg grating (MFBG) can be effectively single mode, simplifying the demultiplexing and demodulation processes. MFBG exhibits high sensitivity to contact force and an MFBG-based force sensor was also constructed and tested to investigate their suitability for use as an invasive surgery device. Performance of the contact force sensor packaged in a conforming elastomer material compares favourably to one of the best-performing commercial contact force sensors in catheterization applications. The proposed sensor features extremely high sensitivity up to 1.37-mN, miniature size (2.4-mm) that meets standard specification, excellent linearity, low hysteresis, and magnetic resonance imaging compatibility.

  13. Advanced imaging techniques for the detection of breast cancer.

    PubMed

    Jochelson, Maxine

    2012-01-01

    Mammography is the only breast imaging examination that has been shown to reduce breast cancer mortality. Population-based sensitivity is 75% to 80%, but sensitivity in high-risk women with dense breasts is only in the range of 50%. Breast ultrasound and contrast-enhanced breast magnetic resonance imaging (MRI) have become additional standard modalities used in the diagnosis of breast cancer. In high-risk women, ultrasound is known to detect approximately four additional cancers per 1,000 women. MRI is exquisitely sensitive for the detection of breast cancer. In high-risk women, it finds an additional four to five cancers per 100 women. However, both ultrasound and MRI are also known to lead to a large number of additional benign biopsies and short-term follow-up examinations. Many new breast imaging tools have improved and are being developed to improve on our current ability to diagnose early-stage breast cancer. These can be divided into two groups. The first group is those that are advances in current techniques, which include digital breast tomosynthesis and contrast-enhanced mammography and ultrasound with elastography or microbubbles. The other group includes new breast imaging platforms such as breast computed tomography (CT) scanning and radionuclide breast imaging. These are exciting advances. However, in this era of cost and radiation containment, it is imperative to look at all of them objectively to see which will provide clinically relevant additional information. PMID:24451711

  14. Multiple advanced surgical techniques to treat acquired seminal duct obstruction

    PubMed Central

    Jiang, Hong-Tao; Yuan, Qian; Liu, Yu; Liu, Zeng-Qin; Zhou, Zhen-Yu; Xiao, Ke-Feng; Yang, Jiang-Gen

    2014-01-01

    The aim of this study was to evaluate the outcomes of multiple advanced surgical treatments (i.e. microsurgery, laparoscopic surgery and endoscopic surgery) for acquired obstructive azoospermia. We analyzed the surgical outcomes of 51 patients with suspected acquired obstructive azoospermia consecutively who enrolled at our center between January 2009 and May 2013. Modified vasoepididymostomy, laparoscopically assisted vasovasostomy and transurethral incision of the ejaculatory duct with holmium laser were chosen and performed based on the different obstruction sites. The mean postoperative follow-up time was 22 months (range: 9 months to 52 months). Semen analyses were initiated at four postoperative weeks, followed by trimonthly (months 3, 6, 9 and 12) semen analyses, until no sperm was found at 12 months or until pregnancy was achieved. Patency was defined as >10,000 sperm ml−1 of semen. The obstruction sites, postoperative patency and natural pregnancy rate were recorded. Of 51 patients, 47 underwent bilateral or unilateral surgical reconstruction; the other four patients were unable to be treated with surgical reconstruction because of pelvic vas or intratesticular tubules obstruction. The reconstruction rate was 92.2% (47/51), and the patency rate and natural pregnancy rate were 89.4% (42/47) and 38.1% (16/42), respectively. No severe complications were observed. Using multiple advanced surgical techniques, more extensive range of seminal duct obstruction was accessible and correctable; thus, a favorable patency and pregnancy rate can be achieved. PMID:25337841

  15. Recent advances on polyoxometalate-based molecular and composite materials.

    PubMed

    Song, Yu-Fei; Tsunashima, Ryo

    2012-11-21

    Polyoxometalates (POMs) are a subset of metal oxides with unique physical and chemical properties, which can be reliably modified through various techniques and methods to develop sophisticated materials and devices. In parallel with the large number of new crystal structures reported in the literature, the application of these POMs towards multifunctional materials has attracted considerable attention. This critical review summarizes recent progress on POM-based molecular and composite materials, and particularly highlights the emerging areas that are closely related to surface, electronic, energy, environment, life science, etc. (171 references). PMID:22850732

  16. Advances in the Rising Bubble Technique for discharge measurement

    NASA Astrophysics Data System (ADS)

    Hilgersom, Koen; Luxemburg, Willem; Willemsen, Geert; Bussmann, Luuk

    2014-05-01

    Already in the 19th century, d'Auria described a discharge measurement technique that applies floats to find the depth-integrated velocity (d'Auria, 1882). The basis of this technique was that the horizontal distance that the float travels on its way to the surface is the image of the integrated velocity profile over depth. Viol and Semenov (1964) improved this method by using air bubbles as floats, but still distances were measured manually until Sargent (1981) introduced a technique that could derive the distances from two photographs simultaneously taken from each side of the river bank. Recently, modern image processing techniques proved to further improve the applicability of the method (Hilgersom and Luxemburg, 2012). In the 2012 article, controlling and determining the rising velocity of an air bubble still appeared a major challenge for the application of this method. Ever since, laboratory experiments with different nozzle and tube sizes lead to advances in our self-made equipment enabling us to produce individual air bubbles with a more constant rising velocity. Also, we introduced an underwater camera to on-site determine the rising velocity, which is dependent on the water temperature and contamination, and therefore is site-specific. Camera measurements of the rising velocity proved successful in a laboratory and field setting, although some improvements to the setup are necessary to capture the air bubbles also at depths where little daylight penetrates. References D'Auria, L.: Velocity of streams; A new method to determine correctly the mean velocity of any perpendicular in rivers and canals, (The) American Engineers, 3, 1882. Hilgersom, K.P. and Luxemburg, W.M.J.: Technical Note: How image processing facilitates the rising bubble technique for discharge measurement, Hydrology and Earth System Sciences, 16(2), 345-356, 2012. Sargent, D.: Development of a viable method of stream flow measurement using the integrating float technique, Proceedings of the Institution of Civil Engineers (London), Part 2, 71, 1-15, 1981. Viol, V. and Semenov, V.: Experiments in measuring discharges in canals by the photo-integration method, Soviet Hydrol. Selected Pap, 2, 198-199, 1964.

  17. Characterising chromosome rearrangements: recent technical advances in molecular cytogenetics

    PubMed Central

    Le Scouarnec, S; Gribble, S M

    2012-01-01

    Genomic rearrangements can result in losses, amplifications, translocations and inversions of DNA fragments thereby modifying genome architecture, and potentially having clinical consequences. Many genomic disorders caused by structural variation have initially been uncovered by early cytogenetic methods. The last decade has seen significant progression in molecular cytogenetic techniques, allowing rapid and precise detection of structural rearrangements on a whole-genome scale. The high resolution attainable with these recently developed techniques has also uncovered the role of structural variants in normal genetic variation alongside single-nucleotide polymorphisms (SNPs). We describe how array-based comparative genomic hybridisation, SNP arrays, array painting and next-generation sequencing analytical methods (read depth, read pair and split read) allow the extensive characterisation of chromosome rearrangements in human genomes. PMID:22086080

  18. Characterising chromosome rearrangements: recent technical advances in molecular cytogenetics.

    PubMed

    Le Scouarnec, S; Gribble, S M

    2012-01-01

    Genomic rearrangements can result in losses, amplifications, translocations and inversions of DNA fragments thereby modifying genome architecture, and potentially having clinical consequences. Many genomic disorders caused by structural variation have initially been uncovered by early cytogenetic methods. The last decade has seen significant progression in molecular cytogenetic techniques, allowing rapid and precise detection of structural rearrangements on a whole-genome scale. The high resolution attainable with these recently developed techniques has also uncovered the role of structural variants in normal genetic variation alongside single-nucleotide polymorphisms (SNPs). We describe how array-based comparative genomic hybridisation, SNP arrays, array painting and next-generation sequencing analytical methods (read depth, read pair and split read) allow the extensive characterisation of chromosome rearrangements in human genomes. PMID:22086080

  19. Advanced molecular dynamics simulation methods for kinase drug discovery.

    PubMed

    Aci-Sèche, Samia; Ziada, Sonia; Braka, Abdennour; Arora, Rohit; Bonnet, Pascal

    2016-04-01

    Interest in the application of molecular dynamics (MD) simulations has increased in the field of protein kinase (PK) drug discovery. PKs belong to an important drug target class because they are directly involved in a number of diseases, including cancer. MD methods simulate dynamic biological and chemical events at an atomic level. This information can be combined with other in silico and experimental methods to efficiently target selected receptors. In this review, we present common and advanced methods of MD simulations and we focus on the recent applications of MD-based methodologies that provided significant insights into the elucidation of biological mechanisms involving PKs and into the discovery of novel kinase inhibitors. PMID:27054816

  20. Molecular diagnosis of endemic and invasive mycoses: advances and challenges.

    PubMed

    Gómez, Beatriz L

    2014-01-01

    The diagnosis of endemic and invasive fungal disease remains challenging. Molecular techniques for identification of fungi now play a significant and growing role in clinical mycology and offer distinct advantages as they are faster, more sensitive and more specific. The aim of this mini-review is to provide an overview of the state of the art of molecular diagnosis of endemic and invasive fungal diseases, and to emphasize the challenges and current need for standardization of the different methods. The European Aspergillus PCR Initiative (EAPCRI) has made significant progress in developing a standard for Aspergillus polymerase chain reaction (PCR), but recognizes that the process will not be finished until clinical utility has been established in formal and extensive clinical trials. Similar efforts should be implemented for the diagnosis of the other mycoses in order to fully validate the current methods or reinforce the need to design new ones. This manuscript is part of the series of works presented at the "V International Workshop: Molecular genetic approaches to the study of human pathogenic fungi" (Oaxaca, Mexico, 2012). PMID:24252827

  1. Advanced Cell Culture Techniques for Cancer Drug Discovery

    PubMed Central

    Lovitt, Carrie J.; Shelper, Todd B.; Avery, Vicky M.

    2014-01-01

    Human cancer cell lines are an integral part of drug discovery practices. However, modeling the complexity of cancer utilizing these cell lines on standard plastic substrata, does not accurately represent the tumor microenvironment. Research into developing advanced tumor cell culture models in a three-dimensional (3D) architecture that more prescisely characterizes the disease state have been undertaken by a number of laboratories around the world. These 3D cell culture models are particularly beneficial for investigating mechanistic processes and drug resistance in tumor cells. In addition, a range of molecular mechanisms deconstructed by studying cancer cells in 3D models suggest that tumor cells cultured in two-dimensional monolayer conditions do not respond to cancer therapeutics/compounds in a similar manner. Recent studies have demonstrated the potential of utilizing 3D cell culture models in drug discovery programs; however, it is evident that further research is required for the development of more complex models that incorporate the majority of the cellular and physical properties of a tumor. PMID:24887773

  2. Advances in Molecular Serotyping and Subtyping of Escherichia coli†

    PubMed Central

    Fratamico, Pina M.; DebRoy, Chitrita; Liu, Yanhong; Needleman, David S.; Baranzoni, Gian Marco; Feng, Peter

    2016-01-01

    Escherichia coli plays an important role as a member of the gut microbiota; however, pathogenic strains also exist, including various diarrheagenic E. coli pathotypes and extraintestinal pathogenic E. coli that cause illness outside of the GI-tract. E. coli have traditionally been serotyped using antisera against the ca. 186 O-antigens and 53 H-flagellar antigens. Phenotypic methods, including bacteriophage typing and O- and H- serotyping for differentiating and characterizing E. coli have been used for many years; however, these methods are generally time consuming and not always accurate. Advances in next generation sequencing technologies have made it possible to develop genetic-based subtyping and molecular serotyping methods for E. coli, which are more discriminatory compared to phenotypic typing methods. Furthermore, whole genome sequencing (WGS) of E. coli is replacing established subtyping methods such as pulsed-field gel electrophoresis, providing a major advancement in the ability to investigate food-borne disease outbreaks and for trace-back to sources. A variety of sequence analysis tools and bioinformatic pipelines are being developed to analyze the vast amount of data generated by WGS and to obtain specific information such as O- and H-group determination and the presence of virulence genes and other genetic markers. PMID:27199968

  3. Ciceromics: Advancement in Genomics and Recent Molecular Techniques

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomics is a branch of science that decodes the encrypted information in DNA and reveals information such as the number of genes, genome organization and content. This information has tremendous application in agriculture, evolutionary biology and other areas of science. Although genomics has allow...

  4. Azalea phylogeny reconstructed by means of molecular techniques.

    PubMed

    De Keyser, Ellen; Scariot, Valentina; Kobayashi, Nobuo; Handa, Takashi; De Riek, Jan

    2010-01-01

    Plants belonging to the Rhododendron subgenera Pentanthera (deciduous) and Tsutsusi and Azaleastrum (evergreen) are called azaleas. Concerning their mutual phylogenetic positions, the Pentanthera subgenus is closer to evergreen rhododendrons (subgenera Rhododendron and Hymenanthes) than to the Tsutsusi subgenus. Both azalea types are important ornamentals with a long breeding tradition. Different hybrid groups are often named after the supposed principal ancestor species. Molecular techniques for phylogenetic and kinship research have been evaluated to a great extent. First, some studies using comparative gene sequencing are presented; this approach was then widened to the use of molecular markers to reveal more detailed genetic relationships. Finally, the use of candidate genes as functional markers for the assessment of genetic diversity is presented. This opens new research lines to the genetic mapping of plant traits and azalea genomics. PMID:20099114

  5. Molecular dynamics techniques in the studies of the bacterial ribosome

    NASA Astrophysics Data System (ADS)

    Panecka, Joanna; Trylska, Joanna

    2012-06-01

    We summarize here the recent applications of molecular dynamics (MD) and enhanced sampling methods used to elucidate the role of flexibility in ribosome functioning. In the last decade, many atomic resolution structures of the bacterial ribosome have been solved, which allowed for extensive all-atom MD studies of this system. However, the time scale of such simulations is often not sufficient due to the large number of atoms building the ribosome complex. One of the ways to overcome this problem are enhanced sampling techniques. For instance, steered MD gave us knowledge about the dynamics of nascent peptide chain in the ribosomal exit tunnel. Targeted MD was used to study pathways of tRNA accommodation into the ribosome. Other MD-based techniques (MDFF and MDfit) allowed for generation of full-atom models from mediumresolution cryo-electron microscopy (cryo-EM) maps. Also, the studies on models of ribosomal aminoacyl-tRNA binding site (A-site) improved our understanding of the mRNA decoding process. For example, replica exchange molecular dynamics (REMD) was used to study the movement of the two key adenines, involved in the mRNA decoding process. The REMD extensive sampling allowed for construction of free energy landscapes. In summary, the MD-based techniques are very helpful in expanding our knowledge of the ribosome functioning and they successfully complement the experimental studies.

  6. A Sensitive TLRH Targeted Imaging Technique for Ultrasonic Molecular Imaging

    PubMed Central

    Hu, Xiaowen; Zheng, Hairong; Kruse, Dustin E.; Sutcliffe, Patrick; Stephens, Douglas N.; Ferrara, Katherine W.

    2010-01-01

    The primary goals of ultrasound molecular imaging are the detection and imaging of ultrasound contrast agents (microbubbles), which are bound to specific vascular surface receptors. Imaging methods that can sensitively and selectively detect and distinguish bound microbubbles from freely circulating microbubbles (free microbubbles) and surrounding tissue are critically important for the practical application of ultrasound contrast molecular imaging. Microbubbles excited by low frequency acoustic pulses emit wide-band echoes with a bandwidth extending beyond 20 MHz; we refer to this technique as TLRH (transmission at a low frequency and reception at a high frequency). Using this wideband, transient echo, we have developed and implemented a targeted imaging technique incorporating a multi-frequency co-linear array and the Siemens Antares imaging system. The multi-frequency co-linear array integrates a center 5.4 MHz array, used to receive echoes and produce radiation force, and two outer 1.5 MHz arrays used to transmit low frequency incident pulses. The targeted imaging technique makes use of an acoustic radiation force sub-sequence to enhance accumulation and a TLRH imaging sub-sequence to detect bound microbubbles. The radiofrequency (RF) data obtained from the TLRH imaging sub-sequence are processsed to separate echo signatures between tissue, free microbubbles, and bound microbubbles. By imaging biotin-coated microbubbles targeted to avidin-coated cellulose tubes, we demonstrate that the proposed method has a high contrast-to-tissue ratio (up to 34 dB) and a high sensitivity to bound microbubbles (with the ratio of echoes from bound microbubbles versus free microbubbles extending up to 23 dB). The effects of the imaging pulse acoustic pressure, the radiation force sub-sequence and the use of various slow-time filters on the targeted imaging quality are studied. The TLRH targeted imaging method is demonstrated in this study to provide sensitive and selective detection of bound microbubbles for ultrasound molecularly-targeted imaging. PMID:20178897

  7. A review of hemorheology: Measuring techniques and recent advances

    NASA Astrophysics Data System (ADS)

    Sousa, Patrícia C.; Pinho, Fernando T.; Alves, Manuel A.; Oliveira, Mónica S. N.

    2016-02-01

    Significant progress has been made over the years on the topic of hemorheology, not only in terms of the development of more accurate and sophisticated techniques, but also in terms of understanding the phenomena associated with blood components, their interactions and impact upon blood properties. The rheological properties of blood are strongly dependent on the interactions and mechanical properties of red blood cells, and a variation of these properties can bring further insight into the human health state and can be an important parameter in clinical diagnosis. In this article, we provide both a reference for hemorheological research and a resource regarding the fundamental concepts in hemorheology. This review is aimed at those starting in the field of hemodynamics, where blood rheology plays a significant role, but also at those in search of the most up-to-date findings (both qualitative and quantitative) in hemorheological measurements and novel techniques used in this context, including technical advances under more extreme conditions such as in large amplitude oscillatory shear flow or under extensional flow, which impose large deformations comparable to those found in the microcirculatory system and in diseased vessels. Given the impressive rate of increase in the available knowledge on blood flow, this review is also intended to identify areas where current knowledge is still incomplete, and which have the potential for new, exciting and useful research. We also discuss the most important parameters that can lead to an alteration of blood rheology, and which as a consequence can have a significant impact on the normal physiological behavior of blood.

  8. Synthetic biology and molecular genetics in non-conventional yeasts: Current tools and future advances.

    PubMed

    Wagner, James M; Alper, Hal S

    2016-04-01

    Coupling the tools of synthetic biology with traditional molecular genetic techniques can enable the rapid prototyping and optimization of yeast strains. While the era of yeast synthetic biology began in the well-characterized model organism Saccharomyces cerevisiae, it is swiftly expanding to include non-conventional yeast production systems such as Hansenula polymorpha, Kluyveromyces lactis, Pichia pastoris, and Yarrowia lipolytica. These yeasts already have roles in the manufacture of vaccines, therapeutic proteins, food additives, and biorenewable chemicals, but recent synthetic biology advances have the potential to greatly expand and diversify their impact on biotechnology. In this review, we summarize the development of synthetic biological tools (including promoters and terminators) and enabling molecular genetics approaches that have been applied in these four promising alternative biomanufacturing platforms. An emphasis is placed on synthetic parts and genome editing tools. Finally, we discuss examples of synthetic tools developed in other organisms that can be adapted or optimized for these hosts in the near future. PMID:26701310

  9. Advanced Techniques for Power System Identification from Measured Data

    SciTech Connect

    Pierre, John W.; Wies, Richard; Trudnowski, Daniel

    2008-11-25

    Time-synchronized measurements provide rich information for estimating a power-system's electromechanical modal properties via advanced signal processing. This information is becoming critical for the improved operational reliability of interconnected grids. A given mode's properties are described by its frequency, damping, and shape. Modal frequencies and damping are useful indicators of power-system stress, usually declining with increased load or reduced grid capacity. Mode shape provides critical information for operational control actions. This project investigated many advanced techniques for power system identification from measured data focusing on mode frequency and damping ratio estimation. Investigators from the three universities coordinated their effort with Pacific Northwest National Laboratory (PNNL). Significant progress was made on developing appropriate techniques for system identification with confidence intervals and testing those techniques on field measured data and through simulation. Experimental data from the western area power system was provided by PNNL and Bonneville Power Administration (BPA) for both ambient conditions and for signal injection tests. Three large-scale tests were conducted for the western area in 2005 and 2006. Measured field PMU (Phasor Measurement Unit) data was provided to the three universities. A 19-machine simulation model was enhanced for testing the system identification algorithms. Extensive simulations were run with this model to test the performance of the algorithms. University of Wyoming researchers participated in four primary activities: (1) Block and adaptive processing techniques for mode estimation from ambient signals and probing signals, (2) confidence interval estimation, (3) probing signal design and injection method analysis, and (4) performance assessment and validation from simulated and field measured data. Subspace based methods have been use to improve previous results from block processing techniques. Bootstrap techniques have been developed to estimate confidence intervals for the electromechanical modes from field measured data. Results were obtained using injected signal data provided by BPA. A new probing signal was designed that puts more strength into the signal for a given maximum peak to peak swing. Further simulations were conducted on a model based on measured data and with the modifications of the 19-machine simulation model. Montana Tech researchers participated in two primary activities: (1) continued development of the 19-machine simulation test system to include a DC line; and (2) extensive simulation analysis of the various system identification algorithms and bootstrap techniques using the 19 machine model. Researchers at the University of Alaska-Fairbanks focused on the development and testing of adaptive filter algorithms for mode estimation using data generated from simulation models and on data provided in collaboration with BPA and PNNL. There efforts consist of pre-processing field data, testing and refining adaptive filter techniques (specifically the Least Mean Squares (LMS), the Adaptive Step-size LMS (ASLMS), and Error Tracking (ET) algorithms). They also improved convergence of the adaptive algorithms by using an initial estimate from block processing AR method to initialize the weight vector for LMS. Extensive testing was performed on simulated data from the 19 machine model. This project was also extensively involved in the WECC (Western Electricity Coordinating Council) system wide tests carried out in 2005 and 2006. These tests involved injecting known probing signals into the western power grid. One of the primary goals of these tests was the reliable estimation of electromechanical mode properties from measured PMU data. Applied to the system were three types of probing inputs: (1) activation of the Chief Joseph Dynamic Brake, (2) mid-level probing at the Pacific DC Intertie (PDCI), and (3) low-level probing on the PDCI. The Chief Joseph Dynamic Brake is a 1400 MW disturbance to the system and is injected for a half of a second. For the mid and low-level probing, the Celilo terminal of the PDCI is modulated with a known probing signal. Similar but less extensive tests were conducted in June of 2000. The low-level probing signals were designed at the University of Wyoming. A number of important design factors are considered. The designed low-level probing signal used in the tests is a multi-sine signal. Its frequency content is focused in the range of the inter-area electromechanical modes. The most frequently used of these low-level multi-sine signals had a period of over two minutes, a root-mean-square (rms) value of 14 MW, and a peak magnitude of 20 MW. Up to 15 cycles of this probing signal were injected into the system resulting in a processing gain of 15. The resulting measured response at points throughout the system was not much larger than the ambient noise present in the measurements.

  10. Miniaturization of molecular biological techniques for gene assay.

    PubMed

    Lien, Kang-Yi; Lee, Gwo-Bin

    2010-07-01

    The rapid diagnosis of various diseases is a critical advantage of many emerging biomedical tools. Due to advances in preventive medicine, tools for the accurate analysis of genetic mutation and associated hereditary diseases have attracted significant interests in recent years. The entire diagnostic process usually involves two critical steps, namely, sample pre-treatment and genetic analysis. The sample pre-treatment processes such as extraction and purification of the target nucleic acids prior to genetic analysis are essential in molecular diagnostics. The genetic analysis process may require specialized apparatus for nucleic acid amplification, sequencing and detection. Traditionally, pre-treatment of clinical biological samples (e.g. the extraction of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA)) and the analysis of genetic polymorphisms associated with genetic diseases are typically a lengthy and costly process. These labor-intensive and time-consuming processes usually result in a high-cost per diagnosis and hinder their practical applications. Besides, the accuracy of the diagnosis may be affected owing to potential contamination from manual processing. Alternatively, due to significant advances in micro-electro-mechanical-systems (MEMS) and microfluidic technology, there are numerous miniature systems employed in biomedical applications, especially for the rapid diagnosis of genetic diseases. A number of advantages including automation, compactness, disposability, portability, lower cost, shorter diagnosis time, lower sample and reagent consumption, and lower power consumption can be realized by using these microfluidic-based platforms. As a result, microfluidic-based systems are becoming promising platforms for genetic analysis, molecular biology and for the rapid detection of genetic diseases. In this review paper, microfluidic-based platforms capable of identifying genetic sequences and diagnosis of genetic mutations are surveyed and reviewed. Some critical issues with the use of microfluidic-based systems for diagnosis of genetic diseases are also highlighted. PMID:20390199

  11. Development of advanced strain diagnostic techniques for reactor environments.

    SciTech Connect

    Fleming, Darryn D.; Holschuh, Thomas Vernon,; Miller, Timothy J.; Hall, Aaron Christopher; Urrea, David Anthony,; Parma, Edward J.,

    2013-02-01

    The following research is operated as a Laboratory Directed Research and Development (LDRD) initiative at Sandia National Laboratories. The long-term goals of the program include sophisticated diagnostics of advanced fuels testing for nuclear reactors for the Department of Energy (DOE) Gen IV program, with the future capability to provide real-time measurement of strain in fuel rod cladding during operation in situ at any research or power reactor in the United States. By quantifying the stress and strain in fuel rods, it is possible to significantly improve fuel rod design, and consequently, to improve the performance and lifetime of the cladding. During the past year of this program, two sets of experiments were performed: small-scale tests to ensure reliability of the gages, and reactor pulse experiments involving the most viable samples in the Annulated Core Research Reactor (ACRR), located onsite at Sandia. Strain measurement techniques that can provide useful data in the extreme environment of a nuclear reactor core are needed to characterize nuclear fuel rods. This report documents the progression of solutions to this issue that were explored for feasibility in FY12 at Sandia National Laboratories, Albuquerque, NM.

  12. Dissecting cell adhesion architecture using advanced imaging techniques

    PubMed Central

    Morton, Penny E

    2011-01-01

    Cell adhesion to extracellular matrix proteins or to other cells is essential for the control of embryonic development, tissue integrity, immune function and wound healing. Adhesions are tightly spatially regulated structures containing over one hundred different proteins that coordinate both dynamics and signaling events at these sites. Extensive biochemical and morphological analysis of adhesion types over the past three decades has greatly improved understanding of individual protein contributions to adhesion signaling and, in some cases, dynamics. However, it is becoming increasingly clear that these diverse macromolecular complexes contain a variety of protein sub-networks, as well as distinct sub-domains that likely play important roles in regulating adhesion behavior. Until recently, resolving these structures, which are often less than a micron in size, was hampered by the limitations of conventional light microscopy. However, recent advances in optical techniques and imaging methods have revealed exciting insight into the intricate control of adhesion structure and assembly. Here we provide an overview of the recent data arising from such studies of cell:matrix and cell:cell contact and an overview of the imaging strategies that have been applied to study the intricacies and hierarchy of proteins within adhesions. PMID:21785274

  13. Pediatric Cardiopulmonary Resuscitation: Advances in Science, Techniques, and Outcomes

    PubMed Central

    Topjian, Alexis A.; Berg, Robert A.; Nadkarni, Vinay M.

    2009-01-01

    More than 25% of children survive to hospital discharge after in-hospital cardiac arrests, and 5% to 10% survive after out-of-hospital cardiac arrests. This review of pediatric cardiopulmonary resuscitation addresses the epidemiology of pediatric cardiac arrests, mechanisms of coronary blood flow during cardiopulmonary resuscitation, the 4 phases of cardiac arrest resuscitation, appropriate interventions during each phase, special resuscitation circumstances, extracorporeal membrane oxygenation cardiopulmonary resuscitation, and quality of cardiopulmonary resuscitation. The key elements of pathophysiology that impact and match the timing, intensity, duration, and variability of the hypoxic-ischemic insult to evidence-based interventions are reviewed. Exciting discoveries in basic and applied-science laboratories are now relevant for specific subpopulations of pediatric cardiac arrest victims and circumstances (eg, ventricular fibrillation, neonates, congenital heart disease, extracorporeal cardiopulmonary resuscitation). Improving the quality of interventions is increasingly recognized as a key factor for improving outcomes. Evolving training strategies include simulation training, just-in-time and just-in-place training, and crisis-team training. The difficult issue of when to discontinue resuscitative efforts is addressed. Outcomes from pediatric cardiac arrests are improving. Advances in resuscitation science and state-of-the-art implementation techniques provide the opportunity for further improvement in outcomes among children after cardiac arrest. PMID:18977991

  14. Sculpting 3D worlds with music: advanced texturing techniques

    NASA Astrophysics Data System (ADS)

    Greuel, Christian; Bolas, Mark T.; Bolas, Niko; McDowall, Ian E.

    1996-04-01

    Sound within the virtual environment is often considered to be secondary to the graphics. In a typical scenario, either audio cues are locally associated with specific 3D objects or a general aural ambiance is supplied in order to alleviate the sterility of an artificial experience. This paper discusses a completely different approach, in which cues are extracted from live or recorded music in order to create geometry and control object behaviors within a computer- generated environment. Advanced texturing techniques used to generate complex stereoscopic images are also discussed. By analyzing music for standard audio characteristics such as rhythm and frequency, information is extracted and repackaged for processing. With the Soundsculpt Toolkit, this data is mapped onto individual objects within the virtual environment, along with one or more predetermined behaviors. Mapping decisions are implemented with a user definable schedule and are based on the aesthetic requirements of directors and designers. This provides for visually active, immersive environments in which virtual objects behave in real-time correlation with the music. The resulting music-driven virtual reality opens up several possibilities for new types of artistic and entertainment experiences, such as fully immersive 3D `music videos' and interactive landscapes for live performance.

  15. Nanocrystalline materials: recent advances in crystallographic characterization techniques

    PubMed Central

    Ringe, Emilie

    2014-01-01

    Most properties of nanocrystalline materials are shape-dependent, providing their exquisite tunability in optical, mechanical, electronic and catalytic properties. An example of the former is localized surface plasmon resonance (LSPR), the coherent oscillation of conduction electrons in metals that can be excited by the electric field of light; this resonance frequency is highly dependent on both the size and shape of a nanocrystal. An example of the latter is the marked difference in catalytic activity observed for different Pd nanoparticles. Such examples highlight the importance of particle shape in nanocrystalline materials and their practical applications. However, one may ask ‘how are nanoshapes created?’, ‘how does the shape relate to the atomic packing and crystallography of the material?’, ‘how can we control and characterize the external shape and crystal structure of such small nanocrystals?’. This feature article aims to give the reader an overview of important techniques, concepts and recent advances related to these questions. Nucleation, growth and how seed crystallography influences the final synthesis product are discussed, followed by shape prediction models based on seed crystallography and thermodynamic or kinetic parameters. The crystallographic implications of epitaxy and orientation in multilayered, core-shell nanoparticles are overviewed, and, finally, the development and implications of novel, spatially resolved analysis tools are discussed. PMID:25485133

  16. [Targeted molecular therapy based on advanced cancer stem cell model].

    PubMed

    Hirao, Atsushi

    2015-08-01

    Improvement of cell purification and transplantation techniques have contributed to the identification of cell populations known as tumor-initiating cells (TICs). Although it was hypothesized that tumors are organized as hierarchies of tumor cells that are sustained by rare TICs, like normal tissue stem cells, there are several controversies towards such cancer stem cell model, e.g. reversible change of stem cell like population based on epigenetic changes, clonal genetic evolution and problems in xenotransplantation system. Despite complexity in cancer stem cell models, studies in cancer stem cell field have revealed that there are close relationship between cancer malignancy and stem cell properties, called "stemness". Understanding molecular mechanisms for controlling stemness would contribute to establishment of novel diagnostics or therapeutics for cancer. PMID:26281675

  17. Hybrid inverse lithography techniques for advanced hierarchical memories

    NASA Astrophysics Data System (ADS)

    Xiao, Guangming; Hooker, Kevin; Irby, Dave; Zhang, Yunqiang; Ward, Brian; Cecil, Tom; Hall, Brett; Lee, Mindy; Kim, Dave; Lucas, Kevin

    2014-03-01

    Traditional segment-based model-based OPC methods have been the mainstream mask layout optimization techniques in volume production for memory and embedded memory devices for many device generations. These techniques have been continually optimized over time to meet the ever increasing difficulties of memory and memory periphery patterning. There are a range of difficult issues for patterning embedded memories successfully. These difficulties include the need for a very high level of symmetry and consistency (both within memory cells themselves and between cells) due to circuit effects such as noise margin requirements in SRAMs. Memory cells and access structures consume a large percentage of area in embedded devices so there is a very high return from shrinking the cell area as much as possible. This aggressive scaling leads to very difficult resolution, 2D CD control and process window requirements. Additionally, the range of interactions between mask synthesis corrections of neighboring areas can extend well beyond the size of the memory cell, making it difficult to fully take advantage of the inherent designed cell hierarchy in mask pattern optimization. This is especially true for non-traditional (i.e., less dependent on geometric rule) OPC/RET methods such as inverse lithography techniques (ILT) which inherently have more model-based decisions in their optimizations. New inverse methods such as model-based SRAF placement and ILT are, however, well known to have considerable benefits in finding flexible mask pattern solutions to improve process window, improve 2D CD control, and improve resolution in ultra-dense memory patterns. They also are known to reduce recipe complexity and provide native MRC compliant mask pattern solutions. Unfortunately, ILT is also known to be several times slower than traditional OPC methods due to the increased computational lithographic optimizations it performs. In this paper, we describe and present results for a methodology to greatly improve the ability of ILT to optimize advanced embedded memory designs while retaining significant hierarchy and cell design symmetry, therefore, have good turnaround time and CD uniformity. This paper will explain the enhancements which have been developed in order to overcome the traditional difficulties listed above. These enhancements are in the categories of local CD control, global chip processing options, process window benefit, turn-around time and hierarchy retention.

  18. Double-Edge Molecular Technique for Doppler Lidar Wind Measurement

    NASA Technical Reports Server (NTRS)

    Flesia, Cristina; Korb, C. Laurence

    1998-01-01

    The double-edge lidar technique for measuring the wind using molecular backscatter is described. Two high spectral resolution edge filters are located in the wings of the Rayleigh-Brillouin profile. This doubles the signal change per unit Doppler shift, the sensitivity, and gives nearly a factor of two improvement in measurement accuracy. The use of a crossover region is described where the sensitivity of a molecular and aerosol-based measurement are equal. This desensitizes the molecular measurement to the effects of aerosol scattering over a frequency range of +/- 100 m/s. We give methods for correcting for short-term frequency jitter and drift using a laser reference frequency measurement and methods for long-term frequency correction using a servo control system. The effects of Rayleigh-Brillouin scattering on the measurement are shown to be significant and are included in the analysis. Simulations for a conical scanning satellite-based lidar at 355 nm show an accuracy of 2-3 m/s for altitudes of 2 to 15 km for a 1 km vertical resolution, a satellite altitude of 400 km and a 200 km x 200 km spatial resolution. Results of ground based wind measurements are presented.

  19. 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.

  20. Molecular Genetic Tools and Techniques in Fission Yeast.

    PubMed

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

    2016-01-01

    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. PMID:27140925

  1. Advanced small bowel adenocarcinoma: Molecular characteristics and therapeutic perspectives.

    PubMed

    Zaaimi, Yosra; Aparicio, Thomas; Laurent-Puig, Pierre; Taieb, Julien; Zaanan, Aziz

    2016-04-01

    Small bowel cancer represents less than 5% of all gastrointestinal cancers, while small bowel adenocarcinoma (SBA) accounts for about one third of all cancers of the small bowel. Although SBA frequently appears sporadically, some diseases are risk factors, such as Crohn's disease and some genetic predispositions to cancer. Progress in the identification of molecular alterations suggests some similarities in carcinogenesis between SBA and colorectal cancer. Evidence levels for the treatment and prognosis of these tumors are insufficient because of the scarcity of this disease and the absence of randomized trials. Chemotherapy based on fluoropyrimidine plus a platinum salt appears to be the most effective treatment regimen in non-randomized prospective trials for advanced SBA. Targeted therapy, against the angiogenic pathway or the epidermal growth factor receptor (EGFR) pathway, for example, is not yet established, but seems promising given the over-expression of vascular epithelial growth factor (VEGF)-A or EGFR observed in SBA. Phase I and II studies are currently evaluating the safety and efficacy of these targeted therapies in SBA treatment. The low incidence of SBA should promote the development of international collaborations to improve our knowledge of the biological mechanisms underlying these tumors and to set up therapeutic trials. PMID:26547136

  2. Advanced Techniques for Simulating the Behavior of Sand

    NASA Astrophysics Data System (ADS)

    Clothier, M.; Bailey, M.

    2009-12-01

    Computer graphics and visualization techniques continue to provide untapped research opportunities, particularly when working with earth science disciplines. Through collaboration with the Oregon Space Grant and IGERT Ecosystem Informatics programs we are developing new techniques for simulating sand. In addition, through collaboration with the Oregon Space Grant, we’ve been communicating with the Jet Propulsion Laboratory (JPL) to exchange ideas and gain feedback on our work. More specifically, JPL’s DARTS Laboratory specializes in planetary vehicle simulation, such as the Mars rovers. This simulation utilizes a virtual "sand box" to test how planetary rovers respond to different terrains while traversing them. Unfortunately, this simulation is unable to fully mimic the harsh, sandy environments of those found on Mars. Ideally, these simulations should allow a rover to interact with the sand beneath it, particularly for different sand granularities and densities. In particular, there may be situations where a rover may become stuck in sand due to lack of friction between the sand and wheels. In fact, in May 2009, the Spirit rover became stuck in the Martian sand and has provided additional motivation for this research. In order to develop a new sand simulation model, high performance computing will play a very important role in this work. More specifically, graphics processing units (GPUs) are useful due to their ability to run general purpose algorithms and ability to perform massively parallel computations. In prior research, simulating vast quantities of sand has been difficult to compute in real-time due to the computational complexity of many colliding particles. With the use of GPUs however, each particle collision will be parallelized, allowing for a dramatic performance increase. In addition, spatial partitioning will also provide a speed boost as this will help limit the number of particle collision calculations. However, since the goal of this research is to simulate the look and behavior of sand, this work will go beyond simple particle collision. In particular, we can continue to use our parallel algorithms not only on single particles but on particle “clumps” that consist of multiple combined particles. Since sand is typically not spherical in nature, these particle “clumps” help to simulate the coarse nature of sand. In a simulation environment, multiple combined particles could be used to simulate the polygonal and granular nature of sand grains. Thus, a diversity of sand particles can be generated. The interaction between these particles can then be parallelized using GPU hardware. As such, this research will investigate different graphics and physics techniques and determine the tradeoffs in performance and visual quality for sand simulation. An enhanced sand model through the use of high performance computing and GPUs has great potential to impact research for both earth and space scientists. Interaction with JPL has provided an opportunity for us to refine our simulation techniques that can ultimately be used for their vehicle simulator. As an added benefit of this work, advancements in simulating sand can also benefit scientists here on earth, especially in regard to understanding landslides and debris flows.

  3. ADVANCED TECHNIQUES FOR RESERVOIR SIMULATION AND MODELING OF NONCONVENTIONAL WELLS

    SciTech Connect

    Louis J. Durlofsky; Khalid Aziz

    2004-08-20

    Nonconventional wells, which include horizontal, deviated, multilateral and ''smart'' wells, offer great potential for the efficient management of oil and gas reservoirs. These wells are able to contact larger regions of the reservoir than conventional wells and can also be used to target isolated hydrocarbon accumulations. The use of nonconventional wells instrumented with downhole inflow control devices allows for even greater flexibility in production. Because nonconventional wells can be very expensive to drill, complete and instrument, it is important to be able to optimize their deployment, which requires the accurate prediction of their performance. However, predictions of nonconventional well performance are often inaccurate. This is likely due to inadequacies in some of the reservoir engineering and reservoir simulation tools used to model and optimize nonconventional well performance. A number of new issues arise in the modeling and optimization of nonconventional wells. For example, the optimal use of downhole inflow control devices has not been addressed for practical problems. In addition, the impact of geological and engineering uncertainty (e.g., valve reliability) has not been previously considered. In order to model and optimize nonconventional wells in different settings, it is essential that the tools be implemented into a general reservoir simulator. This simulator must be sufficiently general and robust and must in addition be linked to a sophisticated well model. Our research under this five year project addressed all of the key areas indicated above. The overall project was divided into three main categories: (1) advanced reservoir simulation techniques for modeling nonconventional wells; (2) improved techniques for computing well productivity (for use in reservoir engineering calculations) and for coupling the well to the simulator (which includes the accurate calculation of well index and the modeling of multiphase flow in the wellbore); and (3) accurate approaches to account for the effects of reservoir heterogeneity and for the optimization of nonconventional well deployment. An overview of our progress in each of these main areas is as follows. A general purpose object-oriented research simulator (GPRS) was developed under this project. The GPRS code is managed using modern software management techniques and has been deployed to many companies and research institutions. The simulator includes general black-oil and compositional modeling modules. The formulation is general in that it allows for the selection of a wide variety of primary and secondary variables and accommodates varying degrees of solution implicitness. Specifically, we developed and implemented an IMPSAT procedure (implicit in pressure and saturation, explicit in all other variables) for compositional modeling as well as an adaptive implicit procedure. Both of these capabilities allow for efficiency gains through selective implicitness. The code treats cell connections through a general connection list, which allows it to accommodate both structured and unstructured grids. The GPRS code was written to be easily extendable so new modeling techniques can be readily incorporated. Along these lines, we developed a new dual porosity module compatible with the GPRS framework, as well as a new discrete fracture model applicable for fractured or faulted reservoirs. Both of these methods display substantial advantages over previous implementations. Further, we assessed the performance of different preconditioners in an attempt to improve the efficiency of the linear solver. As a result of this investigation, substantial improvements in solver performance were achieved.

  4. Weldability and joining techniques for advanced fossil energy system alloys

    SciTech Connect

    Lundin, C.D.; Qiao, C.Y.P.; Liu, W.; Yang, D.; Zhou, G.; Morrison, M.

    1998-05-01

    The efforts represent the concerns for the basic understanding of the weldability and fabricability of the advanced high temperature alloys so necessary to affect increases in the efficiency of the next generation Fossil Energy Power Plants. The effort was divided into three tasks with the first effort dealing with the welding and fabrication behavior of 310HCbN (HR3C), the second task details the studies aimed at understanding the weldability of a newly developed 310TaN high temperature stainless (a modification of 310 stainless) and Task 3 addressed the cladding of austenitic tubing with Iron-Aluminide using the GTAW process. Task 1 consisted of microstructural studies on 310HCbN and the development of a Tube Weldability test which has applications to production welding techniques as well as laboratory weldability assessments. In addition, the evaluation of ex-service 310HCbN which showed fireside erosion and cracking at the attachment weld locations was conducted. Task 2 addressed the behavior of the newly developed 310 TaN modification of standard 310 stainless steel and showed that the weldability was excellent and that the sensitization potential was minimal for normal welding and fabrication conditions. The microstructural evolution during elevated temperature testing was characterized and the second phase particles evolved upon aging were identified. Task 3 details the investigation undertaken to clad 310HCbN tubing with Iron Aluminide and developed welding conditions necessary to provide a crack free cladding. The work showed that both a preheat and a post-heat was necessary for crack free deposits and the effect of a third element on the cracking potential was defined together with the effect of the aluminum level for optimum weldability.

  5. The Evolution of Advanced Molecular Diagnostics for the Detection and Characterization of Mycoplasma pneumoniae.

    PubMed

    Diaz, Maureen H; Winchell, Jonas M

    2016-01-01

    Over the past decade there have been significant advancements in the methods used for detecting and characterizing Mycoplasma pneumoniae, a common cause of respiratory illness and community-acquired pneumonia worldwide. The repertoire of available molecular diagnostics has greatly expanded from nucleic acid amplification techniques (NAATs) that encompass a variety of chemistries used for detection, to more sophisticated characterizing methods such as multi-locus variable-number tandem-repeat analysis (MLVA), Multi-locus sequence typing (MLST), matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS), single nucleotide polymorphism typing, and numerous macrolide susceptibility profiling methods, among others. These many molecular-based approaches have been developed and employed to continually increase the level of discrimination and characterization in order to better understand the epidemiology and biology of M. pneumoniae. This review will summarize recent molecular techniques and procedures and lend perspective to how each has enhanced the current understanding of this organism and will emphasize how Next Generation Sequencing may serve as a resource for researchers to gain a more comprehensive understanding of the genomic complexities of this insidious pathogen. PMID:27014191

  6. The Evolution of Advanced Molecular Diagnostics for the Detection and Characterization of Mycoplasma pneumoniae

    PubMed Central

    Diaz, Maureen H.; Winchell, Jonas M.

    2016-01-01

    Over the past decade there have been significant advancements in the methods used for detecting and characterizing Mycoplasma pneumoniae, a common cause of respiratory illness and community-acquired pneumonia worldwide. The repertoire of available molecular diagnostics has greatly expanded from nucleic acid amplification techniques (NAATs) that encompass a variety of chemistries used for detection, to more sophisticated characterizing methods such as multi-locus variable-number tandem-repeat analysis (MLVA), Multi-locus sequence typing (MLST), matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF MS), single nucleotide polymorphism typing, and numerous macrolide susceptibility profiling methods, among others. These many molecular-based approaches have been developed and employed to continually increase the level of discrimination and characterization in order to better understand the epidemiology and biology of M. pneumoniae. This review will summarize recent molecular techniques and procedures and lend perspective to how each has enhanced the current understanding of this organism and will emphasize how Next Generation Sequencing may serve as a resource for researchers to gain a more comprehensive understanding of the genomic complexities of this insidious pathogen. PMID:27014191

  7. Investigation of joining techniques for advanced austenitic alloys

    SciTech Connect

    Lundin, C.D.; Qiao, C.Y.P.; Kikuchi, Y.; Shi, C.; Gill, T.P.S.

    1991-05-01

    Modified Alloys 316 and 800H, designed for high temperature service, have been developed at Oak Ridge National Laboratory. Assessment of the weldability of the advanced austenitic alloys has been conducted at the University of Tennessee. Four aspects of weldability of the advanced austenitic alloys were included in the investigation.

  8. 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

  9. Development of efficient molecular simulation techniques for engineering applications

    NASA Astrophysics Data System (ADS)

    Subramaniyan, Arun Karthi

    Engineering Molecular Mechanics (EMM) was developed as an alternative to conventional molecular simulation techniques to model high temperature (T > 0 K) phenomena. The EMM methodology was developed using thermal expansion and thermal energy as key thermal properties. Temperature dependent interatomic potentials were developed to account for thermal effects. Lennard-Jones and Morse potentials were used to build temperature dependent potentials. The validity and effectiveness of EMM simulations were demonstrated by simulating temperature dependent properties such as thermal expansion, elastic constants and thermal stress in copper and nickel. EMM simulations were significantly faster than molecular dynamics (MD) simulations for the same accuracy. A controversy regarding the definition of stress in an atomic system was resolved. Using theoretical arguments and numerical examples, the equivalence of virial stress and Cauchy stress was proved. It was shown that neglecting the velocity term in the definition of virial stress (as suggested by some researchers) can cause significant errors in MD simulations at high temperatures. The nanoscale instabilities during phase transformation in Ni-Al shape memory alloys were studied using MD and EMM simulations. The phase transformation temperatures predicted by MD simulations agreed well with experiments. Some limitations of the EMM methodology and the minimization algorithm were discussed. The possibility of nanoscale material design of Ni-Al shape memory alloys was investigated. It was found that the distribution of nickel and aluminum atoms in the alloy can affect the phase transformation characteristics significantly. A new design criterion based on thermal expansion mismatch was introduced. The predicted results using the new criterion matched well with the phase transformation temperature and strain calculated using MD simulations. The new one parameter design criterion was shown to be effective for designing Ni-Al shape memory alloys.

  10. 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. PMID:26116421

  11. Integrating advanced materials simulation techniques into an automated data analysis workflow at the Spallation Neutron Source

    SciTech Connect

    Borreguero Calvo, Jose M; Campbell, Stuart I; Delaire, Olivier A; Doucet, Mathieu; Goswami, Monojoy; Hagen, Mark E; Lynch, Vickie E; Proffen, Thomas E; Ren, Shelly; Savici, Andrei T; Sumpter, Bobby G

    2014-01-01

    This presentation will review developments on the integration of advanced modeling and simulation techniques into the analysis step of experimental data obtained at the Spallation Neutron Source. A workflow framework for the purpose of refining molecular mechanics force-fields against quasi-elastic neutron scattering data is presented. The workflow combines software components to submit model simulations to remote high performance computers, a message broker interface for communications between the optimizer engine and the simulation production step, and tools to convolve the simulated data with the experimental resolution. A test application shows the correction to a popular fixed-charge water model in order to account polarization effects due to the presence of solvated ions. Future enhancements to the refinement workflow are discussed. This work is funded through the DOE Center for Accelerating Materials Modeling.

  12. 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

  13. Simple technique for sequential q-switching of molecular lasers.

    PubMed

    Lucht, R A; Allario, F; Jarrett, O

    1972-07-01

    A simple technique for sequentially Q-switching molecular lasers (e.g., CO(2), CO, HF) is discussed in which an optical scanner is used as an optical folding element in a laser cavity consisting of a stationary diffraction grating and partially reflecting mirror. Sequential Q-swtiching of a conventional CO(2) laser is demonstrated in which over sixty-two transitions between 9.2 micro and 10.8 micro are observed. Rapid repetition rates (200 Hz) and narrow laser pulses (<5 microsec) allow conventional signal processing techniques to be used with this multi-wavelength laser source which is a versatile tool for laser propagation studies, absorption spectroscopy, and gain measurements. Results of a preliminary experiment demonstrating the utility of measuring selective absorption of CO(2) laser wavelengths by C(2)H(4) is shown, but selective absorption by atmospheric CO(2), NH(3), and O(3) can also be studied. With appropriate optical sca ners and diffraction gratings, sequential Q-switching of CO and HF lasers is possible. PMID:20119187

  14. Advances in the integration of optical and mass spectrometry molecular imaging technologies: from omics data to molecular signature discovery.

    PubMed

    Belizrio, Jos E; Sangiuliano, Beatriz A; Perez-Sosa, Marcela; Santos, Beatriz V; Machado-Santelli, Glucia

    2015-12-01

    Many molecular mechanisms in complex biological processes of diseases cannot be fully understood without direct visualization. In the last decades, advances in imaging principles and technologies have expanded our ability to capture and analyze the morphology of tissues and cells' components on conventional widefield optical and fluorescence microscopies and their derivatives confocal and multiphoton fluorescence laser-scanning microscopes, as well as transmission electron microscopes. Innovative imaging technologies are now emerging for constructing fine structural features, precise localization and the dynamic interplay of single and macromolecular assemblies that drive cell growth, differentiation and cell death as well as stromal and chromatin remodeling within many cellular context. The newer super-resolution microscopies capture images with unprecedented sensitivity and clarity allowing the exploration of interactions between individual molecules with a distance resolution as low as 20 nm. But these techniques are not robust enough to quantitate molecules on a genome-wide scale. Mass spectrometry imaging is a high-throughput chemical imaging technique for the identification, quantitation and distribution of proteins, lipids and chemical metabolites at picomol level within a single-cell and complex multicellular tissue. Here we provide an overview on imaging instrumentations and computational platforms to store, data mining, analyze and retrieving genomic, proteomic and immunohistochemistry digital image information which are available for multilevel academic-private collaborations. The expansion of these data sets will lead to a merge picture from it we will retrieve knowledge for more rational-design systems to basic and clinical research in near future. PMID:26760983

  15. Techniques in molecular spectroscopy: from broad bandwidth to high resolution

    NASA Astrophysics Data System (ADS)

    Cossel, Kevin C.

    This thesis presents a range of different experiments all seeking to extended the capabilities of molecular spectroscopy and enable new applications. The new technique of cavity-enhanced direct frequency comb spectroscopy (CE-DFCS) provides a unique combination of broad bandwidth, high resolution, and high sensitivity that can be useful for a wide range of applications. Previous demonstrations of CE-DFCS were confined to the visible or near-infrared and operated over a limited bandwidth: for many applications it is desirable to increase the spectral coverage and to extend to the mid-infrared where strong, fundamental vibrational modes of molecules occur. There are several key requirements for CE-DFCS: a frequency comb source that provides broad bandwidth and high resolution, an optical cavity for high sensitivity, and a detection system capable of multiplex detection of the comb spectrum transmitted through the cavity. We first discuss comb sources with emphasis on the coherence properties of spectral broadening in nonlinear fiber and the development of a high-power frequency comb source in the mid-infrared based on an optical-parametric oscillator (OPO). To take advantage of this new mid-infrared comb source for spectroscopy, we also discuss the development of a rapid-scan Fourier-transform spectrometer (FTS). We then discuss the first demonstration of CE-DFCS with spectrally broadened light from a highly nonlinear fiber with the application to measurements of impurities in semiconductor manufacturing gases. We also cover our efforts towards extending CE-DFCS to the mid-infrared using the mid-infrared OPO and FTS to measure ppb levels of various gases important for breath analysis and atmospheric chemistry and highlight some future applications of this system. In addition to the study of neutral molecules, broad-bandwidth and high-resolution spectra of molecular ions are useful for astrochemistry where many of the observed molecules are ionic, for studying molecules such as CH5 + with highly non-classical behavior, and for tests of fundamental physics. We have developed a new technique---frequency comb velocity-modulation spectroscopy---that is the first system to enable rapid, broadband spectroscopy of molecular ions with high resolution. We have demonstrated the ability to record 150 cm-1 of spectra consisting of 45,000 points in 30 minutes and have used this system to record over 1000 cm-1 of spectra of HfF+ in the near-infrared around 800 nm. After improvements, the system can now cover more than 3250 cm-1 (700-900 nm). We have combined this with standard velocity-modulation spectroscopy to measure and analyze 19 ro-vibronic bands of HfF+. These measurements enabled precision spectroscopy of trapped HfF + for testing time-reversal symmetry. For this experiment, we perform Ramsey spectroscopy between spin states in the metastable 3Delta 1 level to look for a permanent electric dipole moment of the electron with what we believe is the narrowest line observed in a molecular system (Fourier limited with 500 ms of coherence time). The long coherence time is a major advantage of using ions, but there are also some added complexities. We discuss various aspects metastable state preparation, state detection, and spectroscopy in a rotating frame (due to the necessary rotating electric bias field) that were particular challenging. In addition, we discuss limits to the coherence time---in particular, ion-ion collisions---as well as the sensitivity of the current measurements and provide a path towards a new limit on the electric dipole moment of the electron.

  16. Visualizing epigenetics: current advances and advantages in HDAC PET imaging techniques

    PubMed Central

    Wang, Changning; Schroeder, Frederick A.; Hooker, Jacob M.

    2013-01-01

    Abnormal gene regulation as a consequence of flawed epigenetic mechanisms may be central to the initiation and persistence of many human diseases. However, the association of epigenetic dysfunction with disease and the development of therapeutic agents for treatment are slow. Developing new methodologies used to visualize chromatin modifying enzymes and their function in the human brain would be valuable for diagnosis of brain disorders and drug discovery. We provide an overview of current invasive and noninvasive techniques for measuring expression and functions of chromatin modifying enzymes in the brain, emphasizing tools applicable to histone deacetylase (HDAC) enzymes as a leading example. The majority of current techniques are invasive and difficult to translate to what is happening within a human brain in vivo. However, recent progress in molecular imaging provides new, noninvasive ways to visualize epigenetics in human brain. Neuroimaging tool development presents a unique set of challenges in order to identify and validate CNS radiotracers for HDACs and other histone modifying enzymes. We summarize advances in the effort to image HDACs and HDAC inhibitory effects in the brain using PET and highlight generalizable techniques that can be adapted to investigate other specific components of epigenetic machinery. Translational tools like neuroimaging by PET and MRI provide the best way to link our current understanding of epigenetic changes with in vivo function in normal and diseased brain. These tools will be a critical addition to ex vivo methods to evaluate - and intervene - in CNS dysfunction. PMID:24051365

  17. Advanced Millimeter-Wave Security Portal Imaging Techniques

    SciTech Connect

    Sheen, David M.; Bernacki, Bruce E.; McMakin, Douglas L.

    2012-04-01

    Millimeter-wave imaging is rapidly gaining acceptance for passenger screening at airports and other secured facilities. This paper details a number of techniques developed over the last several years including novel image reconstruction and display techniques, polarimetric imaging techniques, array switching schemes, as well as high frequency high bandwidth techniques. Implementation of some of these methods will increase the cost and complexity of the mm-wave security portal imaging systems. RF photonic methods may provide new solutions to the design and development of the sequentially switched linear mm-wave arrays that are the key element in the mm-wave portal imaging systems.

  18. How Molecular Structure Affects Mechanical Properties of an Advanced Polymer

    NASA Technical Reports Server (NTRS)

    Nicholson, Lee M.; Whitley, Karen S.; Gates, Thomas S.; Hinkley, Jeffrey A.

    2000-01-01

    density was performed over a range of temperatures below the glass transition temperature. The physical characterization, elastic properties and notched tensile strength all as a function of molecular weight and test temperature were determined. For the uncrosslinked SI material, it was shown that notched tensile strength is a strong function of both temperature and molecular weight, whereas stiffness is only a strong function of temperature. For the crosslinked PETI-SI material, it was shown that the effect of crosslinking significantly enhances the mechanical performance of the low molecular weight material; comparable to that exhibited by the high molecular weight material.

  19. 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

  20. Advanced Characterization of Molecular Interactions in TALSPEAK-like Separations Systems

    SciTech Connect

    Nash, Kenneth; Guelis, Artem; Lumetta, Gregg J.; Sinkov, Sergey

    2015-10-21

    Combining unit operations in advanced aqueous reprocessing schemes brings obvious process compactness advantages, but at the same time greater complexity in process design and operation. Unraveling these interactions requires increasingly sophisticated analytical tools and unique approaches for adequate analysis and characterization that probe molecular scale interactions. Conventional slope analysis methods of solvent extraction are too indirect to provide much insight into such interactions. This project proposed the development and verification of several analytical tools based on studies of TALSPEAK-like aqueous processes. As such, the chemistry of trivalent fission product lanthanides, americium, curium, plutonium, neptunium and uranium figure prominently in these studies. As the project was executed, the primary focus fell upon the chemistry or trivalent lanthanides and actinides. The intent of the investigation was to compare and contrast the results from these various complementary techniques/studies to provide a stronger basis for predicting the performance of extractant/diluent mixtures as media for metal ion separations. As many/most of these techniques require the presence of metal ions at elevated concentrations, it was expected that these studies would take this investigation into the realm of patterns of supramolecular organization of metal complexes and extractants in concentrated aqueous/organic media. We expected to advance knowledge of the processes that enable and limit solvent extraction reactions as a result of the application of fundamental chemical principles to explaining interactions in complex media.

  1. Recent advances in microscopic techniques for visualizing leukocytes in vivo

    PubMed Central

    Jain, Rohit; Tikoo, Shweta; Weninger, Wolfgang

    2016-01-01

    Leukocytes are inherently motile and interactive cells. Recent advances in intravital microscopy approaches have enabled a new vista of their behavior within intact tissues in real time. This brief review summarizes the developments enabling the tracking of immune responses in vivo.

  2. Recent advances in microscopic techniques for visualizing leukocytes in vivo.

    PubMed

    Jain, Rohit; Tikoo, Shweta; Weninger, Wolfgang

    2016-01-01

    Leukocytes are inherently motile and interactive cells. Recent advances in intravital microscopy approaches have enabled a new vista of their behavior within intact tissues in real time. This brief review summarizes the developments enabling the tracking of immune responses in vivo. PMID:27239292

  3. Bricklaying Curriculum: Advanced Bricklaying Techniques. Instructional Materials. Revised.

    ERIC Educational Resources Information Center

    Turcotte, Raymond J.; Hendrix, Laborn J.

    This curriculum guide is designed to assist bricklaying instructors in providing performance-based instruction in advanced bricklaying. Included in the first section of the guide are units on customized or architectural masonry units; glass block; sills, lintels, and copings; and control (expansion) joints. The next two units deal with cut,…

  4. Advanced NDE techniques for quantitative characterization of aircraft

    NASA Technical Reports Server (NTRS)

    Heyman, Joseph S.; Winfree, William P.

    1990-01-01

    Recent advances in nondestructive evaluation (NDE) at NASA Langley Research Center and their applications that have resulted in quantitative assessment of material properties based on thermal and ultrasonic measurements are reviewed. Specific applications include ultrasonic determination of bolt tension, ultrasonic and thermal characterization of bonded layered structures, characterization of composite materials, and disbonds in aircraft skins.

  5. Investigation of PACVD protective coating processes using advanced diagnostics techniques

    SciTech Connect

    Roman, W.C.

    1993-05-07

    Objective is to understand the mechanisms governing nonequilibrium plasma atomistic or molecular deposition of hard face coatings. Laser diagnostic methods include coherent anti-Stokes Raman spectroscopy (CARS) and laser-induced fluorescence. TiB[sub 2] and diamonds were used as the hard face coating materials. Diborane was used as precursor to TiB[sub 2].

  6. The advancing clinical impact of molecular imaging in CVD.

    PubMed

    Osborn, Eric A; Jaffer, Farouc A

    2013-12-01

    Molecular imaging seeks to unravel critical molecular and cellular events in living subjects by providing complementary biological information to current structural clinical imaging modalities. In recent years, molecular imaging efforts have marched forward into the clinical cardiovascular arena, and are now actively illuminating new biology in a broad range of conditions, including atherosclerosis, myocardial infarction, thrombosis, vasculitis, aneurysm, cardiomyopathy, and valvular disease. Development of novel molecular imaging reporters is occurring for many clinical cardiovascular imaging modalities (positron emission tomography, single-photon emission computed tomography, magnetic resonance imaging), as well as in translational platforms such as intravascular fluorescence imaging. The ability to image, track, and quantify molecular biomarkers in organs not routinely amenable to biopsy (e.g., the heart and vasculature) open new clinical opportunities to tailor therapeutics based on a cardiovascular disease molecular profile. In addition, molecular imaging is playing an increasing role in atherosclerosis drug development in phase II clinical trials. Here, we present state-of-the-art clinical cardiovascular molecular imaging strategies, and explore promising translational approaches positioned for clinical testing in the near term. PMID:24332285

  7. The Advancing Clinical Impact of Molecular Imaging in Cardiovascular Disease

    PubMed Central

    Osborn, Eric A; Jaffer, Farouc A

    2013-01-01

    Molecular imaging seeks to unravel critical molecular and cellular events in living subjects by providing complementary biological information to current structural clinical imaging modalities. In recent years, molecular imaging efforts have marched forward into the clinical cardiovascular arena, and are now actively illuminating new biology in a broad range of conditions, including atherosclerosis, myocardial infarction, thrombosis, vasculitis, aneurysm, cardiomyopathy, and valvular disease. Development of novel molecular imaging reporters is occurring for many clinical cardiovascular imaging modalities (PET, SPECT, MRI), as well in translational platforms such as intravascular fluorescence imaging. The ability to image, track, and quantify molecular biomarkers in organs not routinely amenable to biopsy (e.g. the heart and vasculature) open new clinical opportunities to tailor therapeutics based on a cardiovascular disease molecular profile. In addition, molecular imaging is playing an increasing role in atherosclerosis drug development in Phase II clinical trials. Here we present state-of-the-art clinical cardiovascular molecular imaging strategies, and explore promising translational approaches positioned for clinical testing in the near term. PMID:24332285

  8. 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 ?-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. PMID:24369423

  9. Clinical application of high throughput molecular screening techniques for pharmacogenomics

    PubMed Central

    Wiita, Arun P; Schrijver, Iris

    2011-01-01

    Genetic analysis is one of the fastest-growing areas of clinical diagnostics. Fortunately, as our knowledge of clinically relevant genetic variants rapidly expands, so does our ability to detect these variants in patient samples. Increasing demand for genetic information may necessitate the use of high throughput diagnostic methods as part of clinically validated testing. Here we provide a general overview of our current and near-future abilities to perform large-scale genetic testing in the clinical laboratory. First we review in detail molecular methods used for high throughput mutation detection, including techniques able to monitor thousands of genetic variants for a single patient or to genotype a single genetic variant for thousands of patients simultaneously. These methods are analyzed in the context of pharmacogenomic testing in the clinical laboratories, with a focus on tests that are currently validated as well as those that hold strong promise for widespread clinical application in the near future. We further discuss the unique economic and clinical challenges posed by pharmacogenomic markers. Our ability to detect genetic variants frequently outstrips our ability to accurately interpret them in a clinical context, carrying implications both for test development and introduction into patient management algorithms. These complexities must be taken into account prior to the introduction of any pharmacogenomic biomarker into routine clinical testing. PMID:23226057

  10. 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.

  11. Optimization techniques for parallel molecular dynamics using domain decomposition

    NASA Astrophysics Data System (ADS)

    Pütz, M.; Kolb, A.

    1998-10-01

    In this paper we describe the implementation of a new parallelized Molecular Dynamics code for many-particle problems with short-ranged interactions. While the basic algorithms have their foundation in the fairly standard methods of domain decomposition, linked-cell pair search and Verlet pair list, we have developed some refined techniques for optimizing them. The rewards of these optimizations are a up to 45% overall improvement in the scalar performance and very good scaling behavior in the number of processors even down to a few hundred particles per processor on a CRAY T3E. The best speedup can be obtained for systems with pair forces only since then the data structures can be organized in a very simple manner. To deal with more complex situations as well, we have developed a partial replicated data scheme which is suitable to simulate many molecules consisting of many simple particles (e.g. polymer chains) for many types of short-range interactions.

  12. [Molecular techniques applied in species identification of Toxocara].

    PubMed

    Fogt, Renata

    2006-01-01

    Toxocarosis is still an important and actual problem in human medicine. It can manifest as visceral (VLM), ocular (OLM) or covert (CT) larva migrans syndroms. Complicated life cycle of Toxocara, lack of easy and practical methods of species differentiation of the adult nematode and embarrassing in recognition of the infection in definitive hosts create difficulties in fighting with the infection. Although studies on human toxocarosis have been continued for over 50 years there is no conclusive answer, which of species--T. canis or T. cati constitutes a greater risk of transmission of the nematode to man. Neither blood serological examinations nor microscopic observations of the morphological features of the nematode give the satisfied answer on the question. Since the 90-ths molecular methods were developed for species identification and became useful tools being widely applied in parasitological diagnosis. This paper cover the survey of methods of DNA analyses used for identification of Toxocara species. The review may be helpful for researchers focused on Toxocara and toxocarosis as well as on detection of new species. The following techniques are described: PCR (Polymerase Chain Reaction), RFLP (Restriction Fragment Length Polymorphism), RAPD (Random Amplified Polymorphic DNA) and SSCP (Single Strand Conformation Polymorphism). PMID:17007334

  13. Advances in pituitary pathology: use of novel techniques.

    PubMed

    Lloyd, Ricardo V

    2004-01-01

    Many new techniques are rapidly being developed and applied to the study of normal and neoplastic pituitary tissues. These range from techniques used for the past few decades such as in situ hybridization to more recent developments such as comparative genomic hybridization, laser capture microdissection, DNA and tissue arrays, proteomics, and RNA interference technology. These approaches have been applied to answer many challenging questions about pituitary function and pathophysiology. This chapter reviews many of these recent developments and shows their applications to pituitary biology in order to demonstrate how these new techniques are providing insights about basic aspects, clinical, and pharmacologic knowledge of the pituitary gland and of pituitary tumors. PMID:15281345

  14. Backscattered Electron Microscopy as an Advanced Technique in Petrography.

    ERIC Educational Resources Information Center

    Krinsley, David Henry; Manley, Curtis Robert

    1989-01-01

    Three uses of this method with sandstone, desert varnish, and granite weathering are described. Background information on this technique is provided. Advantages of this type of microscopy are stressed. (CW)

  15. Advanced millimeter-wave security portal imaging techniques

    NASA Astrophysics Data System (ADS)

    Sheen, David M.; Bernacki, Bruce E.; McMakin, Douglas L.

    2012-03-01

    Millimeter-wave (mm-wave) imaging is rapidly gaining acceptance as a security tool to augment conventional metal detectors and baggage x-ray systems for passenger screening at airports and other secured facilities. This acceptance indicates that the technology has matured; however, many potential improvements can yet be realized. The authors have developed a number of techniques over the last several years including novel image reconstruction and display techniques, polarimetric imaging techniques, array switching schemes, and high-frequency high-bandwidth techniques. All of these may improve the performance of new systems; however, some of these techniques will increase the cost and complexity of the mm-wave security portal imaging systems. Reducing this cost may require the development of novel array designs. In particular, RF photonic methods may provide new solutions to the design and development of the sequentially switched linear mm-wave arrays that are the key element in the mm-wave portal imaging systems. Highfrequency, high-bandwidth designs are difficult to achieve with conventional mm-wave electronic devices, and RF photonic devices may be a practical alternative. In this paper, the mm-wave imaging techniques developed at PNNL are reviewed and the potential for implementing RF photonic mm-wave array designs is explored.

  16. New molecularly targeted therapies against advanced hepatocellular carcinoma: From molecular pathogenesis to clinical trials and future directions.

    PubMed

    Chuma, Makoto; Terashita, Katsumi; Sakamoto, Naoya

    2015-10-01

    Hepatocellular carcinoma (HCC) can be lethal due to its aggressive course and lack of effective systemic therapies for advanced disease. Sorafenib is the only systemic therapy that has demonstrated an overall survival benefit in patients with advanced HCC, and new agents for treatment of advanced HCC are needed. The multiple pathways involved in HCC oncogenesis, proliferation and survival provide many opportunities for the development of molecularly targeted therapies. Molecular targets of interest have expanded from angiogenesis to cancer cell-directed oncogenic signaling pathways for treatment of advanced HCC. Agents targeting vascular endothelial growth factor receptor, epidermal growth factor receptor, fibroblast growth factor receptor, platelet-derived growth factor receptor, c-mesenchymal-epithelial transition factor-1 and mammalian target of rapamycin signaling have been actively explored. This article focuses on the evaluation of molecular agents targeting pathogenic HCC and provides a review of recently completed phase III drug studies (e.g. involving sorafenib, sunitinib, brivanib, linifanib, erlotinib, everolimus, ramucirumab or orantinib) and ongoing drug studies (e.g. involving lenvatinib, regorafenib, tivantinib or cabozantinib) of molecularly targeted agents in advanced HCC, including a brief description of the biologic rationale behind these agents. PMID:25472913

  17. 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

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

    PubMed

    Badial, Peres R; Tallmadge, Rebecca L; Miller, Steven; Stokol, Tracy; Richards, Kristy; Borges, Alexandre S; Felippe, M Julia B

    2015-11-01

    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

  19. [Advances in molecular targeted therapy of thyroid carcinoma].

    PubMed

    Feng, Huihao; Cheng, Xiaoming; Zeng, Feng

    2015-12-01

    Thyroid carcinoma is the most common endocrine maligancy, and the worldwide incidence has been rising in recent years. Differentiated thyroid carcinoma is the most common thyroid malignancy, which include thyroid papillary carcinoma and follicular thyroid carcinoma, accounting for about 90 percent of thyroid carcinoma incidence. Currently, surgical treatment, iodine radiotherapy and TSH suppressive therapy are the commonly accepted effective treatments for differentiated thyroid carcinoma, and most patients can be cured. But there are still some patients not sensitive to the general treatments, who have lost the treatment of opportunity. Molecular targeted therapy is an agonistic or suppressive treatment for molecular biology targets of malignant tumor, and currently is a frontier research in the field of malignancy treatment. By retrieving and analyzing the related literature of molecular targeted therapy of thyroid carcinoma through PUBMED in the past 5 years, the article introduced the current status of molecular targeted therapy of thyroid carcinoma. PMID:27093829

  20. Advances in directed molecular evolution of reporter genes.

    PubMed

    Xiong, Ai-Sheng; Peng, Ri-He; Zhuang, Jing; Davies, Jim; Zhang, Jian; Yao, Quan-Hong

    2012-06-01

    Many reporter genes, such as gfp, gusA, and lacZ, are widely used for research into plants, animals, and microorganisms. Reporter genes, which offer high levels of sensitivity and convenience of detection, have been utilized in transgenic technology, promoter analysis, drug screening, and other areas. Directed molecular evolution is a powerful molecular tool for the creation of designer proteins for industrial and research applications, including studies of protein structure and function. Directed molecular evolution is based mainly on in vitro recombination methods, such as error-prone PCR and DNA shuffling. The strategies of directed evolution of enzyme biocatalysts have been the subject of several recent reviews. Here, we briefly summarize successes in the field of directed molecular evolution of reporter genes and discuss some of the applications. PMID:21774740

  1. Advances in genetics. Volume 22: Molecular genetics of plants

    SciTech Connect

    Scandalios, J.G.; Caspari, E.W.

    1984-01-01

    This book contains the following four chapters: Structural Variation in Mitochondrial DNA; The Structure and Expression of Nuclear Genes in Higher Plants; Chromatin Structure and Gene Regulation in Higher Plants; and The Molecular Genetics of Crown Gall Tumorigenesis.

  2. Artificial nanomachines based on interlocked molecular species: recent advances.

    PubMed

    Balzani, Vincenzo; Credi, Alberto; Silvi, Serena; Venturi, Margherita

    2006-11-01

    The bottom-up construction and operation of nanoscale machines and motors, that is, supramolecular systems wherein the molecular components can be set in motion in a controlled manner for ultimately accomplishing a function, is a topic of great interest in nanoscience and a fascinating challenge of nanotechnology. The field of artificial molecular machines and motors is growing at an astonishing rate and is attracting a great deal of interest. Research in the last decade has shown that species made of interlocked molecular components like rotaxanes, catenanes and related systems are most attractive candidates. In recent times, the evolution of the structural and functional design of such systems has led to the construction and operation of complex molecular machines that, in some cases, are able to do specific tasks. This tutorial review is intended to discuss the design principles for nanomachines based on interlocked molecules, and to provide a timely overview on representative prototype systems. PMID:17057842

  3. [Advance in molecular genetic research on primary congenital glaucoma].

    PubMed

    Li, Xiulan; Liu, Haotian; Zhang, Dingding

    2016-04-01

    Primary congenital glaucoma (PCG) is one of the major diseases causing blindness in children, but its pathogenesis has remained unclear. Genetic factors play an important role in the pathogenesis of PCG. Molecular genetics of candidate genes such as CYP1B1, MYOC, LTBP2 and FOXC1 has so far been explored, but no disease-causing gene has been identified. Molecular genetic research on PCG including candidate gene screening and research strategies are reviewed here. PMID:27060330

  4. Molecular behavior study in mediated biosensing technique and nanotechnology research

    NASA Astrophysics Data System (ADS)

    Dang, Bachlien Thi

    Phenothiazines have been considered as very promising artificial redox mediators in the development of reagent-less electrochemical biosensors. Due to the intrinsic low redox potentials of phenothiazines (approximately -0.20 V vs. Ag/AgCl), the new biosensors are expected to possess many technical advantages: highly selective, completely oxygen-independent, and suitable for a broad range of in-vivo and in-vitro applications. However, although various approaches have been attempted in order to immobilize the mediator molecules and the glucose oxidase enzyme in chitosan polymer matrix, poor stability of the resulting biosensors has always been a major technical drawback, while the cause of this problem is unclear. In this work, we will try to find out the answer through a systematic study using cyclovoltammetry and UV/Vis spectroscopy. Carbon nanotubes (CNTs), when decorated with certain metals, have exhibited exciting properties that rival state-of-the-art materials used in fuel cells, sensors, reinforced composites, electromagnetic interference shielding applications, and fabrication of sophisticated nanostructures. Further explorations in these areas strongly demand significant advances in mass-production of the metal/CNT composites. Among the existing metallization techniques, physisorption involves separate preparation for metal particulates and takes a long sonication process to mix with CNTs, where dislodging of the metal particulates is often observed due to the loose attachment. Electroless deposition usually requires a harsh oxidative pretreatment followed by a complex activation-sensitization procedure, which is disruptive to the intrinsic CNT structure and properties. On the contrary, electrochemical deposition is of particular interest due to its simplicity and manageability, although it was challenging to make reliable electrical contact with bulk CNT samples via previous approaches, such as in-situ CNT growth on a conducting template, microlithography, electrophoresis, sputtering and thermal evaporation, all of which are too complicated or expensive to be scaled up in industrial level manufacturing. We will develop a superb platform, where metal nanostructures, varying from dense and uniformly distributed atom clusters (approximately 1nm in diameter) to continuous ultra-thin coatings with variable surface morphologies, can be electro-deposited on CNTs promptly. This unique technique should be facile, versatile, scalable, inexpensive, and non-disruptive to CNT structures. We also plan to study the effects of CNTs on the curing process of epoxy resin-based composites and comprehensively characterize the metallized CNT-filled epoxy composites.

  5. Nondestructive Evaluation of Thick Concrete Using Advanced Signal Processing Techniques

    SciTech Connect

    Clayton, Dwight A; Barker, Alan M; Santos-Villalobos, Hector J; Albright, Austin P; Hoegh, Kyle; Khazanovich, Lev

    2015-09-01

    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 [1]. Since many important safety structures in an NPP are constructed of concrete, inspection techniques must be developed and tested to evaluate the internal condition. In-service containment structures generally do not allow for the destructive measures necessary to validate the accuracy of these inspection techniques. This creates a need for comparative testing of the various nondestructive evaluation (NDE) measurement techniques on concrete specimens with known material properties, voids, internal microstructure flaws, and reinforcement locations.

  6. Advances in enantioselective separations using electromigration capillary techniques.

    PubMed

    Preinerstorfer, Beatrix; Lämmerhofer, Michael; Lindner, Wolfgang

    2009-01-01

    The most recent literature dealing with enantioselective separations and stereoselective analyses of chiral entities including especially pharmaceuticals, phytochemicals, biochemicals, agrochemicals, fine chemicals and specific test compounds by electromigration techniques such as CE, MEKC, MEEKC, CEC and microchip CE is reviewed. The review covers literature from 2007 until mid-2008, i.e. studies that were published after the appearance of the latest review article on that topic in Electrophoresis by Gübitz and Schmid (see Electrophoresis 2007, 28, 114). Particular attention is given to the description of new chiral selector systems, studies on separation mechanisms and applications in the above-specified electromigration techniques. PMID:19107703

  7. Application of advanced coating techniques to rocket engine components

    NASA Technical Reports Server (NTRS)

    Verma, S. K.

    1988-01-01

    The materials problem in the space shuttle main engine (SSME) is reviewed. Potential coatings and the method of their application for improved life of SSME components are discussed. A number of advanced coatings for turbine blade components and disks are being developed and tested in a multispecimen thermal fatigue fluidized bed facility at IIT Research Institute. This facility is capable of producing severe strains of the degree present in blades and disk components of the SSME. The potential coating systems and current efforts at IITRI being taken for life extension of the SSME components are summarized.

  8. Transcranial Doppler: Techniques and advanced applications: Part 2

    PubMed Central

    Sharma, Arvind K.; Bathala, Lokesh; Batra, Amit; Mehndiratta, Man Mohan; Sharma, Vijay K.

    2016-01-01

    Transcranial Doppler (TCD) is the only diagnostic tool that can provide continuous information about cerebral hemodynamics in real time and over extended periods. In the previous paper (Part 1), we have already presented the basic ultrasound physics pertaining to TCD, insonation methods, and various flow patterns. This article describes various advanced applications of TCD such as detection of right-to-left shunt, emboli monitoring, vasomotor reactivity (VMR), monitoring of vasospasm in subarachnoid hemorrhage (SAH), monitoring of intracranial pressure, its role in stoke prevention in sickle cell disease, and as a supplementary test for confirmation of brain death. PMID:27011639

  9. Development of Advanced In-Situ Techniques for Chemistry Monitoring and Corrosion Mitigation in SCWO Environments

    SciTech Connect

    Macdonald, D. D.; Lvov, S. N.

    2000-03-31

    This project is developing sensing technologies and corrosion monitoring techniques for use in super critical water oxidation (SCWO) systems to reduce the volume of mixed low-level nuclear waste by oxidizing organic components in a closed cycle system where CO2 and other gaseous oxides are produced, leaving the radioactive elements concentrated in ash. The technique uses water at supercritical temperatures under highly oxidized conditions by maintaining a high fugacity of molecular oxygen in the system, which causes high corrosion rates of even the most corrosive resistant reactor materials. This project significantly addresses the high corrosion shortcoming through development of (a) advanced electrodes and sensors for in situ potentiometric monitoring of pH in high subcritical and supercritical aqueous solutions, (b) an approach for evaluating the association constants for 1-1 aqueous electrolytes using a flow-through electrochemical thermocell; (c) an electrochemical noise sensor for the in situ measurement of corrosion rate in subcritical and supercritical aqueous systems; (d) a model for estimating the effect of pressure on reaction rates, including corrosion reactions, in high subcritical and supercritical aqueous systems. The project achieved all objectives, except for installing some of the sensors into a fully operating SCWO system.

  10. Advancing the Frontiers in Nanocatalysis, Biointerfaces, and Renewable Energy Conversion by Innovations of Surface Techniques

    SciTech Connect

    Somorjai, G.A.; Frei, H.; Park, J.Y.

    2009-07-23

    The challenge of chemistry in the 21st century is to achieve 100% selectivity of the desired product molecule in multipath reactions ('green chemistry') and develop renewable energy based processes. Surface chemistry and catalysis play key roles in this enterprise. Development of in situ surface techniques such as high-pressure scanning tunneling microscopy, sum frequency generation (SFG) vibrational spectroscopy, time-resolved Fourier transform infrared methods, and ambient pressure X-ray photoelectron spectroscopy enabled the rapid advancement of three fields: nanocatalysts, biointerfaces, and renewable energy conversion chemistry. In materials nanoscience, synthetic methods have been developed to produce monodisperse metal and oxide nanoparticles (NPs) in the 0.8-10 nm range with controlled shape, oxidation states, and composition; these NPs can be used as selective catalysts since chemical selectivity appears to be dependent on all of these experimental parameters. New spectroscopic and microscopic techniques have been developed that operate under reaction conditions and reveal the dynamic change of molecular structure of catalysts and adsorbed molecules as the reactions proceed with changes in reaction intermediates, catalyst composition, and oxidation states. SFG vibrational spectroscopy detects amino acids, peptides, and proteins adsorbed at hydrophobic and hydrophilic interfaces and monitors the change of surface structure and interactions with coadsorbed water. Exothermic reactions and photons generate hot electrons in metal NPs that may be utilized in chemical energy conversion. The photosplitting of water and carbon dioxide, an important research direction in renewable energy conversion, is discussed.

  11. Advances in Direct Detection Doppler Lidar Technology and Techniques

    NASA Technical Reports Server (NTRS)

    Gentry, Bruce; Einaudi, Franco (Technical Monitor)

    2001-01-01

    In this paper we will describe the ground based Doppler lidar system which is mounted in a modified delivery van to allow field deployment and operations. The system includes an aerosol double edge receiver optimized for aerosol backscatter Doppler measurements at 1064 nm and a molecular double edge receiver which operates at 355 nm. The lidar system will be described including details of the injection seeded diode pumped laser transmitter and the piezoelectrically tunable high spectral resolution Fabry Perot etalon which is used to measure the Doppler shift. Examples of tropospheric wind profiles obtained with the system will also be presented to demonstrate its capabilities.

  12. A Coupled Meshless Technique/Molecular Dynamics Approach for Deformation Characterization of Mono-crystalline Metal

    SciTech Connect

    Gu, Y. T.; Yarlagadda, Prasad K. D. V.

    2010-05-21

    This paper presents a multiscale study using the coupled Meshless technique/Molecular Dynamics (M{sup 2}) for exploring the deformation mechanism of mono-crystalline metal (focus on copper) under uniaxial tension. In M{sup 2}, an advanced transition algorithm using transition particles is employed to ensure the compatibility of both displacements and their gradients, and an effective local quasi-continuum approach is also applied to obtain the equivalent continuum strain energy density based on the atomistic potentials and Cauchy-Born rule. The key parameters used in M{sup 2} are firstly investigated using a benchmark problem. Then, M{sup 2} is applied to the multiscale simulation for a mono-crystalline copper bar. It has found that the mono-crystalline copper has very good elongation property, and the ultimate strength and Young's modulus are much higher than those obtained in macro-scale.

  13. Benefits of advanced software techniques for mission planning systems

    NASA Technical Reports Server (NTRS)

    Gasquet, A.; Parrod, Y.; Desaintvincent, A.

    1994-01-01

    The increasing complexity of modern spacecraft, and the stringent requirement for maximizing their mission return, call for a new generation of Mission Planning Systems (MPS). In this paper, we discuss the requirements for the Space Mission Planning and the benefits which can be expected from Artificial Intelligence techniques through examples of applications developed by Matra Marconi Space.

  14. In Situ Techniques for Monitoring Electrochromism: An Advanced Laboratory Experiment

    ERIC Educational Resources Information Center

    Saricayir, Hakan; Uce, Musa; Koca, Atif

    2010-01-01

    This experiment employs current technology to enhance and extend existing lab content. The basic principles of spectroscopic and electroanalytical techniques and their use in determining material properties are covered in some detail in many undergraduate chemistry programs. However, there are limited examples of laboratory experiments with in…

  15. Advances in reduction techniques for tire contact problems

    NASA Technical Reports Server (NTRS)

    Noor, Ahmed K.

    1995-01-01

    Some recent developments in reduction techniques, as applied to predicting the tire contact response and evaluating the sensitivity coefficients of the different response quantities, are reviewed. The sensitivity coefficients measure the sensitivity of the contact response to variations in the geometric and material parameters of the tire. The tire is modeled using a two-dimensional laminated anisotropic shell theory with the effects of variation in geometric and material parameters, transverse shear deformation, and geometric nonlinearities included. The contact conditions are incorporated into the formulation by using a perturbed Lagrangian approach with the fundamental unknowns consisting of the stress resultants, the generalized displacements, and the Lagrange multipliers associated with the contact conditions. The elemental arrays are obtained by using a modified two-field, mixed variational principle. For the application of reduction techniques, the tire finite element model is partitioned into two regions. The first region consists of the nodes that are likely to come in contact with the pavement, and the second region includes all the remaining nodes. The reduction technique is used to significantly reduce the degrees of freedom in the second region. The effectiveness of the computational procedure is demonstrated by a numerical example of the frictionless contact response of the space shuttle nose-gear tire, inflated and pressed against a rigid flat surface. Also, the research topics which have high potential for enhancing the effectiveness of reduction techniques are outlined.

  16. Tagging and Purifying Proteins to Teach Molecular Biology and Advanced Biochemistry

    ERIC Educational Resources Information Center

    Roecklein-Canfield, Jennifer A.; Lopilato, Jane

    2004-01-01

    Two distinct courses, "Molecular Biology" taught by the Biology Department and "Advanced Biochemistry" taught by the Chemistry Department, complement each other and, when taught in a coordinated and integrated way, can enhance student learning and understanding of complex material. "Molecular Biology" is a comprehensive lecture-based course with a…

  17. 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

  18. Application of advanced cytometric and molecular technologies to minimal residual disease monitoring

    NASA Astrophysics Data System (ADS)

    Leary, James F.; He, Feng; Reece, Lisa M.

    2000-04-01

    Minimal residual disease monitoring presents a number of theoretical and practical challenges. Recently it has been possible to meet some of these challenges by combining a number of new advanced biotechnologies. To monitor the number of residual tumor cells requires complex cocktails of molecular probes that collectively provide sensitivities of detection on the order of one residual tumor cell per million total cells. Ultra-high-speed, multi parameter flow cytometry is capable of analyzing cells at rates in excess of 100,000 cells/sec. Residual tumor selection marker cocktails can be optimized by use of receiver operating characteristic analysis. New data minimizing techniques when combined with multi variate statistical or neural network classifications of tumor cells can more accurately predict residual tumor cell frequencies. The combination of these techniques can, under at least some circumstances, detect frequencies of tumor cells as low as one cell in a million with an accuracy of over 98 percent correct classification. Detection of mutations in tumor suppressor genes requires insolation of these rare tumor cells and single-cell DNA sequencing. Rare residual tumor cells can be isolated at single cell level by high-resolution single-cell cell sorting. Molecular characterization of tumor suppressor gene mutations can be accomplished using a combination of single- cell polymerase chain reaction amplification of specific gene sequences followed by TA cloning techniques and DNA sequencing. Mutations as small as a single base pair in a tumor suppressor gene of a single sorted tumor cell have been detected using these methods. Using new amplification procedures and DNA micro arrays it should be possible to extend the capabilities shown in this paper to screening of multiple DNA mutations in tumor suppressor and other genes on small numbers of sorted metastatic tumor cells.

  19. Advances in simulation study on organic small molecular solar cells

    NASA Astrophysics Data System (ADS)

    Zhang, Xuan; Guo, Wenge; Li, Ming; Ma, Wentao; Meng, Sen

    2015-02-01

    Recently, more focuses have been put on organic semiconductors because of its advantages, such as its flexibility, ease of fabrication and potential low cost, etc. The reasons we pay highlight on small molecular photovoltaic material are its ease of purification, easy to adjust and determine structure, easy to assemble range units and get high carrier mobility, etc. Simulation study on organic small molecular solar cells before the experiment can help the researchers find relationship between the efficiency and structure parameters, properties of material, estimate the performance of the device, bring the optimization of guidance. Also, the applicability of the model used in simulation can be discussed by comparison with experimental data. This paper summaries principle, structure, progress of numerical simulation on organic small molecular solar cells.

  20. [Advance of pesticide residue analysis techniques based on biological principle].

    PubMed

    He, Yonghong; Gao, Zhixian; Chao, Fuhuan

    2004-01-01

    The application of pesticide residue analysis techniques based on biological principle, such as immunoassay, biosensor and direct test the influence of pesticide upon the activity of the enzyme and the growth of the propagation, was reviewed in this paper. Immunoassay is a kind of precise and sensitive method, but it's not easy to produce the antibody of pesticide. The strongpoint of biosensor is the process of the detection is quickly and real time, but the sensitivity and stability of biosensor still need improve. The tests based on the activity of the enzyme and the growth of the propagation are simple and inexpensive, and are useful in the situation of acute-poisoning and severe contamination. These techniques general work fast, cost inexpensive, and do not need large-volume unit, so they have a good large potential in extensive pesticide residue monitoring and spot assays. PMID:15098494

  1. Some advanced testing techniques for concentrator photovoltaic cells and lenses

    SciTech Connect

    Wiczer, J.J.; Chaffin, R.J.; Hibray, R.E.

    1982-09-01

    The authors describe two separate test techniques for evaluating concentrator photovoltaic components. For convenient characterization of concentrator solar cells, they have developed a method for measuring the entire illuminated I-V curve of a photovoltaic cell with a single flash of intense simulated sunlight. This method reduces the heat input to the cell and the time required to test a cell, thus making possible quick indoor measurements of photovoltaic conversion efficiency at concentrated illumination levels without the use of elaborate cell mounting fixtures or heat sink attachments. The other test method provides a technique to analyze the spatially dependent, spectral distribution of intense sunlight collected and focused by lenses designed for use in photovoltaic concentrator systems. This information is important in the design of multijunction photovoltaic receivers, secondary concentrators, and in optimizing the performance of conventional silicon cell concentrator systems.

  2. Developments and advances concerning the hyperpolarisation technique SABRE.

    PubMed

    Mewis, Ryan E

    2015-10-01

    To overcome the inherent sensitivity issue in NMR and MRI, hyperpolarisation techniques are used. Signal Amplification By Reversible Exchange (SABRE) is a hyperpolarisation technique that utilises parahydrogen, a molecule that possesses a nuclear singlet state, as the source of polarisation. A metal complex is required to break the singlet order of parahydrogen and, by doing so, facilitates polarisation transfer to analyte molecules ligated to the same complex through the J-coupled network that exists. The increased signal intensities that the analyte molecules possess as a result of this process have led to investigations whereby their potential as MRI contrast agents has been probed and to understand the fundamental processes underpinning the polarisation transfer mechanism. As well as discussing literature relevant to both of these areas, the chemical structure of the complex, the physical constraints of the polarisation transfer process and the successes of implementing SABRE at low and high magnetic fields are discussed. PMID:26264565

  3. Characterization of PTFE Using Advanced Thermal Analysis Techniques

    NASA Astrophysics Data System (ADS)

    Blumm, J.; Lindemann, A.; Meyer, M.; Strasser, C.

    2010-10-01

    Polytetrafluoroethylene (PTFE) is a synthetic fluoropolymer used in numerous industrial applications. It is often referred to by its trademark name, Teflon. Thermal characterization of a PTFE material was carried out using various thermal analysis and thermophysical properties test techniques. The transformation energetics and specific heat were measured employing differential scanning calorimetry. The thermal expansion and the density changes were determined employing pushrod dilatometry. The viscoelastic properties (storage and loss modulus) were analyzed using dynamic mechanical analysis. The thermal diffusivity was measured using the laser flash technique. Combining thermal diffusivity data with specific heat and density allows calculation of the thermal conductivity of the polymer. Measurements were carried out from - 125 °C up to 150 °C. Additionally, measurements of the mechanical properties were carried out down to - 170 °C. The specific heat tests were conducted into the fully molten regions up to 370 °C.

  4. Advances in epidemiology survey methodology and techniques in schistosomiasis

    PubMed Central

    Mott, K. E.; Cline, B. L.

    1980-01-01

    Quantitative techniques are now recognized to contribute to the validity and comparability of data from epidemiological studies in schistosomiasis. These methods have been developed and tested in field investigations in areas where Schistosoma mansoni is endemic and, to a lesser extent, S. haematobium endemic areas. Carefully planned epidemiological investigations using standardized and quantitative methods have contributed to our understanding of the relationships between intensity of infection and morbidity, as well as to the development of improved control strategies relevant to these areas. This article reviews the newer parasitological techniques, methods of morbidity assessment, and data analysis procedures employed in current epidemiological studies in schistosomiasis, as well as the analytical questions involved in research on the epidemiology of schistosomiasis. PMID:6969136

  5. Advanced materials and techniques for fibre-optic sensing

    NASA Astrophysics Data System (ADS)

    Henderson, Philip J.

    2014-06-01

    Fibre-optic monitoring systems came of age in about 1999 upon the emergence of the world's first significant commercialising company - a spin-out from the UK's collaborative MAST project. By using embedded fibre-optic technology, the MAST project successfully measured transient strain within high-performance composite yacht masts. Since then, applications have extended from smart composites into civil engineering, energy, military, aerospace, medicine and other sectors. Fibre-optic sensors come in various forms, and may be subject to embedment, retrofitting, and remote interrogation. The unique challenges presented by each implementation require careful scrutiny before widespread adoption can take place. Accordingly, various aspects of design and reliability are discussed spanning a range of representative technologies that include resonant microsilicon structures, MEMS, Bragg gratings, advanced forms of spectroscopy, and modern trends in nanotechnology. Keywords: Fibre-optic sensors, fibre Bragg gratings, MEMS, MOEMS, nanotechnology, plasmon.

  6. Development of processing techniques for advanced thermal protection materials

    NASA Technical Reports Server (NTRS)

    Selvaduray, Guna S.

    1994-01-01

    The effort, which was focused on the research and development of advanced materials for use in Thermal Protection Systems (TPS), has involved chemical and physical testing of refractory ceramic tiles, fabrics, threads and fibers. This testing has included determination of the optical properties, thermal shock resistance, high temperature dimensional stability, and tolerance to environmental stresses. Materials have also been tested in the Arc Jet 2 x 9 Turbulent Duct Facility (TDF), the 1 atmosphere Radiant Heat Cycler, and the Mini-Wind Tunnel Facility (MWTF). A significant part of the effort hitherto has gone towards modifying and upgrading the test facilities so that meaningful tests can be carried out. Another important effort during this period has been the creation of a materials database. Computer systems administration and support have also been provided. These are described in greater detail below.

  7. Recent advances in the molecular pathophysiology of atrial fibrillation

    PubMed Central

    Wakili, Reza; Voigt, Niels; Kääb, Stefan; Dobrev, Dobromir; Nattel, Stanley

    2011-01-01

    Atrial fibrillation (AF) is an extremely common cardiac rhythm disorder that causes substantial morbidity and contributes to mortality. The mechanisms underlying AF are complex, involving both increased spontaneous ectopic firing of atrial cells and impulse reentry through atrial tissue. Over the past ten years, there has been enormous progress in understanding the underlying molecular pathobiology. This article reviews the basic mechanisms and molecular processes causing AF. We discuss the ways in which cardiac disease states, extracardiac factors, and abnormal genetic control lead to the arrhythmia. We conclude with a discussion of the potential therapeutic implications that might arise from an improved mechanistic understanding. PMID:21804195

  8. Tumor Functional and Molecular Imaging Utilizing Ultrasound and Ultrasound-Mediated Optical Techniques

    PubMed Central

    Yuan, Baohong; Rychak, Joshua

    2014-01-01

    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. PMID:23219728

  9. Advancing weatherization performance: Measured results from the North Carolina field test of an advanced measure selection technique

    SciTech Connect

    Sharp, T.R.

    1993-07-01

    The field performance of weatherizations based on a newly-developed advanced residential energy conservation measure selection technique was tested alongside current Retro-Tech-based weatherizations in North Carolina. The two weatherization approaches were compared based on implementation ease, measures installed, labor and cost requirements, and energy savings achieved. One-hundred twenty low-income, single-family households served by three different weatherization agencies participated in the field test which was conducted between June 1989 and August 1991. Average heating energy savings were 33% for weatherizations based on the new technique and 23% for Retro-Tech-based weatherizations. Weatherizations based on the new technique achieved 43% more heating energy savings, cost around 10% less at two weatherization agencies and considerably more at the third, and were near equivalent in labor requirements. Major findings from the study include: (1) the advanced audit will install some measures in near identical quantities as Retro-Tech-based weatherizations and others in dramatically different quantities, (2) the advanced audit can significantly increase heating energy savings, (3) blower-door-directed air sealing can more than double the air leakage reductions achieved from standard air sealing techniques, (4) North Carolina low-income houses have much higher average leakage rates than similar New York houses but can be sealed as well or better, and (5) using the advanced audit will not increase weatherization costs and may actually lower costs for most weatherization agencies.

  10. Recent advances in yeast molecular biology: recombinant DNA. [Lead abstract

    SciTech Connect

    Not Available

    1982-09-01

    Separate abstracts were prepared for the 25 papers presented at a workshop focusing on chromosomal structure, gene regulation, recombination, DNA repair, and cell type control, that have been obtained by experimental approaches incorporating the new technologies of yeast DNA transformation, molecular cloning, and DNA sequence analysis. (KRM)

  11. Recent Advances in the Molecular Characterization of Sweetpotato Begomoviruses

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although sweetpotato leaf curl disease has been observed on sweetpotato in Japan and Taiwan since 1985, molecular characterization of sweetpotato begomoviruses has only been conducted in recent years. In the U.S., two begomoviruses, Sweet potato leaf curl virus (SPLCV) and Sweet potato leaf curl Ge...

  12. Technical advances in molecular simulation since the 1980s.

    PubMed

    Field, Martin J

    2015-09-15

    This review describes how the theory and practice of molecular simulation have evolved since the beginning of the 1980s when the author started his career in this field. The account is of necessity brief and subjective and highlights the changes that the author considers have had significant impact on his research and mode of working. PMID:25772387

  13. Advances in Coupling of Kinetics and Molecular Scale Tools to Shed Light on Soil Biogeochemical Processes

    SciTech Connect

    Sparks, Donald

    2014-09-02

    Biogeochemical processes in soils such as sorption, precipitation, and redox play critical roles in the cycling and fate of nutrients, metal(loid)s and organic chemicals in soil and water environments. Advanced analytical tools enable soil scientists to track these processes in real-time and at the molecular scale. Our review focuses on recent research that has employed state-of-the-art molecular scale spectroscopy, coupled with kinetics, to elucidate the mechanisms of nutrient and metal(loid) reactivity and speciation in soils. We found that by coupling kinetics with advanced molecular and nano-scale tools major advances have been made in elucidating important soil chemical processes including sorption, precipitation, dissolution, and redox of metal(loids) and nutrients. Such advances will aid in better predicting the fate and mobility of nutrients and contaminants in soils and water and enhance environmental and agricultural sustainability.

  14. Advances in parameter estimation techniques applied to flexible structures

    NASA Technical Reports Server (NTRS)

    Maben, Egbert; Zimmerman, David C.

    1994-01-01

    In this work, various parameter estimation techniques are investigated in the context of structural system identification utilizing distributed parameter models and 'measured' time-domain data. Distributed parameter models are formulated using the PDEMOD software developed by Taylor. Enhancements made to PDEMOD for this work include the following: (1) a Wittrick-Williams based root solving algorithm; (2) a time simulation capability; and (3) various parameter estimation algorithms. The parameter estimations schemes will be contrasted using the NASA Mini-Mast as the focus structure.

  15. Advanced coding techniques for few mode transmission systems.

    PubMed

    Okonkwo, Chigo; van Uden, Roy; Chen, Haoshuo; de Waardt, Huug; Koonen, Ton

    2015-01-26

    We experimentally verify the advantage of employing advanced coding schemes such as space-time coding and 4 dimensional modulation formats to enhance the transmission performance of a 3-mode transmission system. The performance gain of space-time block codes for extending the optical signal-to-noise ratio tolerance in multiple-input multiple-output optical coherent spatial division multiplexing transmission systems with respect to single-mode transmission performance are evaluated. By exploiting the spatial diversity that few-mode-fibers offer, with respect to single mode fiber back-to-back performance, significant OSNR gains of 3.2, 4.1, 4.9, and 6.8 dB at the hard-decision forward error correcting limit are demonstrated for DP-QPSK 8, 16 and 32 QAM, respectively. Furthermore, by employing 4D constellations, 6 × 28Gbaud 128 set partitioned quadrature amplitude modulation is shown to outperform conventional 8 QAM transmission performance, whilst carrying an additional 0.5 bit/symbol. PMID:25835899

  16. Recent Advances in Spaceborne Precipitation Radar Measurement Techniques and Technology

    NASA Technical Reports Server (NTRS)

    Im, Eastwood; Durden, Stephen L.; Tanelli, Simone

    2006-01-01

    NASA is currently developing advanced instrument concepts and technologies for future spaceborne atmospheric radars, with an over-arching objective of making such instruments more capable in supporting future science needs and more cost effective. Two such examples are the Second-Generation Precipitation Radar (PR-2) and the Nexrad-In-Space (NIS). PR-2 is a 14/35-GHz dual-frequency rain radar with a deployable 5-meter, wide-swath scanned membrane antenna, a dual-polarized/dual-frequency receiver, and a realtime digital signal processor. It is intended for Low Earth Orbit (LEO) operations to provide greatly enhanced rainfall profile retrieval accuracy while consuming only a fraction of the mass of the current TRMM Precipitation Radar (PR). NIS is designed to be a 35-GHz Geostationary Earth Orbiting (GEO) radar for providing hourly monitoring of the life cycle of hurricanes and tropical storms. It uses a 35-m, spherical, lightweight membrane antenna and Doppler processing to acquire 3-dimensional information on the intensity and vertical motion of hurricane rainfall.

  17. Element selective detection of molecular species applying chromatographic techniques and diode laser atomic absorption spectrometry.

    PubMed

    Kunze, K; Zybin, A; Koch, J; Franzke, J; Miclea, M; Niemax, K

    2004-12-01

    Tunable diode laser atomic absorption spectroscopy (DLAAS) combined with separation techniques and atomization in plasmas and flames is presented as a powerful method for analysis of molecular species. The analytical figures of merit of the technique are demonstrated by the measurement of Cr(VI) and Mn compounds, as well as molecular species including halogen atoms, hydrogen, carbon and sulfur. PMID:15561625

  18. Advanced experimental techniques for transonic wind tunnels - Final lecture

    NASA Technical Reports Server (NTRS)

    Kilgore, Robert A.

    1987-01-01

    A philosophy of experimental techniques is presented, suggesting that in order to be successful, one should like what one does, have the right tools, stick to the job, avoid diversions, work hard, interact with people, be informed, keep it simple, be self sufficient, and strive for perfection. Sources of information, such as bibliographies, newsletters, technical reports, and technical contacts and meetings are recommended. It is pointed out that adaptive-wall test sections eliminate or reduce wall interference effects, and magnetic suspension and balance systems eliminate support-interference effects, while the problem of flow quality remains with all wind tunnels. It is predicted that in the future it will be possible to obtain wind tunnel results at the proper Reynolds number, and the effects of flow unsteadiness, wall interference, and support interference will be eliminated or greatly reduced.

  19. [Advances in molecular mechanism of bacterial reduction of hexavalent chromium].

    PubMed

    Li, Dou; Zhao, You-Cai; Song, Li-Yan; Yin, Ya-Jie; Wang, Yang-Qing; Xu, Zhong-Hui

    2014-04-01

    Cr(VI) has been causing serious environmental pollution due to its carcinogenicity, teratogenicity and strong migration. Reduction of Cr( VI) to Cr(III), a precipitation that is much less toxic, is an efficient strategy to control Cr pollution. Within the strategy, bacterial reduction of Cr(VI) to Cr(III) has been considered as one of the best bioremediation methods because of its efficiency, environment friendly, and low cost; however, the molecular mechanism remains large unknown. This review summarizes Cr(VI) reduction bacterial species and its application in pollution control, elaborates the pathways of Cr( VI) reduction and functional proteins involved, concludes the molecular mechanism of baterial reduction Cr(VI), and discusses the orientation of the future research. PMID:24946623

  20. Recent advances in the molecular design of synthetic vaccines

    NASA Astrophysics Data System (ADS)

    Jones, Lyn H.

    2015-12-01

    Vaccines have typically been prepared using whole organisms. These are normally either attenuated bacteria or viruses that are live but have been altered to reduce their virulence, or pathogens that have been inactivated and effectively killed through exposure to heat or formaldehyde. However, using whole organisms to elicit an immune response introduces the potential for infections arising from a reversion to a virulent form in live pathogens, unproductive reactions to vaccine components or batch-to-batch variability. Synthetic vaccines, in which a molecular antigen is conjugated to a carrier protein, offer the opportunity to circumvent these problems. This Perspective will highlight the progress that has been achieved in developing synthetic vaccines using a variety of molecular antigens. In particular, the different approaches used to develop conjugate vaccines using peptide/proteins, carbohydrates and other small molecule haptens as antigens are compared.

  1. Pathological and Molecular Advances in Pediatric Low Grade Astrocytoma

    PubMed Central

    Rodriguez, Fausto J.; Lim, Kah Suan; Bowers, Daniel; Eberhart, Charles G.

    2013-01-01

    Pediatric low grade astrocytomas are the commonest brain tumors in children. They sometimes have similar microscopic and clinical features, making accurate diagnosis difficult. For patients whose tumors are in locations that do not permit full resection, or those with an intrinsically aggressive biology, more effective therapies are required. Until recently, little was known about the molecular changes that drive the initiation and growth of pilocytic and other low grade astrocytomas beyond the association of a minority of cases, primarily in the optic nerve, with neurofibromatosis type 1. Over the last several years, a wide range of studies have implicated the BRAF oncogene and other members of this signaling cascade in the pathobiology of pediatric low grade astrocytoma. In this review, we attempt to summarize this rapidly developing field, and discuss the potential for translating our growing molecular knowledge into improved diagnostic and prognostic biomarkers and new targeted therapies. PMID:23121055

  2. Polycystic liver diseases: advanced insights into the molecular mechanisms

    PubMed Central

    Perugorria, Maria J.; Masyuk, Tatyana V.; Marin, Jose J.; Marzioni, Marco; Bujanda, Luis; LaRusso, Nicholas F.; Banales, Jesus M.

    2015-01-01

    Polycystic liver diseases are genetic disorders characterized by progressive bile duct dilatation and/or cyst development. The large volume of hepatic cysts causes different symptoms and complications such as abdominal distension, local pressure with back pain, hypertension, gastro-oesophageal reflux and dyspnea as well as bleeding, infection and rupture of the cysts. Current therapeutic strategies are based on surgical procedures and pharmacological management, which partially prevent or ameliorate the disease. However, as these treatments only show short-term and/or modest beneficial effects, liver transplantation is the only definitive therapy. Therefore, interest in understanding the molecular mechanisms involved in disease pathogenesis is increasing so that new targets for therapy can be identified. In this Review, the genetic mechanisms underlying polycystic liver diseases and the most relevant molecular pathways of hepatic cystogenesis are discussed. Moreover, the main clinical and preclinical studies are highlighted and future directions in basic as well as clinical research are indicated. PMID:25266109

  3. Cocoa phytochemicals: recent advances in molecular mechanisms on health.

    PubMed

    Kim, Jiyoung; Kim, Jaekyoon; Shim, Jaesung; Lee, Chang Yong; Lee, Ki Won; Lee, Hyong Joo

    2014-01-01

    Recent reports on cocoa are appealing in that a food commonly consumed for pure pleasure might also bring tangible benefits for human health. Cocoa consumption is correlated with reduced health risks of cardiovascular diseases, hypertension, atherosclerosis, and cancer, and the health-promoting effects of cocoa are mediated by cocoa-driven phytochemicals. Cocoa is rich in procyanidins, theobromine, (-)-epicatechin, catechins, and caffeine. Among the phytochemicals present in consumed cocoa, theobromine is most available in human plasma, followed by caffeine, (-)-epicatechin, catechin, and procyanidins. It has been reported that cocoa phytochemicals specifically modulate or interact with specific molecular targets linked to the pathogenesis of chronic human diseases, including cardiovascular diseases, cancer, neurodegenerative diseases, obesity, diabetes, and skin aging. This review summarizes comprehensive recent findings on the beneficial actions of cocoa-driven phytochemicals in molecular mechanisms of human health. PMID:24580540

  4. Recent advances in techniques for tsetse-fly control*

    PubMed Central

    MacLennan, K. J. R.

    1967-01-01

    With the advent of modern persistent insecticides, it has become possible to utilize some of the knowledge that has accumulated on the ecology and bionomics of Glossina and to devise more effective techniques for the control and eventual extermination of these species. The present article, based on experience of the tsetse fly problem in Northern Nigeria, points out that the disadvantages of control techniques—heavy expenditure of money and manpower and undue damage to the biosystem—can now largely be overcome by basing the application of insecticides on knowledge of the habits of the particular species of Glossina in a particular environment. Two factors are essential to the success of a control project: the proper selection of sites for spraying (the concept of restricted application) and the degree of persistence of the insecticide used. Reinfestation from within or outside the project area must also be taken into account. These and other aspects are discussed in relation to experience gained from a successful extermination project carried out in the Sudan vegetation zone and from present control activities in the Northern Guinea vegetation zone. PMID:5301739

  5. Advanced pattern-matching techniques for autonomous acquisition

    NASA Astrophysics Data System (ADS)

    Narendra, P. M.; Westover, B. L.

    1981-01-01

    The key objective of this effort is the development of pattern-matching algorithms which can impart autonomous acquisition capability to precision-guided munitions such as Copperhead and Hellfire. Autonomous acquisition through pattern matching holds the promise of eliminating laser designation and enhancing fire power by multiple target prioritization. The pattern-matching approach being developed under this program is based on a symbolic pattern-matching framework, which is suited for the autonomous acquisition scenario. It is based on matching a symbolic representation derived from the two images, and it can accommodate the stringent pattern-matchine criteria established by the scenario: enormous differences in the scene perspective, aspect and range between the two sensors, differences in sensor characteristics and illumination, and scene changes such as target motion and obscuration from one view point ot the other. This report contains a description of an efficient branch-and-bound technique for symbolic pattern matching. Also presented are the results of applying a simulation of the algorithm to pairs of FLIR images of military vehicles in cluttered environments as well as pairs of images from different sensors (FLIR and silicon TV). The computational requirements are analyzed toward real-time implementation, and avenues of future work are recommended.

  6. Advanced Manufacturing Techniques Demonstrated for Fabricating Developmental Hardware

    NASA Technical Reports Server (NTRS)

    Redding, Chip

    2004-01-01

    NASA Glenn Research Center's Engineering Development Division has been working in support of innovative gas turbine engine systems under development by Glenn's Combustion Branch. These one-of-a-kind components require operation under extreme conditions. High-temperature ceramics were chosen for fabrication was because of the hostile operating environment. During the designing process, it became apparent that traditional machining techniques would not be adequate to produce the small, intricate features for the conceptual design, which was to be produced by stacking over a dozen thin layers with many small features that would then be aligned and bonded together into a one-piece unit. Instead of using traditional machining, we produced computer models in Pro/ENGINEER (Parametric Technology Corporation (PTC), Needham, MA) to the specifications of the research engineer. The computer models were exported in stereolithography standard (STL) format and used to produce full-size rapid prototype polymer models. These semi-opaque plastic models were used for visualization and design verification. The computer models also were exported in International Graphics Exchange Specification (IGES) format and sent to Glenn's Thermal/Fluids Design & Analysis Branch and Applied Structural Mechanics Branch for profiling heat transfer and mechanical strength analysis.

  7. Advances in Current Rating Techniques for Flexible Printed Circuits

    NASA Technical Reports Server (NTRS)

    Hayes, Ron

    2014-01-01

    Twist Capsule Assemblies are power transfer devices commonly used in spacecraft mechanisms that require electrical signals to be passed across a rotating interface. Flexible printed circuits (flex tapes, see Figure 2) are used to carry the electrical signals in these devices. Determining the current rating for a given trace (conductor) size can be challenging. Because of the thermal conditions present in this environment the most appropriate approach is to assume that the only means by which heat is removed from the trace is thru the conductor itself, so that when the flex tape is long the temperature rise in the trace can be extreme. While this technique represents a worst-case thermal situation that yields conservative current ratings, this conservatism may lead to overly cautious designs when not all traces are used at their full rated capacity. A better understanding of how individual traces behave when they are not all in use is the goal of this research. In the testing done in support of this paper, a representative flex tape used for a flight Solar Array Drive Assembly (SADA) application was tested by energizing individual traces (conductors in the tape) in a vacuum chamber and the temperatures of the tape measured using both fine-gauge thermocouples and infrared thermographic imaging. We find that traditional derating schemes used for bundles of wires do not apply for the configuration tested. We also determine that single active traces located in the center of a flex tape operate at lower temperatures than those on the outside edges.

  8. Advances in array detectors for X-ray diffraction techniques.

    PubMed

    Hanley, Quentin S; Denton, M Bonner

    2005-09-01

    Improved focal plane array detector systems are described which can provide improved readout speeds, random addressing and even be employed to simultaneously measure position, intensity and energy. This latter capability promises to rekindle interests in Laue techniques. Simulations of three varieties of foil mask spectrometer in both on- and off-axis configurations indicate that systems of stacked silicon detectors can provide energy measurements within 1% of the true value based on the use of single 'foils' and approximately 10000 photons. An eight-detector hybrid design can provide energy coverage from 4 to 60 keV. Energy resolution can be improved by increased integration time or higher flux experiments. An off-axis spectrometer design in which the angle between the incident beam and the detector system is 45 degrees results in a shift in the optimum energy response of the spectrometer system. In the case of a 200 microm-thick silicon absorber, the energy optimum shifts from 8.7 keV to 10.3 keV as the angle of incidence goes from 0 to 45 degrees. These new designs make better use of incident photons, lower the impact of source flicker through simultaneous rather than sequential collection of intensities, and improve the energy range relative to previously reported systems. PMID:16120985

  9. Nonlinear optical technique for advanced tunable IR lidar

    NASA Astrophysics Data System (ADS)

    Pasmanik, Guerman A.; Matveyev, Alexander Z.; Peterson, Darrel G.; Shilov, Alexander A.; Yakovlev, Ivan V.

    1998-05-01

    A review of nonlinear optical techniques to be used in tunable far IR lidar, radar and spectrometer system is presented. As an example, a tunable IR remote sensing technology demonstrator system operating at 8-12 μm is described. It includes an OPO and OPA pumped by Nd:YAG laser as well as Raman emitter and receiver pumped by the OPA output. Relatively small variations of an OPA wavelength (1.85-2 μm)provide a broad operative range at far IR (8-12 μm). The unique feature of OPO is pumping by two phase conjugated beams. A pulse from the pump laser is transmitted through the OPO. A portion of the transmitted pulse is reflected in a phase conjugate cell, and the remaining pulse energy is semi- compressed in stimulated Brillouin scattering (SBS) cells. These phase conjugate (PC) cells are filled with highly purified and stable SiCl4 and GeCl4 (R=80%). This process reduces the OPO threshold as well as forms short and narrow linewidth pulses. Being amplified up to 140 mJ in a 2 ns pulse in the OPA, these pulses are directed to a hydrogen Raman emitter. Due to auxiliary pumps at 1064 nm and 1907 nm with total energy approximately 30 mJ providing phonon excitation, the SRS conversion of an OPA output in the Stokes wave starts from a relatively high phonon seed so a quantum efficiency of more than 50 percent at far IR is achieved. The high sensitive detector of far IR weak signals (~1000 photons)is based on a Raman-induced four wave mixing of these signals with a delayed OPA output. A subsequent readout of the Raman grating is performed using a 532 nm pulse. The Raman-shifted 683 nm pulse is proportional to that of a weak IR signal.

  10. 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.

  11. Biotechnology Apprenticeship for Secondary-Level Students: Teaching Advanced Cell Culture Techniques for Research

    ERIC Educational Resources Information Center

    Lewis, Jennifer R.; Kotur, Mark S.; Butt, Omar; Kulcarni, Sumant; Riley, Alyssa A.; Ferrell, Nick; Sullivan, Kathryn D.; Ferrari, Mauro

    2002-01-01

    The purpose of this article is to discuss "small-group apprenticeships (SGAs)" as a method to instruct cell culture techniques to high school participants. The study aimed to teach cell culture practices and to introduce advanced imaging techniques to solve various biomedical engineering problems. Participants designed and completed experiments…

  12. Advanced Techniques for Reservoir Simulation and Modeling of Non-Conventional Wells

    SciTech Connect

    Durlofsky, Louis J.

    2000-08-28

    This project targets the development of (1) advanced reservoir simulation techniques for modeling non-conventional wells; (2) improved techniques for computing well productivity (for use in reservoir engineering calculations) and well index (for use in simulation models), including the effects of wellbore flow; and (3) accurate approaches to account for heterogeneity in the near-well region.

  13. Advanced techniques for determining long term compatibility of materials with propellants

    NASA Technical Reports Server (NTRS)

    Green, R. L.; Stebbins, J. P.; Smith, A. W.; Pullen, K. E.

    1973-01-01

    A method for the prediction of propellant-material compatibility for periods of time up to ten years is presented. Advanced sensitive measurement techniques used in the prediction method are described. These include: neutron activation analysis, radioactive tracer technique, and atomic absorption spectroscopy with a graphite tube furnace sampler. The results of laboratory tests performed to verify the prediction method are presented.

  14. Biotechnology Apprenticeship for Secondary-Level Students: Teaching Advanced Cell Culture Techniques for Research.

    ERIC Educational Resources Information Center

    Lewis, Jennifer R.; Kotur, Mark S.; Butt, Omar; Kulcarni, Sumant; Riley, Alyssa A.; Ferrell, Nick; Sullivan, Kathryn D.; Ferrari, Mauro

    2002-01-01

    Discusses small-group apprenticeships (SGAs) as a method for introducing cell culture techniques to high school participants. Teaches cell culture practices and introduces advance imaging techniques to solve various biomedical engineering problems. Clarifies and illuminates the value of small-group laboratory apprenticeships. (Author/KHR)

  15. Recent Advances in Stable Isotope Techniques for N2O Source Partitioning in Soils

    NASA Astrophysics Data System (ADS)

    Baggs, E.; Mair, L.; Mahmood, S.

    2007-12-01

    The use of 13C, 15N and 18O enables us to overcome uncertainties associated with soil C and N processes and to assess the links between species diversity and ecosystem function. Recent advances in stable isotope techniques enable determination of process rates, and are fundamental for examining interactions between C and N cycles. Here we will introduce the 15N-, 18O- and 13C-enrichment techniques we have developed to distinguish between different N2O-producing processes in situ in soils, presenting selected results, and will critically assess their potential, alone and in combination with molecular techniques, to help address key research questions for soil biogeochemistry and microbial ecology. We have developed 15N- 18O-enrichment techniques to distinguish between, and to quantify, N2O production during ammonia oxidation, nitrifier denitrification and denitrification. This provides a great advantage over natural abundance approaches as it enables quantification of N2O from each microbial source, which can be coupled with quantification of N2 production, and used to examine interactions between different processes and cycles. These approaches have also provided new insights into the N cycle and how it interacts with the C cycle. For example, we now know that ammonia oxidising bacteria significantly contribute to N2O emissions from soils, both via the traditionally accepted ammonia oxidation pathway, and also via denitrification (nitrifier denitrification) which can proceed even under aerobic conditions. We are also linking emissions from each source to diversity and activity of relevant microbial functional groups, for example through the development and application of a specific nirK primer for the nitrite reductase in ammonia oxidising bacteria. Recently, isotopomers have been proposed as an alternative for source partitioning N2O at natural abundance levels, and offers the potential to investigate N2O production from nitrate ammonification, and overcomes the need to apply 18O-H2O to determine nitrifier denitrification. However, this only provides an estimated, not a quantified, contribution, and further developments are required for quantification using isotope enrichment. Despite some limitations, such techniques become even more powerful when linked with other recent developments, such as nanoSIMS, gene expression and 13C-stable isotope probing of microbial RNA, and when linked to other disciplines. These may help address remaining questions such as: which microbes are producing N2O in soil, what is the influence of plants and mycorrhizal fungi on rhizosphere processes, and where is denitrification occurring in soil?

  16. 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

  17. Endoscopic therapy for early gastric cancer: Standard techniques and recent advances in ESD

    PubMed Central

    Kume, Keiichiro

    2014-01-01

    The technique of endoscopic submucosal dissection (ESD) is now a well-known endoscopic therapy for early gastric cancer. ESD was introduced to resect large specimens of early gastric cancer in a single piece. ESD can provide precision of histologic diagnosis and can also reduce the recurrence rate. However, the drawback of ESD is its technical difficulty, and, consequently, it is associated with a high rate of complications, the need for advanced endoscopic techniques, and a lengthy procedure time. Various advances in the devices and techniques used for ESD have contributed to overcoming these drawbacks. PMID:24914364

  18. 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

  19. 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...

  20. Molecular targets of isothiocyanates in cancer: recent advances.

    PubMed

    Gupta, Parul; Kim, Bonglee; Kim, Sung-Hoon; Srivastava, Sanjay K

    2014-08-01

    Cancer is a multistep process resulting in uncontrolled cell division. It results from aberrant signaling pathways that lead to uninhibited cell division and growth. Various recent epidemiological studies have indicated that consumption of cruciferous vegetables, such as garden cress, broccoli, etc., reduces the risk of cancer. Isothiocyanates (ITCs) have been identified as major active constituents of cruciferous vegetables. ITCs occur in plants as glucosinolate and can readily be derived by hydrolysis. Numerous mechanistic studies have demonstrated the anticancer effects of ITCs in various cancer types. ITCs suppress tumor growth by generating reactive oxygen species or by inducing cycle arrest leading to apoptosis. Based on the exciting outcomes of preclinical studies, few ITCs have advanced to the clinical phase. Available data from preclinical as well as available clinical studies suggest ITCs to be one of the promising anticancer agents available from natural sources. This is an up-to-date exhaustive review on the preventive and therapeutic effects of ITCs in cancer. PMID:24510468

  1. Recent advances in molecular biology of parasitic viruses.

    PubMed

    Banik, Gouri Rani; Stark, Damien; Rashid, Harunor; Ellis, John T

    2014-01-01

    The numerous protozoa that can inhabit the human gastro-intestinal tract are known, yet little is understood of the viruses which infect these protozoa. The discovery, morphologic details, purification methods of virus-like particles, genome and proteome of the parasitic viruses, Entamoeba histolytica, Giardia lamblia, Trichomonas vaginalis, and the Eimeria sp. are described in this review. The protozoan viruses share many common features: most of them are RNA or double-stranded RNA viruses, ranging between 5 and 8 kilobases, and are spherical or icosahedral in shape with an average diameter of 30-40 nm. These viruses may influence the function and pathogenicity of the protozoa which they infect, and may be important to investigate from a clinical perspective. The viruses may be used as specific genetic transfection vectors for the parasites and may represent a research tool. This review provides an overview on recent advances in the field of protozoan viruses. PMID:25019235

  2. Recent Advances in Methamphetamine Neurotoxicity Mechanisms and Its Molecular Pathophysiology

    PubMed Central

    Yu, Shaobin; Zhu, Ling; Shen, Qiang; Bai, Xue; Di, Xuhui

    2015-01-01

    Methamphetamine (METH) is a sympathomimetic amine that belongs to phenethylamine and amphetamine class of psychoactive drugs, which are widely abused for their stimulant, euphoric, empathogenic, and hallucinogenic properties. Many of these effects result from acute increases in dopamine and serotonin neurotransmission. Subsequent to these acute effects, METH produces persistent damage to dopamine and serotonin release in nerve terminals, gliosis, and apoptosis. This review summarized the numerous interdependent mechanisms including excessive dopamine, ubiquitin-proteasome system dysfunction, protein nitration, endoplasmic reticulum stress, p53 expression, inflammatory molecular, D3 receptor, microtubule deacetylation, and HIV-1 Tat protein that have been demonstrated to contribute to this damage. In addition, the feasible therapeutic strategies according to recent studies were also summarized ranging from drug and protein to gene level. PMID:25861156

  3. Recent Advances in Molecular Mechanisms of Taste Signaling and Modifying.

    PubMed

    Shigemura, Noriatsu; Ninomiya, Yuzo

    2016-01-01

    The sense of taste conveys crucial information about the quality and nutritional value of foods before it is ingested. Taste signaling begins with taste cells via taste receptors in oral cavity. Activation of these receptors drives the transduction systems in taste receptor cells. Then particular transmitters are released from the taste cells and activate corresponding afferent gustatory nerve fibers. Recent studies have revealed that taste sensitivities are defined by distinct taste receptors and modulated by endogenous humoral factors in a specific group of taste cells. Such peripheral taste generations and modifications would directly influence intake of nutritive substances. This review will highlight current understanding of molecular mechanisms for taste reception, signal transduction in taste bud cells, transmission between taste cells and nerves, regeneration from taste stem cells, and modification by humoral factors at peripheral taste organs. PMID:26944619

  4. Multifunctional nanomaterials for advanced molecular imaging and cancer therapy

    NASA Astrophysics Data System (ADS)

    Subramaniam, Prasad

    Nanotechnology offers tremendous potential for use in biomedical applications, including cancer and stem cell imaging, disease diagnosis and drug delivery. The development of nanosystems has aided in understanding the molecular mechanisms of many diseases and permitted the controlled nanoscale manipulation of biological phenomena. In recent years, many studies have focused on the use of several kinds of nanomaterials for cancer and stem cell imaging and also for the delivery of anticancer therapeutics to tumor cells. However, the proper diagnosis and treatment of aggressive tumors such as brain and breast cancer requires highly sensitive diagnostic agents, in addition to the ability to deliver multiple therapeutics using a single platform to the target cells. Addressing these challenges, novel multifunctional nanomaterial-based platforms that incorporate multiple therapeutic and diagnostic agents, with superior molecular imaging and targeting capabilities, has been presented in this work. The initial part of this work presents the development of novel nanomaterials with superior optical properties for efficiently delivering soluble cues such as small interfering RNA (siRNA) into brain cancer cells with minimal toxicity. Specifically, this section details the development of non-toxic quantums dots for the imaging and delivery of siRNA into brain cancer and mesenchymal stem cells, with the hope of using these quantum dots as multiplexed imaging and delivery vehicles. The use of these quantum dots could overcome the toxicity issues associated with the use of conventional quantum dots, enabled the imaging of brain cancer and stem cells with high efficiency and allowed for the delivery of siRNA to knockdown the target oncogene in brain cancer cells. The latter part of this thesis details the development of nanomaterial-based drug delivery platforms for the co-delivery of multiple anticancer drugs to brain tumor cells. In particular, this part of the thesis focuses on the synthesis and use of a biodegradable dendritic polypeptide-based nanocarrier for the delivery of multiple anticancer drugs and siRNA to brain tumor cells. The co-delivery of important anticancer agents using a single platform was shown to increase the efficacy of the drugs manyfold, ensuring the cancer cell-specific delivery and minimizing dose limiting toxicities of the individual drugs. This would be of immense importance when used in vivo.

  5. Recent advances toward a molecular mechanism of efflux pump inhibition

    PubMed Central

    Opperman, Timothy J.; Nguyen, Son T.

    2015-01-01

    Multidrug resistance (MDR) in Gram-negative pathogens, such as the Enterobacteriaceae and Pseudomonas aeruginosa, poses a significant threat to our ability to effectively treat infections caused by these organisms. A major component in the development of the MDR phenotype in Gram-negative bacteria is overexpression of Resistance-Nodulation-Division (RND)-type efflux pumps, which actively pump antibacterial agents and biocides from the periplasm to the outside of the cell. Consequently, bacterial efflux pumps are an important target for developing novel antibacterial treatments. Potent efflux pump inhibitors (EPIs) could be used as adjunctive therapies that would increase the potency of existing antibiotics and decrease the emergence of MDR bacteria. Several potent inhibitors of RND-type efflux pump have been reported in the literature, and at least three of these EPI series were optimized in a pre-clinical development program. However, none of these compounds have been tested in the clinic. One of the major hurdles to the development of EPIs has been the lack of biochemical, computational, and structural methods that could be used to guide rational drug design. Here, we review recent reports that have advanced our understanding of the mechanism of action of several potent EPIs against RND-type pumps. PMID:25999939

  6. Progress of Molecular Targeted Therapies for Advanced Renal Cell Carcinoma

    PubMed Central

    Santoni, Matteo; Amantini, Consuelo; Burattini, Luciano; Berardi, Rossana; Santoni, Giorgio; Cascinu, Stefano; Muzzonigro, Giovanni

    2013-01-01

    Vascular endothelial growth factor (VEGF) plays a crucial role in tumor angiogenesis. VEGF expression in metastatic renal cell carcinoma (mRCC) is mostly regulated by hypoxia, predominantly via the hypoxia-induced factor (HIF)/Von Hippel-Lindau (VHL) pathway. Advances in our knowledge of VEGF role in tumor angiogenesis, growth, and progression have permitted development of new approaches for the treatment of mRCC, including several agents targeting VEGF and VEGF receptors: tyrosine kinase pathway, serine/threonine kinases, α5β1-integrin, deacetylase, CD70, mammalian target of rapamycin (mTOR), AKT, and phosphatidylinositol 3′-kinase (PI3K). Starting from sorafenib and sunitinib, several targeted therapies have been approved for mRCC treatment, with a long list of agents in course of evaluation, such as tivozanib, cediranib, and VEGF-Trap. Here we illustrate the main steps of tumor angiogenesis process, defining the pertinent therapeutic targets and the efficacy and toxicity profiles of these new promising agents. PMID:24093097

  7. Molecular Targets of Isothiocyanates in Cancer: Recent Advances

    PubMed Central

    Gupta, Parul; Kim, Bonglee; Kim, Sung-Hoon; Srivastava, Sanjay K.

    2014-01-01

    Cancer is a multistep process resulting in uncontrolled cell division. It results from aberrant signaling pathways that lead to uninhibited cell division and growth. Various recent epidemiological studies have indicated that consumption of cruciferous vegetables such as garden cress, broccoli, etc., reduces the risk of cancer. Isothiocyanates (ITC) have been identified as major active constituents of cruciferous vegetables. ITCs occur in plants as glucosinolate and can readily be derived by hydrolysis. Numerous mechanistic studies have demonstrated the anti-cancer effects of ITCs in various cancer types. ITCs suppress tumor growth by generating reactive oxygen species or by inducing cycle arrest leading to apoptosis. Based on the exciting outcomes of pre-clinical studies, few ITCs have advanced to the clinical phase. Available data from pre-clinical as well as available clinical studies suggests ITCs to be one of the promising anti-cancer agents available from natural sources. This is an up-to-date exhaustive review on the preventive and therapeutic effects of ITCs in cancer. PMID:24510468

  8. Advances in the molecular genetics of non-syndromic polydactyly.

    PubMed

    Deng, Hao; Tan, Ting; Yuan, Lamei

    2015-01-01

    Polydactyly is one of the most common inherited limb abnormalities, characterised by supernumerary fingers or toes. It results from disturbances in the normal programme of the anterior-posterior axis of the developing limb, with diverse aetiology and variable inter- and intra-familial clinical features. Polydactyly can occur as an isolated disorder (non-syndromic polydactyly) or as a part of an anomaly syndrome (syndromic polydactyly). On the basis of the anatomic location of the duplicated digits, non-syndromic polydactyly is divided into three kinds, including preaxial polydactyly, axial polydactyly and postaxial polydactyly. Non-syndromic polydactyly frequently exhibits an autosomal dominant inheritance with variable penetrance. To date, in human, at least ten loci and four disease-causing genes, including the GLI3 gene, the ZNF141 gene, the MIPOL1 gene and the PITX1 gene, have been identified. In this paper, we review clinical features of non-syndromic polydactyly and summarise the recent progress in the molecular genetics, including loci and genes that are responsible for the disorder, the signalling pathways that these genetic factors are involved in, as well as animal models of the disorder. These progresses will improve our understanding of the complex disorder and have implications on genetic counselling such as prenatal diagnosis. PMID:26515020

  9. Advances in molecular-replacement procedures: the REVAN pipeline.

    PubMed

    Carrozzini, Benedetta; Cascarano, Giovanni Luca; Giacovazzo, Carmelo; Mazzone, Annamaria

    2015-09-01

    The REVAN pipeline aiming at the solution of protein structures via molecular replacement (MR) has been assembled. It is the successor to REVA, a pipeline that is particularly efficient when the sequence identity (SI) between the target and the model is greater than 0.30. The REVAN and REVA procedures coincide when the SI is >0.30, but differ substantially in worse conditions. To treat these cases, REVAN combines a variety of programs and algorithms (REMO09, REFMAC, DM, DSR, VLD, free lunch, Coot, Buccaneer and phenix.autobuild). The MR model, suitably rotated and positioned, is first refined by a standard REFMAC refinement procedure, and the corresponding electron density is then submitted to cycles of DM-VLD-REFMAC. The next REFMAC applications exploit the better electron densities obtained at the end of the VLD-EDM sections (a procedure called vector refinement). In order to make the model more similar to the target, the model is submitted to mutations, in which Coot plays a basic role, and it is then cyclically resubmitted to REFMAC-EDM-VLD cycles. The phases thus obtained are submitted to free lunch and allow most of the test structures studied by DiMaio et al. [(2011), Nature (London), 473, 540-543] to be solved without using energy-guided programs. PMID:26327375

  10. Advances in the Molecular Genetics of Non-syndromic Syndactyly

    PubMed Central

    Deng, Hao; Tan, Ting

    2015-01-01

    Syndactyly, webbing of adjacent digits with or without bony fusion, is one of the most common hereditary limb malformations. It occurs either as an isolated abnormality or as a component of more than 300 syndromic anomalies. There are currently nine types of phenotypically diverse nonsyndromic syndactyly. Non-syndromic syndactyly is usually inherited as an autosomal dominant trait, although the more severe presenting types and subtypes may show autosomal recessive or X-linked pattern of inheritance. The phenotype appears to be not only caused by a main gene, but also dependant on genetic background and subsequent signaling pathways involved in limb formation. So far, the principal genes identified to be involved in congenital syndactyly are mainly involved in the zone of polarizing activity and sonic hedgehog pathway. This review summarizes the recent progress made in the molecular genetics, including known genes and loci responsible for non-syndromic syndactyly, and the signaling pathways those genetic factors involved in, as well as clinical features and animal models. We hope our review will contribute to the understanding of underlying pathogenesis of this complicated disorder and have implication on genetic counseling. PMID:26069458

  11. A Novel Microcharacterization Technique in the Measurement of Strain and Orientation Gradient in Advanced Materials

    NASA Technical Reports Server (NTRS)

    Garmestai, H.; Harris, K.; Lourenco, L.

    1997-01-01

    Representation of morphology and evolution of the microstructure during processing and their relation to properties requires proper experimental techniques. Residual strains, lattice distortion, and texture (micro-texture) at the interface and the matrix of a layered structure or a functionally gradient material and their variation are among parameters important in materials characterization but hard to measure with present experimental techniques. Current techniques available to measure changes in interred material parameters (residual stress, micro-texture, microplasticity) produce results which are either qualitative or unreliable. This problem becomes even more complicated in the case of a temperature variation. These parameters affect many of the mechanical properties of advanced materials including stress-strain relation, ductility, creep, and fatigue. A review of some novel experimental techniques using recent advances in electron microscopy is presented here to measure internal stress, (micro)texture, interracial strength and (sub)grain formation and realignment. Two of these techniques are combined in the chamber of an Environmental Scanning Electron Microscope to measure strain and orientation gradients in advanced materials. These techniques which include Backscattered Kikuchi Diffractometry (BKD) and Microscopic Strain Field Analysis are used to characterize metallic and intermetallic matrix composites and superplastic materials. These techniques are compared with the more conventional x-ray diffraction and indentation techniques.

  12. Hairy cell leukemia: Update on molecular profiling and therapeutic advances.

    PubMed

    Grever, Michael R; Blachly, James S; Andritsos, Leslie A

    2014-09-01

    Hairy cell leukemia was initially described as a clinicopathologic entity more than 50 years ago. We have subsequently discovered that HCL is really at least two diseases: classical HCL and the hairy cell leukemia variant. The former is among a small group of cancers exceptional for being (nearly) unified by a single genetic lesion, the BRAF V600E mutation. Over the past three decades, tremendous progress in both diagnostic and prognostic clarification has been accompanied by therapeutic advances in classical HCL. Consequently, this once uniformly fatal disease has been converted in most cases into a chronic illness enabling patients to live long and productive lives. In response to standard therapy, patients have high complete remission rates. Unfortunately, the long-term survival curves have not plateaued, revealing that this disease is controlled but not cured. Though rare and representing only about 10% of an already rare disease, those patients with the variant fare exceptionally poorly with standard therapy: complete response rates to purine nucleoside analogs are reported to be less than 50%, whereas the complete response rates in classical HCL are up to 90%. Novel small molecules targeting BRAF and the B-cell receptor signaling complex, and biologic agents like antibodies and immunotoxin conjugates are being explored for those patients who have relapsed. Substantial opportunities for continued research remain. This complex and multi-faceted disease incorporates challenges from altered immunity associated with the underlying disease and its treatments. Considering the rarity of this malignancy, optimization of patient management requires multi-institutional collaboration. The Hairy Cell Leukemia Foundation (www.hairycellleukemia.org) was formed to coordinate these efforts. PMID:25110197

  13. Analysis of leading edge and trailing edge cover glass samples before and after treatment with advanced satellite contamination removal techniques

    NASA Technical Reports Server (NTRS)

    Hotaling, S. P.

    1993-01-01

    Two samples from Long Duration Exposure Facility (LDEF) experiment M0003-4 were analyzed for molecular and particulate contamination prior to and following treatment with advanced satellite contamination removal techniques (CO2 gas/solid jet spray and oxygen ion beam). The pre- and post-cleaning measurements and analyses are presented. The jet spray removed particulates in seconds. The low energy reactive oxygen ion beam removed 5,000 A of photo polymerized organic hydrocarbon contamination in less than 1 hour. Spectroscopic analytical techniques were applied to the analysis of cleaning efficiency including: Fourier transform infrared, Auger, x ray photoemissions, energy dispersive x ray, and ultraviolet/visible. The results of this work suggest that the contamination studied here was due to spacecraft self-contamination enhanced by atomic oxygen plasma dynamics and solar UV radiation. These results also suggest the efficacy for the jet spray and ion beam contamination control technologies for spacecraft optical surfaces.

  14. 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,

  15. 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,…

  16. MO-C-BRE-01: The WMIS-AAPM Joint Symposium: Advances in Molecular Imaging

    SciTech Connect

    Contag, C; Pogue, B; Lewis, J

    2014-06-15

    This joint symposium of the World Molecular Imaging Society (WMIS) and the AAPM includes three luminary speakers discussing work in new paradigms of molecular imaging in cancer (Contag), applications of optical imaging technologies to radiation therapy (Pogue) and an update on PET imaging as a surrogate biomarker for cancer progression and response to therapy. Learning Objectives: Appreciate the current trends in molecular and systems imaging. Understand how optical imaging technologies, and particularly Cerenkov detectors, can be used in advancing radiation oncology. Stay current on new PET tracers - and targets - of interest in cancer treatment.

  17. Current molecular techniques for the detection of microbial pathogens.

    PubMed

    Galluzzi, Luca; Magnani, Mauro; Saunders, Nick; Harms, Carsten; Bruce, Ian James

    2007-01-01

    Traditionally the detection of microbial pathogens in clinical, environmental or food samples has commonly needed the prelevation of cells by culture before the application ofthe detection strategy. This is done to increase cell number thereby overcoming problems associated with the sensitivity of classical detection strategies. However, culture-based methods have the disadvantages of taking longer, usually are more complex and require skilled personnel as well as not being able to detect viable but non cultivable microbial species. A number of molecular methods have been developed in the last 10 to 15 years to overcome these issues and to facilitate the rapid, accurate, sensitive and cost effective identification and enumeration of microorganisms which are designed to replace and/or support classical approaches to microbial detection. Amongst these new methods, ones based on the polymerase chain reaction and nucleic acid hybridization have been shown to be particularly suitable for this purpose. This review generally summarizes some of the current and emerging nucleic acid based molecular approaches for the detection, discrimination andquantification ofmicrobes in environmental, food and clinical samples and includes reference to the recently developing areas of microfluidics and nanotechnology "Lab-on-a-chip". PMID:17455764

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

    PubMed Central

    Sevick-Muraca, Eva M.; Rasmussen, John C.

    2010-01-01

    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. PMID:19021311

  19. Molecular beam epitaxy for advanced gate stack materials and processes

    NASA Astrophysics Data System (ADS)

    Locquet, Jean-Pierre

    2005-03-01

    The material requirements for future CMOS generations - as given by the ITRS roadmap - are very challenging. This includes a high K dielectric without a low K interfacial layer, a high mobility channel and the appropriate metal gate. With the help of two projects INVEST and ET4US, we are building up a molecular beam epitaxy (MBE) infrastructure to grow this material set on large area wafers that can be further processed into small scale devices. In the INVEST project, we have developed an MBE system for the growth of complex oxides on semiconductors. The system follows the overall design of a production tool and is equipped with an RF atomic oxygen source, effusion cells, e-beam evaporators and a differential pumping stage. The oxide growth process starts with desorbing the initial surface oxide on the Si wafers in ultra-high vacuum and high temperature to create a clean reconstructed 2x1 surface. Using the atomic oxygen it is possible to oxidize the surface in a well controlled manner at low temperature and to grow very thin and dense SiOx layers, followed by the growth of 2-6 nm amorphous high K dielectrics. The process parameters permit to tune the interface layer from a SiOx rich to a silicide rich interface with a significant impact on the capacitance and the leakage. Initial focus is on developing an optimized growth recipe for high quality amorphous HfO2 and LaHfO3.5 films. This recipe was subsequently used to make wafers for a transistor batch that gave us the first N short channel MBE MOSFET's (100 nm) using an etched gate process flow. Some highlights of the first batch for 3nm HfO2 MOSFET are a high mobility (> 270 cm^2/Vs) with a corresponding low leakage current of 2 mA/cm^2). While there were some process issues for LaHfO3.5, the 3 nm MOSFET showed very low leakage currents below 10-6 A/cm^2. Interestingly all the LaHFO3.5 MOSFETs showed very low threshold voltage instabilities. In collaboration with C. Marchiori, M. Sousa, A.Guiller, H. Siegwart, D. Caimi, J. Fompeyrine, D. J Webb, C. Rossel, R. Germann of IBM Research GmbH Zurich Switzerland; L. Pantisano, M. Claes, T. Conard, M. Demand, W. Deweerd, S. DeGendt, M. Heyns, M. Houssa, M. Aoulaiche, G. Lujan, L. Ragnarsson, E. Rohr, T. Schram of IMEC Leuven Belgium; J. Hooker, Z.M Rittersma, Y. Furukawa of Philips Research Leuven Belgium and J. W. Seo of EPFL Lausanne Switzerland.

  20. Modulation/demodulation techniques for satellite communications. Part 2: Advanced techniques. The linear channel

    NASA Technical Reports Server (NTRS)

    Omura, J. K.; Simon, M. K.

    1982-01-01

    A theory is presented for deducing and predicting the performance of transmitter/receivers for bandwidth efficient modulations suitable for use on the linear satellite channel. The underlying principle used is the development of receiver structures based on the maximum-likelihood decision rule. The application of the performance prediction tools, e.g., channel cutoff rate and bit error probability transfer function bounds to these modulation/demodulation techniques.

  1. Biomarkers and Molecular Imaging as Predictors of Response to Neoadjuvant Chemoradiotherapy in Patients With Locally Advanced Rectal Cancer.

    PubMed

    Molinari, Chiara; Matteucci, Federica; Caroli, Paola; Passardi, Alessandro

    2015-12-01

    Standard treatment of patients with locally advanced rectal cancer (LARC) includes neoadjuvant chemoradiotherapy (NCRT) followed by surgery. Tumor regression after NCRT varies substantially among individuals and pathological complete response is a known prognostic factor for LARC. The identification of a predictive model for response to chemoradiotherapy would help clinicians to identify patients who would probably benefit from multimodal treatment and to perform an early assessment of individual prognosis. Carcinoembryonic antigen has proven to be a good predictor of response in several clinical trials. Other widely studied predictive models in LARC include molecular biomarkers, analyzed at various levels and by different techniques, and molecular imaging, in particular magnetic resonance imaging and positron emission tomography/computed tomography. Although none of the studied markers have been approved in clinical practice, their evaluation in larger, prospective trials and in combined predictive models could be of use to define tailored therapeutic strategies. PMID:26170142

  2. POC-Scale Testing of an Advanced Fine Coal Dewatering Equipment/Technique

    SciTech Connect

    B. K. Karekh; D. Tao; J. G. Groppo

    1998-08-28

    Froth flotation technique is an effective and efficient process for recovering of ultra-fine (minus 74 mm) clean coal. Economical dewatering of an ultra-fine clean coal product to a 20% level moisture will be an important step in successful implementation of the advanced cleaning processes. This project is a step in the Department of Energy's program to show that ultra-clean coal could be effectively dewatered to 20% or lower moisture using either conventional or advanced dewatering techniques. The cost-sharing contract effort is for 45 months beginning September 30, 1994. This report discusses technical progress made during the quarter from January 1 � March 31, 1998.

  3. Clinical applications of recent molecular advances in urologic malignancies: no longer chasing a "mirage"?

    PubMed

    Netto, George J

    2013-05-01

    As our understanding of the molecular events leading to the development and progression of genitourologic malignancies, new markers of detection, prognostication, and therapy prediction can be exploited in the management of these prevalent tumors. The current review discusses the recent advances in prostate, bladder, renal, and testicular neoplasms that are pertinent to the anatomic pathologist. PMID:23574774

  4. Polymicrobial chronic endophthalmitis diagnosed by culture and molecular technique.

    PubMed

    Mukherjee, A; Pramanik, S; Das, D; Roy, R; Therese, K L

    2014-01-01

    Accurate etiological diagnosis is the key to prevention of ocular morbidity in endophthalmitis cases. A 66 year old male was suffering from chronic endophthalmitis post-cataract surgery. Polymerase chain reaction examination on anterior chamber fluid was positive for Propionibacterium acnes but negative for the panfungal genome. He was advised vitrectomy with intravitreal injections. Polymerase chain reaction of vitreous aspirate was positive for P.acnes as well as panfungal genome. The vitreous sample also grew yeast in culture which was identified as Candida pseudotropicalis. Patient was treated on an alternate day regimen of intravitreal Vancomycin and Amphotericin B in the post-operative period. There was improvement in vision at final follow up. Chronic endophthalmitis can have polymicrobial etiology which will require appropriate diagnostic and therapeutic strategies. The role of molecular testing is vital in these cases as growth in culture is often negative. PMID:25008833

  5. Acetone preservation: a practical technique for molecular analysis.

    PubMed

    Fukatsu, T

    1999-11-01

    In attempts to establish a convenient and reliable method for field collection and archival preservation of insects and their endosymbiotic microorganisms for molecular analysis, acetone, ethanol, and other organic solvents were tested for DNA preservability of the pea aphid Acyrthosiphon pisum and its intracellular symbiotic bacterium Buchnera sp. After 6 months' storage, not only the band of high-molecular-size DNA but also the bands of rRNA were well preserved in acetone, ethanol, 2-propanol, diethyl ether and ethyl acetate. Polymerase chain reaction (PCR) assays confirmed that the DNA of both the insects and their symbionts was well preserved in these solvents. In contrast, methanol and chloroform showed poor DNA preservability. When water-containing series of acetone and ethanol were examined for DNA preservability, acetone was apparently more robust against water contamination than ethanol. Considering that most biological materials contain high amounts of water, acetone may be a more recommendable preservative for DNA analysis than ethanol which has been widely used for this purpose. The DNA of various insects could be preserved in acetone at room temperature in good condition for several years. In addition to the DNA of the host insects, the DNA of their endosymbionts, including Buchnera and other mycetocyte symbionts, Wolbachia, and gut bacteria, was amplified by PCR after several years of acetone storage. The RNA and protein of the pea aphid and its endosymbiont were also preserved for several years in acetone. After 2 years' storage in acetone, proteins of A. pisum could be analysed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and immunoblotting, and the endosymbiotic bacteria were successfully detected by immunohistochemistry and in situ hybridization on the tissue sections. PMID:10620236

  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 a chance…

  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 a chance

  8. Modulation/demodulation techniques for satellite communications. Part 3: Advanced techniques. The nonlinear channel

    NASA Technical Reports Server (NTRS)

    Omura, J. K.; Simon, M. K.

    1982-01-01

    A theory for deducing and predicting the performance of transmitter/receivers for bandwidth efficient modulations suitable for use on the nonlinear satellite channel is presented. The underlying principle used throughout is the development of receiver structures based on the maximum likelihood decision rule and aproximations to it. The bit error probability transfer function bounds developed in great detail in Part 4 is applied to these modulation/demodulation techniques. The effects of the various degrees of receiver mismatch are considered both theoretically and by numerous illustrative examples.

  9. Ultrasmall volume molecular isothermal amplification in microfluidic chip with advanced surface processing

    NASA Astrophysics Data System (ADS)

    Huang, Guoliang; Ma, Li; Yang, Xiaoyong; Yang, Xu

    2011-01-01

    In this paper, we developed a metal micro-fluidic chip with advanced surface processing for ultra-small volume molecular isothermal amplification. This method takes advantages of the nucleic acid amplification with good stability and consistency, high sensitivity about 31 genomic DNA copies and bacteria specific gene identification. Based on the advanced surface processing, the bioreaction assays of nucleic acid amplification was dropped about 392nl in volume. A high numerical aperture confocal optical detection system was advanced to sensitively monitor the DNA amplification with low noise and high power collecting fluorescence near to the optical diffraction limit. A speedy nucleic acid isothermal amplification was performed in the ultra-small volume microfluidic chip, where the time at the inflexions of second derivative to DNA exponential amplified curves was brought forward and the sensitivity was improved about 65 folds to that of in current 25?l Ep-tube amplified reaction, which indicates a promising clinic molecular diagnostics in the droplet amplification.

  10. Pushing CT and MR Imaging to the Molecular Level for Studying the “Omics”: Current Challenges and Advancements

    PubMed Central

    Huang, Hsuan-Ming; Shih, Yi-Yu

    2014-01-01

    During the past decade, medical imaging has made the transition from anatomical imaging to functional and even molecular imaging. Such transition provides a great opportunity to begin the integration of imaging data and various levels of biological data. In particular, the integration of imaging data and multiomics data such as genomics, metabolomics, proteomics, and pharmacogenomics may open new avenues for predictive, preventive, and personalized medicine. However, to promote imaging-omics integration, the practical challenge of imaging techniques should be addressed. In this paper, we describe key challenges in two imaging techniques: computed tomography (CT) and magnetic resonance imaging (MRI) and then review existing technological advancements. Despite the fact that CT and MRI have different principles of image formation, both imaging techniques can provide high-resolution anatomical images while playing a more and more important role in providing molecular information. Such imaging techniques that enable single modality to image both the detailed anatomy and function of tissues and organs of the body will be beneficial in the imaging-omics field. PMID:24738056

  11. Application of Advanced Magnetic Resonance Imaging Techniques in Evaluation of the Lower Extremity

    PubMed Central

    Braun, Hillary J.; Dragoo, Jason L.; Hargreaves, Brian A.; Levenston, Marc E.; Gold, Garry E.

    2012-01-01

    Synopsis This article reviews current magnetic resonance imaging techniques for imaging the lower extremity, focusing on imaging of the knee, ankle, and hip joints. Recent advancements in MRI include imaging at 7 Tesla, using multiple receiver channels, T2* imaging, and metal suppression techniques, allowing more detailed visualization of complex anatomy, evaluation of morphological changes within articular cartilage, and imaging around orthopedic hardware. PMID:23622097

  12. Detecting Molecular Properties by Various Laser-Based Techniques

    SciTech Connect

    Tse-Ming Hsin

    2007-08-03

    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 {approx}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.

  13. Reflection mass spectrometry technique for monitoring and controlling composition during molecular beam epitaxy

    DOEpatents

    Brennan, T.M.; Hammons, B.E.; Tsao, J.Y.

    1992-12-15

    A method for on-line accurate monitoring and precise control of molecular beam epitaxial growth of Groups III-III-V or Groups III-V-V layers in an advanced semiconductor device incorporates reflection mass spectrometry. The reflection mass spectrometry is responsive to intentional perturbations in molecular fluxes incident on a substrate by accurately measuring the molecular fluxes reflected from the substrate. The reflected flux is extremely sensitive to the state of the growing surface and the measurements obtained enable control of newly forming surfaces that are dynamically changing as a result of growth. 3 figs.

  14. Reflection mass spectrometry technique for monitoring and controlling composition during molecular beam epitaxy

    DOEpatents

    Brennan, Thomas M.; Hammons, B. Eugene; Tsao, Jeffrey Y.

    1992-01-01

    A method for on-line accurate monitoring and precise control of molecular beam epitaxial growth of Groups III-III-V or Groups III-V-V layers in an advanced semiconductor device incorporates reflection mass spectrometry. The reflection mass spectrometry is responsive to intentional perturbations in molecular fluxes incident on a substrate by accurately measuring the molecular fluxes reflected from the substrate. The reflected flux is extremely sensitive to the state of the growing surface and the measurements obtained enable control of newly forming surfaces that are dynamically changing as a result of growth.

  15. 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

  16. Softform for facial rejuvenation: historical review, operative techniques, and recent advances.

    PubMed

    Miller, P J; Levine, J; Ahn, M S; Maas, C S; Constantinides, M

    2000-01-01

    The deep nasolabial fold and other facial furrows and wrinkles have challenged the facial plastic surgeon. A variety of techniques have been used in the past to correct these troublesome defects. Advances in the last five years in new materials and design have created a subcutaneous implant that has excellent properties. This article reviews the development and use of Softform facial implant. PMID:11802342

  17. Advanced Diffusion-Weighted Magnetic Resonance Imaging Techniques of the Human Spinal Cord

    PubMed Central

    Andre, Jalal B.; Bammer, Roland

    2012-01-01

    Unlike those of the brain, advances in diffusion-weighted imaging (DWI) of the human spinal cord have been challenged by the more complicated and inhomogeneous anatomy of the spine, the differences in magnetic susceptibility between adjacent air and fluid-filled structures and the surrounding soft tissues, and the inherent limitations of the initially used echo-planar imaging techniques used to image the spine. Interval advances in DWI techniques for imaging the human spinal cord, with the specific aims of improving the diagnostic quality of the images, and the simultaneous reduction in unwanted artifacts have resulted in higher-quality images that are now able to more accurately portray the complicated underlying anatomy and depict pathologic abnormality with improved sensitivity and specificity. Diffusion tensor imaging (DTI) has benefited from the advances in DWI techniques, as DWI images form the foundation for all tractography and DTI. This review provides a synopsis of the many recent advances in DWI of the human spinal cord, as well as some of the more common clinical uses for these techniques, including DTI and tractography. PMID:22158130

  18. Real-time application of advanced three-dimensional graphic techniques for research aircraft simulation

    NASA Technical Reports Server (NTRS)

    Davis, Steven B.

    1990-01-01

    Visual aids are valuable assets to engineers for design, demonstration, and evaluation. Discussed here are a variety of advanced three-dimensional graphic techniques used to enhance the displays of test aircraft dynamics. The new software's capabilities are examined and possible future uses are considered.

  19. Recognizing and Managing Complexity: Teaching Advanced Programming Concepts and Techniques Using the Zebra Puzzle

    ERIC Educational Resources Information Center

    Crabtree, John; Zhang, Xihui

    2015-01-01

    Teaching advanced programming can be a challenge, especially when the students are pursuing different majors with diverse analytical and problem-solving capabilities. The purpose of this paper is to explore the efficacy of using a particular problem as a vehicle for imparting a broad set of programming concepts and problem-solving techniques. We…

  20. Recognizing and Managing Complexity: Teaching Advanced Programming Concepts and Techniques Using the Zebra Puzzle

    ERIC Educational Resources Information Center

    Crabtree, John; Zhang, Xihui

    2015-01-01

    Teaching advanced programming can be a challenge, especially when the students are pursuing different majors with diverse analytical and problem-solving capabilities. The purpose of this paper is to explore the efficacy of using a particular problem as a vehicle for imparting a broad set of programming concepts and problem-solving techniques. We

  1. Advanced techniques for high resolution spectroscopic observations of cosmic gamma-ray sources

    NASA Technical Reports Server (NTRS)

    Matteson, J. L.; Pelling, M. R.; Peterson, L. E.; Lin, R. P.; Anderson, K. A.; Pehl, R. H.; Hurley, K. C.; Vedrenne, G.; Sniel, M.; Durouchoux, P.

    1985-01-01

    An advanced gamma-ray spectrometer that is currently in development is described. It will obtain a sensitivity of 0.0001 ph/sq cm./sec in a 6 hour balloon observation and uses innovative techniques for background reduction and source imaging.

  2. A User-Oriented Interface for Generalised Informetric Analysis Based on Applying Advanced Data Modelling Techniques.

    ERIC Educational Resources Information Center

    Jarvelin, Kalervo; Ingwersen, Peter; Niemi, Timo

    2000-01-01

    Presents a user-oriented interface for generalized informetric analysis and demonstrates how informetric calculations can be specified through advanced data modeling techniques. Topics include bibliographic data; online information retrieval systems; citation networks; query interface; impact factors; data restructuring; and multi-level…

  3. Fabrication of advanced electrochemical energy materials using sol-gel processing techniques

    NASA Technical Reports Server (NTRS)

    Chu, C. T.; Chu, Jay; Zheng, Haixing

    1995-01-01

    Advanced materials play an important role in electrochemical energy devices such as batteries, fuel cells, and electrochemical capacitors. They are being used as both electrodes and electrolytes. Sol-gel processing is a versatile solution technique used in fabrication of ceramic materials with tailored stoichiometry, microstructure, and properties. The application of sol-gel processing in the fabrication of advanced electrochemical energy materials will be presented. The potentials of sol-gel derived materials for electrochemical energy applications will be discussed along with some examples of successful applications. Sol-gel derived metal oxide electrode materials such as V2O5 cathodes have been demonstrated in solid-slate thin film batteries; solid electrolytes materials such as beta-alumina for advanced secondary batteries had been prepared by the sol-gel technique long time ago; and high surface area transition metal compounds for capacitive energy storage applications can also be synthesized with this method.

  4. Performance Characterization of Molecular Dynamics Techniques for Biomolecular Simulations

    SciTech Connect

    Alam, Sadaf R

    2006-03-01

    Large-scale simulations and computational modeling using molecular dynamics (MD) continues to make significant impacts in the field of biology. It is well known that simulations of biological events at native time and length scales requires computing power several orders of magnitude beyond today's commonly available systems. Supercomputers, such as IBM Blue Gene/L and Cray XT3, will soon make tens to hundreds of teraFLOP/s of computing power available by utilizing thousands of processors. The popular algorithms and MD applications, however, were not initially designed to run on thousands of processors. In this paper, we present detailed investigations of the performance issues, which are crucial for improving the scalability of the MD-related algorithms and applications on massively parallel processing (MPP) architectures. Due to the varying characteristics of biological input problems, we study two prototypical biological complexes that use the MD algorithm: an explicit solvent and an implicit solvent. In particular, we study the AMBER application, which supports a variety of these types of input problems. For the explicit solvent problem, we focused on the particle mesh Ewald (PME) method for calculating the electrostatic energy, and for the implicit solvent model, we targeted the Generalized Born (GB) calculation. We uncovered and subsequently modified a limitation in AMBER that restricted the scaling beyond 128 processors. We collected performance data for experiments on up to 2048 Blue Gene/L and XT3 processors and subsequently identified that the scaling is largely limited by the underlying algorithmic characteristics and also by the implementation of the algorithms. Furthermore, we found that the input problem size of biological system is constrained by memory available per node. In conclusion, our results indicate that MD codes can significantly benefit from the current generation architectures with relatively modest optimization efforts. Nevertheless, the key for enabling scientific breakthroughs lies in exploiting the full potential of these new architectures.

  5. Detection and Sizing of Fatigue Cracks in Steel Welds with Advanced Eddy Current Techniques

    NASA Astrophysics Data System (ADS)

    Todorov, E. I.; Mohr, W. C.; Lozev, M. G.

    2008-02-01

    Butt-welded specimens were fatigued to produce cracks in the weld heat-affected zone. Advanced eddy current (AEC) techniques were used to detect and size the cracks through a coating. AEC results were compared with magnetic particle and phased-array ultrasonic techniques. Validation through destructive crack measurements was also conducted. Factors such as geometry, surface treatment, and crack tightness interfered with depth sizing. AEC inspection techniques have the potential of providing more accurate and complete sizing flaw data for manufacturing and in-service inspections.

  6. The development of optical microscopy techniques for the advancement of single-particle studies

    SciTech Connect

    Marchuk, Kyle

    2013-05-15

    Single particle orientation and rotational tracking (SPORT) has recently become a powerful optical microscopy tool that can expose many molecular motions. Unfortunately, there is not yet a single microscopy technique that can decipher all particle motions in all environmental conditions, thus there are limitations to current technologies. Within, the two powerful microscopy tools of total internal reflection and interferometry are advanced to determine the position, orientation, and optical properties of metallic nanoparticles in a variety of environments. Total internal reflection is an optical phenomenon that has been applied to microscopy to produce either fluorescent or scattered light. The non-invasive far-field imaging technique is coupled with a near-field illumination scheme that allows for better axial resolution than confocal microscopy and epi-fluorescence microscopy. By controlling the incident illumination angle using total internal reflection fluorescence (TIRF) microscopy, a new type of imaging probe called “non-blinking” quantum dots (NBQDs) were super-localized in the axial direction to sub-10-nm precision. These particles were also used to study the rotational motion of microtubules being propelled by the motor protein kinesin across the substrate surface. The same instrument was modified to function under total internal reflection scattering (TIRS) microscopy to study metallic anisotropic nanoparticles and their dynamic interactions with synthetic lipid bilayers. Utilizing two illumination lasers with opposite polarization directions at wavelengths corresponding to the short and long axis surface plasmon resonance (SPR) of the nanoparticles, both the in-plane and out-of-plane movements of many particles could be tracked simultaneously. When combined with Gaussian point spread function (PSF) fitting for particle super-localization, the binding status and rotational movement could be resolved without degeneracy. TIRS microscopy was also used to find the 3D orientation of stationary metallic anisotropic nanoparticles utilizing only long-axis SPR enhancement. The polarization direction of the illuminating light was rotated causing the relative intensity of p-polarized and s-polarized light within the evanescent field to change. The interaction of the evanescent field with the particles is dependent on the orientation of the particle producing an intensity curve. This curve and the in-plane angle can be compared with simulations to accurately determine the 3D orientation. Differential interference contrast (DIC) microscopy is another non-invasive far-field technique based upon interferometry that does not rely on staining or other contrast enhancing techniques. In addition, high numerical aperture condensers and objectives can be used to give a very narrow depth of field allowing for the optical tomography of samples, which makes it an ideal candidate to study biological systems. DIC microscopy has also proven itself in determining the orientation of gold nanorods in both engineered environments and within cells. Many types of nanoparticles and nanostructures have been synthesized using lithographic techniques on silicon wafer substrates. Traditionally, reflective mode DIC microscopes have been developed and applied to the topographical study of reflective substrates and the imaging of chips on silicon wafers. Herein, a laser-illuminated reflected-mode DIC was developed for studying nanoparticles on reflective surfaces.

  7. The development of optical microscopy techniques for the advancement of single-particle studies

    NASA Astrophysics Data System (ADS)

    Marchuk, Kyle

    Single particle orientation and rotational tracking (SPORT) has recently become a powerful optical microscopy tool that can expose many molecular motions. Unfortunately, there is not yet a single microscopy technique that can decipher all particle motions in all environmental conditions, thus there are limitations to current technologies. Within, the two powerful microscopy tools of total internal reflection and interferometry are advanced to determine the position, orientation, and optical properties of metallic nanoparticles in a variety of environments. Total internal reflection is an optical phenomenon that has been applied to microscopy to produce either fluorescent or scattered light. The non-invasive far-field imaging technique is coupled with a near-field illumination scheme that allows for better axial resolution than confocal microscopy and epi-fluorescence microscopy. By controlling the incident illumination angle using total internal reflection fluorescence (TIRF) microscopy, a new type of imaging probe called "non-blinking" quantum dots (NBQDs) were super-localized in the axial direction to sub-10-nm precision. These particles were also used to study the rotational motion of microtubules being propelled by the motor protein kinesin across the substrate surface. The same instrument was modified to function under total internal reflection scattering (TIRS) microscopy to study metallic anisotropic nanoparticles and their dynamic interactions with synthetic lipid bilayers. Utilizing two illumination lasers with opposite polarization directions at wavelengths corresponding to the short and long axis surface plasmon resonance (SPR) of the nanoparticles, both the in-plane and out-of-plane movements of many particles could be tracked simultaneously. When combined with Gaussian point spread function (PSF) fitting for particle super-localization, the binding status and rotational movement could be resolved without degeneracy. TIRS microscopy was also used to find the 3D orientation of stationary metallic anisotropic nanoparticles utilizing only long-axis SPR enhancement. The polarization direction of the illuminating light was rotated causing the relative intensity of p-polarized and s-polarized light within the evanescent field to change. The interaction of the evanescent field with the particles is dependent on the orientation of the particle producing an intensity curve. This curve and the in-plane angle can be compared with simulations to accurately determine the 3D orientation. Differential interference contrast (DIC) microscopy is another non-invasive far-field technique based upon interferometry that does not rely on staining or other contrast enhancing techniques. In addition, high numerical aperture condensers and objectives can be used to give a very narrow depth of field allowing for the optical tomography of samples, which makes it an ideal candidate to study biological systems. DIC microscopy has also proven itself in determining the orientation of gold nanorods in both engineered environments and within cells. Many types of nanoparticles and nanostructures have been synthesized using lithographic techniques on silicon wafer substrates. Traditionally, reflective mode DIC microscopes have been developed and applied to the topographical study of reflective substrates and the imaging of chips on silicon wafers. Herein, a laser-illuminated reflected-mode DIC was developed for studying nanoparticles on reflective surfaces.

  8. Chronic phase advance alters circadian physiological rhythms and peripheral molecular clocks.

    PubMed

    Wolff, Gretchen; Duncan, Marilyn J; Esser, Karyn A

    2013-08-01

    Shifting the onset of light, acutely or chronically, can profoundly affect responses to infection, tumor progression, development of metabolic disease, and mortality in mammals. To date, the majority of phase-shifting studies have focused on acute exposure to a shift in the timing of the light cycle, whereas the consequences of chronic phase shifts alone on molecular rhythms in peripheral tissues such as skeletal muscle have not been studied. In this study, we tested the effect of chronic phase advance on the molecular clock mechanism in two phenotypically different skeletal muscles. The phase advance protocol (CPA) involved 6-h phase advances (earlier light onset) every 4 days for 8 wk. Analysis of the molecular clock, via bioluminescence recording, in the soleus and flexor digitorum brevis (FDB) muscles and lung demonstrated that CPA advanced the phase of the rhythm when studied immediately after CPA. However, if the mice were placed into free-running conditions (DD) for 2 wk after CPA, the molecular clock was not phase shifted in the two muscles but was still shifted in the lung. Wheel running behavior remained rhythmic in CPA mice; however, the endogenous period length of the free-running rhythm was significantly shorter than that of control mice. Core body temperature, cage activity, and heart rate remained rhythmic throughout the experiment, although the onset of the rhythms was significantly delayed with CPA. These results provide clues that lifestyles associated with chronic environmental desynchrony, such as shift work, can have disruptive effects on the molecular clock mechanism in peripheral tissues, including both types of skeletal muscle. Whether this can contribute, long term, to increased incidence of insulin resistance/metabolic disease requires further study. PMID:23703115

  9. Panel 4: Recent Advances in Otitis Media in Molecular Biology, Biochemistry, Genetics, and Animal Models

    PubMed Central

    Li, Jian-Dong; Hermansson, Ann; Ryan, Allen F.; Bakaletz, Lauren O.; Brown, Steve D.; Cheeseman, Michael T.; Juhn, Steven K.; Jung, Timothy T. K.; Lim, David J.; Lim, Jae Hyang; Lin, Jizhen; Moon, Sung-Kyun; Post, J. Christopher

    2014-01-01

    Background Otitis media (OM) is the most common childhood bacterial infection and also the leading cause of conductive hearing loss in children. Currently, there is an urgent need for developing novel therapeutic agents for treating OM based on full understanding of molecular pathogenesis in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. Objective To provide a state-of-the-art review concerning recent advances in OM in the areas of molecular biology, biochemistry, genetics, and animal model studies and to discuss the future directions of OM studies in these areas. Data Sources and Review Methods A structured search of the current literature (since June 2007). The authors searched PubMed for published literature in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. Results Over the past 4 years, significant progress has been made in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. These studies brought new insights into our understanding of the molecular and biochemical mechanisms underlying the molecular pathogenesis of OM and helped identify novel therapeutic targets for OM. Conclusions and Implications for Practice Our understanding of the molecular pathogenesis of OM has been significantly advanced, particularly in the areas of inflammation, innate immunity, mucus overproduction, mucosal hyperplasia, middle ear and inner ear interaction, genetics, genome sequencing, and animal model studies. Although these studies are still in their experimental stages, they help identify new potential therapeutic targets. Future preclinical and clinical studies will help to translate these exciting experimental research findings into clinical applications. PMID:23536532

  10. Molecular Acoustic Angiography: A New Technique for High-resolution Superharmonic Ultrasound Molecular Imaging.

    PubMed

    Shelton, Sarah E; Lindsey, Brooks D; Tsuruta, James K; Foster, F Stuart; Dayton, Paul A

    2016-03-01

    Ultrasound molecular imaging utilizes targeted microbubbles to bind to vascular targets such as integrins, selectins and other extracellular binding domains. After binding, these microbubbles are typically imaged using low pressures and multi-pulse imaging sequences. In this article, we present an alternative approach for molecular imaging using ultrasound that relies on superharmonic signals produced by microbubble contrast agents. Bound bubbles were insonified near resonance using a low frequency (4 MHz) element and superharmonic echoes were received at high frequencies (25-30 MHz). Although this approach was observed to produce declining image intensity during repeated imaging in both in vitro and in vivo experiments because of bubble destruction, the feasibility of superharmonic molecular imaging was demonstrated for transmit pressures, which are sufficiently high to induce shell disruption in bound microbubbles. This approach was validated using microbubbles targeted to the αvβ3 integrin in a rat fibrosarcoma model (n = 5) and combined with superharmonic images of free microbubbles to produce high-contrast, high-resolution 3-D volumes of both microvascular anatomy and molecular targeting. Image intensity over repeated scans and the effect of microbubble diameter were also assessed in vivo, indicating that larger microbubbles yield increased persistence in image intensity. Using ultrasound-based acoustic angiography images rather than conventional B-mode ultrasound to provide the underlying anatomic information facilitates anatomic localization of molecular markers. Quantitative analysis of relationships between microvasculature and targeting information indicated that most targeting occurred within 50 μm of a resolvable vessel (>100 μm diameter). The combined information provided by these scans may present new opportunities for analyzing relationships between microvascular anatomy and vascular targets, subject only to limitations of the current mechanically scanned system and microbubble persistence to repeated imaging at moderate mechanical indices. PMID:26678155

  11. Advance of Molecular Imaging Technology and Targeted Imaging Agent in Imaging and Therapy

    PubMed Central

    Chen, Zhi-Yi; Wang, Yi-Xiang; Lin, Yan; Zhang, Jin-Shan; Yang, Feng; Zhou, Qiu-Lan; Liao, Yang-Ying

    2014-01-01

    Molecular imaging is an emerging field that integrates advanced imaging technology with cellular and molecular biology. It can realize noninvasive and real time visualization, measurement of physiological or pathological process in the living organism at the cellular and molecular level, providing an effective method of information acquiring for diagnosis, therapy, and drug development and evaluating treatment of efficacy. Molecular imaging requires high resolution and high sensitive instruments and specific imaging agents that link the imaging signal with molecular event. Recently, the application of new emerging chemical technology and nanotechnology has stimulated the development of imaging agents. Nanoparticles modified with small molecule, peptide, antibody, and aptamer have been extensively applied for preclinical studies. Therapeutic drug or gene is incorporated into nanoparticles to construct multifunctional imaging agents which allow for theranostic applications. In this review, we will discuss the characteristics of molecular imaging, the novel imaging agent including targeted imaging agent and multifunctional imaging agent, as well as cite some examples of their application in molecular imaging and therapy. PMID:24689058

  12. Diagnosis of dissolved organic matter removal by GAC treatment in biologically treated papermill effluents using advanced organic characterisation techniques.

    PubMed

    Antony, Alice; Bassendeh, Mojgan; Richardson, Desmond; Aquilina, Simon; Hodgkinson, Andrew; Law, Ian; Leslie, Greg

    2012-02-01

    Granular activated carbon (GAC) exhaustion rates on pulp and paper effluent from South East Australia were found to be a factor of three higher (3.62cf. 1.47kgm(-3)) on Kraft mills compared to mills using Thermomechanical pulping supplemented by Recycled Fibre (TMP/RCF). Biological waste treatment at both mills resulted in a final effluent COD of 240mgL(-1). The dissolved organic carbon (DOC) was only 1.2 times higher in the Kraft effluent (70 vs. 58mgL(-1)), however, GAC treatment of Kraft and TMP/RCF effluent was largely different on the DOC persisted after biological treatment. The molecular mass (636 vs. 534gmol(-1)) and aromaticity (5.35 vs. 4.67Lmg(-1)m(-1)) of humic substances (HS) were slightly higher in the Kraft effluent. The HS aromaticity was decreased by a factor of 1.0Lmg(-1)m(-1) in both Kraft and TMP/RCF effluent. The molecular mass of the Kraft effluent increased by 50gmol(-1) while the molecular mass of the TMP/RCF effluent was essentially unchanged after GAC treatment; the DOC removal efficiency of the GAC on Kraft effluent was biased towards the low molecular weight humic compounds. The rapid adsorption of this fraction, coupled with the slightly higher aromaticity of the humic components resulted in early breakthrough on the Kraft effluent. Fluorescence excitation-emission matrix analysis of the each GAC treated effluent indicated that the refractory components were higher molecular weight humics on the Kraft effluent and protein-like compounds on the TMP/RCF effluent. Although the GAC exhaustion rates are too high for an effective DOC removal option for biologically treated pulp and paper mill effluents, the study indicates that advanced organic characterisation techniques can be used to diagnose GAC performance on complex effluents with comparable bulk DOC and COD loads. PMID:22209320

  13. Advanced techniques for determining long term compatibility of materials with propellants

    NASA Technical Reports Server (NTRS)

    Green, R. L.

    1972-01-01

    The search for advanced measurement techniques for determining long term compatibility of materials with propellants was conducted in several parts. A comprehensive survey of the existing measurement and testing technology for determining material-propellant interactions was performed. Selections were made from those existing techniques which were determined could meet or be made to meet the requirements. Areas of refinement or changes were recommended for improvement of others. Investigations were also performed to determine the feasibility and advantages of developing and using new techniques to achieve significant improvements over existing ones. The most interesting demonstration was that of the new technique, the volatile metal chelate analysis. Rivaling the neutron activation analysis in terms of sensitivity and specificity, the volatile metal chelate technique was fully demonstrated.

  14. Advanced analytical techniques for the extraction and characterization of plant-derived essential oils by gas chromatography with mass spectrometry.

    PubMed

    Waseem, Rabia; Low, Kah Hin

    2015-02-01

    In recent years, essential oils have received a growing interest because of the positive health effects of their novel characteristics such as antibacterial, antifungal, and antioxidant activities. For the extraction of plant-derived essential oils, there is the need of advanced analytical techniques and innovative methodologies. An exhaustive study of hydrodistillation, supercritical fluid extraction, ultrasound- and microwave-assisted extraction, solid-phase microextraction, pressurized liquid extraction, pressurized hot water extraction, liquid-liquid extraction, liquid-phase microextraction, matrix solid-phase dispersion, and gas chromatography (one- and two-dimensional) hyphenated with mass spectrometry for the extraction through various plant species and analysis of essential oils has been provided in this review. Essential oils are composed of mainly terpenes and terpenoids with low-molecular-weight aromatic and aliphatic constituents that are particularly important for public health. PMID:25403494

  15. Nondestructive Characterization by Advanced Synchrotron Light Techniques: Spectromicroscopy and Coherent Radiology

    PubMed Central

    Margaritondo, Giorgio; Hwu, Yeukuang; Je, Jung Ho

    2008-01-01

    The advanced characteristics of synchrotron light has led in recent years to the development of a series of new experimental techniques to investigate chemical and physical properties on a microscopic scale. Although originally developed for materials science and biomedical research, such techniques find increasing applications in other domains – and could be quite useful for the study and conservation of cultural heritage. Specifically, they can nondestructively provide detailed chemical composition information that can be useful for the identification of specimens, for the discovery of historical links based on the sources of chemical raw materials and on chemical processes, for the analysis of damage, their causes and remedies and for many other issues. Likewise, morphological and structural information on a microscopic scale is useful for the identification, study and preservation of many different cultural and historical specimens. We concentrate here on two classes of techniques: in the first case, photoemission spectromicroscopy. This is the result of the advanced evolution of photoemission techniques like ESCA (Electron Microscopy for Chemical Analysis). By combining high lateral resolution to spectroscopy, photoemission spectromicroscopy can deliver fine chemical information on a microscopic scale in a nondestructive fashion. The second class of techniques exploits the high lateral coherence of modern synchrotron sources, a byproduct of the quest for high brightness or brilliance. We will see that such techniques now push radiology into the submicron scale and the submillisecond time domain. Furthermore, they can be implemented in a tomographic mode, increasing the information and becoming potentially quite useful for the analysis of cultural heritage specimens.

  16. Recent advances in 3D computed tomography techniques for simulation and navigation in hepatobiliary pancreatic surgery.

    PubMed

    Uchida, Masafumi

    2014-04-01

    A few years ago it could take several hours to complete a 3D image using a 3D workstation. Thanks to advances in computer science, obtaining results of interest now requires only a few minutes. Many recent 3D workstations or multimedia computers are equipped with onboard 3D virtual patient modeling software, which enables patient-specific preoperative assessment and virtual planning, navigation, and tool positioning. Although medical 3D imaging can now be conducted using various modalities, including computed tomography (CT), magnetic resonance imaging (MRI), positron emission tomography (PET), and ultrasonography (US) among others, the highest quality images are obtained using CT data, and CT images are now the most commonly used source of data for 3D simulation and navigation image. If the 2D source image is bad, no amount of 3D image manipulation in software will provide a quality 3D image. In this exhibition, the recent advances in CT imaging technique and 3D visualization of the hepatobiliary and pancreatic abnormalities are featured, including scan and image reconstruction technique, contrast-enhanced techniques, new application of advanced CT scan techniques, and new virtual reality simulation and navigation imaging. PMID:24464989

  17. Molecular testing to optimize therapeutic decision making in advanced colorectal cancer.

    PubMed

    Semrad, Thomas J; Kim, Edward J

    2016-04-01

    Colorectal cancer (CRC) is a leading cause of cancer death in the United States. In recent years, therapeutic advances have prolonged the survival of patients with advanced disease. Along with the addition of new treatments, an increasing body of literature explores the potential benefit of using molecular testing to define tumor, circulating, or host biomarkers of benefit to specific treatment strategies. At present, testing for specific mutations in exons 2, 3, and 4 of KRAS and NRAS has become accepted practice to select patients for treatment with epidermal growth factor receptor (EGFR)-targeted agents. Additionally, testing for the BRAF V600E mutation is used to refine decisions based on patient prognosis. The presence of the uridine diphosphate glucuronosyltransferase 1A1 (UGT1A1) *28 polymorphism is associated with toxicity from irinotecan, although it has not been universally applied. Nonetheless, molecular markers to predict response and toxicity of cytotoxic therapy are evolving. While the development of selection biomarkers for anti-angiogenic treatments has not proved fruitful to date, improved development strategies and novel targeted agents are anticipated to revolutionize the approach to treatment of advanced CRC in the near future. This review summarizes currently available data to select treatment strategies in patients with advanced CRC. PMID:27034809

  18. Molecular testing to optimize therapeutic decision making in advanced colorectal cancer

    PubMed Central

    Kim, Edward J.

    2016-01-01

    Colorectal cancer (CRC) is a leading cause of cancer death in the United States. In recent years, therapeutic advances have prolonged the survival of patients with advanced disease. Along with the addition of new treatments, an increasing body of literature explores the potential benefit of using molecular testing to define tumor, circulating, or host biomarkers of benefit to specific treatment strategies. At present, testing for specific mutations in exons 2, 3, and 4 of KRAS and NRAS has become accepted practice to select patients for treatment with epidermal growth factor receptor (EGFR)-targeted agents. Additionally, testing for the BRAF V600E mutation is used to refine decisions based on patient prognosis. The presence of the uridine diphosphate glucuronosyltransferase 1A1 (UGT1A1) *28 polymorphism is associated with toxicity from irinotecan, although it has not been universally applied. Nonetheless, molecular markers to predict response and toxicity of cytotoxic therapy are evolving. While the development of selection biomarkers for anti-angiogenic treatments has not proved fruitful to date, improved development strategies and novel targeted agents are anticipated to revolutionize the approach to treatment of advanced CRC in the near future. This review summarizes currently available data to select treatment strategies in patients with advanced CRC. PMID:27034809

  19. Unified Instrumentation: Examining the Simultaneous Application of Advanced Measurement Techniques for Increased Wind Tunnel Testing Capability

    NASA Technical Reports Server (NTRS)

    Fleming, Gary A. (Editor); Bartram, Scott M.; Humphreys, William M., Jr.; Jenkins, Luther N.; Jordan, Jeffrey D.; Lee, Joseph W.; Leighty, Bradley D.; Meyers, James F.; South, Bruce W.; Cavone, Angelo A.; Ingram, JoAnne L.

    2002-01-01

    A Unified Instrumentation Test examining the combined application of Pressure Sensitive Paint, Projection Moire Interferometry, Digital Particle Image Velocimetry, Doppler Global Velocimetry, and Acoustic Microphone Array has been conducted at the NASA Langley Research Center. The fundamental purposes of conducting the test were to: (a) identify and solve compatibility issues among the techniques that would inhibit their simultaneous application in a wind tunnel, and (b) demonstrate that simultaneous use of advanced instrumentation techniques is feasible for increasing tunnel efficiency and identifying control surface actuation / aerodynamic reaction phenomena. This paper provides summary descriptions of each measurement technique used during the Unified Instrumentation Test, their implementation for testing in a unified fashion, and example results identifying areas of instrument compatibility and incompatibility. Conclusions are drawn regarding the conditions under which the measurement techniques can be operated simultaneously on a non-interference basis. Finally, areas requiring improvement for successfully applying unified instrumentation in future wind tunnel tests are addressed.

  20. POC-scale testing of an advanced fine coal dewatering equipment/technique

    SciTech Connect

    1998-09-01

    Froth flotation technique is an effective and efficient process for recovering of ultra-fine (minus 74 pm) clean coal. Economical dewatering of an ultra-fine clean-coal product to a 20% level moisture will be an important step in successful implementation of the advanced cleaning processes. This project is a step in the Department of Energy`s program to show that ultra-clean coal could be effectively dewatered to 20% or lower moisture using either conventional or advanced dewatering techniques. The cost-sharing contract effort is for 36 months beginning September 30, 1994. This report discusses technical progress made during the quarter from July 1 - September 30, 1997.

  1. Flaw Detection for Composite Materials Improved by Advanced Thermal Image Reconstruction Techniques

    NASA Technical Reports Server (NTRS)

    Martin, Richard E.; Gyekenyesi, Andrew L.

    2003-01-01

    The development of advanced composite materials for use in space and propulsion components has seen considerable growth over the past few years. In addition to improvements that have been made in material properties and processing techniques, similar growth must be seen in the development of methods for the detection of flaws, either generated in service or during manufacturing. Thermal imaging techniques have proven to be successful for the nondestructive evaluation (NDE) of composite materials, but their detection capabilities decrease as flaw depth increases. The purpose of this research is to investigate advanced thermal imaging methods and thermal image processing technologies to increase the maximum depth below surface that a flaw can be detected and improve the contrast between flawed regions and sound regions.

  2. Development of advanced electron holographic techniques and application to industrial materials and devices.

    PubMed

    Yamamoto, Kazuo; Hirayama, Tsukasa; Tanji, Takayoshi

    2013-06-01

    The development of a transmission electron microscope equipped with a field emission gun paved the way for electron holography to be put to practical use in various fields. In this paper, we review three advanced electron holography techniques: on-line real-time electron holography, three-dimensional (3D) tomographic holography and phase-shifting electron holography, which are becoming important techniques for materials science and device engineering. We also describe some applications of electron holography to the analysis of industrial materials and devices: GaAs compound semiconductors, solid oxide fuel cells and all-solid-state lithium ion batteries. PMID:23536696

  3. The investigation of advanced remote sensing techniques for the measurement of aerosol characteristics

    NASA Technical Reports Server (NTRS)

    Deepak, A.; Becher, J.

    1979-01-01

    Advanced remote sensing techniques and inversion methods for the measurement of characteristics of aerosol and gaseous species in the atmosphere were investigated. Of particular interest were the physical and chemical properties of aerosols, such as their size distribution, number concentration, and complex refractive index, and the vertical distribution of these properties on a local as well as global scale. Remote sensing techniques for monitoring of tropospheric aerosols were developed as well as satellite monitoring of upper tropospheric and stratospheric aerosols. Computer programs were developed for solving multiple scattering and radiative transfer problems, as well as inversion/retrieval problems. A necessary aspect of these efforts was to develop models of aerosol properties.

  4. An example of requirements for Advanced Subsonic Civil Transport (ASCT) flight control system using structured techniques

    NASA Technical Reports Server (NTRS)

    Mclees, Robert E.; Cohen, Gerald C.

    1991-01-01

    The requirements are presented for an Advanced Subsonic Civil Transport (ASCT) flight control system generated using structured techniques. The requirements definition starts from initially performing a mission analysis to identify the high level control system requirements and functions necessary to satisfy the mission flight. The result of the study is an example set of control system requirements partially represented using a derivative of Yourdon's structured techniques. Also provided is a research focus for studying structured design methodologies and in particular design-for-validation philosophies.

  5. New test techniques and analytical procedures for understanding the behavior of advanced propellers

    NASA Technical Reports Server (NTRS)

    Stefko, G. L.; Bober, L. J.; Neumann, H. E.

    1983-01-01

    Analytical procedures and experimental techniques were developed to improve the capability to design advanced high speed propellers. Some results from the propeller lifting line and lifting surface aerodynamic analysis codes are compared with propeller force data, probe data and laser velocimeter data. In general, the code comparisons with data indicate good qualitative agreement. A rotating propeller force balance demonstrated good accuracy and reduced test time by 50 percent. Results from three propeller flow visualization techniques are shown which illustrate some of the physical phenomena occurring on these propellers.

  6. Combined preputial advancement and phallopexy as a revision technique for treating paraphimosis in a dog.

    PubMed

    Wasik, S M; Wallace, A M

    2014-11-01

    A 7-year-old neutered male Jack Russell terrier-cross was presented for signs of recurrent paraphimosis, despite previous surgical enlargement of the preputial ostium. Revision surgery was performed using a combination of preputial advancement and phallopexy, which resulted in complete and permanent coverage of the glans penis by the prepuce, and at 1 year postoperatively, no recurrence of paraphimosis had been observed. The combined techniques allow preservation of the normal penile anatomy, are relatively simple to perform and provide a cosmetic result. We recommend this combination for the treatment of paraphimosis in the dog, particularly when other techniques have failed. PMID:25348145

  7. [Principles and advanced techniques for better internetpresentations in obstetrics and gynecology].

    PubMed

    Seufert, R; Molitor, N; Pollow, K; Woernle, F; Hawighorst-Knapstein, S

    2001-08-01

    Internet presentations are common tools for better medical communication and better scientific work. Meanwhile a great number of gynecological and obstetrical institutions present data via the world wide web within a wide range of quality and performance. Specific HTML editors offer quick and easy presentations, but only advanced internet techniques enable interesting multimedia presentations. N-tier applications are the future standard and we must integrate them in general informatical systems. New Concepts, actual tools and general problems will be discussed and new principles similar to actual E commerce techniques are able to solve our special medical demands. PMID:11562809

  8. Advanced digital modulation: Communication techniques and monolithic GaAs technology

    NASA Technical Reports Server (NTRS)

    Wilson, S. G.; Oliver, J. D., Jr.; Kot, R. C.; Richards, C. R.

    1983-01-01

    Communications theory and practice are merged with state-of-the-art technology in IC fabrication, especially monolithic GaAs technology, to examine the general feasibility of a number of advanced technology digital transmission systems. Satellite-channel models with (1) superior throughput, perhaps 2 Gbps; (2) attractive weight and cost; and (3) high RF power and spectrum efficiency are discussed. Transmission techniques possessing reasonably simple architectures capable of monolithic fabrication at high speeds were surveyed. This included a review of amplitude/phase shift keying (APSK) techniques and the continuous-phase-modulation (CPM) methods, of which MSK represents the simplest case.

  9. Comparison of selected analytical techniques for protein sizing, quantitation and molecular weight determination.

    PubMed

    Goetz, H; Kuschel, M; Wulff, T; Sauber, C; Miller, C; Fisher, S; Woodward, C

    2004-09-30

    Protein analysis techniques are developing fast due to the growing number of proteins obtained by recombinant DNA techniques. In the present paper we compare selected techniques, which are used for protein sizing, quantitation and molecular weight determination: sodium dodecylsulfate-polyacrylamide gel electrophoresis (SDS-PAGE), lab-on-a-chip or microfluidics technology (LoaC), size exclusion chromatography (SEC) and mass spectrometry (MS). We compare advantages and limitations of each technique in respect to different application areas, analysis time, protein sizing and quantitation performance. PMID:15345296

  10. Study of advanced techniques for determining the long term performance of components

    NASA Technical Reports Server (NTRS)

    1973-01-01

    The application of existing and new technology to the problem of determining the long-term performance capability of liquid rocket propulsion feed systems is discussed. The long term performance of metal to metal valve seats in a liquid propellant fuel system is stressed. The approaches taken in conducting the analysis are: (1) advancing the technology of characterizing components through the development of new or more sensitive techniques and (2) improving the understanding of the physical of degradation.

  11. The Double Edge Aerosol and Molecular Techniques for Doppler Lidar Wind Measurement

    NASA Technical Reports Server (NTRS)

    Korb, C. Laurence; Flesia, Cristina

    1998-01-01

    We have developed the theory for aerosol- and molecular-based lidar measurements of the wind using double edge versions of the edge technique. Aerosol-based wind measurements have been made at Goddard Space Flight Center and molecular-based wind measurements at the University of Geneva. We have demonstrated atmospheric measurements using these techniques for altitudes from 1 to more than 10 km. Measurement accuracies of better than 1.25 m/s have been obtained with integration times from 5 to 30 seconds. The measurements can be scaled to space and agree, within a factor of two, with satellite-based simulations of performance based on Poisson statistics.

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

    PubMed

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

    2009-07-01

    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. PMID:19148900

  13. POC-scale testing of an advanced fine coal dewatering equipment/technique

    SciTech Connect

    Groppo, J.G.; Parekh, B.K.; Rawls, P.

    1995-11-01

    Froth flotation technique is an effective and efficient process for recovering of ultra-fine (minus 74 {mu}m) clean coal. Economical dewatering of an ultra-fine clean coal product to a 20 percent level moisture will be an important step in successful implementation of the advanced cleaning processes. This project is a step in the Department of Energy`s program to show that ultra-clean coal could be effectively dewatered to 20 percent or lower moisture using either conventional or advanced dewatering techniques. As the contract title suggests, the main focus of the program is on proof-of-concept testing of a dewatering technique for a fine clean coal product. The coal industry is reluctant to use the advanced fine coal recovery technology due to the non-availability of an economical dewatering process. in fact, in a recent survey conducted by U.S. DOE and Battelle, dewatering of fine clean coal was identified as the number one priority for the coal industry. This project will attempt to demonstrate an efficient and economic fine clean coal slurry dewatering process.

  14. Integrating Organic Matter Structure with Ecosystem Function using Advanced Analytical Chemistry Techniques

    NASA Astrophysics Data System (ADS)

    Boot, C. M.

    2012-12-01

    Microorganisms are the primary transformers of organic matter in terrestrial and aquatic ecosystems. The structure of organic matter controls its bioavailability and researchers have long sought to link the chemical characteristics of the organic matter pool to its lability. To date this effort has been primarily attempted using low resolution descriptive characteristics (e.g. organic matter content, carbon to nitrogen ratio, aromaticity, etc .). However, recent progress in linking these two important ecosystem components has been advanced using advanced high resolution tools (e.g. nuclear magnetic resonance (NMR) spectroscopy, and mass spectroscopy (MS)-based techniques). A series of experiments will be presented that highlight the application of high resolution techniques in a variety of terrestrial and aquatic ecosystems with the focus on how these data explicitly provide the foundation for integrating organic matter structure into our concept of ecosystem function. The talk will highlight results from a series of experiments including: an MS-based metabolomics and fluorescence excitation emission matrix approach evaluating seasonal and vegetation based changes in dissolved organic matter (DOM) composition from arctic soils; Fourier transform ion cyclotron resonance (FTICR) MS and MS metabolomics analysis of DOM from three lakes in an alpine watershed; and the transformation of 13C labeled glucose track with NMR during a rewetting experiment from Colorado grassland soils. These data will be synthesized to illustrate how the application of advanced analytical techniques provides novel insight into our understanding of organic matter processing in a wide range of ecosystems.

  15. PET/SPECT molecular imaging in clinical neuroscience: recent advances in the investigation of CNS diseases

    PubMed Central

    Lu, Feng-Mei

    2015-01-01

    Molecular imaging is an attractive technology widely used in clinical practice that greatly enhances our understanding of the pathophysiology and treatment in central nervous system (CNS) diseases. It is a novel multidisciplinary technique that can be defined as real-time visualization, in vivo characterization and qualification of biological processes at the molecular and cellular level. It involves the imaging modalities and the corresponding imaging agents. Nowadays, molecular imaging in neuroscience has provided tremendous insights into disturbed human brain function. Among all of the molecular imaging modalities, positron emission tomography (PET) and single photon emission computed tomography (SPECT) have occupied a particular position that visualize and measure the physiological processes using high-affinity and high-specificity molecular radioactive tracers as imaging probes in intact living brain. In this review, we will put emphasis on the PET/SPECT applications in Alzheimer’s disease (AD) and Parkinson’s disease (PD) as major CNS disorders. We will first give an overview of the main classical molecular neuroimaging modalities. Then, the major clinical applications of PET and SPECT along with molecular probes in the fields of psychiatry and neurology will be discussed. PMID:26029646

  16. The rapidly evolving therapies for advanced melanoma-Towards immunotherapy, molecular targeted therapy, and beyond.

    PubMed

    Zhu, Ziqiang; Liu, Wei; Gotlieb, Vladimir

    2016-03-01

    The incidence of melanoma in both males and females continues to rise during the past 40 years despite the stable or declining trends for most cancer types. Due to the tremendous advance in immunobiology and molecular biology, breakthroughs in both immunotherapies and molecular targeted therapies have recently revolutionized the standard of care for patients with advanced melanoma. In 2011, US Food and Drug Administration (FDA) approved ipilimumab, an anti-cytotoxic T-lymphocyte antigen-4 (CTLA-4) antibody for metastatic melanoma therapy. Since then, novel drugs including antibodies to programmed cell death 1 (PD-1) such as pembrolizumab and nivolumab (both approved in 2014), selective BRAF inhibitors such as vemurafenib (approved in 2011), dabrafenib (approved in 2013); and MEK inhibitor trametinib (approved in 2013), have greatly extended the potential of immunotherapy and molecular targeted therapy for advanced melanoma. All of which have been demonstrated a significant increase in overall survival rate, and long-term benefits in multiple large clinical trials. Several new agents and novel therapies are currently under phase III clinical trials with the hope of being approved in the near future. We already entered a golden era in oncology that are providing significant survival improvement. In the meantime, new challenges for clinicians also started to emerge. In this review, we presented the existing evidence for the newest treatments for advanced melanoma, including CTLA-4, PD-1/PD-L1 checkpoint inhibitors and BRAF, MEK inhibitors. We also discussed the strengths, limitations and challenges of using these novel therapies, and potential solutions as well as highlighted the areas requiring further research. PMID:26708040

  17. Advances in Rosetta structure prediction for difficult molecular-replacement problems

    SciTech Connect

    DiMaio, Frank

    2013-11-01

    Modeling advances using Rosetta structure prediction to aid in solving difficult molecular-replacement problems are discussed. Recent work has shown the effectiveness of structure-prediction methods in solving difficult molecular-replacement problems. The Rosetta protein structure modeling suite can aid in the solution of difficult molecular-replacement problems using templates from 15 to 25% sequence identity; Rosetta refinement guided by noisy density has consistently led to solved structures where other methods fail. In this paper, an overview of the use of Rosetta for these difficult molecular-replacement problems is provided and new modeling developments that further improve model quality are described. Several variations to the method are introduced that significantly reduce the time needed to generate a model and the sampling required to improve the starting template. The improvements are benchmarked on a set of nine difficult cases and it is shown that this improved method obtains consistently better models in less running time. Finally, strategies for best using Rosetta to solve difficult molecular-replacement problems are presented and future directions for the role of structure-prediction methods in crystallography are discussed.

  18. Accelerated Testing Methodology in Constant Stress-Rate Testing for Advanced Structural Ceramics: A Preloading Technique

    NASA Technical Reports Server (NTRS)

    Choi, Sung R.; Gyekenyesi, John P.; Huebert, Dean; Bartlett, Allen; Choi, Han-Ho

    2001-01-01

    Preloading technique was used as a means of an accelerated testing methodology in constant stress-rate (dynamic fatigue) testing for two different brittle materials. The theory developed previously for fatigue strength as a function of preload was further verified through extensive constant stress-rate testing for glass-ceramic and CRT glass in room temperature distilled water. The preloading technique was also used in this study to identify the prevailing failure mechanisms at elevated temperatures, particularly at lower test rates in which a series of mechanisms would be associated simultaneously with material failure, resulting in significant strength increase or decrease. Two different advanced ceramics including SiC whisker-reinforced composite silicon nitride and 96 wt% alumina were used at elevated temperatures. It was found that the preloading technique can be used as an additional tool to pinpoint the dominant failure mechanism that is associated with such a phenomenon of considerable strength increase or decrease.

  19. Accelerated Testing Methodology in Constant Stress-Rate Testing for Advanced Structural Ceramics: A Preloading Technique

    NASA Technical Reports Server (NTRS)

    Choi, Sung R.; Gyekenyesi, John P.; Huebert, Dean; Bartlett, Allen; Choi, Han-Ho

    2001-01-01

    Preloading technique was used as a means of an accelerated testing methodology in constant stress-rate ('dynamic fatigue') testing for two different brittle materials. The theory developed previously for fatigue strength as a function of preload was further verified through extensive constant stress-rate testing for glass-ceramic and CRT glass in room temperature distilled water. The preloading technique was also used in this study to identify the prevailing failure mechanisms at elevated temperatures, particularly at lower test rate in which a series of mechanisms would be associated simultaneously with material failure, resulting in significant strength increase or decrease. Two different advanced ceramics including SiC whisker-reinforced composite silicon nitride and 96 wt% alumina were used at elevated temperatures. It was found that the preloading technique can be used as an additional tool to pinpoint the dominant failure mechanism that is associated with such a phenomenon of considerable strength increase or decrease.

  20. 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

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

    PubMed

    Ding, Chang; He, Jianzhong

    2012-05-01

    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

  2. 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

  3. 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 previously "shadowed" less abundant species available for PCR amplification. These PCR products obtained with and without PMA treatment will then be subjected to downstream diversity analyses such as sequencing and DNA microarray. It is expected that PMA-coupled PCR will amplify the "minority population" and help in understanding microbial diversity spectrum of an environmental sample at a much deeper level. This new protocol aims to overcome the major potential biases faced when analyzing microbial 16S rRNA gene diversity. This study will lead to a technological advancement and a commercial product that will aid microbial ecologists in understanding microbial diversity from various environmental niches. Implementation of this technique may lead to discoveries of novel microbes and their functions in sustenance of the ecosystem.

  4. Towards a molecular risk map--recent advances on the etiology of inflammatory bowel disease.

    PubMed

    Rosenstiel, Philip; Sina, Christian; Franke, Andre; Schreiber, Stefan

    2009-12-01

    Recent advances have enabled a comprehensive understanding of the genetic architecture of inflammatory bowel disease (IBD) with over 30 identified and replicated disease loci. The pathophysiological consequences of disease gene variants in Crohn disease and ulcerative colitis, the two main subentities of IBD, so far are only understood on the single disease gene level, yet complex network analyses linking the individual risk factors into a molecular risk map are still missing. In this review, we will focus on recent pathways and cellular functions that emerged from the genetic studies (e.g. innate immunity, autophagy) and delineate the existence of shared (e.g. IL23R, IL12B) and unique (e.g. NOD2 for CD) risk factors for the disease subtypes. Ultimately, the defined molecular profiles may identify individuals at risk early in life and may serve as a guidance to administer personalized interventions for causative therapies and/or early targeted prevention strategies. Due to this comparatively advanced level of molecular understanding in the field, IBD may represent precedent also for future developments of individualized genetic medicine in other polygenic disorders in general. PMID:19926490

  5. Advanced spatio-temporal filtering techniques for photogrammetric image sequence analysis in civil engineering material testing

    NASA Astrophysics Data System (ADS)

    Liebold, F.; Maas, H.-G.

    2016-01-01

    The paper shows advanced spatial, temporal and spatio-temporal filtering techniques which may be used to reduce noise effects in photogrammetric image sequence analysis tasks and tools. As a practical example, the techniques are validated in a photogrammetric spatio-temporal crack detection and analysis tool applied in load tests in civil engineering material testing. The load test technique is based on monocular image sequences of a test object under varying load conditions. The first image of a sequence is defined as a reference image under zero load, wherein interest points are determined and connected in a triangular irregular network structure. For each epoch, these triangles are compared to the reference image triangles to search for deformations. The result of the feature point tracking and triangle comparison process is a spatio-temporally resolved strain value field, wherein cracks can be detected, located and measured via local discrepancies. The strains can be visualized as a color-coded map. In order to improve the measuring system and to reduce noise, the strain values of each triangle must be treated in a filtering process. The paper shows the results of various filter techniques in the spatial and in the temporal domain as well as spatio-temporal filtering techniques applied to these data. The best results were obtained by a bilateral filter in the spatial domain and by a spatio-temporal EOF (empirical orthogonal function) filtering technique.

  6. Review of recent advances in analytical techniques for the determination of neurotransmitters

    PubMed Central

    Perry, Maura; Li, Qiang; Kennedy, Robert T.

    2009-01-01

    Methods and advances for monitoring neurotransmitters in vivo or for tissue analysis of neurotransmitters over the last five years are reviewed. The review is organized primarily by neurotransmitter type. Transmitter and related compounds may be monitored by either in vivo sampling coupled to analytical methods or implanted sensors. Sampling is primarily performed using microdialysis, but low-flow push-pull perfusion may offer advantages of spatial resolution while minimizing the tissue disruption associated with higher flow rates. Analytical techniques coupled to these sampling methods include liquid chromatography, capillary electrophoresis, enzyme assays, sensors, and mass spectrometry. Methods for the detection of amino acid, monoamine, neuropeptide, acetylcholine, nucleoside, and soluable gas neurotransmitters have been developed and improved upon. Advances in the speed and sensitivity of these methods have enabled improvements in temporal resolution and increased the number of compounds detectable. Similar advances have enabled improved detection at tissue samples, with a substantial emphasis on single cell and other small samples. Sensors provide excellent temporal and spatial resolution for in vivo monitoring. Advances in application to catecholamines, indoleamines, and amino acids have been prominent. Improvements in stability, sensitivity, and selectivity of the sensors have been of paramount interest. PMID:19800472

  7. Molecular tagging techniques and their applications to the study of complex thermal flow phenomena

    NASA Astrophysics Data System (ADS)

    Chen, Fang; Li, Haixing; Hu, Hui

    2015-08-01

    This review article reports the recent progress in the development of a new group of molecule-based flow diagnostic techniques, which include molecular tagging velocimetry (MTV) and molecular tagging thermometry (MTT), for both qualitative flow visualization of thermally induced flow structures and quantitative whole-field measurements of flow velocity and temperature distributions. The MTV and MTT techniques can also be easily combined to result in a so-called molecular tagging velocimetry and thermometry (MTV&T) technique, which is capble of achieving simultaneous measurements of flow velocity and temperature distribution in fluid flows. Instead of using tiny particles, the molecular tagging techniques (MTV, MTT, and MTV&T) use phosphorescent molecules, which can be turned into long-lasting glowing marks upon excitation by photons of appropriate wavelength, as the tracers for the flow velocity and temperature measurements. The unique attraction and implementation of the molecular tagging techniques are demonstrated by three application examples, which include: (1) to quantify the unsteady heat transfer process from a heated cylinder to the surrounding fluid flow in order to examine the thermal effects on the wake instabilities behind the heated cylinder operating in mixed and forced heat convection regimes, (2) to reveal the time evolution of unsteady heat transfer and phase changing process inside micro-sized, icing water droplets in order to elucidate the underlying physics pertinent to aircraft icing phenomena, and (3) to achieve simultaneous droplet size, velocity and temperature measurements of "in-flight" droplets to characterize the dynamic and thermodynamic behaviors of flying droplets in spray flows.

  8. 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

  9. Recent advances in discovery, heterologous expression, and molecular engineering of cyclodextrin glycosyltransferase for versatile applications.

    PubMed

    Han, Ruizhi; Li, Jianghua; Shin, Hyun-Dong; Chen, Rachel R; Du, Guocheng; Liu, Long; Chen, Jian

    2014-01-01

    Cyclodextrin glycosyltransferase (CGTase) is an important enzyme with multiple functions, in particular the production of cyclodextrins. It is also widely applied in baking and carbohydrate glycosylation because it participates in various types of catalytic reactions. New applications are being found with novel CGTases being isolated from various organisms. Heterologous expression is performed for the overproduction of CGTases to meet the requirements of these applications. In addition, various directed evolution techniques have been applied to modify the molecular structure of CGTase for improved performance in industrial applications. In recent years, substantial progress has been made in the heterologous expression and molecular engineering of CGTases. In this review, we systematically summarize the heterologous expression strategies used for enhancing the production of CGTases. We also outline and discuss the molecular engineering approaches used to improve the production, secretion, and properties (e.g., product and substrate specificity, catalytic efficiency, and thermal stability) of CGTase. PMID:24361954

  10. Application of Advanced Atomic Force Microscopy Techniques to Study Quantum Dots and Bio-materials

    NASA Astrophysics Data System (ADS)

    Guz, Nataliia

    In recent years, there has been an increase in research towards micro- and nanoscale devices as they have proliferated into diverse areas of scientific exploration. Many of the general fields of study that have greatly affected the advancement of these devices includes the investigation of their properties. The sensitivity of Atomic Force Microscopy (AFM) allows detecting charges up to the single electron value in quantum dots in ambient conditions, the measurement of steric forces on the surface of the human cell brush, determination of cell mechanics, magnetic forces, and other important properties. Utilizing AFM methods, the fast screening of quantum dot efficiency and the differences between cancer, normal (healthy) and precancer (immortalized) human cells has been investigated. The current research using AFM techniques can help to identify biophysical differences of cancer cells to advance our understanding of the resistance of the cells against the existing medicine.

  11. New molecular targeted therapies for advanced non-small-cell lung cancer

    PubMed Central

    Méndez, Míriam; Custodio, Ana; Provencio, Mariano

    2011-01-01

    Non-small-cell lung cancer (NSCLC) is a uniformly fatal disease and most patients will present with advanced stage. Treatment outcomes remain unsatisfactory, with low long-term survival rates. Standard treatment, such as palliative chemotherapy and radiotherapy, offers a median survival not exceeding 1 year. Hence, considerable efforts have started to be made in order to identify new biological agents which may safely and effectively be administered to advanced NSCLC patients. Two cancer cell pathways in particular have been exploited, the epidermal growth factor receptor (EGFR) and the vascular endothelial growth factor receptor (VEGFR) pathways. However, novel targeted therapies that interfere with other dysregulated pathways in lung cancer are already in the clinic. This review outlines the most promising research approaches to the treatment of NSCLC, discussed according to the specific molecular pathway targeted. PMID:22263060

  12. Lipophilic Statins as Anticancer Agents: Molecular Targeted Actions and Proposal in Advanced Gynaecological Malignancies.

    PubMed

    Gizzo, Salvatore; Quaranta, Michela; Nardelli, Giovanni Battista; Noventa, Marco

    2015-01-01

    Despite adequate surgery, women affected by advanced-stage gynaecological cancers (ovarian/ endometrial malignancies) carry an extremely poor prognosis; an improved oncological prognosis could largely depend upon the enhancement of adjuvant treatment. Recent data showed that, among women affected by endometrial/ovarian malignancies, a reduced cancer-related mortality was noted in statin-users compared to non-users, suggesting the need for clinical trials to define the anticancerproperties of statins. In vitro/in vivo evidences suggest a potential chemo-preventive effect through induction of cancer-cell apoptosis and inhibition of cancer-cell growth, proliferation, invasion, and metastasis. The potential oncological impact of this discovery compels us to investigate all possible molecular targets for anticancer activities of statins in order to identify a rationale in proposing their administration in association with standard chemotherapy/radiotherapy protocols after adequate surgical-treatment for advanced-stages gynaecological malignancies. PMID:25901529

  13. Advanced MRI techniques to improve our understanding of experience-induced neuroplasticity.

    PubMed

    Tardif, Christine Lucas; Gauthier, Claudine Joëlle; Steele, Christopher John; Bazin, Pierre-Louis; Schäfer, Andreas; Schaefer, Alexander; Turner, Robert; Villringer, Arno

    2016-05-01

    Over the last two decades, numerous human MRI studies of neuroplasticity have shown compelling evidence for extensive and rapid experience-induced brain plasticity in vivo. To date, most of these studies have consisted of simply detecting a difference in structural or functional images with little concern for their lack of biological specificity. Recent reviews and public debates have stressed the need for advanced imaging techniques to gain a better understanding of the nature of these differences - characterizing their extent in time and space, their underlying biological and network dynamics. The purpose of this article is to give an overview of advanced imaging techniques for an audience of cognitive neuroscientists that can assist them in the design and interpretation of future MRI studies of neuroplasticity. The review encompasses MRI methods that probe the morphology, microstructure, function, and connectivity of the brain with improved specificity. We underline the possible physiological underpinnings of these techniques and their recent applications within the framework of learning- and experience-induced plasticity in healthy adults. Finally, we discuss the advantages of a multi-modal approach to gain a more nuanced and comprehensive description of the process of learning. PMID:26318050

  14. New Strategies in Pediatric Gliomas: Molecular Advances in Pediatric Low-Grade Gliomas as a Model

    PubMed Central

    Raabe, Eric; Kieran, Mark W.; Cohen, Kenneth J.

    2015-01-01

    Pediatric low-grade gliomas (pLGG) account for more brain tumors in children than any other histologic subtype. While surgery, chemotherapy and radiation remain the mainstay of upfront treatment, recent advances in molecular interrogation of pLGG have shown a small number of recurring genetic mutations in these tumors that might be exploited therapeutically. Notable findings include abnormalities in the RAS/MAP kinase pathway such as NF-1 loss or BRAF activation and mTOR activation. Recent identification of activating re-arrangements in c-MYB and MYBL1 in pediatric diffuse astrocytoma also provide candidates for therapeutic intervention. Targeting these molecularly identified pathways may allow for improved outcomes for patients as pediatric oncology moves into the era of biology-driven medicine. PMID:23881924

  15. Molecularly targeted therapy for advanced hepatocellular carcinoma - a drug development crisis?

    PubMed Central

    Thillai, Kiruthikah; Ross, Paul; Sarker, Debashis

    2016-01-01

    Hepatocellular carcinoma is the fastest growing cause of cancer related death globally. Sorafenib, a multi-targeted kinase inhibitor, is the only drug proven to improve outcomes in patients with advanced disease offering modest survival benefit. Although comprehensive genomic mapping has improved understanding of the genetic aberrations in hepatocellular cancer (HCC), this knowledge has not yet impacted clinical care. The last few years have seen the failure of several first and second line phase III clinical trials of novel molecularly targeted therapies, warranting a change in the way new therapies are investigated in HCC. Potential reasons for these failures include clinical and molecular heterogeneity, trial design and a lack of biomarkers. This review discusses the current crisis in HCC drug development and how we should learn from recent trial failures to develop a more effective personalised treatment paradigm for patients with HCC. PMID:26909132

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

    NASA Astrophysics Data System (ADS)

    Kilgour, Michael; Segal, Dvira

    2015-07-01

    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, kBT/ɛB > 1/25, with ɛB 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.

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

    PubMed

    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, kBT/ϵB > 1/25, with ϵB 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. PMID:26178094

  18. ADVANCING THE FUNDAMENTAL UNDERSTANDING AND SCALE-UP OF TRISO FUEL COATERS VIA ADVANCED MEASUREMENT AND COMPUTATIONAL TECHNIQUES

    SciTech Connect

    Biswas, Pratim; Al-Dahhan, Muthanna

    2012-11-01

    Tri-isotropic (TRISO) fuel particle coating is critical for the future use of nuclear energy produced byadvanced gas reactors (AGRs). The fuel kernels are coated using chemical vapor deposition in a spouted fluidized bed. The challenges encountered in operating TRISO fuel coaters are due to the fact that in modern AGRs, such as High Temperature Gas Reactors (HTGRs), the acceptable level of defective/failed coated particles is essentially zero. This specification requires processes that produce coated spherical particles with even coatings having extremely low defect fractions. Unfortunately, the scale-up and design of the current processes and coaters have been based on empirical approaches and are operated asœblack boxes. Hence, a voluminous amount of experimental development and trial and error work has been conducted. It has been clearly demonstrated that the quality of the coating applied to the fuel kernels is impacted by the hydrodynamics, solids flow field, and flow regime characteristics of the spouted bed coaters, which themselves are influenced by design parameters and operating variables. Further complicating the outlook for future fuel-coating technology and nuclear energy production is the fact that a variety of new concepts will involve fuel kernels of different sizes and with compositions of different densities. Therefore, without a fundamental understanding the underlying phenomena of the spouted bed TRISO coater, a significant amount of effort is required for production of each type of particle with a significant risk of not meeting the specifications. This difficulty will significantly and negatively impact the applications of AGRs for power generation and cause further challenges to them as an alternative source of commercial energy production. Accordingly, the proposed work seeks to overcome such hurdles and advance the scale-up, design, and performance of TRISO fuel particle spouted bed coaters. The overall objectives of the proposed work are to advance the fundamental understanding of the hydrodynamics by systematically investigating the effect of design and operating variables, to evaluate the reported dimensionless groups as scaling factors, and to establish a reliable scale-up methodology for the TRISO fuel particle spouted bed coaters based on hydrodynamic similarity via advanced measurement and computational techniques. An additional objective is to develop an on-line non-invasive measurement technique based on gamma ray densitometry (i.e. Nuclear Gauge Densitometry) that can be installed and used for coater process monitoring to ensure proper performance and operation and to facilitate the developed scale-up methodology. To achieve the objectives set for the project, the work will use optical probes and gamma ray computed tomography (CT) (for the measurements of solids/voidage holdup cross-sectional distribution and radial profiles along the bed height, spouted diameter, and fountain height) and radioactive particle tracking (RPT) (for the measurements of the 3D solids flow field, velocity, turbulent parameters, circulation time, solids lagrangian trajectories, and many other of spouted bed related hydrodynamic parameters). In addition, gas dynamic measurement techniques and pressure transducers will be utilized to complement the obtained information. The measurements obtained by these techniques will be used as benchmark data to evaluate and validate the computational fluid dynamic (CFD) models (two fluid model or discrete particle model) and their closures. The validated CFD models and closures will be used to facilitate the developed methodology for scale-up, design and hydrodynamic similarity. Successful execution of this work and the proposed tasks will advance the fundamental understanding of the coater flow field and quantify it for proper and safe design, scale-up, and performance. Such achievements will overcome the barriers to AGR applications and will help assure that the US maintains nuclear energy as a feasible option to meet the nation’s needs for energy and environmental safety. In addition, the outcome of the proposed study will have a broader impact on other processes that utilize spouted beds, such as coal gasification, granulation, drying, catalytic reactions, etc.

  19. Advanced Intensity-Modulation Continuous-Wave Lidar Techniques for Column CO2 Measurements

    NASA Astrophysics Data System (ADS)

    Campbell, J. F.; Lin, B.; Nehrir, A. R.; Harrison, F. W.; Obland, M. D.; Ismail, S.; Meadows, B.; Browell, E. V.

    2014-12-01

    Global atmospheric carbon dioxide (CO2) measurements for the NASA Active Sensing of CO2 Emissions over Nights, Days, and Seasons (ASCENDS) space mission are critical for improving our understanding of global CO2 sources and sinks. Advanced Intensity-Modulated Continuous-Wave (IM-CW) lidar techniques are investigated as a means of facilitating CO2 measurements from space to meet the ASCENDS measurement requirements. In recent numerical, laboratory and flight experiments we have successfully used the Binary Phase Shift Keying (BPSK) modulation technique to uniquely discriminate surface lidar returns from intermediate aerosol and cloud contamination. We demonstrate the utility of BPSK to eliminate sidelobes in the range profile as a means of making Integrated Path Differential Absorption (IPDA) column CO2 measurements in the presence of optically thin clouds, thereby eliminating the need to correct for sidelobe bias errors caused by the clouds. Furthermore, high accuracy and precision ranging to the surface as well as to the top of intermediate cloud layers, which is a requirement for the inversion of column CO2 number density measurements to column CO2 mixing ratios, has been demonstrated using new hyperfine interpolation techniques that takes advantage of the periodicity of the modulation waveforms. This approach works well for both BPSK and linear swept-frequency modulation techniques. The BPSK technique under investigation has excellent auto-correlation properties while possessing a finite bandwidth. A comparison of BPSK and linear swept-frequency is also discussed in this paper.

  20. Advanced techniques and technology for efficient data storage, access, and transfer

    NASA Technical Reports Server (NTRS)

    Rice, Robert F.; Miller, Warner

    1991-01-01

    Advanced techniques for efficiently representing most forms of data are being implemented in practical hardware and software form through the joint efforts of three NASA centers. These techniques adapt to local statistical variations to continually provide near optimum code efficiency when representing data without error. Demonstrated in several earlier space applications, these techniques are the basis of initial NASA data compression standards specifications. Since the techniques clearly apply to most NASA science data, NASA invested in the development of both hardware and software implementations for general use. This investment includes high-speed single-chip very large scale integration (VLSI) coding and decoding modules as well as machine-transferrable software routines. The hardware chips were tested in the laboratory at data rates as high as 700 Mbits/s. A coding module's definition includes a predictive preprocessing stage and a powerful adaptive coding stage. The function of the preprocessor is to optimally process incoming data into a standard form data source that the second stage can handle.The built-in preprocessor of the VLSI coder chips is ideal for high-speed sampled data applications such as imaging and high-quality audio, but additionally, the second stage adaptive coder can be used separately with any source that can be externally preprocessed into the 'standard form'. This generic functionality assures that the applicability of these techniques and their recent high-speed implementations should be equally broad outside of NASA.

  1. [Recent advances in the techniques of protein-protein interaction study].

    PubMed

    Wang, Ming-Qiang; Wu, Jin-Xia; Zhang, Yu-Hong; Han, Ning; Bian, Hong-Wu; Zhu, Mu-Yuan

    2013-11-01

    Protein-protein interactions play key roles in the development of organisms and the response to biotic and abiotic stresses. Several wet-lab methods have been developed to study this challenging area,including yeast two-hybrid system, tandem affinity purification, Co-immunoprecipitation, GST Pull-down, bimolecular fluorescence complementation, fluorescence resonance energy transfer and surface plasmon resonance analysis. In this review, we discuss theoretical principles and relative advantages and disvantages of these techniques,with an emphasis on recent advances to compensate for limitations. PMID:24579310

  2. Determination of Electromagnetic Properties of Mesh Material Using Advanced Radiometer Techniques

    NASA Technical Reports Server (NTRS)

    Arrington, R. F.; Blume, H. J. C.

    1985-01-01

    The need for a large diameter deployable antenna to map soil moisture with a 10 kilometer or better resolution using a microwave radiometer is discussed. A 6 meter deployable antenna is also needed to map sea surface temperature on the Navy Remote Ocean Sensor System (NROSS). Both of these deployable antennas require a mesh membrane material as the reflecting surface. The determination of the electromagnetic properties of mesh materials is a difficult problem. The Antenna and Microwave Research Branch (AMRB) of Langley Research Center was asked to measure the material to be used on MROSS by NRL. A cooperative program was initiated to measure this mesh material using two advanced radiometer techniques.

  3. Advances in gas-mediated electron beam-induced etching and related material processing techniques

    NASA Astrophysics Data System (ADS)

    Toth, Milos

    2014-12-01

    Electron beam-induced etching (EBIE) has traditionally been used for top-down, direct-write, chemical dry etching, and iterative editing of materials. The present article reviews recent advances in EBIE modeling and emerging applications, with an emphasis on use cases in which the approaches that have conventionally been used to realize EBIE are instead used for material analysis, surface functionalization, or bottom-up growth of nanostructured materials. Such applications are used to highlight the shortcomings of existing quantitative EBIE models and to identify physicochemical phenomena that must be accounted for in order to enable full exploitation and predictive modeling of EBIE and related electron beam fabrication techniques.

  4. Imaging mass spectrometry of the visual system: Advancing the molecular understanding of retina degenerations.

    PubMed

    Bowrey, Hannah E; Anderson, David M; Pallitto, Patrick; Gutierrez, Danielle B; Fan, Jie; Crouch, Rosalie K; Schey, Kevin L; Ablonczy, Zsolt

    2016-04-01

    Visual sensation is fundamental for quality of life, and loss of vision to retinal degeneration is a debilitating condition. The eye is the only part of the central nervous system that can be noninvasively observed with optical imaging. In the clinics, various spectroscopic methods provide high spatial resolution images of the fundus and the developing degenerative lesions. However, the currently utilized tools are not specific enough to establish the molecular underpinnings of retinal diseases. In contrast, mass spectrometric imaging (MSI) is a powerful tool to identify molecularly specific disease indicators and classification markers. This technique is particularly well suited to the eye, where molecular information can be correlated with clinical data collected via noninvasive diagnostic imaging modalities. Recent studies during the last few recent years have uncovered a plethora of new spatially defined molecular information on several vision-threatening diseases, including age-related macular degeneration, Stargardt disease, glaucoma, cataract, as well as lipid disorders. Even though MS inside the eye cannot be performed noninvasively, by linking diagnostic and molecular information, these studies are the first step toward the development of smart ophthalmic diagnostic and surgical tools. Here, we provide an overview of current approaches applying MSI technology to ocular pathology. PMID:26586164

  5. Effects of Molecular Structure in Macroscopic Mechanical Properties of an Advanced Polymer (LARC(sup TM)-SI)

    NASA Technical Reports Server (NTRS)

    Nicholson, Lee M.; Hinkley, Jeffrey A.; Whitley, Karen S.; Gates, Thomas S.

    2004-01-01

    Mechanical testing of an advanced polymer resin with known variations in molecular weight was performed over a range of temperatures below the glass transition temperature. The elastic properties, inelastic elongation behavior, and notched tensile strength all as a function of molecular weight and test temperature were determined. It was shown that notched tensile strength is a strong function of both temperature and molecular weight, whereas stiffness is only a strong function of temperature.

  6. 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

  7. Probing detonation physics and chemistry using molecular dynamics and quantum chemistry techniques

    SciTech Connect

    Cook, M.D.; Fellows, J.; Haskins, P.J.

    1996-07-01

    Modern quantum chemistry and molecular dynamics computer codes are powerful tools with which to study the physics and chemistry of energetic materials at the molecular level. Quantum chemistry calculations, on one or two energetic molecules, can give valuable information about the initial steps in their decomposition. Molecular dynamics calculations, even with empirical potentials, can yield important information about the physical processes involved in the initiation and growth of reaction of energetic materials. The combination of molecular dynamics and quantum chemistry techniques offers the potential to probe energetic material reaction chemistry in real systems, in some detail, in the near future. Such an approach is vital if one is to be able to create new realistic macroscopic models within hydrocodes that can describe the initiation and growth of reaction in explosives. This paper gives an overview of the approach being adopted at DRA Fort Halstead to understanding energetic materials at the molecular level. In particular, the use of quantum chemistry and molecular dynamics to help construct new macroscopic models will be discussed.

  8. Recent advances in coupling capillary electrophoresis based separation techniques to ESI and MALDI MS

    PubMed Central

    Zhong, Xuefei; Zhang, Zichuan; Jiang, Shan; Li, Lingjun

    2014-01-01

    Coupling capillary electrophoresis (CE) based separation techniques to mass spectrometry creates a powerful platform for analysis of a wide range of biomolecules from complex samples because it combines the high separation efficiency of CE and the sensitivity and selectivity of MS detection. ESI and MALDI, as the most common soft ionization techniques employed for CE and MS coupling, offer distinct advantages for biomolecular characterization. This review is focused primarily on technological advances in combining CE and chip-based CE with ESI and MALDI MS detection in the past five years. Selected applications in the analyses of metabolites, peptides, and proteins with the recently developed CE-MS platforms are also highlighted. PMID:24170529

  9. A comparison of conventional and advanced ultrasonic inspection techniques in the characterization of TMC materials

    NASA Technical Reports Server (NTRS)

    Holland, Mark R.; Handley, Scott M.; Miller, James G.; Reighard, Mark K.

    1992-01-01

    Results obtained with a conventional ultrasonic inspection technique as well as those obtained with more advanced ultrasonic NDE methods in the characterization of an 8-ply quasi-isotropic titanium matrix composite (TMC) specimen are presented. Images obtained from a conventional ultrasonic inspection of TMC material are compared with those obtained using more sophisticated ultrasonic inspection methods. It is suggested that the latter techniques are able to provide quantitative images of TMC material. They are able to reveal the same potential defect indications while simultaneously providing more quantitative information concerning the material's inherent properties. Band-limited signal loss and slope-of-attenuation images provide quantitative data on the inherent material characteristics and defects in TMC.

  10. Recent Advances and New Techniques in Visualization of Ultra-short Relativistic Electron Bunches

    SciTech Connect

    Xiang, Dao; /SLAC

    2012-06-05

    Ultrashort electron bunches with rms length of {approx} 1 femtosecond (fs) can be used to generate ultrashort x-ray pulses in FELs that may open up many new regimes in ultrafast sciences. It is also envisioned that ultrashort electron bunches may excite {approx}TeV/m wake fields for plasma wake field acceleration and high field physics studies. Recent success of using 20 pC electron beam to drive an x-ray FEL at LCLS has stimulated world-wide interests in using low charge beam (1 {approx} 20 pC) to generate ultrashort x-ray pulses (0.1 fs {approx} 10 fs) in FELs. Accurate measurement of the length (preferably the temporal profile) of the ultrashort electron bunch is essential for understanding the physics associated with the bunch compression and transportation. However, the shorter and shorter electron bunch greatly challenges the present beam diagnostic methods. In this paper we review the recent advances in the measurement of ultra-short electron bunches. We will focus on several techniques and their variants that provide the state-of-the-art temporal resolution. Methods to further improve the resolution of these techniques and the promise to break the 1 fs time barrier is discussed. We review recent advances in the measurement of ultrashort relativistic electron bunches. We will focus on several techniques and their variants that are capable of breaking the femtosecond time barrier in measurements of ultrashort bunches. Techniques for measuring beam longitudinal phase space as well as the x-ray pulse shape in an x-ray FEL are also discussed.

  11. Recent advancements in sensing techniques based on functional materials for organophosphate pesticides.

    PubMed

    Kumar, Pawan; Kim, Ki-Hyun; Deep, Akash

    2015-08-15

    The use of organophosphate pesticides (OPs) for pest control in agriculture has caused serious environmental problems throughout the world. OPs are highly toxic with the potential to cause neurological disorders in humans. As the application of OPs has greatly increased in various agriculture activities, it has become imperative to accurately monitor their concentration levels for the protection of ecological systems and food supplies. Although there are many conventional methods available for the detection of OPs, the development of portable sensors is necessary to facilitate routine analysis with more convenience. Some of these potent alternative techniques based on functional materials include fluorescence nanomaterials based sensors, molecular imprinted (MIP) sensors, electrochemical sensors, and biosensors. This review explores the basic features of these sensing approaches through evaluation of their performance. The discussion is extended further to describe the challenges and opportunities for these unique sensing techniques. PMID:25864041

  12. Methods for Quantification of Soil-Transmitted Helminths in Environmental Media: Current Techniques and Recent Advances.

    PubMed

    Collender, Philip A; Kirby, Amy E; Addiss, David G; Freeman, Matthew C; Remais, Justin V

    2015-12-01

    Limiting the environmental transmission of soil-transmitted helminths (STHs), which infect 1.5 billion people worldwide, will require sensitive, reliable, and cost-effective methods to detect and quantify STHs in the environment. We review the state-of-the-art of STH quantification in soil, biosolids, water, produce, and vegetation with regard to four major methodological issues: environmental sampling; recovery of STHs from environmental matrices; quantification of recovered STHs; and viability assessment of STH ova. We conclude that methods for sampling and recovering STHs require substantial advances to provide reliable measurements for STH control. Recent innovations in the use of automated image identification and developments in molecular genetic assays offer considerable promise for improving quantification and viability assessment. PMID:26440788

  13. Linking microbial community structure, interactions and function in anaerobic digesters using new molecular techniques.

    PubMed

    Vanwonterghem, Inka; Jensen, Paul D; Ho, Dang P; Batstone, Damien J; Tyson, Gene W

    2014-06-01

    Over the last decade there has been a rapid development in culture-independent techniques for exploring microbial communities, which have led to new insights into their structure and function in both natural environments and engineered systems. This review focuses on some of the most important recent advances and their applications to the diverse microbial communities associated with anaerobic digestion. The use of these approaches in combination with complementary imaging techniques, chemical isotope analyses and detailed reactor performance measurements provides a new opportunity to develop a fundamental understanding of how microbial community dynamics, interactions and functionality influence digester efficiency and stability. PMID:24863897

  14. Advancement of an Infra-Red Technique for Whole-Field Concentration Measurements in Fluidized Beds.

    PubMed

    Medrano, Jose A; de Nooijer, Niek C A; Gallucci, Fausto; van Sint Annaland, Martin

    2016-01-01

    For a better understanding and description of the mass transport phenomena in dense multiphase gas-solids systems such as fluidized bed reactors, detailed and quantitative experimental data on the concentration profiles is required, which demands advanced non-invasive concentration monitoring techniques with a high spatial and temporal resolution. A novel technique based on the selective detection of a gas component in a gas mixture using infra-red properties has been further developed. The first stage development was carried out using a very small sapphire reactor and CO₂ as tracer gas. Although the measuring principle was demonstrated, the real application was hindered by the small reactor dimensions related to the high costs and difficult handling of large sapphire plates. In this study, a new system has been developed, that allows working at much larger scales and yet with higher resolution. In the new system, propane is used as tracer gas and quartz as reactor material. In this study, a thorough optimization and calibration of the technique is presented which is subsequently applied for whole-field measurements with high temporal resolution. The developed technique allows the use of a relatively inexpensive configuration for the measurement of detailed concentration fields and can be applied to a large variety of important chemical engineering topics. PMID:26927127

  15. Advanced condition monitoring techniques and plant life extension studies at EBR-2

    SciTech Connect

    Singer, R.M.; Gross, K.C. ); Perry, W.H.; King, R.W. )

    1991-01-01

    Numerous advanced techniques have been evaluated and tested at EBR-2 as part of a plant-life extension program for detection of degradation and other abnormalities in plant systems. Two techniques have been determined to be of considerable assistance in planning for the extended-life operation of EBR-2. The first, a computer-based pattern-recognition system (System State Analyzer or SSA) is used for surveillance of the primary system instrumentation, primary sodium pumps and plant heat balances. This surveillance has indicated that the SSA can detect instrumentation degradation and system performance degradation over varying time intervals and can be used to provide derived signal values to replace signals from failed sensors. The second technique, also a computer-based pattern-recognition system (Sequential Probability Ratio Test or SPRT) is used to validate signals and to detect incipient failures in sensors and components or systems. It is being used on the failed fuel detection system and is experimentally used on the primary coolant pumps. Both techniques are described and experience with their operation presented.

  16. Data requirements for advancing techniques to predict dredge-induced sediment and contaminant releases -- A review

    SciTech Connect

    Averett, D.E.

    1995-12-31

    In many areas of the world, contaminated sediments are being considered a major factor in the redistribution of toxic chemicals in the environment. While removal of contaminated sediments from the aquatic environment is often the preferred alternative for reducing the potential impacts of contaminated sediment, regulatory agencies and the public often express concern about contaminant releases during dredging operations. The US Army Corps of Engineers continues to develop techniques for making a priori estimates of the sediment resuspension rates and contaminant releases during hydraulic and mechanical dredging activities. However, appropriate field data to verify and refine these techniques for a wide range of conditions are currently limited. Data needs include physical and operational characteristics of the dredge, waterway characteristics, sediment characteristics, sediment contaminant data, and water quality data collected during the dredging activity. This paper discusses key parameters required to improve the current predictive techniques and outlines the type of monitoring program needed to improve the comparability of the techniques to measured releases. The recommended monitoring program is derived from experiences with previous monitoring efforts. Planners of future dredging demonstrations are encouraged to collect similar data in order to advance the state of the art for predicting sediment and contaminant releases associated with dredging.

  17. Applications of Advanced, Waveform Based AE Techniques for Testing Composite Materials

    NASA Technical Reports Server (NTRS)

    Prosser, William H.

    1996-01-01

    Advanced, waveform based acoustic emission (AE) techniques have been previously used to evaluate damage progression in laboratory tests of composite coupons. In these tests, broad band, high fidelity acoustic sensors were used to detect signals which were then digitized and stored for analysis. Analysis techniques were based on plate mode wave propagation characteristics. This approach, more recently referred to as Modal AE, provides an enhanced capability to discriminate and eliminate noise signals from those generated by damage mechanisms. This technique also allows much more precise source location than conventional, threshold crossing arrival time determination techniques. To apply Modal AE concepts to the interpretation of AE on larger composite structures, the effects of wave propagation over larger distances and through structural complexities must be well characterized and understood. In this research, measurements were made of the attenuation of the extensional and flexural plate mode components of broad band simulated AE signals in large composite panels. As these materials have applications in a cryogenic environment, the effects of cryogenic insulation on the attenuation of plate mode AE signals were also documented.

  18. Advancement of an Infra-Red Technique for Whole-Field Concentration Measurements in Fluidized Beds

    PubMed Central

    Medrano, Jose A.; de Nooijer, Niek C. A.; Gallucci, Fausto; van Sint Annaland, Martin

    2016-01-01

    For a better understanding and description of the mass transport phenomena in dense multiphase gas-solids systems such as fluidized bed reactors, detailed and quantitative experimental data on the concentration profiles is required, which demands advanced non-invasive concentration monitoring techniques with a high spatial and temporal resolution. A novel technique based on the selective detection of a gas component in a gas mixture using infra-red properties has been further developed. The first stage development was carried out using a very small sapphire reactor and CO2 as tracer gas. Although the measuring principle was demonstrated, the real application was hindered by the small reactor dimensions related to the high costs and difficult handling of large sapphire plates. In this study, a new system has been developed, that allows working at much larger scales and yet with higher resolution. In the new system, propane is used as tracer gas and quartz as reactor material. In this study, a thorough optimization and calibration of the technique is presented which is subsequently applied for whole-field measurements with high temporal resolution. The developed technique allows the use of a relatively inexpensive configuration for the measurement of detailed concentration fields and can be applied to a large variety of important chemical engineering topics. PMID:26927127

  19. Biotechnology Apprenticeship for Secondary-Level Students: Teaching Advanced Cell Culture Techniques for Research

    PubMed Central

    Lewis, Jennifer R.; Kotur, Mark S.; Butt, Omar; Kulcarni, Sumant; Riley, Alyssa A.; Ferrell, Nick; Sullivan, Kathryn D.; Ferrari, Mauro

    2002-01-01

    The purpose of this article is to discuss small-group apprenticeships (SGAs) as a method to instruct cell culture techniques to high school participants. The study aimed to teach cell culture practices and to introduce advanced imaging techniques to solve various biomedical engineering problems. Participants designed and completed experiments using both flow cytometry and laser scanning cytometry during the 1-month summer apprenticeship. In addition to effectively and efficiently teaching cell biology laboratory techniques, this course design provided an opportunity for research training, career exploration, and mentoring. Students participated in active research projects, working with a skilled interdisciplinary team of researchers in a large research institution with access to state-of-the-art instrumentation. The instructors, composed of graduate students, laboratory managers, and principal investigators, worked well together to present a real and worthwhile research experience. The students enjoyed learning cell culture techniques while contributing to active research projects. The institution's researchers were equally enthusiastic to instruct and serve as mentors. In this article, we clarify and illuminate the value of small-group laboratory apprenticeships to the institution and the students by presenting the results and experiences of seven middle and high school participants and their instructors. PMID:12587031

  20. Advanced grazing-incidence techniques for modern soft-matter materials analysis

    SciTech Connect

    Hexemer, Alexander; Müller-Buschbaum, Peter

    2015-01-01

    The complex nano-morphology of modern soft-matter materials is successfully probed with advanced grazing-incidence techniques. Based on grazing-incidence small- and wide-angle X-ray and neutron scattering (GISAXS, GIWAXS, GISANS and GIWANS), new possibilities arise which are discussed with selected examples. Due to instrumental progress, highly interesting possibilities for local structure analysis in this material class arise from the use of micro- and nanometer-sized X-ray beams in micro- or nanofocused GISAXS and GIWAXS experiments. The feasibility of very short data acquisition times down to milliseconds creates exciting possibilities forin situandin operandoGISAXS and GIWAXS studies. Tuning the energy of GISAXS and GIWAXS in the soft X-ray regime and in time-of flight GISANS allows the tailoring of contrast conditions and thereby the probing of more complex morphologies. In addition, recent progress in software packages, useful for data analysis for advanced grazing-incidence techniques, is discussed.

  1. Advanced grazing-incidence techniques for modern soft-matter materials analysis

    PubMed Central

    Hexemer, Alexander; Müller-Buschbaum, Peter

    2015-01-01

    The complex nano-morphology of modern soft-matter materials is successfully probed with advanced grazing-incidence techniques. Based on grazing-incidence small- and wide-angle X-ray and neutron scattering (GISAXS, GIWAXS, GISANS and GIWANS), new possibilities arise which are discussed with selected examples. Due to instrumental progress, highly interesting possibilities for local structure analysis in this material class arise from the use of micro- and nanometer-sized X-ray beams in micro- or nanofocused GISAXS and GIWAXS experiments. The feasibility of very short data acquisition times down to milliseconds creates exciting possibilities for in situ and in operando GISAXS and GIWAXS studies. Tuning the energy of GISAXS and GIWAXS in the soft X-ray regime and in time-of flight GISANS allows the tailoring of contrast conditions and thereby the probing of more complex morphologies. In addition, recent progress in software packages, useful for data analysis for advanced grazing-incidence techniques, is discussed. PMID:25610632

  2. Advanced grazing-incidence techniques for modern soft-matter materials analysis

    DOE PAGESBeta

    Hexemer, Alexander; Müller-Buschbaum, Peter

    2015-01-01

    The complex nano-morphology of modern soft-matter materials is successfully probed with advanced grazing-incidence techniques. Based on grazing-incidence small- and wide-angle X-ray and neutron scattering (GISAXS, GIWAXS, GISANS and GIWANS), new possibilities arise which are discussed with selected examples. Due to instrumental progress, highly interesting possibilities for local structure analysis in this material class arise from the use of micro- and nanometer-sized X-ray beams in micro- or nanofocused GISAXS and GIWAXS experiments. The feasibility of very short data acquisition times down to milliseconds creates exciting possibilities forin situandin operandoGISAXS and GIWAXS studies. Tuning the energy of GISAXS and GIWAXS in themore » soft X-ray regime and in time-of flight GISANS allows the tailoring of contrast conditions and thereby the probing of more complex morphologies. In addition, recent progress in software packages, useful for data analysis for advanced grazing-incidence techniques, is discussed.« less

  3. Use of Advanced Magnetic Resonance Imaging Techniques in Neuromyelitis Optica Spectrum Disorder

    PubMed Central

    Kremer, Stephane; Renard, Felix; Achard, Sophie; Lana-Peixoto, Marco A.; Palace, Jacqueline; Asgari, Nasrin; Klawiter, Eric C.; Tenembaum, Silvia N.; Banwell, Brenda; Greenberg, Benjamin M.; Bennett, Jeffrey L.; Levy, Michael; Villoslada, Pablo; Saiz, Albert; Fujihara, Kazuo; Chan, Koon Ho; Schippling, Sven; Paul, Friedemann; Kim, Ho Jin; de Seze, Jerome; Wuerfel, Jens T.

    2016-01-01

    Brain parenchymal lesions are frequently observed on conventional magnetic resonance imaging (MRI) scans of patients with neuromyelitis optica (NMO) spectrum disorder, but the specific morphological and temporal patterns distinguishing them unequivocally from lesions caused by other disorders have not been identified. This literature review summarizes the literature on advanced quantitative imaging measures reported for patients with NMO spectrum disorder, including proton MR spectroscopy, diffusion tensor imaging, magnetization transfer imaging, quantitative MR volumetry, and ultrahigh-field strength MRI. It was undertaken to consider the advanced MRI techniques used for patients with NMO by different specialists in the field. Although quantitative measures such as proton MR spectroscopy or magnetization transfer imaging have not reproducibly revealed diffuse brain injury, preliminary data from diffusion-weighted imaging and brain tissue volumetry indicate greater white matter than gray matter degradation. These findings could be confirmed by ultrahigh-field MRI. The use of nonconventional MRI techniques may further our understanding of the pathogenic processes in NMO spectrum disorders and may help us identify the distinct radiographic features corresponding to specific phenotypic manifestations of this disease. PMID:26010909

  4. Use of Advanced Magnetic Resonance Imaging Techniques in Neuromyelitis Optica Spectrum Disorder.

    PubMed

    Kremer, Stephane; Renard, Felix; Achard, Sophie; Lana-Peixoto, Marco A; Palace, Jacqueline; Asgari, Nasrin; Klawiter, Eric C; Tenembaum, Silvia N; Banwell, Brenda; Greenberg, Benjamin M; Bennett, Jeffrey L; Levy, Michael; Villoslada, Pablo; Saiz, Albert; Fujihara, Kazuo; Chan, Koon Ho; Schippling, Sven; Paul, Friedemann; Kim, Ho Jin; de Seze, Jerome; Wuerfel, Jens T; Cabre, Philippe; Marignier, Romain; Tedder, Thomas; van Pelt, Danielle; Broadley, Simon; Chitnis, Tanuja; Wingerchuk, Dean; Pandit, Lekha; Leite, Maria Isabel; Apiwattanakul, Metha; Kleiter, Ingo; Prayoonwiwat, Naraporn; Han, May; Hellwig, Kerstin; van Herle, Katja; John, Gareth; Hooper, D Craig; Nakashima, Ichiro; Sato, Douglas; Yeaman, Michael R; Waubant, Emmanuelle; Zamvil, Scott; Stüve, Olaf; Aktas, Orhan; Smith, Terry J; Jacob, Anu; O'Connor, Kevin

    2015-07-01

    Brain parenchymal lesions are frequently observed on conventional magnetic resonance imaging (MRI) scans of patients with neuromyelitis optica (NMO) spectrum disorder, but the specific morphological and temporal patterns distinguishing them unequivocally from lesions caused by other disorders have not been identified. This literature review summarizes the literature on advanced quantitative imaging measures reported for patients with NMO spectrum disorder, including proton MR spectroscopy, diffusion tensor imaging, magnetization transfer imaging, quantitative MR volumetry, and ultrahigh-field strength MRI. It was undertaken to consider the advanced MRI techniques used for patients with NMO by different specialists in the field. Although quantitative measures such as proton MR spectroscopy or magnetization transfer imaging have not reproducibly revealed diffuse brain injury, preliminary data from diffusion-weighted imaging and brain tissue volumetry indicate greater white matter than gray matter degradation. These findings could be confirmed by ultrahigh-field MRI. The use of nonconventional MRI techniques may further our understanding of the pathogenic processes in NMO spectrum disorders and may help us identify the distinct radiographic features corresponding to specific phenotypic manifestations of this disease. PMID:26010909

  5. Advanced intensity-modulation continuous-wave lidar techniques for ASCENDS CO2 column measurements

    NASA Astrophysics Data System (ADS)

    Campbell, Joel F.; Lin, Bing; Nehrir, Amin R.; Harrison, F. W.; Obland, Michael D.; Meadows, Byron

    2015-10-01

    Global atmospheric carbon dioxide (CO2) measurements for the NASA Active Sensing of CO2 Emissions over Nights, Days, and Seasons (ASCENDS) space mission are critical for improving our understanding of global CO2 sources and sinks. Advanced Intensity- Modulated Continuous-Wave (IM-CW) lidar techniques are investigated as a means of facilitating CO2 measurements from space to meet the ASCENDS measurement requirements. In recent numerical, laboratory and flight experiments we have successfully used the Binary Phase Shift Keying (BPSK) modulation technique to uniquely discriminate surface lidar returns from intermediate aerosol and cloud contamination. We demonstrate the utility of BPSK to eliminate sidelobes in the range profile as a means of making Integrated Path Differential Absorption (IPDA) column CO2 measurements in the presence of optically thin clouds, thereby eliminating the need to correct for sidelobe bias errors caused by the clouds. Furthermore, high accuracy and precision ranging to the surface as well as to the top of intermediate cloud layers, which is a requirement for the inversion of column CO2 number density measurements to column CO2 mixing ratios, has been demonstrated using new hyperfine interpolation techniques that takes advantage of the periodicity of the modulation waveforms. This approach works well for both BPSK and linear swept-frequency modulation techniques. The BPSK technique under investigation has excellent auto-correlation properties while possessing a finite bandwidth. A comparison of BPSK and linear swept-frequency is also discussed in this paper. These results are extended to include Richardson-Lucy deconvolution techniques to extend the resolution of the lidar beyond that implied by limit of the bandwidth of the modulation, where it is shown useful for making tree canopy measurements.

  6. Advanced Intensity-Modulation Continuous-Wave Lidar Techniques for ASCENDS O2 Column Measurements

    NASA Technical Reports Server (NTRS)

    Campbell, Joel F.; Lin, Bing; Nehrir, Amin R.; Harrison, F. Wallace; Obland, Michael D.; Meadows, Byron

    2015-01-01

    Global atmospheric carbon dioxide (CO2) measurements for the NASA Active Sensing of CO2 Emissions over Nights, Days, and Seasons (ASCENDS) space mission are critical for improving our understanding of global CO2 sources and sinks. Advanced Intensity- Modulated Continuous-Wave (IM-CW) lidar techniques are investigated as a means of facilitating CO2 measurements from space to meet the ASCENDS measurement requirements. In recent numerical, laboratory and flight experiments we have successfully used the Binary Phase Shift Keying (BPSK) modulation technique to uniquely discriminate surface lidar returns from intermediate aerosol and cloud contamination. We demonstrate the utility of BPSK to eliminate sidelobes in the range profile as a means of making Integrated Path Differential Absorption (IPDA) column CO2 measurements in the presence of optically thin clouds, thereby eliminating the need to correct for sidelobe bias errors caused by the clouds. Furthermore, high accuracy and precision ranging to the surface as well as to the top of intermediate cloud layers, which is a requirement for the inversion of column CO2 number density measurements to column CO2 mixing ratios, has been demonstrated using new hyperfine interpolation techniques that takes advantage of the periodicity of the modulation waveforms. This approach works well for both BPSK and linear swept-frequency modulation techniques. The BPSK technique under investigation has excellent auto-correlation properties while possessing a finite bandwidth. A comparison of BPSK and linear swept-frequency is also discussed in this paper. These results are extended to include Richardson-Lucy deconvolution techniques to extend the resolution of the lidar beyond that implied by limit of the bandwidth of the modulation, where it is shown useful for making tree canopy measurements.

  7. Study of solid oxide fuel cell interconnects, protective coatings and advanced physical vapor deposition techniques

    NASA Astrophysics Data System (ADS)

    Gannon, Paul Edward

    High energy conversion efficiency, decreased environmentally-sensitive emissions and fuel flexibility have attracted increasing attention toward solid oxide fuel cell (SOFC) systems for stationary, transportation and portable power generation. Critical durability and cost issues, however, continue to impede wide-spread deployment. Many intermediate temperature (600-800°C) planar SOFC systems employ metallic alloy interconnect components, which physically connect individual fuel cells into electric series, facilitate gas distribution to appropriate SOFC electrode chambers (fuel/anode and oxidant[air]/cathode) and provide SOFC stack mechanical support. These demanding multifunctional requirements challenge commercially-available and inexpensive metallic alloys due to corrosion and related effects. Many ongoing investigations are aimed at enabling inexpensive metallic alloys (via bulk and/or surface modifications) as SOFC interconnects (SOFC(IC)s). In this study, two advanced physical vapor deposition (PVD) techniques: large area filtered vacuum arc deposition (LAFAD), and filtered arc plasma-assisted electron beam PVD (FA-EBPVD) were used to deposit a wide-variety of protective nanocomposite (amorphous/nanocrystalline) ceramic thin-film (<5microm) coatings on commercial and specialty stainless steels with different surface finishes. Both bare and coated steel specimens were subjected to SOFC(IC)-relevant exposures and evaluated using complimentary surface analysis techniques. Significant improvements were observed under simulated SOFC(IC) exposures with many coated specimens at ˜800°C relative to uncoated specimens: stable surface morphology; low area specific resistance (ASR <100mO·cm 2 >1,000 hours); and, dramatically reduced Cr volatility (>30-fold). Analyses and discussions of SOFC(IC) corrosion, advanced PVD processes and protective coating behavior are intended to advance understanding and accelerate the development of durable and commercially-viable SOFC systems.

  8. System Design Techniques for Reducing the Power Requirements of Advanced life Support Systems

    NASA Technical Reports Server (NTRS)

    Finn, Cory; Levri, Julie; Pawlowski, Chris; Crawford, Sekou; Luna, Bernadette (Technical Monitor)

    2000-01-01

    The high power requirement associated with overall operation of regenerative life support systems is a critical Z:p technological challenge. Optimization of individual processors alone will not be sufficient to produce an optimized system. System studies must be used in order to improve the overall efficiency of life support systems. Current research efforts at NASA Ames Research Center are aimed at developing approaches for reducing system power and energy usage in advanced life support systems. System energy integration and energy reuse techniques are being applied to advanced life support, in addition to advanced control methods for efficient distribution of power and thermal resources. An overview of current results of this work will be presented. The development of integrated system designs that reuse waste heat from sources such as crop lighting and solid waste processing systems will reduce overall power and cooling requirements. Using an energy integration technique known as Pinch analysis, system heat exchange designs are being developed that match hot and cold streams according to specific design principles. For various designs, the potential savings for power, heating and cooling are being identified and quantified. The use of state-of-the-art control methods for distribution of resources, such as system cooling water or electrical power, will also reduce overall power and cooling requirements. Control algorithms are being developed which dynamically adjust the use of system resources by the various subsystems and components in order to achieve an overall goal, such as smoothing of power usage and/or heat rejection profiles, while maintaining adequate reserves of food, water, oxygen, and other consumables, and preventing excessive build-up of waste materials. Reductions in the peak loading of the power and thermal systems will lead to lower overall requirements. Computer simulation models are being used to test various control system designs.

  9. Advancing Molecular-Guided Surgery through probe development and testing in a moderate cost evaluation pipeline

    PubMed Central

    Pogue, Brian W; Paulsen, Keith D; Hull, Sally M.; Samkoe, Kimberly S.; Gunn, Jason; Hoopes, Jack; Roberts, David W.; Strong, Theresa V.; Draney, Daniel; Feldwisch, Joachim

    2015-01-01

    Molecular guided oncology surgery has the potential to transform the way decisions about resection are done, and can be critically important in areas such as neurosurgery where the margins of tumor relative to critical normal tissues are not readily apparent from visual or palpable guidance. Yet there are major financial barriers to advancing agents into clinical trials with commercial backing. We observe that development of these agents in the standard biological therapeutic paradigm is not viable, due to the high up front financial investment needed and the limitations in the revenue models of contrast agents for imaging. The hypothesized solution to this problem is to develop small molecular biologicals tagged with an established fluorescent reporter, through the chemical agent approval pathway, targeting a phase 0 trials initially, such that the initial startup phase can be completely funded by a single NIH grant. In this way, fast trials can be completed to de-risk the development pipeline, and advance the idea of fluorescence-guided surgery (FGS) reporters into human testing. As with biological therapies the potential successes of each agent are still moderate, but this process will allow the field to advance in a more stable and productive manner, rather than relying upon isolated molecules developed at high cost and risk. The pathway proposed and tested here uses peptide synthesis of an epidermal growth factor receptor (EGFR)-binding Affibody molecules, uniquely conjugated to IRDye 800CW, developed and tested in academic and industrial laboratories with well-established records for GMP production, fill & finish, toxicity testing, and early phase clinical trials with image guidance. PMID:25914500

  10. Advancing molecular-guided surgery through probe development and testing in a moderate cost evaluation pipeline

    NASA Astrophysics Data System (ADS)

    Pogue, Brian W.; Paulsen, Keith D.; Hull, Sally M.; Samkoe, Kimberley S.; Gunn, Jason; Hoopes, Jack; Roberts, David W.; Strong, Theresa V.; Draney, Daniel; Feldwisch, Joachim

    2015-03-01

    Molecular guided oncology surgery has the potential to transform the way decisions about resection are done, and can be critically important in areas such as neurosurgery where the margins of tumor relative to critical normal tissues are not readily apparent from visual or palpable guidance. Yet there are major financial barriers to advancing agents into clinical trials with commercial backing. We observe that development of these agents in the standard biological therapeutic paradigm is not viable, due to the high up front financial investment needed and the limitations in the revenue models of contrast agents for imaging. The hypothesized solution to this problem is to develop small molecular biologicals tagged with an established fluorescent reporter, through the chemical agent approval pathway, targeting a phase 0 trials initially, such that the initial startup phase can be completely funded by a single NIH grant. In this way, fast trials can be completed to de-risk the development pipeline, and advance the idea of fluorescence-guided surgery (FGS) reporters into human testing. As with biological therapies the potential successes of each agent are still moderate, but this process will allow the field to advance in a more stable and productive manner, rather than relying upon isolated molecules developed at high cost and risk. The pathway proposed and tested here uses peptide synthesis of an epidermal growth factor receptor (EGFR)-binding Affibody molecules, uniquely conjugated to IRDye 800CW, developed and tested in academic and industrial laboratories with well-established records for GMP production, fill and finish, toxicity testing, and early phase clinical trials with image guidance.

  11. 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.

  12. Molecular Profiling-Selected Therapy for Treatment of Advanced Pancreaticobiliary Cancer: A Retrospective Multicenter Study

    PubMed Central

    Epelbaum, Ron; Shacham-Shmueli, Einat; Klein, Baruch; Agbarya, Abed; Brenner, Baruch; Brenner, Ronen; Gez, Eliahu; Golan, Talia; Hubert, Ayala; Purim, Ofer; Temper, Mark; Tepper, Ella; Voss, Andreas; Russell, Kenneth; Dvir, Addie; Soussan-Gutman, Lior; Stemmer, Salomon M.; Geva, Ravit

    2015-01-01

    This multicenter cohort study assessed the impact of molecular profiling (MP) on advanced pancreaticobiliary cancer (PBC). The study included 30 patients treated with MP-guided therapy after failing ≥1 therapy for advanced PBC. Treatment was considered as having benefit for the patient if the ratio between the longest progression-free survival (PFS) on MP-guided therapy and the PFS on the last therapy before MP was ≥1.3. The null hypothesis was that ≤15% of patients gain such benefit. Overall, ≥1 actionable (i.e., predictive of response to specific therapies) biomarker was identified/patient. Immunohistochemistry (the most commonly used method for guiding treatment decisions) identified 1–6 (median: 4) actionable biomarkers per patient. After MP, patients received 1–4 (median: 1) regimens/patient (most commonly, FOLFIRI/XELIRI). In a decision-impact analysis, of the 27 patients for whom treatment decisions before MP were available, 74.1% experienced a treatment decision change in the first line after MP. Twenty-four patients were evaluable for clinical outcome analysis; in 37.5%, the PFS ratio was ≥1.3. In one-sided exact binomial test versus the null hypothesis, P = 0.0015; therefore, the null hypothesis was rejected. In conclusion, our analysis demonstrated the feasibility, clinical decision impact, and potential clinical benefits of MP-guided therapy in advanced PBC. PMID:26161408

  13. 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 18.7nm in resonance wavelength is recorded for this profenofos concentration range. The maximum sensitivity of the sensor is 12.7nm/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. PMID:26706813

  14. Molecular subtype analysis determines the association of advanced breast cancer in Egypt with favorable biology

    PubMed Central

    2011-01-01

    Background Prognostic markers and molecular breast cancer subtypes reflect underlying biological tumor behavior and are important for patient management. Compared to Western countries, women in North Africa are less likely to be prognosticated and treated based on well-characterized markers such as the estrogen receptor (ER), progesterone receptor (PR) and Her2. We conducted this study to determine the prevalence of breast cancer molecular subtypes in the North African country of Egypt as a measure of underlying biological characteristics driving tumor manifestations. Methods To determine molecular subtypes we characterized over 200 tumor specimens obtained from Egypt by performing ER, PR, Her2, CK5/6, EGFR and Ki67 immunohistochemistry. Results Our study demonstrated that the Luminal A subtype, associated with favorable prognosis, was found in nearly 45% of cases examined. However, the basal-like subtype, associated with poor prognosis, was found in 11% of cases. These findings are in sharp contrast to other parts of Africa in which the basal-like subtype is over-represented. Conclusions Egyptians appear to have favorable underlying biology, albeit having advanced disease at diagnosis. These data suggest that Egyptians would largely profit from early detection of their disease. Intervention at the public health level, including education on the benefits of early detection is necessary and would likely have tremendous impact on breast cancer outcome in Egypt. PMID:21961708

  15. Biosynthesis of Polyunsaturated Fatty Acids in Marine Invertebrates: Recent Advances in Molecular Mechanisms

    PubMed Central

    Monroig, Óscar; Tocher, Douglas R.; Navarro, Juan C.

    2013-01-01

    Virtually all polyunsaturated fatty acids (PUFA) originate from primary producers but can be modified by bioconversions as they pass up the food chain in a process termed trophic upgrading. Therefore, although the main primary producers of PUFA in the marine environment are microalgae, higher trophic levels have metabolic pathways that can produce novel and unique PUFA. However, little is known about the pathways of PUFA biosynthesis and metabolism in the levels between primary producers and fish that are largely filled by invertebrates. It has become increasingly apparent that, in addition to trophic upgrading, de novo synthesis of PUFA is possible in some lower animals. The unequivocal identification of PUFA biosynthetic pathways in many invertebrates is complicated by the presence of other organisms within them. These organisms include bacteria and algae with PUFA biosynthesis pathways, and range from intestinal flora to symbiotic relationships that can involve PUFA translocation to host organisms. This emphasizes the importance of studying biosynthetic pathways at a molecular level, and the continual expansion of genomic resources and advances in molecular analysis is facilitating this. The present paper highlights recent research into the molecular and biochemical mechanisms of PUFA biosynthesis in marine invertebrates, particularly focusing on cephalopod molluscs. PMID:24152561

  16. Application of Molecular Profiling in Clinical Trials for Advanced Metastatic Cancers

    PubMed Central

    Williams, P. Mickey; Lih, Chih-Jian; Polley, Eric C.; Chen, Alice P.; Rubinstein, Larry V.; Zhao, Yingdong; Simon, Richard M.; Conley, Barbara A.; Doroshow, James H.

    2015-01-01

    There is growing interest in the application of molecular profiling, including sequencing, genotyping, and/or mRNA expression profiling, to the analysis of patient tumors with the objective of applying these data to inform therapeutic choices for patients with advanced cancers. Multiple clinical trials that are attempting to validate this personalized or precision medicine approach are in various stages of development and execution. Although preliminary data from some of these efforts have fueled excitement about the value and utility of these studies, their execution has also provoked many questions about the best way to approach complicating factors such as tumor heterogeneity and the choice of which genetic mutations to target. This commentary highlights some of the challenges confronting the clinical application of molecular tumor profiling and the various trial designs being utilized to address these challenges. Randomized trials that rigorously test patient response to molecularly targeted agents assigned based on the presence of a defined set of mutations in putative cancer-driving pathways are required to address some of the current challenges and to identify patients likely to benefit from this approach. PMID:25663694

  17. 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.

  18. PREFACE: 16th International workshop on Advanced Computing and Analysis Techniques in physics research (ACAT2014)

    NASA Astrophysics Data System (ADS)

    Fiala, L.; Lokajicek, M.; Tumova, N.

    2015-05-01

    This volume of the IOP Conference Series is dedicated to scientific contributions presented at the 16th International Workshop on Advanced Computing and Analysis Techniques in Physics Research (ACAT 2014), this year the motto was ''bridging disciplines''. The conference took place on September 1-5, 2014, at the Faculty of Civil Engineering, Czech Technical University in Prague, Czech Republic. The 16th edition of ACAT explored the boundaries of computing system architectures, data analysis algorithmics, automatic calculations, and theoretical calculation technologies. It provided a forum for confronting and exchanging ideas among these fields, where new approaches in computing technologies for scientific research were explored and promoted. This year's edition of the workshop brought together over 140 participants from all over the world. The workshop's 16 invited speakers presented key topics on advanced computing and analysis techniques in physics. During the workshop, 60 talks and 40 posters were presented in three tracks: Computing Technology for Physics Research, Data Analysis - Algorithms and Tools, and Computations in Theoretical Physics: Techniques and Methods. The round table enabled discussions on expanding software, knowledge sharing and scientific collaboration in the respective areas. ACAT 2014 was generously sponsored by Western Digital, Brookhaven National Laboratory, Hewlett Packard, DataDirect Networks, M Computers, Bright Computing, Huawei and PDV-Systemhaus. Special appreciations go to the track liaisons Lorenzo Moneta, Axel Naumann and Grigory Rubtsov for their work on the scientific program and the publication preparation. ACAT's IACC would also like to express its gratitude to all referees for their work on making sure the contributions are published in the proceedings. Our thanks extend to the conference liaisons Andrei Kataev and Jerome Lauret who worked with the local contacts and made this conference possible as well as to the program coordinator Federico Carminati and the conference chair Denis Perret-Gallix for their global supervision. Further information on ACAT 2014 can be found at http://www.particle.cz/acat2014

  19. Advances in the molecular dynamics flexible fitting method for cryo-EM modeling.

    PubMed

    McGreevy, Ryan; Teo, Ivan; Singharoy, Abhishek; Schulten, Klaus

    2016-05-01

    Molecular Dynamics Flexible Fitting (MDFF) is an established technique for fitting all-atom structures of molecules into corresponding cryo-electron microscopy (cryo-EM) densities. The practical application of MDFF is simple but requires a user to be aware of and take measures against a variety of possible challenges presented by each individual case. Some of these challenges arise from the complexity of a molecular structure or the limited quality of available structural models and densities to be interpreted, while others stem from the intricacies of MDFF itself. The current article serves as an overview of the strategies that have been developed since MDFF's inception to overcome common challenges and successfully perform MDFF simulations. PMID:26804562

  20. Molecular interactions of benzophenone UV filters with human serum albumin revealed by spectroscopic techniques and molecular modeling.

    PubMed

    Zhang, Feng; Zhang, Jing; Tong, Changlun; Chen, Yadong; Zhuang, Shulin; Liu, Weiping

    2013-12-15

    Benzophenone (BP)-type UV filters have been widely used in many personal care products to protect human from UV exposure. Their dermal applications can cause direct human health risk following accumulation in bloodstream. Few studies have addressed whether BP-type UV filters could bind and alter the structure and function of human serum albumin (HSA), the major carrier protein in plasma. Four benzophenones, BP-1, BP-2, BP-3 and BP-8 were selected to investigate their potentially toxic interactions with HSA and the intrinsic binding mechanism using combined spectroscopies and molecular docking techniques. Four benzophenones significantly quench the intrinsic fluorescence of HSA via static mode. The competitive binding fluorescence assay and molecular docking both revealed that the benzophenones bind at site II of HSA. Their binding constants range from 1.91 × 10(4)M(-1) to 12.96 × 10(4)M(-1) at 296 K. BP-8 interacts with HSA mainly through hydrogen bonding interactions and van der Waals interactions, while hydrophobic interactions and electrostatic interactions are dominant for interactions between BP-1, BP-2, BP-3 and HSA. Molecular docking revealed that the changes in structural moiety and hydrophobicity of four benzophenones account for their different binding affinities. As further revealed by circular dichroism and time-resolved fluorescence decay, these benzophenones cause global and local structural changes of HSA, which illustrates their potential toxicity to cause structural damage of HSA. Two degradation products of BP-3 have higher binding affinities to HSA, suggesting higher potencies in causing adverse effects on human health. PMID:24231334

  1. Contemporary molecular tools in microbial ecology and their application to advancing biotechnology.

    PubMed

    Rashid, Mamoon; Stingl, Ulrich

    2015-12-01

    Novel methods in microbial ecology are revolutionizing our understanding of the structure and function of microbes in the environment, but concomitant advances in applications of these tools to biotechnology are mostly lagging behind. After more than a century of efforts to improve microbial culturing techniques, about 70-80% of microbial diversity - recently called the "microbial dark matter" - remains uncultured. In early attempts to identify and sample these so far uncultured taxonomic lineages, methods that amplify and sequence ribosomal RNA genes were extensively used. Recent developments in cell separation techniques, DNA amplification, and high-throughput DNA sequencing platforms have now made the discovery of genes/genomes of uncultured microorganisms from different environments possible through the use of metagenomic techniques and single-cell genomics. When used synergistically, these metagenomic and single-cell techniques create a powerful tool to study microbial diversity. These genomics techniques have already been successfully exploited to identify sources for i) novel enzymes or natural products for biotechnology applications, ii) novel genes from extremophiles, and iii) whole genomes or operons from uncultured microbes. More can be done to utilize these tools more efficiently in biotechnology. PMID:26409315

  2. 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. PMID:23834846

  3. New advanced surface modification technique: titanium oxide ceramic surface implants: long-term clinical results

    NASA Astrophysics Data System (ADS)

    Szabo, Gyorgy; Kovacs, Lajos; Barabas, Jozsef; Nemeth, Zsolt; Maironna, Carlo

    2001-11-01

    The purpose of this paper is to discuss the background to advanced surface modification technologies and to present a new technique, involving the formation of a titanium oxide ceramic coating, with relatively long-term results of its clinical utilization. Three general techniques are used to modify surfaces: the addition or removal of material and the change of material already present. Surface properties can also be changed without the addition or removal of material, through the laser or electron beam thermal treatment. The new technique outlined in this paper relates to the production of a corrosion-resistant 2000-2500 A thick, ceramic oxide layer with a coherent crystalline structure on the surface of titanium implants. The layer is grown electrochemically from the bulk of the metal and is modified by heat treatment. Such oxide ceramic-coated implants have a number of advantageous properties relative to implants covered with various other coatings: a higher external hardness, a greater force of adherence between the titanium and the oxide ceramic coating, a virtually perfect insulation between the organism and the metal (no possibility of metal allergy), etc. The coated implants were subjected to various physical, chemical, electronmicroscopic, etc. tests for a qualitative characterization. Finally, these implants (plates, screws for maxillofacial osteosynthesis and dental root implants) were applied in surgical practice for a period of 10 years. Tests and the experience acquired demonstrated the good properties of the titanium oxide ceramic-coated implants.

  4. Measurements of the subcriticality using advanced technique of shooting source during operation of NPP reactors

    SciTech Connect

    Lebedev, G. V. Petrov, V. V.; Bobylyov, V. T.; Butov, R. I.; Zhukov, A. M.; Sladkov, A. A.

    2014-12-15

    According to the rules of nuclear safety, the measurements of the subcriticality of reactors should be carried out in the process of performing nuclear hazardous operations. An advanced technique of shooting source of neutrons is proposed to meet this requirement. As such a source, a pulsed neutron source (PNS) is used. In order to realize this technique, it is recommended to enable a PNS with a frequency of 1–20 Hz. The PNS is stopped after achieving a steady-state (on average) number of neutrons in the reactor volume. The change in the number of neutrons in the reactor volume is measured in time with an interval of discreteness of ∼0.1 s. The results of these measurements with the application of a system of point-kinetics equations are used in order to calculate the sought subcriticality. The basic idea of the proposed technique used to measure the subcriticality is elaborated in a series of experiments on the Kvant assembly. The conditions which should be implemented in order to obtain a positive result of measurements are formulated. A block diagram of the basic version of the experimental setup is presented, whose main element is a pulsed neutron generator.

  5. Advances of Peripheral Nerve Repair Techniques to Improve Hand Function: A Systematic Review of Literature

    PubMed Central

    P, Mafi; S, Hindocha; M, Dhital; M, Saleh

    2012-01-01

    Concepts of neuronal damage and repair date back to ancient times. The research in this topic has been growing ever since and numerous nerve repair techniques have evolved throughout the years. Due to our greater understanding of nerve injuries and repair we now distinguish between central and peripheral nervous system. In this review, we have chosen to concentrate on peripheral nerve injuries and in particular those involving the hand. There are no reviews bringing together and summarizing the latest research evidence concerning the most up-to-date techniques used to improve hand function. Therefore, by identifying and evaluating all the published literature in this field, we have summarized all the available information about the advances in peripheral nerve techniques used to improve hand function. The most important ones are the use of resorbable poly[(R)-3-hydroxybutyrate] (PHB), epineural end-to-end suturing, graft repair, nerve transfer, side to side neurorrhaphy and end to side neurorrhaphy between median, radial and ulnar nerves, nerve transplant, nerve repair, external neurolysis and epineural sutures, adjacent neurotization without nerve suturing, Agee endoscopic operation, tourniquet induced anesthesia, toe transfer and meticulous intrinsic repair, free auto nerve grafting, use of distal based neurocutaneous flaps and tubulization. At the same time we found that the patient’s age, tension of repair, time of repair, level of injury and scar formation following surgery affect the prognosis. Despite the thorough findings of this systematic review we suggest that further research in this field is needed. PMID:22431951

  6. Molecular techniques to detect and identify protozoan parasites in the environment.

    PubMed

    Cacciò, Simone M

    2003-01-01

    The environmental route of transmission is important for many protozoan and helminth parasites, with water, soil and food being particularly significant. Both the potential for producing large numbers of transmissive stages and their environmental robustness pose persistent threats to public and veterinary health. The introduction of molecular techniques, in particular those based on the amplification of nucleic acids, has provided researchers with highly sensitive and specific assays for the detection and identification of these pathogens. The application of these techniques to clinical, environmental, and food samples is instrumental for a thorough understanding of the epidemiology of the infection and for the implementation of control measures. Here, the advantages and drawbacks of some molecular techniques (Polymerase Chain Reaction--PCR; Reverse-Transcriptase PCR--RT-PCR; Real-time PCR--qPCR; Nucleic Acid Sequence-Based Amplification--NASBA) will be briefly reviewed. Some application of these techniques will be illustrated with reference to two important and widespread human parasites, the apicomplexan Cryptosporidium and the flagellate Giardia. PMID:15058811

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

    NASA Astrophysics Data System (ADS)

    Schierz, Philipp; Zierenberg, Johannes; Janke, Wolfhard

    2015-10-01

    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.

  8. 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.

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

    PubMed

    Schierz, Philipp; Zierenberg, Johannes; Janke, Wolfhard

    2015-10-01

    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. PMID:26450299

  10. Evaluation of targeted therapies in advanced breast cancer: the need for large-scale molecular screening and transformative clinical trial designs.

    PubMed

    Fadoukhair, Z; Zardavas, D; Chad, M A; Goulioti, T; Aftimos, P; Piccart, M

    2016-04-01

    Breast cancer (BC) has been classified into four intrinsic subtypes through seminal studies employing gene expression profiling analysis of primary tumours, namely the luminal A and B subtypes, the human epidermal growth factor receptor 2-like subtype and the basal-like subtype. More recently, the emergence of high-throughput genomic sequencing techniques, such as next-generation or massive parallel sequencing has expanded our understanding of the complex genomic landscapes of BC, with marked intertumour heterogeneity seen among different patients. In addition, increasing evidence indicates intratumour heterogeneity, with molecular differences observed within one patient, both spatially and longitudinally. These phenomena have an impact on the clinical development of molecularly targeted agents, with the classical paradigm of population-based clinical trials being no longer efficient. In the era of genomically driven oncology, three complementary tools can accelerate the clinical development of targeted agents for advanced BC as follows: (i) the implementation of molecular profiling of metastatic tumour lesions, as exemplified by the AURORA (Aiming to Understand the Molecular Aberrations in Metastatic Breast Cancer) programme; (ii) serial assessments of circulating tumour DNA, allowing a more thorough molecular interrogation of metastatic tumour burden; and (iii) new innovative clinical trial designs able to address the challenges of the increasing molecular fragmentation of BC. PMID:26119941

  11. Effects of age, system experience, and navigation technique on driving with an advanced traveler information system.

    PubMed

    Dingus, T A; Hulse, M C; Mollenhauer, M A; Fleischman, R N; McGehee, D V; Manakkal, N

    1997-06-01

    This paper explores the effects of age, system experience, and navigation technique on driving, navigation performance, and safety for drivers who used TravTek, an Advanced Traveler Information System. The first two studies investigated various route guidance configurations on the road in a specially equipped instrumented vehicle with an experimenter present. The third was a naturalistic quasi-experimental field study that collected data unobtrusively from more than 1200 TravTek rental car drivers with no in-vehicle experimenter. The results suggest that with increased experience, drivers become familiar with the system and develop strategies for substantially more efficient and safer use. The results also showed that drivers over age 65 had difficulty driving and navigating concurrently. They compensated by driving slowly and more cautiously. Despite this increased caution, older drivers made more safety-related errors than did younger drivers. The results also showed that older drivers benefited substantially from a well-designed ATIS driver interface. PMID:9302887

  12. Visualisation of Ecohydrological Processes and Relationships for Teaching Using Advanced Techniques

    NASA Astrophysics Data System (ADS)

    Guan, H.; Wang, H.; Gutierrez-Jurado, H. A.; Yang, Y.; Deng, Z.

    2014-12-01

    Ecohydrology is an emerging discipline with a rapid research growth. This calls for enhancing ecohydrology education in both undergraduate and postgraduate levels. In other hydrology disciplines, hydrological processes are commonly observed in environments (e.g. streamflow, infiltration) or easily demonstrated in labs (e.g. Darcy's column). It is relatively difficult to demonstrate ecohydrological concepts and processes (e.g. soil-vegetation water relationship) in teaching. In this presentation, we report examples of using some advanced techniques to illustrate ecohydrological concepts, relationships, and processes, with measurements based on a native vegetation catchment in South Australia. They include LIDAR images showing the relationship between topography-control hdyroclimatic conditions and vegetation distribution, electrical resistivity tomography derived images showing stem structures, continuous stem water potential monitoring showing diurnal variations of plant water status, root zone moisture depletion during dry spells, and responses to precipitation inputs, and incorporating sapflow measurements to demonstrate environmental stress on plant stomatal behaviours.

  13. Advances in the transient dc photocurrent technique for excited state dipole moment measurements

    SciTech Connect

    Smirnov, S.N.; Braun, C.L.

    1998-08-01

    Recent advances in the transient dc photocurrent technique for measuring excited state dipole moments, developed in our group, are discussed. A variety of approaches with detailed analyses of their advantages and disadvantages including cell design, circuit construction tricks, the data acquisition procedure, calibration, and the theoretical treatment of different conditions, are presented. Sensitivity, time resolution limitations, and newly developed features, such as the signal{close_quote}s dependence on light polarization as well as charge separation at interfaces are outlined. Dipole moments of a few molecules (diphenylcyclopropenone, bianthryl, dimethylaminonitrostilbene, Coumarin 153, and fluoroprobe) suitable for calibration purpose are reported{emdash}some of them for the first time. {copyright} {ital 1998 American Institute of Physics.}

  14. Planning and scheduling the Hubble Space Telescope: Practical application of advanced techniques

    NASA Technical Reports Server (NTRS)

    Miller, Glenn E.

    1994-01-01

    NASA's Hubble Space Telescope (HST) is a major astronomical facility that was launched in April, 1990. In late 1993, the first of several planned servicing missions refurbished the telescope, including corrections for a manufacturing flaw in the primary mirror. Orbiting above the distorting effects of the Earth's atmosphere, the HST provides an unrivaled combination of sensitivity, spectral coverage and angular resolution. The HST is arguably the most complex scientific observatory ever constructed and effective use of this valuable resource required novel approaches to astronomical observation and the development of advanced software systems including techniques to represent scheduling preferences and constraints, a constraint satisfaction problem (CSP) based scheduler and a rule based planning system. This paper presents a discussion of these systems and the lessons learned from operational experience.

  15. Locally advanced and metastatic basal cell carcinoma: molecular pathways, treatment options and new targeted therapies.

    PubMed

    Ruiz Salas, Veronica; Alegre, Marta; Garcés, Joan Ramón; Puig, Lluis

    2014-06-01

    The hedgehog (Hh) signaling pathway has been identified as important to normal embryonic development in living organisms and it is implicated in processes including cell proliferation, differentiation and tissue patterning. Aberrant Hh pathway has been involved in the pathogenesis and chemotherapy resistance of different solid and hematologic malignancies. Basal cell carcinoma (BCC) and medulloblastoma are two well-recognized cancers with mutations in components of the Hh pathway. Vismodegib has recently approved as the first inhibitor of one of the components of the Hh pathway (smoothened). This review attempts to provide current data on the molecular pathways involved in the development of BCC and the therapeutic options available for the treatment of locally advanced and metastatic BCC, and the new targeted therapies in development. PMID:24611655

  16. Advancement of polarizable force field and its use for molecular modeling and design.

    PubMed

    Xu, Peijun; Wang, Jinguang; Xu, Yong; Chu, Huiying; Liu, Jiahui; Zhao, Meixia; Zhang, Depeng; Mao, Yingchen; Li, Beibei; Ding, Yang; Li, Guohui

    2015-01-01

    The most important requirement of biomolecular modeling is to deal with electrostatic energies. The electrostatic polarizability is an important part of electrostatic interaction for simulation systems. However, AMBER, CHARMM, OPLS, GROMOS, MMFF force fields etc. used in the past mostly apply fixed atomic center point charge to describe electrostatic energies, and are not sufficient for considering the influence of the electrostatic polarization. The emergence of polarizable force fields has solved this problem. In recent years, quickly developed polarizable force fields have involved a lot of fields. The chapter relating to polarizable force fields spread over several aspects. Firstly, we reviewed the history of the classical force fields and compared with polarizable force fields to elucidate the advancements of polarizable force fields. Secondly, it is introduced that the application of polarizable force fields to small molecules and biological macromolecules simulation, including molecular design. Finally, a brief development trend and perspective is given on rapidly growing polarizable force fields. PMID:25387957

  17. Characterization of ACLV for advanced technology nodes using scatterometer-based lens fingerprinting technique

    NASA Astrophysics Data System (ADS)

    Wang, ChangAn; Zhang, Guohong; DeMoor, Stephen; Tan, Colin; Ilzhoefer, John; Atkinson, Chris; Wickman, Chad; Hansen, Steve; Geh, Bernd; Flagello, Donis G.; Boehm, Mark

    2004-05-01

    Gate CD control is crucial to transistor fabrication for advanced technology nodes at and beyond 65 nm. ACLV (across chip linewidth variation) has been identified as a major contributor to overall CD budget for low k1 lithography. In this paper, we present a detailed characterization of ACLV performance on the latest ASML scanner using Texas Instruments proprietary scatterometer based lens fingerprinting technique (ScatterLith). We are able to decompose a complex ACLV signature including patterns placed in both vertical and horizontal directions and trace the CD errors back to various scanner components such as lens aberrations, illumination source shape, dynamic image field, and scan synchronization. Lithography simulation plays an important role in bringing together the wafer and tool metrology for direct correlation and providing a quantitative understanding of pattern sensitivity to lens and illuminator errors for a particular process setup. A new ACLV characterization methodology is enabled by combining wafer metrology ScattereLith, scanner metrology and lithography simulation. Implementation of this methodology improves tool-to-tool matching and control on ACLV and V-H bias across multiple scanners to meet tight yield and speed requirements for advanced chip manufacturing.

  18. PREFACE: 14th International Workshop on Advanced Computing and Analysis Techniques in Physics Research (ACAT 2011)

    NASA Astrophysics Data System (ADS)

    Teodorescu, Liliana; Britton, David; Glover, Nigel; Heinrich, Gudrun; Lauret, Jérôme; Naumann, Axel; Speer, Thomas; Teixeira-Dias, Pedro

    2012-06-01

    ACAT2011 This volume of Journal of Physics: Conference Series is dedicated to scientific contributions presented at the 14th International Workshop on Advanced Computing and Analysis Techniques in Physics Research (ACAT 2011) which took place on 5-7 September 2011 at Brunel University, UK. The workshop series, which began in 1990 in Lyon, France, brings together computer science researchers and practitioners, and researchers from particle physics and related fields in order to explore and confront the boundaries of computing and of automatic data analysis and theoretical calculation techniques. It is a forum for the exchange of ideas among the fields, exploring and promoting cutting-edge computing, data analysis and theoretical calculation techniques in fundamental physics research. This year's edition of the workshop brought together over 100 participants from all over the world. 14 invited speakers presented key topics on computing ecosystems, cloud computing, multivariate data analysis, symbolic and automatic theoretical calculations as well as computing and data analysis challenges in astrophysics, bioinformatics and musicology. Over 80 other talks and posters presented state-of-the art developments in the areas of the workshop's three tracks: Computing Technologies, Data Analysis Algorithms and Tools, and Computational Techniques in Theoretical Physics. Panel and round table discussions on data management and multivariate data analysis uncovered new ideas and collaboration opportunities in the respective areas. This edition of ACAT was generously sponsored by the Science and Technology Facility Council (STFC), the Institute for Particle Physics Phenomenology (IPPP) at Durham University, Brookhaven National Laboratory in the USA and Dell. We would like to thank all the participants of the workshop for the high level of their scientific contributions and for the enthusiastic participation in all its activities which were, ultimately, the key factors in the success of the workshop. Further information on ACAT 2011 can be found at http://acat2011.cern.ch Dr Liliana Teodorescu Brunel University ACATgroup The PDF also contains details of the workshop's committees and sponsors.

  19. Characterization of water movement in a reconstructed slope in Keokuk, Iowa, using advanced geophysical techniques

    NASA Astrophysics Data System (ADS)

    Schettler, Megan Elizabeth

    This project addresses the topic of evaluating water movement inside a hillslope using a combination of conventional and advanced geophysical techniques. While slope dynamics have been widely studied, ground water movement in hills is still poorly understood. A combination of piezometers, ground-penetrating radar (GPR), and electrical resistivity (ER) surveys were used in an effort to monitor fluctuations in the subsurface water level in a reengineered slope near Keokuk, Iowa. This information, integrated with rainfall data, formed a picture of rainfall-groundwater response dynamics. There were two hypotheses: 1) that the depth and fluctuation of the water table could be accurately sensed using a combination of monitoring wells, ground-penetrating radar and resistivity surveys; and 2) that the integration of data from the instrumentation array and the geophysical surveys would enable the characterization of water movement in the slope in response to rainfall events. This project also sought to evaluate the utility and limitations of using these techniques in landslide and hydrology studies, advance our understanding of hillslope hydrology, and improve our capacity to better determine when slope failure may occur. Results from monitoring wells, stratigraphy, and resistivity surveys at the study site indicated the presence of a buried swale, channelizing subsurface storm flow and creating variations in groundwater. Although there was some success in defining hydrologic characteristics and response of the slope using this integrated approach, it was determined that GPR was ultimately not well suited to this site. However, the use of GPR as part of an integrated approach to study hillslope hydrology still appears to hold potential, and future work to further evaluate the applicability and potential of this approach would be warranted.

  20. Theory of the double-edge molecular technique for Doppler lidar wind measurement.

    PubMed

    Flesia, C; Korb, C L

    1999-01-20

    The theory of the double-edge lidar technique for measuring the wind with molecular backscatter is described. Two high-spectral-resolution edge filters are located in the wings of the Rayleigh-Brillouin profile. This doubles the signal change per unit Doppler shift, the sensitivity, and improves measurement accuracy relative to the single-edge technique by nearly a factor of 2. The use of a crossover region where the sensitivity of a molecular- and an aerosol-based measurement is equal is described. Use of this region desensitizes the molecular measurement to the effects of aerosol scattering over a velocity range of +/-100 m/s. We give methods for correcting short-term, shot-to-shot, frequency jitter and drift with a laser reference frequency measurement and methods for long-term frequency correction with a servo control system. The effects of Rayleigh-Brillouin scattering on the measurement are shown to be significant and are included in the analysis. Simulations for a conical scanning satellite-based lidar at 355 nm show an accuracy of 2-3 m/s for altitudes of 2-15 km for a 1-km vertical resolution, a satellite altitude of 400 km, and a 200 km x 200 km spatial resolution. PMID:18305631

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

    PubMed

    Fu, Ji; Lin, Guole

    2016-01-25

    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. PMID:26797832

  2. A multiscale modeling technique for bridging molecular dynamics with finite element method

    SciTech Connect

    Lee, Yongchang Basaran, Cemal

    2013-11-15

    In computational mechanics, molecular dynamics (MD) and finite element (FE) analysis are well developed and most popular on nanoscale and macroscale analysis, respectively. MD can very well simulate the atomistic behavior, but cannot simulate macroscale length and time due to computational limits. FE can very well simulate continuum mechanics (CM) problems, but has the limitation of the lack of atomistic level degrees of freedom. Multiscale modeling is an expedient methodology with a potential to connect different levels of modeling such as quantum mechanics, molecular dynamics, and continuum mechanics. This study proposes a new multiscale modeling technique to couple MD with FE. The proposed method relies on weighted average momentum principle. A wave propagation example has been used to illustrate the challenges in coupling MD with FE and to verify the proposed technique. Furthermore, 2-Dimensional problem has also been used to demonstrate how this method would translate into real world applications. -- Highlights: •A weighted averaging momentum method is introduced for bridging molecular dynamics (MD) with finite element (FE) method. •The proposed method shows excellent coupling results in 1-D and 2-D examples. •The proposed method successfully reduces the spurious wave reflection at the border of MD and FE regions. •Big advantages of the proposed method are simplicity and inexpensive computational cost of multiscale analysis.

  3. Advances in functional X-ray imaging techniques and contrast agents

    PubMed Central

    Chen, Hongyu; Rogalski, Melissa M.

    2012-01-01

    X-rays have been used for non-invasive high-resolution imaging of thick biological specimens since their discovery in 1895. They are widely used for structural imaging of bone, metal implants, and cavities in soft tissue. Recently, a number of new contrast methodologies have emerged which are expanding X-ray’s biomedical applications to functional as well as structural imaging. These techniques are promising to dramatically improve our ability to study in situ biochemistry and disease pathology. In this review, we discuss how X-ray absorption, X-ray fluorescence, and X-ray excited optical luminescence can be used for physiological, elemental, and molecular imaging of vasculature, tumours, pharmaceutical distribution, and the surface of implants. Imaging of endogenous elements, exogenous labels, and analytes detected with optical indicators will be discussed. PMID:22962667

  4. A comparative assessment of molecular biological and direct microscopic techniques for assessing aquatic systems.

    PubMed

    Knapp, C W; Findlay, D L; Kidd, K A; Graham, D W

    2008-10-01

    Molecular techniques have clear value for community characterization; however, almost all previous datasets are based upon non-molecular measurements and it is hard to compare "old" data with "new" data because few correlations have been made. Therefore, the purpose of this evaluation was to simultaneously use molecular and non-molecular methods within the same sampling program to determine how data compare. Three methods were used for characterizing microbial populations in Lake 260 (L260) at Experimental Lakes Area (Ontario, Canada) during a whole-lake exposure study. Methods included whole-cell microscopic counts (for bacteria, cyanobacteria, algae and zooplankton), chlorophyll a, and small sub-unit (ssu)-rRNA hybridization using EUB-338, EUB-785, CYAN-785-a/b, EUCA-1379 and UNIV-1390 gene probes. Strong correlations were found between the EUB-785 probe signal and "bacteria minus cyanobacteria" direct counts, and the EUB-338 probe signal and "bacteria plus cyanobacteria" counts. Furthermore, the difference in probe signal between EUB-338 and EUB-785 (a presumptive signature for cyanobacteria and plastids) correlated with cyanobacterial direct counts and also with chlorophyll a. However, EUCA-1379 probe signal did not correlate with algae counts, and UNIV-1390 probe signal only correlated with total bacteria counts. Results suggest that, although ssu-rRNA methods are fast, reproducible, and specifically detect "viable" organisms, their use may be limited to non-eukaryotic populations unless new probes are developed that are more specific. PMID:18071916

  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 photogrammetry (for model attitude and deformation measurement) are excluded to limit the scope of this report. Other physical probes such as heat flux gauges, total temperature probes are also excluded. We further exclude measurement techniques that require particle seeding though particle based methods may still be useful in many high speed flow applications. This manuscript details some of the more widely used molecular-based measurement techniques for studying transition and turbulence: laser-induced fluorescence (LIF), Rayleigh and Raman Scattering and coherent anti-Stokes Raman scattering (CARS). These techniques are emphasized, in part, because of the prior experience of the authors. Additional molecular based techniques are described, albeit in less detail. Where possible, an effort is made to compare the relative advantages and disadvantages of the various measurement techniques, although these comparisons can be subjective views of the authors. Finally, the manuscript concludes by evaluating the different measurement techniques in view of the precision requirements described in this chapter. Additional requirements and considerations are discussed to assist with choosing an optical measurement technique for a given application.

  6. STED-FLCS: An Advanced Tool to Reveal Spatiotemporal Heterogeneity of Molecular Membrane Dynamics.

    PubMed

    Vicidomini, Giuseppe; Ta, Haisen; Honigmann, Alf; Mueller, Veronika; Clausen, Mathias P; Waithe, Dominic; Galiani, Silvia; Sezgin, Erdinc; Diaspro, Alberto; Hell, Stefan W; Eggeling, Christian

    2015-09-01

    Heterogeneous diffusion dynamics of molecules play an important role in many cellular signaling events, such as of lipids in plasma membrane bioactivity. However, these dynamics can often only be visualized by single-molecule and super-resolution optical microscopy techniques. Using fluorescence lifetime correlation spectroscopy (FLCS, an extension of fluorescence correlation spectroscopy, FCS) on a super-resolution stimulated emission depletion (STED) microscope, we here extend previous observations of nanoscale lipid dynamics in the plasma membrane of living mammalian cells. STED-FLCS allows an improved determination of spatiotemporal heterogeneity in molecular diffusion and interaction dynamics via a novel gated detection scheme, as demonstrated by a comparison between STED-FLCS and previous conventional STED-FCS recordings on fluorescent phosphoglycerolipid and sphingolipid analogues in the plasma membrane of live mammalian cells. The STED-FLCS data indicate that biophysical and biochemical parameters such as the affinity for molecular complexes strongly change over space and time within a few seconds. Drug treatment for cholesterol depletion or actin cytoskeleton depolymerization not only results in the already previously observed decreased affinity for molecular interactions but also in a slight reduction of the spatiotemporal heterogeneity. STED-FLCS specifically demonstrates a significant improvement over previous gated STED-FCS experiments and with its improved spatial and temporal resolution is a novel tool for investigating how heterogeneities of the cellular plasma membrane may regulate biofunctionality. PMID:26235350

  7. STED-FLCS: An Advanced Tool to Reveal Spatiotemporal Heterogeneity of Molecular Membrane Dynamics

    PubMed Central

    2015-01-01

    Heterogeneous diffusion dynamics of molecules play an important role in many cellular signaling events, such as of lipids in plasma membrane bioactivity. However, these dynamics can often only be visualized by single-molecule and super-resolution optical microscopy techniques. Using fluorescence lifetime correlation spectroscopy (FLCS, an extension of fluorescence correlation spectroscopy, FCS) on a super-resolution stimulated emission depletion (STED) microscope, we here extend previous observations of nanoscale lipid dynamics in the plasma membrane of living mammalian cells. STED-FLCS allows an improved determination of spatiotemporal heterogeneity in molecular diffusion and interaction dynamics via a novel gated detection scheme, as demonstrated by a comparison between STED-FLCS and previous conventional STED-FCS recordings on fluorescent phosphoglycerolipid and sphingolipid analogues in the plasma membrane of live mammalian cells. The STED-FLCS data indicate that biophysical and biochemical parameters such as the affinity for molecular complexes strongly change over space and time within a few seconds. Drug treatment for cholesterol depletion or actin cytoskeleton depolymerization not only results in the already previously observed decreased affinity for molecular interactions but also in a slight reduction of the spatiotemporal heterogeneity. STED-FLCS specifically demonstrates a significant improvement over previous gated STED-FCS experiments and with its improved spatial and temporal resolution is a novel tool for investigating how heterogeneities of the cellular plasma membrane may regulate biofunctionality. PMID:26235350

  8. Advanced contrast nanoagents for photoacoustic molecular imaging, cytometry, blood test and photothermal theranostics†

    PubMed Central

    de la Zerda, Adam; Kim, Jin-Woo; Galanzha, Ekaterina I.; Gambhir, Sanjiv S.; Zharov, Vladimir P.

    2013-01-01

    Various nanoparticles have raised significant interest over the past decades for their unique physical and optical properties and biological utilities. Here we summarize the vast applications of advanced nanoparticles with a focus on carbon nanotube (CNT)-based or CNT-catalyzed contrast agents for photoacoustic (PA) imaging, cytometry and theranostics applications based on the photothermal (PT) effect. We briefly review the safety and potential toxicity of the PA/PT contrast nanoagents, while showing how the physical properties as well as multiple biological coatings change their toxicity profiles and contrasts. We provide general guidelines needed for the validation of a new molecular imaging agent in living subjects, and exemplify these guidelines with single-walled CNTs targeted to αvβ3, an integrin associated with tumor angiogenesis, and golden carbon nanotubes targeted to LYVE-1, endothelial lymphatic receptors. An extensive review of the potential applications of advanced contrast agents is provided, including imaging of static targets such as tumor angiogenesis receptors, in vivo cytometry of dynamic targets such as circulating tumor cells and nanoparticles in blood, lymph, bones and plants, methods to enhance the PA and PT effects with transient and stationary bubble conjugates, PT/PA Raman imaging and multispectral histology. Finally, theranostic applications are reviewed, including the nanophotothermolysis of individual tumor cells and bacteria with clustered nanoparticles, nanothrombolysis of blood clots, detection and purging metastasis in sentinel lymph nodes, spectral hole burning and multiplex therapy with ultrasharp rainbow nanoparticles. PMID:22025336

  9. Advances in the clinicopathological and molecular classification of cutaneous mesenchymal neoplasms.

    PubMed

    Costigan, Danielle C; Doyle, Leona A

    2016-05-01

    In recent years, there have been several important refinements in the classification of cutaneous mesenchymal neoplasms, including the description of new tumour types, along with the identification of novel and recurrent molecular genetic findings. In addition to providing new insights into tumour biology, many of these advances have had significant clinical consequences with regard to diagnostics, management, and prognostication. Newly described entities include pseudomyogenic haemangioendothelioma, haemosiderotic fibrolipomatous tumour, and fibroblastic connective tissue naevus, which are reviewed in the context of the principal differential diagnoses and significant clinical implications. Genetic characterization of several soft tissue tumour types that occur in the skin has resulted in the identification of diagnostically useful markers: ALK gene rearrangement with corresponding ALK protein expression by immunohistochemistry in epithelioid fibrous histiocytoma; the WWTR1-CAMTA1 fusion gene with CAMTA1 protein expression in epithelioid haemangioendothelioma; MYC amplification and overexpression in radiation-associated angiosarcoma; and EWSR1 gene rearrangement in cutaneous myoepithelial tumours. Finally, the classification of intradermal smooth muscle tumours and unclassified/pleomorphic dermal sarcoma has been refined, resulting in both improved classification and improved prognostication. Many of the tumour types listed above are encountered not only by specialist dermatopathologists, but also by practising general surgical pathologists, and this review should therefore provide a widely applicable update on the histological and molecular classification of cutaneous mesenchymal neoplasms, along with the appropriate use of ancillary diagnostic tests, in particular immunohistochemistry, in the evaluation of such lesions and their histological mimics. PMID:26763770

  10. Advancements in sensing and perception using structured lighting techniques :an LDRD final report.

    SciTech Connect

    Novick, David Keith; Padilla, Denise D.; Davidson, Patrick A. Jr.; Carlson, Jeffrey J.

    2005-09-01

    This report summarizes the analytical and experimental efforts for the Laboratory Directed Research and Development (LDRD) project entitled ''Advancements in Sensing and Perception using Structured Lighting Techniques''. There is an ever-increasing need for robust, autonomous ground vehicles for counterterrorism and defense missions. Although there has been nearly 30 years of government-sponsored research, it is undisputed that significant advancements in sensing and perception are necessary. We developed an innovative, advanced sensing technology for national security missions serving the Department of Energy, the Department of Defense, and other government agencies. The principal goal of this project was to develop an eye-safe, robust, low-cost, lightweight, 3D structured lighting sensor for use in broad daylight outdoor applications. The market for this technology is wide open due to the unavailability of such a sensor. Currently available laser scanners are slow, bulky and heavy, expensive, fragile, short-range, sensitive to vibration (highly problematic for moving platforms), and unreliable for outdoor use in bright sunlight conditions. Eye-safety issues are a primary concern for currently available laser-based sensors. Passive, stereo-imaging sensors are available for 3D sensing but suffer from several limitations : computationally intensive, require a lighted environment (natural or man-made light source), and don't work for many scenes or regions lacking texture or with ambiguous texture. Our approach leveraged from the advanced capabilities of modern CCD camera technology and Center 6600's expertise in 3D world modeling, mapping, and analysis, using structured lighting. We have a diverse customer base for indoor mapping applications and this research extends our current technology's lifecycle and opens a new market base for outdoor 3D mapping. Applications include precision mapping, autonomous navigation, dexterous manipulation, surveillance and reconnaissance, part inspection, geometric modeling, laser-based 3D volumetric imaging, simultaneous localization and mapping (SLAM), aiding first responders, and supporting soldiers with helmet-mounted LADAR for 3D mapping in urban-environment scenarios. The technology developed in this LDRD overcomes the limitations of current laser-based 3D sensors and contributes to the realization of intelligent machine systems reducing manpower need.

  11. Screening Platform toward New Anti-HIV Aptamers Set on Molecular Docking and Fluorescence Quenching Techniques.

    PubMed

    Oliviero, Giorgia; Stornaiuolo, Mariano; D'Atri, Valentina; Nici, Fabrizia; Yousif, Ali Munaim; D'Errico, Stefano; Piccialli, Gennaro; Mayol, Luciano; Novellino, Ettore; Marinelli, Luciana; Grieco, Paolo; Carotenuto, Alfonso; Noppen, Sam; Liekens, Sandra; Balzarini, Jan; Borbone, Nicola

    2016-02-16

    By using a new rapid screening platform set on molecular docking simulations and fluorescence quenching techniques, three new anti-HIV aptamers targeting the viral surface glycoprotein 120 (gp120) were selected, synthesized, and assayed. The use of the short synthetic fluorescent peptide V35-Fluo mimicking the V3 loop of gp120, as the molecular target for fluorescence-quenching binding affinity studies, allowed one to measure the binding affinities of the new aptamers for the HIV-1 gp120 without the need to obtain and purify the full recombinant gp120 protein. The almost perfect correspondence between the calculated Kd and the experimental EC50 on HIV-infected cells confirmed the reliability of the platform as an alternative to the existing methods for aptamer selection and measuring of aptamer-protein equilibria. PMID:26810800

  12. 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.

  13. Direct pulse technique for spontaneous polarization dynamics and molecular reorientation processes in ferroelectric liquid crystals

    NASA Astrophysics Data System (ADS)

    Bawa, S. S.; Biradar, A. M.; Saxena, K.; Chandra, Subhas

    1988-09-01

    A method has been devised for studying the spontaneous polarization, dynamics of polarization reversal, and the molecular reorientation processes that occur in the bulk and surfaces of ferroelectric liquid crystals. These studies have been carried out by analyzing the current response to triangular- and square-wave forms. The current response to a triangular wave yields the spontaneous polarization by conveniently subtracting the background contribution due to the conductive and capacitive currents. Molecular reorientation processes which take place within the bulk and the boundary surface layer can be studied by the appearance of polarization current peaks on the triangular-wave response. The dynamics of polarization reversal between bistable states and of the polarization change between the zero-field relaxed state and either of the saturation remanent polarization states have been studied by applying ``symmetric'' and ``asymmetric'' square waves. The technique can also be successfully applied to solid ferroelectrics for studying the spontaneous polarization and the domain dynamics during switching.

  14. Advanced 3D-Sonographic Imaging as a Precise Technique to Evaluate Tumor Volume

    PubMed Central

    Pflanzer, R.; Hofmann, M.; Shelke, A.; Habib, A.; Derwich, W.; Schmitz-Rixen, T.; Bernd, A.; Kaufmann, R.; Bereiter-Hahn, J.

    2014-01-01

    Determination of tumor volume in subcutaneously inoculated xenograft models is a standard procedure for clinical and preclinical evaluation of tumor response to treatment. Practitioners frequently use a hands-on caliper method in conjunction with a simplified formula to assess tumor volume. Non-invasive and more precise techniques as investigation by MR or (μ)CT exist but come with various adverse effects in terms of radiation, complex setup or elevated cost of investigations. Therefore, we propose an advanced three-dimensional sonographic imaging technique to determine small tumor volumes in xenografts with high precision and minimized observer variability. We present a study on xenograft carcinoma tumors from which volumes and shapes were calculated with the standard caliper method as well as with a clinically available three-dimensional ultrasound scanner and subsequent processing software. Statistical analysis reveals the suitability of this non-invasive approach for the purpose of a quick and precise calculation of tumor volume in small rodents. PMID:25500076

  15. Recoil separators for radiative capture using radioactive ion beams. Recent advances and detection techniques

    NASA Astrophysics Data System (ADS)

    Ruiz, Chris; Greife, Uwe; Hager, Ulrike

    2014-06-01

    Radiative capture reactions involving the fusion of hydrogen or helium are ubiquitous in the stellar history of the universe, and are some of the most important reactions in the processes that govern nucleosynthesis and energy generation in both static and explosive scenarios. However, radiative capture reactions pose some of the most difficult experimental challenges due to extremely small cross sections. With the advent of recoil separators and techniques in inverse kinematics, it is now possible to measure radiative capture reactions on very short-lived radioactive nuclei, and in the presence of high experimental backgrounds. In this paper we review the experimental needs for making measurements of astrophysical importance on radiative capture reactions. We also review some of the important historical advances in the field of recoil separators as well as describe current techniques and performance milestones, including descriptions of some of the separators most recently working at radioactive ion beam facilities, such as DRAGON at TRIUMF and the DRS at the Holifield Radioactive Ion Beam Facility. We will also summarize some of the scientific highlight measurements at the RIB facilities.

  16. Advanced Modeling Techniques to Study Anthropogenic Influences on Atmospheric Chemical Budgets

    NASA Technical Reports Server (NTRS)

    Mathur, Rohit

    1997-01-01

    This research work is a collaborative effort between research groups at MCNC and the University of North Carolina at Chapel Hill. The overall objective of this research is to improve the level of understanding of the processes that determine the budgets of chemically and radiatively active compounds in the atmosphere through development and application of advanced methods for calculating the chemical change in atmospheric models. The research performed during the second year of this project focused on four major aspects: (1) The continued development and refinement of multiscale modeling techniques to address the issue of the disparate scales of the physico-chemical processes that govern the fate of atmospheric pollutants; (2) Development and application of analysis methods utilizing process and mass balance techniques to increase the interpretive powers of atmospheric models and to aid in complementary analysis of model predictions and observations; (3) Development of meteorological and emission inputs for initial application of the chemistry/transport model over the north Atlantic region; and, (4) The continued development and implementation of a totally new adaptive chemistry representation that changes the details of what is represented as the underlying conditions change.

  17. Comments on advanced, time-resolved imaging techniques for free-electron laser (FEL) experiments

    SciTech Connect

    Lumpkin, A.H.

    1992-11-01

    An extensive set of time-resolved imaging experiments has been performed on rf-linac driven free-electron lasers (FELs) over the past few years. These experiments have addressed both micropulse and macropulse timescales on both the charged-particle beam and the wiggler/undulator outputs (spontaneous emission and lasing). A brief review of first measurements on photoinjecter micropulse elongation, submacropulse phase slew in drive lasers, submacropulse wavelength shifts in lasers, etc. is presented. This is followed by discussions of new measurements of 35-MeV electron beam micropulse bunch length (<10 ps) using optical transition radiation, some of the first single bend synchrotron radiation beam profile measurements at gamma <80, and comments on the low-jitter synchroscan streak camera tuner. These techniques will be further developed on the 200-650 MeV linac test stand at the Advanced Photon Source (APS) in the next few years. Such techniques should be adaptable to many of the present FEL designs and to some aspects of the next generation of light sources.

  18. Comments on advanced, time-resolved imaging techniques for free-electron laser (FEL) experiments

    SciTech Connect

    Lumpkin, A.H.

    1992-01-01

    An extensive set of time-resolved imaging experiments has been performed on rf-linac driven free-electron lasers (FELs) over the past few years. These experiments have addressed both micropulse and macropulse timescales on both the charged-particle beam and the wiggler/undulator outputs (spontaneous emission and lasing). A brief review of first measurements on photoinjecter micropulse elongation, submacropulse phase slew in drive lasers, submacropulse wavelength shifts in lasers, etc. is presented. This is followed by discussions of new measurements of 35-MeV electron beam micropulse bunch length (<10 ps) using optical transition radiation, some of the first single bend synchrotron radiation beam profile measurements at gamma <80, and comments on the low-jitter synchroscan streak camera tuner. These techniques will be further developed on the 200-650 MeV linac test stand at the Advanced Photon Source (APS) in the next few years. Such techniques should be adaptable to many of the present FEL designs and to some aspects of the next generation of light sources.

  19. Updates in advanced diffusion-weighted magnetic resonance imaging techniques in the evaluation of prostate cancer

    PubMed Central

    Vargas, Hebert Alberto; Lawrence, Edward Malnor; Mazaheri, Yousef; Sala, Evis

    2015-01-01

    Diffusion-weighted magnetic resonance imaging (DW-MRI) is considered part of the standard imaging protocol for the evaluation of patients with prostate cancer. It has been proven valuable as a functional tool for qualitative and quantitative analysis of prostate cancer beyond anatomical MRI sequences such as T2-weighted imaging. This review discusses ongoing controversies in DW-MRI acquisition, including the optimal number of b-values to be used for prostate DWI, and summarizes the current literature on the use of advanced DW-MRI techniques. These include intravoxel incoherent motion imaging, which better accounts for the non-mono-exponential behavior of the apparent diffusion coefficient as a function of b-value and the influence of perfusion at low b-values. Another technique is diffusion kurtosis imaging (DKI). Metrics from DKI reflect excess kurtosis of tissues, representing its deviation from Gaussian diffusion behavior. Preliminary results suggest that DKI findings may have more value than findings from conventional DW-MRI for the assessment of prostate cancer. PMID:26339460

  20. Advanced system identification techniques for wind turbine structures with special emphasis on modal parameters

    SciTech Connect

    Bialasiewicz, J.T.

    1995-06-01

    The goal of this research is to develop advanced system identification techniques that can be used to accurately measure the frequency response functions of a wind-turbine structure immersed in wind noise. To allow for accurate identification, the authors have developed a special test signal called the Pseudo-Random Binary Sequence (PRBS). The Matlab program that generates this signal allows the user to interactively tailor its parameters for the frequency range of interest based on the response of the wind turbine under test. By controlling NREL`s Mobile Hydraulic Shaker System, which is attached to the wind turbine structure, the PRBS signal produces the wide-band excitation necessary to perform system identification in the presence of wind noise. The techniques presented here will enable researchers to obtain modal parameters from an operating wind turbine, including frequencies, damping coefficients, and mode shapes. More importantly, the algorithms they have developed and tested (so far using input-output data from a simulated structure) permit state-space representation of the system under test, particularly the modal state space representation. This is the only system description that reveals the internal behavior the system, such as the interaction between the physical parameters, and which, in contrast to transfer functions, is valid for non-zero initial conditions.

  1. Procedural guidance using advance imaging techniques for percutaneous edge-to-edge mitral valve repair.

    PubMed

    Quaife, Robert A; Salcedo, Ernesto E; Carroll, John D

    2014-02-01

    The complexity of structural heart disease interventions such as edge-to edge mitral valve repair requires integration of multiple highly technical imaging modalities. Real time imaging with 3-dimensional (3D) echocardiography is a relatively new technique that first, allows clear volumetric imaging of target structures such as the mitral valve for both pre-procedural diagnosis and planning in patients with degenerative or functional mitral valve regurgitation. Secondly it provides intra-procedural, real-time panoramic volumetric 3D view of structural heart disease targets that facilitates eye-hand coordination while manipulating devices within the heart. X-ray fluoroscopy and RT 3D TEE images are used in combination to display specific targets and movement of catheter based technologies in 3D space. This integration requires at least two different image display monitors and mentally fusing the individual datasets by the operator. Combined display technology such as this, allow rotation and orientation of both dataset perspectives necessary to define targets and guidance of structural disease device procedures. The inherently easy concept of direct visual feedback and eye-hand coordination allows safe and efficient completion of MitraClip procedures. This technology is now merged into a single structural heart disease guidance mode called EchoNavigator(TM) (Philips Medical Imaging Andover, MA). These advanced imaging techniques have revolutionized the field of structural heart disease interventions and this experience is exemplified by a cooperative imaging approach used for guidance of edge-to-edge mitral valve repair procedures. PMID:24430014

  2. Investigation to advance prediction techniques of the low-speed aerodynamics of V/STOL aircraft

    NASA Technical Reports Server (NTRS)

    Maskew, B.; Strash, D.; Nathman, J.; Dvorak, F. A.

    1985-01-01

    A computer program, VSAERO, has been applied to a number of V/STOL configurations with a view to advancing prediction techniques for the low-speed aerodynamic characteristics. The program couples a low-order panel method with surface streamline calculation and integral boundary layer procedures. The panel method--which uses piecewise constant source and doublet panels-includes an iterative procedure for wake shape and models boundary layer displacement effect using the source transpiration technique. Certain improvements to a basic vortex tube jet model were installed in the code prior to evaluation. Very promising results were obtained for surface pressures near a jet issuing at 90 deg from a flat plate. A solid core model was used in the initial part of the jet with a simple entrainment model. Preliminary representation of the downstream separation zone significantly improve the correlation. The program accurately predicted the pressure distribution inside the inlet on the Grumman 698-411 design at a range of flight conditions. Furthermore, coupled viscous/potential flow calculations gave very close correlation with experimentally determined operational boundaries dictated by the onset of separation inside the inlet. Experimentally observed degradation of these operational boundaries between nacelle-alone tests and tests on the full configuration were also indicated by the calculation. Application of the program to the General Dynamics STOL fighter design were equally encouraging. Very close agreement was observed between experiment and calculation for the effects of power on pressure distribution, lift and lift curve slope.

  3. Coulomb-explosion technique for determining geometrical structures of molecular ions

    SciTech Connect

    Gemmell, D.S.

    1981-01-01

    Traditional experimental techniques (e.g. studies on photon absorption or emission) for determining the sterochemical structures of neutral molecules are extremeley difficult to apply to molecular ions because of problems in obtaining a sufficient spatial density of the ions to be studied. Recent high-resolution measurements on the energy and angle distributions of the fragments produced when fast (MeV) molecular-ion beams from an electrostatic accelerator dissociate (Coulomb explode) in thin foils and in gases, offer promising possibilities for deducing the sterochemical structures of the molecular ions constituting the incident beams. Bond lengths have been determined in this way for several diatomic projectiles (H/sub 2//sup +/, HeH/sup +/, CH/sup +/, NH/sup +/, OH/sup +/, N/sub 2//sup +/, O/sub 2//sup +/, etc.) with an accuracy of approx. 0.01 A. H/sub 3//sup +/ has been demonstrated (for the first time) to be equilateral triangular and the interproton distance measured. Measurements on single fragments from CO/sub 2//sup +/, N/sub 2/O/sup +/, C/sub 3/H/sub 3//sup +/, and CH/sub n//sup +/ have revealed the gross structures of the projectiles. An apparatus has recently been constructed at Argonne to permit precise measurements on fragments in coincidence. The apparatus has been tested on a known structure (OH/sub 2//sup +/). The O-H bond length was found to be 1.0 +- 0.04 A and the H-O-H bond angle was measured as 110 --- 2/sup 0/. These values are in excellent agreement with those found in optical experiments (0.999 A and 110.5/sup 0/). This Coulomb explosion technique can be expected to be refined in accuracy and to be extended to a wide range of molecular ions whose structures are inaccessible by other means.

  4. Penicillium marneffei Infection and Recent Advances in the Epidemiology and Molecular Biology Aspects

    PubMed Central

    Vanittanakom, Nongnuch; Cooper, Chester R.; Fisher, Matthew C.; Sirisanthana, Thira

    2006-01-01

    Penicillium marneffei infection is an important emerging public health problem, especially among patients infected with human immunodeficiency virus in the areas of endemicity in southeast Asia, India, and China. Within these regions, P. marneffei infection is regarded as an AIDS-defining illness, and the severity of the disease depends on the immunological status of the infected individual. Early diagnosis by serologic and molecular assay-based methods have been developed and are proving to be important in diagnosing infection. The occurrence of natural reservoirs and the molecular epidemiology of P. marneffei have been studied; however, the natural history and mode of transmission of the organism remain unclear. Soil exposure, especially during the rainy season, has been suggested to be a critical risk factor. Using a highly discriminatory molecular technique, multilocus microsatellite typing, to characterize this fungus, several isolates from bamboo rats and humans were shown to share identical multilocus genotypes. These data suggest either that transmission of P. marneffei may occur from rodents to humans or that rodents and humans are coinfected from common environmental sources. These putative natural cycles of P. marneffei infection need further investigation. Studies on the fungal genetics of P. marneffei have been focused on the characterization of genetic determinants that may play important roles in asexual development, mycelial-to-yeast phase transition, and the expression of antigenic determinants. Molecular studies have identified several genes involved in germination, hyphal development, conidiogenesis, and yeast cell polarity. A number of functionally important genes, such as the malate synthase- and catalase-peroxidase protein-encoding genes, have been identified as being upregulated in the yeast phase. Future investigations pertaining to the roles of these genes in host-fungus interactions may provide the key knowledge to understanding the pathogenicity of P. marneffei. PMID:16418525

  5. The Synergy Between Total Scattering and Advanced Simulation Techniques: Quantifying Geopolymer Gel Evolution

    SciTech Connect

    White, Claire; Bloomer, Breaunnah E.; Provis, John L.; Henson, Neil J.; Page, Katharine L.

    2012-05-16

    With the ever increasing demands for technologically advanced structural materials, together with emerging environmental consciousness due to climate change, geopolymer cement is fast becoming a viable alternative to traditional cements due to proven mechanical engineering characteristics and the reduction in CO2 emitted (approximately 80% less CO2 emitted compared to ordinary Portland cement). Nevertheless, much remains unknown regarding the kinetics of the molecular changes responsible for nanostructural evolution during the geopolymerization process. Here, in-situ total scattering measurements in the form of X-ray pair distribution function (PDF) analysis are used to quantify the extent of reaction of metakaolin/slag alkali-activated geopolymer binders, including the effects of various activators (alkali hydroxide/silicate) on the kinetics of the geopolymerization reaction. Restricting quantification of the kinetics to the initial ten hours of reaction does not enable elucidation of the true extent of the reaction, but using X-ray PDF data obtained after 128 days of reaction enables more accurate determination of the initial extent of reaction. The synergies between the in-situ X-ray PDF data and simulations conducted by multiscale density functional theory-based coarse-grained Monte Carlo analysis are outlined, particularly with regard to the potential for the X-ray data to provide a time scale for kinetic analysis of the extent of reaction obtained from the multiscale simulation methodology.

  6. PREFACE: 15th International Workshop on Advanced Computing and Analysis Techniques in Physics Research (ACAT2013)

    NASA Astrophysics Data System (ADS)

    Wang, Jianxiong

    2014-06-01

    This volume of Journal of Physics: Conference Series is dedicated to scientific contributions presented at the 15th International Workshop on Advanced Computing and Analysis Techniques in Physics Research (ACAT 2013) which took place on 16-21 May 2013 at the Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China. The workshop series brings together computer science researchers and practitioners, and researchers from particle physics and related fields to explore and confront the boundaries of computing and of automatic data analysis and theoretical calculation techniques. This year's edition of the workshop brought together over 120 participants from all over the world. 18 invited speakers presented key topics on the universe in computer, Computing in Earth Sciences, multivariate data analysis, automated computation in Quantum Field Theory as well as computing and data analysis challenges in many fields. Over 70 other talks and posters presented state-of-the-art developments in the areas of the workshop's three tracks: Computing Technologies, Data Analysis Algorithms and Tools, and Computational Techniques in Theoretical Physics. The round table discussions on open-source, knowledge sharing and scientific collaboration stimulate us to think over the issue in the respective areas. ACAT 2013 was generously sponsored by the Chinese Academy of Sciences (CAS), National Natural Science Foundation of China (NFSC), Brookhaven National Laboratory in the USA (BNL), Peking University (PKU), Theoretical Physics Cernter for Science facilities of CAS (TPCSF-CAS) and Sugon. We would like to thank all the participants for their scientific contributions and for the en- thusiastic participation in all its activities of the workshop. Further information on ACAT 2013 can be found at http://acat2013.ihep.ac.cn. Professor Jianxiong Wang Institute of High Energy Physics Chinese Academy of Science Details of committees and sponsors are available in the PDF

  7. 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.

  8. Recent Research and Progress in Food, Feed and Nutrition with Advanced Synchrotron-based SR-IMS and DRIFT Molecular Spectroscopy.

    PubMed

    Liu, Na; Yu, Peiqiang

    2016-04-25

    Ultraspatially resolved synchrotron radiation based infrared microspectroscopy is able to detect the structure features of a food or feed tissue at cellular and molecular levels. However, to date, this advanced synchrotron-based technique is almost unknown to food and feed scientists. The objective of this article was to introduce this novel analytical technology, ultra-spatially resolved synchrotron radiation based infrared microspectroscopy (SR-IMS) to food, feed, conventional nutrition, and molecular nutrition scientists. The emphasis of this review focused on the following areas: (1) Principles of molecular spectroscopy for food and feed structure research, such as protein molecular structure, carbohydrate conformation, heating induced protein structure changes, and effect of gene-transformation on food and feed structure; (2) Molecular spectral analysis methodology; (3) Biological applications of synchrotron SR-IMS and DRIFT spectroscopy; and (4) Recent progress in food, feed and nutrition research program. The information described in this article gives better insight in food structure research progress and update. PMID:25148108

  9. Strategies for improved accuracy and efficiency with advanced intensity modulated radiation therapy techniques

    NASA Astrophysics Data System (ADS)

    Westerly, David C.

    2009-11-01

    The development of advanced intensity modulated radiation therapy (IMRT) techniques has led to significant improvements in our ability to treat complicated target volumes with minimal collateral damage to the surrounding healthy tissue. These techniques however, come at the cost of increased complexity; which translates into increased sensitivity of the optimized treatment plans to inaccuracies in the planning and delivery processes, and can also result in longer treatment times. The aim of this work is investigate various strategies designed to improve the accuracy and efficiency of two advanced forms of IMRT: helical tomotherapy and intensity modulated proton therapy (IMPT). Helical tomotherapy is form of X-ray IMRT that uses a compact linear accelerator mounted on a CT ring gantry to rotationally deliver intensity modulated fan-beams of radiation to a patient for treatment. Failure to select judicious values for certain planning parameters can result in plans with long treatment times that are difficult for the machine to accurately deliver. This situation was observed for a series of patients scheduled for treatment at the University of Wisconsin. Treatment planning methods designed to avoid these difficulties have been investigated and are discussed. While the vast majority of IMRT treatments are performed using mega-voltage X-rays, there has recently been a great deal of interest in the use of IMPT for a variety of clinical indications. Current methods of IMPT are limited in their applicability however, due to restrictions imposed by the current delivery paradigm. An alternative method for IMPT delivery using a fan-beam geometry has been examined. Another challenge with IMPT pertains to the accuracy of proton dose calculations in the presence of complex tissue heterogeneities. Monte Carlo methods provide the most accurate means of dose calculation; however, the computational requirements of current radiation transport codes makes Monte Carlo methods unsuitable for routine treatment planning. As an alternative, analytical pencil beam algorithms are used to calculate dose. For this work, an analytical proton dose calculator was developed. Two heterogeneity correction schemes have been incorporated into the algorithm and the accuracy of these methods compared with Monte Carlo is examined in a variety of heterogeneous phantom geometries.

  10. Study of DNA interactions with bifenthrin by spectroscopic techniques and molecular modeling

    NASA Astrophysics Data System (ADS)

    Zhu, Pan; Zhang, Guowen; Ma, Yadi; Zhang, Yepeng; Miao, Hong; Wu, Yongning

    2013-08-01

    The interaction between bifenthrin (BF) and calf thymus DNA (ctDNA) in physiological buffer (pH 7.4) was investigated by UV-vis absorption, fluorescence, circular dichroism (CD), and Fourier transform infrared (FT-IR) spectroscopy, coupled with viscosity measurements and molecular docking techniques. It was found that BF molecular could intercalate into the base pairs of ctDNA as evidenced by significant increases in absorption intensity, fluorescence polarization and relative viscosity of ctDNA, decrease in iodide quenching effect, and induced CD spectral changes. The association constant of BF with ctDNA was evaluated to be in the order of 104 L mol-1. Thermodynamic analysis of the binding data obtained at different temperatures suggested that the binding process was primarily driven by hydrogen bonds and van der Waals forces, as the values of the enthalpy change (ΔH) and the entropy change (ΔS) were calculated to be -31.13 ± 1.89 kJ mol-1 and -22.79 ± 1.21 J mol-1 K-1, respectively. The results of FT-IR spectra and molecular docking showed that a specific binding mainly existed between BF and adenine and guanine bases.

  11. 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

  12. 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

    2014-08-01

    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

  13. An effusive molecular beam technique for studies of polyatomic gas-surface reactivity and energy transfer

    NASA Astrophysics Data System (ADS)

    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(Tg, Ts; ϑ), on metal surfaces for which the impinging gas temperature, Tg, and surface temperature, Ts, can be independently varied, along with the angle of incidence, ϑ, of the impinging gas. Effusive beam experiments with Tg = Ts = 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(Tg, Ts; ϑ) measurements for which Tg ≠ Ts 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 Tg 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).

  14. Current Molecular Targeted Therapy in Advanced Gastric Cancer: A Comprehensive Review of Therapeutic Mechanism, Clinical Trials, and Practical Application.

    PubMed

    Li, Kaichun; Li, Jin

    2016-01-01

    Despite the great progress in the treatment of gastric cancer, it is still the third leading cause of cancer death worldwide. Patients often miss the opportunity for a surgical cure, because the cancer has already developed into advanced cancer when identified. Compared to best supportive care, chemotherapy can improve quality of life and prolong survival time, but the overall survival is often short. Due to the molecular study of gastric cancer, new molecular targeted drugs have entered the clinical use. Trastuzumab, an antibody targeting human epidermal growth factor receptor 2 (HER2), can significantly improve survival in advanced gastric cancer patients with HER2 overexpression. Second-line treatment of advanced gastric cancer with ramucirumab, an antibody targeting VEGFR-2, alone or in combination with paclitaxel, has been proved to provide a beneficial effect. The VEGFR-2 tyrosine kinase inhibitor, apatinib, can improve the survival of advanced gastric cancer patients after second-line chemotherapy failure. Unfortunately, none of the EGFR targeting antibodies (cetuximab or panitumumab), VEGF targeting monoclonal antibodies (bevacizumab), mTOR inhibitor (everolimus), or HGF/MET pathway targeting drugs has a significant survival benefit. Many other clinical trials based on molecular markers are underway. This review will summarize targeted therapies for advanced gastric cancer. PMID:26880889

  15. Current Molecular Targeted Therapy in Advanced Gastric Cancer: A Comprehensive Review of Therapeutic Mechanism, Clinical Trials, and Practical Application

    PubMed Central

    Li, Kaichun; Li, Jin

    2016-01-01

    Despite the great progress in the treatment of gastric cancer, it is still the third leading cause of cancer death worldwide. Patients often miss the opportunity for a surgical cure, because the cancer has already developed into advanced cancer when identified. Compared to best supportive care, chemotherapy can improve quality of life and prolong survival time, but the overall survival is often short. Due to the molecular study of gastric cancer, new molecular targeted drugs have entered the clinical use. Trastuzumab, an antibody targeting human epidermal growth factor receptor 2 (HER2), can significantly improve survival in advanced gastric cancer patients with HER2 overexpression. Second-line treatment of advanced gastric cancer with ramucirumab, an antibody targeting VEGFR-2, alone or in combination with paclitaxel, has been proved to provide a beneficial effect. The VEGFR-2 tyrosine kinase inhibitor, apatinib, can improve the survival of advanced gastric cancer patients after second-line chemotherapy failure. Unfortunately, none of the EGFR targeting antibodies (cetuximab or panitumumab), VEGF targeting monoclonal antibodies (bevacizumab), mTOR inhibitor (everolimus), or HGF/MET pathway targeting drugs has a significant survival benefit. Many other clinical trials based on molecular markers are underway. This review will summarize targeted therapies for advanced gastric cancer. PMID:26880889

  16. Application of Energy Integration Techniques to the Design of Advanced Life Support Systems

    NASA Technical Reports Server (NTRS)

    Levri, Julie; Finn, Cory

    2000-01-01

    Exchanging heat between hot and cold streams within an advanced life support system can save energy. This savings will reduce the equivalent system mass (ESM) of the system. Different system configurations are examined under steady-state conditions for various percentages of food growth and waste treatment. The scenarios investigated represent possible design options for a Mars reference mission. Reference mission definitions are drawn from the ALSS Modeling and Analysis Reference Missions Document, which includes definitions for space station evolution, Mars landers, and a Mars base. For each scenario, streams requiring heating or cooling are identified and characterized by mass flow, supply and target temperatures and heat capacities. The Pinch Technique is applied to identify good matches for energy exchange between the hot and cold streams and to calculate the minimum external heating and cooling requirements for the system. For each pair of hot and cold streams that are matched, there will be a reduction in the amount of external heating and cooling required, and the original heating and cooling equipment will be replaced with a heat exchanger. The net cost savings can be either positive or negative for each stream pairing, and the priority for implementing each pairing can be ranked according to its potential cost savings. Using the Pinch technique, a complete system heat exchange network is developed and heat exchangers are sized to allow for calculation of ESM. The energy-integrated design typically has a lower total ESM than the original design with no energy integration. A comparison of ESM savings in each of the scenarios is made to direct future Pinch Analysis efforts.

  17. Craniospinal Irradiation Techniques: A Dosimetric Comparison of Proton Beams With Standard and Advanced Photon Radiotherapy

    SciTech Connect

    Yoon, Myonggeun; Shin, Dong Ho; Kim, Jinsung; Kim, Jong Won; Kim, Dae Woong; Park, Sung Yong; Lee, Se Byeong; Kim, Joo Young; Park, Hyeon-Jin; Park, Byung Kiu; Shin, Sang Hoon

    2011-11-01

    Purpose: To evaluate the dosimetric benefits of advanced radiotherapy techniques for craniospinal irradiation in cancer in children. Methods and Materials: Craniospinal irradiation (CSI) using three-dimensional conformal radiotherapy (3D-CRT), tomotherapy (TOMO), and proton beam treatment (PBT) in the scattering mode was planned for each of 10 patients at our institution. Dosimetric benefits and organ-specific radiation-induced cancer risks were based on comparisons of dose-volume histograms (DVHs) and on the application of organ equivalent doses (OEDs), respectively. Results: When we analyzed the organ-at-risk volumes that received 30%, 60%, and 90% of the prescribed dose (PD), we found that PBT was superior to TOMO and 3D-CRT. On average, the doses delivered by PBT to the esophagus, stomach, liver, lung, pancreas, and kidney were 19.4 Gy, 0.6 Gy, 0.3 Gy, 2.5 Gy, 0.2 Gy, and 2.2 Gy for the PD of 36 Gy, respectively, which were significantly lower than the doses delivered by TOMO (22.9 Gy, 4.5 Gy, 6.1 Gy, 4.0 Gy, 13.3 Gy, and 4.9 Gy, respectively) and 3D-CRT (34.6 Gy, 3.6 Gy, 8.0 Gy, 4.6 Gy, 22.9 Gy, and 4.3 Gy, respectively). Although the average doses delivered by PBT to the chest and abdomen were significantly lower than those of 3D-CRT or TOMO, these differences were reduced in the head-and-neck region. OED calculations showed that the risk of secondary cancers in organs such as the stomach, lungs, thyroid, and pancreas was much higher when 3D-CRT or TOMO was used than when PBT was used. Conclusions: Compared with photon techniques, PBT showed improvements in most dosimetric parameters for CSI patients, with lower OEDs to organs at risk.

  18. Advances in turbulent mixing techniques to study microsecond protein folding reactions

    PubMed Central

    Kathuria, Sagar V.; Chan, Alexander; Graceffa, Rita; Nobrega, R. Paul; Matthews, C. Robert; Irving, Thomas C.; Perot, Blair; Bilsel, Osman

    2013-01-01

    Recent experimental and computational advances in the protein folding arena have shown that the readout of the one-dimensional sequence information into three-dimensional structure begins within the first few microseconds of folding. The initiation of refolding reactions has been achieved by several means, including temperature jumps, flash photolysis, pressure jumps and rapid mixing methods. One of the most commonly used means of initiating refolding of chemically-denatured proteins is by turbulent flow mixing with refolding dilution buffer, where greater than 99% mixing efficiency has been achieved within 10’s of microseconds. Successful interfacing of turbulent flow mixers with complementary detection methods, including time-resolved Fluorescence Spectroscopy (trFL), Förster Resonance Energy Transfer (FRET), Circular Dichroism (CD), Small-Angle X-ray Scattering (SAXS), Hydrogen Exchange (HX) followed by Mass Spectrometry (MS) and Nuclear Magnetic Resonance Spectroscopy (NMR), Infrared Spectroscopy (IR), and Fourier Transform IR Spectroscopy (FTIR), has made this technique very attractive for monitoring various aspects of structure formation during folding. Although continuous-flow (CF) mixing devices interfaced with trFL detection have a dead time of only 30 µs, burst-phases have been detected in this time scale during folding of peptides and of large proteins (e.g., CheY and TIM barrels). Furthermore, a major limitation of CF mixing technique has been the requirement of large quantities of sample. In this brief communication, we will discuss the recent flurry of activity in micromachining and microfluidics, guided by computational simulations, that are likely to lead to dramatic improvements in time resolution and sample consumption for CF mixers over the next few years. PMID:23868289

  19. Strategic steps for advanced molecular imaging with magnetic resonance-based diagnostic modalities.

    PubMed

    Belkic, Dž; Belkic, K

    2015-02-01

    With the rapidly-expanding sophistication in our understanding of cancer cell biology, molecular imaging offers a critical bridge to oncology. Molecular imaging through magnetic resonance spectroscopy (MRS) can provide information about many metabolites at the same time. Since MRS entails no ionizing radiation, repeated monitoring, including screening can be performed. However, MRS via the fast Fourier transform (FFT) has poor resolution and signal-to-noise ratio (SNR). Moreover, subjective and non-unique (ambiguous) fittings of FFT spectra cannot provide reliable quantification of clinical usefulness. In sharp contrast, objective and unique (unambiguous) signal processing by the fast Padé transform (FPT) can increase resolution and retrieve the true quantitative metabolic information. To illustrate, we apply the FPT to in vitro MRS data as encoded from malignant ovarian cyst fluid and perform detailed analysis. This problem area is particularly in need of timely diagnostics by more advanced modalities, such as high-resolution MRS, since conventional methods usually detect ovarian cancers at late stages with poor prognosis, whereas at an early stage the prognosis is excellent. The reliability and robustness of the FPT is assessed for time signals contaminated with varying noise levels. In the presence of higher background noise, all physical metabolites were unequivocally identified and their concentrations precisely extracted, using small fractions of the total signal length. Via the "signal-noise separation" concept alongside the "stability test", all non-physical information was binned, such that fully denoised spectra were generated. These results imply that a reformulation of data acquisition is needed, as guided by the FPT in MRS, since a small number of short transient time signals can provide high resolution and good SNR. This would enhance the diagnostic accuracy of MRS and shorten examination times, thereby improving efficiency and cost-effectiveness of this high throughput cancer diagnostic modality. Such advantages could be particularly important for more effective ovarian cancer detection, as well as more broadly for improved diagnostics and treatment within oncology. PMID:24354757

  20. On Advanced Estimation Techniques for Exoplanet Detection and Characterization using Ground-based Coronagraphs

    NASA Technical Reports Server (NTRS)

    Lawson, Peter; Frazin, Richard

    2012-01-01

    The direct imaging of planets around nearby stars is exceedingly difficult. Only about 14 exoplanets have been imaged to date that have masses less than 13 times that of Jupiter. The next generation of planet-finding coronagraphs, including VLT-SPHERE, the Gemini Planet Imager, Palomar P1640, and Subaru HiCIAO have predicted contrast performance of roughly a thousand times less than would be needed to detect Earth-like planets. In this paper we review the state of the art in exoplanet imaging, most notably the method of Locally Optimized Combination of Images (LOCI), and we investigate the potential of improving the detectability of faint exoplanets through the use of advanced statistical methods based on the concepts of the ideal observer and the Hotelling observer. We propose a formal comparison of techniques using a blind data challenge with an evaluation of performance using the Receiver Operating Characteristic (ROC) and Localization ROC (LROC) curves. We place particular emphasis on the understanding and modeling of realistic sources of measurement noise in ground-based AO-corrected coronagraphs. The work reported in this paper is the result of interactions between the co-authors during a week-long workshop on exoplanet imaging that was held in Squaw Valley, California, in March of 2012

  1. An advanced noise source identification technique using the inverse boundary-element method

    NASA Astrophysics Data System (ADS)

    Martinus, Ferdy

    2005-09-01

    The application of the inverse BEM method as an advanced, non-contact noise source identification technique will be discussed. In the first and most conventional experiment, the inverse BEM is used to reconstruct the vibration pattern on the surface of a motorcycle engine oil pan cover. In the second experiment, the inverse BEM is used to determine the distribution of particle velocity on the open end of a rectangular duct. Measurements of the particle velocity using the two-microphone method are compared to those predicted using the inverse BEM. In the third experiment, the inverse BEM is used to identify the mechanism of an aeroacoustics noise problem (a vortex tone) created by flow over a circular rod. The spectrum of the tonal sound within the flow field is reconstructed using the inverse BEM, and a near field spatial reconstruction of the sound pressure shows clearly the nature of the vortex source. This paper will also show that only a relatively small number sound pressure measurements are required for the inverse BEM and that these measurements need not be in the near field of the source nor conformal to it to obtain good results.

  2. On Advanced Estimation Techniques for Exoplanet Detection and Characterization using Ground-Based Coronagraphs

    NASA Technical Reports Server (NTRS)

    Lawson, Peter R.; Frazin, Richard; Barrett, Harrison; Caucci, Luca; Devaney, Nicholas; Furenlid, Lars; Gladysz, Szymon; Guyon, Olivier; Krist, John; Maire, Jerome; Marois, Christian; Mawet, Dimitri; Mouillet, David; Mugnier, Laurent; Perrin, Marshall; Poyneer, Lisa; Pueyo, Laurent; Savransky, Dmitry; Soummer, Remi

    2012-01-01

    The direct imaging of planets around nearby stars is exceedingly difficult. Only about 14 exoplanets have been imaged to date that have masses less than 13 times that of Jupiter. The next generation of planet-finding coronagraphs, including VLT-SPHERE, the Gemini Planet Imager, Palomar P1640, and Subaru HiCIAO have predicted contrast performance of roughly a thousand times less than would be needed to detect Earth-like planets. In this paper we review the state of the art in exoplanet imaging, most notably the method of Locally Optimized Combination of Images (LOCI), and we investigate the potential of improving the detectability of faint exoplanets through the use of advanced statistical methods based on the concepts of the ideal observer and the Hotelling observer. We provide a formal comparison of techniques through a blind data challenge and evaluate performance using the Receiver Operating Characteristic (ROC) and Localization ROC (LROC) curves. We place particular emphasis on the understanding and modeling of realistic sources of measurement noise in ground-based AO-corrected coronagraphs. The work reported in this paper is the result of interactions between the co-authors during a week-long workshop on exoplanet imaging that was held in Squaw Valley, California, in March of 2012.

  3. Classification of human colonic tissues using FTIR spectra and advanced statistical techniques

    NASA Astrophysics Data System (ADS)

    Zwielly, A.; Argov, S.; Salman, A.; Bogomolny, E.; Mordechai, S.

    2010-04-01

    One of the major public health hazards is colon cancer. There is a great necessity to develop new methods for early detection of cancer. If colon cancer is detected and treated early, cure rate of more than 90% can be achieved. In this study we used FTIR microscopy (MSP), which has shown a good potential in the last 20 years in the fields of medical diagnostic and early detection of abnormal tissues. Large database of FTIR microscopic spectra was acquired from 230 human colonic biopsies. Five different subgroups were included in our database, normal and cancer tissues as well as three stages of benign colonic polyps, namely, mild, moderate and severe polyps which are precursors of carcinoma. In this study we applied advanced mathematical and statistical techniques including principal component analysis (PCA) and linear discriminant analysis (LDA), on human colonic FTIR spectra in order to differentiate among the mentioned subgroups' tissues. Good classification accuracy between normal, polyps and cancer groups was achieved with approximately 85% success rate. Our results showed that there is a great potential of developing FTIR-micro spectroscopy as a simple, reagent-free viable tool for early detection of colon cancer in particular the early stages of premalignancy among the benign colonic polyps.

  4. Analysis of deformation patterns through advanced DINSAR techniques in Istanbul megacity

    NASA Astrophysics Data System (ADS)

    Balik Sanli, F.; Calò, F.; Abdikan, S.; Pepe, A.; Gorum, T.

    2014-09-01

    As result of the Turkey's economic growth and heavy migration processes from rural areas, Istanbul has experienced a high urbanization rate, with severe impacts on the environment in terms of natural resources pressure, land-cover changes and uncontrolled sprawl. As a consequence, the city became extremely vulnerable to natural and man-made hazards, inducing ground deformation phenomena that threaten buildings and infrastructures and often cause significant socio-economic losses. Therefore, the detection and monitoring of such deformation patterns is of primary importance for hazard and risk assessment as well as for the design and implementation of effective mitigation strategies. Aim of this work is to analyze the spatial distribution and temporal evolution of deformations affecting the Istanbul metropolitan area, by exploiting advanced Differential SAR Interferometry (DInSAR) techniques. In particular, we apply the Small BAseline Subset (SBAS) approach to a dataset of 43 TerraSAR-X images acquired, between November 2010 and June 2012, along descending orbits with an 11-day revisit time and a 3 m × 3 m spatial resolution. The SBAS processing allowed us to remotely detect and monitor subsidence patterns over all the urban area as well as to provide detailed information at the scale of the single building. Such SBAS measurements, effectively integrated with ground-based monitoring data and thematic maps, allows to explore the relationship between the detected deformation phenomena and urbanization, contributing to improve the urban planning and management.

  5. Recent Advance in Liquid Chromatography/Mass Spectrometry Techniques for Environmental Analysis in Japan

    PubMed Central

    Suzuki, Shigeru

    2014-01-01

    The techniques and measurement methods developed in the Environmental Survey and Monitoring of Chemicals by Japan’s Ministry of the Environment, as well as a large amount of knowledge archived in the survey, have led to the advancement of environmental analysis. Recently, technologies such as non-target liquid chromatography/high resolution mass spectrometry and liquid chromatography with micro bore column have further developed the field. Here, the general strategy of a method developed for the liquid chromatography/mass spectrometry (LC/MS) analysis of environmental chemicals with a brief description is presented. Also, a non-target analysis for the identification of environmental pollutants using a provisional fragment database and “MsMsFilter,” an elemental composition elucidation tool, is presented. This analytical method is shown to be highly effective in the identification of a model chemical, the pesticide Bendiocarb. Our improved micro-liquid chromatography injection system showed substantially enhanced sensitivity to perfluoroalkyl substances, with peak areas 32–71 times larger than those observed in conventional LC/MS. PMID:26819891

  6. On advanced estimation techniques for exoplanet detection and characterization using ground-based coronagraphs

    NASA Astrophysics Data System (ADS)

    Lawson, Peter R.; Poyneer, Lisa; Barrett, Harrison; Frazin, Richard; Caucci, Luca; Devaney, Nicholas; Furenlid, Lars; Gładysz, Szymon; Guyon, Olivier; Krist, John; Maire, Jérôme; Marois, Christian; Mawet, Dimitri; Mouillet, David; Mugnier, Laurent; Pearson, Iain; Perrin, Marshall; Pueyo, Laurent; Savransky, Dmitry

    2012-07-01

    The direct imaging of planets around nearby stars is exceedingly difficult. Only about 14 exoplanets have been imaged to date that have masses less than 13 times that of Jupiter. The next generation of planet-finding coronagraphs, including VLT-SPHERE, the Gemini Planet Imager, Palomar P1640, and Subaru HiCIAO have predicted contrast performance of roughly a thousand times less than would be needed to detect Earth-like planets. In this paper we review the state of the art in exoplanet imaging, most notably the method of Locally Optimized Combination of Images (LOCI), and we investigate the potential of improving the detectability of faint exoplanets through the use of advanced statistical methods based on the concepts of the ideal observer and the Hotelling observer. We propose a formal comparison of techniques using a blind data challenge with an evaluation of performance using the Receiver Operating Characteristic (ROC) and Localization ROC (LROC) curves. We place particular emphasis on the understanding and modeling of realistic sources of measurement noise in ground-based AO-corrected coronagraphs. The work reported in this paper is the result of interactions between the co-authors during a week-long workshop on exoplanet imaging that was held in Squaw Valley, California, in March of 2012.

  7. On Advanced Estimation Techniques for Exoplanet Detection and Characterization Using Ground-based Coronagraphs

    PubMed Central

    Lawson, Peter R.; Poyneer, Lisa; Barrett, Harrison; Frazin, Richard; Caucci, Luca; Devaney, Nicholas; Furenlid, Lars; Gładysz, Szymon; Guyon, Olivier; Krist, John; Maire, Jérôme; Marois, Christian; Mawet, Dimitri; Mouillet, David; Mugnier, Laurent; Pearson, Iain; Perrin, Marshall; Pueyo, Laurent; Savransky, Dmitry

    2015-01-01

    The direct imaging of planets around nearby stars is exceedingly difficult. Only about 14 exoplanets have been imaged to date that have masses less than 13 times that of Jupiter. The next generation of planet-finding coronagraphs, including VLT-SPHERE, the Gemini Planet Imager, Palomar P1640, and Subaru HiCIAO have predicted contrast performance of roughly a thousand times less than would be needed to detect Earth-like planets. In this paper we review the state of the art in exoplanet imaging, most notably the method of Locally Optimized Combination of Images (LOCI), and we investigate the potential of improving the detectability of faint exoplanets through the use of advanced statistical methods based on the concepts of the ideal observer and the Hotelling observer. We propose a formal comparison of techniques using a blind data challenge with an evaluation of performance using the Receiver Operating Characteristic (ROC) and Localization ROC (LROC) curves. We place particular emphasis on the understanding and modeling of realistic sources of measurement noise in ground-based AO-corrected coronagraphs. The work reported in this paper is the result of interactions between the co-authors during a week-long workshop on exoplanet imaging that was held in Squaw Valley, California, in March of 2012. PMID:26347393

  8. Nanocasting technique to prepare lotus-leaf-like superhydrophobic electroactive polyimide as advanced anticorrosive coatings.

    PubMed

    Chang, Kung-Chin; Lu, Hsin-I; Peng, Chih-Wei; Lai, Mei-Chun; Hsu, Sheng-Chieh; Hsu, Min-Hsiang; Tsai, Yuan-Kai; Chang, Chi-Hao; Hung, Wei-I; Wei, Yen; Yeh, Jui-Ming

    2013-02-01

    Nanocasting technique was used to obtain a biomimetic superhydrophobic electroactive polyimide (SEPI) surface structure from a natural Xanthosoma sagittifolium leaf. An electroactive polyimide (EPI) was first synthesized through thermal imidization. An impression of the superhydrophobic Xanthosoma sagittifolium leaf was then nanocasted onto the surface of the EPI so that the resulting EPI was superhydrophobic and would prevent corrosion. Polydimethylsiloxane (PDMS) was then used as a negative template to transfer the impression of the superhydrophobic surface of the biomimetic EPI onto a cold-rolled steel (CRS) electrode. The superhydrophobic electroactive material could be used as advanced coatings that protect metals against corrosion. The morphology of the surface of the as-synthesized SEPI coating was investigated using scanning electron microscopy (SEM). The surface showed numerous micromastoids, each decorated with many nanowrinkles. The water contact angle (CA) for the SEPI coating was 155°, which was significantly larger than that for the EPI coating (i.e., CA = 87°). The significant increase in the contact angle indicated that the biomimetic morphology effectively repelled water. Potentiodynamic and electrochemical impedance spectroscopic measurements indicated that the SEPI coating offered better protection against corrosion than the EPI coating did. PMID:23384046

  9. Molecular Advances Leading to Treatment Implications for Fragile X Premutation Carriers

    PubMed Central

    Polussa, Jonathan; Schneider, Andrea; Hagerman, Randi

    2014-01-01

    Fragile X syndrome (FXS) is the most common single gene cause of intellectual disability and it is characterized by a CGG expansion of more than 200 repeats in the FMR1 gene, leading to methylation of the promoter and gene silencing. The fragile X premutation, characterized by a 55 to 200 CGG repeat expansion, causes health problems and developmental difficulties in some, but not all, carriers. The premutation causes primary ovarian insufficiency in approximately 20% of females, psychiatric problems (including depression and/or anxiety) in approximately 50% of carriers and a neurodegenerative disorder, the fragile X-associated tremor ataxia syndrome (FXTAS), in approximately 40% of males and 16% of females later in life. Recent clinical studies in premutation carriers have expanded the health problems that may be seen. Advances in the molecular pathogenesis of the premutation have shown significant mitochondrial dysfunction and oxidative stress in neurons which may be amenable to treatment. Here we review the clinical problems of carriers and treatment recommendations. PMID:25436181

  10. Advanced Glycation End Products: A Molecular Target for Vascular Complications in Diabetes

    PubMed Central

    Yamagishi, Sho-ichi; Nakamura, Nobutaka; Suematsu, Mika; Kaseda, Kuniyoshi; Matsui, Takanori

    2015-01-01

    A nonenzymatic reaction between reducing sugars and amino groups of proteins, lipids and nucleic acids contributes to the aging of macromolecules and subsequently alters their structural integrity and function. This process has been known to progress at an accelerated rate under hyperglycemic and/or oxidative stress conditions. Over a course of days to weeks, early glycation products undergo further reactions such as rearrangements and dehydration to become irreversibly cross-linked, fluorescent and senescent macroprotein derivatives termed advanced glycation end products (AGEs). There is a growing body of evidence indicating that interaction of AGEs with their receptor (RAGE) elicits oxidative stress generation and as a result evokes proliferative, inflammatory, thrombotic and fibrotic reactions in a variety of cells. This evidence supports AGEs’ involvement in diabetes- and aging-associated disorders such as diabetic vascular complications, cancer, Alzheimer’s disease and osteoporosis. Therefore, inhibition of AGE formation could be a novel molecular target for organ protection in diabetes. This report summarizes the pathophysiological role of AGEs in vascular complications in diabetes and discusses the potential clinical utility of measurement of serum levels of AGEs for evaluating organ damage in diabetes. PMID:26605646

  11. Inherited pancreatic endocrine tumor syndromes: advances in molecular pathogenesis, diagnosis, management, and controversies.

    PubMed

    Jensen, Robert T; Berna, Marc J; Bingham, David B; Norton, Jeffrey A

    2008-10-01

    Pancreatic endocrine tumors (PETs) can occur as part of 4 inherited disorders, including Multiple Endocrine Neoplasia type 1 (MEN1), von Hippel-Lindau disease (VHL), neurofibromatosis 1 (NF-1) (von Recklinghausen disease), and the tuberous sclerosis complex (TSC). The relative frequency with which patients who have these disorders develop PETs is MEN1>VHL>NF-1>TSC. Over the last few years, there have been major advances in the understanding of the genetics and molecular pathogenesis of these disorders as well in the localization and the medical and surgical treatment of PETs in such patients. The study of PETs in these disorders not only has provided insights into the possible pathogenesis of sporadic PETs but also has presented several unique management and treatment issues, some of which are applicable to patients with sporadic PETs. Therefore, the study of PETs in these uncommon disorders has provided valuable insights that, in many cases, are applicable to the general group of patients with sporadic PETs. In this article, these areas are reviewed briefly along with the current state of knowledge of the PETs in these disorders, and the controversies that exist in their management are summarized briefly and discussed. PMID:18798544

  12. Oculopharyngeal muscular dystrophy: recent advances in the understanding of the molecular pathogenic mechanisms and treatment strategies.

    PubMed

    Abu-Baker, Aida; Rouleau, Guy A

    2007-02-01

    Oculopharyngeal muscular dystrophy (OPMD) is an adult-onset disorder characterized by progressive eyelid drooping, swallowing difficulties and proximal limb weakness. OPMD is caused by a small expansion of a short polyalanine tract in the poly (A) binding protein nuclear 1 protein (PABPN1). The mechanism by which the polyalanine expansion mutation in PABPN1 causes disease is unclear. PABPN1 is a nuclear multi-functional protein which is involved in pre-mRNA polyadenylation, transcription regulation, and mRNA nucleocytoplasmic transport. The distinct pathological hallmark of OPMD is the presence of filamentous intranuclear inclusions (INIs) in patient's skeletal muscle cells. The exact relationship between mutant PABPN1 intranuclear aggregates and pathology is not clear. OPMD is a unique disease sharing common pathogenic features with other polyalanine disorders, as well as with polyglutamine and dystrophic disorders. This chapter aims to review the rapidly growing body of knowledge concerning OPMD. First, we outline the background of OPMD. Second, we compare OPMD with other trinucleotide repeat disorders. Third, we discuss the recent advances in the understanding of the molecular mechanisms underlying OPMD pathogenesis. Finally, we review recent therapeutic strategies for OPMD. PMID:17110089

  13. Recent advances and perspectives in molecular epidemiology of Taenia solium cysticercosis.

    PubMed

    Ito, Akira; Yanagida, Tetsuya; Nakao, Minoru

    2016-06-01

    Cysticercosis caused by accidental ingestion of eggs of Taenia solium is spreading all over the world through globalization and is one of the most neglected, neglected tropical diseases (NTDs) or neglected zoonotic diseases (NZDs). In the present study, the reason why T. solium cysticercosis has been neglected is discussed at first, and followed with an overview on the most recent advances and perspectives in molecular approaches for epidemiology of T. solium taeniasis/cysticercosis, since although taeniasis does not constitute recognized zoonoses, transmission and complete development are dependent on human definitive hosts. Main topics are discussions on (1) the two, Asian and Afro/American, genotypes of T. solium, (2) comparative analysis of mitochondrial (haploid) and nuclear (diploid) genes, and (3) the presence of hybrids of these two genotypes which indicates out-crossing of two genotypes in hermaphrodite tapeworms in Madagascar. Additional topics are on (4) the usefulness of phylogeographic analyses to discuss where the infection was acquired from, and (5) miscellaneous unsolved topics around these genetic diversity of T. solium. PMID:26112071

  14. 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…

  15. APPLICATION OF ADVANCED IN VITRO TECHNIQUES TO MEASURE, UNDERSTAND AND PREDICT THE KINETICS AND MECHANISMS OF XENOBIOTIC METABOLISM

    EPA Science Inventory

    We have developed a research program in metabolism that involves numerous collaborators across EPA as well as other federal and academic labs. A primary goal is to develop and apply advanced in vitro techniques to measure, understand and predict the kinetics and mechanisms of xen...

  16. 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

  17. A study on the molecular interaction of PPG 3000 and its blend using ultrasonic technique

    NASA Astrophysics Data System (ADS)

    Venkatramanan, K.; Padmanaban, R.; Arumugam, V.

    2012-05-01

    Ultrasonic study has become an important research tool in the field of polymers for investigating the structure and molecular interactions in multi component system. Ultrasonic studies were carried out on Polypropylene glycol [PPG 3000] at different concentrations [0-1%] in toluene at 303K. Various parameters like adiabatic compressibility, free volume and internal pressure were calculated. The ultrasonic velocity increases with increase in the concentration. An attempt has been made to blend Polypropylene glycol [PPG] 400 with PPG 3000 at 303K at various compositions and the miscibility nature of the blend is analyzed through ultrasonic study. The variation of ultrasonic velocity with blend composition is nonlinear and follows S-type pattern, which shows that the blend is immiscible. The miscibility nature of the blend is further confirmed through other techniques like viscosity and optical studies.

  18. Bacterial community structures of deep-sea water investigated by molecular biological techniques.

    PubMed

    Terahara, Takeshi; Yamada, Katsuhisa; Nakayama, Jiro; Igarashi, Yasuhiro; Kobayashi, Takeshi; Imada, Chiaki

    2016-02-01

    The aim of the present study was to investigate the bacterial community structures of deep-sea water (DSW) and surface seawater (SSW) samples in Japan by molecular biological techniques. DGGE analyses and pyrosequencing analysis revealed that bacterial community structures of DSW were diverse and differed from those of SSW. This is the first report on the horizontal variation of bacterial community structures of DSW throughout Japan. In addition, pyrosequencing analysis revealed that the number of phyla in DSW was larger than that in SSW, and specific phyla, such as Firmicutes and Planctomycetes, were characterized by a higher proportion of the bacterial community structure in DSW than in SSW. Taken together, these results indicate that a variety of bacteria that are specifically adapted to the DSW environments can be expected to be found in DSW, and DSW would thus be a potential resource for novel or unique microorganisms and compounds. PMID:26475936

  19. Congenital candidiasis: confirmation of mother-neonate transmission using molecular analysis techniques.

    PubMed

    Tiraboschi, Iris Carla Niveyro; Niveyro, Carla; Mandarano, Ana Maria; Messer, Shawn A; Bogdanowicz, Elizabeth; Kurlat, Isabel; Lasala, María Beatriz

    2010-02-01

    We describe a case of congenital acquired candidiasis in a preterm female delivered through Caesarean section due to the premature rupture of the amniotic membrane. The neonate presented with suspected chorioamnionitis and erythematous desquamative skin. Candida albicans was isolated from the placenta, mouth, groin, and periumbilical lesions. The infant developed candidemia due to Candida albicans and the same yeast was also isolated from a catheter. Culture inoculated with swabs from the mouth and vagina of the mother yielded C. albicans and C. krusei. All C. albicans isolates from the mother and the neonate were visually indistinguishable by molecular typing techniques which included chromosomal karyotyping and restriction endonuclease analysis followed by pulsed-field gel electrophoresis. These findings allowed the clinical condition to be confirmed as congenital acquisition of candidiasis in this case. PMID:19306215

  20. 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 United Kingdom occupational exposure limit. PMID:8000490

  1. Development of anti-viral agents using molecular modeling and virtual screening techniques.

    PubMed

    Kirchmair, Johannes; Distinto, Simona; Liedl, Klaus Roman; Markt, Patrick; Rollinger, Judith Maria; Schuster, Daniela; Spitzer, Gudrun Maria; Wolber, Gerhard

    2011-02-01

    Computational chemistry has always played a key role in anti-viral drug development. The challenges and the quickly rising public interest when a virus is becoming a threat has significantly influenced computational drug discovery. The most obvious example is anti-AIDS research, where HIV protease and reverse transcriptase have triggered enormous efforts in developing and improving computational methods. Methods applied to anti-viral research include (i) ligand-based approaches that rely on known active compounds to extrapolate biological activity, such as machine learning techniques or classical QSAR, (ii) structure-based methods that rely on an experimentally determined 3D structure of the targets, such as molecular docking or molecular dynamics, and (iii) universal approaches that can be applied in a structure- or ligand-based way, such as 3D QSAR or 3D pharmacophore elucidation. In this review we summarize these molecular modeling approaches as they were applied to fight anti-viral diseases and highlight their importance for anti-viral research. We discuss the role of computational chemistry in the development of small molecules as agents against HIV integrase, HIV-1 protease, HIV-1 reverse transcriptase, the influenza virus M2 channel protein, influenza virus neuraminidase, the SARS coronavirus main proteinase and spike protein, thymidine kinases of herpes viruses, hepatitis c virus proteins and other flaviviruses as well as human rhinovirus coat protein and proteases, and other picornaviridae. We highlight how computational approaches have helped in discovering anti-viral activities of natural products and give an overview on polypharmacology approaches that help to optimize drugs against several viruses or help to optimize the metabolic profile of and anti-viral drug. PMID:21303343

  2. Electrospinning as a new technique to control the crystal morphology and molecular orientation of polyoxymethylene nanofibers.

    PubMed

    Kongkhlang, Thontree; Tashiro, Kohji; Kotaki, Masaya; Chirachanchai, Suwabun

    2008-11-19

    Electrospinning is widely accepted as a simple and versatile technique for producing nanofibers. The present work, however, introduces a new concept of the electrospinning method for controlling the crystal morphology and molecular orientation of the nanofibers through an illustration of a case study of polyoxymethylene (POM) nanofibers. Isotropic and anisotropic electrospun POM nanofibers are successfully prepared by using a stationary collector and a rotating disk collector. By controlling the voltage and the take-up velocity of the disk rotator, the morphology changes between an extended chain crystal (ECC) and a folded chain crystal (FCC) as clarified by a detailed analysis of the X-ray diffraction and polarized infrared spectra of the POM nanofibers. Herman's orientation function and dichroic ratio lead us to a schematic conclusion--that (i) molecular orientation is parallel to the fiber axis in both isotropic and anisotropic POM nanofibers, (ii) a single nanofiber consists of a nanofibril assembly with a size of 60-70 A and tilting at a certain degree, and (iii) the higher the take-up velocity, the smaller the nanofibril under the (9/5) helical structure of the POM chains. It should be emphasized here that the electrospinning method is no longer a single nanofiber producer but that it can be applied as a new instrument to control the morphology and chain orientation characteristics of polymer materials, opening a new research field in polymer science where we can understand the relationship between structure at the molecular level and the properties and performance at the macroscopic level. PMID:18950171

  3. Landslide detection and long-term monitoring in urban area by means of advanced interferometric techniques

    NASA Astrophysics Data System (ADS)

    Cigna, Francesca; Del Ventisette, Chiara; Liguori, Vincenzo; Casagli, Nicola

    2010-05-01

    This work aims at illustrating the potential of advanced interferometric techniques for detection and long-term monitoring of landslide ground deformations at local scale. Space-born InSAR (Synthetic Aperture Radar Interferometry) has been successfully exploited in recent years to measure ground deformations associated to processes with slow kinematics, such as landslides, tectonic motions, subsidence or volcanic activity, thanks to both the standard single-interferogram approach (centimeter accuracy) and advanced time-series analyses of long temporal radar satellite data stacks (millimeter accuracy), such as Persistent Scatterers Interferometry (PSI) techniques. In order to get a complete overview and an in-depth knowledge of an investigated landslide, InSAR satellite measures can support conventional in situ data. This methodology allows studying the spatial pattern and the temporal evolution of ground deformations, improving the spatial coverage and overcoming issues related to installation of ground-based instrumentation and data acquisition in unstable areas. Here we describe the application of the above-mentioned methodology on the test area of Agrigento, Sicily (Italy), affected by hydrogeological risk. The town is located in Southern Sicily, at edge of the Apennine-Maghrebian thrust belt, on the Plio-Pleistocene and Miocene sediments of the Gela Nappe. Ground instabilities affect the urban area and involve the infrastructures of its NW side, such as the Cathedral, the Seminary and many private buildings. An integration between InSAR analyses and conventional field investigations (e.g. structural damages and fractures surveys) was therefore carried out, to support Regional Civil Protection authorities for emergency management and risk mitigation. The results of InSAR analysis highlighted a general stability of the whole urban area between 1992 and 2007. However, very high deformation rates (up to 10-12 mm/y) were identified in 1992-2000 in the W slope of the town, within the crown and the main scarp area of the Addolorata landslide (occurred in July 1966), and thus was highlighted that the phenomenon was still active. The time-series analysis performed in the NW area of the town, also allowed measuring acceleration (up to 13 mm/y) of the deformation rates near the main Cathedral, starting from August 2006 and persisting until the end of the monitoring period (2007). The new information about the state of activity of these landslides were discussed with the Civil Protection authorities to plan further field investigations and structural surveys to be carried out in the areas at higher risk. The analysis on Agrigento confirmed the capabilities of this integrated approach for detection of ground deformations, long-term monitoring of landslides and, finally, management and mitigation of hydrogeological risk in urban area at local scale.

  4. Inelastic effects in molecular transport junctions: The probe technique at high bias

    NASA Astrophysics Data System (ADS)

    Kilgour, Michael; Segal, Dvira

    2016-03-01

    We extend the Landauer-Büttiker probe formalism for conductances to the high bias regime and study the effects of environmentally induced elastic and inelastic scattering on charge current in single molecule junctions, focusing on high-bias effects. The probe technique phenomenologically incorporates incoherent elastic and inelastic effects to the fully coherent case, mimicking a rich physical environment at trivial cost. We further identify environmentally induced mechanisms which generate an asymmetry in the current, manifested as a weak diode behavior. This rectifying behavior, found in two types of molecular junction models, is absent in the coherent-elastic limit and is only active in the case with incoherent-inelastic scattering. Our work illustrates that in the low bias-linear response regime, the commonly used "dephasing probe" (mimicking only elastic decoherence effects) operates nearly indistinguishably from a "voltage probe" (admitting inelastic-dissipative effects). However, these probes realize fundamentally distinct I-V characteristics at high biases, reflecting the central roles of dissipation and inelastic scattering processes on molecular electronic transport far-from-equilibrium.

  5. Inelastic effects in molecular transport junctions: The probe technique at high bias.

    PubMed

    Kilgour, Michael; Segal, Dvira

    2016-03-28

    We extend the Landauer-Büttiker probe formalism for conductances to the high bias regime and study the effects of environmentally induced elastic and inelastic scattering on charge current in single molecule junctions, focusing on high-bias effects. The probe technique phenomenologically incorporates incoherent elastic and inelastic effects to the fully coherent case, mimicking a rich physical environment at trivial cost. We further identify environmentally induced mechanisms which generate an asymmetry in the current, manifested as a weak diode behavior. This rectifying behavior, found in two types of molecular junction models, is absent in the coherent-elastic limit and is only active in the case with incoherent-inelastic scattering. Our work illustrates that in the low bias-linear response regime, the commonly used "dephasing probe" (mimicking only elastic decoherence effects) operates nearly indistinguishably from a "voltage probe" (admitting inelastic-dissipative effects). However, these probes realize fundamentally distinct I-V characteristics at high biases, reflecting the central roles of dissipation and inelastic scattering processes on molecular electronic transport far-from-equilibrium. PMID:27036427

  6. Inquiry-based learning: inflammation as a model to teach molecular techniques for assessing gene expression.

    PubMed

    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

  7. 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. PMID:24927237

  8. Molecular contrast in optical coherence tomography using a pump-probe technique

    NASA Astrophysics Data System (ADS)

    Rao, K. D.; Choma, Michael A.; Yazdanfar, Siavash; Rollins, Andrew M.; Izatt, Joseph A.

    2003-07-01

    Optical coherence tomography (OCT) is an emerging tool for real time in-situ tissue imaging with micrometer-scale resolution. Real-time OCT systems have been integrated into clinical medical diagnostics, and functional extensions such as polarization-sensitive, Doppler, and spectroscopic OCT have recently been introduced. However, OCT imaging technology has not yet taken advantage of molecular-specific contrast mechanisms which have revolutionized other medical and biological imaging modalities such as MRI, PET, SPECT, and fluorescence microscopy. OCT is by definition insensitive to incoherent scattering processes such fluorescence or spontaneous Raman scattering. We have previously proposed the use of spectroscopic OCT for detection of light from coherent inelastic scattering processes such as stimulated emission, stimulate Raman scattering, and other four-wave mixing processes. In this report we present a new technique which we call pump probe OCT (PPOCT), which is a novel extension of OCT for enhancing the contrast of OCT images based on transient absorption in the sample induced by an external pump beam. We show preliminary data for PPOCT using methylene blue as a molecular contrast agent and show depth resolved PPOCT M-scans that localize the presence of dye in a well phantom.

  9. 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

  10. 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). PMID:21529024

  11. Utilizing advanced polymerization techniques for simplifying polymer grafting from silica colloidal crystal substrates

    NASA Astrophysics Data System (ADS)

    Yerneni, Charu K.

    Polyacrylamide has been well established as a biocompatible material when Polyacrylamide gel electrophoresis (PAGE) came into existence in the 1960s. Under aqueous buffer conditions it becomes non-adsorptive to proteins and due to its molecular level pore forming nature could be used in size based biomolecule separations. Since then considerable research has been done to explore the non-adsorptive nature of polyacrylamide on a platform or substrate. Attempts were made to grow polyacrylamide chains from silica as a substrate which can then be used in various protein separation techniques. Based on an ionic polymerization method which was used for gel casting in PAGE, polymers were grown on silica gel. Though considerable thickness could be achieved, polymerization was not just confined to the surface. Therefore a rigid polymer brush layer could not be achieved. Atom transfer radical polymerization (ATRP) method showed the solution to this problem. Polymer brush layers with acceptable thickness could now be achieved for growing polyacrylamide from silica gel. Yet it still suffered from several disadvantages such as the need of an inert atmosphere for polymerization and limited thickness. Many developments have taken place in the past decade which led to improvements in substrate and polymerization methods. This research used non porous sub-micron silica as the substrate and AGET ATRP (Activator generated electron transfer atom transfer radical polymerization) for surface grafting polyacrylamide. Non porous submicron silica has been shown to be a better stationary phase substrate for protein separations than conventional substrates. AGET ATRP enables polymerization to be performed under ambient conditions and in water based solutions which gives thicknesses much higher than conventional ATRP. Data from various analytical techniques showed that within the experimental range the polymerization is linear and has decent control. This means silica nanoparticles coated with polyacrylamide of varying thickness can be produced by varying the reaction time. Linear polymerization kinetics was studied using IR spectroscopy, elemental analysis, ellipsometry, GPC etc. All of them closely agree with each other. Attempts were made to expand the applicability of this novel way of material synthesis. HILIC is known as a premium separation mode for polar analytes. Glycoproteins form an important class of analytes which need better separation columns. Polyacrylamide coated nonporous colloidal silica is shown here to be a better column packing material. Combined results show that AGET ATRP can be a better and simpler alternative to ATRP for grafting polyacrylamide onto silica based substrates. Future efforts can possibly lead to the expansion of the applicability of this method for making materials for many other separation methods.

  12. 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 sufficient for the complete information on the properties of the system. In this report we review the modified group projector technique, giving detailed algorithm for its application, which is also a clear prescription for its numerical implementation. Generality of the method allows unified treatment of the most important dynamical models for ions (lattice dynamics within harmonic approximation), electrons (tight-binding method for the quantum states) and spin subsystem (spin waves in quasi classical approach), with specific details considered separately. Finally, relaxation techniques, optimization of the structure and of the spin ordering are analyzed, in order to provide the most efficient symmetry based procedures.

  13. Advanced Sensing and Control Techniques to Facilitate Semi-Autonomous Decommissioning

    SciTech Connect

    Schalkoff, Robert J.

    1999-06-01

    This research is intended to advance the technology of semi-autonomous teleoperated robotics as applied to Decontamination and Decommissioning (D&D) tasks. Specifically, research leading to a prototype dual-manipulator mobile work cell is underway. This cell is supported and enhanced by computer vision, virtual reality and advanced robotics technology.

  14. [Recent advances of anastomosis techniques of esophagojejunostomy after laparoscopic totally gastrectomy in gastric tumor].

    PubMed

    Li, Xi; Ke, Chongwei

    2015-05-01

    The esophageal jejunum anastomosis of the digestive tract reconstruction techniques in laparoscopic total gastrectomy includes two categories: circular stapler anastomosis techniques and linear stapler anastomosis techniques. Circular stapler anastomosis techniques include manual anastomosis method, purse string instrument method, Hiki improved special anvil anastomosis technique, the transorally inserted anvil(OrVil(TM)) and reverse puncture device technique. Linear stapler anastomosis techniques include side to side anastomosis technique and Overlap side to side anastomosis technique. Esophageal jejunum anastomosis technique has a wide selection of different technologies with different strengths and the corresponding limitations. This article will introduce research progress of laparoscopic total gastrectomy esophagus jejunum anastomosis from both sides of the development of anastomosis technology and the selection of anastomosis technology. PMID:26013872

  15. 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.

  16. Capillary nano-immunoassays: advancing quantitative proteomics analysis, biomarker assessment, and molecular diagnostics.

    PubMed

    Chen, Jin-Qiu; Wakefield, Lalage M; Goldstein, David J

    2015-01-01

    There is an emerging demand for the use of molecular profiling to facilitate biomarker identification and development, and to stratify patients for more efficient treatment decisions with reduced adverse effects. In the past decade, great strides have been made to advance genomic, transcriptomic and proteomic approaches to address these demands. While there has been much progress with these large scale approaches, profiling at the protein level still faces challenges due to limitations in clinical sample size, poor reproducibility, unreliable quantitation, and lack of assay robustness. A novel automated capillary nano-immunoassay (CNIA) technology has been developed. This technology offers precise and accurate measurement of proteins and their post-translational modifications using either charge-based or size-based separation formats. The system not only uses ultralow nanogram levels of protein but also allows multi-analyte analysis using a parallel single-analyte format for increased sensitivity and specificity. The high sensitivity and excellent reproducibility of this technology make it particularly powerful for analysis of clinical samples. Furthermore, the system can distinguish and detect specific protein post-translational modifications that conventional Western blot and other immunoassays cannot easily capture. This review will summarize and evaluate the latest progress to optimize the CNIA system for comprehensive, quantitative protein and signaling event characterization. It will also discuss how the technology has been successfully applied in both discovery research and clinical studies, for signaling pathway dissection, proteomic biomarker assessment, targeted treatment evaluation and quantitative proteomic analysis. Lastly, a comparison of this novel system with other conventional immuno-assay platforms is performed. PMID:26048678

  17. Visceral Leishmaniasis: Advancements in Vaccine Development via Classical and Molecular Approaches

    PubMed Central

    Joshi, Sumit; Rawat, Keerti; Yadav, Narendra Kumar; Kumar, Vikash; Siddiqi, Mohammad Imran; Dube, Anuradha

    2014-01-01

    Visceral leishmaniasis (VL) or kala-azar, a vector-borne protozoan disease, shows endemicity in larger areas of the tropical, subtropical and the Mediterranean countries. WHO report suggested that an annual incidence of VL is nearly 200,000 to 400,000 cases, resulting in 20,000 to 30,000 deaths per year. Treatment with available anti-leishmanial drugs are not cost effective, with varied efficacies and higher relapse rate, which poses a major challenge to current kala-azar control program in Indian subcontinent. Therefore, a vaccine against VL is imperative and knowing the fact that recovered individuals developed lifelong immunity against re-infection, it is feasible. Vaccine development program, though time taking, has recently gained momentum with the emergence of omic era, i.e., from genomics to immunomics. Classical as well as molecular methodologies have been overtaken with alternative strategies wherein proteomics based knowledge combined with computational techniques (immunoinformatics) speed up the identification and detailed characterization of new antigens for potential vaccine candidates. This may eventually help in the designing of polyvalent synthetic and recombinant chimeric vaccines as an effective intervention measures to control the disease in endemic areas. This review focuses on such newer approaches being utilized for vaccine development against VL. PMID:25202307

  18. 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.

  19. Advances and challenges in the molecular biology and treatment of glioblastoma—is there any hope for the future?

    PubMed Central

    Veliz, Ignacio; Loo, Yong; Castillo, Omar; Karachaliou, Niki; Nigro, Olga

    2015-01-01

    Malignant gliomas, such as glioblastoma multiforme (GBM), present some of the greatest challenges in the management of cancer patients worldwide. Even with aggressive surgical resections and recent advances in radiotherapy and chemotherapy, the prognosis for GBM patients remains dismal and quality of life is poor. Although new molecular pathways crucial to the biology and invasive ability of GBM are coming to light, translation of basic science achievements into clinical practice is slow. Optimal management requires a multidisciplinary approach and knowledge of potential complications arising from both disease and treatment. To help illustrate “where we are going” with GBM, we here include a detailed depiction of the molecular alterations underlying this fatal disease, as well as intensive research over the past two decades that has led to considerable advances in the understanding of basic GBM biology, pathogenesis and therapeutic approaches. PMID:25705639

  20. An advanced technique for speciation of organic nitrogen in atmospheric aerosols

    NASA Astrophysics Data System (ADS)

    Samy, S.; Robinson, J.; Hays, M. D.

    2011-12-01

    The chemical composition of organic nitrogen (ON) in the environment is a research topic of broad significance. The topic intersects the branches of atmospheric, aquatic, and ecological science; thus, a variety of instrumentation, analytical methods, and data interpretation tools have evolved for determination of ON. Recent studies that focus on atmospheric particulate nitrogen (N) suggest a significant fraction (20-80%) of total N is bound in organic compounds. The sources, bioavailability and transport mechanisms of these N-containing compounds can differ, producing a variety of environmental consequences. Amino acids (AA) are a key class of atmospheric ON compounds that can contribute to secondary organic aerosol (SOA) formation and potentially influence water cycles, air pollutant scavenging, and the radiation balance. AA are water-soluble organic compounds (WSOC) that can significantly alter the acid-base chemistry of aerosols, and may explain the buffering capacity that impacts heterogeneous atmospheric chemistry. The chemical transformations that N-containing organic compounds (including AA) undergo can increase the light-absorbing capacity of atmospheric carbon via formation of 'brown carbon'. Suggested sources of atmospheric AA include: marine surface layer transport from bursting sea bubbles, the suspension of bacteria, fungi, algae, pollen, spores, or biomass burning. Methodology for detection of native (underivatized) amino acids (AA) in atmospheric aerosols has been developed and validated (Samy et al., 2011). This presentation describes the use of LC-MS (Q-TOF) and microwave-assisted gas phase hydrolysis for detection of free and combined amino acids in aerosols collected in a Southeastern U.S. forest environment. Accurate mass detection and the addition of isotopically labeled surrogates prior to sample preparation allows for sensitive quantitation of target AA in a complex aerosol matrix. A total of 16 native AA were detected above the reporting threshold as water-soluble free AA, with an average concentration of 22 9 ng m-3 (N=13). Following microwave-assisted gas phase hydrolysis, the total AA concentration in the forest environment increased significantly (70 35 ng m-3) and additional compounds (methionine, isoleucine) were detected above the reporting threshold. The ability to quantify AA in aerosol samples without derivatization reduces time consuming preparation procedures while providing the advancement of selective mass determination that eliminates potential interferences associated with traditional fluorescence detection. This step forward in precise mass determination with the use of internal standardization, improves the confidence of compound identification. With the increasing focus on WSOC (including ON) characterization in the atmospheric science community, native detection by LC-MS (Q-TOF) will play a central role in determining the most direct approach to quantify an increasing fraction of the co-extracted polar organic compounds. Method application for further characterization of atmospheric ON will be discussed. Reference: Samy, S., Robinson, J., and M.D. Hays. "An Advanced LC-MS (Q-TOF) Technique for the Detection of Amino Acids in Atmospheric Aerosols", Analytical Bioanalytical Chemistry, 2011, DOI: 10.1007/s00216-011-5238-2