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Sample records for enhanced afci sampling

  1. Enhanced AFCI Sampling, Analysis, and Safeguards Technology Review

    SciTech Connect

    John Svoboda

    2009-09-01

    The focus of this study includes the investigation of sampling technologies used in industry and their potential application to nuclear fuel processing. The goal is to identify innovative sampling methods using state of the art techniques that could evolve into the next generation sampling and analysis system for metallic elements. Sampling and analysis of nuclear fuel recycling plant processes is required both to monitor the operations and ensure Safeguards and Security goals are met. In addition, environmental regulations lead to additional samples and analysis to meet licensing requirements. The volume of samples taken by conventional means, can restrain productivity while results samples are analyzed, require process holding tanks that are sized to meet analytical issues rather than process issues (and that create a larger facility footprint), or, in some cases, simply overwhelm analytical laboratory capabilities. These issues only grow when process flowsheets propose new separations systems and new byproduct material for transmutation purposes. Novel means of streamlining both sampling and analysis are being evaluated to increase the efficiency while meeting all requirements for information. This report addresses just a part of the effort to develop and study novel methods by focusing on the sampling and analysis of aqueous samples for metallic elements. It presents an overview of the sampling requirements, including frequency, sensitivity, accuracy, and programmatic drivers, to demonstrate the magnitude of the task. The sampling and analysis system needed for metallic element measurements is then discussed, and novel options being applied to other industrial analytical needs are presented. Inductively coupled mass spectrometry instruments are the most versatile for metallic element analyses and are thus chosen as the focus for the study. Candidate novel means of process sampling, as well as modifications that are necessary to couple such instruments to

  2. AFCI Safeguards Enhancement Study: Technology Development Roadmap

    SciTech Connect

    Smith, Leon E.; Dougan, A.; Tobin, Stephen; Cipiti, B.; Ehinger, Michael H.; Bakel, A. J.; Bean, Robert; Grate, Jay W.; Santi, P.; Bryan, Steven; Kinlaw, M. T.; Schwantes, Jon M.; Burr, Tom; Lehn, Scott A.; Tolk, K.; Chichester, David; Menlove, H.; Vo, D.; Duckworth, Douglas C.; Merkle, P.; Wang, T. F.; Duran, F.; Nakae, L.; Warren, Glen A.; Friedrich, S.; Rabin, M.

    2008-12-31

    The Advanced Fuel Cycle Initiative (AFCI) Safeguards Campaign aims to develop safeguards technologies and processes that will significantly reduce the risk of proliferation in the U.S. nuclear fuel cycle of tomorrow. The Safeguards Enhancement Study was chartered with identifying promising research and development (R&D) directions over timescales both near-term and long-term, and under safeguards oversight both domestic and international. This technology development roadmap documents recognized gaps and needs in the safeguarding of nuclear fuel cycles, and outlines corresponding performance targets for each of those needs. Drawing on the collective expertise of technologists and user-representatives, a list of over 30 technologies that have the potential to meet those needs was developed, along with brief summaries of each candidate technology. Each summary describes the potential impact of that technology, key research questions to be addressed, and prospective development milestones that could lead to a definitive viability or performance assessment. Important programmatic linkages between U.S. agencies and offices are also described, reflecting the emergence of several safeguards R&D programs in the U.S. and the reinvigoration of nuclear fuel cycles across the globe.

  3. 2014 AFCI Glovebox Event Executive Summary

    SciTech Connect

    Campbell, Joseph Lenard

    2016-01-01

    One of the primary INL missions is to support development of advanced fuels with the goal of creating reactor fuels that produce less waste and are easier to store. The Advanced Fuel Cycle Initiative (AFCI) Glovebox in the Fuel Manufacturing Facility (FMF) is used for several fuel fabrication steps that involve transuranic elements, including americium. The AFCI glove box contains equipment used for fuel fabrication, including an arc melter – a small, laboratory-scale version of an electric arc furnace used to make new metal alloys for research – and an americium distillation apparatus. This overview summarizes key findings related to the investigation into the releases of airborne radioactivity that occurred in the AFCI glovebox room in late August and early September 2014. The full report (AFCI Glovebox Radiological Release – Evaluation, Corrective Actions and Testing, INL/INL-15-36996) provides details of the identified issues, corrective actions taken as well as lessons learned

  4. Quality Assurance Protocol for AFCI Advanced Structural Materials Testing

    SciTech Connect

    Busby, Jeremy T

    2009-05-01

    application of NQA-1 requirements at the site. The current program is being revised to incorporate changes imposed through the recently revised AFCI Technical Integration Office QA requirements. Testing conducted under the AFCI QA program for the advanced structural materials effort shall incorporate the following quality assurance expectations: (1) personnel are adequately trained to perform assigned work; (2) activities are controlled to ensure consistency of results; (3) records necessary to substantiate how the work was performed are maintained (dedicated laboratory notebooks will be used); (4) the pedigree and traceability of the various tested materials are maintained throughout the described processes using consistent sample numbering and adequate record keeping; (5) equipment with the potential to affect the quality of the planned work is calibrated and maintained in accordance with applicable operating requirements. In addition, all reporting or related dissemination by ORNL personnel of the results of the work described in this subcontract shall be conducted in accordance with the requirements described or referenced in the ORNL Standards Based Management System subject area entitled Scientific and Technical Information. Reporting or publications at other institutions will be conducted in accordance with the requirements of that institution. Successful implementation of these protocols will provide a sound basis for future decisions and research. In addition, these steps will also help ensure that results can also be applied to licensing discussions at a future date.

  5. MDD Status Letter Report (AFCI CETE Milestone)

    SciTech Connect

    Vedder, Raymond James; Jubin, Robert Thomas

    2009-09-01

    understanding of the chemistry of the uranium-ammonium double nitrate salt was developed. Later pilot-scale studies produced kilogram quantities of UO{sub 3} using engineering-scale (1 kg/hour), continuously-operated equipment, while establishing the reliability of the process and equipment. The current work was performed in support of the Advanced Fuel Cycle Initiative (AFCI), utilizing glove-box-contained equipment (100 g/hour) to produce UO{sub 3}, PuO{sub 2}, and mixed oxides of uranium, plutonium, neptunium, and americium from a nitrate solution of those actinides. Then the MDD glove-box system was utilized in the Coupled-End-To-End (CETE) project to convert the U-Pu-Np and uranium product solutions into oxide powders. As part of the CETE project, a powder characterization laboratory was established in gloveboxes with instruments required for the determination of: (1) surface area by the BET methodology; (2) tap density by using a Quantachrome AutoTap; (3) flow properties by using a Freeman technology powder rheometer; (4) material composition and crystalline structure by using a powder X-ray diffractometer; (5) particle size distribution by using a laser light-scattering analyzer; and (6) imaging of the powders with a stereomicroscope. These instruments can be used to characterize the products and to determine the effects of MDD operating parameters on product powder morphology. Ultimately, the powder characteristics necessary to produce high-density, sintered MOX pellets can be determined.

  6. AFCI-2.0 Library of Neutron Cross Section Covariances

    SciTech Connect

    Herman, M.; Herman,M.; Oblozinsky,P.; Mattoon,C.; Pigni,M.; Hoblit,S.; Mughabghab,S.F.; Sonzogni,A.; Talou,P.; Chadwick,M.B.; Hale.G.M.; Kahler,A.C.; Kawano,T.; Little,R.C.; Young,P.G.

    2011-06-26

    Neutron cross section covariance library has been under development by BNL-LANL collaborative effort over the last three years. The primary purpose of the library is to provide covariances for the Advanced Fuel Cycle Initiative (AFCI) data adjustment project, which is focusing on the needs of fast advanced burner reactors. The covariances refer to central values given in the 2006 release of the U.S. neutron evaluated library ENDF/B-VII. The preliminary version (AFCI-2.0beta) has been completed in October 2010 and made available to the users for comments. In the final 2.0 release, covariances for a few materials were updated, in particular new LANL evaluations for {sup 238,240}Pu and {sup 241}Am were adopted. BNL was responsible for covariances for structural materials and fission products, management of the library and coordination of the work, while LANL was in charge of covariances for light nuclei and for actinides.

  7. Code qualification of structural materials for AFCI advanced recycling reactors.

    SciTech Connect

    Natesan, K.; Li, M.; Majumdar, S.; Nanstad, R.K.; Sham, T.-L.

    2012-05-31

    This report summarizes the further findings from the assessments of current status and future needs in code qualification and licensing of reference structural materials and new advanced alloys for advanced recycling reactors (ARRs) in support of Advanced Fuel Cycle Initiative (AFCI). The work is a combined effort between Argonne National Laboratory (ANL) and Oak Ridge National Laboratory (ORNL) with ANL as the technical lead, as part of Advanced Structural Materials Program for AFCI Reactor Campaign. The report is the second deliverable in FY08 (M505011401) under the work package 'Advanced Materials Code Qualification'. The overall objective of the Advanced Materials Code Qualification project is to evaluate key requirements for the ASME Code qualification and the Nuclear Regulatory Commission (NRC) approval of structural materials in support of the design and licensing of the ARR. Advanced materials are a critical element in the development of sodium reactor technologies. Enhanced materials performance not only improves safety margins and provides design flexibility, but also is essential for the economics of future advanced sodium reactors. Code qualification and licensing of advanced materials are prominent needs for developing and implementing advanced sodium reactor technologies. Nuclear structural component design in the U.S. must comply with the ASME Boiler and Pressure Vessel Code Section III (Rules for Construction of Nuclear Facility Components) and the NRC grants the operational license. As the ARR will operate at higher temperatures than the current light water reactors (LWRs), the design of elevated-temperature components must comply with ASME Subsection NH (Class 1 Components in Elevated Temperature Service). However, the NRC has not approved the use of Subsection NH for reactor components, and this puts additional burdens on materials qualification of the ARR. In the past licensing review for the Clinch River Breeder Reactor Project (CRBRP) and the

  8. Enhanced conformational sampling using enveloping distribution sampling.

    PubMed

    Lin, Zhixiong; van Gunsteren, Wilfred F

    2013-10-14

    To lessen the problem of insufficient conformational sampling in biomolecular simulations is still a major challenge in computational biochemistry. In this article, an application of the method of enveloping distribution sampling (EDS) is proposed that addresses this challenge and its sampling efficiency is demonstrated in simulations of a hexa-β-peptide whose conformational equilibrium encompasses two different helical folds, i.e., a right-handed 2.7(10∕12)-helix and a left-handed 3(14)-helix, separated by a high energy barrier. Standard MD simulations of this peptide using the GROMOS 53A6 force field did not reach convergence of the free enthalpy difference between the two helices even after 500 ns of simulation time. The use of soft-core non-bonded interactions in the centre of the peptide did enhance the number of transitions between the helices, but at the same time led to neglect of relevant helical configurations. In the simulations of a two-state EDS reference Hamiltonian that envelops both the physical peptide and the soft-core peptide, sampling of the conformational space of the physical peptide ensures that physically relevant conformations can be visited, and sampling of the conformational space of the soft-core peptide helps to enhance the transitions between the two helices. The EDS simulations sampled many more transitions between the two helices and showed much faster convergence of the relative free enthalpy of the two helices compared with the standard MD simulations with only a slightly larger computational effort to determine optimized EDS parameters. Combined with various methods to smoothen the potential energy surface, the proposed EDS application will be a powerful technique to enhance the sampling efficiency in biomolecular simulations.

  9. AFCI-2.0 Neutron Cross Section Covariance Library

    SciTech Connect

    Herman, M.; Herman, M; Oblozinsky, P.; Mattoon, C.M.; Pigni, M.; Hoblit, S.; Mughabghab, S.F.; Sonzogni, A.; Talou, P.; Chadwick, M.B.; Hale, G.M.; Kahler, A.C.; Kawano, T.; Little, R.C.; Yount, P.G.

    2011-03-01

    The cross section covariance library has been under development by BNL-LANL collaborative effort over the last three years. The project builds on two covariance libraries developed earlier, with considerable input from BNL and LANL. In 2006, international effort under WPEC Subgroup 26 produced BOLNA covariance library by putting together data, often preliminary, from various sources for most important materials for nuclear reactor technology. This was followed in 2007 by collaborative effort of four US national laboratories to produce covariances, often of modest quality - hence the name low-fidelity, for virtually complete set of materials included in ENDF/B-VII.0. The present project is focusing on covariances of 4-5 major reaction channels for 110 materials of importance for power reactors. The work started under Global Nuclear Energy Partnership (GNEP) in 2008, which changed to Advanced Fuel Cycle Initiative (AFCI) in 2009. With the 2011 release the name has changed to the Covariance Multigroup Matrix for Advanced Reactor Applications (COMMARA) version 2.0. The primary purpose of the library is to provide covariances for AFCI data adjustment project, which is focusing on the needs of fast advanced burner reactors. Responsibility of BNL was defined as developing covariances for structural materials and fission products, management of the library and coordination of the work; LANL responsibility was defined as covariances for light nuclei and actinides. The COMMARA-2.0 covariance library has been developed by BNL-LANL collaboration for Advanced Fuel Cycle Initiative applications over the period of three years, 2008-2010. It contains covariances for 110 materials relevant to fast reactor R&D. The library is to be used together with the ENDF/B-VII.0 central values of the latest official release of US files of evaluated neutron cross sections. COMMARA-2.0 library contains neutron cross section covariances for 12 light nuclei (coolants and moderators), 78 structural

  10. Enhanced sampling of rare events

    NASA Astrophysics Data System (ADS)

    Melchionna, Simone

    2000-12-01

    We present a method to enhance sampling of a given reaction coordinate by projecting part of the random thermal noise along a preferential direction. The approach is promising to study rough energy landscapes and highly activated barriers that can be overcome by increasing the attempt frequency. Furthermore it allows us to rescale a given reaction coordinate without biasing the configurational properties of the system. A major advantage of the method is its simplicity in the analytical derivation and numerical implementation.

  11. AFCI Transmutation Fuel Processes and By-Products Planning: Interim Report

    SciTech Connect

    Eric L. Shaber

    2005-09-01

    The goals of the Advanced Fuel Cycle Initiative (AFCI) Program are to reduce high-level waste volume, reduce long-lived and radiotoxic elements, and reclaim valuable energy content of spent nuclear fuel. The AFCI chartered the Fuel Development Working Group (FDWG) to develop advanced fuels in support of the AFCI goals. The FDWG organized a phased strategy of fuel development that is designed to match the needs of the AFCI program: Phase 1 - High-burnup fuels for light-water reactors (LWRs) and tri-isotopic (TRISO) fuel for gas-cooled reactors Phase 2 – Mixed oxide fuels with minor actinides for LWRs, Am transmutation targets for LWRs, inert matrix fuels for LWRs, and TRISO fuel containing Pu and other transuranium for gas-cooled reactors Phase 3 – Fertile free or low-fertile metal, ceramic, ceramic dispersed in a metal matrix (CERMET), and ceramics dispersed in a ceramic matrix (CERCER) that would be used primarily in fast reactors. Development of advanced fuels requires the fabrication, assembly, and irradiation of prototypic fuel under bounding reactor conditions. At specialized national laboratory facilities small quantities of actinides are being fabricated into such fuel for irradiation tests. Fabrication of demonstration quantities of selected fuels for qualification testing is needed but not currently feasible, because existing manual glovebox fabrication approaches result in significant radiation exposures when larger quantities of actinides are involved. The earliest demonstration test fuels needed in the AFCI program are expected to be variants of commercial mixed oxide fuel for use in an LWR as lead test assemblies. Manufacture of such test assemblies will require isolated fabrication lines at a facility not currently available in the U.S. Such facilities are now being planned as part of an Advanced Fuel Cycle Facility (AFCF). Adequate planning for and specification of actinide fuel fabrication facilities capable of producing transmutation fuels

  12. Progress on Nuclear Data Covariances: AFCI-1.2 Covariance Library

    SciTech Connect

    Oblozinsky,P.; Oblozinsky,P.; Mattoon,C.M.; Herman,M.; Mughabghab,S.F.; Pigni,M.T.; Talou,P.; Hale,G.M.; Kahler,A.C.; Kawano,T.; Little,R.C.; Young,P.G

    2009-09-28

    Improved neutron cross section covariances were produced for 110 materials including 12 light nuclei (coolants and moderators), 78 structural materials and fission products, and 20 actinides. Improved covariances were organized into AFCI-1.2 covariance library in 33-energy groups, from 10{sup -5} eV to 19.6 MeV. BNL contributed improved covariance data for the following materials: {sup 23}Na and {sup 55}Mn where more detailed evaluation was done; improvements in major structural materials {sup 52}Cr, {sup 56}Fe and {sup 58}Ni; improved estimates for remaining structural materials and fission products; improved covariances for 14 minor actinides, and estimates of mubar covariances for {sup 23}Na and {sup 56}Fe. LANL contributed improved covariance data for {sup 235}U and {sup 239}Pu including prompt neutron fission spectra and completely new evaluation for {sup 240}Pu. New R-matrix evaluation for {sup 16}O including mubar covariances is under completion. BNL assembled the library and performed basic testing using improved procedures including inspection of uncertainty and correlation plots for each material. The AFCI-1.2 library was released to ANL and INL in August 2009.

  13. Summary of Off-Normal Events in US Fuel Cycle Facilities for AFCI Applications

    SciTech Connect

    L. C. Cadwallader; S. J. Piet; S. O. Sheetz; D. H. McGuire; W. B. Boore

    2005-09-01

    This report is a collection and review of system operation and failure experiences for facilities comprising the fission reactor fuel cycle, with the exception of reactor operations. This report includes mines, mills, conversion plants, enrichment plants, fuel fabrication plants, transportation of fuel materials between these centers, and waste storage facilities. Some of the facilities discussed are no longer operating; others continue to produce fuel for the commercial fission power plant industry. Some of the facilities discussed have been part of the military’s nuclear effort; these are included when the processes used are similar to those used for commercial nuclear power. When reading compilations of incidents and accidents, after repeated entries it is natural to form an opinion that there exists nothing but accidents. For this reason, production or throughput values are described when available. These adverse operating experiences are compiled to support the design and decisions needed for the Advanced Fuel Cycle Initiative (AFCI). The AFCI is to weigh options for a new fission reactor fuel cycle that is efficient, safe, and productive for US energy security.

  14. Detectivity enhancement in THz electrooptical sampling

    SciTech Connect

    Ahmed, Saima; Savolainen, Janne; Hamm, Peter

    2014-01-15

    We demonstrate and discuss a simple scheme that significantly enhances the detectivity of THz electro-optical sampling by introducing a sequence of Brewster windows that increases the ellipticity of the probe beam. By varying the window material or the number of Brewster windows, the enhancement factor can be adjusted; we demonstrate an enhancement factor of ≈20 with four ZnSe Brewster windows. The scheme is particularly useful when very small THz fields are to be measured in connection with low-repetition rate amplified Ti:S laser systems.

  15. AFCI UFP, Final Technical Report DE-FC07-00AL67053

    SciTech Connect

    Cathy Dixon

    2005-02-21

    The project ''Creating an Educational Consortium to Support the Recruitment and Retention of Expertise for the Nuclear Weapons Complex'' was also known as the Advanced Fuel Cycle Initiative (AFCI) University Fellowship Program. Since its inception, the Advanced Fuel Cycle Initiative program and its predecessor, the Advanced Accelerator Applications (AAA) program, have engaged university researchers and students in the sciences necessary to answer technical questions related to reducing high-level waste volumes, optimizing the economics and performance of Yucca Mountain, reducing the technical need for a second repository, reducing the long-term inventories of plutonium in spent fuel, and enabling the proliferation-resistant recovery of the energy contained in spent fuel. The Advanced Fuel Cycle University Fellowship Program is intended to support top students across the nation in a variety of disciplines that will be required to support transmutation research and technology development in the coming decades.

  16. AFCI Fuel Irradiation Test Plan, Test Specimens AFC-1Æ and AFC-1F

    SciTech Connect

    D. C. Crawford; S. L. Hayes; B. A. Hilton; M. K. Meyer; R. G. Ambrosek; G. S. Chang; D. J. Utterbeck

    2003-11-01

    The U. S. Advanced Fuel Cycle Initiative (AFCI) seeks to develop and demonstrate the technologies needed to transmute the long-lived transuranic actinide isotopes contained in spent nuclear fuel into shorter-lived fission products, thereby dramatically decreasing the volume of material requiring disposition and the long-term radiotoxicity and heat load of high-level waste sent to a geologic repository (DOE, 2003). One important component of the technology development is actinide-bearing transmutation fuel forms containing plutonium, neptunium, americium (and possibly curium) isotopes. There are little irradiation performance data available on non-fertile fuel forms, which would maximize the destruction rate of plutonium, and low-fertile (i.e., uranium-bearing) fuel forms, which would support a sustainable nuclear energy option. Initial scoping level irradiation tests on a variety of candidate fuel forms are needed to establish a transmutation fuel form design and evaluate deployment of transmutation fuels.

  17. Enhanced sampling techniques in biomolecular simulations.

    PubMed

    Spiwok, Vojtech; Sucur, Zoran; Hosek, Petr

    2015-11-01

    Biomolecular simulations are routinely used in biochemistry and molecular biology research; however, they often fail to match expectations of their impact on pharmaceutical and biotech industry. This is caused by the fact that a vast amount of computer time is required to simulate short episodes from the life of biomolecules. Several approaches have been developed to overcome this obstacle, including application of massively parallel and special purpose computers or non-conventional hardware. Methodological approaches are represented by coarse-grained models and enhanced sampling techniques. These techniques can show how the studied system behaves in long time-scales on the basis of relatively short simulations. This review presents an overview of new simulation approaches, the theory behind enhanced sampling methods and success stories of their applications with a direct impact on biotechnology or drug design. Copyright © 2014 Elsevier Inc. All rights reserved.

  18. Reactor physics studies for the Advanced Fuel Cycle Initiative (AFCI) Reactor-Accelerator Coupling Experiments (RACE) Project

    NASA Astrophysics Data System (ADS)

    Stankovskiy, Evgeny Yuryevich

    In the recently completed RACE Project of the AFCI, accelerator-driven subcritical systems (ADS) experiments were conducted to develop technology of coupling accelerators to nuclear reactors. In these experiments electron accelerators induced photon-neutron reactions in heavy-metal targets to initiate fission reactions in ADS. Although the Idaho State University (ISU) RACE ADS was constructed only to develop measurement techniques for advanced experiments, many reactor kinetics experiments were conducted there. In the research reported in this dissertation, a method was developed to calculate kinetics parameters for measurement and calculation of the reactivity of ADS, a safety parameter that is necessary for control and monitoring of power production. Reactivity is measured in units of fraction of delayed versus prompt neutron from fission, a quantity that cannot be directly measured in far-subcritical reactors such as the ISU RACE configuration. A new technique is reported herein to calculate it accurately and to predict kinetic behavior of a far-subcritical ADS. Experiments conducted at ISU are first described and experimental data are presented before development of the kinetic theory used in the new computational method. Because of the complexity of the ISU ADS, the Monte-Carlo method as applied in the MCNP code is most suitable for modeling reactor kinetics. However, the standard method of calculating the delayed neutron fraction produces inaccurate values. A new method was developed and used herein to evaluate actual experiments. An advantage of this method is that its efficiency is independent of the fission yield of delayed neutrons, which makes it suitable for fuel with a minor actinide component (e.g. transmutation fuels). The implementation of this method is based on a correlated sampling technique which allows the accurate evaluation of delayed and prompt neutrons. The validity of the obtained results is indicated by good agreement between experimental

  19. Designing an enhanced groundwater sample collection system

    SciTech Connect

    Schalla, R.

    1994-10-01

    As part of an ongoing technical support mission to achieve excellence and efficiency in environmental restoration activities at the Laboratory for Energy and Health-Related Research (LEHR), Pacific Northwest Laboratory (PNL) provided guidance on the design and construction of monitoring wells and identified the most suitable type of groundwater sampling pump and accessories for monitoring wells. The goal was to utilize a monitoring well design that would allow for hydrologic testing and reduce turbidity to minimize the impact of sampling. The sampling results of the newly designed monitoring wells were clearly superior to those of the previously installed monitoring wells. The new wells exhibited reduced turbidity, in addition to improved access for instrumentation and hydrologic testing. The variable frequency submersible pump was selected as the best choice for obtaining groundwater samples. The literature references are listed at the end of this report. Despite some initial difficulties, the actual performance of the variable frequency, submersible pump and its accessories was effective in reducing sampling time and labor costs, and its ease of use was preferred over the previously used bladder pumps. The surface seals system, called the Dedicator, proved to be useful accessory to prevent surface contamination while providing easy access for water-level measurements and for connecting the pump. Cost savings resulted from the use of the pre-production pumps (beta units) donated by the manufacturer for the demonstration. However, larger savings resulted from shortened field time due to the ease in using the submersible pumps and the surface seal access system. Proper deployment of the monitoring wells also resulted in cost savings and ensured representative samples.

  20. 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

  1. Enhancement of canonical sampling by virtual-state transitions

    NASA Astrophysics Data System (ADS)

    Higo, Junichi; Kasahara, Kota; Dasgupta, Bhaskar; Nakamura, Haruki

    2017-01-01

    A novel method was developed to enhance canonical sampling. A system is divided into virtually introduced sub-states, called "virtual states," which does not exist in reality. The configuration sampling is achieved by a standard canonical sampling method, the Metropolis Monte Carlo method, and confined in a virtual state for a while. In contrast, inter-virtual state motions are controlled by transition probabilities, which can be set arbitrarily. A simple recursive equation was introduced to determine the inter-virtual state transition probabilities, by which the sampling is enhanced considerably. We named this method "virtual-system coupled canonical Monte Carlo (VcMC) sampling." A simple method was proposed to reconstruct a canonical distribution function at a certain temperature from the resultant VcMC sampling data. Two systems, a one-dimensional double-well potential and a three-dimensional ligand-receptor binding/unbinding model, were examined. VcMC produced an accurate canonical distribution much more quickly than a conventional canonical Monte Carlo simulation does.

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

    PubMed

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

    2015-05-01

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

  3. Enhanced, targeted sampling of high-dimensional free-energy landscapes using variationally enhanced sampling, with an application to chignolin.

    PubMed

    Shaffer, Patrick; Valsson, Omar; Parrinello, Michele

    2016-02-02

    The capabilities of molecular simulations have been greatly extended by a number of widely used enhanced sampling methods that facilitate escaping from metastable states and crossing large barriers. Despite these developments there are still many problems which remain out of reach for these methods which has led to a vigorous effort in this area. One of the most important problems that remains unsolved is sampling high-dimensional free-energy landscapes and systems that are not easily described by a small number of collective variables. In this work we demonstrate a new way to compute free-energy landscapes of high dimensionality based on the previously introduced variationally enhanced sampling, and we apply it to the miniprotein chignolin.

  4. Enhanced, targeted sampling of high-dimensional free-energy landscapes using variationally enhanced sampling, with an application to chignolin

    PubMed Central

    Shaffer, Patrick; Valsson, Omar; Parrinello, Michele

    2016-01-01

    The capabilities of molecular simulations have been greatly extended by a number of widely used enhanced sampling methods that facilitate escaping from metastable states and crossing large barriers. Despite these developments there are still many problems which remain out of reach for these methods which has led to a vigorous effort in this area. One of the most important problems that remains unsolved is sampling high-dimensional free-energy landscapes and systems that are not easily described by a small number of collective variables. In this work we demonstrate a new way to compute free-energy landscapes of high dimensionality based on the previously introduced variationally enhanced sampling, and we apply it to the miniprotein chignolin. PMID:26787868

  5. Avoiding traps in trajectory space: Metadynamics enhanced transition path sampling

    NASA Astrophysics Data System (ADS)

    Borrero, E. E.; Dellago, C.

    2016-10-01

    We propose a transition path sampling (TPS) scheme designed to enhance sampling in systems with multiple reaction channels. In this method, based on a combination of the metadynamics algorithm with the TPS shooting move, a history dependent bias drives the simulation towards unexplored reaction channels. The bias, constructed as a superposition of repulsive Gaussian potentials deposited on the trajectories harvested in the course of the simulation, acts only during the initial stage of the trajectory generation, but leaves the dynamics along the trajectories unaffected such that the sampled pathways are true dynamical trajectories. Simulations carried out for two test systems indicate that the new approach effortlessly switches between distinct reaction channels even if they are separated by high barriers in trajectory space.

  6. A Variational Approach to Enhanced Sampling and Free Energy Calculations

    NASA Astrophysics Data System (ADS)

    Parrinello, Michele

    2015-03-01

    The presence of kinetic bottlenecks severely hampers the ability of widely used sampling methods like molecular dynamics or Monte Carlo to explore complex free energy landscapes. One of the most popular methods for addressing this problem is umbrella sampling which is based on the addition of an external bias which helps overcoming the kinetic barriers. The bias potential is usually taken to be a function of a restricted number of collective variables. However constructing the bias is not simple, especially when the number of collective variables increases. Here we introduce a functional of the bias which, when minimized, allows us to recover the free energy. We demonstrate the usefulness and the flexibility of this approach on a number of examples which include the determination of a six dimensional free energy surface. Besides the practical advantages, the existence of such a variational principle allows us to look at the enhanced sampling problem from a rather convenient vantage point.

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

    SciTech Connect

    Hanks, D

    2010-06-07

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

  8. AFCI Options Study

    SciTech Connect

    R. Wigeland; T. Taiwo; M. Todosow; W. Halsey; J. Gehin

    2009-09-01

    This report describes the background and framework for both organizing the discussion and providing information on the potential for nuclear energy R&D to develop alternative nuclear fuel cycles that would address the issues with the current implementations of nuclear power, including nuclear waste disposal, proliferation risk, safety, security, economics, and sustainability. The disposition of used fuel is the cause of many of the concerns, and the possible approaches to used fuel management identify a number of basic technology areas that need to be considered. The basic science in each of the technology areas is discussed, emphasizing what science is currently available, where scientific knowledge may be insufficient, and especially to identify specific areas where transformational discoveries may allow achievement of performance goals not currently attainable. These discussions lead to the wide range of technical options that have been the basis for past and current research and development on advanced nuclear fuel cycles in the United States. The results of this work are then briefly reviewed to show the extent to which such approaches are capable of addressing the issues with nuclear power, the potential for moving further, and the inherent limitations.

  9. Hierarchical Protein Free Energy Landscapes from Variationally Enhanced Sampling.

    PubMed

    Shaffer, Patrick; Valsson, Omar; Parrinello, Michele

    2016-12-13

    In recent work, we demonstrated that it is possible to obtain approximate representations of high-dimensional free energy surfaces with variationally enhanced sampling ( Shaffer, P.; Valsson, O.; Parrinello, M. Proc. Natl. Acad. Sci. , 2016 , 113 , 17 ). The high-dimensional spaces considered in that work were the set of backbone dihedral angles of a small peptide, Chignolin, and the high-dimensional free energy surface was approximated as the sum of many two-dimensional terms plus an additional term which represents an initial estimate. In this paper, we build on that work and demonstrate that we can calculate high-dimensional free energy surfaces of very high accuracy by incorporating additional terms. The additional terms apply to a set of collective variables which are more coarse than the base set of collective variables. In this way, it is possible to build hierarchical free energy surfaces, which are composed of terms that act on different length scales. We test the accuracy of these free energy landscapes for the proteins Chignolin and Trp-cage by constructing simple coarse-grained models and comparing results from the coarse-grained model to results from atomistic simulations. The approach described in this paper is ideally suited for problems in which the free energy surface has important features on different length scales or in which there is some natural hierarchy.

  10. ENHANCED DAPI STAINING FOR CRYPTOSPORIDIUM IN WATER SAMPLES

    EPA Science Inventory

    The U.S. Environmental Protection Agency's Method 1623 is used to detect and quantify the presence of {ital Cryptosporidium} spp. oocysts in water. The protocol consists of concentrating a sample, staining this concentrate with a fluorescent antibody, and examining the sample mi...

  11. ENHANCED DAPI STAINING FOR CRYPTOSPORIDIUM IN WATER SAMPLES

    EPA Science Inventory

    The U.S. Environmental Protection Agency's Method 1623 is used to detect and quantify the presence of {ital Cryptosporidium} spp. oocysts in water. The protocol consists of concentrating a sample, staining this concentrate with a fluorescent antibody, and examining the sample mi...

  12. Enhanced Sampling and Analysis, Selection of Technology for Testing

    SciTech Connect

    Svoboda, John; Meikrantz, David

    2010-02-01

    The focus of this study includes the investigation of sampling technologies used in industry and their potential application to nuclear fuel processing. The goal is to identify innovative sampling methods using state of the art techniques that could evolve into the next generation sampling and analysis system for metallic elements. This report details the progress made in the first half of FY 2010 and includes a further consideration of the research focus and goals for this year. Our sampling options and focus for the next generation sampling method are presented along with the criteria used for choosing our path forward. We have decided to pursue the option of evaluating the feasibility of microcapillary based chips to remotely collect, transfer, track and supply microliters of sample solutions to analytical equipment in support of aqueous processes for used nuclear fuel cycles. Microchip vendors have been screened and a choice made for the development of a suitable microchip design followed by production of samples for evaluation by ANL, LANL, and INL on an independent basis.

  13. From thermodynamics to kinetics: enhanced sampling of rare events.

    PubMed

    Yang, Lijiang; Liu, Cheng-Wen; Shao, Qiang; Zhang, Jun; Gao, Yi Qin

    2015-04-21

    Despite great advances in molecular dynamics simulations, there remain large gaps between the simulations and experimental observations in terms of the time and length scales that can be approached. Developing fast and accurate algorithms and methods is of ultimate importance to bridge these gaps. In this Account, we briefly summarize recent efforts in such directions. In particular, we focus on integrated tempering sampling. The efficiency of this sampling method has been demonstrated by applications to a range of chemical and biological problems: protein folding, molecular cluster structure searches, and chemical reactions. The combination of integrated tempering sampling and a trajectory sampling method allows the calculation of rate constants and reaction pathways without predefined collective coordinates.

  14. Enhancing sampling design in mist-net bat surveys by accounting for sample size optimization

    PubMed Central

    Trevelin, Leonardo Carreira; Novaes, Roberto Leonan Morim; Colas-Rosas, Paul François; Benathar, Thayse Cristhina Melo; Peres, Carlos A.

    2017-01-01

    The advantages of mist-netting, the main technique used in Neotropical bat community studies to date, include logistical implementation, standardization and sampling representativeness. Nonetheless, study designs still have to deal with issues of detectability related to how different species behave and use the environment. Yet there is considerable sampling heterogeneity across available studies in the literature. Here, we approach the problem of sample size optimization. We evaluated the common sense hypothesis that the first six hours comprise the period of peak night activity for several species, thereby resulting in a representative sample for the whole night. To this end, we combined re-sampling techniques, species accumulation curves, threshold analysis, and community concordance of species compositional data, and applied them to datasets of three different Neotropical biomes (Amazonia, Atlantic Forest and Cerrado). We show that the strategy of restricting sampling to only six hours of the night frequently results in incomplete sampling representation of the entire bat community investigated. From a quantitative standpoint, results corroborated the existence of a major Sample Area effect in all datasets, although for the Amazonia dataset the six-hour strategy was significantly less species-rich after extrapolation, and for the Cerrado dataset it was more efficient. From the qualitative standpoint, however, results demonstrated that, for all three datasets, the identity of species that are effectively sampled will be inherently impacted by choices of sub-sampling schedule. We also propose an alternative six-hour sampling strategy (at the beginning and the end of a sample night) which performed better when resampling Amazonian and Atlantic Forest datasets on bat assemblages. Given the observed magnitude of our results, we propose that sample representativeness has to be carefully weighed against study objectives, and recommend that the trade-off between

  15. Enhancing sampling design in mist-net bat surveys by accounting for sample size optimization.

    PubMed

    Trevelin, Leonardo Carreira; Novaes, Roberto Leonan Morim; Colas-Rosas, Paul François; Benathar, Thayse Cristhina Melo; Peres, Carlos A

    2017-01-01

    The advantages of mist-netting, the main technique used in Neotropical bat community studies to date, include logistical implementation, standardization and sampling representativeness. Nonetheless, study designs still have to deal with issues of detectability related to how different species behave and use the environment. Yet there is considerable sampling heterogeneity across available studies in the literature. Here, we approach the problem of sample size optimization. We evaluated the common sense hypothesis that the first six hours comprise the period of peak night activity for several species, thereby resulting in a representative sample for the whole night. To this end, we combined re-sampling techniques, species accumulation curves, threshold analysis, and community concordance of species compositional data, and applied them to datasets of three different Neotropical biomes (Amazonia, Atlantic Forest and Cerrado). We show that the strategy of restricting sampling to only six hours of the night frequently results in incomplete sampling representation of the entire bat community investigated. From a quantitative standpoint, results corroborated the existence of a major Sample Area effect in all datasets, although for the Amazonia dataset the six-hour strategy was significantly less species-rich after extrapolation, and for the Cerrado dataset it was more efficient. From the qualitative standpoint, however, results demonstrated that, for all three datasets, the identity of species that are effectively sampled will be inherently impacted by choices of sub-sampling schedule. We also propose an alternative six-hour sampling strategy (at the beginning and the end of a sample night) which performed better when resampling Amazonian and Atlantic Forest datasets on bat assemblages. Given the observed magnitude of our results, we propose that sample representativeness has to be carefully weighed against study objectives, and recommend that the trade-off between

  16. Variational Approach to Enhanced Sampling and Free Energy Calculations

    NASA Astrophysics Data System (ADS)

    Valsson, Omar; Parrinello, Michele

    2014-08-01

    The ability of widely used sampling methods, such as molecular dynamics or Monte Carlo simulations, to explore complex free energy landscapes is severely hampered by the presence of kinetic bottlenecks. A large number of solutions have been proposed to alleviate this problem. Many are based on the introduction of a bias potential which is a function of a small number of collective variables. However constructing such a bias is not simple. Here we introduce a functional of the bias potential and an associated variational principle. The bias that minimizes the functional relates in a simple way to the free energy surface. This variational principle can be turned into a practical, efficient, and flexible sampling method. A number of numerical examples are presented which include the determination of a three-dimensional free energy surface. We argue that, beside being numerically advantageous, our variational approach provides a convenient and novel standpoint for looking at the sampling problem.

  17. Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics

    PubMed Central

    Bonomi, Massimiliano; Camilloni, Carlo; Vendruscolo, Michele

    2016-01-01

    Accurate and precise structural ensembles of proteins and macromolecular complexes can be obtained with metainference, a recently proposed Bayesian inference method that integrates experimental information with prior knowledge and deals with all sources of errors in the data as well as with sample heterogeneity. The study of complex macromolecular systems, however, requires an extensive conformational sampling, which represents a separate challenge. To address such challenge and to exhaustively and efficiently generate structural ensembles we combine metainference with metadynamics and illustrate its application to the calculation of the free energy landscape of the alanine dipeptide. PMID:27561930

  18. Enhanced spot preparation for liquid extractive sampling and analysis

    DOEpatents

    Van Berkel, Gary J.; King, Richard C.

    2015-09-22

    A method for performing surface sampling of an analyte, includes the step of placing the analyte on a stage with a material in molar excess to the analyte, such that analyte-analyte interactions are prevented and the analyte can be solubilized for further analysis. The material can be a matrix material that is mixed with the analyte. The material can be provided on a sample support. The analyte can then be contacted with a solvent to extract the analyte for further processing, such as by electrospray mass spectrometry.

  19. Enhancing Paradynamics for QM/MM Sampling of Enzymatic Reactions.

    PubMed

    Lameira, Jerônimo; Kupchencko, Ilya; Warshel, Arieh

    2016-03-10

    Despite the enormous increase in computer power, it is still extremely challenging to obtain computationally converging sampling of ab initio QM/MM (QM(ai)/MM) free energy surfaces in condensed phases. The sampling problem can be significantly reduced by the use of the reference potential paradynamics (PD) approach, but even this approach still requires major computer time in studies of enzymatic reactions. To further reduce the sampling problem we developed here a new PD version where we use an empirical valence bond reference potential that has a minimum rather than a maximum at the transition state region of the target potential (this is accomplished conveniently by shifting the EVB of the product state). Hence, we can map the TS region in a more efficient way. Here, we introduce and validate the inverted EVB PD approach. The validation involves the study of the S(N)2 step of the reaction catalyzed by haloakene dehalogenase (DhlA) and the GTP hydrolysis in the RasGAP system. In addition, we have also studied the corresponding reaction in water for each of the systems described here and the reaction involving trimethylsulfonium and dimethylamine in solution. The results are encouraging and the new strategy appears to provide a powerful way of evaluating QM(ai)/MM activation free energies.

  20. Extruded dielectric sample tubes of complex cross section for EPR signal enhancement of aqueous samples

    NASA Astrophysics Data System (ADS)

    Sidabras, Jason W.; Mett, Richard R.; Hyde, James S.

    2017-04-01

    This paper builds on the work of Mett and Hyde (2003) and Sidabras et al. (2005) where multiple flat aqueous sample cells placed perpendicular to electric fields in microwave cavities were used to reduce the RF losses and increase the EPR signal. In this work, we present three novel sample holders for loop-gap resonators (LGRs) and cylindrical cavity geometries. Two sample holders have been commissioned and built by polytetrafluoroethylene (PTFE) extrusion techniques: a 1 mm O.D. capillary with a septum down the middle, named DoubleDee, and a 3.5 mm O.D. star shaped sample holder, named AquaStar. Simulations and experimental results at X-band show that the EPR signal intensity increases by factors of 1.43 and 3.87 in the DoubleDee and AquaStar respectively, over the current TPX 0.9 mm O.D. sample tube in a two-loop-one-gap LGR. Finally, combining the insight gained from the constructed sample holders and finite-element solutions, a third multi-lumen sample holder for a cylindrical TE011 cavity is optimized, named AquaSun, where simulations show an EPR signal intensity increase by a factor of 8.2 over a standard 1 mm capillary.

  1. Extruded dielectric sample tubes of complex cross section for EPR signal enhancement of aqueous samples.

    PubMed

    Sidabras, Jason W; Mett, Richard R; Hyde, James S

    2017-04-01

    This paper builds on the work of Mett and Hyde (2003) and Sidabras et al. (2005) where multiple flat aqueous sample cells placed perpendicular to electric fields in microwave cavities were used to reduce the RF losses and increase the EPR signal. In this work, we present three novel sample holders for loop-gap resonators (LGRs) and cylindrical cavity geometries. Two sample holders have been commissioned and built by polytetrafluoroethylene (PTFE) extrusion techniques: a 1mm O.D. capillary with a septum down the middle, named DoubleDee, and a 3.5mm O.D. star shaped sample holder, named AquaStar. Simulations and experimental results at X-band show that the EPR signal intensity increases by factors of 1.43 and 3.87 in the DoubleDee and AquaStar respectively, over the current TPX 0.9mm O.D. sample tube in a two-loop-one-gap LGR. Finally, combining the insight gained from the constructed sample holders and finite-element solutions, a third multi-lumen sample holder for a cylindrical TE011 cavity is optimized, named AquaSun, where simulations show an EPR signal intensity increase by a factor of 8.2 over a standard 1mm capillary. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Active sampling technique to enhance chemical signature of buried explosives

    NASA Astrophysics Data System (ADS)

    Lovell, John S.; French, Patrick D.

    2004-09-01

    Deminers and dismounted countermine engineers commonly use metal detectors, ground penetrating radar and probes to locate mines. Many modern landmines have a very low metal content, which severely limits the effectiveness of metal detectors. Canines have also been used for landmine detection for decades. Experiments have shown that canines smell the explosives which are known to leak from most types of landmines. The fact that dogs can detect landmines indicates that vapor sensing is a viable approach to landmine detection. Several groups are currently developing systems to detect landmines by "sniffing" for the ultra-trace explosive vapors above the soil. The amount of material that is available to passive vapor sensing systems is limited to no more than the vapor in equilibrium with the explosive related chemicals (ERCs) distributed in the surface soils over and near the landmine. The low equilibrium vapor pressure of TNT in the soil/atmosphere boundary layer and the limited volume of the boundary layer air imply that passive chemical vapor sensing systems require sensitivities in the picogram range, or lower. ADA is working to overcome many of the limitations of passive sampling methods, by the use of an active sampling method that employs a high-powered (1,200+ joules) strobe lamp to create a highly amplified plume of vapor and/or ERC-bearing fine particulates. Initial investigations have demonstrated that this approach can amplify the detectability of TNT by two or three orders of magnitude. This new active sampling technique could be used with any suitable explosive sensor.

  3. Enhanced activities of organically bound tritium in biota samples.

    PubMed

    Svetlik, I; Fejgl, M; Malátová, I; Tomaskova, L

    2014-11-01

    A pilot study aimed on possible occurrence of elevated activity of non-exchangable organically bound tritium (NE-OBT) in biota was performed. The first results showed a significant surplus of NE-OBT activity in biota of the valley of Mohelno reservoir and Jihlava river. The liquid releases of HTO from the nuclear power plant Dukovany is the source of tritium in this area. This area can be a source of various types of natural samples for future studies of tritium pathways.

  4. The mutual effect of metal sample and turboflame in LIBS signal enhancement

    NASA Astrophysics Data System (ADS)

    Ghezelbash, M.; Mousavi, S. J.; Majd, A. E.; Darbani, S. M. R.; Saghafifar, H.; Maleki, A.

    2016-08-01

    The main aim of the present study is to evaluate the mutual effect of copper sample and turboflame in laser induced breakdown spectroscopy (LIBS) signal enhancement. The use of copper sample leads to a signal enhancement in CN ( B 2Σ+- X 2Σ+) 384.2-388.4 nm molecular transition, N742nm, N744nm, N746nm (a triplet generated by the fine splitting of the 2 s 22 p 2(3 P)3 s-2 s 22 p 2(3 P)3 p transition) and Hα, 656.3 nm (as a flame inductor) atomic lines analysis. Additionally, increase in copper sample temperature with flame can enhance the Cu atomic line intensities (as copper sample inductors). Moreover, in this paper, the comparison between turboflame and alcohol flame on LIBS analysis was studied. LIBS signal intensity variation in a turboflame and turboflame coupled with copper sample at different laser pulse energies indicated that the low laser pulse energy could be compensated by using a copper sample that is coupled with turboflame and improved LIBS signal enhancement. For flames analysis, the use of metal sample in LIBS method is demonstrated to be costeffective, compact, and capable of signal enhancement.

  5. Enhanced Sampling in Free Energy Calculations: Combining SGLD with the Bennett's Acceptance Ratio and Enveloping Distribution Sampling Methods.

    PubMed

    König, Gerhard; Miller, Benjamin T; Boresch, Stefan; Wu, Xiongwu; Brooks, Bernard R

    2012-10-09

    One of the key requirements for the accurate calculation of free energy differences is proper sampling of conformational space. Especially in biological applications, molecular dynamics simulations are often confronted with rugged energy surfaces and high energy barriers, leading to insufficient sampling and, in turn, poor convergence of the free energy results. In this work, we address this problem by employing enhanced sampling methods. We explore the possibility of using self-guided Langevin dynamics (SGLD) to speed up the exploration process in free energy simulations. To obtain improved free energy differences from such simulations, it is necessary to account for the effects of the bias due to the guiding forces. We demonstrate how this can be accomplished for the Bennett's acceptance ratio (BAR) and the enveloping distribution sampling (EDS) methods. While BAR is considered among the most efficient methods available for free energy calculations, the EDS method developed by Christ and van Gunsteren is a promising development that reduces the computational costs of free energy calculations by simulating a single reference state. To evaluate the accuracy of both approaches in connection with enhanced sampling, EDS was implemented in CHARMM. For testing, we employ benchmark systems with analytical reference results and the mutation of alanine to serine. We find that SGLD with reweighting can provide accurate results for BAR and EDS where conventional molecular dynamics simulations fail. In addition, we compare the performance of EDS with other free energy methods. We briefly discuss the implications of our results and provide practical guidelines for conducting free energy simulations with SGLD.

  6. Enhancing Bioaerosol Sampling by Andersen Impactors Using Mineral-Oil-Spread Agar Plate

    PubMed Central

    Xu, Zhenqiang; Wei, Kai; Wu, Yan; Shen, Fangxia; Chen, Qi; Li, Mingzhen; Yao, Maosheng

    2013-01-01

    As a bioaerosol sampling standard, Andersen type impactor is widely used since its invention in 1950s, including the investigation of the anthrax attacks in the United States in 2001. However, its related problems such as impaction and desiccation stress as well as particle bounce have not been solved. Here, we improved its biological collection efficiencies by plating a mineral oil layer (100 µL) onto the agar plate. An Andersen six-stage sampler and a BioStage impactor were tested with mineral-oil-spread agar plates in collecting indoor and outdoor bacterial and fungal aerosols. The effects of sampling times (5, 10 and 20 min) were also studied using the BioStage impactor when sampling environmental bioaerosols as well as aerosolized Bacillus subtilis (G+) and Escherichia coli (G-). In addition, particle bounce reduction by mineral-oil-plate was also investigated using an optical particle counter (OPC). Experimental results revealed that use of mineral-oil-spread agar plate can substantially enhance culturable bioaerosol recoveries by Andersen type impactors (p-values<0.05). The recovery enhancement was shown to depend on bioaerosol size, type, sampling time and environment. In general, more enhancements (extra 20%) were observed for last stage of the Andersen six-stage samplers compared to the BioStage impactor for 10 min sampling. When sampling aerosolized B. subtilis, E. coli and environmental aerosols, the enhancement was shown to increase with increasing sampling time, ranging from 50% increase at 5 min to ∼100% at 20 min. OPC results indicated that use of mineral oil can effectively reduce the particle bounce with an average of 66% for 10 min sampling. Our work suggests that enhancements for fungal aerosols were primarily attributed to the reduced impaction stress, while for bacterial aerosols reduced impaction, desiccation and particle bounce played major roles. The developed technology can readily enhance the agar-based techniques including those high

  7. Enhancing bioaerosol sampling by Andersen impactors using mineral-oil-spread agar plate.

    PubMed

    Xu, Zhenqiang; Wei, Kai; Wu, Yan; Shen, Fangxia; Chen, Qi; Li, Mingzhen; Yao, Maosheng

    2013-01-01

    As a bioaerosol sampling standard, Andersen type impactor is widely used since its invention in 1950s, including the investigation of the anthrax attacks in the United States in 2001. However, its related problems such as impaction and desiccation stress as well as particle bounce have not been solved. Here, we improved its biological collection efficiencies by plating a mineral oil layer (100 µL) onto the agar plate. An Andersen six-stage sampler and a BioStage impactor were tested with mineral-oil-spread agar plates in collecting indoor and outdoor bacterial and fungal aerosols. The effects of sampling times (5, 10 and 20 min) were also studied using the BioStage impactor when sampling environmental bioaerosols as well as aerosolized Bacillus subtilis (G+) and Escherichia coli (G-). In addition, particle bounce reduction by mineral-oil-plate was also investigated using an optical particle counter (OPC). Experimental results revealed that use of mineral-oil-spread agar plate can substantially enhance culturable bioaerosol recoveries by Andersen type impactors (p-values<0.05). The recovery enhancement was shown to depend on bioaerosol size, type, sampling time and environment. In general, more enhancements (extra 20%) were observed for last stage of the Andersen six-stage samplers compared to the BioStage impactor for 10 min sampling. When sampling aerosolized B. subtilis, E. coli and environmental aerosols, the enhancement was shown to increase with increasing sampling time, ranging from 50% increase at 5 min to ∼100% at 20 min. OPC results indicated that use of mineral oil can effectively reduce the particle bounce with an average of 66% for 10 min sampling. Our work suggests that enhancements for fungal aerosols were primarily attributed to the reduced impaction stress, while for bacterial aerosols reduced impaction, desiccation and particle bounce played major roles. The developed technology can readily enhance the agar-based techniques including those high

  8. Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review.

    PubMed

    Miao, Yinglong; McCammon, J Andrew

    Free energy calculations are central to understanding the structure, dynamics and function of biomolecules. Yet insufficient sampling of biomolecular configurations is often regarded as one of the main sources of error. Many enhanced sampling techniques have been developed to address this issue. Notably, enhanced sampling methods based on biasing collective variables (CVs), including the widely used umbrella sampling, adaptive biasing force and metadynamics, have been discussed in a recent excellent review (Abrams and Bussi, Entropy, 2014). Here, we aim to review enhanced sampling methods that do not require predefined system-dependent CVs for biomolecular simulations and as such do not suffer from the hidden energy barrier problem as encountered in the CV-biasing methods. These methods include, but are not limited to, replica exchange/parallel tempering, self-guided molecular/Langevin dynamics, essential energy space random walk and accelerated molecular dynamics. While it is overwhelming to describe all details of each method, we provide a summary of the methods along with the applications and offer our perspectives. We conclude with challenges and prospects of the unconstrained enhanced sampling methods for accurate biomolecular free energy calculations.

  9. Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review

    PubMed Central

    Miao, Yinglong; McCammon, J. Andrew

    2016-01-01

    Free energy calculations are central to understanding the structure, dynamics and function of biomolecules. Yet insufficient sampling of biomolecular configurations is often regarded as one of the main sources of error. Many enhanced sampling techniques have been developed to address this issue. Notably, enhanced sampling methods based on biasing collective variables (CVs), including the widely used umbrella sampling, adaptive biasing force and metadynamics, have been discussed in a recent excellent review (Abrams and Bussi, Entropy, 2014). Here, we aim to review enhanced sampling methods that do not require predefined system-dependent CVs for biomolecular simulations and as such do not suffer from the hidden energy barrier problem as encountered in the CV-biasing methods. These methods include, but are not limited to, replica exchange/parallel tempering, self-guided molecular/Langevin dynamics, essential energy space random walk and accelerated molecular dynamics. While it is overwhelming to describe all details of each method, we provide a summary of the methods along with the applications and offer our perspectives. We conclude with challenges and prospects of the unconstrained enhanced sampling methods for accurate biomolecular free energy calculations. PMID:27453631

  10. Enhanced sampling simulations to construct free-energy landscape of protein-partner substrate interaction.

    PubMed

    Ikebe, Jinzen; Umezawa, Koji; Higo, Junichi

    2016-03-01

    Molecular dynamics (MD) simulations using all-atom and explicit solvent models provide valuable information on the detailed behavior of protein-partner substrate binding at the atomic level. As the power of computational resources increase, MD simulations are being used more widely and easily. However, it is still difficult to investigate the thermodynamic properties of protein-partner substrate binding and protein folding with conventional MD simulations. Enhanced sampling methods have been developed to sample conformations that reflect equilibrium conditions in a more efficient manner than conventional MD simulations, thereby allowing the construction of accurate free-energy landscapes. In this review, we discuss these enhanced sampling methods using a series of case-by-case examples. In particular, we review enhanced sampling methods conforming to trivial trajectory parallelization, virtual-system coupled multicanonical MD, and adaptive lambda square dynamics. These methods have been recently developed based on the existing method of multicanonical MD simulation. Their applications are reviewed with an emphasis on describing their practical implementation. In our concluding remarks we explore extensions of the enhanced sampling methods that may allow for even more efficient sampling.

  11. Enhanced Conformational Sampling of N-glycans in Solution with Replica State Exchange Metadynamics.

    PubMed

    Galvelis, Raimondas; Re, Suyong; Sugita, Yuji

    2017-04-11

    Molecular dynamics (MD) simulation of a N-glycan in solution is challenging due to high- energy barriers of the glycosidic linkages, functional group rotational barriers, and numerous intra- and inter-molecular hydrogen bonds. In this study, we apply different enhanced conformational sampling approaches, namely, metadynamics (MTD), the replica-exchange MD (REMD), and the recently proposed replica state exchange MTD (RSE-MTD), to a N-glycan in solution and compare their conformational sampling efficiencies. MTD helps to cross the high- energy barrier along the ω angle by utilizing a bias potential, but it cannot enhance sampling of the other degrees of freedom. REMD ensures moderate-energy barrier crossings by exchanging temperatures between replicas, while it hardly crosses the barriers along ω. In contrast, RSE- MTD succeeds to cross the high-energy barrier along ω as well as to enhance sampling of the other degrees of freedom. We tested two RSE-MTD schemes: in one scheme, 64 replicas were simulated with the bias potential along ω at different temperatures, while simulations of 4 replicas were performed with the bias potentials for different CVs at 300 K. In both schemes, one unbiased replica at 300 K was included to compute conformational properties of the glycan. The conformational sampling of the former is better than the other enhanced sampling methods, while the latter shows reasonable performance without spending large computational resources. The latter scheme is likely to be useful when a N-glycan-attached protein is simulated.

  12. Metal-Enhanced Fluorescence (MEF): Physical Characterization of Siver-Island Films and Exploring Sample Geometries.

    PubMed

    Pribik, R; Dragan, A I; Zhang, Y; Gaydos, C; Geddes, C D

    2009-08-01

    In this study we have analyzed metal-enhanced fluorescence (MEF) effects from different density silver island films (SiFs) and the effects of sample geometry on the observed enhancement of fluorescence (EF). It is shown that silver islands grow exponentially with SiF deposition time (DT<7min), optical density of SiFs almost linearly depends on DT; electrical conductivity is zero. At DT>7 min, silver islands merge, exhibiting a sharp increase in electrical conductivity. It has been shown that the newly proposed SiF-Glass sample geometry exhibits higher EF values than the commonly used in MEF studies SiF-SiF sample geometry. The SiF-Glass geometry demonstrates high sensitivity for surface immunoassays, a growing application of metal-enhanced fluorescence.

  13. Communication: Multiple atomistic force fields in a single enhanced sampling simulation

    SciTech Connect

    Hoang Viet, Man; Derreumaux, Philippe; Nguyen, Phuong H.

    2015-07-14

    The main concerns of biomolecular dynamics simulations are the convergence of the conformational sampling and the dependence of the results on the force fields. While the first issue can be addressed by employing enhanced sampling techniques such as simulated tempering or replica exchange molecular dynamics, repeating these simulations with different force fields is very time consuming. Here, we propose an automatic method that includes different force fields into a single advanced sampling simulation. Conformational sampling using three all-atom force fields is enhanced by simulated tempering and by formulating the weight parameters of the simulated tempering method in terms of the energy fluctuations, the system is able to perform random walk in both temperature and force field spaces. The method is first demonstrated on a 1D system and then validated by the folding of the 10-residue chignolin peptide in explicit water.

  14. Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach.

    PubMed

    Burusco, Kepa K; Bruce, Neil J; Alibay, Irfan; Bryce, Richard A

    2015-10-26

    Free energy simulations are an established computational tool in modelling chemical change in the condensed phase. However, sampling of kinetically distinct substates remains a challenge to these approaches. As a route to addressing this, we link the methods of thermodynamic integration (TI) and swarm-enhanced sampling molecular dynamics (sesMD), where simulation replicas interact cooperatively to aid transitions over energy barriers. We illustrate the approach by using alchemical alkane transformations in solution, comparing them with the multiple independent trajectory TI (IT-TI) method. Free energy changes for transitions computed by using IT-TI grew increasingly inaccurate as the intramolecular barrier was heightened. By contrast, swarm-enhanced sampling TI (sesTI) calculations showed clear improvements in sampling efficiency, leading to more accurate computed free energy differences, even in the case of the highest barrier height. The sesTI approach, therefore, has potential in addressing chemical change in systems where conformations exist in slow exchange.

  15. Latin Hypercube Sampling (LHS) at variable resolutions for enhanced watershed scale Soil Sampling and Digital Soil Mapping.

    NASA Astrophysics Data System (ADS)

    Hamalainen, Sampsa; Geng, Xiaoyuan; He, Juanxia

    2017-04-01

    Latin Hypercube Sampling (LHS) at variable resolutions for enhanced watershed scale Soil Sampling and Digital Soil Mapping. Sampsa Hamalainen, Xiaoyuan Geng, and Juanxia, He. AAFC - Agriculture and Agr-Food Canada, Ottawa, Canada. The Latin Hypercube Sampling (LHS) approach to assist with Digital Soil Mapping has been developed for some time now, however the purpose of this work was to complement LHS with use of multiple spatial resolutions of covariate datasets and variability in the range of sampling points produced. This allowed for specific sets of LHS points to be produced to fulfil the needs of various partners from multiple projects working in the Ontario and Prince Edward Island provinces of Canada. Secondary soil and environmental attributes are critical inputs that are required in the development of sampling points by LHS. These include a required Digital Elevation Model (DEM) and subsequent covariate datasets produced as a result of a Digital Terrain Analysis performed on the DEM. These additional covariates often include but are not limited to Topographic Wetness Index (TWI), Length-Slope (LS) Factor, and Slope which are continuous data. The range of specific points created in LHS included 50 - 200 depending on the size of the watershed and more importantly the number of soil types found within. The spatial resolution of covariates included within the work ranged from 5 - 30 m. The iterations within the LHS sampling were run at an optimal level so the LHS model provided a good spatial representation of the environmental attributes within the watershed. Also, additional covariates were included in the Latin Hypercube Sampling approach which is categorical in nature such as external Surficial Geology data. Some initial results of the work include using a 1000 iteration variable within the LHS model. 1000 iterations was consistently a reasonable value used to produce sampling points that provided a good spatial representation of the environmental

  16. Multiscale enhanced sampling for protein systems: An extension via adiabatic separation

    NASA Astrophysics Data System (ADS)

    Moritsugu, Kei; Terada, Tohru; Kidera, Akinori

    2016-09-01

    Multiscale enhanced sampling (MSES) calculates the configurational ensemble of all-atom (MM) protein systems with the help of coupling to a coarse-grained (CG) model. Here, for further improvement of the sampling efficiency, the approximation of adiabatic separation was introduced to the original MSES, by adopting a high CG temperature limit. An application to the folding of chignolin in explicit solvent demonstrated that the MSES formula based on adiabatic separation correctly sampled the canonical ensemble with excellent efficiency and robustness against the parameter selection, and thus MSES successfully achieved the scalability for applications to large protein systems.

  17. Breast cancer detection based on serum sample surface enhanced Raman spectroscopy.

    PubMed

    Vargas-Obieta, Enrique; Martínez-Espinosa, Juan Carlos; Martínez-Zerega, Brenda Esmeralda; Jave-Suárez, Luis Felipe; Aguilar-Lemarroy, Adriana; González-Solís, José Luis

    2016-09-01

    Raman spectroscopy is a vibrational technique which provides information about the chemical structure. Nevertheless, since many chemicals are present in a sample at very low concentration, the Raman signal observed is extremely weak. In surface enhanced Raman scattering (SERS), Raman signals can be enhanced by many orders of magnitude when nanoparticles are used. To the best of our knowledge, this is the first report in the breast cancer detection based on serum SERS. The serum samples were obtained from 12 patients who were clinically diagnosed with advanced breast cancer and 15 controls. In the same proportion, the serum samples were mixed with colloidal gold nanoparticles of 40 nm using sonication. At least 10 spectra were collected of each serum sample using a Jobin-Yvon LabRAM Raman Spectrometer with a laser of 830 nm. Raw spectra were processed by carrying baseline correction, smoothing, and normalization and then analyzed using principle component analysis (PCA) and linear discriminant analysis (LDA). Raman spectra showed strongly enhanced bands in the 600-1800 cm (-1) range due to the nanoparticle colloidal clusters observed. These Raman bands allowed identifying biomolecules present at low concentration as amide I and III, β carotene, glutathione, tryptophan, tyrosine, and phenylalanine. Preliminary results demonstrated that SERS and PCA-LDA can be used to discriminate between control and cancer samples with high sensitivity and specificity. SERS allowed short exposures and required a minimal sample preparation. The preliminary results suggest that SERS and PCA-LDA could be an excellent support technique for the breast cancer detection using serum samples.

  18. Performance tuning non-uniform sampling for sensitivity enhancement of signal-limited biological NMR

    PubMed Central

    Palmer, Melissa R.; Wenrich, Broc R.; Stahlfeld, Phillip

    2014-01-01

    Non-uniform sampling (NUS) has been established as a route to obtaining true sensitivity enhancements when recording indirect dimensions of decaying signals in the same total experimental time as traditional uniform incrementation of the indirect evolution period. Theory and experiments have shown that NUS can yield up to two-fold improvements in the intrinsic signal-to-noise ratio (SNR) of each dimension, while even conservative protocols can yield 20–40 % improvements in the intrinsic SNR of NMR data. Applications of biological NMR that can benefit from these improvements are emerging, and in this work we develop some practical aspects of applying NUS nD-NMR to studies that approach the traditional detection limit of nD-NMR spectroscopy. Conditions for obtaining high NUS sensitivity enhancements are considered here in the context of enabling 1H,15N-HSQC experiments on natural abundance protein samples and 1H,13C-HMBC experiments on a challenging natural product. Through systematic studies we arrive at more precise guidelines to contrast sensitivity enhancements with reduced line shape constraints, and report an alternative sampling density based on a quarter-wave sinusoidal distribution that returns the highest fidelity we have seen to date in line shapes obtained by maximum entropy processing of non-uniformly sampled data. PMID:24682944

  19. Preserving, Enhancing, and Continuing the Scientific Legacy of the Apollo Sample Suite

    NASA Technical Reports Server (NTRS)

    Zeigler, Ryan; Evans, Cindy; Cai, Yue; Lehnert, Kerstin; Todd, Nancy; Blumenfeld, Erika

    2016-01-01

    From 1969 to 1972, Apollo astronauts collected 382 kg of rocks, soils, and core samples from six geologically diverse locations on the Moon. In the nearly 50 years since the samples were collected, over 3000 different studies have been conducted using the nearly 2200 different Apollo samples. Despite the maturity of the sample collection, many new studies of lunar samples are undertaken each year, with an average of more than 55 requests and more than 600 distinct subsamples allocated annually over the past five years. The Apollo samples are a finite resource, however. Although new studies are encouraged, it is important that new studies do not duplicate previous studies, and where possible, leverage previous results to inform and enhance the current studies. This helps to preserve the samples and scientific funding, both of which are precious resources. We have initiated several new efforts to rescue some of the early analyses from these samples, including unpublished analytical data. We are actively scanning NASA documentation in paper form that is related to the Apollo missions and sample processing, and we are collaborating with IEDA to establish a geochemical data base called MoonDB. To populate this database, we are actively working with about a dozen prominent lunar PIs to organize and transcribe years of both published and unpublished data, making it available to all researchers. This effort will also take advantage of new online analytical tools like PetDB. There have already been tangible results from the MoonDB data rescue effort. A pilot project involving the rescue of geochemical data of John Delano on Apollo pyroclastic glasses has already been referenced in multiple Apollo sample requests, and in fact, the compiled data was used as part of one of the new studies. Similarly, scanned sample handling reports have been utilized to find previously analyzed samples that were appropriate to fulfill new sample requests. We have also begun to image the Apollo

  20. Preserving, Enhancing, and Continuing the Scientific Legacy of the Apollo Sample Suite

    NASA Astrophysics Data System (ADS)

    Zeigler, R. A.; Evans, C. A.; Lehnert, K.; Cai, Y.; Todd, N. S.

    2016-12-01

    From 1969 to 1972, Apollo astronauts collected 382 kg of rocks, soils, and core samples from six geologically diverse locations on the Moon. In the nearly 50 years since the samples were collected, over 3000 different studies have been conducted using the nearly 2200 different Apollo samples. Despite the maturity of the sample collection, many new studies of lunar samples are undertaken each year, with an average of >55 requests and >600 distinct subsamples allocated annually over the past five years. The Apollo samples are a finite resource, however. Although new studies are encouraged, it is important that new studies do not duplicate previous studies, and where possible, leverage previous results to inform and enhance the current studies. This helps to preserve the samples and scientific funding, both of which are precious resources. We have initiated several new efforts to rescue some of the early analyses from these samples, including unpublished analytical data. We are actively scanning NASA documentation in paper form that is related to the Apollo missions and sample processing, and we are collaborating with IEDA to establish a geochemical data base called MoonDB. To populate this database, we are actively working with about a dozen prominent lunar PIs to organize and transcribe years of both published and unpublished data, making it available to all researchers. This effort will also take advantage of new online analytical tools like PetDB. There have already been tangible results from the MoonDB data rescue effort. A pilot project involving the rescue of geochemical data of John Delano on Apollo pyroclastic glasses has already been referenced in multiple Apollo sample requests, and in fact, the compiled data was used as part of one of the new studies. Similarly, scanned sample handling reports have been utilized to find previously analyzed samples that were appropriate to fulfill new sample requests. We have also begun to image the Apollo samples using (1

  1. Enhancing resolution of free-flow zone electrophoresis via a simple sheath-flow sample injection.

    PubMed

    Yang, Ying; Kong, Fan-Zhi; Liu, Ji; Li, Jun-Min; Liu, Xiao-Ping; Li, Guo-Qing; Wang, Ju-Fang; Xiao, Hua; Fan, Liu-Yin; Cao, Cheng-Xi; Li, Shan

    2016-07-01

    In this work, a simple and novel sheath-flow sample injection method (SFSIM) is introduced to reduce the band broadening of free-flow zone electrophoresis separation in newly developed self-balance free-flow electrophoresis instrument. A needle injector was placed in the center of the separation inlet, into which the BGE and sample solution were pumped simultaneously. BGE formed sheath flow outside the sample stream, resulting in less band broadening related to hydrodynamics and electrodynamics. Hemoglobin and C-phycocyanin were successfully separated by the proposed method in contrast to the poor separation of free-flow electrophoresis with the traditional injection method without sheath flow. About 3.75 times resolution enhancement could be achieved by sheath-flow sample injection method.

  2. Microbial activity in subsurface samples before and during nitrate-enhanced bioremediation

    SciTech Connect

    Thomas, J.M.; Gordy, V.R.; Bruce, C.L.; Ward, C.H.; Hutchins, S.R.; Sinclair, J.L.

    1995-12-31

    A study was conducted to determine the microbial activity at a site contaminated with JP-4 jet fuel before and during nitrate-enhanced bioremediation. Samples at three depths from six different locations were collected aseptically under anaerobic conditions before and during treatment. Cores were located in or close to the source of contamination, downgradient of the source, or outside the zone of contamination. Parameters for microbial characterization included (1) viable counts of aerobic heterotrophic, JP-4 degrading, and oligotrophic bacteria; (2) the most probable number (MPN) of aerobic and anaerobic protozoa; (3) the MPN of total denitrifiers; and (4) the MPN of denitrifiers in hydrocarbon-amended microcosms. The results indicate that the total number of denitrifiers increased by an order of magnitude during nitrate-enhanced bioremediation in most samples. The number of total heterotrophs and JP-4-degrading microorganisms growing aerobically also increased. In addition, the first anaerobic protozoa associated with hydrocarbon-contaminated subsurface materials were detected.

  3. Fast sampling in the slow manifold: The momentum-enhanced hybrid Monte Carlo method

    NASA Astrophysics Data System (ADS)

    Andricioaei, Ioan

    2005-03-01

    We will present a novel dynamic algorithm, the MEHMC method, which enhances sampling and at the same time yielding correct Boltzmann weighted statistical distributions. The gist of the MEHMC method is to use momentum averaging to identify the slow manifold and bias along this manifold the Maxwell distribution of momenta usually employed in Hybrid Monte Carlo. Several tests and applications are to exemplify the method.

  4. Bremsstrahlung enhancement in electron probe microanalysis for homogeneous samples using Monte Carlo simulation.

    PubMed

    Petaccia, M; Segui, S; Castellano, G

    2016-11-01

    Fluorescence enhancement in samples irradiated in a scanning electron microscope or an electron microprobe should be appropriately assessed in order not to distort quantitative analyses. Several models have been proposed to take into account this effect and current quantification routines are based on them, many of which have been developed under the assumption that bremsstrahlung fluorescence correction is negligible when compared to characteristic enhancement; however, no concluding arguments have been provided in order to support this assumption. As detectors are unable to discriminate primary from secondary characteristic X-rays, Monte Carlo simulation of radiation transport becomes a determinant tool in the study of this fluorescence enhancement. In this work, bremsstrahlung fluorescence enhancement in electron probe microanalysis has been studied by using the interaction forcing routine offered by penelope 2008 as a variance reduction alternative. The developed software allowed us to show that bremsstrahlung and characteristic fluorescence corrections are in fact comparable in the studied cases. As an extra result, the interaction forcing approach appears as a most efficient method, not only in the computation of the continuum enhancement but also for the assessment of the characteristic fluorescence correction.

  5. Utilizing transmembrane convection to enhance solute sampling and delivery by microdialysis: theory and in vitro validation

    PubMed Central

    Bungay, Peter M.; Wang, Tianli; Yang, Hua; Elmquist, William F.

    2009-01-01

    Microdialysis is a well-developed membrane-based tool relying on diffusion to sample diffusible constituents of complex media, such as biological tissue. The objective of this research is to expand the utility of microdialysis by combining transmembrane convection with diffusion to enhance solute exchange between microdialysis probes and the surrounding medium. We have developed a mathematical model to describe probe performance and performed validation experiments utilizing tracer solutes and commercially available probes with 100-kDa molecular weight cutoff membranes. Diffusive and fluid permeabilities of the probe membranes are evaluated for probes immersed in well-stirred bathing media in vitro. Transmembrane convection alters the solute extraction fraction, i.e., the fractional loss of a solute from the probe perfusate during delivery and the fractional gain by the perfusate during sampling. The extraction fraction change depends upon the magnitude and direction (inward or outward) of fluid movement across the membrane. However, for solutes with zero reflection coefficients, equality is maintained between these delivery and sampling extraction fractions. This equality is a prerequisite for probe calibration approaches that rely on analyte delivery from the perfusate. Thus, we have provided the theoretical and experimental basis for exploiting convection in a quantitative manner to enhance solute delivery and sampling in microdialysis applications. PMID:20161534

  6. Extended Phase-Space Methods for Enhanced Sampling in Molecular Simulations: A Review

    PubMed Central

    Fujisaki, Hiroshi; Moritsugu, Kei; Matsunaga, Yasuhiro; Morishita, Tetsuya; Maragliano, Luca

    2015-01-01

    Molecular Dynamics simulations are a powerful approach to study biomolecular conformational changes or protein–ligand, protein–protein, and protein–DNA/RNA interactions. Straightforward applications, however, are often hampered by incomplete sampling, since in a typical simulated trajectory the system will spend most of its time trapped by high energy barriers in restricted regions of the configuration space. Over the years, several techniques have been designed to overcome this problem and enhance space sampling. Here, we review a class of methods that rely on the idea of extending the set of dynamical variables of the system by adding extra ones associated to functions describing the process under study. In particular, we illustrate the Temperature Accelerated Molecular Dynamics (TAMD), Logarithmic Mean Force Dynamics (LogMFD), and Multiscale Enhanced Sampling (MSES) algorithms. We also discuss combinations with techniques for searching reaction paths. We show the advantages presented by this approach and how it allows to quickly sample important regions of the free-energy landscape via automatic exploration. PMID:26389113

  7. Detection of metronidazole and ronidazole from environmental samples by surface enhanced Raman spectroscopy.

    PubMed

    Han, Caiqin; Chen, Jing; Wu, Xiaomeng; Huang, Yao-Wen; Zhao, Yiping

    2014-10-01

    In this study, the surface enhanced Raman spectra (SERS) of two prohibited veterinary drugs, metronidazole (MNZ) and ronidazole (RNZ), have been acquired, and compared to the theoretically calculated spectra using density function theory (DFT). The experimental Raman and SERS spectra of MNZ and RNZ exhibit high resemblance with the DFT calculations. SERS detection of MNZ and RNZ from standard solutions as well as real environmental samples (tap, lake, swamp waters and soil) was performed on highly sensitive and reproducible silver nanorod array substrates. The limits of detection for MNZ and RNZ are 10 and 1 µg/mL in methanol and ultra-pure water, respectively, and 10-50 µg/mL in the environmental samples. The SERS-based method demonstrates its potential as a rapid, simple, and inexpensive means for the onsite screening of banned antibiotics from the aquatic and sediment environments, with minimal requirement for sample pretreatment.

  8. Enhanced contrast separation in scanning electron microscopes via a suspended-thin sample approach.

    PubMed

    Ji, Yuan; Wang, Li; Guo, Zhenxi; Wei, Bin; Zhao, Jie; Wang, Xiaodong; Zhang, Yinqi; Sui, Manling; Han, Xiaodong

    2014-11-01

    A suspended-thin-sample (STS) approach for signal selection and contrast separation is developed in scanning electron microscopes with commonly used primary beam energies and traditional detectors. Topography contrast, electron channeling contrast and composition contrast are separated and largely enhanced from suspended thin samples of several hundred nanometers in thickness, which is less than the escape depth of backscattered electrons. This imaging technique enables to detect relatively pure secondary electron and elastic backscattered electron singles, whereas suppress multiple inelastic scattering effects. The provided contrast features are different from those of bulk samples, which are largely mixed with inelastic scattering effects. The STS imaging concept and method could be expected to have more applications in distinguishing materials of nanostructures, multilayers, compounds and composites, as well as in SEM-based electron backscatter diffraction, cathodoluminesence, and x-ray microanalysis.

  9. Identification of Metal Oxide Nanoparticles in Histological Samples by Enhanced Darkfield Microscopy and Hyperspectral Mapping.

    PubMed

    Roth, Gary A; Sosa Peña, Maria del Pilar; Neu-Baker, Nicole M; Tahiliani, Sahil; Brenner, Sara A

    2015-12-08

    Nanomaterials are increasingly prevalent throughout industry, manufacturing, and biomedical research. The need for tools and techniques that aid in the identification, localization, and characterization of nanoscale materials in biological samples is on the rise. Currently available methods, such as electron microscopy, tend to be resource-intensive, making their use prohibitive for much of the research community. Enhanced darkfield microscopy complemented with a hyperspectral imaging system may provide a solution to this bottleneck by enabling rapid and less expensive characterization of nanoparticles in histological samples. This method allows for high-contrast nanoscale imaging as well as nanomaterial identification. For this technique, histological tissue samples are prepared as they would be for light-based microscopy. First, positive control samples are analyzed to generate the reference spectra that will enable the detection of a material of interest in the sample. Negative controls without the material of interest are also analyzed in order to improve specificity (reduce false positives). Samples can then be imaged and analyzed using methods and software for hyperspectral microscopy or matched against these reference spectra in order to provide maps of the location of materials of interest in a sample. The technique is particularly well-suited for materials with highly unique reflectance spectra, such as noble metals, but is also applicable to other materials, such as semi-metallic oxides. This technique provides information that is difficult to acquire from histological samples without the use of electron microscopy techniques, which may provide higher sensitivity and resolution, but are vastly more resource-intensive and time-consuming than light microscopy.

  10. Identification of Metal Oxide Nanoparticles in Histological Samples by Enhanced Darkfield Microscopy and Hyperspectral Mapping

    PubMed Central

    Roth, Gary A.; Sosa Peña, Maria del Pilar; Neu-Baker, Nicole M.; Tahiliani, Sahil; Brenner, Sara A.

    2015-01-01

    Nanomaterials are increasingly prevalent throughout industry, manufacturing, and biomedical research. The need for tools and techniques that aid in the identification, localization, and characterization of nanoscale materials in biological samples is on the rise. Currently available methods, such as electron microscopy, tend to be resource-intensive, making their use prohibitive for much of the research community. Enhanced darkfield microscopy complemented with a hyperspectral imaging system may provide a solution to this bottleneck by enabling rapid and less expensive characterization of nanoparticles in histological samples. This method allows for high-contrast nanoscale imaging as well as nanomaterial identification. For this technique, histological tissue samples are prepared as they would be for light-based microscopy. First, positive control samples are analyzed to generate the reference spectra that will enable the detection of a material of interest in the sample. Negative controls without the material of interest are also analyzed in order to improve specificity (reduce false positives). Samples can then be imaged and analyzed using methods and software for hyperspectral microscopy or matched against these reference spectra in order to provide maps of the location of materials of interest in a sample. The technique is particularly well-suited for materials with highly unique reflectance spectra, such as noble metals, but is also applicable to other materials, such as semi-metallic oxides. This technique provides information that is difficult to acquire from histological samples without the use of electron microscopy techniques, which may provide higher sensitivity and resolution, but are vastly more resource-intensive and time-consuming than light microscopy. PMID:26709947

  11. Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms☆

    PubMed Central

    Mori, Takaharu; Miyashita, Naoyuki; Im, Wonpil; Feig, Michael; Sugita, Yuji

    2016-01-01

    This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins. Guest Editors: J.C. Gumbart and Sergei Noskov. PMID:26766517

  12. Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms.

    PubMed

    Mori, Takaharu; Miyashita, Naoyuki; Im, Wonpil; Feig, Michael; Sugita, Yuji

    2016-07-01

    This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  13. Adaptive k-space sampling design for edge-enhanced DCE-MRI using compressed sensing.

    PubMed

    Raja, Rajikha; Sinha, Neelam

    2014-09-01

    The critical challenge in dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is the trade-off between spatial and temporal resolution due to the limited availability of acquisition time. To address this, it is imperative to under-sample k-space and to develop specific reconstruction techniques. Our proposed method reconstructs high-quality images from under-sampled dynamic k-space data by proposing two main improvements; i) design of an adaptive k-space sampling lattice and ii) edge-enhanced reconstruction technique. A high-resolution data set obtained before the start of the dynamic phase is utilized. The sampling pattern is designed to adapt to the nature of k-space energy distribution obtained from the static high-resolution data. For image reconstruction, the well-known compressed sensing-based total variation (TV) minimization constrained reconstruction scheme is utilized by incorporating the gradient information obtained from the static high-resolution data. The proposed method is tested on seven real dynamic time series consisting of 2 breast data sets and 5 abdomen data sets spanning 1196 images in all. For data availability of only 10%, performance improvement is seen across various quality metrics. Average improvements in Universal Image Quality Index and Structural Similarity Index Metric of up to 28% and 24% on breast data and about 17% and 9% on abdomen data, respectively, are obtained for the proposed method as against the baseline TV reconstruction with variable density random sampling pattern. Copyright © 2014 Elsevier Inc. All rights reserved.

  14. Enhanced Cleaning of Genesis Solar Wind Sample 61348 for Film Residue Removal

    NASA Technical Reports Server (NTRS)

    Allums, K. K.; Gonzalez, C. P.; Kuhlman, K. R.; Allton, J. H.

    2015-01-01

    The Genesis mission returned to Earth on September 8, 2004, experiencing a nonnominal reentry. During the recovery of the collector materials from the capsule, many of the collector fragments were placed on the adhesive protion of post-it notes to prevent the fragments from moving during transport back to Johnson Space Center. This unknowingly provided an additional contaminate that would prove difficult to remove with the limited chemistries allowed in the Genesis Curation Laboratory. Generally when collector material samples are prepared for allocation to PIs, the samples are cleaned front side only with Ultra-Pure Water (UPW) via megasonic dispersion to the collector surface to remove crash debris and contamination. While this cleaning method works well on samples that were not placed on post-its during recovery, it has caused movement of the residue on the back of the sample to be deposited on the front in at least two examples. Therefore, samples placed on the adhesive portion on post-it note, require enhanced cleaning methods since post-it residue has proved resistant to UPW cleaning.

  15. Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering

    PubMed Central

    2015-01-01

    The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated in a Hamiltonian replica-exchange scheme. The ladder of replicas is built with different strengths of the bias potential exploiting the tunability of well-tempered metadynamics. Using this method, free-energy barriers of individual collective variables are significantly reduced compared with simple force-field scaling. The introduced methodology is flexible and allows adaptive bias potentials to be self-consistently constructed for a large number of simple collective variables, such as distances and dihedral angles. The method is tested on alanine dipeptide and applied to the difficult problem of conformational sampling in a tetranucleotide. PMID:25838811

  16. Highly sensitive detection of zearalenone in feed samples using competitive surface-enhanced Raman scattering immunoassay.

    PubMed

    Liu, Jianzhi; Hu, Yongjun; Zhu, Guichi; Zhou, Xiaoming; Jia, Li; Zhang, Tao

    2014-08-20

    Accurate and quantitative analysis of mycotoxin (such as zearalenone) is particularly imperative in the field of food safety and animal husbandry. Here, we develop a sensitive and specific method for zearalenone detection using competitive surface-enhanced Raman scattering (SERS) immunoassay. In this assay, a functional gold nanoparticle was labeled with the Raman reporter and the zearalenone antibody, and a modified substrate was assembled with the zearalenone-bovine serum albumin. With the addition of free zearalenone, the competitive immune reaction between free zearalenone and zearalenone-bovine serum albumin was initiated for binding with zearalenone antibody labeled on gold nanoparticle, resulting in the change of SERS signal intensity. The proposed method exhibits high sensitivity with a detection limit of 1 pg/mL and a wide dynamic range from 1 to 1000 pg/mL. Furthermore, this method can be further applied to analyze the multiple natural feed samples contaminated with zearalenone, holding great potential for real sample detection.

  17. Systematic application of multiplex PCR enhances the detection of bacteria, parasites, and viruses in stool samples.

    PubMed

    McAuliffe, Gary N; Anderson, Trevor P; Stevens, Mary; Adams, Jacqui; Coleman, Robyn; Mahagamasekera, Patalee; Young, Sheryl; Henderson, Tom; Hofmann, Maria; Jennings, Lance C; Murdoch, David R

    2013-08-01

    To determine whether systematic testing of faecal samples with a broad range multiplex PCR increases the diagnostic yield in patients with diarrhoea compared with conventional methods and a clinician initiated testing strategy. 1758 faecal samples from 1516 patients with diarrhoea submitted to two diagnostic laboratories were tested for viral, bacterial, and parasitic pathogens by Fast-Track Diagnostics multiplex real-time PCR kits and conventional diagnostic tests. Multiplex PCR detected pathogens in 530 samples (30%): adenovirus (51, 3%), astrovirus (95, 5%), norovirus (172, 10%), rotavirus (3, 0.2%), Campylobacter jejuni/coli (85, 5%), Salmonella spp. (22, 1%), Clostridium difficile (72, 4%), entero-haemorrhagic Escherichia coli (21, 1%), Cryptosporidium spp. (3, 0.2%), Entamoeba histolytica (1, 0.1%), and Giardia lamblia (59, 3%). In contrast, conventional testing detected a pathogen in 324 (18%) samples. Using a systematic approach to the diagnosis of gastroenteritis improved diagnostic yield. This enhanced detection with PCR was achieved by a combination of improved detection of individual pathogens and detection of pathogens not requested or unable to be tested by conventional tests. This approach also allowed earlier identification for most pathogens and created a workflow which is likely to adapt well for many diagnostic laboratories. Copyright © 2013 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

  18. Sampling and Selection Factors that Enhance the Diversity of Microbial Collections: Application to Biopesticide Development

    PubMed Central

    Park, Jun-Kyung; Lee, Seung-Hwan; Lee, Jang-Hoon; Han, Songhee; Kang, Hunseung; Kim, Jin-Cheol; Kim, Young Cheol; Gardener, Brian McSpadden

    2013-01-01

    Diverse bacteria are known to colonize plants. However, only a small fraction of that diversity has been evaluated for their biopesticide potential. To date, the criteria for sampling and selection in such bioprospecting endeavors have not been systematically evaluated in terms of the relative amount of diversity they provide for analysis. The present study aimed to enhance the success of bio-prospecting efforts by increasing the diversity while removing the genotypic redundancy often present in large collections of bacteria. We developed a multivariate sampling and marker-based selection strategy that significantly increase the diversity of bacteria recovered from plants. In doing so, we quantified the effects of varying sampling intensity, media composition, incubation conditions, plant species, and soil source on the diversity of recovered isolates. Subsequent sequencing and high-throughput phenotypic analyses of a small fraction of the collected isolates revealed that this approach led to the recovery of over a dozen rare and, to date, poorly characterized genera of plant-associated bacteria with significant biopesticide activities. Overall, the sampling and selection approach described led to an approximately 5-fold improvement in efficiency and the recovery of several novel strains of bacteria with significant biopesticide potential. PMID:25288941

  19. Enhanced procedural blank control for organic geochemical studies of critical sample material.

    PubMed

    Leider, A; Schumacher, T C; Hallmann, C

    2016-09-01

    . Artificial black shale pellets can provide enhanced contamination control in biomarker studies - particularly for exceptionally vulnerable samples such as Precambrian rocks, meteorites or extraterrestrial sample-return material. © 2016 John Wiley & Sons Ltd.

  20. Determination of amphetamines in biological samples using electro enhanced solid-phase microextraction-gas chromatography.

    PubMed

    Zeng, Jingbin; Chen, Jingjing; Li, Min; Subhan, Fazle; Chong, Fayun; Wen, Chongying; Yu, Jianfeng; Cui, Bingwen; Chen, Xi

    2015-09-01

    In this work, an ordered mesoporous carbon (OMC)/Nafion coated fiber for solid-phase microextraction (SPME) was prepared and used as the working electrode for electro-enhanced SPME (EE-SPME) of amphetamines. The EE-SPME strategy is primarily based on the electro-migration and complementary charge interaction between fiber coating and ionic compounds. Compared with traditional SPME, EE-SPME exhibited excellent extraction efficiency for amphetamine (AP) and methamphetamine (MA) with an enhancement factor of 7.8 and 12.1, respectively. The present strategy exhibited good linearity for the determination of AP and MA in urine samples in the range of 10-1000ngmL(-1) and 20-1000ngmL(-1), respectively. The detection limits were found to be 1.2ngmL(-1) for AP and 4.8ngmL(-1) for MA. The relative standard deviations were calculated to be 6.2% and 8.5% for AP and MA, respectively. Moreover, the practical application of the proposed method was demonstrated by analyzing the amphetamines in urine and serum samples with satisfactory results.

  1. New Approach Based on Compressive Sampling for Sample Rate Enhancement in DASs for Low-Cost Sensing Nodes

    PubMed Central

    Bonavolontà, Francesco; D'Apuzzo, Massimo; Liccardo, Annalisa; Vadursi, Michele

    2014-01-01

    The paper deals with the problem of improving the maximum sample rate of analog-to-digital converters (ADCs) included in low cost wireless sensing nodes. To this aim, the authors propose an efficient acquisition strategy based on the combined use of high-resolution time-basis and compressive sampling. In particular, the high-resolution time-basis is adopted to provide a proper sequence of random sampling instants, and a suitable software procedure, based on compressive sampling approach, is exploited to reconstruct the signal of interest from the acquired samples. Thanks to the proposed strategy, the effective sample rate of the reconstructed signal can be as high as the frequency of the considered time-basis, thus significantly improving the inherent ADC sample rate. Several tests are carried out in simulated and real conditions to assess the performance of the proposed acquisition strategy in terms of reconstruction error. In particular, the results obtained in experimental tests with ADC included in actual 8- and 32-bits microcontrollers highlight the possibility of achieving effective sample rate up to 50 times higher than that of the original ADC sample rate. PMID:25313493

  2. 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.

  3. Energy Landscape of All-Atom Protein-Protein Interactions Revealed by Multiscale Enhanced Sampling

    PubMed Central

    Moritsugu, Kei; Terada, Tohru; Kidera, Akinori

    2014-01-01

    Protein-protein interactions are regulated by a subtle balance of complicated atomic interactions and solvation at the interface. To understand such an elusive phenomenon, it is necessary to thoroughly survey the large configurational space from the stable complex structure to the dissociated states using the all-atom model in explicit solvent and to delineate the energy landscape of protein-protein interactions. In this study, we carried out a multiscale enhanced sampling (MSES) simulation of the formation of a barnase-barstar complex, which is a protein complex characterized by an extraordinary tight and fast binding, to determine the energy landscape of atomistic protein-protein interactions. The MSES adopts a multicopy and multiscale scheme to enable for the enhanced sampling of the all-atom model of large proteins including explicit solvent. During the 100-ns MSES simulation of the barnase-barstar system, we observed the association-dissociation processes of the atomistic protein complex in solution several times, which contained not only the native complex structure but also fully non-native configurations. The sampled distributions suggest that a large variety of non-native states went downhill to the stable complex structure, like a fast folding on a funnel-like potential. This funnel landscape is attributed to dominant configurations in the early stage of the association process characterized by near-native orientations, which will accelerate the native inter-molecular interactions. These configurations are guided mostly by the shape complementarity between barnase and barstar, and lead to the fast formation of the final complex structure along the downhill energy landscape. PMID:25340714

  4. Adaptive Splitting Integrators for Enhancing Sampling Efficiency of Modified Hamiltonian Monte Carlo Methods in Molecular Simulation.

    PubMed

    Akhmatskaya, Elena; Fernández-Pendás, Mario; Radivojević, Tijana; Sanz-Serna, J M

    2017-08-02

    The modified Hamiltonian Monte Carlo (MHMC) methods, i.e., importance sampling methods that use modified Hamiltonians within a Hybrid Monte Carlo (HMC) framework, often outperform in sampling efficiency standard techniques such as molecular dynamics (MD) and HMC. The performance of MHMC may be enhanced further through the rational choice of the simulation parameters and by replacing the standard Verlet integrator with more sophisticated splitting algorithms. Unfortunately, it is not easy to identify the appropriate values of the parameters that appear in those algorithms. We propose a technique, that we call MAIA (Modified Adaptive Integration Approach), which, for a given simulation system and a given time step, automatically selects the optimal integrator within a useful family of two-stage splitting formulas. Extended MAIA (or e-MAIA) is an enhanced version of MAIA, which additionally supplies a value of the method-specific parameter that, for the problem under consideration, keeps the momentum acceptance rate at a user-desired level. The MAIA and e-MAIA algorithms have been implemented, with no computational overhead during simulations, in MultiHMC-GROMACS, a modified version of the popular software package GROMACS. Tests performed on well-known molecular models demonstrate the superiority of the suggested approaches over a range of integrators (both standard and recently developed), as well as their capacity to improve the sampling efficiency of GSHMC, a noticeable method for molecular simulation in the MHMC family. GSHMC combined with e-MAIA shows a remarkably good performance when compared to MD and HMC coupled with the appropriate adaptive integrators.

  5. Energy landscape of all-atom protein-protein interactions revealed by multiscale enhanced sampling.

    PubMed

    Moritsugu, Kei; Terada, Tohru; Kidera, Akinori

    2014-10-01

    Protein-protein interactions are regulated by a subtle balance of complicated atomic interactions and solvation at the interface. To understand such an elusive phenomenon, it is necessary to thoroughly survey the large configurational space from the stable complex structure to the dissociated states using the all-atom model in explicit solvent and to delineate the energy landscape of protein-protein interactions. In this study, we carried out a multiscale enhanced sampling (MSES) simulation of the formation of a barnase-barstar complex, which is a protein complex characterized by an extraordinary tight and fast binding, to determine the energy landscape of atomistic protein-protein interactions. The MSES adopts a multicopy and multiscale scheme to enable for the enhanced sampling of the all-atom model of large proteins including explicit solvent. During the 100-ns MSES simulation of the barnase-barstar system, we observed the association-dissociation processes of the atomistic protein complex in solution several times, which contained not only the native complex structure but also fully non-native configurations. The sampled distributions suggest that a large variety of non-native states went downhill to the stable complex structure, like a fast folding on a funnel-like potential. This funnel landscape is attributed to dominant configurations in the early stage of the association process characterized by near-native orientations, which will accelerate the native inter-molecular interactions. These configurations are guided mostly by the shape complementarity between barnase and barstar, and lead to the fast formation of the final complex structure along the downhill energy landscape.

  6. A new class of enhanced kinetic sampling methods for building Markov state models

    NASA Astrophysics Data System (ADS)

    Bhoutekar, Arti; Ghosh, Susmita; Bhattacharya, Swati; Chatterjee, Abhijit

    2017-10-01

    Markov state models (MSMs) and other related kinetic network models are frequently used to study the long-timescale dynamical behavior of biomolecular and materials systems. MSMs are often constructed bottom-up using brute-force molecular dynamics (MD) simulations when the model contains a large number of states and kinetic pathways that are not known a priori. However, the resulting network generally encompasses only parts of the configurational space, and regardless of any additional MD performed, several states and pathways will still remain missing. This implies that the duration for which the MSM can faithfully capture the true dynamics, which we term as the validity time for the MSM, is always finite and unfortunately much shorter than the MD time invested to construct the model. A general framework that relates the kinetic uncertainty in the model to the validity time, missing states and pathways, network topology, and statistical sampling is presented. Performing additional calculations for frequently-sampled states/pathways may not alter the MSM validity time. A new class of enhanced kinetic sampling techniques is introduced that aims at targeting rare states/pathways that contribute most to the uncertainty so that the validity time is boosted in an effective manner. Examples including straightforward 1D energy landscapes, lattice models, and biomolecular systems are provided to illustrate the application of the method. Developments presented here will be of interest to the kinetic Monte Carlo community as well.

  7. Reconstruction of enhancer-target networks in 935 samples of human primary cells, tissues and cell lines.

    PubMed

    Cao, Qin; Anyansi, Christine; Hu, Xihao; Xu, Liangliang; Xiong, Lei; Tang, Wenshu; Mok, Myth T S; Cheng, Chao; Fan, Xiaodan; Gerstein, Mark; Cheng, Alfred S L; Yip, Kevin Y

    2017-10-01

    We propose a new method for determining the target genes of transcriptional enhancers in specific cells and tissues. It combines global trends across many samples and sample-specific information, and considers the joint effect of multiple enhancers. Our method outperforms existing methods when predicting the target genes of enhancers in unseen samples, as evaluated by independent experimental data. Requiring few types of input data, we are able to apply our method to reconstruct the enhancer-target networks in 935 samples of human primary cells, tissues and cell lines, which constitute by far the largest set of enhancer-target networks. The similarity of these networks from different samples closely follows their cell and tissue lineages. We discover three major co-regulation modes of enhancers and find defense-related genes often simultaneously regulated by multiple enhancers bound by different transcription factors. We also identify differentially methylated enhancers in hepatocellular carcinoma (HCC) and experimentally confirm their altered regulation of HCC-related genes.

  8. Coarse graining from variationally enhanced sampling applied to the Ginzburg–Landau model

    PubMed Central

    Invernizzi, Michele; Valsson, Omar; Parrinello, Michele

    2017-01-01

    A powerful way to deal with a complex system is to build a coarse-grained model capable of catching its main physical features, while being computationally affordable. Inevitably, such coarse-grained models introduce a set of phenomenological parameters, which are often not easily deducible from the underlying atomistic system. We present a unique approach to the calculation of these parameters, based on the recently introduced variationally enhanced sampling method. It allows us to obtain the parameters from atomistic simulations, providing thus a direct connection between the microscopic and the mesoscopic scale. The coarse-grained model we consider is that of Ginzburg–Landau, valid around a second-order critical point. In particular, we use it to describe a Lennard–Jones fluid in the region close to the liquid–vapor critical point. The procedure is general and can be adapted to other coarse-grained models. PMID:28292890

  9. Coarse graining from variationally enhanced sampling applied to the Ginzburg-Landau model.

    PubMed

    Invernizzi, Michele; Valsson, Omar; Parrinello, Michele

    2017-03-28

    A powerful way to deal with a complex system is to build a coarse-grained model capable of catching its main physical features, while being computationally affordable. Inevitably, such coarse-grained models introduce a set of phenomenological parameters, which are often not easily deducible from the underlying atomistic system. We present a unique approach to the calculation of these parameters, based on the recently introduced variationally enhanced sampling method. It allows us to obtain the parameters from atomistic simulations, providing thus a direct connection between the microscopic and the mesoscopic scale. The coarse-grained model we consider is that of Ginzburg-Landau, valid around a second-order critical point. In particular, we use it to describe a Lennard-Jones fluid in the region close to the liquid-vapor critical point. The procedure is general and can be adapted to other coarse-grained models.

  10. Entropic and Enthalpic Contributions to Stereospecific Ligand Binding from Enhanced Sampling Methods

    PubMed Central

    2013-01-01

    The stereoselective binding of R- and S-propranolol to the metabolic enzyme cytochrome P450 2D6 and its mutant F483A was studied using various computational approaches. Previously reported free-energy differences from Hamiltonian replica exchange simulations, combined with thermodynamic integration, are compared to the one-step perturbation approach, combined with local-elevation enhanced sampling, and an excellent agreement between methods was obtained. Further, the free-energy differences are interpreted in terms of enthalpic and entropic contributions where it is shown that exactly compensating contributions obscure a molecular interpretation of differences in the affinity while various reduced terms allow a more detailed analysis, which agree with heuristic observations on the interactions. PMID:24372516

  11. Enhanced Sampling Methods for the Computation of Conformational Kinetics in Macromolecules

    NASA Astrophysics Data System (ADS)

    Grazioli, Gianmarc

    Calculating the kinetics of conformational changes in macromolecules, such as proteins and nucleic acids, is still very much an open problem in theoretical chemistry and computational biophysics. If it were feasible to run large sets of molecular dynamics trajectories that begin in one configuration and terminate when reaching another configuration of interest, calculating kinetics from molecular dynamics simulations would be simple, but in practice, configuration spaces encompassing all possible configurations for even the simplest of macromolecules are far too vast for such a brute force approach. In fact, many problems related to searches of configuration spaces, such as protein structure prediction, are considered to be NP-hard. Two approaches to addressing this problem are to either develop methods for enhanced sampling of trajectories that confine the search to productive trajectories without loss of temporal information, or coarse-grained methodologies that recast the problem in reduced spaces that can be exhaustively searched. This thesis will begin with a description of work carried out in the vein of the second approach, where a Smoluchowski diffusion equation model was developed that accurately reproduces the rate vs. force relationship observed in the mechano-catalytic disulphide bond cleavage observed in thioredoxin-catalyzed reduction of disulphide bonds. Next, three different novel enhanced sampling methods developed in the vein of the first approach will be described, which can be employed either separately or in conjunction with each other to autonomously define a set of energetically relevant subspaces in configuration space, accelerate trajectories between the interfaces dividing the subspaces while preserving the distribution of unassisted transition times between subspaces, and approximate time correlation functions from the kinetic data collected from the transitions between interfaces.

  12. Enhancing the speech envelope of continuous interleaved sampling processors for cochlear implants.

    PubMed

    Geurts, L; Wouters, J

    1999-04-01

    A new method to code the speech envelope in continuous interleaved sampling (CIS) processors for cochlear implants is proposed. In this enhanced envelope, the rapid adaptation seen in the response of auditory nerves to sound stimuli is incorporated. Two strategies, one using the standard envelope (CIS) and one using the enhanced envelope (EECIS), were tested perceptually with six postlingually deafened users of the LAURA cochlear implant. The tests included identification of stop consonants in three different vowel contexts and monosyllabic consonant-vowel-consonant (CVC) words. Significant improvements in correct identification scores were observed for stop consonants in intervocalic /a/ context (p = 0.026): average results varied from 46% correct for CIS to 55% for EECIS. This improvement was mainly due to the better transmission of place of articulation. The differences in identification scores for stop consonants in /i/ and /u/ context were not significant. The identification scores for the medial vowels of the CVC words were significantly higher when the EECIS strategy was used: average results increased from 39% correct to 46% correct (p = 0.018). No significant differences were observed between the results for initial and final consonants of the CVC words. The present results demonstrate that the inclusion of the rapid adaptation in the speech processing for cochlear implants can improve speech intelligibility.

  13. Enhanced Sampling and Overfitting Analyses in Structural Refinement of Nucleic Acids into Electron Microscopy Maps

    PubMed Central

    Vashisth, Harish; Skiniotis, Georgios; Brooks, Charles L.

    2013-01-01

    Flexible-fitting computational algorithms are often useful to interpret low resolution maps of many macromolecular complexes generated by electron microscopy (EM) imaging. One such atomistic simulation technique is molecular dynamics flexible fitting (MDFF), which has been widely applied to generate structural models of large ribonucleoprotein assemblies such as the ribosome. We have previously shown that MDFF simulations of globular proteins are sensitive to the resolution of the target EM map, and the strength of restraints used to preserve the secondary structure elements during fitting (Vashisth et al. Structure 2012, 20, 1453–1462). In this work, we aim to systematically examine the quality of structural models of various nucleic acids obtained via MDFF by varying the map resolution and the strength of structural restraints. We also demonstrate how an enhanced conformational sampling technique for proteins, temperatureaccelerated molecular dynamics (TAMD), can be combined with MDFF for the structural refinement of nucleic acids in EMmaps. Finally, we also demonstrate application of TAMD-assisted MDFF (TAMDFF) on a RNA/protein complex and suggest that TAMDFF is a viable strategy for enhanced conformational fitting in target maps of ribonucleoprotein complexes. PMID:23506287

  14. Field enhancement sample stacking for analysis of organic acids in traditional Chinese medicine by capillary electrophoresis.

    PubMed

    Zhu, Qianqian; Xu, Xueqin; Huang, Yuanyuan; Xu, Liangjun; Chen, Guonan

    2012-07-13

    A technique known as field enhancement sample stacking (FESS) and capillary electrophoresis (CE) separation has been developed to analyze and detect organic acids in the three traditional Chinese medicines (such as Portulaca oleracea L., Crataegus pinnatifida and Aloe vera L.). In FESS, a reverse electrode polarity-stacking mode (REPSM) was applied as on-line preconcentration strategy. Under the optimized condition, the baseline separation of eight organic acids (linolenic acid, lauric acid, p-coumaric acid, ascorbic acid, benzoic acid, caffeic acid, succinic acid and fumaric acid) could be achieved within 20 min. Validation parameters of this method (such as detection limits, linearity and precision) were also evaluated. The detection limits ranged from 0.4 to 60 ng/mL. The results indicated that the proposed method was effective for the separation of mixtures of organic acids. Satisfactory recoveries were also obtained in the analysis of these organic acids in the above traditional Chinese medicine samples. Copyright © 2012 Elsevier B.V. All rights reserved.

  15. Sensitivity enhancing injection from a sample reservoir and channel interface in microchip electrophoresis.

    PubMed

    Wuethrich, Alain; Quirino, Joselito P

    2017-02-01

    The stacking of a cationic analyte (i.e., rhodamine B) at the interface between a sample reservoir and channel in a microchip electrophoresis device is described for the first time. Stacking at negative polarity was by micelle to solvent stacking where the dye was prepared in a micellar solution (5 mM sodium dodecyl sulfate in 25 mM phosphoric acid, pH 2.5) and the channel was filled with high methanol content background solution (70% methanol in 50 mM phosphoric acid, pH 2.5). The injection of the stacked dye into the channel was by simple reversal of the voltage polarity with the sample solution and background solution at the anodic and cathodic reservoirs of the straight channel, respectively. The enrichment of rhodamine B at the interface and injection of the stacked dye into the channel was clearly visualized using an inverted fluorescence microscope. A notable sensitivity enhancement factor of up to 150 was achieved after 2 min at 1 kV of micelle to solvent stacking. The proposed technique will be useful as a concentration step for analyte mixtures in simple and classical cross-channel microchip electrophoresis devices or for the controlled delivery of enriched reagents or analytes as narrow plugs in advanced microchip electrophoresis devices. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. In Situ Passive Sampling of Sediment Porewater Enhanced by Periodic Vibration.

    PubMed

    Jalalizadeh, Mehregan; Ghosh, Upal

    2016-08-16

    Passive sampling for the measurement of freely dissolved concentrations of organic pollutants in sediment porewater has emerged as a promising approach, but in situ measurements are complicated by slow mass transfer of strongly hydrophobic compounds. The primary resistance to mass transfer arises in the sediment side where a concentration depletion layer develops in the vicinity of the polymeric passive sampling material. The slow mass transfer results in underequilibrated passive sampler measurements that need to be corrected for equilibrium, typically by extrapolation of the loss kinetics of performance reference compounds. Such corrections are prone to large errors, especially when deviation from equilibrium is large. In this research we address the challenge of slow mass transfer by disrupting the external depletion layer around an in situ passive sampler. We report an engineering innovation of adapting low-cost vibration motors for periodically disrupting the depletion layer in a passive sampler deployed in sediments. The uptake of 16 polycyclic aromatic hydrocarbons into polyethylene passive samplers was measured after 7, 14, 28, and 56 days of exposure to sediment under static, vibrating, and fully mixed modes. We demonstrate through laboratory experiments and numerical mass transfer modeling that short periodic shaking of a passive sampler deployed in static sediment enhances the rate of mass transfer and reduces the difference in the extent of equilibrium achieved compared to a well-mixed laboratory equilibrium. The improvement over static sediment deployment is especially evident for the high molecular weight compounds such as benzo(a)pyrene.

  17. Highly sensitive quantitation of human serum albumin in clinical samples for hypoproteinemia using metal-enhanced fluorescence.

    PubMed

    Zhang, Yongxia; Mali, Buddha L; Aitken, Caroleann; Geddes, Chris D

    2013-01-01

    In this paper, we have explored metal-enhanced fluorescence (MEF) of the Human serum albumin indicators: Albumin Blue 580, Merocyanine 540 and Bromophenol Blue in close proximity to silver nano-particles, SiFs, from both buffered and clinical samples. The photostability of the Albumin Blue 580 is shown to be much more prolonged from the SiFs as compared to glass (a control sample), potentially allowing for longer detection times to further improve assay statistics. Our findings suggest the widespread use of nanoparticulate SiFs surfaces for the enhanced detection of HSA, particularly for Hypoproteinemia, where an enhanced assay performance at low protein abundance is required.

  18. Graphene-enhanced plasmonic nanohole arrays for environmental sensing in aqueous samples

    PubMed Central

    Genslein, Christa; Hausler, Peter; Kirchner, Eva-Maria; Bierl, Rudolf; Baeumner, Antje J

    2016-01-01

    The label-free nature of surface plasmon resonance techniques (SPR) enables a fast, specific, and sensitive analysis of molecular interactions. However, detection of highly diluted concentrations and small molecules is still challenging. It is shown here that in contrast to continuous gold films, gold nanohole arrays can significantly improve the performance of SPR devices in angle-dependent measurement mode, as a signal amplification arises from localized surface plasmons at the nanostructures. This leads consequently to an increased sensing capability of molecules bound to the nanohole array surface. Furthermore, a reduced graphene oxide (rGO) sensor surface was layered over the nanohole array. Reduced graphene oxide is a 2D nanomaterial consisting of sp2-hybridized carbon atoms and is an attractive receptor surface for SPR as it omits any bulk phase and therefore allows fast response times. In fact, it was found that nanohole arrays demonstrated a higher shift in the resonance angle of 250–380% compared to a continuous gold film. At the same time the nanohole array structure as characterized by its diameter-to-periodicity ratio had minimal influence on the binding capacity of the sensor surface. As a simple and environmentally highly relevant model, binding of the plasticizer diethyl phthalate (DEP) via π-stacking was monitored on the rGO gold nanohole array realizing a limit of detection of as low as 20 nM. The concentration-dependent signal change was studied with the best performing rGO-modified nanohole arrays. Compared to continuous gold films a diameter-to-periodicity ratio (D/P) of 0.43 lead to a 12-fold signal enhancement. Finally, the effect of environmental waters on the sensor was evaluated using samples from sea, lake and river waters spiked with analytically relevant amounts of DEP during which significant changes in the SPR signal are observed. It is expected that this concept can be successfully transferred to enhance the sensitivity in SPR

  19. Graphene-enhanced plasmonic nanohole arrays for environmental sensing in aqueous samples.

    PubMed

    Genslein, Christa; Hausler, Peter; Kirchner, Eva-Maria; Bierl, Rudolf; Baeumner, Antje J; Hirsch, Thomas

    2016-01-01

    The label-free nature of surface plasmon resonance techniques (SPR) enables a fast, specific, and sensitive analysis of molecular interactions. However, detection of highly diluted concentrations and small molecules is still challenging. It is shown here that in contrast to continuous gold films, gold nanohole arrays can significantly improve the performance of SPR devices in angle-dependent measurement mode, as a signal amplification arises from localized surface plasmons at the nanostructures. This leads consequently to an increased sensing capability of molecules bound to the nanohole array surface. Furthermore, a reduced graphene oxide (rGO) sensor surface was layered over the nanohole array. Reduced graphene oxide is a 2D nanomaterial consisting of sp(2)-hybridized carbon atoms and is an attractive receptor surface for SPR as it omits any bulk phase and therefore allows fast response times. In fact, it was found that nanohole arrays demonstrated a higher shift in the resonance angle of 250-380% compared to a continuous gold film. At the same time the nanohole array structure as characterized by its diameter-to-periodicity ratio had minimal influence on the binding capacity of the sensor surface. As a simple and environmentally highly relevant model, binding of the plasticizer diethyl phthalate (DEP) via π-stacking was monitored on the rGO gold nanohole array realizing a limit of detection of as low as 20 nM. The concentration-dependent signal change was studied with the best performing rGO-modified nanohole arrays. Compared to continuous gold films a diameter-to-periodicity ratio (D/P) of 0.43 lead to a 12-fold signal enhancement. Finally, the effect of environmental waters on the sensor was evaluated using samples from sea, lake and river waters spiked with analytically relevant amounts of DEP during which significant changes in the SPR signal are observed. It is expected that this concept can be successfully transferred to enhance the sensitivity in SPR

  20. Depletion of cells and abundant proteins from biological samples by enhanced dielectrophoresis✩

    PubMed Central

    Gupta, C.; Provine, J.; Davis, R.W.; Howe, R.T.

    2016-01-01

    Platforms that are sensitive and specific enough to assay low-abundance protein biomarkers, in a high throughput multiplex format, within a complex biological fluid specimen, are necessary to enable protein biomarker based diagnostics for diseases such as cancer. The signal from an assay for a low-abundance protein biomarker in a biological fluid sample like blood is typically buried in a background that arises from the presence of blood cells and from high-abundance proteins that make up 90% of the assayed protein mass. We present an automated on-chip platform for the depletion of cells and highly abundant serum proteins in blood. Our platform consists of two components, the first of which is a microfluidic mixer that mixes beads containing antibodies against the highly abundant proteins in the whole blood. This complex mixture (consisting of beads, cells, and serum proteins) is then injected into the second component of our microfluidic platform, which comprises a filter trench to capture all the cells and the beads. The size-based trapping of the cells and beads into the filter trench is significantly enhanced by leveraging additional negative dielectrophoretic forces to push the micron sized particles (cells and beads which have captured the highly abundant proteins) down into the trench, allowing the serum proteins of lower abundance to flow through. In general, dielectrophoresis using bare electrodes is incapable of producing forces beyond the low piconewton range that tend to be insufficient for separation applications. However, by using electrodes passivated with atomic layer deposition, we demonstrate the application of enhanced negative DEP electrodes together with size-based flltration induced by the filter trench, to deplete 100% of the micron sized particles in the mixture. PMID:26924893

  1. Applications of Raman and Surface-Enhanced Raman Scattering to the Analysis of Eukaryotic Samples

    NASA Astrophysics Data System (ADS)

    Schulte, Franziska; Joseph, Virginia; Panne, Ulrich; Kneipp, Janina

    In this chapter, we discuss Raman scattering and surface-enhanced Raman scattering (SERS) for the analysis of cellular samples of plant and animal origin which are several tens to hundreds of microns in size. As was shown in the past several years, the favorable properties of noble metal nanostructures can be used to generate SERS signals in very complex biological samples such as cells, and result in an improved sensitivity and spatial resolution. Pollen grains, the physiological containers that produce the male gametes of seed plants, consist of a few vegetative cells and one generative cell, surrounded by a biopolymer shell. Their chemical composition has been a subject of research of plant physiologists, biochemists [1, 2], and lately even materials scientists [3, 4] for various reasons. In spite of a multitude of applied analytical approaches it could not be elucidated in its entirety yet. Animal cells from cell cultures have been a subject of intense studies due to their application in virtually all fields of biomedical research, ranging from studies of basic biological mechanisms to models for pharmaceutical and diagnostic research. Many aspects of all kinds of cellular processes including signalling, transport, and gene regulation have been elucidated, but many more facts about cell biology will need to be understood in order to efficiently address issues such as cancer, viral infection or genetic disorder. Using the information from spectroscopic methods, in particular combining normal Raman spectroscopy and SERS may open up new perspectives on cellular biochemistry. New sensitive Raman-based tools are being developed for the biochemical analysis of cellular processes [5-8].

  2. On the Use of Accelerated Molecular Dynamics to Enhance Configurational Sampling in Ab Initio Simulations

    PubMed Central

    2011-01-01

    We have implemented the accelerated molecular dynamics approach (Hamelberg, D.; Mongan, J.; McCammon, J. A. J. Chem. Phys. 2004, 120 (24), 11919) in the framework of ab initio MD (AIMD). Using three simple examples, we demonstrate that accelerated AIMD (A-AIMD) can be used to accelerate solvent relaxation in AIMD simulations and facilitate the detection of reaction coordinates: (i) We show, for one cyclohexane molecule in the gas phase, that the method can be used to accelerate the rate of the chair-to-chair interconversion by a factor of ∼1 × 105, while allowing for the reconstruction of the correct canonical distribution of low-energy states; (ii) We then show, for a water box of 64 H2O molecules, that A-AIMD can also be used in the condensed phase to accelerate the sampling of water conformations, without affecting the structural properties of the solvent; and (iii) The method is then used to compute the potential of mean force (PMF) for the dissociation of Na−Cl in water, accelerating the convergence by a factor of ∼3−4 compared to conventional AIMD simulations.(2) These results suggest that A-AIMD is a useful addition to existing methods for enhanced conformational and phase-space sampling in solution. While the method does not make the use of collective variables superfluous, it also does not require the user to define a set of collective variables that can capture all the low-energy minima on the potential energy surface. This property may prove very useful when dealing with highly complex multidimensional systems that require a quantum mechanical treatment. PMID:21494425

  3. Silver nanoparticles enhanced flow injection chemiluminescence determination of gatifloxacin in pharmaceutical formulation and spiked urine sample

    NASA Astrophysics Data System (ADS)

    Wabaidur, Saikh mohammad; Alam, Seikh Mafiz; Alothman, Zeid A.; Mohsin, Kazi

    2015-06-01

    Silver nanoparticles have been utilized for the enhanced chemiluminogenic estimation of fluoroquinolone antibiotic gatifloxacin. It has been found that the weak chemiluminescence intensity produced from the reaction between calcein and KMnO4 can further be strengthened by the addition of silver nanoparticles in the presence of gatifloxacin. This phenomenon has been exploited to the quantitative determination of gatifloxacin. Under the optimum experimental conditions, the calibration curves are linear over the range of 8.9 × 10-9-4.0 × 10-6 M, while the limits of detections were found to be 2.6 × 10-9 M with correlation coefficient value (r2) 0.9999. The relative standard deviation calculated from six replicate measurements (1.0 × 10-4 M gatifloxacin) was 1.70%. The method was applied to pharmaceutical preparations and the results obtained were in reasonable agreement with the amount labeled on the formulations. The proposed method was also used for the determination of gatifloxacin in spiked urine samples with satisfactory results. No interference effects from some common excipients used in pharmaceutical preparations have been found.

  4. Dynamics and Kinetics Study of "In-Water" Chemical Reactions by Enhanced Sampling of Reactive Trajectories.

    PubMed

    Zhang, Jun; Yang, Y Isaac; Yang, Lijiang; Gao, Yi Qin

    2015-11-12

    High potential energy barriers and engagement of solvent coordinates set challenges for in silico studies of chemical reactions, and one is quite commonly limited to study reactions along predefined reaction coordinate(s). A systematic protocol, QM/MM MD simulations using enhanced sampling of reactive trajectories (ESoRT), is established to quantitatively study chemical transitions in complex systems. A number of trajectories for Claisen rearrangement in water and toluene were collected and analyzed, respectively. Evidence was found that the bond making and breaking during this reaction are concerted processes in solutions, preferentially through a chairlike configuration. Water plays an important dynamic role that helps stabilize the transition sate, and the dipole-dipole interaction between water and the solute also lowers the transition barrier. The calculated rate coefficient is consistent with the experimental measurement. Compared with water, the reaction pathway in toluene is "narrower" and the reaction rate is slower by almost three orders of magnitude due to the absence of proper interactions to stabilize the transition state. This study suggests that the "in-water" nature of the Claisen rearrangement in aqueous solution influences its thermodynamics, kinetics, as well as dynamics.

  5. Tip-enhanced laser ablation sample transfer for biomolecule mass spectrometry.

    PubMed

    Ghorai, Suman; Seneviratne, Chinthaka A; Murray, Kermit K

    2015-01-01

    Atomic force microscope (AFM) tip-enhanced laser ablation was used to transfer molecules from thin films to a suspended silver wire for off-line mass spectrometry using laser desorption ionization (LDI) and matrix-assisted laser desorption ionization (MALDI). An AFM with a 30 nm radius gold-coated silicon tip was used to image the sample and to hold the tip 15 nm from the surface for material removal using a 355 nm Nd:YAG laser. The ablated material was captured on a silver wire that was held 300 μm vertically and 100 μm horizontally from the tip. For the small molecules anthracene and rhodamine 6G, the wire was cut and affixed to a metal target using double-sided conductive tape and analyzed by LDI using a commercial laser desorption time-of-flight mass spectrometer. Approximately 100 fg of material was ablated from each of the 1 μm ablation spots and transferred with approximately 3% efficiency. For larger polypeptide molecules angiotensin II and bovine insulin, the captured material was dissolved in saturated matrix solution and deposited on a target for MALDI analysis.

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

    PubMed

    Pang, Yuan-Ping

    2014-09-26

    CLN025 is one of the smallest fast-folding proteins. Until now it has not been reported that CLN025 can autonomously fold to its native conformation in a classical, all-atom, and isothermal-isobaric molecular dynamics (MD) simulation. This article reports the autonomous and repeated folding of CLN025 from a fully extended backbone conformation to its native conformation in explicit solvent in multiple 500-ns MD simulations at 277K and 1atm with the first folding event occurring as early as 66.1ns. These simulations were accomplished by using AMBER forcefield derivatives with atomic masses reduced by 10-fold on Apple Mac Pros. By contrast, no folding event was observed when the simulations were repeated using the original AMBER forcefields of FF12SB and FF14SB. The results demonstrate that low-mass MD simulation is a simple and generic technique to enhance configurational sampling. This technique may propel autonomous folding of a wide range of miniature proteins in classical, all-atom, and isothermal-isobaric MD simulations performed on commodity computers-an important step forward in quantitative biology. Copyright © 2014 The Author. Published by Elsevier Inc. All rights reserved.

  7. Enhanced Method for Molybdenum Separation and Isotopic Determination in Geological Samples and Uranium-Rich Materials

    NASA Astrophysics Data System (ADS)

    Migeon, V.; Bourdon, B.; Pili, E.

    2014-12-01

    Molybdenum (Mo) shares analogous geochemical properties with uranium. Mo ispresent as a minor or a trace element in uranium ores under two main oxidation states: +IVand +VI. Mo has seven stable isotopes (92, 94, 95, 96, 97, 98 and 100). In natural systems,Mo and Mo isotopes were shown to fractionate during redox reactions. Because Morepresents an impurity difficult to separate in the nuclear fuel cycle, it has the potential to beused as an indicator of the origins of uranium concentrates, in the framework of nuclearforensics. This work focuses on developing an enhanced separation method for Mo from auranium-rich matrix (uranium ore, uranium concentrate) in order to analyze the massfractionation induced by processes typical of the nuclear fuel cycle. Purification of Mo forisotope ratio measurements is performed with a three-step separation on ion-exchange resins,with yields between 45 and 82%. Matrix and isobaric interferences (Zr, Ru) were reduced ingeological and uranium standards, such as U/Mo ≤ 2*10-4, Zr/Mo ≤ 1*10-3, Ru/Mo ≤ 6*10-4and Fe/Mo ≤ 4*10-3. Mo isotopic compositions were measured on a Neptune Plus MC-ICPMSequipped with Jet cones, for a concentration of 30 ng/ml. The achieved sensitivity is~1200-1800 V/ppm with interferences below 10 mV and an overall reproducibility of 0.02 ‰on the δ98Mo values. A double spike, with 97Mo and 100Mo, was added to the samples beforethe purification. It allows for correction of the chemical and instrumental mass fractionations,without requiring a quantitative yield. For igneous rocks, δ98Mo values range between -0.55and -0.03 ‰, relative to the NIST-SRM 3134 molybdenum standard. Fractionation amonguranium ore concentrates is higher, with δ98Mo ranging between 0.02 and -2.84 ‰.

  8. Enhanced Conformational Sampling Using Replica Exchange with Concurrent Solute Scaling and Hamiltonian Biasing Realized in One Dimension

    PubMed Central

    2015-01-01

    Replica exchange (REX) is a powerful computational tool for overcoming the quasi-ergodic sampling problem of complex molecular systems. Recently, several multidimensional extensions of this method have been developed to realize exchanges in both temperature and biasing potential space or the use of multiple biasing potentials to improve sampling efficiency. However, increased computational cost due to the multidimensionality of exchanges becomes challenging for use on complex systems under explicit solvent conditions. In this study, we develop a one-dimensional (1D) REX algorithm to concurrently combine the advantages of overall enhanced sampling from Hamiltonian solute scaling and the specific enhancement of collective variables using Hamiltonian biasing potentials. In the present Hamiltonian replica exchange method, termed HREST-BP, Hamiltonian solute scaling is applied to the solute subsystem, and its interactions with the environment to enhance overall conformational transitions and biasing potentials are added along selected collective variables associated with specific conformational transitions, thereby balancing the sampling of different hierarchical degrees of freedom. The two enhanced sampling approaches are implemented concurrently allowing for the use of a small number of replicas (e.g., 6 to 8) in 1D, thus greatly reducing the computational cost in complex system simulations. The present method is applied to conformational sampling of two nitrogen-linked glycans (N-glycans) found on the HIV gp120 envelope protein. Considering the general importance of the conformational sampling problem, HREST-BP represents an efficient procedure for the study of complex saccharides, and, more generally, the method is anticipated to be of general utility for the conformational sampling in a wide range of macromolecular systems. PMID:26082676

  9. Direct DNA amplification from crude clinical samples using a PCR enhancer cocktail and novel mutants of Taq.

    PubMed

    Zhang, Zhian; Kermekchiev, Milko B; Barnes, Wayne M

    2010-03-01

    PCR-based clinical and forensic tests often have low sensitivity or even false-negative results caused by potent PCR inhibitors found in blood and soil. It is widely accepted that purification of target DNA before PCR is necessary for successful amplification. In an attempt to overcome PCR inhibition, enhance PCR amplification, and simplify the PCR protocol, we demonstrate improved PCR-enhancing cocktails containing nonionic detergent, l-carnitine, d-(+)-trehalose, and heparin. These cocktails, in combination with two inhibitor-resistant Taq mutants, OmniTaq and Omni Klentaq, enabled efficient amplification of exogenous, endogenous, and high-GC content DNA targets directly from crude samples containing human plasma, serum, and whole blood without DNA purification. In the presence of these enhancer cocktails, the mutant enzymes were able to tolerate at least 25% plasma, serum, or whole blood and as high as 80% GC content templates in PCR reactions. These enhancer cocktails also improved the performance of the novel Taq mutants in real-time PCR amplification using crude samples, both in SYBR Green fluorescence detection and TaqMan assays. The novel enhancer mixes also facilitated DNA amplification from crude samples with various commercial Taq DNA polymerases.

  10. Influence of high-conductivity buffer composition on field-enhanced sample injection coupled to sweeping in CE.

    PubMed

    Anres, Philippe; Delaunay, Nathalie; Vial, Jérôme; Thormann, Wolfgang; Gareil, Pierre

    2013-02-01

    The aim of this work was to clarify the mechanism taking place in field-enhanced sample injection coupled to sweeping and micellar EKC (FESI-Sweep-MEKC), with the utilization of two acidic high-conductivity buffers (HCBs), phosphoric acid or sodium phosphate buffer, in view of maximizing sensitivity enhancements. Using cationic model compounds in acidic media, a chemometric approach and simulations with SIMUL5 were implemented. Experimental design first enabled to identify the significant factors and their potential interactions. Simulation demonstrates the formation of moving boundaries during sample injection, which originate at the initial sample/HCB and HCB/buffer discontinuities and gradually change the compositions of HCB and BGE. With sodium phosphate buffer, the HCB conductivity increased during the injection, leading to a more efficient preconcentration by staking (about 1.6 times) than with phosphoric acid alone, for which conductivity decreased during injection. For the same injection time at constant voltage, however, a lower amount of analytes was injected with sodium phosphate buffer than with phosphoric acid. Consequently sensitivity enhancements were lower for the whole FESI-Sweep-MEKC process. This is why, in order to maximize sensitivity enhancements, it is proposed to work with sodium phosphate buffer as HCB and to use constant current during sample injection. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Phylogenomic analysis of ants, bees and stinging wasps: Improved taxon sampling enhances understanding of hymenopteran evolution

    USDA-ARS?s Scientific Manuscript database

    The importance of taxon sampling in phylogenetic accuracy is a topic of active debate. We investigated the role of taxon sampling in causing incongruent results between two recent phylogenomic studies of stinging wasps (Hymenoptera: Aculeata), a diverse lineage that includes ants, bees and the major...

  12. Cloud point sample clean-up and capillary zone electrophoresis with field enhanced sample injection and micelle to solvent stacking for the analysis of herbicides in milk.

    PubMed

    Kukusamude, Chunyapuk; Srijaranai, Supalax; Kato, Masaru; Quirino, Joselito P

    2014-07-18

    Sample clean-up by cloud point phase separation and analysis by capillary electrophoresis with stacking was developed for quaternary ammonium herbicides (i.e., paraquat and diquat) in milk. For sample clean-up, a mixture of 845μL of milk sample, 5μL of 100mM phosphoric acid, and 150μL of Triton X-114 was heated (60°C for 2min) and centrifugated (3000rpm for 2min) in 2-mL Eppendorf tube. The upper phase was directly analysed by capillary electrophoresis via electrokinetic injection at 10kV for 150s. The separation electrolyte was 100mM phosphate buffer with 20% acetonitrile at pH 2.5. Before sample injection, a micellar solution (10mM SDS in 80mM phosphate buffer at pH 2.5) and an organic solvent rich solution (30% ACN) was hydrodynamically introduced into the capillary. These solutions provided the necessary conditions for stacking the cationic herbicides via the combination of field enhanced sample injection and micelle to solvent stacking. The LODs (S/N=3) obtained from the entire strategy for paraquat and diquat in milk was 0.004 and 0.018μg/mL, respectively. This is 1.5 to >2 orders of magnitude better than the corresponding LODs obtained from the electrophoretic analysis of herbicide standards prepared in the separation electrolyte. The strategy was also successfully applied to 5 milk samples available in the market. Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.

  13. Enhanced Ligand Sampling for Relative Protein–Ligand Binding Free Energy Calculations

    PubMed Central

    2016-01-01

    Free energy calculations are used to study how strongly potential drug molecules interact with their target receptors. The accuracy of these calculations depends on the accuracy of the molecular dynamics (MD) force field as well as proper sampling of the major conformations of each molecule. However, proper sampling of ligand conformations can be difficult when there are large barriers separating the major ligand conformations. An example of this is for ligands with an asymmetrically substituted phenyl ring, where the presence of protein loops hinders the proper sampling of the different ring conformations. These ring conformations become more difficult to sample when the size of the functional groups attached to the ring increases. The Adaptive Integration Method (AIM) has been developed, which adaptively changes the alchemical coupling parameter λ during the MD simulation so that conformations sampled at one λ can aid sampling at the other λ values. The Accelerated Adaptive Integration Method (AcclAIM) builds on AIM by lowering potential barriers for specific degrees of freedom at intermediate λ values. However, these methods may not work when there are very large barriers separating the major ligand conformations. In this work, we describe a modification to AIM that improves sampling of the different ring conformations, even when there is a very large barrier between them. This method combines AIM with conformational Monte Carlo sampling, giving improved convergence of ring populations and the resulting free energy. This method, called AIM/MC, is applied to study the relative binding free energy for a pair of ligands that bind to thrombin and a different pair of ligands that bind to aspartyl protease β-APP cleaving enzyme 1 (BACE1). These protein–ligand binding free energy calculations illustrate the improvements in conformational sampling and the convergence of the free energy compared to both AIM and AcclAIM. PMID:25906170

  14. The enhanced forest inventory and analysis program - national sampling design and estimation procedures

    Treesearch

    William A. Bechtold; Paul L. Patterson; [Editors

    2005-01-01

    The Forest Inventory and Analysis (FIA) Program of the U.S. Department of Agriculture Forest Service is in the process of moving from a system of quasiindependent, regional, periodic inventories to an enhanced program featuring greater national consistency, annual measurement of a proportion of plots in each State, new reporting requirements, and integration with the...

  15. Star Formation Enhancement in z=0 Close Major Mergers --- Spitzer Observations of a K-Band Selected Sample

    NASA Astrophysics Data System (ADS)

    Xu, C. Kevin; Domingue, D.; Cheng, Y.; Lu, N.; Huang, J.; Gao, Y.; Mazzarella, J. M.; Cutri, R.; Sun, W.; Surace, J.

    2010-05-01

    We present Spitzer observations for a sample of close major-merger galaxy pairs (KPAIR sample) selected from 2MASS/SDSS-DR3 cross-matches. The goals are to study the star formation activity in these galaxies and to set a local bench mark for the cosmic evolution of close major mergers. The Spitzer sample (27 pairs, 54 galaxies) includes all spectroscopically confirmed spiral-spiral (S+S) and spiral-elliptical (S+E) pairs in a parent sample that is complete for primaries brighter than K=12.5 mag, projected separations of 5sample (one-to-one mass-matched to 39 non-AGN spirals in the pair sample), only spiral galaxies in S+S pairs show significantly enhanced specific star formation rate (sSFR=SFR/M), whereas spiral galaxies in S+E pairs do not. Furthermore, the SFR enhancement of spiral galaxies in S+S pairs is highly mass-dependent: Only those with mass higher than 1010.5 Msun (H0=75, Salpeter IMF) show significant enhancement. Relatively low mass ( 1010 Msun) spirals in S+S pairs have about the same sSFR compared to their counterparts in the control sample, while those with 1011 Msun have on average a 3 times higher sSFR than single spirals. In S+S pairs, the sSFR's of primaries and secondaries are correlated ("Holmberg effect"), and are equally enhanced. There is no significant difference in the sSFR between spirals of SEP<1 and those of SEP>1, SEP being the normalized separation parameter. These results reveal that enhanced star formation only occurs in a small fraction of close major-merger galaxies (i.e. some of the massive spirals in S+S pairs), and this is not determined by orbital parameters such as SEP. Our results challenge the current theory for interaction induced star formation.

  16. Differential outcomes enhance accuracy of delayed matching to sample but not resistance to change.

    PubMed

    Nevin, John A; Ward, Ryan D; Jimenez-Gomez, Corina; Odum, Amy L; Shahan, Timothy A

    2009-01-01

    Three experiments assessed the relation between the differential outcomes effect and resistance to change of delayed matching-to-sample performance. Pigeons produced delayed matching-to-sample trials by responding on variable interval schedules in two components of a multiple schedule. In the same-outcome component, the probability of reinforcement was the same for both samples (.9 in Experiments 1 and 2, .5 in Experiment 3); in the different-outcomes component, the probability of reinforcement was .9 for one sample and .1 for the other. In all three experiments, the forgetting functions in the different-outcomes component were higher and shallower than in the same-outcomes component. When total reinforcement was greater in the same-outcomes component (Experiments 1 and 2), resistance to disruption by prefeeding, intercomponent food, extinction, or flashing lights typically was greater in that component. In Experiment 3, when total reinforcement was equated, resistance to disruption was similar across components. Thus, the level and slope of forgetting functions depended on differential reinforcement correlated with the samples, but the resistance to change of forgetting functions depended on total reinforcement in a component. Both aspects of the results can be explained by a model of delayed matching to sample performance. Copyright 2009 APA, all rights reserved.

  17. Differential outcomes enhance accuracy of delayed matching to sample but not resistance to change

    PubMed Central

    Nevin, John A.; Ward, Ryan D.; Jimenez-Gomez, Corina; Odum, Amy L.; Shahan, Timothy A

    2009-01-01

    Three experiments assessed the relation between the differential-outcomes effect and resistance to change of delayed matching-to-sample performance. Pigeons produced delayed matching-to-sample trials by responding on variable-interval schedules in two components of a multiple schedule. In the same-outcome component, the probability of reinforcement was the same for both samples (.9 in Experiments 1 & 2, .5 in Experiment 3); in the different-outcomes component, the probability of reinforcement was .9 for one sample and .1 for the other. In all three experiments, the forgetting functions in the different-outcomes component were higher and shallower than in the same-outcomes component. When total reinforcement was greater in the same-outcomes component (Experiments 1 and 2), resistance to disruption by prefeeding, intercomponent food, extinction, or flashing lights typically was greater in that component. In Experiment 3, when total reinforcement was equated, resistance to disruption was similar across components. Thus, the level and slope of forgetting functions depended on differential reinforcement correlated with the samples, but the resistance to change of forgetting functions depended on total reinforcement in a component. Both aspects of the results can be explained by a model of delayed matching to sample performance. PMID:19159163

  18. Poisson-gap sampling and forward maximum entropy reconstruction for enhancing the resolution and sensitivity of protein NMR data.

    PubMed

    Hyberts, Sven G; Takeuchi, Koh; Wagner, Gerhard

    2010-02-24

    The Fourier transform has been the gold standard for transforming data from the time domain to the frequency domain in many spectroscopic methods, including NMR spectroscopy. While reliable, it has the drawback that it requires a grid of uniformely sampled data points, which is not efficient for decaying signals, and it also suffers from artifacts when dealing with nondecaying signals. Over several decades, many alternative sampling and transformation schemes have been proposed. Their common problem is that relative signal amplitudes are not well-preserved. Here we demonstrate the superior performance of a sine-weighted Poisson-gap distribution sparse-sampling scheme combined with forward maximum entropy (FM) reconstruction. While the relative signal amplitudes are well-preserved, we also find that the signal-to-noise ratio is enhanced up to 4-fold per unit of data acquisition time relative to traditional linear sampling.

  19. Pieces of Other Worlds - Enhance YSS Education and Public Outreach Events with Extraterrestrial Samples

    NASA Astrophysics Data System (ADS)

    Allen, C.

    2010-12-01

    During the Year of the Solar System spacecraft will encounter two comets; orbit the asteroid Vesta, continue to explore Mars with rovers, and launch robotic explorers to the Moon and Mars. We have pieces of all these worlds in our laboratories. Extensive information about these unique materials, as well as actual lunar samples and meteorites, is available for display and education. The Johnson Space Center (JSC) curates NASA's extraterrestrial samples to support research, education, and public outreach. At the current time JSC curates five types of extraterrestrial samples: Moon rocks and soils collected by the Apollo astronauts Meteorites collected on US expeditions to Antarctica (including rocks from the Moon, Mars, and many asteroids including Vesta) “Cosmic dust” (asteroid and comet particles) collected by high-altitude aircraft Solar wind atoms collected by the Genesis spacecraft Comet and interstellar dust particles collected by the Stardust spacecraft These rocks, soils, dust particles, and atoms continue to be studied intensively by scientists around the world. Descriptions of the samples, research results, thousands of photographs, and information on how to request research samples are on the JSC Curation website: http://curator.jsc.nasa.gov/ NASA is eager for scientists and the public to have access to these exciting samples through our various loan procedures. NASA provides a limited number of Moon rock samples for either short-term or long-term displays at museums, planetariums, expositions, and professional events that are open to the public. The JSC Public Affairs Office handles requests for such display samples. Requestors should apply in writing to Mr. Louis Parker, JSC Exhibits Manager. He will advise successful applicants regarding provisions for receipt, display, and return of the samples. All loans will be preceded by a signed loan agreement executed between NASA and the requestor's organization. Email address: louis.a.parker@nasa.gov Sets

  20. Combined Dynamic Contrast Enhanced Liver MRI and MRA Using Interleaved Variable Density Sampling

    PubMed Central

    Rahimi, Mahdi Salmani; Korosec, Frank R.; Wang, Kang; Holmes, James H.; Motosugi, Utaroh; Bannas, Peter; Reeder, Scott B.

    2014-01-01

    Purpose To develop and evaluate a method for volumetric contrast-enhanced MR imaging of the liver, with high spatial and temporal resolutions, for combined dynamic imaging and MR angiography using a single injection of contrast. Methods An interleaved variable density (IVD) undersampling pattern was implemented in combination with a real-time-triggered, time-resolved, dual-echo 3D spoiled gradient echo sequence. Parallel imaging autocalibration lines were acquired only once during the first time-frame. Imaging was performed in ten subjects with focal nodular hyperplasia (FNH) and compared with their clinical MRI. The angiographic phase of the proposed method was compared to a dedicated MR angiogram acquired during a second injection of contrast. Results A total of 21 FNH, 3 cavernous hemangiomas, and 109 arterial segments were visualized in 10 subjects. The temporally-resolved images depicted the characteristic arterial enhancement pattern of the lesions with a 4 s update rate. Images were graded as having significantly higher quality compared to the clinical MRI. Angiograms produced from the IVD method provided non-inferior diagnostic assessment compared to the dedicated MRA. Conclusion Using an undersampled IVD imaging method, we have demonstrated the feasibility of obtaining high spatial and temporal resolution dynamic contrast-enhanced imaging and simultaneous MRA of the liver. PMID:24639130

  1. Improved sample preparation and counting techniques for enhanced tritium measurement sensitivity

    NASA Astrophysics Data System (ADS)

    Moran, J.; Aalseth, C.; Bailey, V. L.; Mace, E. K.; Overman, C.; Seifert, A.; Wilcox Freeburg, E. D.

    2015-12-01

    Tritium (T) measurements offer insight to a wealth of environmental applications including hydrologic tracking, discerning ocean circulation patterns, and aging ice formations. However, the relatively short half-life of T (12.3 years) limits its effective age dating range. Compounding this limitation is the decrease in atmospheric T content by over two orders of magnitude (from 1000-2000 TU in 1962 to < 10 TU currently) since the cessation of above ground nuclear testing in the 1960's. We are developing sample preparation methods coupled to direct counting of T via ultra-low background proportional counters which, when combined, offer improved T measurement sensitivity (~4.5 mmoles of H2 equivalent) and will help expand the application of T age dating to smaller sample sizes linked to persistent environmental questions despite the limitations above. For instance, this approach can be used to T date ~ 2.2 mmoles of CH4 collected from sample-limited systems including microbial communities, soils, or subsurface aquifers and can be combined with radiocarbon dating to distinguish the methane's formation age from C age in a system. This approach can also expand investigations into soil organic C where the improved sensitivity will permit resolution of soil C into more descriptive fractions and provide direct assessments of the stability of specific classes of organic matter in soils environments. We are employing a multiple step sample preparation system whereby organic samples are first combusted with resulting CO2 and H2O being used as a feedstock to synthesize CH4. This CH4 is mixed with Ar and loaded directly into an ultra-low background proportional counter for measurement of T β decay in a shallow underground laboratory. Analysis of water samples requires only the addition of geologic CO2 feedstock with the sample for methane synthesis. The chemical nature of the preparation techniques enable high sample throughput with only the final measurement requiring T decay

  2. Micro-organism extraction from biological samples using DEP forces enhanced by osmotic shock.

    PubMed

    Bisceglia, Emilie; Cubizolles, Myriam; Mallard, Frédéric; Vinet, Françoise; Français, Olivier; Le Pioufle, Bruno

    2013-03-07

    On the road towards efficient diagnostics of infectious diseases, sample preparation is considered as the key step and remains a real technical challenge. Finding new methods for extraction of micro-organisms from a complex biological sample remains a major challenge prior to pathogen detection and analysis. This paper reports a new technique for capturing and isolating micro-organisms from a complex sample. To achieve the segregation of pathogens and blood cells, dielectrophoretic forces applied to bioparticles previously subjected to an osmotic shock are successfully implemented within a dedicated microfluidic device. Our device involves an electrode array of interdigitated electrodes, coated with an insulating layer, to minimize electrochemical reactions with the electrolyte and to enable long-time use. The electric field intensity inside the device is optimized, considering the insulating layer, for a given frequency bandwidth, enabling the separation of bioparticles by dielectrophoretic forces. Our predictions are based on analytical models, consistent with numerical simulations (using COMSOL Multiphysics) and correlated to experimental results. The method and device have been shown to extract different types of micro-organisms spiked in a blood cell sample. We strongly believe that this new separation approach may open the way towards a simple device for pathogen extraction from blood and more generally complex samples, with potential advantages of genericness and simplicity.

  3. Enhanced Detection of Rift Valley Fever Virus using Molecular Assays on Whole Blood Samples

    PubMed Central

    Grolla, Allen; Mehedi, Masfique; Lindsay, Robbin; Bosio, Catharine; Duse, Adriano; Feldmann, Heinz

    2012-01-01

    Background Rift Valley fever (RVF) is an emerging arthropod-borne zoonoses of global agricultural and public health importance. In December 2006, an RVF outbreak was recognized in Kenya which led to the deployment of international response laboratory teams to the area. Objectives A field laboratory was operated in Malindi, Kenya to provide safe sample handling and molecular testing for RVF virus (RVFV) as well as selected other pathogens for differential diagnosis. Study Design Safe sample handling was carried out using a negative pressure flexible film isolator (glovebox) and commercial reagents to inactivate clinical specimens and purify nucleic acid. Whole blood was routinely used for diagnostic testing although paired plasma samples were also tested in select cases. Subsequently, human macrophages were tested in vitro for their susceptibility to RVFV. Results The field laboratory received samples from 33 individuals and a definite laboratory diagnosis was provided in 16 of these cases. Using molecular diagnostic techniques, RVFV was more consistently detected in whole blood than in plasma samples most likely due to association of RVFV with blood cells. Subsequent in vitro studies identified macrophages as a target cell for RVFV replication. Conclusions RVFV appears to replicate in blood cells such as macrophages. Thus, the sensitivity of molecular diagnostic testing is improved if whole blood is used as the clinical specimen rather than plasma or serum. PMID:22632901

  4. Enhanced Resolution of Chiral Amino Acids with Capillary Electrophoresis for Biosignature Detection in Extraterrestrial Samples.

    PubMed

    Creamer, Jessica S; Mora, Maria F; Willis, Peter A

    2017-01-17

    Amino acids are fundamental building blocks of terrestrial life as well as ubiquitous byproducts of abiotic reactions. In order to distinguish between amino acids formed by abiotic versus biotic processes it is possible to use chemical distributions to identify patterns unique to life. This article describes two capillary electrophoresis methods capable of resolving 17 amino acids found in high abundance in both biotic and abiotic samples (seven enantiomer pairs d/l-Ala, -Asp, -Glu, -His, -Leu, -Ser, -Val and the three achiral amino acids Gly, β-Ala, and GABA). To resolve the 13 neutral amino acids one method utilizes a background electrolyte containing γ-cyclodextrin and sodium taurocholate micelles. The acidic amino acid enantiomers were resolved with γ-cyclodextrin alone. These methods allow detection limits down to 5 nM for the neutral amino acids and 500 nM for acidic amino acids and were used to analyze samples collected from Mono Lake with minimal sample preparation.

  5. Enhancing Gibbs sampling method for motif finding in DNA with initial graph representation of sequences.

    PubMed

    Stepančič, Ziva

    2014-10-01

    Finding short patterns with residue variation in a set of sequences is still an open problem in genetics, since motif-finding techniques on DNA and protein sequences are inconclusive on real data sets and their performance varies on different species. Hence, finding new algorithms and evolving established methods are vital to further understanding of genome properties and the mechanisms of protein development. In this work, we present an approach to finding functional motifs in DNA sequences in connection to Gibbs sampling method. Starting points in the search space are partly determined via graphical representation of input sequences opposed to completely random initial points with the standard Gibbs sampling. Our algorithm is evaluated on synthetic as well as on real data sets by using several statistics, such as sensitivity, positive predictive value, specificity, performance, and correlation coefficient. Additionally, a comparison between our algorithm and the basic standard Gibbs sampling algorithm is made to show improvement in accuracy, repeatability, and performance.

  6. Enhancing sample preparation capabilities for accelerator mass spectrometry radiocarbon and radiocalcium studies

    SciTech Connect

    Taylor, R E

    1991-08-20

    With support provided by the LLNL Accelerator Mass Spectrometry Laboratory, the UCR Radiocarbon Laboratory continued its studies involving sample pretreatment and target preparation for both AMS radiocarbon ({sup 14}C) and radiocalcium ({sup 41}Ca) involving applications to archaeologically -- and paleoanthropologically- related samples. With regard to AMS {sup 14}C-related studies, we have extended the development of a series of procedures which have, as their initial goal, the capability to combust several hundred microgram amounts of a chemically-pretreated organic sample and convert the resultant CO{sub 2} to graphitic carbon which will consistently yield relatively high {sup 13}C{sup {minus}} ion currents and blanks which will yield, on a consistent basis, {sup 14}C count rates at or below 0.20% modern, giving an 2 sigma age limit of >50,000 yr BP.

  7. Enhancing sample preparation capabilities for accelerator mass spectrometry radiocarbon and radiocalcium studies

    SciTech Connect

    Taylor, R.E.

    1991-08-20

    With support provided by the LLNL Accelerator Mass Spectrometry Laboratory, the UCR Radiocarbon Laboratory continued its studies involving sample pretreatment and target preparation for both AMS radiocarbon ({sup 14}C) and radiocalcium ({sup 41}Ca) involving applications to archaeologically -- and paleoanthropologically- related samples. With regard to AMS {sup 14}C-related studies, we have extended the development of a series of procedures which have, as their initial goal, the capability to combust several hundred microgram amounts of a chemically-pretreated organic sample and convert the resultant CO{sub 2} to graphitic carbon which will consistently yield relatively high {sup 13}C{sup {minus}} ion currents and blanks which will yield, on a consistent basis, {sup 14}C count rates at or below 0.20% modern, giving an 2 sigma age limit of >50,000 yr BP.

  8. Enhanced sensory sampling precedes self-initiated locomotion in an electric fish.

    PubMed

    Jun, James J; Longtin, André; Maler, Leonard

    2014-10-15

    Cortical activity precedes self-initiated movements by several seconds in mammals; this observation has led into inquiries on the nature of volition. Preparatory neural activity is known to be associated with decision making and movement planning. Self-initiated locomotion has been linked to increased active sensory sampling; however, the precise temporal relationship between sensory acquisition and voluntary movement initiation has not been established. Based on long-term monitoring of sensory sampling activity that is readily observable in freely behaving pulse-type electric fish, we show that heightened sensory acquisition precedes spontaneous initiation of swimming. Gymnotus sp. revealed a bimodal distribution of electric organ discharge rate (EODR) demonstrating down- and up-states of sensory sampling and neural activity; movements only occurred during up-states and up-states were initiated before movement onset. EODR during voluntary swimming initiation exhibited greater trial-to-trial variability than the sound-evoked increases in EODR. The sampling variability declined after voluntary movement onset as previously observed for the neural variability associated with decision making in primates. Spontaneous movements occurred randomly without a characteristic timescale, and no significant temporal correlation was found between successive movement intervals. Using statistical analyses of spontaneous exploratory behaviours and associated preparatory sensory sampling increase, we conclude that electric fish exhibit key attributes of volitional movements, and that voluntary behaviours in vertebrates may generally be preceded by increased sensory sampling. Our results suggest that comparative studies of the neural basis of volition may therefore be possible in pulse-type electric fish, given the substantial homologies between the telencephali of teleost fish and mammals. © 2014. Published by The Company of Biologists Ltd.

  9. Minimizing tip-sample forces and enhancing sensitivity in atomic force microscopy with dynamically compliant cantilevers

    NASA Astrophysics Data System (ADS)

    Keyvani, Aliasghar; Sadeghian, Hamed; Tamer, Mehmet Selman; Goosen, Johannes Frans Loodewijk; van Keulen, Fred

    2017-06-01

    Due to the harmonic motion of the cantilever in Tapping Mode Atomic Force Microscopy, it is seemingly impossible to estimate the tip-sample interactions from the motion of the cantilever. Not directly observing the interaction force, it is possible to damage the surface or the tip by applying an excessive mechanical load. The tip-sample interactions scale with the effective stiffness of the probe. Thus, the reduction of the mechanical load is usually limited by the manufacturability of low stiffness probes. However, the one-to-one relationship between spring constant and applied force only holds when higher modes of the cantilever are not excited. In this paper, it is shown that, by passively tuning higher modes of the cantilever, it is possible to reduce the peak repulsive force. These tuned probes can be dynamically more compliant than conventional probes with the same static spring constant. Both theoretical and experimental results show that a proper tuning of dynamic modes of cantilevers reduces the contact load and increases the sensitivity considerably. Moreover, due to the contribution of higher modes, the tuned cantilevers provide more information on the tip-sample interaction. This extra information from the higher harmonics can be used for mapping and possibly identification of material properties of samples.

  10. Ultra-deep imaging of turbid samples by enhanced photon harvesting

    NASA Astrophysics Data System (ADS)

    Crosignani, Viera; Dvornikov, Alexander; Gratton, Enrico

    2013-02-01

    We constructed an advanced detection system for two-photon fluorescence microscopy that allows us to image in biological tissue and tissue phantoms up to the depth of a few mm with micron resolution. The innovation lies in the detection system which is much more sensitive to low level fluorescence signals than the fluorescence detection configuration used in conventional two-photon fluorescence microscopes. A wide area photocathode photomultiplier tube (PMT) was used to detect fluorescence photons directly from a wide (1 inch diameter) area of the turbid sample, as opposed to the photon collection by the microscope objective which can only collect light from a relatively small area of the sample. The optical path between the sample and the photocathode is refractive index matched to curtail losses at the boundaries due to reflections. The system has been successfully employed in the imaging of tissue phantoms simulating brain optical properties and in biological tissues, such as murine small intestine, colon, tumors, and other samples. The system has in-depth fluorescence lifetime imaging (FLIM) capabilities and is also highly suitable for SHG signal detection, such as collagen fibers and muscles, due to the intrinsically forward-directed propagation of SHG photons.

  11. Individualized Sampling Parameters for Behavioral Observations: Enhancing the Predictive Validity of Competing Stimulus Assessments

    ERIC Educational Resources Information Center

    DeLeon, Iser G.; Toole, Lisa M.; Gutshall, Katharine A.; Bowman, Lynn G.

    2005-01-01

    Recent studies have used pretreatment analyses, termed competing stimulus assessments, to identify items that most effectively displace the aberrant behavior of individuals with developmental disabilities. In most studies, there appeared to have been no systematic basis for selecting the sampling period (ranging from 30 s to 10 min) in which items…

  12. Development in release testing of topical dosage forms: use of the Enhancer Cell with automated sampling.

    PubMed

    Rege, P R; Vilivalam, V D; Collins, C C

    1998-09-01

    The aim of this study was to evaluate an automated method using the Enhancer Cell and compare the release of the corticosteroid triamcinolone acetonide (TA) from commercial semisolid formulations. The method used a modified USP Apparatus 2 using the Enhancer Cell in 200 ml capacity flasks instead of the standard 900 ml flasks. The additional equipment included an adapter plate to position the flasks in the center, a cover to reduce the receptor phase evaporation and smaller sized (1/4 in.) shaft and collets. All products were evaluated prior to their expiration date. Effects of system variables such as the temperature and composition of the receptor medium, stirring speed, and the choice of membrane on the drug release were evaluated. Statistical analysis was carried out using SAS Ver. 6.07 and the slopes and intercepts (of the cumulative release/unit area versus square root of time plots) were compared. TA release was a linear function of the square root of time (P < or = 0.0001), in accordance with Higuchi's model (r2 > or = 0.9 in most cases). Temperature (32 and 37 degrees C) did not affect the drug release (P > 0.32) but a significantly higher release rate was observed (P < or = 0.0001) at 50 degrees C. Stirring speed (50, 100, 200 rpm) (P > 0.26) and receptor media composition (38 and 76% ethanol) (P > 0.68) did not significantly alter the release rates. Membrane selection (regenerated cellulose, polyethylene, and rat skin) was found to be a significant variable (P < or = 0.004). This study demonstrates the use of the Enhancer Cell as an automated quality control tool in the in vitro release testing procedure for semisolid drug formulations.

  13. Determination of 2-methoxyestradiol in serum samples and pharmaceutical preparations by silver nanoparticles-enhanced chemiluminescence.

    PubMed

    Zhang, Min; Xiao, Xiangqin; Zeng, Wenyuan; Zeng, Xiaoying; Yao, Hanchun

    2014-03-01

    Silver nanoparticles (AgNPs) exhibited better chemiluminescence (CL) catalysis activity and smaller nanoparticles have stronger catalysis ability in luminol-K3Fe(CN)6 system among the synthesized AgNPs of different size. 10±2 nm nanoparticles was used as catalysts to enhance the reaction sensitivity. It was found that the CL intensity of AgNPs-luminol-K3Fe(CN)6 was strongly inhibited in the presence of 2-methoxyestradiol (2-ME) and the relative CL intensity was in linear correlation with the concentration of 2-ME. Thus, the silver nanoparticles-enhanced CL method for the determination of 2-ME was developed. The proposed method has a detection limit (3 Sb/K) of 5.0×10(-10) mol L(-1) with a relative standard deviation of 0.75% for 5.0×10(-8) mol L(-1) 2-ME. The method was successfully applied for determination of 2-ME in human serum and pharmaceutical preparations. The possible CL reaction mechanism was also discussed briefly. Oxygen radicals played an important role in the catalytic process.

  14. A critical evaluation of sample extraction techniques for enhanced proteomic analysis of recalcitrant plant tissues.

    PubMed

    Saravanan, Ramu S; Rose, Jocelyn K C

    2004-09-01

    Most published proteomics studies of bulk plant tissues use a procedure in which proteins are precipitated with trichloroacetic acid (TCA) and acetone (TCA-A), but few attempts have been made to contrast this approach in a systematic way with alternative methods against a spectrum of tissues. To address this, TCA-A was compared with another acetone-based protocol (TCA-B) or a phenol (Phe)-based method, targeting a range of tomato tissues and three species of fruits that contain high levels of contaminating compounds: banana, avocado and orange. The Phe method gave a higher protein yield and typically greater resolution and spot intensity, particularly with extracts from tissues containing high levels of soluble polysaccharides. The methods also generated remarkably different two-dimensional gel electrophoresis (2-DE) protein spot patterns. Peptide mass fingerprinting was used to identify polypeptides that were common to multiple extracts or uniquely present in one extract type. While no clear pattern emerged to explain the basis for the differential protein extraction, it was noted that the Phe method showed enhanced extraction of glycoproteins. These results suggest that the Phe protocol is highly effective with more recalcitrant tissues and that a combination of TCA-A and Phe methods provides enhanced 2-DE based proteomic analyses of most plant tissues.

  15. Enhancing temporal cues to voice pitch in continuous interleaved sampling cochlear implants

    NASA Astrophysics Data System (ADS)

    Green, Tim; Faulkner, Andrew; Rosen, Stuart

    2004-10-01

    The limited spectral resolution of cochlear implant systems means that voice pitch perception depends on weak temporal envelope cues. Enhancement of such cues was investigated in implant users and in acoustic simulations. Subjects labeled the pitch movement of processed synthetic diphthongal glides. In standard processing, noise carriers (simulations) or pulse trains (implant users) were modulated by 400 Hz low-pass envelopes. In modified processing, carriers were modulated by two components: (1) Slow-rate (<32 Hz) envelope modulations, conveying dynamic spectral shape changes crucial for speech; (2) a simplified waveform (e.g., a sawtooth) matching the periodicity of the input diphthong. In both normal listeners and implant users performance was better with modified processing, though temporal envelope cues were less effective with higher F0. Factors contributing to the advantage for modified processing may include increased modulation depth and use of a modulation waveform featuring a rapid onset in each period, resulting in a clearer representation of F0 in the neural firing pattern. Eliminating slow-rate spectral dynamics, so that within-channel amplitude changes solely reflected F0, showed that dynamic spectral variation obscured temporal pitch cues. Though significant, advantages for modified processing were small, suggesting that the potential for developing strategies delivering enhanced pitch perception is limited. .

  16. Application of Enhanced Sampling Monte Carlo Methods for High-Resolution Protein-Protein Docking in Rosetta

    PubMed Central

    Zhang, Zhe; Schindler, Christina E. M.; Lange, Oliver F.; Zacharias, Martin

    2015-01-01

    The high-resolution refinement of docked protein-protein complexes can provide valuable structural and mechanistic insight into protein complex formation complementing experiment. Monte Carlo (MC) based approaches are frequently applied to sample putative interaction geometries of proteins including also possible conformational changes of the binding partners. In order to explore efficiency improvements of the MC sampling, several enhanced sampling techniques, including temperature or Hamiltonian replica exchange and well-tempered ensemble approaches, have been combined with the MC method and were evaluated on 20 protein complexes using unbound partner structures. The well-tempered ensemble method combined with a 2-dimensional temperature and Hamiltonian replica exchange scheme (WTE-H-REMC) was identified as the most efficient search strategy. Comparison with prolonged MC searches indicates that the WTE-H-REMC approach requires approximately 5 times fewer MC steps to identify near native docking geometries compared to conventional MC searches. PMID:26053419

  17. Sampling of prenatal and postnatal offspring from individual rat dams enhances animal use without compromising development

    NASA Technical Reports Server (NTRS)

    Alberts, J. R.; Burden, H. W.; Hawes, N.; Ronca, A. E.

    1996-01-01

    To assess prenatal and postnatal developmental status in the offspring of a group of animals, it is typical to examine fetuses from some of the dams as well as infants born to the remaining dams. Statistical limitations often arise, particularly when the animals are rare or especially precious, because all offspring of the dam represent only a single statistical observation; littermates are not independent observations (biologically or statistically). We describe a study in which pregnant laboratory rats were laparotomized on day 7 of gestation (GD7) to ascertain the number and distribution of uterine implantation sites and were subjected to a simulated experience on a 10-day space shuttle flight. After the simulated landing on GD18, rats were unilaterally hysterectomized, thus providing a sample of fetuses from 10 independent uteruses, followed by successful vaginal delivery on GD22, yielding postnatal samples from 10 uteruses. A broad profile of maternal and offspring morphologic and physiologic measures indicated that these novel sampling procedures did not compromise maternal well-being and maintained normal offspring development and function. Measures included maternal organ weights and hormone concentrations, offspring body size, growth, organ weights, sexual differentiation, and catecholamine concentrations.

  18. Sampling of prenatal and postnatal offspring from individual rat dams enhances animal use without compromising development

    NASA Technical Reports Server (NTRS)

    Alberts, J. R.; Burden, H. W.; Hawes, N.; Ronca, A. E.

    1996-01-01

    To assess prenatal and postnatal developmental status in the offspring of a group of animals, it is typical to examine fetuses from some of the dams as well as infants born to the remaining dams. Statistical limitations often arise, particularly when the animals are rare or especially precious, because all offspring of the dam represent only a single statistical observation; littermates are not independent observations (biologically or statistically). We describe a study in which pregnant laboratory rats were laparotomized on day 7 of gestation (GD7) to ascertain the number and distribution of uterine implantation sites and were subjected to a simulated experience on a 10-day space shuttle flight. After the simulated landing on GD18, rats were unilaterally hysterectomized, thus providing a sample of fetuses from 10 independent uteruses, followed by successful vaginal delivery on GD22, yielding postnatal samples from 10 uteruses. A broad profile of maternal and offspring morphologic and physiologic measures indicated that these novel sampling procedures did not compromise maternal well-being and maintained normal offspring development and function. Measures included maternal organ weights and hormone concentrations, offspring body size, growth, organ weights, sexual differentiation, and catecholamine concentrations.

  19. Specific PCR, bacterial culture, serology and pharyngeal sampling to enhance the aetiological diagnosis of cellulitis.

    PubMed

    Toleman, Michelle S; Vipond, I Barry; Brindle, Richard

    2016-01-01

    It is often difficult to obtain a bacteriological diagnosis in patients with cellulitis. We examined the utility of molecular techniques and skin and throat cultures, as well as serology, in providing evidence of either Staphylococcus aureus or group A Streptococcus (GAS) presence inpatients with cellulitis. Samples were collected from patients with a clinical diagnosis of cellulitis who were recruited into a prospective placebo-controlled clinical trial (C4C study, EudraCT 2013-001218-14). Specific PCR, paired serology and culture for both organisms were carried out on a variety of samples where appropriate. Despite utilizing a range of diagnostic methods,a bacteriological diagnosis was only achieved in 43 % of patients with a clinical diagnosis of cellulitis. Seventeen per cent of patients tested positive for GAS by any method but only 4 % were positive by PCR, whilst S. aureus was detected in 34% of samples. Bacterial diagnosis in cases of cellulitis remains challenging. This is probably due to a very low bacterial burden with toxin production resulting in inflammation mediating skin damage. Further consideration for the need for long courses of antimicrobial therapy for cellulitis therefore appears merited.

  20. Comparison of field-enhanced and pressure-assisted field-enhanced sample injection techniques for the analysis of water-soluble vitamins using CZE.

    PubMed

    Liu, Qingqing; Liu, Yaling; Guan, Yu; Jia, Li

    2009-04-01

    A new online concentration method, namely pressure-assisted field-enhanced sample injection (PA-FESI), was developed and compared with FESI for the analysis of water-soluble vitamins by CZE with UV detection. In PA-FESI, negative voltage and positive pressure were simultaneously applied to initialize PA-FESI. PA-FESI uses the hydrodynamic flow generated by the positive pressure to counterbalance the reverse EOF in the capillary column during electrokinetic sample injection, which allowed a longer injection time than usual FESI mode without compromising the separation efficiency. Using the PA-FESI method, the LODs of the vitamins were at ng/mL level based on the S/N of 3 and the RSDs of migration time and peak area for each vitamin (1 microg/mL) were less than 5.1%. The developed method was applied to the analysis of water-soluble vitamins in corns.

  1. Enhanced Stability of Blood Matrices Using a Dried Sample Spot Assay to Measure Human Butyrylcholinesterase Activity and Nerve Agent Adducts

    PubMed Central

    Perez, Jonas W.; Pantazides, Brooke G.; Watson, Caroline M.; Thomas, Jerry D.; Blake, Thomas A.; Johnson, Rudolph C.

    2015-01-01

    Dried matrix spots are safer to handle and easier to store than wet blood products, but factors such as intra-spot variability and unknown sample volumes have limited their appeal as a sampling format for quantitative analyses. In this work, we introduce a dried spot activity assay for quantifying butyrylcholinesterase (BChE) specific activity which is BChE activity normalized to the total protein content in a sample spot. The method was demonstrated with blood, serum, and plasma spotted on specimen collection devices (cards) which were extracted to measure total protein and BChE activity using a modified Ellman assay. Activity recovered from dried spots was ∼80% of the initial spotted activity for blood and >90% for plasma and serum. Measuring total protein in the sample and calculating specific activity substantially improved quantification and reduced intra-spot variability. Analyte stability of nerve agent adducts was also evaluated, and the results obtained via BChE-specific activity measurements were confirmed by quantification of BChE adducts using a previously established LC-MS/MS method. The spotted samples were up to 10-times more resistant to degradation compared to unspotted control samples when measuring BChE inhibition by the nerve agents sarin and VX. Using this method, both BChE activity and adducts can be accurately measured from a dried sample spot. This use of a dried sample spot with normalization to total protein is robust, demonstrates decreased intra-spot variability without the need to control for initial sample volume, and enhances analyte stability. PMID:25955132

  2. Determination of low-aliphatic aldehydes indoors by micellar electrokinetic chromatography using sample dissolution manipulation for signal enhancement.

    PubMed

    Pereira, Elisabete A; Cardoso, Arnaldo A; Tavares, Marina F M

    2003-02-01

    This work describes a novel approach for the analysis of selected aldehydes (formaldehyde, acetaldehyde, propionaldehyde, and acrolein) and acetone in environmental samples using micellar electrokinetic chromatography (MEKC). The method is based on the reaction of carbonyl compounds with 3-methyl-2-benzothiazoline hydrazone (MBTH) that gives an azine intermediate with maximum absorbance at 216 nm. A systematic evaluation of sample dissolution medium was conducted as a means to enhancing sensitivity. In the best condition, samples were dissolved in 0.030 mol.L(-1) tetraborate solution. This condition presented enhancement factors in the range of 35-54 for the aldehydes under investigation, computed as the improvement of the concentration limits of detection (LODs) with reference to the sample dissolved in pure water. The running buffer was 0.020 mol.L(-1) tetraborate, pH 9.3, containing 0.050 mol.L(-1) sodium dodecyly sulfate (SDS). The overall methodology presented several advantages over established methods for aldehydes. Worthy mentioning that MBTH is available in high purity degree, dispensing laborious reagent purification procedures. A few method validation parameters were determined revealing good migration time repeatability (< 2.5% coefficient of variation, CV) and area repeatability (< 4% CV), excellent linearity (20-120 micro g/L, r > 0.995) and adequate sensitivity for environmental applications. The LODs with respect to each single aldehyde were in the range of 0.54-4.0 micro g.L(-1) and 11 micro g.L(-1) for acetone. The methodology was applied to the determination of aldehydes indoors. Samples were collected in an impinger flask containing 0.05% MBTH solution, at a flow rate of 0.80 L.min(-1), during 2.5 h, at different times during the day. The most abundant carbonyls in the samples were acetone, followed by formaldehyde and acetaldehyde, with estimate peak concentrations of 452, 5.2 and 2.2 ppbv, respectively.

  3. Classification of bacterial samples as negative or positive for a UTI and antibiogram using surface enhanced Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Kastanos, Evdokia; Hadjigeorgiou, Katerina; Kyriakides, Alexandros; Pitris, Costas

    2011-03-01

    Urinary tract infection (UTI) diagnosis requires an overnight culture to identify a sample as positive or negative for a UTI. Additional cultures are required to identify the pathogen responsible for the infection and to test its sensitivity to antibiotics. A rise in ineffective treatments, chronic infections, rising health care costs and antibiotic resistance are some of the consequences of this prolonged waiting period of UTI diagnosis. In this work, Surface Enhanced Raman Spectroscopy (SERS) is used for classifying bacterial samples as positive or negative for UTI. SERS spectra of serial dilutions of E.coli bacteria, isolated from a urine culture, were classified as positive (105-108 cells/ml) or negative (103-104 cells/ml) for UTI after mixing samples with gold nanoparticles. A leave-one-out cross validation was performed using the first two principal components resulting in the correct classification of 82% of all samples. Sensitivity of classification was 88% and specificity was 67%. Antibiotic sensitivity testing was also done using SERS spectra of various species of gram negative bacteria collected 4 hours after exposure to antibiotics. Spectral analysis revealed clear separation between the spectra of samples exposed to ciprofloxacin (sensitive) and amoxicillin (resistant). This study can become the basis for identifying urine samples as positive or negative for a UTI and determining their antibiogram without requiring an overnight culture.

  4. Examination of pterins using surface-enhanced Raman spectroscopy using low-volume samples

    NASA Astrophysics Data System (ADS)

    Mehigan, Sam; Smyth, Ciarán.; McCabe, Eithne M.

    2013-02-01

    Raman spectroscopy is a very useful tool for analysing compounds, however its ability to detect low concentrations of a substance are very limited. Surface Enhanced Raman Spectroscopy (SERS) overcomes that issue and is reported to have achieved single molecule detection. Its main shortcoming is the reproducibility of SERS spectra. The variation in signal strength prevents SERS from being usable as a quantitative analytical technique. This variability have been investigated in this work and key factors in improving reproducibility have been considered. Pterins, such as xanthopterin are studied in this paper. Pterins are a group of biological compounds that are found in nature in colour pigmentation and in mammal's metabolic pathways. Moreover, they have been identified in abnormal concentrations in the urine of people suffering from certain kinds of cancer. The potential for pterin's use as a cancer diagnostic points to the importance of SERS detection for pterins.

  5. Mapping Chemical and Structural Composition of Pharmaceutical and Biological Samples by Raman, Surface-Enhanced Raman and Fluorescence Spectral Imaging

    NASA Astrophysics Data System (ADS)

    Chourpa, Igor; Cohen-Jonathan, Simone; Dubois, Pierre

    Raman spectroscopy is an analytical technique recognised for its structural and conformational specificity. The efficient discrimination of molecular species by Raman is particularly potent for multidimensional microscopic imaging of complex biological environment, as demonstrated in the present book. The commonly admitted problem of Raman, low sensitivity, can often be circumvented due to high output instruments and via approaches like RRS (resonance Raman scattering), SERS (surface-enhanced Raman scattering), TERS (tip-enhanced Raman scattering) or CARS (coherent anti-Stokes Raman scattering). In contrast to the latter, RRS and SERS are realizable with less sophisticated set-up based on common Raman systems. Although more invasive than RRS, SERS provides better sensitivity and quenching of fluorescence. SERRS (surface-enhanced resonance Raman scattering) spectroscopy can be used in coupling with fluorescence and competes in selectivity and sensitivity with spectrofluorimetry. In the chapter below, we use recent applications made in our group to illustrate the use of Raman and SERRS spectral imaging for characterization of biological samples (animal subcutaneous tissue, human cancer cells) and pharmaceutical samples (microparticles for drug delivery, fibres for wound dressing). After a brief description of experimental details on spectral imaging, the chapter will focus on results concerning (i) biocompatible pharmaceutical materials made of alginates and (ii) anticancer drugs in pharmaceutical forms and in biological systems.

  6. Avoiding Ethanol Presence in DNA Samples Enhances the Performance of Ultraviolet Resonance Raman Spectroscopy Analysis.

    PubMed

    Cammisuli, Francesca; Pascolo, Lorella; Morgutti, Marcello; Gessini, Alessandro; Masciovecchio, Claudio; D'Amico, Francesco

    2017-01-01

    Ethanol is an essential chemical reagent in DNA preparation as its use increases the yield of extraction. All methodologies for DNA isolation involve the use of ethanol in order to prevent DNA dissolution in water and to optimize the binding of DNA to chromatographic membranes. In this note, we show how the presence of ethanol traces in DNA aqueous solution affects ultraviolet Raman spectra, leading to possible misinterpretations. We report a simple method to remove the ethanol Raman features from the spectra, based on heating the DNA sample at 80 ℃, followed by a slow cooling procedure.

  7. Enhancing backbone sampling in Monte Carlo simulations using internal coordinates normal mode analysis.

    PubMed

    Gil, Victor A; Lecina, Daniel; Grebner, Christoph; Guallar, Victor

    2016-10-15

    Normal mode methods are becoming a popular alternative to sample the conformational landscape of proteins. In this study, we describe the implementation of an internal coordinate normal mode analysis method and its application in exploring protein flexibility by using the Monte Carlo method PELE. This new method alternates two different stages, a perturbation of the backbone through the application of torsional normal modes, and a resampling of the side chains. We have evaluated the new approach using two test systems, ubiquitin and c-Src kinase, and the differences to the original ANM method are assessed by comparing both results to reference molecular dynamics simulations. The results suggest that the sampled phase space in the internal coordinate approach is closer to the molecular dynamics phase space than the one coming from a Cartesian coordinate anisotropic network model. In addition, the new method shows a great speedup (∼5-7×), making it a good candidate for future normal mode implementations in Monte Carlo methods.

  8. Informatics Enhanced SNP Microarray Analysis of 30 Miscarriage Samples Compared to Routine Cytogenetics

    PubMed Central

    Lathi, Ruth B.; Loring, Megan; Massie, Jamie A. M.; Demko, Zachary P.; Johnson, David; Sigurjonsson, Styrmir; Gemelos, George; Rabinowitz, Matthew

    2012-01-01

    Purpose The metaphase karyotype is often used as a diagnostic tool in the setting of early miscarriage; however this technique has several limitations. We evaluate a new technique for karyotyping that uses single nucleotide polymorphism microarrays (SNP). This technique was compared in a blinded, prospective fashion, to the traditional metaphase karyotype. Methods Patients undergoing dilation and curettage for first trimester miscarriage between February and August 2010 were enrolled. Samples of chorionic villi were equally divided and sent for microarray testing in parallel with routine cytogenetic testing. Results Thirty samples were analyzed, with only four discordant results. Discordant results occurred when the entire genome was duplicated or when a balanced rearrangement was present. Cytogenetic karyotyping took an average of 29 days while microarray-based karytoyping took an average of 12 days. Conclusions Molecular karyotyping of POC after missed abortion using SNP microarray analysis allows for the ability to detect maternal cell contamination and provides rapid results with good concordance to standard cytogenetic analysis. PMID:22403611

  9. Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation.

    PubMed

    Iida, Shinji; Nakamura, Haruki; Higo, Junichi

    2016-06-15

    We introduce various, recently developed, generalized ensemble methods, which are useful to sample various molecular configurations emerging in the process of protein-protein or protein-ligand binding. The methods introduced here are those that have been or will be applied to biomolecular binding, where the biomolecules are treated as flexible molecules expressed by an all-atom model in an explicit solvent. Sampling produces an ensemble of conformations (snapshots) that are thermodynamically probable at room temperature. Then, projection of those conformations to an abstract low-dimensional space generates a free-energy landscape. As an example, we show a landscape of homo-dimer formation of an endothelin-1-like molecule computed using a generalized ensemble method. The lowest free-energy cluster at room temperature coincided precisely with the experimentally determined complex structure. Two minor clusters were also found in the landscape, which were largely different from the native complex form. Although those clusters were isolated at room temperature, with rising temperature a pathway emerged linking the lowest and second-lowest free-energy clusters, and a further temperature increment connected all the clusters. This exemplifies that the generalized ensemble method is a powerful tool for computing the free-energy landscape, by which one can discuss the thermodynamic stability of clusters and the temperature dependence of the cluster networks.

  10. Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation

    PubMed Central

    Iida, Shinji; Nakamura, Haruki; Higo, Junichi

    2016-01-01

    We introduce various, recently developed, generalized ensemble methods, which are useful to sample various molecular configurations emerging in the process of protein–protein or protein–ligand binding. The methods introduced here are those that have been or will be applied to biomolecular binding, where the biomolecules are treated as flexible molecules expressed by an all-atom model in an explicit solvent. Sampling produces an ensemble of conformations (snapshots) that are thermodynamically probable at room temperature. Then, projection of those conformations to an abstract low-dimensional space generates a free-energy landscape. As an example, we show a landscape of homo-dimer formation of an endothelin-1-like molecule computed using a generalized ensemble method. The lowest free-energy cluster at room temperature coincided precisely with the experimentally determined complex structure. Two minor clusters were also found in the landscape, which were largely different from the native complex form. Although those clusters were isolated at room temperature, with rising temperature a pathway emerged linking the lowest and second-lowest free-energy clusters, and a further temperature increment connected all the clusters. This exemplifies that the generalized ensemble method is a powerful tool for computing the free-energy landscape, by which one can discuss the thermodynamic stability of clusters and the temperature dependence of the cluster networks. PMID:27288028

  11. Interleaved variable density sampling with a constrained parallel imaging reconstruction for dynamic contrast-enhanced MR angiography.

    PubMed

    Wang, Kang; Busse, Reed F; Holmes, James H; Beatty, Philip J; Brittain, Jean H; Francois, Christopher J; Reeder, Scott B; Du, Jiang; Korosec, Frank R

    2011-08-01

    For MR applications such as contrast-enhanced MR angiography, it is desirable to achieve simultaneously high spatial and temporal resolution. The current clinical standard uses view-sharing methods combined with parallel imaging; however, this approach still provides limited spatial and temporal resolution. To improve on the clinical standard, we present an interleaved variable density (IVD) sampling method that pseudorandomly undersamples each individual frame of a 3D Cartesian ky-kz plane combined with parallel imaging acceleration. From this dataset, time-resolved images are reconstructed with a method that combines parallel imaging with a multiplicative constraint. Total acceleration factors on the order of 20 are achieved for contrast-enhanced MR angiography of the lower extremities, and improvements in temporal fidelity of the depiction of the contrast bolus passage are demonstrated relative to the clinical standard. Copyright © 2011 Wiley-Liss, Inc.

  12. Sampling Error: Impact on the Quantitative Analysis of Nanoparticle-Based Surface-Enhanced Raman Scattering Immunoassays.

    PubMed

    Crawford, Alexis C; Skuratovsky, Aleksander; Porter, Marc D

    2016-06-21

    This paper examines the impact of the sampling error caused by the small size of the focused laser spot when using surface-enhanced Raman scattering (SERS) as a quantitative readout tool to analyze a sandwich immunoassay. The assay consists of a thin-film gold substrate that is modified with a layer of capture monoclonal antibodies (mAbs) and extrinsic Raman labels (ERLs) that consist of gold nanoparticle cores (60 nm diameter) coated with a monolayer of a Raman reporter molecule and a layer of human IgG mAbs to tag the captured antigen. The contribution of sampling error to the measurement is delineated first by constructing and analyzing an antigenic random accumulation model; this is followed by an experimental study of the analysis of an assay substrate using two different laser spot sizes. Both sets of findings indicate that the analysis with a small laser spot can lead to a sampling error (i.e., undersampling) much like that found when the size of a measured soil sample fails to accurately match that of a larger, more representative sample. That is, the smaller the laser spot size, the larger probable deviation in the accuracy of the measurement and the greater the imprecision of the measurement. Possible implications of these results with respect to the general application of SERS for quantitative measurements are also briefly discussed.

  13. Compact OAM microscope for edge enhancement of biomedical and object samples

    NASA Astrophysics Data System (ADS)

    Gozali, Richard; Nguyen, Thien-An; Bendau, Ethan; Alfano, Robert R.

    2017-09-01

    The production of orbital angular momentum (OAM) by using a q-plate, which functions as an electrically tunable spatial frequency filter, provides a simple and efficient method of edge contrast in biological and medical sample imaging for histological evaluation of tissue, smears, and PAP smears. An instrument producing OAM, such as a q-plate, situated at the Fourier plane of a 4f lens system, similar to the use of a high-pass spatial filter, allows the passage of high spatial frequencies and enables the production of an image with highly illuminated edges contrasted against a dark background for both opaque and transparent objects. Compared with ordinary spiral phase plates and spatial light modulators, the q-plate has the added advantage of electric control and tunability.

  14. Enhanced Molecular Dynamics Sampling Methods Applied to Existing and Novel Polypeptide Systems

    NASA Astrophysics Data System (ADS)

    Hayre, Natha Robert

    This thesis consists of the application of certain advanced physics-based theoretical-computational approaches to the exploration of the structure and dynamics of polypeptides --- the key chemical constituents of proteins, a class of biologically essential molecules. Improved statistical-mechanical sampling methods and advanced computational methods were combined in studies that informed both theory and experiment. Part of this work was devoted to the development of improved sampling capabilities simultaneously on three fronts: (1) the ubiquitous use of generalized-ensemble techniques to broadly explore molecular energy landscapes, (2) efficient approximative multi-scale integration techniques for molecular dynamics, and (3) the deployment of novel parallel computational facilities capable of order-of-magnitude speed-ups in the evaluation of biomolecular models. Herein, biophysical experiments inform molecular-mechanical theory and vice versa. In one study, the known folding stability of a small beta-hairpin peptide was compared with the same from simulations using variant model parameterizations, while the more accurate of these latter enabled insight into mechanisms for stability. In another study, the observed stability of a native left-handed beta-helical peptide segment verified the accuracy of two refined parameter sets, while further simulations on diverse sequences suggest mechanisms for the folding behavior of the beta-helical motif. Furthermore, the sequences that were chosen for this latter study open up exciting avenues for more systematic theoretical study of homopolypeptides such as polyglutamine; variants of prion protein and other amyloidogenic sequences; and heuristically-designed super-stable beta-helical sequences. Indeed, the relative stability analysis presented herein is general to any structure or sequence, and could be extended to the study of other rare or novel folding motifs beyond the beta-helix.

  15. Electro-enhanced hollow fiber membrane liquid phase microextraction of Cr(VI) oxoanions in drinking water samples.

    PubMed

    Chanthasakda, Nattaporn; Nitiyanontakit, Sira; Varanusupakul, Pakorn

    2016-02-01

    Hollow fiber membrane liquid phase microextraction (HF-LPME) of metal oxoanions was studied using an ionic carrier enhanced by the application of an electric field (electro-enhanced HF-LPME). The Cr(VI) oxoanion was used as the model. The transportation of Cr(VI) oxoanions across the supported liquid membrane (SLM) was explored via the ion-exchange process and electrokinetic migration. The type of SLM, type of acceptor solution, extraction time, electric potential, and stirring rate were investigated and optimized using MilliQ water. Electro-enhanced HF-LPME provided a much higher enrichment factor compared to conventional HF-LPME (no electric potential) for the same extraction time. A mixture of an anion exchange carrier (methyltrialkyl-ammonium chloride, Aliquat 336) in the SLM facilitated the transportation of Cr(VI) oxoanions. The SLM that gave the best performance was 1-heptanol mixed with 5% Aliquat 336 with 1M NaOH as the acceptor. Linearity was obtained in the working range of 3-15 µg L(-1) Cr(VI) (R(2)>0.99) at 30 V with a 5 min extraction time. The limit of detection was below 5 µg L(-1). The relative standard deviation was less than 12%. The method was applied to drinking water samples. The recoveries of spiked Cr(VI) in drinking water samples were in the range of 96-101% based on the matrix-matched calibration curves. The method was limited to samples containing low levels of ions due to the occurrence of electrolysis. The type of SLM, particularly regarding its resistance, should be tuned to control this problematic phenomenon. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Mimicking coarse-grained simulations without coarse-graining: Enhanced sampling by damping short-range interactions

    NASA Astrophysics Data System (ADS)

    Wei, Dongshan; Wang, Feng

    2010-08-01

    The damped-short-range-interaction (DSRI) method is proposed to mimic coarse-grained simulations by propagating an atomistic scale system on a smoothed potential energy surface. The DSRI method has the benefit of enhanced sampling provided by a typical coarse-grained simulation without the need to perform coarse-graining. Our method was used to simulate liquid water, alanine dipeptide folding, and the self-assembly of dimyristoylphosphatidylcholine lipid. In each case, our method appreciably accelerated the dynamics without significantly changing the free energy surface. Additional insights from DSRI simulations and the promise of coupling our DSRI method with Hamiltonian replica-exchange molecular dynamics are discussed.

  17. A comb-sampling method for enhanced mass analysis in linear electrostatic ion traps

    SciTech Connect

    Greenwood, J. B.; Kelly, O.; Calvert, C. R.; Duffy, M. J.; King, R. B.; Belshaw, L.; Graham, L.; Alexander, J. D.; Williams, I. D.; Bryan, W. A.; Turcu, I. C. E.; Cacho, C. M.; Springate, E.

    2011-04-15

    In this paper an algorithm for extracting spectral information from signals containing a series of narrow periodic impulses is presented. Such signals can typically be acquired by pickup detectors from the image-charge of ion bunches oscillating in a linear electrostatic ion trap, where frequency analysis provides a scheme for high-resolution mass spectrometry. To provide an improved technique for such frequency analysis, we introduce the CHIMERA algorithm (Comb-sampling for High-resolution IMpulse-train frequency ExtRAaction). This algorithm utilizes a comb function to generate frequency coefficients, rather than using sinusoids via a Fourier transform, since the comb provides a superior match to the data. This new technique is developed theoretically, applied to synthetic data, and then used to perform high resolution mass spectrometry on real data from an ion trap. If the ions are generated at a localized point in time and space, and the data is simultaneously acquired with multiple pickup rings, the method is shown to be a significant improvement on Fourier analysis. The mass spectra generated typically have an order of magnitude higher resolution compared with that obtained from fundamental Fourier frequencies, and are absent of large contributions from harmonic frequency components.

  18. Forensic Sampling and Analysis from a Single Substrate: Surface-Enhanced Raman Spectroscopy Followed by Paper Spray Mass Spectrometry.

    PubMed

    Fedick, Patrick W; Bills, Brandon J; Manicke, Nicholas E; Cooks, R Graham

    2017-10-03

    Sample preparation is the most common bottleneck in the analysis and processing of forensic evidence. Time-consuming steps in many forensic tests involve complex separations, such as liquid and gas chromatography or various types of extraction techniques, typically coupled with mass spectrometry (e.g., LC-MS). Ambient ionization ameliorates these slow steps by reducing or even eliminating sample preparation. While some ambient ionization techniques have been adopted by the forensic community, there is significant resistance to discarding chromatography as most forensic analyses require both an identification and a confirmation technique. Here, we describe the use of a paper substrate, the surface of which has been inkjet printed with silver nanoparticles, for surface enhanced Raman spectroscopy (SERS). The same substrate can also act as the paper substrate for paper spray mass spectrometry. The coupling of SERS and paper spray ionization creates a quick, forensically feasible combination.

  19. Exploring Thermoresponsive Affinity Agents to Enhance Microdialysis Sampling Efficiency of Proteins

    NASA Astrophysics Data System (ADS)

    Vasicek, Thaddeus

    with the new affinity agents will lead to increased affinity agent use for microdiaylsis protein sampling.

  20. Enhanced conformational sampling technique provides an energy landscape view of large-scale protein conformational transitions.

    PubMed

    Shao, Qiang

    2016-10-26

    Large-scale conformational changes in proteins are important for their functions. Tracking the conformational change in real time at the level of a single protein molecule, however, remains a great challenge. In this article, we present a novel in silico approach with the combination of normal mode analysis and integrated-tempering-sampling molecular simulation (NMA-ITS) to give quantitative data for exploring the conformational transition pathway in multi-dimensional energy landscapes starting only from the knowledge of the two endpoint structures of the protein. The open-to-closed transitions of three proteins, including nCaM, AdK, and HIV-1 PR, were investigated using NMA-ITS simulations. The three proteins have varied structural flexibilities and domain communications in their respective conformational changes. The transition state structure in the conformational change of nCaM and the associated free-energy barrier are in agreement with those measured in a standard explicit-solvent REMD simulation. The experimentally measured transition intermediate structures of the intrinsically flexible AdK are captured by the conformational transition pathway measured here. The dominant transition pathways between the closed and fully open states of HIV-1 PR are very similar to those observed in recent REMD simulations. Finally, the evaluated relaxation times of the conformational transitions of three proteins are roughly at the same level as reported experimental data. Therefore, the NMA-ITS method is applicable for a variety of cases, providing both qualitative and quantitative insights into the conformational changes associated with the real functions of proteins.

  1. Order parameter free enhanced sampling of the vapor-liquid transition using the generalized replica exchange method

    NASA Astrophysics Data System (ADS)

    Lu, Qing; Kim, Jaegil; Straub, John E.

    2013-03-01

    The generalized Replica Exchange Method (gREM) is extended into the isobaric-isothermal ensemble, and applied to simulate a vapor-liquid phase transition in Lennard-Jones fluids. Merging an optimally designed generalized ensemble sampling with replica exchange, gREM is particularly well suited for the effective simulation of first-order phase transitions characterized by "backbending" in the statistical temperature. While the metastable and unstable states in the vicinity of the first-order phase transition are masked by the enthalpy gap in temperature replica exchange method simulations, they are transformed into stable states through the parameterized effective sampling weights in gREM simulations, and join vapor and liquid phases with a succession of unimodal enthalpy distributions. The enhanced sampling across metastable and unstable states is achieved without the need to identify a "good" order parameter for biased sampling. We performed gREM simulations at various pressures below and near the critical pressure to examine the change in behavior of the vapor-liquid phase transition at different pressures. We observed a crossover from the first-order phase transition at low pressure, characterized by the backbending in the statistical temperature and the "kink" in the Gibbs free energy, to a continuous second-order phase transition near the critical pressure. The controlling mechanisms of nucleation and continuous phase transition are evident and the coexistence properties and phase diagram are found in agreement with literature results.

  2. Ultrasound-assisted surfactant-enhanced emulsification microextraction for the determination of Cd and Ni in tea and water samples.

    PubMed

    Ezoddin, Maryam; Taghizadeh, Tayebeh; Majidi, Behrooz

    2014-01-01

    A microextraction method based on ultrasound-assisted surfactant-enhanced emulsification using solidification of a floating organic droplet (UASEME-SFO) was evaluated for simultaneous determination of Cd and Ni in water and tea samples followed by flame atomic absorption spectrometry. In the UASEME-SFO technique, Triton X-100 was used as an emulsifier to accelerate the emulsification of the extraction solvent into a sample solution and hasten the mass transfer of the analytes. Analytes form a complex and are extracted into 1-dodecanol which was used as an extraction solvent. Some parameters such as type and volume of the extraction solvent, the type and concentration of the surfactant, ultrasound extraction time, reagent concentration, centrifuge conditions and salt concentration were investigated. Under optimum conditions, calibration curves were linear in the range of 0.3-100 and 0.6-180 microg L(-1) with detection limits of 0.11 and 0.20 microg L(-1) for Cd and Ni, respectively. The accuracy of the method was confirmed by parallel analyses using the certified reference material of water and tea samples. The recoveries of the analytes in tea leaves, tea infusions and water samples were in the range of 96.5-105.1%.

  3. Surface-enhanced Raman spectroscopy analysis of house paint and wallpaper samples from an 18th century historic property.

    PubMed

    Harroun, S G; Bergman, J; Jablonski, E; Brosseau, C L

    2011-09-07

    Conservation efforts for heritage buildings require a substantial knowledge of the chemical makeup of materials that were used throughout the lifetime of the property. In particular, conservators are often concerned with the identification of colorants used in both interior and exterior wall treatments (paint, wallpaper, etc.) in order to gain perspective into how the building may have appeared during a certain time period in its existence. Ideally, such an analysis requires a technique that provides molecular level information as to the identity of the colorant as well as other sample components (binders, fillers, etc.), which is useful for dating purposes. In addition, the technique should be easily applied to paint layer samples which can be extremely thin and fragile. Herein we report the surface-enhanced Raman spectroscopy (SERS) analysis of paint and wallpaper samples taken from exterior and interior surfaces of a historic building. Several pigments were identified in the samples, which ranged from early inorganic pigments (lead white, barium sulfate, calcium carbonate, anhydrous chromium(III) oxide) which have been used in house paints for centuries, to a more modern pigment (phthalocyanine blue), developed in the middle of the 20th century. This analysis highlights the usefulness of SERS in such a conservation effort, and demonstrates for the first time pigment identification in house paints and wallpaper using SERS, which has far-reaching implications not only in the field of conservation, but also in forensics, industrial process control, and environmental health and safety.

  4. Order parameter free enhanced sampling of the vapor-liquid transition using the generalized replica exchange method.

    PubMed

    Lu, Qing; Kim, Jaegil; Straub, John E

    2013-03-14

    The generalized Replica Exchange Method (gREM) is extended into the isobaric-isothermal ensemble, and applied to simulate a vapor-liquid phase transition in Lennard-Jones fluids. Merging an optimally designed generalized ensemble sampling with replica exchange, gREM is particularly well suited for the effective simulation of first-order phase transitions characterized by "backbending" in the statistical temperature. While the metastable and unstable states in the vicinity of the first-order phase transition are masked by the enthalpy gap in temperature replica exchange method simulations, they are transformed into stable states through the parameterized effective sampling weights in gREM simulations, and join vapor and liquid phases with a succession of unimodal enthalpy distributions. The enhanced sampling across metastable and unstable states is achieved without the need to identify a "good" order parameter for biased sampling. We performed gREM simulations at various pressures below and near the critical pressure to examine the change in behavior of the vapor-liquid phase transition at different pressures. We observed a crossover from the first-order phase transition at low pressure, characterized by the backbending in the statistical temperature and the "kink" in the Gibbs free energy, to a continuous second-order phase transition near the critical pressure. The controlling mechanisms of nucleation and continuous phase transition are evident and the coexistence properties and phase diagram are found in agreement with literature results.

  5. Comparing the Ability of Enhanced Sampling Molecular Dynamics Methods To Reproduce the Behavior of Fluorescent Labels on Proteins.

    PubMed

    Walczewska-Szewc, Katarzyna; Deplazes, Evelyne; Corry, Ben

    2015-07-14

    Adequately sampling the large number of conformations accessible to proteins and other macromolecules is one of the central challenges in molecular dynamics (MD) simulations; this activity can be difficult, even for relatively simple systems. An example where this problem arises is in the simulation of dye-labeled proteins, which are now being widely used in the design and interpretation of Förster resonance energy transfer (FRET) experiments. In this study, MD simulations are used to characterize the motion of two commonly used FRET dyes attached to an immobilized chain of polyproline. Even in this simple system, the dyes exhibit complex behavior that is a mixture of fast and slow motions. Consequently, very long MD simulations are required to sufficiently sample the entire range of dye motion. Here, we compare the ability of enhanced sampling methods to reproduce the behavior of fluorescent labels on proteins. In particular, we compared Accelerated Molecular Dynamics (AMD), metadynamics, Replica Exchange Molecular Dynamics (REMD), and High Temperature Molecular Dynamics (HTMD) to equilibrium MD simulations. We find that, in our system, all of these methods improve the sampling of the dye motion, but the most significant improvement is achieved using REMD.

  6. Comparison of hot hydroxylamine hydrochloride and oxalic acid leaching of stream sediment and coated rock samples as anomaly enhancement techniques

    USGS Publications Warehouse

    Filipek, L.H.; Chao, T.T.; Theobald, P.K.

    1982-01-01

    A hot hydroxylamine hydrochloride (H-Hxl) extraction in 25% acetic acid is compared with the commonly used oxalic acid extraction as a method of anomaly enhancement for Cu and Zn in samples from two very different metal deposits and climatic environments. Results obtained on minus-80-mesh stream sediments from an area near the Magruder massive sulfide deposit in Lincoln County, Georgia, where the climate is humid subtropical, indicate that H-Hxl enhances the anomaly for Cu by a factor of 2 and for Zn by a factor of 1.5, compared to the oxalic method. Analyses of Fe oxide-coated rock samples from outcrops overlying the North Silver Bell porphyry copper deposit near Tucson, Arizona, where the climate is semi-arid to arid, indicate that both techniques effectively outline the zones of hydrothermal alteration. The H-Hxl extraction can also perform well in high-carbonate or high-clay environments, where other workers have suggested that oxalic acid is not very effective. Therefore, the H-Hxl method is recommended for general exploration use. ?? 1982.

  7. Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment.

    PubMed

    Huang, Xuhui; Bowman, Gregory R; Pande, Vijay S

    2008-05-28

    We have implemented the serial replica exchange method (SREM) and simulated tempering (ST) enhanced sampling algorithms in a global distributed computing environment. Here we examine the helix-coil transition of a 21 residue alpha-helical peptide in explicit solvent. For ST, we demonstrate the efficacy of a new method for determining initial weights allowing the system to perform a random walk in temperature space based on short trial simulations. These weights are updated throughout the production simulation by an adaptive weighting method. We give a detailed comparison of SREM, ST, as well as standard MD and find that SREM and ST give equivalent results in reasonable agreement with experimental data. In addition, we find that both enhanced sampling methods are much more efficient than standard MD simulations. The melting temperature of the Fs peptide with the AMBER99phi potential was calculated to be about 310 K, which is in reasonable agreement with the experimental value of 334 K. We also discuss other temperature dependent properties of the helix-coil transition. Although ST has certain advantages over SREM, both SREM and ST are shown to be powerful methods via distributed computing and will be applied extensively in future studies of complex bimolecular systems.

  8. Determination of fluoxetine in pharmaceutical and biological samples based on the silver nanoparticle enhanced fluorescence of fluoxetine-terbium complex.

    PubMed

    Lotfi, Ali; Manzoori, Jamshid L

    2016-11-01

    In this study, a simple and sensitive spectrofluorimetric method is presented for the determination of fluoxetine based on the enhancing effect of silver nanoparticles (AgNPs) on the terbium-fluoxetine fluorescence emission. The AgNPs were prepared by a simple reduction method and characterized by UV-Vis spectroscopy and transmission electron microscopy. It was indicated that these AgNPs have a remarkable amplifying effect on the terbium-sensitized fluorescence of fluoxetine. The effects of various parameters such as AgNP and Tb(3+) concentration and the pH of the media were investigated. Under obtained optimal conditions, the fluorescence intensity of the terbium-fluoxetine-AgNP system was enhanced linearly by increasing the concentration of fluoxetine in the range of 0.008 to 19 mg/L. The limit of detection (b + 3s) was 8.3 × 10(-4) mg/L. The interference effects of common species found in real samples were also studied. The method had good linearity, recovery, reproducibility and sensitivity, and was satisfactorily applied for the determination of fluoxetine in tablet formulations, human urine and plasma samples. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  9. Sensitivity enhancement and contrasting information provided by free radicals in oriented-sample NMR of bicelle-reconstituted membrane proteins

    NASA Astrophysics Data System (ADS)

    Tesch, Deanna M.; Nevzorov, Alexander A.

    2014-02-01

    Elucidating structure and topology of membrane proteins (MPs) is essential for unveiling functionality of these important biological constituents. Oriented-sample solid-state NMR (OS-NMR) is capable of providing such information on MPs under nearly physiological conditions. However, two dimensional OS-NMR experiments can take several days to complete due to long longitudinal relaxation times combined with the large number of scans to achieve sufficient signal sensitivity in biological samples. Here, free radicals 5-DOXYL stearic acid, TEMPOL, and CAT-1 were added to uniformly 15N-labeled Pf1 coat protein reconstituted in DMPC/DHPC bicelles, and their effect on the longitudinal relaxation times (T1Z) was investigated. The dramatically shortened T1Z's allowed for the signal gain per unit time to be used for either: (i) up to a threefold reduction of the total experimental time at 99% magnetization recovery or (ii) obtaining up to 74% signal enhancement between the control and radical samples during constant experimental time at “optimal” relaxation delays. In addition, through OS-NMR and high-field EPR studies, free radicals were able to provide positional constraints in the bicelle system, which provide a description of the location of each residue in Pf1 coat protein within the bicellar membranes. This information can be useful in the determination of oligomerization states and immersion depths of larger membrane proteins.

  10. Sensitivity enhancement and contrasting information provided by free radicals in oriented-sample NMR of bicelle-reconstituted membrane proteins.

    PubMed

    Tesch, Deanna M; Nevzorov, Alexander A

    2014-02-01

    Elucidating structure and topology of membrane proteins (MPs) is essential for unveiling functionality of these important biological constituents. Oriented-sample solid-state NMR (OS-NMR) is capable of providing such information on MPs under nearly physiological conditions. However, two dimensional OS-NMR experiments can take several days to complete due to long longitudinal relaxation times combined with the large number of scans to achieve sufficient signal sensitivity in biological samples. Here, free radicals 5-DOXYL stearic acid, TEMPOL, and CAT-1 were added to uniformly (15)N-labeled Pf1 coat protein reconstituted in DMPC/DHPC bicelles, and their effect on the longitudinal relaxation times (T1Z) was investigated. The dramatically shortened T1Z's allowed for the signal gain per unit time to be used for either: (i) up to a threefold reduction of the total experimental time at 99% magnetization recovery or (ii) obtaining up to 74% signal enhancement between the control and radical samples during constant experimental time at "optimal" relaxation delays. In addition, through OS-NMR and high-field EPR studies, free radicals were able to provide positional constraints in the bicelle system, which provide a description of the location of each residue in Pf1 coat protein within the bicellar membranes. This information can be useful in the determination of oligomerization states and immersion depths of larger membrane proteins. Copyright © 2013 Elsevier Inc. All rights reserved.

  11. Determination of flavor enhancers in milk powder by one-step sample preparation and two-dimensional liquid chromatography.

    PubMed

    Ma, Jing; Zhang, Bing; Wang, Yunan; Hou, Xiaofang; He, Langchong

    2014-04-01

    Maltol, ethyl maltol, vanillin, and ethyl vanillin are important food additives as flavor enhancers. To quantify the four additives in milk powder, a novel 2D liquid chromatographic (2DLC) method was developed in this article. In such a 2DLC system, the target fractions eluted from the first dimensional column (C4) are stored onto the trapping column (C8) for subsequent analysis; after that, they were switched into the second dimensional column (C18) by a two-position six-port switching valve. A one-step sample preparation method was used prior to 2DLC chromatographic analysis, which was easy and convenient. After optimization of all experimental parameters, the new method was validated in terms of linearity, LODs, and LOQs, intra- and interday precision, and accuracy. A conventional single-dimensional liquid chromatographic method was also proposed in this work for comparison. In order to evaluate the applicability of the new 2DLC method, five brands of commercial milk powder samples (n = 8) were analyzed. Vanillin and ethyl vanillin were detected in two samples, respectively. It is showed that the 2DLC method is effective in quality control programs of milk powder products.

  12. Cryptosporidium oocyst detection in water samples: floatation technique enhanced with immunofluorescence is as effective as immunomagnetic separation method.

    PubMed

    Koompapong, Khuanchai; Sutthikornchai, Chantira; Sukthana, Yowalark

    2009-12-01

    Cryptosporidium can cause gastrointestinal diseases worldwide, consequently posing public health problems and economic burden. Effective techniques for detecting contaminated oocysts in water are important to prevent and control the contamination. Immunomagnetic separation (IMS) method has been widely employed recently due to its efficiency, but, it is costly. Sucrose floatation technique is generally used for separating organisms by using their different specific gravity. It is effective and cheap but time consuming as well as requiring highly skilled personnel. Water turbidity and parasite load in water sample are additional factors affecting to the recovery rate of those 2 methods. We compared the efficiency of IMS and sucrose floatation methods to recover the spiked Cryptosporidium oocysts in various turbidity water samples. Cryptosporidium oocysts concentration at 1, 10(1), 10(2), and 10(3) per 10 microl were spiked into 3 sets of 10 ml-water turbidity (5, 50, and 500 NTU). The recovery rate of the 2 methods was not different. Oocyst load at the concentration < 10(2) per 10 ml yielded unreliable results. Water turbidity at 500 NTU decreased the recovery rate of both techniques. The combination of sucrose floatation and immunofluorescense assay techniques (SF-FA) showed higher recovery rate than IMS and immunofluorescense assay (IMS-FA). We used this SF-FA to detect Cryptosporidium and Giardia from the river water samples and found 9 and 19 out of 30 (30% and 63.3%) positive, respectively. Our results favored sucrose floatation technique enhanced with immunofluorescense assay for detecting contaminated protozoa in water samples in general laboratories and in the real practical setting.

  13. Cryptosporidium Oocyst Detection in Water Samples: Floatation Technique Enhanced with Immunofluorescence Is as Effective as Immunomagnetic Separation Method

    PubMed Central

    Koompapong, Khuanchai; Sutthikornchai, Chantira

    2009-01-01

    Cryptosporidium can cause gastrointestinal diseases worldwide, consequently posing public health problems and economic burden. Effective techniques for detecting contaminated oocysts in water are important to prevent and control the contamination. Immunomagnetic separation (IMS) method has been widely employed recently due to its efficiency, but, it is costly. Sucrose floatation technique is generally used for separating organisms by using their different specific gravity. It is effective and cheap but time consuming as well as requiring highly skilled personnel. Water turbidity and parasite load in water sample are additional factors affecting to the recovery rate of those 2 methods. We compared the efficiency of IMS and sucrose floatation methods to recover the spiked Cryptosporidium oocysts in various turbidity water samples. Cryptosporidium oocysts concentration at 1, 101, 102, and 103 per 10 µl were spiked into 3 sets of 10 ml-water turbidity (5, 50, and 500 NTU). The recovery rate of the 2 methods was not different. Oocyst load at the concentration < 102 per 10 ml yielded unreliable results. Water turbidity at 500 NTU decreased the recovery rate of both techniques. The combination of sucrose floatation and immunofluorescense assay techniques (SF-FA) showed higher recovery rate than IMS and immunofluorescense assay (IMS-FA). We used this SF-FA to detect Cryptosporidium and Giardia from the river water samples and found 9 and 19 out of 30 (30% and 63.3%) positive, respectively. Our results favored sucrose floatation technique enhanced with immunofluorescense assay for detecting contaminated protozoa in water samples in general laboratories and in the real practical setting. PMID:19967082

  14. Aspergillus PCR-Based Investigation of Fresh Tissue and Effusion Samples in Patients with Suspected Invasive Aspergillosis Enhances Diagnostic Capabilities

    PubMed Central

    Reinwald, M.; Spiess, B.; Heinz, W. J.; Heussel, C. P.; Bertz, H.; Cornely, O. A.; Hahn, J.; Lehrnbecher, T.; Kiehl, M.; Laws, H. J.; Wolf, H. H.; Schwerdtfeger, R.; Schultheis, B.; Burchardt, A.; Klein, M.; Dürken, M.; Claus, B.; Schlegel, F.; Hummel, M.; Hofmann, W.-K.

    2013-01-01

    Although it is a severe complication in immunocompromised patients, diagnosing invasive fungal disease (IFD), especially invasive aspergillosis (IA), remains difficult. In certain clinical scenarios, examining tissue samples for identification of the infectious organism becomes important. As culture-based methods rarely yield results, the performance of an Aspergillus-specific nested PCR in fresh tissue or pleural effusion samples was evaluated. Fresh tissue (n = 59) and effusion (n = 47) specimens from 79 immunocompromised patients were subjected to an Aspergillus-specific PCR assay. Twenty-six patients had proven (n = 20) or probable (n = 6) IFD, according to the European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group and National Institute of Allergy and Infectious Diseases Mycoses Study Group (EORTC/MSG) criteria, while the remaining patients were classified as having either possible IFD (n = 30) or no IFD (n = 23). IA was identified as the underlying IFD in 21/26 proven/probable cases. PCR positivity was observed for 18/21 proven/probable and 6 possible IA cases; cases classified as no IA did not show positive signals. Patients with proven IFD (n = 5) with cultures positive for non-Aspergillus molds also had negative Aspergillus PCR results. Aspergillus PCR performance analysis yielded sensitivity and specificity values of 86% (95% confidence interval [CI], 65% to 95%) and 100% (95% CI, 86% to 100%), respectively, thus leading to a diagnostic odds ratio of >200. In this analysis, good diagnostic performance of the PCR assay for detection of IA was observed for tissue samples, while effusion samples showed lower sensitivity rates. PCR testing represents a complementary tool; a positive PCR result strengthens the likelihood of IA, whereas IA seems unlikely in cases with negative results but findings could indicate non-Aspergillus IFD. Thus, PCR testing of these specimens enhances the diagnostic capabilities. PMID

  15. Raman sensitivity enhancement for aqueous absorbing sample using Teflon-AF 2400 liquid core optical fibre cell.

    PubMed

    Tian, Yanjie; Zhang, Liuyang; Zuo, Jian; Li, Zuowei; Gao, Shuqin; Lu, Guohui

    2007-01-02

    The compatibility Teflon-AF 2400 liquid core optical fibre with resonance Raman spectroscopy (RRS-LCOF) was used to detect aqueous biomolecules. The maximum sensitivity enhancement factor for concentrations greater than the detection limit in a conventional cell was 10, and detection limit reduction of about 1000-fold have been achieved for the measurement of aqueous absorbing sample using Teflon-AF 2400 fibre Raman cell compared to the conventional cell. We were able to collect spectra of 2.5 x 10(-9) and 2.5 x 10(-10) M aqueous beta-carotene using 16.2 mW of laser power and 10s integration time. This volume of a 2.5 x 10(-10) M aqueous solution corresponds to only 1.5 fmol or 830 fg of beta-carotene. The results of this preliminary study indicate that RRS-LCOF has potential in bioanalytical and biomedical applications.

  16. Enhanced electron-phonon coupling and critical current density in rapid thermally quenched MgB2 bulk samples

    NASA Astrophysics Data System (ADS)

    Suraj, T. S.; Muralidhar, M.; Sethupathi, K.; Rao, M. S. Ramachandra; Murakami, M.

    2017-08-01

    We report Rapid Thermal Quenching (RTQ) studies on MgB2 samples from optimized sintering temperature of 800 °C down to liquid nitrogen temperature with different sintering duration. Superior electron-phonon coupling strength (λe -E2g ) , critical current density (Jc) and irreversibility fields (Hirr) compared to doped MgB2 were observed without compromising transition temperature Tc. Structural studies showed a contraction of the unit cell due to thermal stress induced by RTQ. Enhanced λe -E2g evaluated from line width, and phonon frequency of Raman spectra using Allen equation was consistent with structural and magnetic studies. Microstructural analysis showed a decrease in grain size resulting in increased Jc and Hirr.

  17. MEASUREMENT OF PYRETHROID RESIDUES IN ENVIRONMENTAL AND FOOD SAMPLES BY ENHANCED SOLVENT EXTRACTION/SUPERCRITICAL FLUID EXTRACTION COUPLED WITH GAS CHROMATOGRAPHY-TANDEM MASS SPECTROMETRY

    EPA Science Inventory

    The abstract summarizes pyrethorid methods development research. It provides a summary of sample preparation and analytical techniques such as supercritical fluid extraction, enhance solvent extraction, gas chromatography and tandem mass spectrometry.

  18. MEASUREMENT OF PYRETHROID RESIDUES IN ENVIRONMENTAL AND FOOD SAMPLES BY ENHANCED SOLVENT EXTRACTION/SUPERCRITICAL FLUID EXTRACTION COUPLED WITH GAS CHROMATOGRAPHY-TANDEM MASS SPECTROMETRY

    EPA Science Inventory

    The abstract summarizes pyrethorid methods development research. It provides a summary of sample preparation and analytical techniques such as supercritical fluid extraction, enhance solvent extraction, gas chromatography and tandem mass spectrometry.

  19. Variation of free‐energy landscape of the p53 C‐terminal domain induced by acetylation: Enhanced conformational sampling

    PubMed Central

    Iida, Shinji; Mashimo, Tadaaki; Kurosawa, Takashi; Hojo, Hironobu; Muta, Hiroya; Goto, Yuji; Fukunishi, Yoshifumi; Nakamura, Haruki

    2016-01-01

    The C‐terminal domain (CTD) of tumor suppressor protein p53 is an intrinsically disordered region that binds to various partner proteins, where lysine of CTD is acetylated/nonacetylated and histidine neutralized/non‐neutralized. Because of the flexibility of the unbound CTD, a free‐energy landscape (FEL) is a useful quantity for determining its statistical properties. We conducted enhanced conformational sampling of CTD in the unbound state via virtual system coupled multicanonical molecular dynamics, in which the lysine was acetylated or nonacetylated and histidine was charged or neutralized. The fragments were expressed by an all‐atom model and were immersed in an explicit solvent. The acetylation and charge‐neutralization varied FEL greatly, which might be convenient to exert a hub property. The acetylation slightly enhanced alpha‐helix structures that are more compact than sheet/loop conformations. The charge‐neutralization produced hairpins. Additionally, circular dichroism experiments confirmed the computational results. We propose possible binding mechanisms of CTD to partners by investigating FEL. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:27735058

  20. Enhanced sampling molecular dynamics identifies PrP(Sc) structures harboring a C-terminal β-core.

    PubMed

    Baillod, Pascal; Garrec, Julian; Colombo, Maria-Carola; Tavernelli, Ivano; Rothlisberger, Ursula

    2012-12-11

    We perform a replica exchange molecular dynamics simulation corresponding to a 2.8 μs total time for the extensive enhanced sampling of the conformational space of the C-terminal part (residues 124-226) of the mouse prion protein (PrP); 1.3% of the conformations sampled display a high level of β-structure (≥19 residues), allowing the assessment of β-propensities along the sequence and highlighting the most structurally labile hot spots. A clustering algorithm is applied to sort the structures of this pool according to their fold. Ten β-rich folds are thus defined and analyzed with regard to their topology, accumulation temperatures, and structural characteristics. In contrast to the so-called spiral and β-helix models suggesting that the β-rich core of the scrapie isoform (PrP(Sc)) comprises the N-terminal tail and part of the C-terminal domain up to helix 1 (H1), we present putative structural models for monomeric precursors of PrP(Sc) and PrP β-oligomers that are characterized by a C-terminal β-rich core, in agreement with the suggestions of a series of recent experiments.

  1. A study on the alkaline hydrolysis of isatin-β-thiosemicarbazone by capillary electrophoresis with enhanced sample loadability.

    PubMed

    Kruk, Pavol; Stankovičová, Henrieta; Bodor, Róbert; Gáplovský, Anton; Masár, Marián

    2012-05-11

    An analytical potential of capillary zone electrophoresis (CZE) with enhanced sample loadability (a 200nL injection volume) in determination of alkaline hydrolysis products of isatin-β-thiosemicarbazone (IBT), a compound with important biological activity, has been studied. The CZE separation conditions for a complete resolution of transformation products, i.e. 2-aminophenylglyoxalate, 2-(2-aminophenyl)-2-semicarbazonoethane, anthranilate and E-Z geometric isomers of 2-(2-aminophenyl)-2-thiosemicarbazonoethane, have been optimized. CZE separations with UV detection at 240 nm were performed using glycine running buffer at high pH (9.2) and containing an uncharged β-cyclodextrin as a complexing agent. High sensitivity (with detection limits ranging from 0.1 to 1.2 μM), good repeatability (RSD of migration times less than 0.4% and 0.4-3.4% RSD of peak areas) and linearity over two orders of magnitude were achieved for the compounds studied. The employed CZE method, characterized by simple sample handling (only dilution step needed) and total analysis time of less than 15 min, has been applied successfully to time monitoring of the transformation of IBT in alkaline media. Under optimized CZE conditions, the effect of pH of reaction media, implemented by different concentration of NaOH (0.1-100mM), on the course of the alkaline hydrolysis of IBT was studied in this respect, as well.

  2. Unambiguous characterization of analytical markers in complex, seized opiate samples using an enhanced ion mobility trace detector-mass spectrometer.

    PubMed

    Liuni, Peter; Romanov, Vladimir; Binette, Marie-Josée; Zaknoun, Hafid; Tam, Maggie; Pilon, Pierre; Hendrikse, Jan; Wilson, Derek J

    2014-11-04

    Ion mobility spectroscopy (IMS)-based trace-compound detectors (TCDs) are powerful and widely implemented tools for the detection of illicit substances. They combine high sensitivity, reproducibility, rapid analysis time, and resistance to dirt with an acceptable false alarm rate. The analytical specificity of TCD-IMS instruments for a given analyte depends strongly on a detailed knowledge of the ion chemistry involved, as well as the ability to translate this knowledge into field-robust analytical methods. In this work, we introduce an enhanced hybrid TCD-IMS/mass spectrometer (TCD-IMS/MS) that combines the strengths of ion-mobility-based target compound detection with unambiguous identification by tandem MS. Building on earlier efforts along these lines (Kozole et al., Anal. Chem. 2011, 83, 8596-8603), the current instrument is capable of positive and negative-mode analyses with tightly controlled gating between the IMS and MS modules and direct measurement of ion mobility profiles. We demonstrate the unique capabilities of this instrument using four samples of opium seized by the Canada Border Services Agency (CBSA), consisting of a mixture of opioid alkaloids and other naturally occurring compounds typically found in these samples. Although many analytical methods have been developed for analyzing naturally occurring opiates, this is the first detailed ion mobility study on seized opium samples. This work demonstrates all available analytical modes for the new IMS-MS system including "single-gate", "dual-gate", MS/MS, and precursor ion scan methods. Using a combination of these modes, we unambiguously identify all signals in the IMS spectra, including previously uncharacterized minor peaks arising from compounds that are common in raw opium.

  3. Exploring the α-enhancement of metal-poor planet-hosting stars. The Kepler and HARPS samples

    NASA Astrophysics Data System (ADS)

    Adibekyan, V. Zh.; Delgado Mena, E.; Sousa, S. G.; Santos, N. C.; Israelian, G.; González Hernández, J. I.; Mayor, M.; Hakobyan, A. A.

    2012-11-01

    Recent studies have shown that at low metallicities Doppler-detected planet-hosting stars tend to have high α-content and to belong to the thick disk. We used the reconnaissance spectra of 87 Kepler planet candidates and data available from the HARPS planet search survey to explore this phenomenon. Using the traditional spectroscopic abundance analysis methods, we derived Ti, Ca, and Cr abundances for the Kepler stars. In the metallicity region -0.65 < [Fe/H] < -0.3 dex, the fraction of Ti-enhanced thick-disk HARPS planet harboring stars is 12.3 ± 4.1%, and for their thin-disk counterparts this fraction is 2.2 ± 1.3%. Binomial statistics give a probability of 0.008 that this could have occurred by chance. Combining the two samples (HARPS and Kepler) reinforces the significance of this result (P ~ 99.97%). Since most of these stars harbor small sized or low-mass planets we can assume that, although terrestrial planets can be found in a low-iron regime, they are mostly enhanced by α-elements. This implies that early formation of rocky planets could start in the Galactic thick disk, where the chemical conditions for their formation are more favorable. Table with chemical abundances is only available at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/547/A36

  4. Enhanced Spatial & Temporal Sampling of Air/Sea Interaction with the NASA CYGNSS MicroSat Constellation

    NASA Astrophysics Data System (ADS)

    Ruf, C. S.; Ridley, A. J.; O'Brien, A.; Johnson, J.; Yi, Y.

    2013-12-01

    The NASA Cyclone Global Navigation Satellite System (CYGNSS) is a new spaceborne mission to address the deficiencies with current tropical cyclone (TC) intensity forecasts related to inadequate observations and modeling of the inner core. The inadequacy results from two causes: 1) much of the inner core ocean surface is obscured from conventional remote sensing instruments by intense precipitation in the eye wall and inner rain bands; and 2) the rapidly evolving (genesis and intensification) stages of the TC life cycle are poorly sampled by conventional polar-orbiting imagers. CYGNSS is specifically designed to address these two limitations by combining the all-weather performance of GNSS-R bistatic ocean surface scatterometry with the enhanced sampling properties of a constellation of satellites. CYGNSS will provide surface wind measurements of the TC inner core that could not previously be measured from space. Mission simulations predict a median(mean) revisit time of 2(5) hours. The CYGNSS wind fields, when combined with as-frequent precipitation fields (e.g. produced by the upcoming Global Precipitation Measurement mission), will resolve the evolution of both the precipitation and underlying wind fields throughout the TC life cycle. They will provide near simultaneous and continuous observations and enable new insights into TC inner core dynamics and energetics. The use of a dense constellation of GNSS-R microsats results in spatial and temporal sampling properties that are markedly different from previous wide swath polar imagers. In particular, revisit times in the tropics are characterized by a probability distribution rather than a single, deterministic number of hours. The asymmetric shape of the probability distribution results in median revisit times that are less than half that of the mean, and mean revisit times that are less than half that of current polar orbiting imagers. CYGNSS is currently in Phase B project development. In parallel with the

  5. Towards high concentration enhancement of microfluidic temperature gradient focusing of sample solutes using combined AC and DC field induced Joule heating.

    PubMed

    Ge, Zhengwei; Wang, Wei; Yang, Chun

    2011-04-07

    It is challenging to continuously concentrate sample solutes in microfluidic channels. We present an improved electrokinetic technique for enhancing microfluidic temperature gradient focusing (TGF) of sample solutes using combined AC and DC field induced Joule heating effects. The introduction of an AC electric field component services dual functions: one is to produce Joule heat for generating temperature gradient; the other is to suppress electroosmotic flow. Consequently the required DC voltages for achieving sample concentration by Joule heating induced TGF are reduced, thereby leading to smaller electroosmotic flow (EOF) and thus backpressure effects. As a demonstration, the proposed technique can lead to concentration enhancement of sample solutes of more than 2500-fold, which is much higher than the existing literature reported microfluidic concentration enhancement by utilizing the Joule heating induced TGF technique.

  6. An enhanced droplet-based liquid microjunction surface sampling system coupled with HPLC-ESI-MS/MS for spatially resolved analysis

    SciTech Connect

    Van Berkel, Gary J.; Weiskittel, Taylor M.; Kertesz, Vilmos

    2014-11-07

    Droplet-based liquid microjunction surface sampling coupled with high-performance liquid chromatography (HPLC)-electrospray ionization (ESI)-tandem mass spectrometry (MS/MS) for spatially resolved analysis provides the possibility of effective analysis of complex matrix samples and can provide a greater degree of chemical information from a single spot sample than is typically possible with a direct analysis of an extract. Described here is the setup and enhanced capabilities of a discrete droplet liquid microjunction surface sampling system employing a commercially available CTC PAL autosampler. The system enhancements include incorporation of a laser distance sensor enabling unattended analysis of samples and sample locations of dramatically disparate height as well as reliably dispensing just 0.5 μL of extraction solvent to make the liquid junction to the surface, wherein the extraction spot size was confined to an area about 0.7 mm in diameter; software modifications improving the spatial resolution of sampling spot selection from 1.0 to 0.1 mm; use of an open bed tray system to accommodate samples as large as whole-body rat thin tissue sections; and custom sample/solvent holders that shorten sampling time to approximately 1 min per sample. Lastly, the merit of these new features was demonstrated by spatially resolved sampling, HPLC separation, and mass spectral detection of pharmaceuticals and metabolites from whole-body rat thin tissue sections and razor blade (“crude”) cut mouse tissue.

  7. An enhanced droplet-based liquid microjunction surface sampling system coupled with HPLC-ESI-MS/MS for spatially resolved analysis

    DOE PAGES

    Van Berkel, Gary J.; Weiskittel, Taylor M.; Kertesz, Vilmos

    2014-11-07

    Droplet-based liquid microjunction surface sampling coupled with high-performance liquid chromatography (HPLC)-electrospray ionization (ESI)-tandem mass spectrometry (MS/MS) for spatially resolved analysis provides the possibility of effective analysis of complex matrix samples and can provide a greater degree of chemical information from a single spot sample than is typically possible with a direct analysis of an extract. Described here is the setup and enhanced capabilities of a discrete droplet liquid microjunction surface sampling system employing a commercially available CTC PAL autosampler. The system enhancements include incorporation of a laser distance sensor enabling unattended analysis of samples and sample locations of dramatically disparatemore » height as well as reliably dispensing just 0.5 μL of extraction solvent to make the liquid junction to the surface, wherein the extraction spot size was confined to an area about 0.7 mm in diameter; software modifications improving the spatial resolution of sampling spot selection from 1.0 to 0.1 mm; use of an open bed tray system to accommodate samples as large as whole-body rat thin tissue sections; and custom sample/solvent holders that shorten sampling time to approximately 1 min per sample. Lastly, the merit of these new features was demonstrated by spatially resolved sampling, HPLC separation, and mass spectral detection of pharmaceuticals and metabolites from whole-body rat thin tissue sections and razor blade (“crude”) cut mouse tissue.« less

  8. Novel flashlamp-based time-resolved fluorescence microscope reduces autofluorescence for 30-fold contrast enhancement in environmental samples

    NASA Astrophysics Data System (ADS)

    Connally, Russell; Veal, Duncan; Piper, James A.

    2003-07-01

    The abundance of naturally fluorescing components (autofluorophors) encountered in environmentally sourced samples can greatly hinder the detection and identification of fluorescently labeled target using fluorescence microscopy. Time-resolved fluorescence microscopy (TRFM) is a technique that reduces the effects of autofluorescence through precisely controlled time delays. Lanthanide chelates have fluorescence lifetimes many orders of magnitude greater than typical autofluorophors, and persist in their luminescence long after autofluorescence has ceased. An intense short pulse of (UV) light is used to excite fluorescence in the sample and after a short delay period the longer persisting fluorescence from the chelate is captured with an image-intensified CCD camera. The choice of pulsed excitation source for TRFM has a large impact on the price and performance of the instrument. A flashlamp with a short pulse duration was selected for our instrument because of the high spectral energy in the UV region and short pulse length. However, flash output decays with an approximate lifetime of 18μs and the TRFM requires a long-lived chelate to ensure probe fluorescence is still visible after decay of the flash plasma. We synthesized a recently reported fluorescent chelate (BHHCT) and conjugated it to a monoclonal antibody directed against the water-borne parasite Giardia lamblia. Fluorescence lifetime of the construct was determined to be 339μs +/- 14μs and provided a 45-fold enhancement of labeled Giardia over background using a gate delay of 100μs. Despite the sub-optimal decay characteristics of the light pulse, flashlamps have many advantages compared to optical chopper wheels and modulated lasers. Their low cost, lack of vibration, ease of interface and small footprint are important factors to consider in TRFM design.

  9. High-speed concatenation of frequency ramps using sampled grating distributed Bragg reflector laser diode sources for OCT resolution enhancement

    NASA Astrophysics Data System (ADS)

    George, Brandon; Derickson, Dennis

    2010-02-01

    Wavelength tunable sampled grating distributed Bragg reflector (SG-DBR) lasers used for telecommunications applications have previously demonstrated the ability for linear frequency ramps covering the entire tuning range of the laser at 100 kHz repetition rates1. An individual SG-DBR laser has a typical tuning range of 50 nm. The InGaAs/InP material system often used with SG-DBR lasers allows for design variations that cover the 1250 to 1650 nm wavelength range. This paper addresses the possibility of concatenating the outputs of tunable SGDBR lasers covering adjacent wavelength ranges for enhancing the resolution of OCT measurements. This laser concatenation method is demonstrated by combining the 1525 nm to 1575 nm wavelength range of a "C Band" SG-DBR laser with the 1570nm to 1620 nm wavelength coverage of an "L-Band" SG-DBR laser. Measurements show that SGDBR lasers can be concatenated with a transition switching time of less than 50 ns with undesired leakage signals attenuated by 50 dB.

  10. U-2012: An improved Lowry protein assay, insensitive to sample color, offering reagent stability and enhanced sensitivity.

    PubMed

    Upreti, Girish C; Wang, Yanming; Finn, Alona; Sharrock, Abigail; Feisst, Nicholas; Davy, Marcus; Jordan, Robert B

    2012-03-01

    Traditional colorimetric protein assays such as Biuret, Lowry, and modified Lowry (U-1988) are unsuitable for colored biological samples. Here we describe an improved Lowry protein assay (U-2012), which utilizes stable reagents and offers enhanced sensitivity over the U-1988 assay. U-2012 circumvents interference from colored pigments and other substances (for example sugars) bound to perchloric acid (PCA) precipitated proteins by hydrogen peroxide (H2O2) induced oxidation at 50°C. Unused hydrogen peroxide is neutralized with sodium pyruvate before protein estimation for a stable end color. The U-2012 assay is carried out on the PCA precipitated protein pellet after neutralization (with Na2CO3 plus NaOH), solubilization (in Triton-NaCl), decolorization (by H2O2) and pyruvate treatment. Protein contents in red wine and homogenates of beetroot and blueberry are calculated from standard curves established for various proteins and generated using a rectangular hyperbola with parameters estimated with Microsoft Excel's Solver add-in. The U-2012 protein assay represents an improvement over U-1988 and gives a more accurate estimation of protein content.

  11. H3 Histone Tail Conformation within the Nucleosome and the Impact of K14 Acetylation Studied Using Enhanced Sampling Simulation

    PubMed Central

    Ikebe, Jinzen; Sakuraba, Shun; Kono, Hidetoshi

    2016-01-01

    Acetylation of lysine residues in histone tails is associated with gene transcription. Because histone tails are structurally flexible and intrinsically disordered, it is difficult to experimentally determine the tail conformations and the impact of acetylation. In this work, we performed simulations to sample H3 tail conformations with and without acetylation. The results show that irrespective of the presence or absence of the acetylation, the H3 tail remains in contact with the DNA and assumes an α-helix structure in some regions. Acetylation slightly weakened the interaction between the tail and DNA and enhanced α-helix formation, resulting in a more compact tail conformation. We inferred that this compaction induces unwrapping and exposure of the linker DNA, enabling DNA-binding proteins (e.g., transcription factors) to bind to their target sequences. In addition, our simulation also showed that acetylated lysine was more often exposed to the solvent, which is consistent with the fact that acetylation functions as a post-translational modification recognition site marker. PMID:26967163

  12. Diazonium Salt-Based Surface-Enhanced Raman Spectroscopy Nanosensor: Detection and Quantitation of Aromatic Hydrocarbons in Water Samples

    PubMed Central

    Tijunelyte, Inga; Betelu, Stéphanie; Moreau, Jonathan; Ignatiadis, Ioannis; Berho, Catherine; Lidgi-Guigui, Nathalie; Guénin, Erwann; David, Catalina; Vergnole, Sébastien; Rinnert, Emmanuel; Lamy de la Chapelle, Marc

    2017-01-01

    Here, we present a surface-enhanced Raman spectroscopy (SERS) nanosensor for environmental pollutants detection. This study was conducted on three polycyclic aromatic hydrocarbons (PAHs): benzo[a]pyrene (BaP), fluoranthene (FL), and naphthalene (NAP). SERS substrates were chemically functionalized using 4-dodecyl benzenediazonium-tetrafluoroborate and SERS analyses were conducted to detect the pollutants alone and in mixtures. Compounds were first measured in water-methanol (9:1 volume ratio) samples. Investigation on solutions containing concentrations ranging from 10−6 g L−1 to 10−3 g L−1 provided data to plot calibration curves and to determine the performance of the sensor. The calculated limit of detection (LOD) was 0.026 mg L−1 (10−7 mol L−1) for BaP, 0.064 mg L−1 (3.2 × 10−7 mol L−1) for FL, and 3.94 mg L−1 (3.1 × 10−5 mol L−1) for NAP, respectively. The correlation between the calculated LOD values and the octanol-water partition coefficient (Kow) of the investigated PAHs suggests that the developed nanosensor is particularly suitable for detecting highly non-polar PAH compounds. Measurements conducted on a mixture of the three analytes (i) demonstrated the ability of the developed technology to detect and identify the three analytes in the mixture; (ii) provided the exact quantitation of pollutants in a mixture. Moreover, we optimized the surface regeneration step for the nanosensor. PMID:28538680

  13. Enhancement motives moderate the relationship between high-arousal positive moods and drinking quantity: Evidence from a 22-day experience sampling study.

    PubMed

    Gautreau, Chantal; Sherry, Simon; Battista, Susan; Goldstein, Abby; Stewart, Sherry

    2015-11-01

    Individuals who consume alcohol may be distinguished by their drinking motives. Enhancement motives involve drinking to enhance positive moods. Research on the moderating effect of enhancement motives on the within-person relation between daily positive mood and drinking has not differentiated between high- (e.g. hyper) and low-arousal (e.g. cheerful) positive moods. The present study addressed this limitation. We hypothesised that enhancement motives would positively moderate the relationship between mid-afternoon high-arousal positive mood and evening drinking. Using a palm pilot-based experience sampling design, 143 undergraduate drinkers answered daily surveys assessing positive mood (mid-afternoon) and drinks (evening) for 22 consecutive days. As hypothesised, enhancement motives strengthened the relation between high-arousal positive moods and drinking. Upon closer examination, the mood-drinking slope for those high in enhancement motives was unexpectedly flat, whereas the mood-drinking slope for those low in enhancement motives was negative. We demonstrated that high enhancement-motivated drinkers exhibit a high, stable drinking level, regardless of the intensity of their high-arousal positive mood. In contrast, low enhancement-motivated drinkers decrease their drinking when in a high-arousal positive mood state. Clinicians may be able to help reduce heavy alcohol consumption in enhancement-motivated drinkers by teaching them to reduce their drinking when in a high-arousal positive mood state. © 2015 Australasian Professional Society on Alcohol and other Drugs.

  14. Thermal Desorption Capability Development for Enhanced On-site Health Risk Assessment: HAPSITE (registered trademark) ER Passive Sampling in the Field

    DTIC Science & Technology

    2015-06-07

    passive (diffusive) sampling systems with the Hazardous Air Pollutants on Site (HAPSITE)® Extended Range (ER) Thermal Desorp- tion (TD) system for ambient...AFRL-RH-WP-TR-2015-0061 THERMAL DESORPTION CAPABILITY DEVELOPMENT FOR ENHANCED ON-SITE HEALTH RISK ASSESSMENT: HAPSITE® ER PASSIVE...2015 Interim November 2013 – July 2015 4. TITLE AND SUBTITLE Thermal Desorption Capability Development for Enhanced On-site Health Risk

  15. Large enhancement of Tc (= 35 K) in a sample synthesized from a starting composition of LaFeAsO1-yHx

    NASA Astrophysics Data System (ADS)

    Miyazawa, Kichi; Ishida, Sigeki; Kihou, Kunihiro; Shirage, Parasharam M.; Kito, Hijiri; Lee, Chul Ho; Uchida, Shinichi; Eisaki, Hiroshi; Tokiwa, Kazuyasu; Iyo, Akira

    2010-03-01

    Large enhancement of superconducting transition temperature (Tc) has been found in a sample synthesized from a nominal composition of LaFeAsO1-yHx. A hydroxide powder of La(OH)3 is mixed with starting materials and the sample is synthesized under high-pressure. The sample shows as high as Tc of 35 K (susceptibility onset) and 38 K (resistivity onset), while the maximum Tc of an oxygen-deficient LaFeAsO1-y is 28 K. A large contraction of lattice is observed in the hydroxide-added samples.

  16. Large-volume constant-concentration sampling technique coupling with surface-enhanced Raman spectroscopy for rapid on-site gas analysis

    NASA Astrophysics Data System (ADS)

    Zhang, Zhuomin; Zhan, Yisen; Huang, Yichun; Li, Gongke

    2017-08-01

    In this work, a portable large-volume constant-concentration (LVCC) sampling technique coupling with surface-enhanced Raman spectroscopy (SERS) was developed for the rapid on-site gas analysis based on suitable derivatization methods. LVCC sampling technique mainly consisted of a specially designed sampling cell including the rigid sample container and flexible sampling bag, and an absorption-derivatization module with a portable pump and a gas flowmeter. LVCC sampling technique allowed large, alterable and well-controlled sampling volume, which kept the concentration of gas target in headspace phase constant during the entire sampling process and made the sampling result more representative. Moreover, absorption and derivatization of gas target during LVCC sampling process were efficiently merged in one step using bromine-thiourea and OPA-NH4+ strategy for ethylene and SO2 respectively, which made LVCC sampling technique conveniently adapted to consequent SERS analysis. Finally, a new LVCC sampling-SERS method was developed and successfully applied for rapid analysis of trace ethylene and SO2 from fruits. It was satisfied that trace ethylene and SO2 from real fruit samples could be actually and accurately quantified by this method. The minor concentration fluctuations of ethylene and SO2 during the entire LVCC sampling process were proved to be < 4.3% and 2.1% respectively. Good recoveries for ethylene and sulfur dioxide from fruit samples were achieved in range of 95.0-101% and 97.0-104% respectively. It is expected that portable LVCC sampling technique would pave the way for rapid on-site analysis of accurate concentrations of trace gas targets from real samples by SERS.

  17. Large-volume constant-concentration sampling technique coupling with surface-enhanced Raman spectroscopy for rapid on-site gas analysis.

    PubMed

    Zhang, Zhuomin; Zhan, Yisen; Huang, Yichun; Li, Gongke

    2017-08-05

    In this work, a portable large-volume constant-concentration (LVCC) sampling technique coupling with surface-enhanced Raman spectroscopy (SERS) was developed for the rapid on-site gas analysis based on suitable derivatization methods. LVCC sampling technique mainly consisted of a specially designed sampling cell including the rigid sample container and flexible sampling bag, and an absorption-derivatization module with a portable pump and a gas flowmeter. LVCC sampling technique allowed large, alterable and well-controlled sampling volume, which kept the concentration of gas target in headspace phase constant during the entire sampling process and made the sampling result more representative. Moreover, absorption and derivatization of gas target during LVCC sampling process were efficiently merged in one step using bromine-thiourea and OPA-NH4(+) strategy for ethylene and SO2 respectively, which made LVCC sampling technique conveniently adapted to consequent SERS analysis. Finally, a new LVCC sampling-SERS method was developed and successfully applied for rapid analysis of trace ethylene and SO2 from fruits. It was satisfied that trace ethylene and SO2 from real fruit samples could be actually and accurately quantified by this method. The minor concentration fluctuations of ethylene and SO2 during the entire LVCC sampling process were proved to be <4.3% and 2.1% respectively. Good recoveries for ethylene and sulfur dioxide from fruit samples were achieved in range of 95.0-101% and 97.0-104% respectively. It is expected that portable LVCC sampling technique would pave the way for rapid on-site analysis of accurate concentrations of trace gas targets from real samples by SERS. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Technical innovation in dynamic contrast-enhanced magnetic resonance imaging of musculoskeletal tumors: an MR angiographic sequence using a sparse k-space sampling strategy.

    PubMed

    Fayad, Laura M; Mugera, Charles; Soldatos, Theodoros; Flammang, Aaron; del Grande, Filippo

    2013-07-01

    We demonstrate the clinical use of an MR angiography sequence performed with sparse k-space sampling (MRA), as a method for dynamic contrast-enhanced (DCE)-MRI, and apply it to the assessment of sarcomas for treatment response. Three subjects with sarcomas (2 with osteosarcoma, 1 with high-grade soft tissue sarcomas) underwent MRI after neoadjuvant therapy/prior to surgery, with conventional MRI (T1-weighted, fluid-sensitive, static post-contrast T1-weighted sequences) and DCE-MRI (MRA, time resolution = 7-10 s, TR/TE 2.4/0.9 ms, FOV 40 cm(2)). Images were reviewed by two observers in consensus who recorded image quality (1 = diagnostic, no significant artifacts, 2 = diagnostic, <25 % artifacts, 3 = nondiagnostic) and contrast enhancement characteristics by static MRI (presence/absence of contrast enhancement, percentage of enhancement) and DCE-MRI (presence/absence of arterial enhancement with time-intensity curves). Results were compared with histological response (defined as <5 % viable tumor [soft tissue sarcoma] or <10 % [bone sarcoma] following resection). Diagnostic quality for all conventional and DCE-MRI sequences was rated as 1. In 2 of the 3 sarcomas, there was good histological response (≤5 % viable tumor); in 1 there was poor response (50 % viable tumor). By static post-contrast T1-weighted sequences, there was enhancement in all sarcomas, regardless of response (up to >75 % with good response, >75 % with poor response). DCE-MRI findings were concordant with histological response (arterial enhancement with poor response, no arterial enhancement with good response). Unlike conventional DCE-MRI sequences, an MRA sequence with sparse k-space sampling is easily integrated into a routine musculoskeletal tumor MRI protocol, with high diagnostic quality. In this preliminary work, tumor enhancement characteristics by DCE-MRI were used to assess treatment response.

  19. Emission enhancement of laser-induced breakdown spectroscopy for aqueous sample analysis based on Au nanoparticles and solid-phase substrate.

    PubMed

    Wen, Xu; Lin, Qingyu; Niu, Guanghui; Shi, Qi; Duan, Yixiang

    2016-08-20

    In this paper, porous electrospun ultrafine fiber with a nanoparticle coating was proposed as an effective approach to enhance the laser-induced breakdown spectroscopy (LIBS) signal for metal ions in aqueous systems. It is known that the LIBS technique is very limited when used for liquid sample analysis. On the other hand, in practical applications, many LIBS measurements have been accomplished in a liquid environment. A signal enhancement method for aqueous sample LIBS analysis was presented in this work, where Au nanoparticles and a solid-phase support were combined for the first time for aqueous sample analysis with LIBS. The system operation was relatively simple, which only required Au nanoparticles being dropped onto the surface of porous electrospun ultrafine fibers before LIBS analysis. Significant signal enhancement was achieved due to the integration of the merits of the Au nanoparticles and the ultrafine fibers. Nanoparticles possess significant LIBS signal enhancement effects by providing several plasma ignition points and then causing more efficient emissions. In addition, Au nanoparticles could also help to decrease the breakdown threshold of target elements for LIBS analysis. The electrospun ultrafine fibers as solid-phase support can accommodate a larger volume of aqueous sample. Meanwhile, the aqueous solution on the fiber surface was easy to evaporate. The experimental results showed that the limits of detection (LODs) with this method were significantly improved, 0.5 μg/mL for Cr, 0.5 μg/mL for Pb, and 1.1 μg/mL for Cu, respectively, compared with 2.0 μg/mL for Cr and 3.3 μg/mL for Cu in the previous research. In the proposed method, signal enhancement could be achieved without any extra equipment, which makes the LIBS technique feasible for direct measurement of an aqueous sample.

  20. Highly sensitive detection of five typical fluoroquinolones in low-fat milk by field-enhanced sample injection-based CE in bubble cell capillary.

    PubMed

    Deng, Yan; Gasilova, Natalia; Qiao, Liang; Zhou, Ying-Lin; Zhang, Xin-Xiang; Girault, Hubert H

    2014-12-01

    Fluoroquinolones are a group of synthetic antibiotics with a broad activity spectrum against mycoplasma, Gram-positive, and Gram-negative bacteria. Due to the extensive use of fluoroquinolones in farming and veterinary science, there is a constant need in the analytical methods able to efficiently monitor their residues in food products of animal origin, regulated by Commission Regulation (European Union) no. 37/2010. Herein, field-enhanced sample injection for sample stacking prior the CZE separation was developed inside a bubble cell capillary for highly sensitive detection of five typical fluoroquinolones in bovine milk. Ethylenediamine was proposed as the main component of BGE for the antibiotics separation. The effect of BGE composition, injection parameters, and water plug length on the field-enhanced sample injection-based CE with UV detection was investigated. Under the optimized conditions, described field-enhanced sample injection-based CE-UV analysis of fluoroquinolones provides LODs varying from 0.4 to 1.3 ng/mL. These LOD values are much lower (from 460 to 1500 times) than those obtained by a conventional CE in a standard capillary without bubble cell. The developed method was finally applied for the analysis of fluoroquinolones in low-fat milk from a Swiss supermarket. Sample recovery values from 93.6 to 106.0% for different fluoroquinolones, and LODs from 0.7 to 2.5 μg/kg, were achieved. Moreover, the proposed ethylenediamine-based BGE as volatile and compatible with MS system, enabled the coupling of the field-enhanced sample injection-based CE with a recently introduced electrostatic spray ionization MS via an iontophoretic fraction collection interface for qualitative fluoroquinolones identification.

  1. [Taking drugs for performance-enhancing at job: a study in a sample of workers in Paris].

    PubMed

    Gay, Vincent; Houdoyer, Eric; Rouzaud, Gilles

    2008-01-01

    the study was to describe the performance-enhancing behavior with licit or illicit substances in working environment, by distinguishing them from dependence behavior. in 2007, 663 workers without dependence at nicotine and alcohol was questioned by anonymous self-questionnaire during the periodic consultation of occupational medicine. Data collected concerned the consumption of substances for job in the last month, socio-professional characteristics, and the levels of stress and job satisfaction. at job, 39.2% of workers had a performance-enhancing behavior, including 24.9% with drugs, 10.3% with tobacco, 7.5% with alcohol, and 2.1% with cannabis. This behavior were more frequent for women and less than 30 years and were related to job constraints. taking drug, licit and illicit substances for the performance-enhancing behavior at work are frequent and cause consumption varied and repeated. One of the risks which could be a passage to the addictive behavior.

  2. Dengue Virus Infection-Enhancing Activity in Serum Samples with Neutralizing Activity as Determined by Using FcγR-Expressing Cells

    PubMed Central

    Moi, Meng Ling; Lim, Chang-Kweng; Chua, Kaw Bing; Takasaki, Tomohiko; Kurane, Ichiro

    2012-01-01

    Background Progress in dengue vaccine development has been hampered by limited understanding of protective immunity against dengue virus infection. Conventional neutralizing antibody titration assays that use FcγR-negative cells do not consider possible infection-enhancement activity. We reasoned that as FcγR-expressing cells are the major target cells of dengue virus, neutralizing antibody titration assays using FcγR-expressing cells that determine the sum of neutralizing and infection-enhancing activity, may better reflect the biological properties of antibodies in vivo. Methods and Findings We evaluated serum samples from 80 residents of a dengue endemic country, Malaysia, for neutralizing activity, and infection-enhancing activity at 1∶10 serum dilution by using FcγR-negative BHK cells and FcγR-expressing BHK cells. The serum samples consisted of a panel of patients with acute DENV infection (31%, 25/80) and a panel of donors without acute DENV infection (69%, 55/80). A high proportion of the tested serum samples (75%, 60/80) demonstrated DENV neutralizing activity (PRNT50≥10) and infection-enhancing activity. Eleven of 18 serum samples from patients with acute secondary DENV infection demonstrated neutralizing activity to the infecting serotype determined by using FcγR-negative BHK cells (PRNT50≥10), but not when determined by using FcγR-expressing cells. Conclusion Human serum samples with low neutralizing activity determined by using FcγR-negative cells showed DENV infection-enhancing activity using FcγR-expressing cells, whereas those with high neutralizing activity determined by using FcγR-negative cells demonstrate low or no infection-enhancing activity using FcγR-expressing cells. The results suggest an inverse relationship between neutralizing antibody titer and infection-enhancing activity, and that neutralizing activity determined by using FcγR-expressing cells, and not the activity determined by using FcγR-negative cells, may

  3. Surfactant-enhanced spectrofluorimetric determination of total aflatoxins from wheat samples after magnetic solid-phase extraction using modified Fe3O4 nanoparticles

    NASA Astrophysics Data System (ADS)

    Manafi, Mohammad Hanif; Allahyari, Mehdi; Pourghazi, Kamyar; Amoli-Diva, Mitra; Taherimaslak, Zohreh

    2015-07-01

    The extraction and preconcentration of total aflatoxins (including aflatoxin B1, B2, G1, and G2) using magnetic nanoparticles based solid phase extraction (MSPE) followed by surfactant-enhanced spectrofluorimetric detection was proposed. Ethylene glycol bis-mercaptoacetate modified silica coated Fe3O4 nanoparticles as an efficient antibody-free adsorbent was successfully applied to extract aflatoxins from wheat samples. High surface area and strong magnetization properties of magnetic nanoparticles were utilized to achieve high enrichment factor (97), and satisfactory recoveries (92-105%) using only 100 mg of the adsorbent. Furthermore, the fast separation time (less than 10 min) avoids many time-consuming cartridge loading or column-passing procedures accompany with the conventional SPE. In determination step, signal enhancement was performed by formation of Triton X-100 micelles around the analytes in 15% (v/v) acetonitrile-water which dramatically increase the sensitivity of the method. Main factors affecting the extraction efficiency and signal enhancement of the analytes including pH of sample solution, desorption conditions, extraction time, sample volume, adsorbent amount, surfactant concentration and volume and time of micelle formation were evaluated and optimized. Under the optimum conditions, wide linear range of 0.1-50 ng mL-1 with low detection limit of 0.03 ng mL-1 were obtained. The developed method was successfully applied to the extraction and preconcentration of aflatoxins in three commercially available wheat samples and the results were compared with the official AOAC method.

  4. A divide-and-conquer strategy in tumor sampling enhances detection of intratumor heterogeneity in routine pathology: A modeling approach in clear cell renal cell carcinoma.

    PubMed

    Lopez, José I; Cortes, Jesús M

    2016-01-01

    Intratumor heterogeneity (ITH) is an inherent process in cancer development which follows for most of the cases a branched pattern of evolution, with different cell clones evolving independently in space and time across different areas of the same tumor. The determination of ITH (in both spatial and temporal domains) is nowadays critical to enhance patient treatment and prognosis. Clear cell renal cell carcinoma (CCRCC) provides a good example of ITH. Sometimes the tumor is too big to be totally analyzed for ITH detection and pathologists decide which parts must be sampled for the analysis. For such a purpose, pathologists follow internationally accepted protocols. In light of the latest findings, however, current sampling protocols seem to be insufficient for detecting ITH with significant reliability. The arrival of new targeted therapies, some of them providing promising alternatives to improve patient survival, pushes the pathologist to obtain a truly representative sampling of tumor diversity in routine practice. How large this sampling must be and how this must be performed are unanswered questions so far.  Here we present a very simple method for tumor sampling that enhances ITH detection without increasing costs. This method follows a divide-and-conquer (DAC) strategy, that is, rather than sampling a small number of large-size tumor-pieces as the routine protocol (RP) advises, we suggest sampling many small-size pieces along the tumor. We performed a computational modeling approach to show that the usefulness of the DAC strategy is twofold: first, we show that DAC outperforms RP with similar laboratory costs, and second, DAC is capable of performing similar to total tumor sampling (TTS) but, very remarkably, at a much lower cost. We thus provide new light to push forward a shift in the paradigm about how pathologists should sample tumors for achieving efficient ITH detection.

  5. A divide-and-conquer strategy in tumor sampling enhances detection of intratumor heterogeneity in routine pathology: A modeling approach in clear cell renal cell carcinoma

    PubMed Central

    Lopez, José I.; Cortes, Jesús M.

    2016-01-01

    Intratumor heterogeneity (ITH) is an inherent process in cancer development which follows for most of the cases a branched pattern of evolution, with different cell clones evolving independently in space and time across different areas of the same tumor. The determination of ITH (in both spatial and temporal domains) is nowadays critical to enhance patient treatment and prognosis. Clear cell renal cell carcinoma (CCRCC) provides a good example of ITH. Sometimes the tumor is too big to be totally analyzed for ITH detection and pathologists decide which parts must be sampled for the analysis. For such a purpose, pathologists follow internationally accepted protocols. In light of the latest findings, however, current sampling protocols seem to be insufficient for detecting ITH with significant reliability. The arrival of new targeted therapies, some of them providing promising alternatives to improve patient survival, pushes the pathologist to obtain a truly representative sampling of tumor diversity in routine practice. How large this sampling must be and how this must be performed are unanswered questions so far.  Here we present a very simple method for tumor sampling that enhances ITH detection without increasing costs. This method follows a divide-and-conquer (DAC) strategy, that is, rather than sampling a small number of large-size tumor-pieces as the routine protocol (RP) advises, we suggest sampling many small-size pieces along the tumor. We performed a computational modeling approach to show that the usefulness of the DAC strategy is twofold: first, we show that DAC outperforms RP with similar laboratory costs, and second, DAC is capable of performing similar to total tumor sampling (TTS) but, very remarkably, at a much lower cost. We thus provide new light to push forward a shift in the paradigm about how pathologists should sample tumors for achieving efficient ITH detection. PMID:27127618

  6. Multisite tumor sampling enhances the detection of intratumor heterogeneity at all different temporal stages of tumor evolution.

    PubMed

    Erramuzpe, Asier; Cortés, Jesús M; López, José I

    2017-08-25

    Intratumor heterogeneity (ITH) is an inherent process of tumor development that has received much attention in previous years, as it has become a major obstacle for the success of targeted therapies. ITH is also temporally unpredictable across tumor evolution, which makes its precise characterization even more problematic since detection success depends on the precise temporal snapshot at which ITH is analyzed. New and more efficient strategies for tumor sampling are needed to overcome these difficulties which currently rely entirely on the pathologist's interpretation. Recently, we showed that a new strategy, the multisite tumor sampling, works better than the routine sampling protocol for the ITH detection when the tumor time evolution was not taken into consideration. Here, we extend this work and compare the ITH detections of multisite tumor sampling and routine sampling protocols across tumor time evolution, and in particular, we provide in silico analyses of both strategies at early and late temporal stages for four different models of tumor evolution (linear, branched, neutral, and punctuated). Our results indicate that multisite tumor sampling outperforms routine protocols in detecting ITH at all different temporal stages of tumor evolution. We conclude that multisite tumor sampling is more advantageous than routine protocols in detecting intratumor heterogeneity.

  7. Exploiting LBL-assembled Au nanoparticles to enhance Raman signals for point-of-care testing of osteoporosis with excreta sample

    NASA Astrophysics Data System (ADS)

    Sun, Jian F.; Liu, Xuan; Guo, Zhi R.; Dong, Jian; Huang, Yawen; Zhang, Jie; Jin, Hui; Gu, Ning

    2017-02-01

    Due to the intrinsic lack of specific biomarkers, there is an increasing demand for degenerative diseases to develop a testing method independent upon the targeting biomolecules. In this paper, we proposed a novel idea for this issue which was to analyze the characteristic information of metabolites with Raman spectrum. First, we achieved the fabrication of stable, uniform and reproducible substrate to enhance the Raman signals, which is crucial to the following analysis of information. This idea was confirmed with the osteoporosis-modeled mice. Furthermore, the testing results with clinical samples also preliminarily exhibited the feasibility of this strategy. The substrate to enhance Raman signal was fabricated by the layer-by-layer assembly of Au nanoparticles. The osteoporosis modeling was made by bilateral ovariectomy. Ten female mice were randomly divided into two groups. The urine and dejecta samples of mice were collected every week. Clinic urine samples were collected from patients with osteoporosis while the controlled samples were from the young students in our university. The LBL-assembled substrate of Au nanoparticles was uniform, stable and reproducible to significantly enhance the Raman signals from tiny amount of samples. With a simple data processing technique, the Raman signal-based method can effectively reflect the development of osteoporosis by comparison with micro-CT characterization. Moreover, the Raman signal from samples of clinic patients also showed the obvious difference with that of the control. Raman spectrum may be a good tool to convey the pathological information of metabolites in molecular level. Our results manifested that the information-based testing is possibly feasible and promising. Our strategy utilizes the characteristic information rather than the biological recognition to test the diseases which are difficult to find specific biomarkers. This will be greatly beneficial to the prevention and diagnosis of degenerative

  8. Enhanced recovery of spermatozoa and comprehensive lysis of epithelial cells from sexual assault samples having a low cell counts or aged up to one year.

    PubMed

    Lounsbury, Jenny A; Nambiar, Shanti M; Karlsson, Anne; Cunniffe, Helina; Norris, Jessica V; Ferrance, Jerome P; Landers, James P

    2014-01-01

    Differential extraction (DE) is the most common method for processing sexual assault samples, allowing for the simultaneous recovery of sperm and epithelial cells from the swab with the separation of sperm cells from epithelial cell DNA by exploiting the differences in the cell membrane susceptibility to detergents. However, sperm cell recovery when using DE is generally 40-50% [1], which can reduce the probability of obtaining a STR profile of the semen contributor, especially if the sample is aged or has a low number of sperm cells. Here, we present a novel buffer, containing SDS and ProK that, when used as an initial incubation buffer, enhances sperm cell recovery to as high as 90%, representing a 200-300% increase over conventional DE buffer. Adjusting the incubation time and temperature provided high, reproducible sperm cell yields. Sample vortexing and replacement of SDS with sodium octyl sulfate (SOS), another sulfate-based anionic detergent, did not provide any further enhancement of the sperm cell recoveries. Furthermore, the one-step buffer provided up to a 300% increase in recovery over the conventional DE buffer when used on samples aged up to one year. STR analysis of samples containing 500 or more sperm cells treated with this buffer showed comparable results (i.e., full STR profiles; 16 of 16 loci) to those obtained using a conventional DE buffer. Finally, when the sample contained only 400 sperm cells (recovered in 100μL volume, then extracted), substantially more STR loci (14 of 16) were generated using the novel buffer in comparison to the conventional DE buffer (4 of 16 loci). This work demonstrates that this buffer may be useful as an alternative for the initial sample incubation step in differential extraction, particularly for aged or samples known to have a low number of sperm cells.

  9. Determination of phthalate esters in liquor samples by vortex-assisted surfactant-enhanced-emulsification liquid-liquid microextraction followed by GC-MS.

    PubMed

    Leng, Geng; Chen, Wenjin; Zhang, Mingfang; Huang, Fang; Cao, Qiming

    2014-03-01

    A novel method using vortex-assisted surfactant-enhanced-emulsification liquid-liquid microextraction has been developed for the extraction of phthalate esters (PAEs) in Chinese liquor samples prior to analysis by GC-MS. In the proposed method, a high-density extraction solvent (carbon tetrachloride) was dispersed into samples with the aid of a surfactant (Triton X-100) and vortex agitation, resulting in a short extraction equilibrium (30 s). After centrifugation, a single microdrop of solvent was easily collected for GC-MS analysis. Key factors that affected the extraction efficiency were optimized. Under the optimum conditions, linearity was found in the range from 0.05 to 50 μg/L. Coefficients of determination varied from 0.9938 to 0.9971. LODs, based on an S/N of 3, ranged from 4.9 to 13 ng/L. Enrichment factors varied from 140 to 184. Reproducibility and recoveries were assessed by testing a series of three liquor samples that were spiked with different concentration levels. Finally, the proposed method was successfully applied to the determination of PAEs in 16 Chinese liquor samples. In this work, high-density-solvent vortex-assisted surfactant-enhanced-emulsification liquid-liquid microextraction was applied for the first time for the extraction of PAEs in Chinese liquor samples and was proved to be simple, rapid, and sensitive.

  10. A device design of an integrated CMOS poly-silicon biosensor-on-chip to enhance performance of biomolecular analytes in serum samples.

    PubMed

    Pei-Wen, Yen; Che-Wei, Huang; Yu-Jie, Huang; Min-Cheng, Chen; Hsin-Hao, Liao; Shey-Shi, Lu; Chih-Ting, Lin

    2014-11-15

    For on-site clinical diagnosis of biomolecules, the detection performances of most point-of-care (POC) biosensor devices are limited by undesired cross-detection of other non-analyte proteins in patient serum samples and other complex samples. To conquer this obstacle, this work presents a fully integrated bottom-gate poly-silcion nanowire (polySi NW) biosensor system-on-chip (SoC) to enhance the detection performance of cardiac-specific troponin-I (cTnI) concentration levels in serum samples. By applying proper electrical potential at the bottom gate under polySi NW biosensor, the biosensor response to cTnI biomarker can be improved by at least 16 fold in 50% phantom serum samples. The experimental result shows its detection range is from 3.2 × 10(-13)M(mol l(-1)) to 3.2 × 10(-10)M. This enhancement can be attributed to the electrostatic interactions between target biomolecules and voltage-applied bottom gate electrodes. This is the first time that a polySi NW CMOS biosensor chip has shown feasibilities to detect specific biomarkers in serum samples. Therefore, the developed technology paves the way toward on-field applications of CMOS compatible SiNW biosensing technologies and it can be employed for future biomolecular analysis in on-site serum diagnosis applications.

  11. Enhanced sample preparation for quantitation of microcystins by matrix-assisted laser desorption/ionisation-time of flight mass spectrometry.

    PubMed

    Puddick, Jonathan; Prinsep, Michèle R; Wood, Susanna A; Craig Cary, S; Hamilton, David P

    2012-01-01

    Microcystins (MCs) are a group of cyanotoxins which pose a serious health threat when present in aquatic systems. Quantitative analysis of MCs by matrix-assisted laser desorption/ionisation-time of flight (MALDI-TOF) mass spectrometry has potential for the processing of large numbers of samples quickly and economically. The existing method uses an expensive internal standard and protocols that are incompatible with automated sample preparation and data acquisition. To produce a MALDI-TOF sample preparation technique for the quantitation of MCs that not only maintains reproducibility and sensitivity, but is also compatible with an automated work-flow. Seven different MALDI-TOF sample preparations were assessed for signal reproducibility (coefficient of variation) and sensitivity (method detection limit) using a cost-effective internal standard (angiotensin I). The best preparation was then assessed for its quantitative performance using three different MC congeners ([Dha⁷] MC-LR, MC-RR and MC-YR). The sensitivity of six of the preparations was acceptable, as was the reproducibility for two thin-layer preparations performed on a polished steel target. Both thin-layer preparations could be used with a MALDI-TOF mass spectrometer that automatically acquires data, and one could be used in an automated sample preparation work-flow. Further investigation using the thin-layer spot preparation demonstrated that linear quantification of three different MC congeners was possible. The study demonstrates that with different sample preparation methods and modern instrumentation, large numbers of samples can be analysed rapidly for MCs at low cost. Copyright © 2011 John Wiley & Sons, Ltd.

  12. Impact of grey zone sample testing by enzyme-linked immunosorbent assay in enhancing blood safety: Experience at a tertiary care hospital in North India.

    PubMed

    Solanki, Archana; Singh, Abhay; Chaudhary, Rajendra

    2016-01-01

    Enzyme-linked immunosorbent assay (ELISA) used for screening blood donors for transfusion transmitted infections (TTIs) can sometimes fail to detect blood donors who are recently infected or possessing the low strength of pathogen. Estimation of a grey zone in ELISA testing and repeat testing of grey zone samples can further help in reducing the risks of TTI in countries where nucleic acid amplification testing for TTIs is not feasible. Grey zone samples with optical density (OD) lying between cut-off OD and 10% below the cut-off OD (cut-off OD × 0.9) were identified during routine ELISA testing. On performing repeat ELISA testing on grey zone samples in duplicate, the samples showing both OD value below grey zone were marked nonreactive, and samples showing one or both OD value in the grey zone were marked indeterminate. The samples on repeat testing showing one or both OD above cut-off value were marked positive. About 119 samples (77 for hepatitis B virus [HBV], 23 for human immunodeficiency virus [HIV], and 19 for hepatitis C virus [HCV]) were found to be in grey zone. On repeat testing of these samples in duplicate, 70 (58.8%) samples (45 for HBV, 12 for HIV, and 13 for HCV) were found to be reactive. Six (5%) samples (four for HBV, one for HIV, and one for HCV) were found to be indeterminate. Seventy donors initially screened negative, were found out to be potentially infectious on repeat grey zone testing. Thus, estimation of grey zone samples with repeat testing can further enhance the safety of blood transfusion.

  13. Sample-based engine noise synthesis using an enhanced pitch-synchronous overlap-and-add method.

    PubMed

    Jagla, Jan; Maillard, Julien; Martin, Nadine

    2012-11-01

    An algorithm for the real time synthesis of internal combustion engine noise is presented. Through the analysis of a recorded engine noise signal of continuously varying engine speed, a dataset of sound samples is extracted allowing the real time synthesis of the noise induced by arbitrary evolutions of engine speed. The sound samples are extracted from a recording spanning the entire engine speed range. Each sample is delimitated such as to contain the sound emitted during one cycle of the engine plus the necessary overlap to ensure smooth transitions during the synthesis. The proposed approach, an extension of the PSOLA method introduced for speech processing, takes advantage of the specific periodicity of engine noise signals to locate the extraction instants of the sound samples. During the synthesis stage, the sound samples corresponding to the target engine speed evolution are concatenated with an overlap and add algorithm. It is shown that this method produces high quality audio restitution with a low computational load. It is therefore well suited for real time applications.

  14. Human Milk Oligosaccharides and Lewis Blood Group: Individual High-Throughput Sample Profiling to Enhance Conclusions From Functional Studies12

    PubMed Central

    Blank, Dennis; Dotz, Viktoria; Geyer, Rudolf; Kunz, Clemens

    2012-01-01

    Human milk oligosaccharides (HMO) are discussed to play a crucial role in an infant’s development. Lewis blood group epitopes, in particular, seem to remarkably contribute to the beneficial effects of HMO. In this regard, large-scale functional human studies could provide evidence of the variety of results from in vitro investigations, although increasing the amount and complexity of sample and data handling. Therefore, reliable screening approaches are needed. To predict the oligosaccharide pattern in milk, the routine serological Lewis blood group typing of blood samples can be applied due to the close relationship between the biosynthesis of HMO and the Lewis antigens on erythrocytes. However, the actual HMO profile of the individual samples does not necessarily correspond to the serological determinations. This review demonstrates the capabilities of merging the traditional serological Lewis blood group typing with the additional information provided by the comprehensive elucidation of individual HMO patterns by means of state-of-the-art analytics. Deduced from the association of the suggested HMO biosynthesis with the Lewis blood group, the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry profiles of oligosaccharides in individual milk samples exemplify the advantages and the limitations of sample assignment to distinct groups. PMID:22585923

  15. Enhanced aerodynamic reach of vapor and aerosol sampling for real-time mass spectrometric detection using Venturi-assisted entrainment and ionization.

    PubMed

    Forbes, Thomas P; Staymates, Matthew

    2017-03-08

    Venturi-assisted ENTrainment and Ionization (VENTI) was developed, demonstrating efficient entrainment, collection, and transport of remotely sampled vapors, aerosols, and dust particulate for real-time mass spectrometry (MS) detection. Integrating the Venturi and Coandă effects at multiple locations generated flow and analyte transport from non-proximate locations and more importantly enhanced the aerodynamic reach at the point of collection. Transport through remote sampling probes up to 2.5 m in length was achieved with residence times on the order of 10(-2) s to 10(-1) s and Reynolds numbers on the order of 10(3) to 10(4). The Venturi-assisted entrainment successfully enhanced vapor collection and detection by greater than an order of magnitude at 20 cm stand-off (limit of simple suction). This enhancement is imperative, as simple suction restricts sampling to the immediate vicinity, requiring close proximity to the vapor source. In addition, the overall aerodynamic reach distance was increased by approximately 3-fold over simple suction under the investigated conditions. Enhanced aerodynamic reach was corroborated and observed with laser-light sheet flow visualization and schlieren imaging. Coupled with atmospheric pressure chemical ionization (APCI), the detection of a range of volatile chemical vapors; explosive vapors; explosive, narcotic, and mustard gas surrogate (methyl salicylate) aerosols; and explosive dust particulate was demonstrated. Continuous real-time Venturi-assisted monitoring of a large room (approximately 90 m(2) area, 570 m(3) volume) was demonstrated for a 60-min period without the remote sampling probe, exhibiting detection of chemical vapors and methyl salicylate at approximately 3 m stand-off distances within 2 min of exposure. Published by Elsevier B.V.

  16. Enhanced bacterial affinity of PVDF membrane: its application as improved sea water sampling tool for environmental monitoring.

    PubMed

    Kumar, Sweta Binod; Sharnagat, Preeti; Manna, Paramita; Bhattacharya, Amit; Haldar, Soumya

    2017-02-01

    Isolation of diversified bacteria from seawater is a major challenge in the field of environmental microbiology. In the present study, an attempt has been made to select specific membrane with improved property of attaching diversified bacteria. Initially, different concentrations (15, 18, and 20% W/W) of polysulfone (PSF) were used to check their affinity for the attachment of selected gram-positive (Bacillus subtilis) and gram-negative (Escherichia coli) bacteria. Among these, 20% W/W PSF showed maximum attachment. Therefore, membrane prepared with other materials such as polyvinylidene fluoride (PVDF) and polyether sulfone (PES) were used with the same concentration (20% W/W) to check their improved bacterial attachment property. Comparative study of bacterial attachment on three different membranes revealed that PVDF possessed the highest affinity towards both the groups of bacteria. This property was confirmed by different analytical methods viz. contact angle, atomic force microscopy, zeta potential, and flux study and further validated with seawater samples collected from seven sites of western coast and Lakshadweep island of India, using Biolog EcoPlate™. All the samples showed that bacterial richness and diversity was high in PVDF membrane in comparison to surrounding seawater samples. Interestingly, affinity for more diversified bacteria was reported to be higher in water sample with less turbidity and low bacteria load. This finding can facilitate the development of PVDF (20% W/W) membrane as a simple, cheap, and less labor intensive environmental sampling tool for the isolation of diversified bacteria from seawater sample wih different physiochemical properties. Graphical abstract ᅟ.

  17. Sparse multidimensional iterative lineshape-enhanced (SMILE) reconstruction of both non-uniformly sampled and conventional NMR data.

    PubMed

    Ying, Jinfa; Delaglio, Frank; Torchia, Dennis A; Bax, Ad

    2016-11-19

    Implementation of a new algorithm, SMILE, is described for reconstruction of non-uniformly sampled two-, three- and four-dimensional NMR data, which takes advantage of the known phases of the NMR spectrum and the exponential decay of underlying time domain signals. The method is very robust with respect to the chosen sampling protocol and, in its default mode, also extends the truncated time domain signals by a modest amount of non-sampled zeros. SMILE can likewise be used to extend conventional uniformly sampled data, as an effective multidimensional alternative to linear prediction. The program is provided as a plug-in to the widely used NMRPipe software suite, and can be used with default parameters for mainstream application, or with user control over the iterative process to possibly further improve reconstruction quality and to lower the demand on computational resources. For large data sets, the method is robust and demonstrated for sparsities down to ca 1%, and final all-real spectral sizes as large as 300 Gb. Comparison between fully sampled, conventionally processed spectra and randomly selected NUS subsets of this data shows that the reconstruction quality approaches the theoretical limit in terms of peak position fidelity and intensity. SMILE essentially removes the noise-like appearance associated with the point-spread function of signals that are a default of five-fold above the noise level, but impacts the actual thermal noise in the NMR spectra only minimally. Therefore, the appearance and interpretation of SMILE-reconstructed spectra is very similar to that of fully sampled spectra generated by Fourier transformation.

  18. Enhanced conformational sampling method for proteins based on the TaBoo SeArch algorithm: application to the folding of a mini-protein, chignolin.

    PubMed

    Harada, Ryuhei; Takano, Yu; Shigeta, Yasuteru

    2015-04-15

    The conformational samplings are indispensible for obtaining reliable canonical ensembles, which provide statistical averages of physical quantities such as free energies. However, the samplings of vast conformational space of biomacromolecules by conventional molecular dynamics (MD) simulations might be insufficient, due to their inadequate accessible time-scales for investigating biological functions. Therefore, the development of methodologies for enhancing the conformational sampling of biomacromolecules still remains as a challenging issue in computational biology. To tackle this problem, we newly propose an efficient conformational search method, which is referred as TaBoo SeArch (TBSA) algorithm. In TBSA, an inverse energy histogram is used to select seeds for the conformational resampling so that states with high frequencies are inhibited, while states with low frequencies are efficiently sampled to explore the unvisited conformational space. As a demonstration, TBSA was applied to the folding of a mini-protein, chignolin, and automatically sampled the native structure (Cα root mean square deviation < 1.0 Å) with nanosecond order computational costs started from a completely extended structure, although a long-time 1-µs normal MD simulation failed to sample the native structure. Furthermore, a multiscale free energy landscape method based on the conformational sampling of TBSA were quantitatively evaluated through free energy calculations with both implicit and explicit solvent models, which enable us to find several metastable states on the folding landscape. © 2015 Wiley Periodicals, Inc.

  19. Accuracy Enhancement of Raman Spectroscopy Using Complementary Laser-Induced Breakdown Spectroscopy (LIBS) with Geologically Mixed Samples.

    PubMed

    Choi, Soojin; Kim, Dongyoung; Yang, Junho; Yoh, Jack J

    2017-04-01

    Quantitative Raman analysis was carried out with geologically mixed samples that have various matrices. In order to compensate the matrix effect in Raman shift, laser-induced breakdown spectroscopy (LIBS) analysis was performed. Raman spectroscopy revealed the geological materials contained in the mixed samples. However, the analysis of a mixture containing different matrices was inaccurate due to the weak signal of the Raman shift, interference, and the strong matrix effect. On the other hand, the LIBS quantitative analysis of atomic carbon and calcium in mixed samples showed high accuracy. In the case of the calcite and gypsum mixture, the coefficient of determination of atomic carbon using LIBS was 0.99, while the signal using Raman was less than 0.9. Therefore, the geological composition of the mixed samples is first obtained using Raman and the LIBS-based quantitative analysis is then applied to the Raman outcome in order to construct highly accurate univariate calibration curves. The study also focuses on a method to overcome matrix effects through the two complementary spectroscopic techniques of Raman spectroscopy and LIBS.

  20. Surface-enhanced Raman spectroscopy (SERS) for identifying traces of adenine in different mineral and rock samples

    NASA Astrophysics Data System (ADS)

    Lafuente, B.; Navarro, R.; Sansano, A.; Rull, F.

    2012-09-01

    The aim of this study is to analyze the potentials of SERS as a technique for in-situ identification of life traces in Mars surface explorations using the Raman instrument (RLS), payload of the ESA Mars mission Exomars. This preliminary study focused on detection of adenine on a variety of rocks soils samples using macro-SERS detection.

  1. Theta- and alpha-power enhancements in the electroencephalogram as an auditory delayed match-to-sample task becomes impossibly difficult.

    PubMed

    Wisniewski, Matthew G; Thompson, Eric R; Iyer, Nandini

    2017-08-09

    Recent studies have related enhancements of theta- (∼4-8 Hz) and alpha-power (∼8-13 Hz) to listening effort based on parallels between enhancement and task difficulty. In contrast, nonauditory works demonstrate that, although increases in difficulty are initially accompanied by increases in effort, effort decreases when a task becomes so difficult as to exceed one's ability. Given the latter, we examined whether theta- and alpha-power enhancements thought to reflect effortful listening show a quadratic trend across levels of listening difficulty from impossible to easy. Listeners (n = 14) performed an auditory delayed match-to-sample task with frequency-modulated tonal sweeps under impossible, difficult (at ∼70.7% correct threshold), and easy (well above threshold) conditions. Frontal midline theta-power and posterior alpha-power enhancements were observed during the retention interval, with greatest enhancement in the difficult condition. Independent component-based analyses of data suggest that theta-power enhancements stemmed from medial frontal sources at or near the anterior cingulate cortex, whereas alpha-power effects stemmed from occipital cortices. Results support the notion that theta- and alpha-power enhancements reflect effortful cognitive processes during listening, related to auditory working memory and the inhibition of task-irrelevant cortical processing regions, respectively. Theta- and alpha-power dynamics can be used to characterize the cognitive processes that make up effortful listening, including qualitatively different types of listening effort. This article has been contributed to by US Government employees and their work is in the public domain in the USA. © 2017 Society for Psychophysiological Research.

  2. Dynamic nuclear polarization-enhanced 1H–13C double resonance NMR in static samples below 20 K

    PubMed Central

    Potapov, Alexey; Thurber, Kent R.; Yau, Wai-Ming; Tycko, Robert

    2012-01-01

    We demonstrate the feasibility of one-dimensional and two-dimensional 1H–13C double resonance NMR experiments with dynamic nuclear polarization (DNP) at 9.4 T and temperatures below 20 K, including both 1H–13C cross-polarization and 1H decoupling, and discuss the effects of polarizing agent type, polarizing agent concentration, temperature, and solvent deuteration. We describe a two-channel low-temperature DNP/NMR probe, capable of carrying the radio-frequency power load required for 1H–13C cross-polarization and high-power proton decoupling. Experiments at 8 K and 16 K reveal a significant T2 relaxation of 13C, induced by electron spin flips. Carr–Purcell experiments and numerical simulations of Carr–Purcell dephasing curves allow us to determine the effective correlation time of electron flips under our experimental conditions. The dependence of the DNP signal enhancement on electron spin concentration shows a maximum near 80 mM. Although no significant difference in the absolute DNP enhancements for triradical (DOTOPA-TEMPO) and biradical (TOTAPOL) dopants was found, the triradical produced greater DNP build-up rates, which are advantageous for DNP experiments. Additionally the feasibility of structural measurements on 13C-labeled biomolecules was demonstrated with a two-dimensional 13C–13C exchange spectrum of selectively 13C-labeled β-amyloid fibrils. PMID:22743540

  3. Molecular dynamics-based approaches for enhanced sampling of long-time, large-scale conformational changes in biomolecules

    PubMed Central

    2009-01-01

    The rugged energy landscape of biomolecules together with shortcomings of traditional molecular dynamics (MD) simulations require specialized methods for capturing large-scale, long-time configurational changes along with chemical dynamics behavior. In this report, MD-based methods for biomolecules are surveyed, involving modification of the potential, simulation protocol, or algorithm as well as global reformulations. While many of these methods are successful at probing the thermally accessible configuration space at the expense of altered kinetics, more sophisticated approaches like transition path sampling or Markov chain models are required to obtain mechanistic information, reaction pathways, and/or reaction rates. Divide-and-conquer methods for sampling and for piecing together reaction rate information are especially suitable for readily available computer cluster networks. Successful applications to biomolecules remain a challenge. PMID:20948633

  4. Enhanced cellular responses and environmental sampling within inner foreskin explants: implications for the foreskin's role in HIV transmission.

    PubMed

    Fahrbach, K M; Barry, S M; Anderson, M R; Hope, T J

    2010-07-01

    The decrease in HIV acquisition after circumcision suggests a role for the foreskin in HIV transmission. However, the mechanism leading to protection remains undefined. Using tissue explant cultures we found that Langerhans cells (LCs) in foreskin alter their cellular protein expression in response to external stimuli. Furthermore, we observe that upon treatment with TNF-alpha, tissue-resident LCs became activated and that stimulatory cytokines can specifically cause an influx of CD4+ T-cells into the epithelial layer. Importantly, both of these changes are significant in the inner, but not outer, foreskin. In addition, we find that LCs in the inner foreskin have increased ability to sample environmental proteins. These results suggest differences in permeability between the inner and outer foreskin and indicate that HIV target cells in the inner foreskin have increased interaction with external factors. This increased responsiveness and sampling provides novel insights into the underlying mechanism of how circumcision can decrease HIV transmission.

  5. Chemometrics enhanced HPLC-DAD performance for rapid quantification of carbamazepine and phenobarbital in human serum samples.

    PubMed

    Vosough, Maryam; Ghafghazi, Shiva; Sabetkasaei, Masoumeh

    2014-02-01

    This paper describes development and validation of a simple and efficient bioanalytical procedure for simultaneous determination of phenobarbital and carbamazepine in human serum samples using high performance liquid chromatography with photodiode-array detection (HPLC-DAD) regarding a fast elution methodology in less than 5 min. Briefly, this method consisted of a simple deproteinization step of serum samples followed by HPLC analysis on a Bonus-RP column using an isocratic mode of elution with acetonitrile/K2HPO4 (pH=7.5) buffer solution (45:55). Due to the presence of serum endogenous components as non-calibrated components in the sample, second-order calibration based on multivariate curve resolution-alternating least squares (MCR-ALS), has been applied on a set of absorbance matrices collected as a function of retention time and wavelengths. Acceptable resolution and quantification results were achieved in the presence of matrix interferences and the second-order advantage was fully exploited. The average recoveries for carbamazepine and phenobarbital were 89.7% and 86.1% and relative standard deviation values were lower than 9%. Additionally, computed elliptical joint confidence region (EJCR) confirmed the accuracy of the proposed method and indicated the absence of both constant and proportional errors in the predicted concentrations. The developed method enabled the determination of the analytes in different serum samples in the presence of overlapped profiles, while keeping experimental time and extraction steps at minimum. Finally, the serum concentration levels of carbamazepine in three time intervals were reported for morphine-dependents who had received carbamazepine for treating their neuropathic pain. © 2013 Elsevier B.V. All rights reserved.

  6. Dynamic multidetector CT and non-contrast-enhanced MR for right adrenal vein imaging: comparison with catheter venography in adrenal venous sampling.

    PubMed

    Ota, Hideki; Seiji, Kazumasa; Kawabata, Masahiro; Satani, Nozomi; Omata, Kei; Ono, Yoshikiyo; Iwakura, Yoshitsugu; Morimoto, Ryo; Matsuura, Tomonori; Kudo, Masataka; Tominaga, Junya; Satoh, Fumitoshi; Ito, Sadayoshi; Takase, Kei

    2016-03-01

    To evaluate visualization of the right adrenal vein (RAV) with multidetector CT and non-contrast-enhanced MR imaging in patients with primary aldosteronism. A total of 125 patients (67 men) scheduled for adrenal venous sampling (AVS) were included. Dynamic 64-detector-row CT and balanced steady-state free precession-based non-contrast-enhanced 3-T MR imaging were performed. RAV visualization based on a four-point score was documented. Both anatomical location and variation on cross-sectional imaging were evaluated, and the findings were compared with catheter venography as the gold standard. The RAV was visualized in 93.2% by CT and 84.8% by MR imaging (p = 0.02). Positive predictive values of RAV visualization were 100% for CT and 95.2% for MR imaging. Imaging score was significantly higher in CT than MR imaging (p < 0.01). The RAV formed a common trunk with an accessory hepatic vein in 16% of patients. The RAV orifice level on cross-sectional imaging was concordant with catheter venography within the range of 1/3 vertebral height in >70% of subjects. Success rate of AVS was 99.2%. Dynamic CT is a reliable way to map the RAV prior to AVS. Non-contrast-enhanced MR imaging is an alternative when there is a risk of complication from contrast media or radiation exposure. Dynamic CT and non-contrast-enhanced MR imaging detect the right adrenal vein (RAV). Dynamic CT can visualize the RAV more than non-contrast-enhanced MR imaging. Mapping the RAV helps to achieve successful adrenal venous sampling. Sixteen per cent of RAVs share the common trunk with accessory hepatic veins.

  7. Overcoming barriers in trajectory space: mechanism and kinetics of rare events via Wang-Landau enhanced transition path sampling.

    PubMed

    Borrero, Ernesto E; Dellago, Christoph

    2010-10-07

    Within the framework of transition path sampling (TPS), activation energies can be computed as path ensemble averages without a priori information about the reaction mechanism [C. Dellago and P. G. Bolhuis, Mol. Simul. 30, 795 (2004)]. Activation energies computed for different conditions can then be used to determine by numerical integration the rate constant for a system of interest from the rate constant known for a reference system. However, in systems with complex potential energy surfaces, multiple reaction pathways may exist making ergodic sampling of trajectory space difficult. Here, we present a combination of TPS with the Wang-Landau (WL) flat-histogram algorithm for an efficient sampling of the transition path ensemble. This method, denoted by WL-TPS, has the advantage that from one single simulation, activation energies at different temperatures can be determined even for systems with multiple reaction mechanisms. The proposed methodology for rate constant calculations does not require the knowledge of the reaction coordinate and is generally applicable to Arrhenius and non-Arrhenius processes. We illustrate the applicability of this technique by studying a two-dimensional toy system consisting of a triatomic molecule immersed in a fluid of repulsive soft disks. We also provide an expression for the calculation of activation volumes from path averages such that the pressure dependence of the rate constant can be obtained by numerical integration.

  8. A novel hybrid mode of sample injection to enhance CZE sensitivity for simultaneous determination of a pyridine-triphenylborane anti-fouling agent and its degradation products.

    PubMed

    Kaewchuay, Netnapit; Yakushiji, Yuki; Fukushi, Keiichi; Saito, Keiitsu; Hirokawa, Takeshi

    2011-06-01

    We developed a novel hybrid sample injection mode (HSIM) that presents the combination of electrokinetic injection and vacuum injection to enhance detection sensitivity in CZE. Samples were introduced using both vacuum and electrokinetic injections simultaneously, with a water plug injected into the capillary prior to sample introduction (i.e. similarly to field-amplified sample injection, FASI). Using a sample mixture containing an anti-fouling agent applied to ship hulls, pyridine-triphenylborane and its degradation products (diphenylborinic acid, phenylboronic acid, and phenol) dissolved in ACN, the length of water plug, time, and voltage for sample introduction were optimized. The signal intensity (peak height) was found to be up to a 30-fold increased using HSIM by applying 4 kV for 4 s at the inlet end of the capillary as the cathode with supplementary vacuum in comparison with only vacuum injection for 4 s. The LODs (at a S/N of 3) for pyridine-triphenylborane, diphenylborinic acid, phenylboronic acid, and phenol were 0.88, 1.0, 21, and 23 μg/L, respectively. At the level of 0.04 mg/L, the RSDs (n=4, intra-day) for the above analytes were in the ranges of 1.9-11, 4.3-9.2, and 0.34-0.66% for peak area, peak height, and migration time, respectively. The HSIM is a simple and promising procedure useful for enhancing the sensitivity for both low-and high-mobility ions in CZE.

  9. An enhanced technique combining pre-enrichment and passive filtration increases the isolation efficiency of Campylobacter jejuni and Campylobacter coli from water and animal fecal samples.

    PubMed

    Jokinen, Cassandra C; Koot, Jacqueline M; Carrillo, Catherine D; Gannon, Victor P J; Jardine, Claire M; Mutschall, Steven K; Topp, Edward; Taboada, Eduardo N

    2012-12-01

    Improved isolation techniques from environmental water and animal samples are vital to understanding Campylobacter epidemiology. In this study, the efficiency of selective enrichment in Bolton Broth (BB) followed by plating on charcoal cefoperazone deoxycholate agar (CCDA) (conventional method) was compared with an approach combining BB enrichment and passive filtration (membrane method) adapted from a method previously developed for testing of broiler meat, in the isolation of thermophilic campylobacters from surface water and animal fecal samples. The conventional method led to recoveries of Campylobacter from 36.7% of the water samples and 78.0% of the fecal samples and similar numbers, 38.3% and 76.0%, respectively, were obtained with the membrane method. To investigate the genetic diversity of Campylobacter jejuni and Campylobacter coli obtained by these two methods, isolates were analyzed using Comparative Genomic Fingerprinting, a high-resolution subtyping technique. The conventional and membrane methods yielded similar numbers of Campylobacter subtypes from water (25 and 28, respectively) and fecal (15 and 17, respectively) samples. Although there was no significant difference in recovery rates between the conventional and membrane methods, a significant improvement in isolation efficiency was obtained by using the membrane method, with a false-positive rate of 1.6% compared with 30.7% obtained using the conventional method. In conclusion, although the two methods are comparable in sensitivity, the membrane method had higher specificity, making it a cost-effective procedure for the enhanced isolation of C. jejuni and C. coli from water and animal fecal samples.

  10. Surfactant-enhanced spectrofluorimetric determination of total aflatoxins from wheat samples after magnetic solid-phase extraction using modified Fe₃O₄ nanoparticles.

    PubMed

    Manafi, Mohammad Hanif; Allahyari, Mehdi; Pourghazi, Kamyar; Amoli-Diva, Mitra; Taherimaslak, Zohreh

    2015-07-05

    The extraction and preconcentration of total aflatoxins (including aflatoxin B1, B2, G1, and G2) using magnetic nanoparticles based solid phase extraction (MSPE) followed by surfactant-enhanced spectrofluorimetric detection was proposed. Ethylene glycol bis-mercaptoacetate modified silica coated Fe3O4 nanoparticles as an efficient antibody-free adsorbent was successfully applied to extract aflatoxins from wheat samples. High surface area and strong magnetization properties of magnetic nanoparticles were utilized to achieve high enrichment factor (97), and satisfactory recoveries (92-105%) using only 100mg of the adsorbent. Furthermore, the fast separation time (less than 10 min) avoids many time-consuming cartridge loading or column-passing procedures accompany with the conventional SPE. In determination step, signal enhancement was performed by formation of Triton X-100 micelles around the analytes in 15% (v/v) acetonitrile-water which dramatically increase the sensitivity of the method. Main factors affecting the extraction efficiency and signal enhancement of the analytes including pH of sample solution, desorption conditions, extraction time, sample volume, adsorbent amount, surfactant concentration and volume and time of micelle formation were evaluated and optimized. Under the optimum conditions, wide linear range of 0.1-50 ng mL(-1) with low detection limit of 0.03 ng mL(-1) were obtained. The developed method was successfully applied to the extraction and preconcentration of aflatoxins in three commercially available wheat samples and the results were compared with the official AOAC method. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. Dynamic nuclear polarization-enhanced ¹H-¹³C double resonance NMR in static samples below 20 K.

    PubMed

    Potapov, Alexey; Thurber, Kent R; Yau, Wai-Ming; Tycko, Robert

    2012-08-01

    We demonstrate the feasibility of one-dimensional and two-dimensional ¹H-¹³C double resonance NMR experiments with dynamic nuclear polarization (DNP) at 9.4 T and temperatures below 20 K, including both ¹H-¹³C cross-polarization and ¹H decoupling, and discuss the effects of polarizing agent type, polarizing agent concentration, temperature, and solvent deuteration. We describe a two-channel low-temperature DNP/NMR probe, capable of carrying the radio-frequency power load required for ¹H-¹³C cross-polarization and high-power proton decoupling. Experiments at 8 K and 16 K reveal a significant T₂ relaxation of ¹³C, induced by electron spin flips. Carr-Purcell experiments and numerical simulations of Carr-Purcell dephasing curves allow us to determine the effective correlation time of electron flips under our experimental conditions. The dependence of the DNP signal enhancement on electron spin concentration shows a maximum near 80 mM. Although no significant difference in the absolute DNP enhancements for triradical (DOTOPA-TEMPO) and biradical (TOTAPOL) dopants was found, the triradical produced greater DNP build-up rates, which are advantageous for DNP experiments. Additionally the feasibility of structural measurements on ¹³C-labeled biomolecules was demonstrated with a two-dimensional ¹³C-¹³C exchange spectrum of selectively ¹³C-labeled β-amyloid fibrils. Copyright © 2012 Elsevier Inc. All rights reserved.

  12. Selective melamine detection in multiple sample matrices with a portable Raman instrument using surface enhanced Raman spectroscopy-active gold nanoparticles.

    PubMed

    Mecker, Laura C; Tyner, Katherine M; Kauffman, John F; Arzhantsev, Sergey; Mans, Daniel J; Gryniewicz-Ruzicka, Connie M

    2012-07-06

    Melamine adulteration of food and pharmaceutical products is a major concern and there is a growing need to protect the public from exposure to contaminated or adulterated products. One approach to reduce this threat is to develop a portable method for on-site rapid testing. We describe a universal and selective method for the detection of melamine in a variety of solid matrices at the 100-200 μg L(-1) level by surface enhanced Raman spectroscopy (SERS) with gold nanoparticles. With minimal sample preparation and the use of a portable Raman spectrometer, this work will lead to field-based screening for melamine adulteration. Citrate coated gold nanoparticles (Au NPs) were investigated for both colorimetric and Raman-based responses. Several non-hazardous solvents were evaluated in order to develop a melamine extraction procedure safe for field applications. Au NP agglomerates formed by the addition of isopropanol (IPA) prior to sample introduction enhanced the Raman signal for melamine and eliminated matrix interference for substrate formation. The melamine Raman signal resulted in a 10(5) enhancement through the use of Au NP agglomerates. To our knowledge, we have developed the first portable SERS method using Au NPs to selectively screen for the presence of melamine adulteration in a variety of food and pharmaceutical matrices, including milk powder, infant formula, lactose, povidone, whey protein, wheat bran and wheat gluten. Published by Elsevier B.V.

  13. Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples.

    PubMed

    Matranga, Christian B; Andersen, Kristian G; Winnicki, Sarah; Busby, Michele; Gladden, Adrianne D; Tewhey, Ryan; Stremlau, Matthew; Berlin, Aaron; Gire, Stephen K; England, Eleina; Moses, Lina M; Mikkelsen, Tarjei S; Odia, Ikponmwonsa; Ehiane, Philomena E; Folarin, Onikepe; Goba, Augustine; Kahn, S Humarr; Grant, Donald S; Honko, Anna; Hensley, Lisa; Happi, Christian; Garry, Robert F; Malboeuf, Christine M; Birren, Bruce W; Gnirke, Andreas; Levin, Joshua Z; Sabeti, Pardis C

    2014-01-01

    We have developed a robust RNA sequencing method for generating complete de novo assemblies with intra-host variant calls of Lassa and Ebola virus genomes in clinical and biological samples. Our method uses targeted RNase H-based digestion to remove contaminating poly(rA) carrier and ribosomal RNA. This depletion step improves both the quality of data and quantity of informative reads in unbiased total RNA sequencing libraries. We have also developed a hybrid-selection protocol to further enrich the viral content of sequencing libraries. These protocols have enabled rapid deep sequencing of both Lassa and Ebola virus and are broadly applicable to other viral genomics studies.

  14. Chemiluminescence determination of moxifloxacin in pharmaceutical and biological samples based on its enhancing effect of the luminol-ferricyanide system using a microfluidic chip.

    PubMed

    Suh, Yeoun Suk; Kamruzzaman, Mohammad; Alam, Al-Mahmnur; Lee, Sang Hak; Kim, Young Ho; Kim, Gyu-Man; Dang, Trung Dung

    2014-05-01

    A sensitive determination of a synthetic fluoroquinolone antibacterial agent, moxifloxacin (MOX), by an enhanced chemiluminescence (CL) method using a microfluidic chip is described. The microfluidic chip was fabricated by a soft-lithographic procedure using polydimethyl siloxane (PDMS). The fabricated PDMS microfluidic chip had three-inlet microchannels for introducing the sample, chemiluminescent reagent and oxidant, and a 500 µm wide, 250 µm deep and 82 mm long microchannel. An enhanced CL system, luminol-ferricyanide, was adopted to analyze the MOX concentration in a sample solution. CL light was emitted continuously after mixing luminol and ferricyanide in the presence of MOX on the PDMS microfluidic chip. The amount of MOX in the luminol-ferricyanide system influenced the intensity of the CL light. The linear range of MOX concentration was 0.14-55.0 ng/mL with a correlation coefficient of 0.9992. The limit of detection (LOD) and limit of quantification (LOQ) were 0.06 and 0.2 ng/mL respectively. The presented method afforded good reproducibility, with a relative standard deviation (RSD) of 1.05% for 10 ng/mL of MOX, and has been successfully applied for the determination of MOX in pharmaceutical and biological samples.

  15. Flow-injection chemiluminescence determination of cloxacillin in water samples and pharmaceutical preparation by using CuO nanosheets-enhanced luminol-hydrogen peroxide system

    NASA Astrophysics Data System (ADS)

    Khataee, Alireza; Iranifam, Mortaza; Fathinia, Mehrangiz; Nikravesh, Mina

    2015-01-01

    In this paper, a rapid and sensitive flow-injection chemiluminescence (flow-CL) system was developed for the determination of cloxacillin sodium in environmental water samples and pharmaceutical preparations. The method was based on the enhancement effect of cloxacillin sodium on the CL reaction of luminal-H2O2-CuO nanosheets (NSs) in alkaline medium. The CuO nanosheets were synthesized using a green sonochemical method. The physical properties of the synthesized CuO nanosheets were characterized by X-ray diffraction (XRD) and scanning electron microscopy (SEM) analyses. The influences of various experimental factors such as H2O2, NaOH, luminol and CuO nanosheets concentrations were investigated. Under the optimum conditions, the enhanced CL intensity was linearly related to the concentration of cloxacillin sodium in the range of the 0.05-30.00 mg L-1 with a correlation coefficient of 0.995. The corresponding detection limit (3σ) was calculated to be 0.026 mg L-1. The relative standard deviation (RSD) of the developed method was 2.21% with 11 repeated measurements of 4.00 mg L-1 cloxacillin sodium. Also, a total analysis time per sample was 30 s which confirmed the rapidity of the proposed method. The analytical applicability of the proposed CL system was assessed by determining cloxacillin sodium in spiked environmental water samples and pharmaceutical preparation. Furthermore, the possible mechanism of CL reaction was discussed.

  16. Flow-injection chemiluminescence determination of cloxacillin in water samples and pharmaceutical preparation by using CuO nanosheets-enhanced luminol-hydrogen peroxide system.

    PubMed

    Khataee, Alireza; Iranifam, Mortaza; Fathinia, Mehrangiz; Nikravesh, Mina

    2015-01-05

    In this paper, a rapid and sensitive flow-injection chemiluminescence (flow-CL) system was developed for the determination of cloxacillin sodium in environmental water samples and pharmaceutical preparations. The method was based on the enhancement effect of cloxacillin sodium on the CL reaction of luminal-H₂O₂-CuO nanosheets (NSs) in alkaline medium. The CuO nanosheets were synthesized using a green sonochemical method. The physical properties of the synthesized CuO nanosheets were characterized by X-ray diffraction (XRD) and scanning electron microscopy (SEM) analyses. The influences of various experimental factors such as H₂O₂, NaOH, luminol and CuO nanosheets concentrations were investigated. Under the optimum conditions, the enhanced CL intensity was linearly related to the concentration of cloxacillin sodium in the range of the 0.05-30.00 mg L(-1) with a correlation coefficient of 0.995. The corresponding detection limit (3σ) was calculated to be 0.026 mg L(-1). The relative standard deviation (RSD) of the developed method was 2.21% with 11 repeated measurements of 4.00 mg L(-1) cloxacillin sodium. Also, a total analysis time per sample was 30 s which confirmed the rapidity of the proposed method. The analytical applicability of the proposed CL system was assessed by determining cloxacillin sodium in spiked environmental water samples and pharmaceutical preparation. Furthermore, the possible mechanism of CL reaction was discussed.

  17. Determination of Lead in Water Samples Using a New Vortex-Assisted, Surfactant-Enhanced Emulsification Liquid-Liquid Microextraction Combined with Graphite Furnace Atomic Absorption Spectrometry.

    PubMed

    Peng, Guilong; He, Qiang; Lu, Ying; Mmereki, Daniel; Pan, Weiliang; Tang, Xiaohui; Zhou, Guangming; Mao, Yufeng; Su, Xaioxuan

    2016-04-01

    A low toxic solvent-based vortex-assisted surfactant-enhanced emulsification liquid-liquid microextraction (LT-VSLLME) combined with graphite furnace atomic absorption spectrometry was developed for the extraction and determination of lead (Pb) in water samples. In the LT-VSLLME method, the extraction solvent was dispersed into the aqueous samples by the assistance of vortex agitator. Meanwhile, the addition of a surfactant, which acted as an emulsifier, could enhance the speed of the mass-transfer from aqueous samples to the extraction solvent. The influences of analytical parameters, including extraction solvent type and its volume, surfactant type and its volume, pH, concentration of chelating agent, salt effect and extraction time were investigated. Under the optimized conditions, a good relative standard deviation of 3.69% at 10 ng L(-1) was obtained. The calibration graph showed a linear pattern in the ranges of 5-30 ngL(-1), with a limit of detection of 0.76 ng L(-1). The linearity was obtained by five points in the concentration range of 5-30 ngL(-1). The enrichment factor was 320. The procedure was applied to wastewater and river water, and the accuracy was assessed through the analysis of the recovery experiments.

  18. Ionic-liquid-based, manual-shaking- and ultrasound-assisted, surfactant-enhanced emulsification microextraction for the determination of three fungicide residues in juice samples.

    PubMed

    Chen, Xiaochu; You, Xiangwei; Liu, Fengmao; Hou, Fan; Zhang, Xu

    2015-01-01

    A novel manual-shaking- and ultrasound-assisted surfactant-enhanced emulsification microextraction method was developed for the determination of three fungicides in juice samples. In this method, the ionic liquid, 1-ethyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]imide, instead of a volatile organic solvent was used as the extraction solvent. The surfactant, NP-10, was used as an emulsifier to enhance the dispersion of the water-immiscible ionic liquid into an aqueous phase, which accelerated the mass transfer of the analytes. Organic dispersive solvent typically required in common dispersive liquid-liquid microextraction methods was not necessary. In addition, manual shaking for 15 s before ultrasound to preliminarily mix the extraction solvent and the aqueous sample could greatly shorten the time for dispersing the ionic liquid into aqueous solution by ultrasound irradiation. Several experimental parameters affecting the extraction efficiency, including type and volume of extraction solvent, type and concentration of surfactant, extraction time, and pH, were optimized. Under the optimized conditions, good linearity with the correlation coefficients (γ) higher than 0.9986 and high sensitivity with the limit of detection ranging from 0.4 to 1.6 μg/L were obtained. The average recoveries ranged from 61.4 to 86.0% for spiked juice, with relative standard deviations from 1.8 to 9.7%. The proposed method was demonstrated to be a simple, fast, and efficient method for the analysis of the target fungicides in juice samples.

  19. Ionic liquid-based dispersive liquid-liquid microextraction and enhanced spectrophotometric determination of molybdenum (VI) in water and plant leaves samples by FO-LADS.

    PubMed

    Gharehbaghi, Maysam; Shemirani, Farzaneh

    2011-02-01

    A new simple and rapid ionic liquid-based dispersive liquid-liquid microextraction (IL-DLLME) has been applied to preconcentrate trace levels of molybdenum (VI) as a prior step to its enhanced determination by fiber optic-linear array detection spectrophotometry (FO-LADS). In this method, a small amount of [Hmim][Tf(2)N] (1-hexyl-3-methylimmidazolium bis (trifluormethylsulfonyl) imid) as an extraction solvent was applied to extract molybdenum - pyrogallol red complex, which was formed in an aqueous solution in the presence of N-cetyl-N-N-N-trimethyl ammonium chloride as a sensitizing agent. Under optimum conditions, enhancement factor, detection limit and relative standard deviation (n=5, for 30 μg L(-1) of molybdenum (VI)) in 10 mL water sample were 72.6, 1.43 μg L(-1) and 2.8%, respectively.

  20. Relative independence of luminol-enhanced intensity of photon emission during oxidative burst from nondiluted human blood on the volume and surface area of the sample

    NASA Astrophysics Data System (ADS)

    Voeikov, Vladimir L.; Novikov, Cyril N.

    1997-05-01

    Parameters of chemiluminescence (CL) from nondiluted human blood were studied. Kinetics and intensity of CL depended upon donor's state of health, time after blood extravasion, conditions of its storage, conditions of its counting. Peculiar dependence of Luminol-enhanced CL on sample volume changes during respiratory burst (RB) was revealed. When 0.5 ml aliquots were consecutively taken from blood and transferred into another vial of the same configuration, each subtraction of blood was followed by an acceleration of CL intensity growth. Summation of portions of blood in the second vial resulted in deceleration of CL intensity increase from it. At equal volumes of blood CL intensity from the first sample was manifold higher than from the second one and this difference was increasing on with further transfers. When blood was transferred back to the first sample, CL intensity from the 'donor' sample began to increase at a faster rate, while CL intensity from the 'recipient' sample stabilized. Such behavior was characteristic of nondiluted healthy donors' blood. Diluted blood or blood of sick people demonstrated different behavior. It is suggested that CL parameters of nondiluted blood may be informative of integrative properties of blood tissue.

  1. Method Comparison for Enhanced Recovery, Isolation and Qualitative Detection of C. jejuni and C. coli from Wastewater Effluent Samples

    PubMed Central

    Ugarte-Ruiz, María; Florez-Cuadrado, Diego; Wassenaar, Trudy M.; Porrero, María Concepción; Domínguez, Lucas

    2015-01-01

    Seeking a sensitive protocol, culture-dependent methods were compared to detect thermophilic Campylobacter species in untreated urban effluents. We evaluated various combinations of selective media, with and without an enrichment steps, as well as an extra filtration step. Culture-independent real-time quantitative PCR was also included and all detected isolates underwent antimicrobial susceptibility testing. All tested water samples contained Campylobacter DNA, but only 64% were positive after culture. Although enrichment using Preston broth resulted in better recovery of potentially stressed Campylobacter than Bolton or Campyfood broth (CFB), there was no significant increase in efficiency compared to direct plating. The type of selective agar media used, on the other hand, had a significant effect, with CASA plates performing better than mCCDA or CFA ones. Inclusion of an enrichment step increased the ratio of C. coli vs. C. jejuni being isolated. Resistances against all antimicrobials tested were observed in C. coli, but fewer instances of resistance were found in C. jejuni isolates. Whether this difference was the result of selection during the enrichment step could not be determined. The presence of Campylobacter in urban effluents can be considered as a valuable proxy for Campylobacter populations present in urban environments. PMID:25739008

  2. Method comparison for enhanced recovery, isolation and qualitative detection of C. jejuni and C. coli from wastewater effluent samples.

    PubMed

    Ugarte-Ruiz, María; Florez-Cuadrado, Diego; Wassenaar, Trudy M; Porrero, María Concepción; Domínguez, Lucas

    2015-03-02

    Seeking a sensitive protocol, culture-dependent methods were compared to detect thermophilic Campylobacter species in untreated urban effluents. We evaluated various combinations of selective media, with and without an enrichment steps, as well as an extra filtration step. Culture-independent real-time quantitative PCR was also included and all detected isolates underwent antimicrobial susceptibility testing. All tested water samples contained Campylobacter DNA, but only 64% were positive after culture. Although enrichment using Preston broth resulted in better recovery of potentially stressed Campylobacter than Bolton or Campyfood broth (CFB), there was no significant increase in efficiency compared to direct plating. The type of selective agar media used, on the other hand, had a significant effect, with CASA plates performing better than mCCDA or CFA ones. Inclusion of an enrichment step increased the ratio of C. coli vs. C. jejuni being isolated. Resistances against all antimicrobials tested were observed in C. coli, but fewer instances of resistance were found in C. jejuni isolates. Whether this difference was the result of selection during the enrichment step could not be determined. The presence of Campylobacter in urban effluents can be considered as a valuable proxy for Campylobacter populations present in urban environments.

  3. Capillary zone electrophoresis with field enhanced sample stacking as a tool for targeted metabolome analysis of adenine nucleotides and coenzymes in Paracoccus denitrificans.

    PubMed

    Musilová, Jindra; Sedlácek, Vojtech; Kucera, Igor; Glatz, Zdenek

    2009-07-01

    The main aim of this work was to demonstrate the applicability of capillary zone electrophoresis in combination with field enhanced sample stacking in targeted metabolome analyses of adenine nucleotides--AMP, ADP, ATP, coenzymes NAD(+), NADP(+) and their reduced forms in Paracoccus denitrificans. Sodium carbonate/hydrogencarbonate buffer (100 mM, pH 9.6) with the addition of beta-CD at a concentration of 10 mM was found to be an effective BGE for their separation within 20 min. Besides this, special attention was paid to the development of the procedure for the extraction of specific metabolites from the bacterium P. denitrificans. This procedure was not only optimised to achieve the highest metabolite yields but also to obtain a sample that was fully compatible with the online preconcetration strategy used. The developed methodology was finally applied in a study of the bacterium P. denitrificans at various stages of the active respiratory chain.

  4. Enhanced resolution of fluorescence anisotropy decays by simultaneous analysis of progressively quenched samples. Applications to anisotropic rotations and to protein dynamics.

    PubMed Central

    Lakowicz, J R; Cherek, H; Gryczynski, I; Joshi, N; Johnson, M L

    1987-01-01

    Enhanced resolution of rapid and complex anisotropy decays was obtained by measurement and analysis of data from progressively quenched samples. Collisional quenching by acrylamide was used to vary the mean decay time of indole or of the tryptophan fluorescence from melittin. Anisotropy decays were obtained from the frequency-response of the polarized emission at frequencies from 4 to 2,000 MHz. Quenching increases the fraction of the total emission, which occurs on the subnanosecond timescale, and thereby provides increased information on picosecond rotational motions or local motions in proteins. For monoexponential subnanosecond anisotropy decays, enhanced resolution is obtained by measurement of the most highly quenched samples. For complex anisotropy decays, such as those due to both local motions and overall protein rotational diffusion, superior resolution is obtained by simultaneous analysis of data from quenched and unquenched samples. We demonstrate that measurement of quenched samples greatly reduces the uncertainty of the 50-ps correlation time of indole in water at 20 degrees C, and allows resolution of the anisotropic rotation of indole with correlation times of 140 and 720 ps. The method was applied to melittin in the monomeric and tetrameric forms. With increased quenching, the anisotropy data showed decreasing contributions from overall protein rotation and increased contribution from picosecond tryptophan motions. The tryptophan residues in both the monomeric and the tetrameric forms of melittin displayed substantial local motions with correlation times near 0.16 and 0.06 ns, respectively. The amplitude of the local motion is twofold less in the tetramer. These highly resolved anisotropy decays should be valuable for comparison with molecular dynamics simulations of melittin. PMID:3593873

  5. Searching for Li-rich giants in a sample of 12 open clusters. Li enhancement in two stars with substellar companions

    NASA Astrophysics Data System (ADS)

    Delgado Mena, E.; Tsantaki, M.; Sousa, S. G.; Kunitomo, M.; Adibekyan, V.; Zaworska, P.; Santos, N. C.; Israelian, G.; Lovis, C.

    2016-03-01

    Aims: The aim of this work is to search for Li-rich giants in a sample of clusters where planets have been searched, thus we can study the planet engulfment scenario to explain Li replenishment using a proper comparison sample of stars without detected giant planets. Methods: We derived Li abundances for a sample of 67 red giant stars in 12 different open clusters using standard spectral synthesis techniques and high-resolution spectra (from HARPS and UVES). We also determined masses, ages, and radius from PARSEC stellar isochrones to constrain the evolutionary stage of these stars. Results: We found three stars in different clusters with clearly enhanced Li abundances compared to other stars within the cluster. Interestingly, the only two stars with a detected substellar companion in our sample belong to that group. One of the planet hosts, NGC 2423 No. 3, might lie close to the luminosity bump on the HR diagram, a phase where Li production by the Cameron-Fowler process is supported by extra-mixing to bring fresh Li up to the surface. On the other hand, NGC 4349 No. 127 is a more massive and more evolved giant that does not seem to be in the evolutionary phase where other Li-rich stars are found. We discuss the possibility that the Li enhancement of this star is triggered by the engulfment of a planet, considering that close-in planets hardly survive the RGB tip and the early AGB phases. Based on observations collected at the La Silla Observatory, ESO (Chile), with HARPS/3.6 m (runs ID 075.C-0140, 076.C-0429, 077.C-0088, and 078.C-0133) and with UVES/VLT at the Cerro Paranal Observatory (run 079.C-0131).

  6. Diazotization-coupling reaction-based selective determination of nitrite in complex samples using shell-isolated nanoparticle-enhanced Raman spectroscopy.

    PubMed

    Zhang, Kaige; Hu, Yuling; Li, Gongke

    2013-11-15

    A simple, rapid and selective method based on diazotization-coupling reaction for determination of nitrite ion in complex samples using shell-isolated nanoparticle-enhanced Raman spectroscopy (SHINERS) was developed. Based on diazotization-coupling reaction, nitrite was transformed into azo dye, which has strong SHINERS activity. Subsequently the concentration of nitrite ion can be determined indirectly from the SHINERS of azo dye. The SHINERS active substrate was composed of gold nanoparticle as core with an ultrathin silica shell having pinhole on the surface. Various factors that influence reaction and SHINERS intensity were investigated. Under the optimal conditions, the linearity was observed in the range of 0.5-6.0 mg L(-1) with good correlation coefficient (r(2)>0.9793). The relative standard deviations (RSDs) for five replicate measurements were less than 14.5%. The limit of detections of the method (S/N=3) were 0.07, 0.08 and 0.10 mg L(-1) at 1137, 1395 and 1432 cm(-1), respectively, without sample preconcentration. The selectivity of the proposed method was also tested. The performance of SHINERS to determine the concentration of nitrite in food, biological and environmental samples was evaluated. The results indicate that SHINERS shows great potential as a useful analytical tool for trace analysis of nitrite in real samples. This proposed method provides a practical protocol for determination of compounds with weak Raman response, and can be expanded for the indirect detection of iodate ion, phenols and aromatic amines.

  7. On-Line Organic Solvent Field Enhanced Sample Injection in Capillary Zone Electrophoresis for Analysis of Quetiapine in Beagle Dog Plasma.

    PubMed

    Cao, Yuqing; Wen, Jun; Zhou, Tingting; Fan, Guorong

    2016-01-21

    A rapid and sensitive capillary zone electrophoresis (CZE) method with field enhanced sample injection (FESI) was developed and validated for the determination of quetiapine fumarate in beagle dog plasma, with a sample pretreatment by LLE in 96-well deep format plate. The optimum separation was carried out in an uncoated 31.2 cm × 75 μm fused-silica capillary with an applied voltage of 13 kV. The electrophoretic analysis was performed by 50 mM phosphate at pH 2.5. The detection wavelength was 210 nm. Under these optimized conditions, FESI with acetonitrile enhanced the sensitivity of quetiapine about 40-50 folds in total. The method was suitably validated with respect to stability, specificity, linearity, lower limit of quantitation, accuracy, precision and extraction recovery. Using mirtazapine as an internal standard (100 ng/mL), the response of quetiapine was linear over the range of 1-1000 ng/mL. The lower limit of quantification was 1 ng/mL. The intra- and inter-day precisions for the assay were within 4.8% and 12.7%, respectively. The method represents the first application of FESI-CZE to the analysis of quetiapine fumarate in beagle dog plasma after oral administration.

  8. Vortex-assisted surfactant-enhanced-emulsification liquid-liquid microextraction for the determination of triazine herbicides in water samples by microemulsion electrokinetic chromatography.

    PubMed

    Li, Ran-Hong; Liu, Dong-Hui; Yang, Zhong-Hua; Zhou, Zhi-Qiang; Wang, Peng

    2012-07-01

    A novel method based on the combination of microemulsion electrokinetic chromatography (MEEKC) and vortex-assisted surfactant-enhanced-emulsification liquid-liquid microextraction (VSLLME) was developed for the determination of five triazine herbicides (simazine, atrazine, ametryn, prometryn, and terbutryn) in water samples. The five triazine herbicides were baseline separated by using the microemulsion buffer containing a 10 mmol/L borate buffer at pH 9.5, 2.5% (w/v) SDS as surfactant, 0.8% (w/v) ethyl acetate as oil phase, and 6.0% (w/v) 1-butanol as cosurfactant. The optimum extraction conditions of VSLLME were as follows: 100 μL chloroform was used as extraction solvent, 5.0 × 10⁻⁵ mol/L Tween-20 was chosen as the surfactant to enhance the emulsification, and the extraction process was carried out by vortex mixing for 3 min. Under these optimum experimental conditions, the calibration curve was linear in the range of 2.0-200.0 ng/mL, with the correlation coefficients (r²) varying from 0.9927 to 0.9958. The detection limits of the method varied from 0.41 to 0.62 ng/mL. The purposed method was applied to the determination of five triazine herbicides in real water samples, and the recoveries were between 80.6 and 107.3%.

  9. myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme

    PubMed Central

    Kasahara, Kota; Ma, Benson; Goto, Kota; Dasgupta, Bhaskar; Higo, Junichi; Fukuda, Ikuo; Mashimo, Tadaaki; Akiyama, Yutaka; Nakamura, Haruki

    2016-01-01

    Molecular dynamics (MD) is a promising computational approach to investigate dynamical behavior of molecular systems at the atomic level. Here, we present a new MD simulation engine named “myPresto/omegagene” that is tailored for enhanced conformational sampling methods with a non-Ewald electrostatic potential scheme. Our enhanced conformational sampling methods, e.g., the virtual-system-coupled multi-canonical MD (V-McMD) method, replace a multi-process parallelized run with multiple independent runs to avoid inter-node communication overhead. In addition, adopting the non-Ewald-based zero-multipole summation method (ZMM) makes it possible to eliminate the Fourier space calculations altogether. The combination of these state-of-the-art techniques realizes efficient and accurate calculations of the conformational ensemble at an equilibrium state. By taking these advantages, myPresto/omegagene is specialized for the single process execution with Graphics Processing Unit (GPU). We performed benchmark simulations for the 20-mer peptide, Trp-cage, with explicit solvent. One of the most thermodynamically stable conformations generated by the V-McMD simulation is very similar to an experimentally solved native conformation. Furthermore, the computation speed is four-times faster than that of our previous simulation engine, myPresto/psygene-G. The new simulator, myPresto/omegagene, is freely available at the following URLs: http://www.protein.osaka-u.ac.jp/rcsfp/pi/omegagene/ and http://presto.protein.osaka-u.ac.jp/myPresto4/. PMID:27924276

  10. myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme.

    PubMed

    Kasahara, Kota; Ma, Benson; Goto, Kota; Dasgupta, Bhaskar; Higo, Junichi; Fukuda, Ikuo; Mashimo, Tadaaki; Akiyama, Yutaka; Nakamura, Haruki

    2016-01-01

    Molecular dynamics (MD) is a promising computational approach to investigate dynamical behavior of molecular systems at the atomic level. Here, we present a new MD simulation engine named "myPresto/omegagene" that is tailored for enhanced conformational sampling methods with a non-Ewald electrostatic potential scheme. Our enhanced conformational sampling methods, e.g., the virtual-system-coupled multi-canonical MD (V-McMD) method, replace a multi-process parallelized run with multiple independent runs to avoid inter-node communication overhead. In addition, adopting the non-Ewald-based zero-multipole summation method (ZMM) makes it possible to eliminate the Fourier space calculations altogether. The combination of these state-of-the-art techniques realizes efficient and accurate calculations of the conformational ensemble at an equilibrium state. By taking these advantages, myPresto/omegagene is specialized for the single process execution with Graphics Processing Unit (GPU). We performed benchmark simulations for the 20-mer peptide, Trp-cage, with explicit solvent. One of the most thermodynamically stable conformations generated by the V-McMD simulation is very similar to an experimentally solved native conformation. Furthermore, the computation speed is four-times faster than that of our previous simulation engine, myPresto/psygene-G. The new simulator, myPresto/omegagene, is freely available at the following URLs: http://www.protein.osaka-u.ac.jp/rcsfp/pi/omegagene/ and http://presto.protein.osaka-u.ac.jp/myPresto4/.

  11. Ultrasonic-energy enhance the ionic liquid-based dual microextraction to preconcentrate the lead in ground and stored rain water samples as compared to conventional shaking method.

    PubMed

    Nizamani, Sooraj; Kazi, Tasneem G; Afridi, Hassan I

    2018-01-01

    An efficient preconcentration technique based on ultrasonic-assisted ionic liquid-based dual microextraction (UA-ILDµE) method has been developed to preconcentrate the lead (Pb(+2)) in ground and stored rain water. In the current proposed method, Pb(+2) was complexed with a chelating agent (dithizone), whereas an ionic liquid (1-butyl-3-methylimidazolium hexafluorophosphate) was used for extraction purpose. The ultrasonic irradiation and electrical shaking system were applied to enhance the dispersion and extraction of Pb(+2) complex in aqueous samples. For second phase, dual microextraction (DµE phase), the enriched Pb(+2) complex in ionic liquid, extracted back into the acidic aqueous solution and finally determined by flame atomic absorption spectrometry. Some major analytical parameters that influenced the extraction efficiency of developed method, such as pH, concentration of ligand, volume of ionic liquid and samples, time of shaking in thermostatic electrical shaker and ultrasonic bath, effect of back extracting HNO3 volume, matrix effect, centrifugation time and rate were optimized. At the sample volume of 25mL, the calculated preconcentration factor was 62.2. The limit of detection of proposed procedure for Pb(+2) ions was found to be 0.54μgL(-1). The validation of developed method was performed by the analysis of certified sample of water SRM 1643e and standard addition method in a real water sample. The extraction recovery of Pb(+2) was enhanced≥2% with shaking time of 80s in ultrasonic bath as compared to used thermostatic electrical shaker, where for optimum recovery up to 10min was required. The developed procedure was successfully used for the enrichment of Pb(+2) in ground and stored rain water (surface water) samples of an endemic region of Pakistan. The resulted data indicated that the ground water samples were highly contaminated with Pb(+2), while some of the surface water samples were also have higher values of Pb(+2) than permissible

  12. Polarization Effects on the Cellulose Dissolution in Ionic Liquids: Molecular Dynamics Simulations with Polarization Model and Integrated Tempering Enhanced Sampling Method.

    PubMed

    Kan, Zigui; Zhu, Qiang; Yang, Lijiang; Huang, Zhixiong; Jin, Biaobing; Ma, Jing

    2017-05-04

    Conformation of cellulose with various degree of polymerization of n = 1-12 in ionic liquid 1,3-dimethylimidazolium chloride ([C1mim]Cl) and the intermolecular interaction between them was studied by means of molecular dynamics (MD) simulations with fixed-charge and charge variable polarizable force fields, respectively. The integrated tempering enhanced sampling method was also employed in the simulations in order to improve the sampling efficiency. Cellulose undergoes significant conformational changes from a gaseous right-hand helical twist along the long axis to a flexible conformation in ionic liquid. The intermolecular interactions between cellulose and ionic liquid were studied by both infrared spectrum measurements and theoretical simulations. Designated by their puckering parameters, the pyranose rings of cellulose oligomers are mainly arranged in a chair conformation. With the increase in the degree of polymerization of cellulose, the boat and skew-boat conformations of cellulose appear in the MD simulations, especially in the simulations with polarization model. The number and population of hydrogen bonds between the cellulose and the chloride anions show that chloride anion is prone to form HBs whenever it approaches the hydroxyl groups of cellulose and, thus, each hydroxyl group is fully hydrogen bonded to the chloride anion. MD simulations with polarization model presented more abundant conformations than that with nonpolarization model. The application of the enhanced sampling method further enlarged the conformational spaces that could be visited by facilitating the system escaping from the local minima. It was found that the electrostatics interactions between the cellulose and ionic liquid contribute more to the total interaction energies than the van der Waals interactions. Although the interaction energy between the cellulose and anion is about 2.9 times that between the cellulose and cation, the role of cation is non-negligible. In contrast

  13. Non-contrast-enhanced 4D MR angiography with STAR spin labeling and variable flip angle sampling: a feasibility study for the assessment of Dural Arteriovenous Fistula.

    PubMed

    Jang, Jinhee; Schmitt, Peter; Kim, Bom-yi; Choi, Hyun Seok; Jung, So-Lyung; Ahn, Kook-Jin; Kim, Inseong; Paek, Munyoung; Kim, Bum-soo

    2014-04-01

    This study aimed to evaluate the feasibility of non-contrast-enhanced 4D magnetic resonance angiography (NCE 4D MRA) with signal targeting with alternative radiofrequency (STAR) spin labeling and variable flip angle (VFA) sampling in the assessment of dural arteriovenous fistula (DAVF) in the transverse sinus. Nine patients underwent NCE 4D MRA for the evaluation of DAVF in the transverse sinus at 3 T. One patient was examined twice, once before and once after the interventional treatment. All patients also underwent digital subtraction angiography (DSA) and/or contrast-enhanced magnetic resonance angiography (CEMRA). For the acquisition of NCE 4D MRA, a STAR spin tagging method was used, and a VFA sampling was applied in the data readout module instead of a constant flip angle. Two readers evaluated the NCE 4D MRA data for the diagnosis of DAVF and its type with consensus. The results were compared with those from DSA and/or CEMRA. All patients underwent NCE 4D MRA without any difficulty. Among seven patients with patent DAVFs, all cases showed an early visualization of the transverse sinus on NCE 4D MRA. Except for one case, the type of DAVF of NCE 4D MRA was agreed with that of reference standard study. Cortical venous reflux (CVR) was demonstrated in two cases out of three patients with CVR. NCE 4D MRA with STAR tagging and VFA sampling is technically and clinically feasible and represents a promising technique for assessment of DAVF in the transverse sinus. Further technical developments should aim at improvements of spatial and temporal coverage.

  14. Sampling Human Indigenous Saliva Peptidome Using a Lollipop-Like Ultrafiltration Probe: Simplify and Enhance Peptide Detection for Clinical Mass Spectrometry

    PubMed Central

    Zhu, Wenhong; Gallo, Richard L.; Huang, Chun-Ming

    2012-01-01

    Although human saliva proteome and peptidome have been revealed 1-2 they were majorly identified from tryptic digests of saliva proteins. Identification of indigenous peptidome of human saliva without prior digestion with exogenous enzymes becomes imperative, since native peptides in human saliva provide potential values for diagnosing disease, predicting disease progression, and monitoring therapeutic efficacy. Appropriate sampling is a critical step for enhancement of identification of human indigenous saliva peptidome. Traditional methods of sampling human saliva involving centrifugation to remove debris 3-4 may be too time-consuming to be applicable for clinical use. Furthermore, debris removal by centrifugation may be unable to clean most of the infected pathogens and remove the high abundance proteins that often hinder the identification of low abundance peptidome. Conventional proteomic approaches that primarily utilize two-dimensional gel electrophoresis (2-DE) gels in conjugation with in-gel digestion are capable of identifying many saliva proteins 5-6. However, this approach is generally not sufficiently sensitive to detect low abundance peptides/proteins. Liquid chromatography-Mass spectrometry (LC-MS) based proteomics is an alternative that can identify proteins without prior 2-DE separation. Although this approach provides higher sensitivity, it generally needs prior sample pre-fractionation 7 and pre-digestion with trypsin, which makes it difficult for clinical use. To circumvent the hindrance in mass spectrometry due to sample preparation, we have developed a technique called capillary ultrafiltration (CUF) probes 8-11. Data from our laboratory demonstrated that the CUF probes are capable of capturing proteins in vivo from various microenvironments in animals in a dynamic and minimally invasive manner 8-11. No centrifugation is needed since a negative pressure is created by simply syringe withdrawing during sample collection. The CUF probes combined

  15. Sampling human indigenous saliva peptidome using a lollipop-like ultrafiltration probe: simplify and enhance peptide detection for clinical mass spectrometry.

    PubMed

    Zhu, Wenhong; Gallo, Richard L; Huang, Chun-Ming

    2012-08-07

    Although human saliva proteome and peptidome have been revealed they were majorly identified from tryptic digests of saliva proteins. Identification of indigenous peptidome of human saliva without prior digestion with exogenous enzymes becomes imperative, since native peptides in human saliva provide potential values for diagnosing disease, predicting disease progression, and monitoring therapeutic efficacy. Appropriate sampling is a critical step for enhancement of identification of human indigenous saliva peptidome. Traditional methods of sampling human saliva involving centrifugation to remove debris may be too time-consuming to be applicable for clinical use. Furthermore, debris removal by centrifugation may be unable to clean most of the infected pathogens and remove the high abundance proteins that often hinder the identification of low abundance peptidome. Conventional proteomic approaches that primarily utilize two-dimensional gel electrophoresis (2-DE) gels in conjugation with in-gel digestion are capable of identifying many saliva proteins. However, this approach is generally not sufficiently sensitive to detect low abundance peptides/proteins. Liquid chromatography-Mass spectrometry (LC-MS) based proteomics is an alternative that can identify proteins without prior 2-DE separation. Although this approach provides higher sensitivity, it generally needs prior sample pre-fractionation and pre-digestion with trypsin, which makes it difficult for clinical use. To circumvent the hindrance in mass spectrometry due to sample preparation, we have developed a technique called capillary ultrafiltration (CUF) probes. Data from our laboratory demonstrated that the CUF probes are capable of capturing proteins in vivo from various microenvironments in animals in a dynamic and minimally invasive manner. No centrifugation is needed since a negative pressure is created by simply syringe withdrawing during sample collection. The CUF probes combined with LC-MS have

  16. Effective extraction of triazines from environmental water samples using magnetism-enhanced monolith-based in-tube solid phase microextraction.

    PubMed

    Mei, Meng; Huang, Xiaojia; Yang, Xiaodong; Luo, Qing

    2016-09-21

    This article reports on the effective extraction of triazines from environmental water samples using magnetism-enhanced monolith-based in-tube solid phase microextraction (ME-MB/IT-SPME). Firstly, monolithic poly (octyl methacrylate-co-ethyleneglycol dimethacrylate) capillary column doped with magnetic nanoparticles was synthesized inside a fused silica. After that, the monolithic capillary column was placed inside a magnetic coil that allowed the exertion of a variable magnetic field during adsorption and desorption steps. The effects of intensity of magnetic field, adsorption and desorption flow rate, volume of sample and desorption solvent, pH value and ionic strength in sample matrix on the performance of ME-MB/IT-SPME for triazines were investigated in details. Under the optimized conditions, the developed ME-MB/IT-SPME showed satisfactory quantitative extraction efficiencies of the target analytes between 64.8% and 99.7%. At the same time, the ME-MB/IT-SPME was combined with high-performance liquid chromatography with diode array detection to detect six triazines in water samples. The limits of detection (S/N = 3) and limits of quantification (S/N = 10) were in the ranges of 0.074-0.23 μg/L and 0.24-0.68 μg/L, respectively. The precision of the proposed method was evaluated in terms of intra- and inter-assay variability calculated as relative standard deviation, and it was found that the values were all below 10%. Finally, the developed method was successfully applied for environmental water samples such as farmland, lake and river water with spiked recoveries in the range of 70.7-119%. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Application of enhanced gas chromatography/triple quadrupole mass spectrometry for monitoring petroleum weathering and forensic source fingerprinting in samples impacted by the Deepwater Horizon oil spill.

    PubMed

    Adhikari, Puspa L; Wong, Roberto L; Overton, Edward B

    2017-10-01

    Accurate characterization of petroleum hydrocarbons in complex and weathered oil residues is analytically challenging. This is primarily due to chemical compositional complexity of both the oil residues and environmental matrices, and the lack of instrumental selectivity due to co-elution of interferences with the target analytes. To overcome these analytical selectivity issues, we used an enhanced resolution gas chromatography coupled with triple quadrupole mass spectrometry in Multiple Reaction Monitoring (MRM) mode (GC/MS/MS-MRM) to eliminate interferences within the ion chromatograms of target analytes found in environmental samples. This new GC/MS/MS-MRM method was developed and used for forensic fingerprinting of deep-water and marsh sediment samples containing oily residues from the Deepwater Horizon oil spill. The results showed that the GC/MS/MS-MRM method increases selectivity, eliminates interferences, and provides more accurate quantitation and characterization of trace levels of alkyl-PAHs and biomarker compounds, from weathered oil residues in complex sample matrices. The higher selectivity of the new method, even at low detection limits, provides greater insights on isomer and homolog compositional patterns and the extent of oil weathering under various environmental conditions. The method also provides flat chromatographic baselines for accurate and unambiguous calculation of petroleum forensic biomarker compound ratios. Thus, this GC/MS/MS-MRM method can be a reliable analytical strategy for more accurate and selective trace level analyses in petroleum forensic studies, and for tacking continuous weathering of oil residues. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Diagnostic Accuracy of the Enhanced Liver Fibrosis (ELF®) Score Using HCV-Infected Serum Samples Cryopreserved for up to 25 Years

    PubMed Central

    Puigvehí, Marc; Hernández, Juanjo; Broquetas, Teresa; Coll, Susanna; Garcia-Retortillo, Montserrat; Cañete, Nuria; Giménez, Maria Dolors; Garcia, Mar; Bory, Felipe; Salvadó, Margarita; Solà, Ricard; Carrión, José A.

    2016-01-01

    Introduction & Aims Cryopreservation of serum samples is a standard procedure for biomedical research in tertiary centers. However, studies evaluating the long-term biological stability of direct liver fibrosis markers using cryopreserved samples are scarce. Methods We compared the stability of hyaluronic acid (HA), tissue inhibitor of metalloproteinases (TIMP-1) and amino-terminal propeptide of type III procollagen (PIIINP) in 225 frozen serum samples of HCV-infected patients with a paired liver biopsy for up to 25 years (1990–2014). Moreover, we assessed the diagnostic accuracy (AUROC) of the Enhanced Liver Fibrosis (ELF®) score to identify significant fibrosis (F2-4) and its predictive capacity to identify clinical events during follow-up. Results Seventy-six patients (39,8%) had mild fibrosis (F0-1) and 115 (60,2%) significant fibrosis (F2-4). HA, PIIINP and TIMP-1 values remained stable during the period from 1995 to 2014 while those of 1990–94 were slightly higher. We did not find significant differences in the median ELF® values during the 20-year period from 1995–2014 in patients with mild (from 8,4 to 8,7) and significant fibrosis (from 9,9 to 10,9) (p = ns between periods and fibrosis stages). The AUROCs of ELF® to identify significant fibrosis were high in all the periods (from 0,85 to 0,91). The ELF® score showed a good predictive capability to identify clinical events during follow-up. Conclusions The biological stability of direct serum markers (HA, PIIINP and TIMP-1) using HCV-infected samples cryopreserved for 20 years is good. Therefore, the diagnostic accuracy of the ELF® score to identify significant fibrosis and clinical events during follow-up is very high. PMID:27984583

  19. A competitive immunoassay for ultrasensitive detection of Hg(2+) in water, human serum and urine samples using immunochromatographic test based on surface-enhanced Raman scattering.

    PubMed

    She, Pei; Chu, Yanxin; Liu, Chunwei; Guo, Xun; Zhao, Kang; Li, Jianguo; Du, Haijing; Zhang, Xiang; Wang, Hong; Deng, Anping

    2016-02-04

    An immunochromatographic test (ICT) strip was developed for ultrasensitive competitive immunoassay of Hg(2+). This strategy was achieved by combining the easy-operation and rapidity of ICT with the high sensitivity of surface-enhanced Raman scattering (SERS). Monoclonal antibody (mAb) against Hg(2+) and Raman active substance 4-mercaptobenzoic acid (MBA) dual labelled gold nanoparticles (GNPs) were prepared as an immunoprobe. The Raman scattering intensity of MBA on the test line of the ICT strip was measured for quantitative determination of Hg(2+). The ICT was able to directly detect Hg(2+) without complexing due to the specific recognition of the mAb with Hg(2+). The IC50 and limit of detection (LOD) of the assay for Hg(2+) detection were 0.12 ng mL(-1) and 0.45 pg mL(-1), respectively. There was no cross-reactivity (CR) of the assay with other nineteen ions and the ICT strips could be kept for 5 weeks without loss of activity. The recoveries of the assay for water, human serum and urine samples spiked with Hg(2+) were in range of 88.3-107.3% with the relative standard deviations (RSD) of 1.5-9.5% (n = 3). The proposed ICT was used for the detection of Hg(2+) in urine samples collected from Occupational Disease Hospital and the results were confirmed by cold-vapor atomic fluorescence spectroscopy (CV-AFS). The assay exhibited high sensitivity, selectivity, stability, precision and accuracy, demonstrating a promising method for the detection of trace amount of Hg(2+) in environmental water samples and biological serum and urine samples. Copyright © 2015 Elsevier B.V. All rights reserved.

  20. Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics-Monte Carlo Simulations Guided by a Coarse-Grained Model.

    PubMed

    Chen, Yunjie; Roux, Benoît

    2015-08-11

    Molecular dynamics (MD) trajectories based on a classical equation of motion provide a straightforward, albeit somewhat inefficient approach, to explore and sample the configurational space of a complex molecular system. While a broad range of techniques can be used to accelerate and enhance the sampling efficiency of classical simulations, only algorithms that are consistent with the Boltzmann equilibrium distribution yield a proper statistical mechanical computational framework. Here, a multiscale hybrid algorithm relying simultaneously on all-atom fine-grained (FG) and coarse-grained (CG) representations of a system is designed to improve sampling efficiency by combining the strength of nonequilibrium molecular dynamics (neMD) and Metropolis Monte Carlo (MC). This CG-guided hybrid neMD-MC algorithm comprises six steps: (1) a FG configuration of an atomic system is dynamically propagated for some period of time using equilibrium MD; (2) the resulting FG configuration is mapped onto a simplified CG model; (3) the CG model is propagated for a brief time interval to yield a new CG configuration; (4) the resulting CG configuration is used as a target to guide the evolution of the FG system; (5) the FG configuration (from step 1) is driven via a nonequilibrium MD (neMD) simulation toward the CG target; (6) the resulting FG configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-ends momentum reversal prescription is used for the neMD trajectories of the FG system to guarantee that the CG-guided hybrid neMD-MC algorithm obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The enhanced sampling achieved with the method is illustrated with a model system with hindered diffusion and explicit-solvent peptide simulations. Illustrative tests indicate that the method can yield a speedup of about 80 times for the model system and up

  1. Enhanced amperometric detection of metronidazole in drug formulations and urine samples based on chitosan protected tetrasulfonated copper phthalocyanine thin-film modified glassy carbon electrode.

    PubMed

    Meenakshi, S; Pandian, K; Jayakumari, L S; Inbasekaran, S

    2016-02-01

    An enhanced electrocatalytic reduction of metronidazole antibiotic drug molecule using chitosan protected tetrasulfonated copper phthalocyanine (Chit/CuTsPc) thin-film modified glassy carbon electrode (GCE) has been developed. An irreversible reduction occurs at -0.47V (vs. Ag/AgCl) using Chit/CuTsPc modified GCE. A maximum peak current value is obtained at pH1 and the electrochemical reduction reaction is a diffusion controlled one. The detection limit is found to be 0.41nM from differential pulse voltammetry (DPV) method. This present investigation method is adopted for electrochemical detection of metronidazole in drug formulation and urine samples by using DPV method.

  2. Ball-and-Stick Local Elevation Umbrella Sampling: Molecular Simulations Involving Enhanced Sampling within Conformational or Alchemical Subspaces of Low Internal Dimensionalities, Minimal Irrelevant Volumes, and Problem-Adapted Geometries.

    PubMed

    Hansen, Halvor S; Hünenberger, Philippe H

    2010-09-14

    A new method, ball-and-stick local elevation umbrella sampling (B&S-LEUS), is proposed to enhance the sampling in computer simulations of (bio)molecular systems. It enables the calculation of conformational free-energy differences between states (or alchemical free-energy differences between molecules), even in situations where the definition of these states relies on a conformational subspace involving more than a few degrees of freedom. The B&S-LEUS method consists of the following steps: (A) choice of a reduced conformational subspace; (B) representation of the relevant states by means of spheres ("balls"), each associated with a biasing potential involving a one-dimensional radial memory-based term and a radial confinement term; (C) definition of a set of lines ("sticks") connecting these spheres, each associated with a biasing potential involving a one-dimensional longitudinal memory-based term and a transverse confinement term; (D) unification of the biasing potentials corresponding to the union of all of the spheres and lines (active subspace) into a single biasing potential according to the enveloping distribution sampling (EDS) scheme; (E) build-up of the memory using the local elevation (LE) procedure, leading to a biasing potential enabling a nearly uniform sampling (radially within the spheres, longitudinally within the lines) of the active subspace; (F) generation of a biased ensemble of configurations using this preoptimized biasing potential, following an umbrella sampling (US) approach; and (G) calculation of the relative free energies of the states via reweighting and state assignment. The main characteristics of this approach are: (i) a low internal dimensionality, that is, the memory only involves one-dimensional grids (acceptable memory requirements); (ii) a minimal irrelevant volume, that is, the conformational volume opened to sampling includes a minimal fraction of irrelevant regions in terms of the free energy of the physical system or of

  3. Sorafenib plus dacarbazine in solid tumors: a phase I study with dynamic contrast-enhanced ultrasonography and genomic analysis of sequential tumor biopsy samples.

    PubMed

    Lazar, Vladimir; Lassau, Nathalie; Meurice, Guillaume; Loriot, Yohann; Peña, Carol; Massard, Christophe; Robert, Caroline; Robert, Thomas; Le Berre, Marie-Aude; de Baere, Thierry; Dessen, Philippe; Soria, Jean-Charles; Armand, Jean-Pierre

    2014-04-01

    Improved prognostic accuracy for treatment response and a wider understanding of drug effects in humans are crucial for enhancing the utility of sorafenib and other promising targeted therapies. We developed a strategy of global genomic investigation of sequential tumor biopsy samples at baseline and 21 days post treatment, and applied this approach in a phase I study of sorafenib plus dacarbazine in patients with solid tumors. The objective of this study was also to validate functional parameters of DCE-US as surrogate markers to predict earlier response. Patients received 21-day cycles of oral sorafenib, 400 mg twice daily and dacarbazine, 1,000 mg/m(2) in a 1-h intravenous infusion on day 1. Efficacy was assessed using response evaluation criteria in solid tumors. Sequential biopsy samples (baseline and day 21) were obtained from the same tumor. Changes from baseline in global gene expression (GE) measured by genomic microarrays and in tumor vascularity at baseline, D8, D21, D 42 and every 2 cycles using dynamic contrast-enhanced ultrasonography (DCE-US) were analyzed for patients with and without a clinical response to treatment at 3 months. Among 23 patients evaluable for treatment efficacy, 17 were eligible for gene expression and DCE-US analyses. One patient achieved a partial response; 14 exhibited stable disease. Ten patients were defined as exhibiting stable disease (SD) and 7, progressive disease (PD) at 3 months. Genomic analyses identified a 237-gene signature that distinguished SD from PD at 3 months. Of note, CDK4 overexpression and PDGFR downregulation were associated with PD. Functional parameters of DCE-US representing the blood volume at baseline, day 8, and day 21 were correlated with disease progression at 3 months. This novel approach of sequential investigations in a phase I trial was feasible, detecting early changes in gene expression and tumor vascularity evaluated using DCE-US that may be predictive of clinical outcome.

  4. Synergistic enhancement effect of room temperature ionic liquids for cloud point extraction combined with UV-vis spectrophotometric determination nickel in environmental samples.

    PubMed

    Zeng, Chujie; Xu, Xili; Zhou, Neng; Lin, Yao

    2012-08-01

    A new method based on enhancement effect of room temperature ionic liquids for cloud point extraction trace amounts of nickel combined with UV-vis spectrophotometric determination was developed. Room temperature ionic liquids (RTILs) and diethyldithiocarbamate (DDTC) were used enhancement reagent and chelating reagent, respectively. The addition of room temperature ionic liquids leads to 3.0 times improvement in the determination of nickel. The nonionic surfactant Triton X-100 was used as the extractant. When the temperature of the system was higher than the cloud point of Triton X-100, Ni-DTC complex was extracted into Triton X-100 and separation of the analyte from the matrix was achieved. Some parameters that influenced cloud point extraction and subsequent determination were evaluated in detail, such as the concentrations of RTILs, DDTC and Triton X-100; pH of sample solution, as well as interferences. Under optimized conditions, an enrichment factor of 72 could be obtained, and the detection limit (LOD) for Ni was 0.5ng mL(-1). Relative standard deviations for five replicate determinations of the standard solution containing 50ng mL(-1) Ni was 3.9%. The proposed method was successfully applied to the determination of nickel in certified reference materials with satisfactory results. Copyright © 2012 Elsevier B.V. All rights reserved.

  5. Sampling Development

    PubMed Central

    Adolph, Karen E.; Robinson, Scott R.

    2011-01-01

    Research in developmental psychology requires sampling at different time points. Accurate depictions of developmental change provide a foundation for further empirical studies and theories about developmental mechanisms. However, overreliance on widely spaced sampling intervals in cross-sectional and longitudinal designs threatens the validity of the enterprise. This article discusses how to sample development in order to accurately discern the shape of developmental change. The ideal solution is daunting: to summarize behavior over 24-hour intervals and collect daily samples over the critical periods of change. We discuss the magnitude of errors due to undersampling, and the risks associated with oversampling. When daily sampling is not feasible, we offer suggestions for sampling methods that can provide preliminary reference points and provisional sketches of the general shape of a developmental trajectory. Denser sampling then can be applied strategically during periods of enhanced variability, inflections in the rate of developmental change, or in relation to key events or processes that may affect the course of change. Despite the challenges of dense repeated sampling, researchers must take seriously the problem of sampling on a developmental time scale if we are to know the true shape of developmental change. PMID:22140355

  6. An enhanced electrochemiluminescence sensor modified with a Ru(bpy)3(2+)/Yb2O3 nanoparticle/nafion composite for the analysis of methadone samples.

    PubMed

    Hosseini, Morteza; Pur, Mohammad Reza Karimi; Norouzi, Parviz; Moghaddam, Mohammad Reza; Ganjali, Mohammad Reza

    2017-07-01

    The sensitive interaction between Ru(bpy)3(2+) and methadone was used for the modification of a solid-state electrochemiluminescence electrode, and it was also successfully applied to determine methadone in the samples. The working electrode was made of a Yb2O3-containing modified carbon paste electrode. The presence of Yb2O3 nanoparticles in the structure of the electrode, was found to enhance its sensitizing effect towards the Ru(bpy)3(2+)-methadone electrochemiluminescence system. The electrodes with the optimal make-up revealed a linear ECL-concentration behavior from 5×10(-9)-3×10(-7)M and reached method detection limit as low as 2.1×10(-10)M with a relative standard deviation of 4.4% (S/N=3). This modified ECL could present a simple yet sensitive and selective route for the determination of methadone in different samples. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. 5-color multiplexed microwave-accelerated metal-enhanced fluorescence: detection and analysis of multiple DNA sequences from within one sample well within a few seconds.

    PubMed

    Dragan, Anatoliy; Geddes, Chris D

    2014-11-01

    We present a potentially highly sensitive and selective bio-assay for the potential detection of any five different DNA sequences from one sample in one well. The assay is based on a DNA "rapid catch and signal" (DNA-RCS) technology developed for the detection of different DNA sequences from a sample well area. Our signal amplification utilizes the metal-enhanced fluorescence (MEF) of dyes attached to the probe-DNAs, which hybridizes with the pre-formed mixture of anchor-DNA scaffolds on silver island films (SiFs). Low-power microwave irradiation accelerates both the formation of the anchor-DNA scaffold on the SiF-surface and anchor/probe DNA hybridization, i.e. "rapid catch" of target DNAs from a bulk solution, decreasing the assay run time from hours to only a few seconds. Localization of signaling dye-labels close to the SiFs make them extremely photostable, which allows for collecting/integrating the signal over a long time period. To demonstrate a 5 color DNA assay (5-plex) we have used a range of readily available Alexa™ dyes. Advantages and perspectives of the RCS-technologies ability to detect 5 different DNA sequences from within one plate-well are discussed.

  8. Application of electro-enhanced solid phase microextraction combined with gas chromatography-mass spectrometry for the determination of tricyclic antidepressants in environmental water samples.

    PubMed

    Xu, Ruyi; Lee, Hian Kee

    2014-07-11

    A fast and efficient method for the determination of tricyclic antidepressants using electro-enhanced solid phase microextraction (SPME) coupled to gas chromatography-mass spectrometry (GC-MS) has been developed. One advantage of this approach is that the mass transfer of target analytes from the sample solution to an SPME fiber can be accelerated by the electrical field, improving extraction selectivity and efficiency. In the present work, the target analytes extracted to the SPME fiber were thermally desorbed in the GC injection port after extraction. Under the optimized extraction conditions, the developed method exhibited low limits of detection (between 0.079 and 0.296μg/L) and good linearity over the concentration range of between 1 and 500μg/L with coefficients of determination (r(2)) of between 0.993 and 0.999. The relative standard deviations were lower than 9.2% for all analytes. The proposed method was applied to extract tricyclic antidepressants in environmental water samples. Copyright © 2014 Elsevier B.V. All rights reserved.

  9. Evaluation of Dietary Supplement Contamination by Xenobiotic and Essential Elements Using Microwave-Enhanced Sample Digestion and Inductively Coupled Plasma-Mass Spectrometry.

    PubMed

    Zinn, Gregory M; Rahman, G M Mizanur; Faber, Scott; Wolle, Mesay Mulugeta; Pamuku, Matt; Kingston, H M Skip

    2016-01-01

    Dietary supplements were analyzed by evaluating the elemental content in six widely consumed products manufactured by four well-known companies. The elements included the neurotoxic and carcinogenic elements cadmium, mercury, aluminum, lead, arsenic, and antimony, as well as the essential elements zinc, selenium, chromium, iron, and copper, which were often not listed as ingredients on the product labels. Contamination from either xenobiotic or essential elements was found in all samples analyzed. The samples were prepared using US Environmental Protection Agency (EPA) Method 3052, microwave-enhanced digestion. The resulting digests were analyzed by Inductively Coupled Plasma-Mass Spectrometry based on EPA Method 6020B. The analytical protocols were validated by analyzing a multivitamin standard reference material, the National Institute of Standards and Technology Standard Reference Material 3280. The application of EPA standard methods demonstrated their utility in making accurate and precise measurements in complex matrices with multiple ingredients and excipients. In the future, the use of these methods could provide a uniform quality assurance protocol that can be implemented along with other industry guidelines to improve the production of dietary supplements.

  10. Ab initio molecular dynamics with enhanced sampling for surface reaction kinetics at finite temperatures: CH2⇌ CH + H on Ni(111) as a case study.

    PubMed

    Sun, Geng; Jiang, Hong

    2015-12-21

    A comprehensive understanding of surface thermodynamics and kinetics based on first-principles approaches is crucial for rational design of novel heterogeneous catalysts, and requires combining accurate electronic structure theory and statistical mechanics modeling. In this work, ab initio molecular dynamics (AIMD) combined with the integrated tempering sampling (ITS) method has been explored to study thermodynamic and kinetic properties of elementary processes on surfaces, using a simple reaction CH2⇌CH+H on the Ni(111) surface as an example. By a careful comparison between the results from ITS-AIMD simulation and those evaluated in terms of the harmonic oscillator (HO) approximation, it is found that the reaction free energy and entropy from the HO approximation are qualitatively consistent with the results from ITS-AIMD simulation, but there are also quantitatively significant discrepancies. In particular, the HO model misses the entropy effects related to the existence of multiple adsorption configurations arising from the frustrated translation and rotation motion of adsorbed species, which are different in the reactant and product states. The rate constants are evaluated from two ITS-enhanced approaches, one using the transition state theory (TST) formulated in terms of the potential of mean force (PMF) and the other one combining ITS with the transition path sampling (TPS) technique, and are further compared to those based on harmonic TST. It is found that the rate constants from the PMF-based TST are significantly smaller than those from the harmonic TST, and that the results from PMF-TST and ITS-TPS are in a surprisingly good agreement. These findings indicate that the basic assumptions of transition state theory are valid in such elementary surface reactions, but the consideration of statistical averaging of all important adsorption configurations and reaction pathways, which are missing in the harmonic TST, are critical for accurate description of

  11. The Use of NanoTrap Particles as a Sample Enrichment Method to Enhance the Detection of Rift Valley Fever Virus

    PubMed Central

    Shafagati, Nazly; Narayanan, Aarthi; Baer, Alan; Fite, Katherine; Pinkham, Chelsea; Bailey, Charles; Kashanchi, Fatah; Lepene, Benjamin; Kehn-Hall, Kylene

    2013-01-01

    Background Rift Valley Fever Virus (RVFV) is a zoonotic virus that is not only an emerging pathogen but is also considered a biodefense pathogen due to the threat it may cause to public health and national security. The current state of diagnosis has led to misdiagnosis early on in infection. Here we describe the use of a novel sample preparation technology, NanoTrap particles, to enhance the detection of RVFV. Previous studies demonstrated that NanoTrap particles lead to both 100 percent capture of protein analytes as well as an improvement of more than 100-fold in sensitivity compared to existing methods. Here we extend these findings by demonstrating the capture and enrichment of viruses. Results Screening of NanoTrap particles indicated that one particle, NT53, was the most efficient at RVFV capture as demonstrated by both qRT-PCR and plaque assays. Importantly, NT53 capture of RVFV resulted in greater than 100-fold enrichment from low viral titers when other diagnostics assays may produce false negatives. NT53 was also capable of capturing and enhancing RVFV detection from serum samples. RVFV that was inactivated through either detergent or heat treatment was still found bound to NT53, indicating the ability to use NanoTrap particles for viral capture prior to transport to a BSL-2 environment. Furthermore, both NP-40-lysed virus and purified RVFV RNA were bound by NT53. Importantly, NT53 protected viral RNA from RNase A degradation, which was not observed with other commercially available beads. Incubation of RVFV samples with NT53 also resulted in increased viral stability as demonstrated through preservation of infectivity at elevated temperatures. Finally, NanoTrap particles were capable of capturing VEEV and HIV, demonstrating the broad applicability of NanoTrap particles for viral diagnostics. Conclusion This study demonstrates NanoTrap particles are capable of capturing, enriching, and protecting RVFV virions. Furthermore, the use of NanoTrap particles

  12. Determination of melamine in soil samples using surfactant-enhanced hollow fiber liquid phase microextraction followed by HPLC–UV using experimental design

    PubMed Central

    Sarafraz Yazdi, Ali; Raouf Yazdinezhad, Samaneh; Heidari, Tahereh

    2014-01-01

    Surfactant-enhanced hollow fiber liquid phase (SE-HF-LPME) microextraction was applied for the extraction of melamine in conjunction with high performance liquid chromatography with UV detection (HPLC–UV). Sodium dodecyl sulfate (SDS) was added firstly to the sample solution at pH 1.9 to form hydrophobic ion-pair with protonated melamine. Then the protonated melamine–dodecyl sulfate ion-pair (Mel–DS) was extracted from aqueous phase into organic phase immobilized in the pores and lumen of the hollow fiber. After extraction, the analyte-enriched 1-octanol was withdrawn into the syringe and injected into the HPLC. Preliminary, one variable at a time method was applied to select the type of extraction solvent. Then, in screening step, the other variables that may affect the extraction efficiency of the analyte were studied using a fractional factorial design. In the next step, a central composite design was applied for optimization of the significant factors having positive effects on extraction efficiency. The optimum operational conditions included: sample volume, 5 mL; surfactant concentration, 1.5 mM; pH 1.9; stirring rate, 1500 rpm and extraction time, 60 min. Using the optimum conditions, the method was analytically evaluated. The detection limit, relative standard deviation and linear range were 0.005 μg mL−1, 4.0% (3 μg mL−1, n = 5) and 0.01–8 μg mL−1, respectively. The performance of the procedure in extraction of melamine from the soil samples was good according to its relative recoveries in different spiking levels (95–109%). PMID:26644934

  13. Lab-on-a-Chip-Surface Enhanced Raman Scattering Combined with the Standard Addition Method: Toward the Quantification of Nitroxoline in Spiked Human Urine Samples.

    PubMed

    Hidi, Izabella J; Jahn, Martin; Weber, Karina; Bocklitz, Thomas; Pletz, Mathias W; Cialla-May, Dana; Popp, Juergen

    2016-09-20

    The emergence of antibacterial resistance and the development of new drugs lead to a continuous change of guidelines for medical treatments. Hence, new analytical tools are required for the detection of drugs in biological fluids. In this study, the first surface enhanced Raman scattering (SERS) detection of nitroxoline (NTX) in purified water and in spiked human urine samples is reported. Insights concerning the nature of the molecule-metal interaction and its influence on the overall SERS signal are provided. Furthermore, three randomly collected urine samples originating from a healthy volunteer were spiked to assess the limit of detection (LOD), the limit of quantification (LOQ), and the linear dynamic range of the lab-on-a-chip SERS (LoC-SERS) method for NTX detection in human urine. The LOD is ∼3 μM (0.57 mg/L), LOQ ∼ 6.5 μM (1.23 mg/L) while the linear range is between 4.28 and 42.8 μM (0.81-8.13 mg/L). This covers the minimum inhibitory concentration (MIC) values of the most commonly encountered uropathogens. Finally, seven clinical samples having an "unknown" NTX concentration were simulated. The LoC-SERS technique combined with the standard addition method and statistical data analysis provided a good prediction of the unknown concentrations. Additionally, it is also demonstrated that the predictions carried out by multicurve resolution alternating least-squares (MCR-ALS) algorithm provides reliable results, and it is preferred to a univariate statistical approach.

  14. Liquid chromatography/tandem mass spectrometry sensitivity enhancement via online sample dilution and trapping: applications in microdosing and dried blood spot (DBS) bioanalysis.

    PubMed

    Li, Fumin; Zulkoski, John P; Ding, Jie; Brown, Wes; Addison, Tom

    2010-09-15

    A simple online sample dilution, enrichment, and cleanup technique was developed for sensitive microdosing and dried blood spot (DBS) liquid chromatography/tandem mass spectrometric (LC/MS/MS) bioanalysis. Samples are diluted online with water and enriched in a trap column which is subsequently switched inline with the analytical column. Excellent lansoprazole (in acetonitrile) peak shape is maintained even with an 80-microL injection. In comparison, similar chromatographic peaks were observed only when a small volume of the same solution, i.e., 1 microL, was injected on a regular high-performance liquid chromatography (HPLC) system, where an injection of 5 microL resulted in severe peak fronting. A substantial enhancement in sensitivity is realized in the trapping mode using large injection volumes. The trap column is washed at the beginning and at the end of each injection with aqueous and organic solvent respectively to remove matrix components. This ultimately leads to reduction of matrix effects and mass spectrometer noise, thus facilitating the utilization of protein precipitation as the sample preparation for plasma samples. A lower limit of quantitation (LLOQ) of 0.5 pg/mL was demonstrated for lansoprazole in human plasma with a signal-to-noise (S/N) ratio of 13 using a 100 microL injection. Excellent intra-day precision and accuracy were established for lansoprazole in human plasma with good linearity (R(2) > 0.999) from 0.5 to 500 pg/mL. This level of LLOQ makes LC/MS/MS a practical alternative for microdosing bioanalysis, where the dose is typically 100 times lower than the therapeutic dose. The same technique was applied to quantitate lansoprazole in human whole blood employing DBS technology. With a single 3-mm punch, i.e. approximately 2 microL of whole blood or approximately 1 microL plasma, a LLOQ of 0.1 ng/mL showed sufficient S/N ratio (40) for lansoprazole when 75 microL of extract was injected. In all, the online sample dilution, cleanup, and

  15. Blind Evaluation of the Microwave-Accelerated Metal-Enhanced Fluorescence Ultrarapid and Sensitive Chlamydia trachomatis Test by Use of Clinical Samples

    PubMed Central

    Melendez, Johan H.; Huppert, Jill S.; Jett-Goheen, Mary; Hesse, Elizabeth A.; Quinn, Nicole; Gaydos, Charlotte A.

    2013-01-01

    Accurate point-of-care (POC) diagnostic tests for Chlamydia trachomatis infection are urgently needed for the rapid treatment of patients. In a blind comparative study, we evaluated microwave-accelerated metal-enhanced fluorescence (MAMEF) assays for ultrafast and sensitive detection of C. trachomatis DNA from vaginal swabs. The results of two distinct MAMEF assays were compared to those of nucleic acid amplification tests (NAATs). The first assay targeted the C. trachomatis 16S rRNA gene, and the second assay targeted the C. trachomatis cryptic plasmid. Using pure C. trachomatis, the MAMEF assays detected as few as 10 inclusion-forming units/ml of C. trachomatis in less than 9 min, including DNA extraction and detection. A total of 257 dry vaginal swabs from 245 female adolescents aged 14 to 22 years were analyzed. Swabs were eluted with water, the solutions were lysed to release and to fragment genomic DNA, and MAMEF-based DNA detection was performed. The prevalence of C. trachomatis by NAATs was 17.5%. Of the 45 samples that were C. trachomatis positive and the 212 samples that were C. trachomatis negative by NAATs, 33/45 and 197/212 were correctly identified by the MAMEF assays if both assays were required to be positive (sensitivity, 73.3%; specificity, 92.9%). Using the plasmid-based assay alone, 37/45 C. trachomatis-positive and 197/212 C. trachomatis-negative samples were detected (sensitivity, 82.2%; specificity, 92.9%). Using the 16S rRNA assay alone, 34/45 C. trachomatis-positive and 197/212 C. trachomatis-negative samples were detected (sensitivity, 75.5%; specificity, 92.9%). The overall rates of agreement with NAAT results for the individual 16S rRNA and cryptic plasmid assays were 89.5% and 91.0%, respectively. Given the sensitivity, specificity, and rapid detection of the plasmid-based assay, the plasmid-based MAMEF assay appears to be suited for clinical POC testing. PMID:23804384

  16. Blind evaluation of the microwave-accelerated metal-enhanced fluorescence ultrarapid and sensitive Chlamydia trachomatis test by use of clinical samples.

    PubMed

    Melendez, Johan H; Huppert, Jill S; Jett-Goheen, Mary; Hesse, Elizabeth A; Quinn, Nicole; Gaydos, Charlotte A; Geddes, Chris D

    2013-09-01

    Accurate point-of-care (POC) diagnostic tests for Chlamydia trachomatis infection are urgently needed for the rapid treatment of patients. In a blind comparative study, we evaluated microwave-accelerated metal-enhanced fluorescence (MAMEF) assays for ultrafast and sensitive detection of C. trachomatis DNA from vaginal swabs. The results of two distinct MAMEF assays were compared to those of nucleic acid amplification tests (NAATs). The first assay targeted the C. trachomatis 16S rRNA gene, and the second assay targeted the C. trachomatis cryptic plasmid. Using pure C. trachomatis, the MAMEF assays detected as few as 10 inclusion-forming units/ml of C. trachomatis in less than 9 min, including DNA extraction and detection. A total of 257 dry vaginal swabs from 245 female adolescents aged 14 to 22 years were analyzed. Swabs were eluted with water, the solutions were lysed to release and to fragment genomic DNA, and MAMEF-based DNA detection was performed. The prevalence of C. trachomatis by NAATs was 17.5%. Of the 45 samples that were C. trachomatis positive and the 212 samples that were C. trachomatis negative by NAATs, 33/45 and 197/212 were correctly identified by the MAMEF assays if both assays were required to be positive (sensitivity, 73.3%; specificity, 92.9%). Using the plasmid-based assay alone, 37/45 C. trachomatis-positive and 197/212 C. trachomatis-negative samples were detected (sensitivity, 82.2%; specificity, 92.9%). Using the 16S rRNA assay alone, 34/45 C. trachomatis-positive and 197/212 C. trachomatis-negative samples were detected (sensitivity, 75.5%; specificity, 92.9%). The overall rates of agreement with NAAT results for the individual 16S rRNA and cryptic plasmid assays were 89.5% and 91.0%, respectively. Given the sensitivity, specificity, and rapid detection of the plasmid-based assay, the plasmid-based MAMEF assay appears to be suited for clinical POC testing.

  17. "One-Stop Shop": Free-Breathing Dynamic Contrast-Enhanced Magnetic Resonance Imaging of the Kidney Using Iterative Reconstruction and Continuous Golden-Angle Radial Sampling.

    PubMed

    Riffel, Philipp; Zoellner, Frank G; Budjan, Johannes; Grimm, Robert; Block, Tobias K; Schoenberg, Stefan O; Hausmann, Daniel

    2016-11-01

    The purpose of the present study was to evaluate a recently introduced technique for free-breathing dynamic contrast-enhanced renal magnetic resonance imaging (MRI) applying a combination of radial k-space sampling, parallel imaging, and compressed sensing. The technique allows retrospective reconstruction of 2 motion-suppressed sets of images from the same acquisition: one with lower temporal resolution but improved image quality for subjective image analysis, and one with high temporal resolution for quantitative perfusion analysis. In this study, 25 patients underwent a kidney examination, including a prototypical fat-suppressed, golden-angle radial stack-of-stars T1-weighted 3-dimensional spoiled gradient-echo examination (GRASP) performed after contrast agent administration during free breathing. Images were reconstructed at temporal resolutions of 55 spokes per frame (6.2 seconds) and 13 spokes per frame (1.5 seconds). The GRASP images were evaluated by 2 blinded radiologists. First, the reconstructions with low temporal resolution underwent subjective image analysis: the radiologists assessed the best arterial phase and the best renal phase and rated image quality score for each patient on a 5-point Likert-type scale.In addition, the diagnostic confidence was rated according to a 3-point Likert-type scale. Similarly, respiratory motion artifacts and streak artifacts were rated according to a 3-point Likert-type scale.Then, the reconstructions with high temporal resolution were analyzed with a voxel-by-voxel deconvolution approach to determine the renal plasma flow, and the results were compared with values reported in previous literature. Reader 1 and reader 2 rated the overall image quality score for the best arterial phase and the best renal phase with a median image quality score of 4 (good image quality) for both phases, respectively. A high diagnostic confidence (median score of 3) was observed. There were no respiratory motion artifacts in any of the

  18. Diagnostic potential for gold nanoparticle-based surface-enhanced Raman spectroscopy to provide colorectal cancer screening using blood serum sample

    NASA Astrophysics Data System (ADS)

    Lin, Duo; Feng, Shangyuan; Pan, Jianji; Chen, Yanping; Lin, Juqiang; Sun, Liqing; Chen, Rong

    2012-03-01

    Surface-enhanced Raman spectroscopy (SERS) is a vibrational spectroscopic technique that is capable of probing the biomolecular changes associated with diseased transformation. The objective of our study was to explore gold nanoparticle based SERS to obtain blood serum biochemical information for non-invasive colorectal cancer detection. SERS measurements were performed on two groups of blood serum samples: one group from patients (n = 38) with pathologically confirmed colorectal cancer and the other group from healthy volunteers (control subjects, n = 45). Tentative assignments of the Raman bands in the measured SERS spectra suggested interesting cancer specific biomolecular changes, including an increase in the relative amounts of nucleic acid, a decrease in the percentage of saccharide and proteins contents in the blood serum of colorectal cancer patients as compared to that of healthy subjects. Principal component analysis (PCA) of the measured SERS spectra separated the spectral features of the two groups into two distinct clusters with little overlaps. Linear discriminate analysis (LDA) based on the PCA generated features differentiated the nasopharyngeal cancer SERS spectra from normal SERS spectra with high sensitivity (97.4%) and specificity (100%). The results from this exploratory study demonstrated that gold nanoparticle based SERS serum analysis combined with PCA-LDA has tremendous potential for the non-invasive detection of colorectal cancers.

  19. Diagnostic potential for gold nanoparticle-based surface-enhanced Raman spectroscopy to provide colorectal cancer screening using blood serum sample

    NASA Astrophysics Data System (ADS)

    Lin, Duo; Feng, Shangyuan; Pan, Jianji; Chen, Yanping; Lin, Juqiang; Sun, Liqing; Chen, Rong

    2011-11-01

    Surface-enhanced Raman spectroscopy (SERS) is a vibrational spectroscopic technique that is capable of probing the biomolecular changes associated with diseased transformation. The objective of our study was to explore gold nanoparticle based SERS to obtain blood serum biochemical information for non-invasive colorectal cancer detection. SERS measurements were performed on two groups of blood serum samples: one group from patients (n = 38) with pathologically confirmed colorectal cancer and the other group from healthy volunteers (control subjects, n = 45). Tentative assignments of the Raman bands in the measured SERS spectra suggested interesting cancer specific biomolecular changes, including an increase in the relative amounts of nucleic acid, a decrease in the percentage of saccharide and proteins contents in the blood serum of colorectal cancer patients as compared to that of healthy subjects. Principal component analysis (PCA) of the measured SERS spectra separated the spectral features of the two groups into two distinct clusters with little overlaps. Linear discriminate analysis (LDA) based on the PCA generated features differentiated the nasopharyngeal cancer SERS spectra from normal SERS spectra with high sensitivity (97.4%) and specificity (100%). The results from this exploratory study demonstrated that gold nanoparticle based SERS serum analysis combined with PCA-LDA has tremendous potential for the non-invasive detection of colorectal cancers.

  20. Flow Measurements and selection of body-body and tip-tip enhanced samples in U+U collisions at STAR

    NASA Astrophysics Data System (ADS)

    Wang, Hui; STAR Collaboration

    2014-09-01

    The azimuthal anisotropy of particle production is commonly used in high-energy nuclear collisions to study the early evolution of the system. The prolate shape of uranium nuclei provides the possibility to study how the initial geometry of the nuclei affects the azimuthal distributions. It also provides a unique opportunity to understand the initial conditions for particle production at mid-rapidity in heavy ion collisions. In this talk, the two- and four- particle cumulant, v2 { 2 } and v2 { 4 } , from U+U collisions at √{sNN} = 193 GeV and Au+Au collisions at √{sNN} = 200 GeV for inclusive charged hadrons will be presented. The STAR Zero Degree Calorimeter is used to subdivide the 0-1% centrality bin into even finer centralities. Differences were observed between the multiplicity dependence of v2 { 2 } for most central Au+Au and U+U collisions. Data were compared with both Monte Carlo Glauber and IP-Glasma models and it was seen that IP-Glasma model does a better job of describing data. It has also been demonstrated that ZDC and multiplicity in combination provide a way to select body-body or tip-tip enhanced samples of central U+U collisions. We will also present preliminary v3 { 2 } results for inclusive charged hadrons from Au+Au and U+U collisions.

  1. In-situ formation of ion-association nanoparticles induced enhancements of resonance Rayleigh scattering intensities for quantitative analysis of trace Hg2 + ions in environmental samples

    NASA Astrophysics Data System (ADS)

    Yang, Qingling; Liu, Jian; Li, Banglin; Hu, Xiaoli; Liu, Shaopu; Chen, Gangcai

    2016-10-01

    In this paper, Hg2 + ions are demonstrated to form anionic [HgI4]2 - complexes after interacting with massive amount of I- ions. Subsequently, the addition of tetradecyl pyridyl bromide (TPB) can make [HgI4]2 - anionic complexes react with univalent tetradecyl pyridyl cationic ions (TP+), forming dispersed ion-association complexes (TP)2(HgI4). Due to the extrusion action of water and Van der Waals force, the hydrophobic ion-association complexes aggregate together, forming dispersed nanoparticles with an average size of about 8.5 nm. Meanwhile, resonance Rayleigh scattering (RRS) intensity is apparently enhanced due to the formation of (TP)2(HgI4) ion-association nanoparticles, contributing to a novel technique for Hg2 + detection. The wavelength of 365 nm is chosen as a detection wavelength and several conditions affecting the RRS responses of Hg2 + are optimized. Under the optimum condition, the developed method is used for the determination of Hg2 + in aqueous solution and the detection limit is estimated to be 0.8 ng mL- 1. Finally, the practical application of the developed method can be confirmed through the detections of Hg2 + in waste and river water samples with satisfactory results.

  2. Performance evaluation of Siemens ADVIA Centaur enhanced estradiol assay and a split sample comparison with liquid chromatography-tandem mass spectrometry.

    PubMed

    Chen, Yu; Kinney, Lois; Soldin, Steven J

    2012-07-01

    The objective of this study was to evaluate the newly developed Siemens ADVIA Centaur enhanced Estradiol (eE2) assay and compare it with a well-established estradiol liquid chromatography-tandem mass spectrometry (LC-MS/MS) method. The Siemens eE2 assay was evaluated using the Clinical and Laboratory Standards Institute evaluation protocols. Split patient samples were compared with the eE2 assay, the current ADVIA Centaur E2-6 Ill assay; and LC-MS/MS method by API5000 mass spectrometer. Within-run and total imprecision of the eE2 assay demonstrated coefficient of variations of 5.7%, 3.2%, 1.5%, and 10.4%, 7.3%, and 6.8%, at levels of 380, 752, and 2051 pmol/L, respectively. The method comparisons showed: eE2=0.903(E2-6 III) -16.2, R(2)=0.938, average bias=-12.3%; and eE2=0.946(LC-MS/MS)+19.5, R(2)=0.925, average bias: 0%. The Siemens eE2 assay correlates well with LC-MS/MS. This method is reliable, and appropriate for routine clinical laboratory use. Copyright © 2012 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

  3. Electrochemical determination of Sudan I in food samples at graphene modified glassy carbon electrode based on the enhancement effect of sodium dodecyl sulphonate.

    PubMed

    Ma, Xinying; Chao, Mingyong; Wang, Zhaoxia

    2013-06-01

    This paper describes a novel electrochemical method for the determination of Sudan I in food samples based on the electrochemical catalytic activity of graphene modified glassy carbon electrode (GMGCE) and the enhancement effect of an anionic surfactant: sodium dodecyl sulphonate (SDS). Using pH 6.0 phosphate buffer solution (PBS) as supporting electrolyte and in the presence of 1.5 × 10(-4)mol L(-1) SDS, Sudan I yielded a well-defined and sensitive oxidation peak at a GMGCE. The oxidation peak current of Sudan I remarkably increased in the presence of SDS. The experimental parameters, such as supporting electrolyte, concentration of SDS, and accumulation time, were optimised for Sudan I determination. The oxidation peak current showed a linear relationship with the concentrations of Sudan I in the range of 7.50 × 10(-8)-7.50 × 10(-6)mol L(-1), with the detection limit of 4.0 × 10(-8)mol L(-1). This new voltammetric method was successfully used to determine Sudan I in food products such as ketchup and chili sauce with satisfactory results.

  4. Contrast-enhanced MR angiography using time resolved interleaved projection sampling with three-dimensional Cartesian phase and slice encoding (TRIPPS).

    PubMed

    Du, Jiang

    2009-04-01

    Undersampled projection reconstruction (PR) techniques provide contrast enhanced MR angiography (CE-MRA) with high temporal resolution, but sensitivity to eddy current, gradient error and off-resonance effects. It is desirable to combine the time efficiency of undersampled PR acquisition with the robustness of Cartesian imaging. In this work we present a technique designed to do this termed time resolved projection sampling with three-dimensional (3D) Cartesian phase and slice encoding (TRIPPS), where 3D Cartesian k-space is partitioned into multiple half projections in the ky-kz plane. The phase and slice encoding are performed along predefined center-out radial trajectories. The whole set of half projections is interleaved into multiple groups of half projections, with each group sparsely but uniformly covering the ky-kz space. A view sharing sliding window reconstruction algorithm is adapted to reconstruct the dynamic images. The feasibility of the TRIPPS technique for CE-MRA was demonstrated on the renal, pulmonary, and intracranial vasculatures of healthy volunteers with a high temporal resolution of 2 s/frame.

  5. Enhanced protein and carbohydrate hydrolyses in plume-associated deepwaters initially sampled during the early stages of the Deepwater Horizon oil spill

    NASA Astrophysics Data System (ADS)

    Ziervogel, Kai; Arnosti, Carol

    2016-07-01

    Oil spilled in the ocean can be biodegraded through a cascade of microbial processes, including direct degradation of petroleum-derived hydrocarbons, as well as subsequent degradation of transformation byproducts and exopolymeric substances (EPS) that are produced by microbes to emulsify hydrocarbons and facilitate access to oil. In the aftermath of the Deepwater Horizon oil spill, we measured enzymatic hydrolysis of carbohydrates and peptides in waters initially collected from within and outside of the deep hydrocarbon plume. The rationale is that the presence of EPS and other transformation byproducts in the deepwater plume may have enhanced heterotrophic bacterial metabolism in the cold deepwater environment. Our investigation targets carbohydrate and peptide hydrolase activities as indicators of the degradation of high molecular weight organic matter, including EPS substrates. Deepwater associated with the hydrocarbon plume revealed higher peptidase activity compared to non-plume deepwater samples. Enzymatic hydrolysis of carbohydrates, measured by the means of exo-acting enzyme activity (β-glucosidase), was also more rapid inside compared to outside the deepwater plume. Hydrolysis rates and patterns of endo-acting polysaccharide hydrolases, measured by means of distinct polysaccharide substrates in longer-term incubations, demonstrated more rapid plume-associated hydrolysis of two (laminarin and xylan) of the three substrates hydrolyzed in deepwaters. Our results indicate that microbial communities associated with the deepwater plume exhibited 'primed' responses to addition of specific substrates, which may structurally resemble components found in bacterial EPS and oil degradation byproducts. Bacterial transformation of oil-degradation byproducts thus likely contributed to microbial growth and respiration measured inside the deepwater plume.

  6. Facilitative effects of the ampakine CX516 on short-term memory in rats: enhancement of delayed-nonmatch-to-sample performance.

    PubMed

    Hampson, R E; Rogers, G; Lynch, G; Deadwyler, S A

    1998-04-01

    Ampakines are a family of drugs that selectively increase AMPA receptor-gated currents and improve performance on several behavioral tasks. This report describes evidence that ampakines cause a cumulative enhancement of performance in a spatial short-term memory task (Deadwyler et al., 1996). Two groups of rats were trained on a spatial variant of the delayed-nonmatch-to-sample (DNMS) paradigm. One group (n = 12) received the ampakine CX516 (Cortex Pharmaceuticals) alternated with vehicle for 17 consecutive days and then only vehicle for an additional 7 d. The second group (n = 6) received only vehicle injections over the same number of days. CX516 improved performance within sessions, particularly on trials with delays of 6-35 sec. In 9 of 12 rats, the positive effect of the drug was also present on nondrug days between CX516 administration and after cessation of CX516 injections. The animals that received only vehicle injections showed no improvement in DNMS performance over the entire 32 d of testing. Three of the 12 animals given CX516 did not exhibit "carryover" effects of the drug to the intervening (vehicle only) test sessions, but nonetheless exhibited superior performance during the first half of the session on days in which the ampakine was administered. Evaluation of errors suggests that the ampakine eliminated the necessity for a shift in response strategy that produced proactive interference on the following trial. Hippocampal involvement in these ampakine effects is discussed as a prelude to the second article in the series (Hampson et al., 1998).

  7. Comparative Investigation of Single Voxel Magnetic Resonance Spectroscopy and Dynamic Contrast Enhancement MR Imaging in Differentiation of Benign and Malignant Breast Lesions in a Sample of Iranian Women.

    PubMed

    Faeghi, Fariborz; Baniasadipour, Banafsheh; Jalalshokouhi, Jalal

    2015-01-01

    To make a comparison of single voxel magnetic resonance spectroscopy (SV-MRS) and dynamic contrast enhancement (DCE) MRI for differentiation of benign and malignant breast lesions in a sample of Iranian women. A total of 30 women with abnormal breast lesions detected in mammography, ultrasound, or clinical breast exam were examined with DCE and SV-MRS. tCho (total choline) resonance in MRS spectra was qualitatively evaluated and detection of a visible tCho peak at 3.2 ppm was defined as a positive finding for malignancy. Different types of DCE curves were persistent (type 1), plateau (type 2), and washout (type 3). At first, lesions were classified according to choline findings and types of DCE curve, finally being compared to pathological results as the standard reference. this study included 19 patients with malignant lesions and 11 patients with benign ones. While 63.6 % of benign lesions (7 of 11) showed type 1 DCE curves and 36.4% (4 of 11) showed type 2, 57.9% (11of 19) of malignant lesions were type 3 and 42.1% (8 of 19) type 2. Choline peaks were detected in 18 of 19 malignant lesions and in 3 of 11 benign counterparts. 1 malignant and 8 benign cases did not show any visible resonance at 3.2 ppm so SV-MRS featured 94.7% sensitivity, 72.7 % specificity and 86.7% accuracy. The present findings indicate that a combined approach using MRS and DCE MRI can improve the specificity of MRI for differentiation of benign and malignant breast lesions.

  8. Surface Enhanced Raman Scattering (SERS) Detection of Ammonium Nitrate (AN) Samples Fabricated Using Drop-on-Demand Inkjet Technology on Commercial and Fabricated SERS Substrates

    DTIC Science & Technology

    2013-04-01

    coffee ring effect, and in (e) a SEM image and photograph of a microdroplet array demonstrating even sample deposition...nitrate and ammonium ions. They also concluded that drying moist samples resulted in a phase IV to III dominant transition. 4 With the...and (c) print head assembly. In (d) graphic and photograph images of drop and dry sample deposition demonstrating coffee ring effect, and in (e) a

  9. IGSN at Work in the Land Down Under: Exploiting an International Sample Identifier System to Enhance Reproducibility of Australian Geochemcial and Geochronological Data.

    NASA Astrophysics Data System (ADS)

    Bastrakova, I.; Klump, J. F.; McInnes, B.; Wyborn, L. A.; Brown, A.

    2015-12-01

    The International Geo-Sample Number (IGSN) provides a globally unique identifier for physical samples used to generate analytical data. This unique identifier provides the ability to link each physical sample to any analytical data undertaken on that sample, as well as to any publications derived from any data derived on the sample. IGSN is particularly important for geochemical and geochronological data, where numerous analytical techniques can be undertaken at multiple analytical facilities not only on the parent rock sample itself, but also on derived sample splits and mineral separates. Australia now has three agencies implementing IGSN: Geoscience Australia, CSIRO and Curtin University. All three have now combined into a single project, funded by the Australian Research Data Services program, to better coordinate the implementation of IGSN in Australia, in particular how these agencies allocate IGSN identifiers. The project will register samples from pilot applications in each agency including the CSIRO National Collection of Mineral Spectra database, the Geoscience Australia sample collection, and the Digital Mineral Library of the John De Laeter Centre for Isotope Research at Curtin University. These local agency catalogues will then be aggregated into an Australian portal, which will ultimately be expanded for all geoscience specimens. The development of this portal will also involve developing a common core metadata schema for the description of Australian geoscience specimens, as well as formulating agreed governance models for registering Australian samples. These developments aim to enable a common approach across Australian academic, research organisations and government agencies for the unique identification of geoscience specimens and any analytical data and/or publications derived from them. The emerging pattern of governance and technical collaboration established in Australia may also serve as a blueprint for similar collaborations internationally.

  10. Tip-enhanced near-field optical microscope with side-on and ATR-mode sample excitation for super-resolution Raman imaging of surfaces

    NASA Astrophysics Data System (ADS)

    Heilman, A. L.; Gordon, M. J.

    2016-06-01

    A tip-enhanced near-field optical microscope with side-on and attenuated total reflectance (ATR) excitation and collection is described and used to demonstrate sub-diffraction-limited (super-resolution) optical and chemical characterization of surfaces. ATR illumination is combined with an Au optical antenna tip to show that (i) the tip can quantitatively transduce the optical near-field (evanescent waves) above the surface by scattering photons into the far-field, (ii) the ATR geometry enables excitation and characterization of surface plasmon polaritons (SPPs), whose associated optical fields are shown to enhance Raman scattering from a thin layer of copper phthalocyanine (CuPc), and (iii) SPPs can be used to plasmonically excite the tip for super-resolution chemical imaging of patterned CuPc via tip-enhanced Raman spectroscopy (TERS). ATR-illumination TERS is also quantitatively compared with the more conventional side-on illumination scheme. In both cases, spatial resolution was better than 40 nm and tip on/tip off Raman enhancement factors were >6500. Furthermore, ATR illumination was shown to provide similar Raman signal levels at lower "effective" pump powers due to additional optical energy delivered by SPPs to the active region in the tip-surface gap.

  11. Tip-enhanced near-field optical microscope with side-on and ATR-mode sample excitation for super-resolution Raman imaging of surfaces

    SciTech Connect

    Heilman, A. L.; Gordon, M. J.

    2016-06-14

    A tip-enhanced near-field optical microscope with side-on and attenuated total reflectance (ATR) excitation and collection is described and used to demonstrate sub-diffraction-limited (super-resolution) optical and chemical characterization of surfaces. ATR illumination is combined with an Au optical antenna tip to show that (i) the tip can quantitatively transduce the optical near-field (evanescent waves) above the surface by scattering photons into the far-field, (ii) the ATR geometry enables excitation and characterization of surface plasmon polaritons (SPPs), whose associated optical fields are shown to enhance Raman scattering from a thin layer of copper phthalocyanine (CuPc), and (iii) SPPs can be used to plasmonically excite the tip for super-resolution chemical imaging of patterned CuPc via tip-enhanced Raman spectroscopy (TERS). ATR-illumination TERS is also quantitatively compared with the more conventional side-on illumination scheme. In both cases, spatial resolution was better than 40 nm and tip on/tip off Raman enhancement factors were >6500. Furthermore, ATR illumination was shown to provide similar Raman signal levels at lower “effective” pump powers due to additional optical energy delivered by SPPs to the active region in the tip-surface gap.

  12. Simulated scaling method for localized enhanced sampling and simultaneous "alchemical" free energy simulations: a general method for molecular mechanical, quantum mechanical, and quantum mechanical/molecular mechanical simulations.

    PubMed

    Li, Hongzhi; Fajer, Mikolai; Yang, Wei

    2007-01-14

    A potential scaling version of simulated tempering is presented to efficiently sample configuration space in a localized region. The present "simulated scaling" method is developed with a Wang-Landau type of updating scheme in order to quickly flatten the distributions in the scaling parameter lambdam space. This proposal is meaningful for a broad range of biophysical problems, in which localized sampling is required. Besides its superior capability and robustness in localized conformational sampling, this simulated scaling method can also naturally lead to efficient "alchemical" free energy predictions when dual-topology alchemical hybrid potential is applied; thereby simultaneously, both of the chemically and conformationally distinct portions of two end point chemical states can be efficiently sampled. As demonstrated in this work, the present method is also feasible for the quantum mechanical and quantum mechanical/molecular mechanical simulations.

  13. Enhanced detection of nitroaromatic explosive vapors combining solid-phase extraction-air sampling, supercritical fluid extraction, and large-volume injection-GC.

    PubMed

    Batlle, Ramón; Carlsson, Håkan; Tollbäck, Petter; Colmsjö, Anders; Crescenzi, Carlo

    2003-07-01

    A complete method for sampling and analyzing of energetic compounds in the atmosphere is described. The method consists of the hyphenation of several techniques: active air sampling using a solid-phase extraction cartridge to collect the analytes, extraction of the sorbed analytes by toluene/methyl tert-butyl ether modified supercritical fluid extraction (SFE), and analysis of the extract by large-volume injection GC-nitrogen/phosphorus detection. The GC system is equipped with a loop-type injection interface with an early solvent vapor exit, a utilizing concurrent solvent evaporation technique. Chemometric approaches, based on a Plackett-Burman screening design and a central composite design for response surface modeling, were used to determine the optimum SFE conditions. The relative standard deviations of the optimized method were determined to be 4.3 to 7.7%, giving raise to method detection limits ranging from 0.06 to 0.36 ng in the sampling cartridge, equivalent to 6.2-36.4 pg/L in the atmosphere, standard sampling volume 10 L. The analytical method was applied to characterize headspace composition above military grade trinitrotoluene (TNT). Results confirm that 2,4-dinitrotoluene (DNT) and 1,3-dinitrobenzene (DNB) constitute the largest vapor flux, but TNT, 2,6-DNT, and trinitrobenzene TNB were also consistently detected in all the samples.

  14. Analysis of urinary neurotransmitters by capillary electrophoresis: sensitivity enhancement using field-amplified sample injection and molecular imprinted polymer solid phase extraction.

    PubMed

    Claude, Bérengère; Nehmé, Reine; Morin, Philippe

    2011-08-12

    Capillary electrophoresis (CE) has been investigated for the analysis of some neurotransmitters, dopamine (DA), 3-methoxytyramine (3-MT) and serotonin (5-hydroxytryptamine, 5-HT) at nanomolar concentrations in urine. Field-amplified sample injection (FASI) has been used to improve the sensitivity through the online pre-concentration samples. The cationic analytes were stacked at the capillary inlet between a zone of low conductivity - sample and pre-injection plug - and a zone of high conductivity - running buffer. Several FASI parameters have been optimized (ionic strength of the running buffer, concentration of the sample protonation agent, composition of the sample solvent and nature of the pre-injection plug). Best results were obtained using H(3)PO(4)-LiOH (pH 4, ionic strength of 80 mmol L(-1)) as running buffer, 100 μmol L(-1) of H(3)PO(4) in methanol-water 90/10 (v/v) as sample solvent and 100 μmol L(-1) of H(3)PO(4) in water for the pre-injection plug. In these conditions, the linearity was verified in the 50-300 nmol L(-1) concentration range for DA, 3-MT and 5-HT with a determination coefficient (r(2)) higher than 0.99. The limits of quantification (10 nmol L(-1) for DA and 3-MT, 5.9 nmol L(-1) for 5-HT) were 500 times lower than those obtained with hydrodynamic injection. However, if this method is applied to the analysis of neurotransmitters in urine, the presence of salts in the matrix greatly reduces the sensitivity of the FASI/CE-UV method.Therefore, a solid phase extraction (SPE) on a dedicated imprinted polymer (MIP) was developed to extract specific neurotransmitters, catecholamines, metanephrines and indolamines, from urine. Matrix salts were thus discarded after sample extraction on AFFINIMIP™ Catecholamine & Metanephrine (100mg) cartridge. Therefore, lower limits of quantification were determined in artificial urine (46 nmol L(-1) for DA, 11 nmol L(-1) for 3-MT and 6 nmol L(-1) for 5-HT).The application of this protocol MIP

  15. Repeated stool sampling and use of multiple techniques enhance the sensitivity of helminth diagnosis: a cross-sectional survey in southern Lao People's Democratic Republic.

    PubMed

    Sayasone, Somphou; Utzinger, Jürg; Akkhavong, Kongsap; Odermatt, Peter

    2015-01-01

    Intestinal parasitic infections are common in Lao People's Democratic Republic (Lao PDR). We investigated the accuracy of the Kato-Katz (KK) technique in relation to varying stool sampling efforts, and determined the effect of the concurrent use of a quantitative formalin-ethyl acetate concentration technique (FECT) for helminth diagnosis and appraisal of concomitant infections. The study was carried out between March and May 2006 in Champasack province, southern Lao PDR. Overall, 485 individuals aged ≥6 months who provided three stool samples were included in the final analysis. All stool samples were subjected to the KK technique. Additionally, one stool sample per individual was processed by FECT. Diagnosis was done under a light microscope by experienced laboratory technicians. Analysis of three stool samples with KK plus a single FECT was considered as diagnostic 'gold' standard and resulted in prevalence estimates of hookworm, Opisthorchis viverrini, Ascaris lumbricoides, Trichuris trichiura and Schistosoma mekongi infection of 77.9%, 65.0%, 33.4%, 26.2% and 24.3%, respectively. As expected, a single KK and a single FECT missed a considerable number of infections. While our diagnostic 'gold' standard produced similar results than those obtained by a mathematical model for most helminth infections, the 'true' prevalence predicted by the model for S. mekongi (28.1%) was somewhat higher than after multiple KK plus a single FECT (24.3%). In the current setting, triplicate KK plus a single FECT diagnosed helminth infections with high sensitivity. Hence, such a diagnostic approach might be utilised for generating high-quality baseline data, assessing anthelminthic drug efficacy and rigorous monitoring of community interventions. Copyright © 2014 Elsevier B.V. All rights reserved.

  16. AirCore-HR: a high-resolution column sampling to enhance the vertical description of CH4 and CO2

    NASA Astrophysics Data System (ADS)

    Membrive, Olivier; Crevoisier, Cyril; Sweeney, Colm; Danis, François; Hertzog, Albert; Engel, Andreas; Bönisch, Harald; Picon, Laurence

    2017-06-01

    An original and innovative sampling system called AirCore was presented by NOAA in 2010 (Karion et al., 2010). It consists of a long (> 100 m) and narrow (< 1 cm) stainless steel tube that can retain a profile of atmospheric air. The captured air sample has then to be analyzed with a gas analyzer for trace mole fraction. In this study, we introduce a new AirCore aiming to improve resolution along the vertical with the objectives to (i) better capture the vertical distribution of CO2 and CH4, (ii) provide a tool to compare AirCores and validate the estimated vertical resolution achieved by AirCores. This (high-resolution) AirCore-HR consists of a 300 m tube, combining 200 m of 0.125 in. (3.175 mm) tube and a 100 m of 0.25 in. (6.35 mm) tube. This new configuration allows us to achieve a vertical resolution of 300 m up to 15 km and better than 500 m up to 22 km (if analysis of the retained sample is performed within 3 h). The AirCore-HR was flown for the first time during the annual StratoScience campaign from CNES in August 2014 from Timmins (Ontario, Canada). High-resolution vertical profiles of CO2 and CH4 up to 25 km were successfully retrieved. These profiles revealed well-defined transport structures in the troposphere (also seen in CAMS-ECMWF high-resolution forecasts of CO2 and CH4 profiles) and captured the decrease of CO2 and CH4 in the stratosphere. The multi-instrument gondola also carried two other low-resolution AirCore-GUF that allowed us to perform direct comparisons and study the underlying processing method used to convert the sample of air to greenhouse gases vertical profiles. In particular, degrading the AirCore-HR derived profiles to the low resolution of AirCore-GUF yields an excellent match between both sets of CH4 profiles and shows a good consistency in terms of vertical structures. This fully validates the theoretical vertical resolution achievable by AirCores. Concerning CO2 although a good agreement is found in terms of vertical structure

  17. 3D-printed polylactic acid supports for enhanced ionization efficiency in desorption electrospray mass spectrometry analysis of liquid and gel samples.

    PubMed

    Elviri, Lisa; Foresti, Ruben; Bianchera, Annalisa; Silvestri, Marco; Bettini, Ruggero

    2016-08-01

    The potential of 3D printing technology was here exploited to prepare tailored polylactic acid (PLA) supports for desorption electrospray ionization (DESI) experiments. PLA rough solid supports presenting wells of different shape (i.e. cylindrical, cubic and hemispherical cavities) were designed to accommodate samples of different physical state. The potentials of such supports in terms of sample loading capacity, sensitivity, signal stability were tested by analysing a peptide (i.e. insulin) and an aminoglycoside antibiotic (i.e. gentamicin sulphate) from solution and a chitosan-based gel. The results obtained were compared with those obtained by using a traditional polytetrafluoroethylene (PTFE) support and discussed. By using PLA support on the flat side, signal intensity improved almost twice with respect to PTFE support, whereas with spherical wells a five times improved signal sensitivity and good stability (RSD<6%) were obtained for the analysis of two model molecules. Limits of detection were in the 3-10nM range and linearity was demonstrated for both analytes in the 0.05-0.5μM range for semi-quantitative or quantitative purposes. The use of a well and the set-up of optimal source parameters allowed the analysis of samples in a gel state with good precision (RSD<10%) and accuracy (86±6-102±9%), otherwise difficult to analyse on a flat smooth surface. These findings are of great interest and stimulus to exploit the advantages of 3D printing technology for the development of devices for a DESI source, presenting different shapes or configuration as a function of the sample types.

  18. Enhanced spectrophotometric detection of Hg in water samples by surface plasmon resonance of Au nanoparticles after preconcentration with vortex-assisted liquid-liquid microextraction

    NASA Astrophysics Data System (ADS)

    Martinis, Estefanía M.; Wuilloud, Rodolfo G.

    2016-10-01

    This article presents an efficient, simple, and cost-effective method for the determination of trace amounts of Hg by vortex-assisted liquid-liquid microextraction (VALLME) coupled to microvolume UV-Vis spectrophotometry. This method correlates changes in the intensity of localized surface plasmon resonance (LSPR) of tetraoctylammonium bromide (TOABr) coated Au nanoparticles (NPs) after interaction with Hg2+ ion. Spectroscopic measurements of the TOABr-coated Au NPs phase with particular absorption properties (strong and well-defined absorption bands) after analyte extraction by VALLME, provide an accurate and sensitive determination of Hg in water samples, comparable with measurements obtained by atomic absorption spectrometry (AAS). Different variables including sample volume, extraction time, and TOABr-coated Au NPs dispersion volume were carefully studied; final experimental conditions were 5 mL, 120 μL and 5 min respectively. The limit of detection (LOD) was 0.8 ng mL- 1. The calibration curve was linear at concentrations between the limit of quantification (LOQ) (4.9 ng mL- 1) and up to at least 120 ng mL- 1 of Hg. The relative standard deviation for six replicate determinations of 20 ng mL- 1 of Hg was 4.7%. This method exhibited an excellent analytical performance in terms of selectivity and sensitivity and it was finally applied for Hg determination in spiked tap and mineral water samples.

  19. Bulk δ(15) N measurements of organic-rich rock samples by elemental analyzer/isotope ratio mass spectrometry with enhanced oxidation ability.

    PubMed

    Han, Wennian; Feng, Lianjun; Li, Hongwei; Liu, Wei

    2017-01-15

    Elemental analyzer/isotope ratio mass spectrometry (EA/IRMS) has been widely used for nitrogen isotope ratio determination in various organic and inorganic samples. However, the extent of the redox reaction in the EA reaction tube can greatly affect the accuracy and precision of measurements, especially in the case of complex geological samples. It is therefore necessary to determine the appropriate reaction conditions to reach a high recovery of nitrogen by complete combustion or thermal decomposition and quantitative reduction. The conventional Dumas dual-inlet method was used to determine the bulk nitrogen isotope composition of SGR-1 (an organic-rich standard sample), which then was analyzed by EA/IRMS under different EA reaction conditions to study the influence of the redox environment on the δ(15) N measurements. The measured data together with the results reported by previous researchers were used to evaluate the effectiveness of the nitrogen extraction for organic-rich rock samples. Our results demonstrated that with the Dumas dual-inlet method more oxidizing agent (CuO) addition to SGR-1 would yield a higher nitrogen content of 0.91% than the recommended content (0.81%) although a δ(15) N value of 17.39 ± 0.09‰ was consistent with the recommended value by USGS. Using EA/IRMS, when more O2 was injected in the reaction tube, a high nitrogen content (0.92 ± 0.01%) and a δ(15) N value (17.43 ± 0.17‰) close to that of the Dumas dual-inlet method were obtained. The addition of V2 O5 or CuO in a continuous-flow system of EA/IRMS could not effectively enable the complete combustion of SGR-1. When measuring the nitrogen isotope composition of organic-rich rock sample dominated by reduced substances with EA/IRMS, greater O2 injection will enable more complete combustion to obtain reliable nitrogen yields compared with the addition of V2 O5 or CuO. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  20. Blocking primers to enhance PCR amplification of rare sequences in mixed samples - a case study on prey DNA in Antarctic krill stomachs.

    PubMed

    Vestheim, Hege; Jarman, Simon N

    2008-07-20

    Identification of DNA sequence diversity is a powerful means for assessing the species present in environmental samples. The most common molecular strategies for estimating taxonomic composition depend upon PCR with universal primers that amplify an orthologous DNA region from a range of species. The diversity of sequences within a sample that can be detected by universal primers is often compromised by high concentrations of some DNA templates. If the DNA within the sample contains a small number of sequences in relatively high concentrations, then less concentrated sequences are often not amplified because the PCR favours the dominant DNA types. This is a particular problem in molecular diet studies, where predator DNA is often present in great excess of food-derived DNA. We have developed a strategy where a universal PCR simultaneously amplifies DNA from food items present in DNA purified from stomach samples, while the predator's own DNA is blocked from amplification by the addition of a modified predator-specific blocking primer. Three different types of modified primers were tested out; one annealing inhibiting primer overlapping with the 3' end of one of the universal primers, another annealing inhibiting primer also having an internal modification of five dI molecules making it a dual priming oligo, and a third elongation arrest primer located between the two universal primers. All blocking primers were modified with a C3 spacer. In artificial PCR mixtures, annealing inhibiting primers proved to be the most efficient ones and this method reduced predator amplicons to undetectable levels even when predator template was present in 1000 fold excess of the prey template. The prey template then showed strong PCR amplification where none was detectable without the addition of blocking primer. Our method was applied to identifying the winter food of one of the most abundant animals in the world, the Antarctic krill, Euphausia superba. Dietary item DNA was PCR

  1. Enhanced sampling molecular dynamics simulation captures experimentally suggested intermediate and unfolded states in the folding pathway of Trp-cage miniprotein

    NASA Astrophysics Data System (ADS)

    Shao, Qiang; Shi, Jiye; Zhu, Weiliang

    2012-09-01

    The ability of molecular dynamics simulation to capturing the transient states within the folding pathway of protein is important to the understanding of protein folding mechanism. In the present study, the integrated-tempering-sampling molecular dynamics (ITS-MD) simulation was performed to investigate the transient states including intermediate and unfolded ones in the folding pathway of a miniprotein, Trp-cage. Three force fields (FF03, FF99SB, and FF96) were tested, and both intermediate and unfolded states with their characteristics in good agreement with experiments were observed during the simulations, which supports the hypothesis that observable intermediates might present in the folding pathway of small polypeptides. In addition, it was demonstrated that FF03 force field as combined with ITS-MD is in overall a more proper force field than the others in reproducing experimentally recorded properties in UVRS, ECD, and NMR, Photo-CIDNP NMR, and IR T-jump experiments, and the folding/unfolding thermodynamics parameters, such as ΔGU, ΔCp, and ΔHU (Tm). In summary, the present study showed that using suitable force field and energy sampling method, molecular dynamics simulation could capture the transient states within the folding pathway of protein which are consistent with the experimental measurements, and thus provide information of protein folding mechanism and thermodynamics.

  2. Modification of sample processing for the Limulus amebocyte lysate assay enhances detection of inflammogenic endotoxin in intact bacteria and organic dust.

    PubMed

    Hoppe Parr, Kimberly A; Hađina, Suzana; Kilburg-Basnyat, Brita; Wang, Yifang; Chavez, Dulce; Thorne, Peter S; Weiss, Jerrold P

    2017-04-01

    The pro-inflammatory potency and causal relationship with asthma of inhaled endotoxins have underscored the importance of accurately assessing the endotoxin content of organic dusts. The Limulus amebocyte lysate (LAL) assay has emerged as the preferred assay, but its ability to measure endotoxin in intact bacteria and organic dusts with similar sensitivity as purified endotoxin is unknown. We used metabolically radiolabeled Neisseria meningitidis and both rough and smooth Escherichia coli to compare dose-dependent activation in the LAL with purified endotoxin from these bacteria and shed outer membrane (OM) blebs. Labeled [(14)C]-3-OH-fatty acids were used to quantify the endotoxin content of the samples. Purified meningococcal and E. coli endotoxins and OM blebs displayed similar specific activity in the LAL assay to the purified LPS standard. In contrast, intact bacteria exhibited fivefold lower specific activity in the LAL assay but showed similar MD-2-dependent potency as purified endotoxin in inducing acute airway inflammation in mice. Pre-treatment of intact bacteria and organic dusts with 0.1 M Tris-HCl/10 mM EDTA increased by fivefold the release of endotoxin. These findings demonstrate that house dust and other organic dusts should be extracted with Tris/EDTA to more accurately assess the endotoxin content and pro-inflammatory potential of these environmental samples.

  3. Extraction and determination of sulfonylurea herbicides in water and soil samples by using ultrasound-assisted surfactant-enhanced emulsification microextraction and analysis by high-performance liquid chromatography.

    PubMed

    Ghobadi, Masoomeh; Yamini, Yadollah; Ebrahimpour, Behnam

    2015-02-01

    An ultrasound-assisted surfactant-enhanced emulsification microextraction (UASEME) with low-density extraction solvents was developed for the extraction of sulfonylurea herbicides from water and soil samples prior to high-performance liquid chromatography coupled with ultraviolet detection (HPLC-UV). In this technique, a surfactant was used as emulsifier which could enhance the dispersion of water-immiscible extraction solvent into aqueous phase and was favorable for the mass-transfer of the analytes from aqueous phase to organic phase. The target analytes were extracted into an extraction phase (Aliquat-336 in 1-octanol) and dispersed in an aqueous solution. After extraction and phase separation, the organic solvent on top of the solution was withdrawn into a syringe and 20 µL of it was injected into a HPLC instrument for analysis. Influential factors in extraction were investigated and optimized. Under optimum experimental conditions, calibration curve was linear in the concentration range from 1 to 100 µg/L, with coefficients of estimation (R(2) values) varying from 0.9928 to 0.9952, and satisfactory repeatabilities (4.7samples, was studied. The obtained results indicated that the proposed method is efficient, fast and inexpensive for extraction and determination of sulfonylurea herbicides in environmental aqueous and soil samples.

  4. Sensitivity and specificity enhanced enzyme-linked immunosorbent assay by rational hapten modification and heterogeneous antibody/coating antigen combinations for the detection of melamine in milk, milk powder and feed samples.

    PubMed

    Cao, Biyun; Yang, Hong; Song, Juan; Chang, Huafang; Li, Shuqun; Deng, Anping

    2013-11-15

    The adulteration of food products with melamine has led to an urgent requirement for sensitive, specific, rapid and reliable quantitative/screening methods. To enhance the sensitivity and specificity of the enzyme-linked immunosorbent assay (ELISA) for the detection of melamine in milk, milk powder and feed samples, rational hapten modification and heterogeneous antibody/coating antigen combinations were adopted. Three melamine derivatives with different length of carboxylic spacer at the end were synthesized and linked to carrier proteins for the production of immunogens and coating antigens. Monoclonal antibody against melamine was produced by hybridoma technology. Under optimal experimental conditions, the standard curves of the ELISAs for melamine were constructed in range of 0.1-100 ng mL(-1). The sensitivity was 10-300 times enhanced compared to those in the published literatures. The cross-reactivity values of the ELISAs also demonstrated the assays exhibited high specificity. Five samples were spiked with melamine at different concentrations and detected by the ELISA. The recovery rates of 72.8-123.0% and intra-assay coefficients of variation of 0.8-18.9% (n=3) were obtained. The ELISA for milk sample was confirmed by high-performance liquid chromatography with a high correlation coefficient of 0.9902 (n=6). The proposed ELISA was proven to be a feasible quantitative/screening method for melamine analysis. Copyright © 2013 Elsevier B.V. All rights reserved.

  5. PG545 enhances anti-cancer activity of chemotherapy in ovarian models and increases surrogate biomarkers such as VEGF in preclinical and clinical plasma samples.

    PubMed

    Winterhoff, Boris; Freyer, Luisa; Hammond, Edward; Giri, Shailendra; Mondal, Susmita; Roy, Debarshi; Teoman, Attila; Mullany, Sally A; Hoffmann, Robert; von Bismarck, Antonia; Chien, Jeremy; Block, Matthew S; Millward, Michael; Bampton, Darryn; Dredge, Keith; Shridhar, Viji

    2015-05-01

    Despite the utility of antiangiogenic drugs in ovarian cancer, efficacy remains limited due to resistance linked to alternate angiogenic pathways and metastasis. Therefore, we investigated PG545, an anti-angiogenic and anti-metastatic agent which is currently in Phase I clinical trials, using preclinical models of ovarian cancer. PG545's anti-cancer activity was investigated in vitro and in vivo as a single agent, and in combination with paclitaxel, cisplatin or carboplatin using various ovarian cancer cell lines and tumour models. PG545, alone, or in combination with chemotherapeutics, inhibited proliferation of ovarian cancer cells, demonstrating synergy with paclitaxel in A2780 cells. PG545 inhibited growth factor-mediated cell migration and reduced HB-EGF-induced phosphorylation of ERK, AKT and EGFR in vitro and significantly reduced tumour burden which was enhanced when combined with paclitaxel in an A2780 model or carboplatin in a SKOV-3 model. Moreover, in the immunocompetent ID8 model, PG545 also significantly reduced ascites in vivo. In the A2780 maintenance model, PG545 initiated with, and following paclitaxel and cisplatin treatment, significantly improved overall survival. PG545 increased plasma VEGF levels (and other targets) in preclinical models and in a small cohort of advanced cancer patients which might represent a potential biomarker of response. Our results support clinical testing of PG545, particularly in combination with paclitaxel, as a novel therapeutic strategy for ovarian cancer. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. Three-dimensional dynamic time-resolved contrast-enhanced MRA using parallel imaging and a variable rate k-space sampling strategy in intracranial arteriovenous malformations.

    PubMed

    Petkova, Mina; Gauvrit, Jean-Yves; Trystram, Denis; Nataf, François; Godon-Hardy, Sylvie; Munier, Thierry; Oppenheim, Catherine; Meder, Jean-François

    2009-01-01

    To evaluate the effectiveness of three-dimensional (3D) dynamic time-resolved contrast-enhanced MRA (TR-CE-MRA) using a combination of a parallel imaging technique (ASSET: array spatial sensitivity encoding technique) and a time-resolved method (TRICKS: time-resolved imaging of contrast kinetics) and to compare it with 3D dynamic TR-CE-MRA using ASSET alone in the assessment of intracranial arteriovenous malformations (AVMs). Twenty consecutive patients with angiographically confirmed AVMs were investigated using both 3D dynamic TR-CE-MRA techniques. Examinations were compared with respect to image quality, spatial resolution, number and type of feeders and drainers, nidus size, presence of early venous filling and temporal resolution. Digital subtraction angiography was used as standard of reference. The higher temporal and spatial resolution of 3D dynamic TR-CE-MRA TRICKS ASSET allowed a better assessment of intracranial vascular malformations, namely better depiction of feeders, drainers and better detection of early venous drainage. There was no significant difference between them in terms of nidus size. 3D dynamic TR-CE-MRA combining parallel imaging and a time-resolved method with subsecond and submillimeter resolution could become the first-line investigation technique in both diagnosis and follow-up of intracranial AVMs.

  7. Determination of the solution-bound conformation of an amino acid binding protein by NMR paramagnetic relaxation enhancement: use of a single flexible paramagnetic probe with improved estimation of its sampling space.

    PubMed

    Bermejo, Guillermo A; Strub, Marie-Paule; Ho, Chien; Tjandra, Nico

    2009-07-15

    We demonstrate the feasibility of elucidating the bound ("closed") conformation of a periplasmic binding protein, the glutamine-binding protein (GlnBP), in solution, using paramagnetic relaxation enhancements (PREs) arising from a single paramagnetic group. GlnBP consists of two globular domains connected by a hinge. Using the ligand-free ("open") conformation as a starting point, conjoined rigid-body/torsion-angle simulated annealing calculations were performed using backbone (1)H(N)-PREs as a major source of distance information. Paramagnetic probe flexibility was accounted for via a multiple-conformer representation. A conventional approach where the entire PRE data set is enforced at once during simulated annealing yielded poor results due to inappropriate conformational sampling of the probe. On the other hand, significant improvements in coordinate accuracy were obtained by estimating the probe sampling space prior to structure calculation. Such sampling is achieved by refining the ensemble of probe conformers with intradomain PREs only, keeping the protein backbone fixed in the open form. Subsequently, while constraining the probe to the previously found conformations, the domains are allowed to move relative to each other under the influence of the non-intradomain PREs, giving the hinge region torsional degrees of freedom. Thus, by partitioning the protocol into "probe sampling" and "backbone sampling" stages, structures significantly closer to the X-ray structure of ligand-bound GlnBP were obtained.

  8. Application of Ultrasound-Assisted Surfactant-Enhanced Emulsification Microextraction Based on Solidification of Floating Organic Droplets and High Performance Liquid Chromatography for Preconcentration and Determination of Alprazolam and Chlordiazepoxide in Human Serum Samples.

    PubMed

    Goudarzi, Nasser; Amirnavaee, Monavar; Arab Chamjangali, Mansour; Farsimadan, Sahar

    2017-03-03

    An improved microextraction method is proposed on the basis of ultrasound-assisted surfactant-enhanced emulsification and solidification of a floating organic droplet procedure combined with high performance liquid chromatography for the preconcentration and quantification of alprazolam (ALP) and chlordiazepoxide (CHL) present in a number of human serum samples. Several parameters affecting the extraction efficiency were investigated by the Plackett -Burman factorial design as the screening design. Then the response surface methodology based on the Box-Behnken design was used to optimize the effective parameters in the proposed procedure. The limits of detection for the proposed method were found to be 3.0 and 3.1 ng mL-1 for CHL and ALP, respectively. The calibration curves obtained for the method were linear in the ranges of 10.0-3,500.0 and 10.0-3,000.0 ng mL-1 for CHL and ALP, respectively, with a good determination coefficient. The recoveries of the drugs in the spiked human serum samples were above 93.0%. The developed method was successfully applied to the analysis of these studied drugs in human serum samples. The pre-treatment of the serum samples was performed using acetonitrile to remove the proteins. The proposed procedure was an accurate and reliable one for the determination and preconcentration of these drugs in blood samples.

  9. Enhancement of the BG-sentinel trap with varying number of mice for field sampling of male and female Aedes albopictus mosquitoes.

    PubMed

    Le Goff, Gilbert; Damiens, David; Payet, Laurent; Ruttee, Abdoul-Hamid; Jean, Frédéric; Lebon, Cyrille; Dehecq, Jean-Sébastien; Gouagna, Louis-Clément

    2016-09-22

    Trapping male mosquitoes in the field is essential for the development of area-wide vector control programs with a sterile insect technique (SIT) component. To determine the optimal temporal and spatial release strategy, an estimation of the wild population density and its temporal dynamics is essential. Among the traps available for such data collection, the BG-Sentinel trap developed by the Biogents company uses a combination of visual cues, convection currents and olfactory signals. Although in numerous cases, this trap has shown high efficiency in sampling Aedes albopictus, in some cases low capture rates of Ae. albopictus males were recorded for the BG-sentinel mosquito trap baited with synthetic attractants. The effects of modifying the BG-sentinel trap (by adding one mouse, two or three live mice to the trap) on the efficiency of trapping Ae. albopictus males and females was tested. The experiment was carried out in three distinct areas on La Réunion that have been selected for pilot field testing of the release of sterile male Ae. albopictus mosquitoes. The effect of four types of attractant (including the generic BG-Lure, one mouse or two to three mice) in baited BGS traps was tested with a Latin square design in order to control for the variability of different sampling positions and dates. At the three studied sites, the number of Ae. albopictus adults caught and the proportion of males per trap consistently increased with the number of mice present in the trap. The results from this study suggest that some new attractants derived from, or similar to, mouse odors could be developed and tested in combination with other existing attractive components, such as CO2 and heat, in order to provide a reliable estimation method for Ae. albopictus adult male abundance in the wild.

  10. High Spatiotemporal Resolution Dynamic Contrast-Enhanced MR Enterography in Crohn Disease Terminal Ileitis Using Continuous Golden-Angle Radial Sampling, Compressed Sensing, and Parallel Imaging.

    PubMed

    Ream, Justin M; Doshi, Ankur; Lala, Shailee V; Kim, Sooah; Rusinek, Henry; Chandarana, Hersh

    2015-06-01

    The purpose of this article was to assess the feasibility of golden-angle radial acquisition with compress sensing reconstruction (Golden-angle RAdial Sparse Parallel [GRASP]) for acquiring high temporal resolution data for pharmacokinetic modeling while maintaining high image quality in patients with Crohn disease terminal ileitis. Fourteen patients with biopsy-proven Crohn terminal ileitis were scanned using both contrast-enhanced GRASP and Cartesian breath-hold (volume-interpolated breath-hold examination [VIBE]) acquisitions. GRASP data were reconstructed with 2.4-second temporal resolution and fitted to the generalized kinetic model using an individualized arterial input function to derive the volume transfer coefficient (K(trans)) and interstitial volume (v(e)). Reconstructions, including data from the entire GRASP acquisition and Cartesian VIBE acquisitions, were rated for image quality, artifact, and detection of typical Crohn ileitis features. Inflamed loops of ileum had significantly higher K(trans) (3.36 ± 2.49 vs 0.86 ± 0.49 min(-1), p < 0.005) and v(e) (0.53 ± 0.15 vs 0.20 ± 0.11, p < 0.005) compared with normal bowel loops. There were no significant differences between GRASP and Cartesian VIBE for overall image quality (p = 0.180) or detection of Crohn ileitis features, although streak artifact was worse with the GRASP acquisition (p = 0.001). High temporal resolution data for pharmacokinetic modeling and high spatial resolution data for morphologic image analysis can be achieved in the same acquisition using GRASP.

  11. Effectiveness of the 'Hold me Tight' Relationship Enhancement Program in a Self-referred and a Clinician-referred Sample: An Emotionally Focused Couples Therapy-Based Approach.

    PubMed

    Conradi, Henk Jan; Dingemanse, Pieter; Noordhof, Arjen; Finkenauer, Catrin; Kamphuis, Jan H

    2017-09-04

    While evidence-based couple therapies are available, only a minority of troubled couples seek help and they often do this too late. To reach more couples earlier, the couple relationship education (CRE) group program "Hold me Tight" (HmT) based on Emotionally Focused Couples Therapy (EFCT) was developed. This study is the first to examine the effectiveness of HmT. Using a three-wave (waiting period, treatment, and follow-up) within-subject design, HmT was delivered to 79 self-referred couples and 50 clinician-referred couples. We applied a comprehensive outcome measure battery. Our main findings were that (1) self-referred couples significantly improved during HmT on all measures, that is relationship satisfaction, security of partner-bond, forgiveness, daily coordination, maintenance behavior, and psychological complaints, with a moderate-to-large mean effect size (d = .63), which was maintained (d = .57) during the 3.5 month follow-up; (2) in clinician-referred couples, who were vulnerable in terms of insecure attachment status and psychopathology, the improvement during HmT was moderate (d = .42), but this was reduced during the 3.5-month follow-up to a small effect (d = .22); (3) emotional functioning (typical HmT target) as well as behavioral functioning (typical Behavioral Couples Therapy-based CRE target) improved during HmT; and (4) individual psychological complaints, although not specifically targeted, were reduced during HmT. These findings suggest that HmT is a promising intervention for enhancement of relationship functioning. Clinical implications are discussed. © 2017 Family Process Institute.

  12. Examination of posttraining supervision of peer counselors in a motivational enhancement intervention to reduce drinking in a sample of heavy-drinking college students.

    PubMed

    Mastroleo, Nadine R; Turrisi, Rob; Carney, Jolynn V; Ray, Anne E; Larimer, Mary E

    2010-10-01

    Importance of peer counselor posttraining supervision on motivational interviewing (MI) microskills and postintervention drinking outcomes were evaluated in a sample of heavy-drinking undergraduate students completing Brief Alcohol Screening and Intervention for College Students (BASICS; L.A. Dimeff, J.S. Baer, D.R. Kivlahan, & G.A. Marlatt, 1999). Two peer counselor groups were trained using identical protocols. Posttraining, one group was randomized to receive supervision, whereas the other received no supervision. Groups were subsequently compared on MI microskills. College students (n = 122) were randomly assigned to either assessment-only control, supervision, or no supervision groups and completed a BASICS intervention. Postintervention drinking outcomes were examined. Results suggested supervision aided peer counselors in reducing use of closed-ended questions. Both treatment groups reduced total drinks per week and heavy-drinking behaviors compared to control. No differences on peak blood alcohol concentration (BAC) or alcohol-related consequences were observed. Differences in supervision did not influence drinking outcomes; however, posttraining supervision for peer counselors deficient in MI microskills may be needed to improve BASICS fidelity.

  13. Examination of Post-Training Supervision of Peer Counselors in a Motivational Enhancement Intervention to Reduce Drinking in a Sample of Heavy Drinking College Students

    PubMed Central

    Mastroleo, Nadine R.; Turrisi, Rob; Carney, JoLynn V.; Ray, Anne E.; Larimer, Mary E.

    2010-01-01

    Importance of peer counselor post-training supervision on Motivational Interviewing microskills and post-intervention drinking outcomes were evaluated in a sample of heavy drinking undergraduate students completing BASICS (Dimeff et al., 1999). Two peer counselor groups were trained using identical protocols. Post-training, one group was randomized to receive supervision, while the other received no supervision. Groups were subsequently compared on MI microskills. College students (N=122) were randomly assigned to either assessment-only control, supervision, or no supervision groups and completed a BASICS intervention. Post-intervention drinking outcomes were examined. Results suggested supervision aided peer counselors in reducing use of closed-ended questions. Both treatment groups reduced total drinks per week and heavy drinking behaviors compared to control. No differences on peak BAC or alcohol related consequences were observed. Differences in supervision did not influence drinking outcomes; however post-training supervision for peer counselors deficient in MI microskills may be needed to improve BASICS fidelity. PMID:20673621

  14. On-line focusing of 5-hydroxy-tryptamine type 3 receptor antagonists via the combination of field-enhanced sample injection and dynamic pH junction in capillary electrophoresis with amperometric detection.

    PubMed

    Li, Libo; Xu, Lei; Huang, Jianshe; You, Tianyan

    2014-02-28

    In the present work, an on-line dual focusing technique based on field-enhance sample injection (FASI) and dynamic pH junction (DypH) was developed for the analysis of two 5-hydroxy-tryptamine type 3 receptor (5-HT3) antagonists ondansetron (Ond) and tropisetron (Tro) by capillary electrophoresis with amperometric detection (CE-AD) system. By preparing the sample in a lower conductivity (FASI condition) and lower pH value (DypH condition) matrix relative to the background electrolyte (BGE) solution, a simple and effective dual focusing approach, FASI-DypH was achieved. In this stacking mode, a large amount of analytes could be electrokinetically injected into the capillary and stacked at the boundary of the sample and the BGE zone as a result of deprotonation and decrease in the electric field. Effects of separation, detection and FASI-DypH focusing conditions were investigated in detail. Under the optimum conditions, good separation for Ond and Tro was achieved within 8min. In comparison with the conventional CE-AD analysis method, the present dual focusing technique enabled the enhancement factors in terms of peak heights to reach 357-fold and 345-fold for Ond and Tro, respectively. The limits of detection (LODs) (S/N=3) for Ond and Tro were 2nM and 5nM, respectively. The intraday and interday repeatabilities (RSDs) were less than 4.5% and 2.9% for peak height and migration time, respectively. The proposed method was successfully applied for the analysis of Ond and Tro in human urine sample. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. Combining poly (methacrylic acid-co-ethylene glycol dimethacrylate) monolith microextraction and octadecyl phosphonic acid-modified zirconia-coated CEC with field-enhanced sample injection for analysis of antidepressants in human plasma and urine.

    PubMed

    Wei, Fang; Fan, Jin; Zheng, Ming-Ming; Feng, Yu-Qi

    2010-01-01

    A method based on poly (methacrylic acid-co-ethylene glycol dimethacrylate) monolith microextraction and octadecylphosphonic acid-modified zirconia-coated CEC followed by field-enhanced sample injection preconcentration technique was proposed for sensitive CE-UV analysis of six antidepressants (doxepin, clozapine, imipramine, paroxetine, fluoxetine and chlorimipramine) in human plasma and urine. A poly(methacrylic acid-co-ethylene glycol dimethacrylate) monolithic capillary column was introduced for the extraction of antidepressants from urine and plasma samples. The hydrophobic main chains and acidic pendant groups of the monolithic column make it a superior material for extraction of basic analytes from aqueous matrix. After extraction, the desorption solvent, which normally provided an excellent medium to ensure direct compatibility for field-enhanced sample injection in CE, was analyzed by CE directly. By the use of alkylphosphonate-modified zirconia-coated CEC for separation of the basic compounds of antidepressants, high separation efficiency and resolution were achieved because that both hydrophobic interaction between analytes and alkylphosphonate-modified zirconia coat and electrophoretic effect work on the separation of antidepressants. The best separation was achieved using a buffer composed of 0.3 M ammonium acetate (adjusted to pH 4.5 with 1 M acetic acid) and 35% ACN v/v, with a temperature and voltage of 20 degrees C and 20 kV, respectively. By applying both preconcentration procedures, LODs of 11.4-51.5 and 3.7-17.0 microg/L were achieved for the six antidepressants in human plasma and urine, respectively. Excellent method of reproducibility was found over a linear range of 50-5000 microg/L in plasma and urine sample.

  16. Sample Design.

    ERIC Educational Resources Information Center

    Ross, Kenneth N.

    1987-01-01

    This article considers various kinds of probability and non-probability samples in both experimental and survey studies. Throughout, how a sample is chosen is stressed. Size alone is not the determining consideration in sample selection. Good samples do not occur by accident; they are the result of a careful design. (Author/JAZ)

  17. Biphasic DC measurement approach for enhanced measurement stability and multi-channel sampling of self-sensing multi-functional structural materials doped with carbon-based additives

    NASA Astrophysics Data System (ADS)

    Downey, Austin; D'Alessandro, Antonella; Ubertini, Filippo; Laflamme, Simon; Geiger, Randall

    2017-06-01

    Investigation of multi-functional carbon-based self-sensing structural materials for structural health monitoring applications is a topic of growing interest. These materials are self-sensing in the sense that they can provide measurable electrical outputs corresponding to physical changes such as strain or induced damage. Nevertheless, the development of an appropriate measurement technique for such materials is yet to be achieved, as many results in the literature suggest that these materials exhibit a drift in their output when measured with direct current (DC) methods. In most of the cases, the electrical output is a resistance and the reported drift is an increase in resistance from the time the measurement starts due to material polarization. Alternating current methods seem more appropriate at eliminating the time drift. However, published results show they are not immune to drift. Moreover, the use of multiple impedance measurement devices (LCR meters) does not allow for the simultaneous multi-channel sampling of multi-sectioned self-sensing materials due to signal crosstalk. The capability to simultaneously monitor multiple sections of self-sensing structural materials is needed to deploy these multi-functional materials for structural health monitoring. Here, a biphasic DC measurement approach with a periodic measure/discharge cycle in the form of a square wave sensing current is used to provide consistent, stable resistance measurements for self-sensing structural materials. DC measurements are made during the measurement region of the square wave while material depolarization is obtained during the discharge region of the periodic signal. The proposed technique is experimentally shown to remove the signal drift in a carbon-based self-sensing cementitious material while providing simultaneous multi-channel measurements of a multi-sectioned self-sensing material. The application of the proposed electrical measurement technique appears promising for real

  18. Vortex-assisted surfactant-enhanced-emulsification liquid-liquid microextraction with solidification of floating organic droplet combined with flame atomic absorption spectrometry for the fast determination of cadmium in water samples.

    PubMed

    Peng, Guilong; Lu, Ying; He, Qiang; Mmereki, Daniel; Tang, Xiaohui; Zhong, Zhihui; Zhao, Xiaolong

    2016-01-01

    A novel vortex-assisted surfactant-enhanced-emulsification liquid-liquid microextraction with solidification of floating organic droplet (VSLLME-SFO) was developed for the fast, simple and efficient determination of cadmium (Cd) in water samples followed by flame atomic absorption spectrometry (FAAS). In the VSLLME-SFO process, the addition of surfactant (as an emulsifier), could enhance the mass transfer from the aqueous solution into the extraction solvent. The extraction solvent could be dispersed into the aqueous phase under vigorous shaking with the vortex. In this paper, we investigated the influences of analytical parameters, including pH, extraction solvent type and its volume, surfactant type and its volume, concentration of chelating agent, salt effect and vortex time, on the extraction efficiency of Cd. Under the optimized conditions, the limit of detection was 0.16 μg/L. The analyte enrichment factor was 37.68. The relative standard deviation was 3.2% (10 μg/L, n = 10) and the calibration graph was linear, ranging from 0.5 to 30 μg/L. The proposed method was successfully applied for the analysis of ultra-trace Cd in river water and wastewater samples.

  19. Employment of 4-(1,2,4-triazol-1-yl)phenol as a signal enhancer of the chemiluminescent luminol-H2O2-horseradish peroxidase reaction for detection of hepatitis C virus in real samples.

    PubMed

    Liu, Jian; Zhang, Lili; Fu, Chuanyun; Wang, Yunshan; Sun, Shanhui

    2015-12-01

    Highly sensitive detection of hepatitis C virus (HCV) in serum is a key method for diagnosing and classifying the extent of HCV infection. In this study, a p-phenol derivative, 4-(1,2,4-triazol-1-yl)phenol (4-TRP), was employed as an efficient enhancer of the luminol-hydrogen peroxide (H2O2)-horseradish peroxidase (HRP) chemiluminescence (CL) system for detection of HCV. Compared with a traditional enhancer, 4-TRP strongly enhanced CL intensity with the effect of prolonging and stabilizing light emission. The developed CL system was applied to detecting HCV core antigen (HCV-cAg) using a sandwich structure inside microwells. Our experimental results showed that there was good linear relationship between CL intensity and HCV-cAg concentration in the 0.6-3.6 pg/mL range (R = 0.99). The intra- and inter-assay coefficients of variation were 4.5-5.8% and 5.0-7.3%, respectively. In addition, sensitive determination of HCV-cAg in serum samples using the luminol-H2O2-HRP-4-TRP CL system was also feasible in clinical settings. Copyright © 2015 John Wiley & Sons, Ltd.

  20. Application of dispersive liquid-liquid microextraction coupled with vortex-assisted hydrophobic magnetic nanoparticles based solid-phase extraction for determination of aflatoxin M1 in milk samples by sensitive micelle enhanced spectrofluorimetry.

    PubMed

    Amoli-Diva, Mitra; Taherimaslak, Zohreh; Allahyari, Mehdi; Pourghazi, Kamyar; Manafi, Mohammad Hanif

    2015-03-01

    An efficient, simple and fast low-density solvent based dispersive liquid-liquid microextraction (LDS-DLLME) followed by vortex-assisted dispersive solid phase extraction (VA-D-SPE) has been developed as a new approach for extraction and preconcentration of aflatoxin M1 in milk samples prior to its micelle enhanced spectrofluorimetic determination. In this LDS-DLLME coupled VA-D-SPE method, milk samples were first treated with methanol/water (80:20, v/v) after removing the fat layer. This solvent was directly used as the dispersing solvent in DLLME along with using 1-heptanol (as a low-density solvent with respect to water) as the extracting solvent. In VA-D-SPE approach, hydrophobic oleic acid modified Fe3O4 nanoparticles were used to retrieve the analyte from the DLLME step. It is considerably that the target of VA-D-SPE was 1-heptanol rather than the aflatoxin M1 directly. The main parameters affecting the efficiency of LDS-DLLME and VA-D-SPE procedures and signal enhancement of aflatoxin M1 were investigated and optimized. Under the optimum conditions, the method was linear in the range from 0.02 to 200 µg L(-1) with the correlation coefficient (R(2)) of 0.9989 and detection limit of 13 ng L(-1). The intra-day precision was 2.9 and 4.3% and the inter-day precision was 2.1 and 3.3% for concentration of 2 and 50 µg L(-1) respectively. The developed method was applied for extraction and preconcentration of AFM1 in three commercially available milk samples and the results were compared with the official AOAC method. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. Capillary sample

    MedlinePlus

    ... using capillary blood sampling. Disadvantages to capillary blood sampling include: Only a limited amount of blood can be drawn using this method. The procedure has some risks (see below). Capillary ...

  2. Laser sampling

    NASA Astrophysics Data System (ADS)

    Gorbatenko, A. A.; Revina, E. I.

    2015-10-01

    The review is devoted to the major advances in laser sampling. The advantages and drawbacks of the technique are considered. Specific features of combinations of laser sampling with various instrumental analytical methods, primarily inductively coupled plasma mass spectrometry, are discussed. Examples of practical implementation of hybrid methods involving laser sampling as well as corresponding analytical characteristics are presented. The bibliography includes 78 references.

  3. An enhanced cerium(IV)-rhodamine 6G chemiluminescence system using guest-host interactions in a lab-on-a-chip platform for estimating the total phenolic content in food samples.

    PubMed

    Al Haddabi, Buthaina; Al Lawati, Haider A J; Suliman, FakhrEldin O

    2016-04-01

    Two chemiluminescence-microfluidic (CL-MF) systems, e.g., Ce(IV)-rhodamine B (RB) and Ce(IV)-rhodamine 6G (R6G), for the determination of the total phenolic content in teas and some sweeteners were evaluated. The results indicated that the Ce(IV)-R6G system was more sensitive in comparison to the Ce(IV)-RB CL system. Therefore, a simple (CL-MF) method based on the CL of Ce(IV)-R6G was developed, and the sensitivity, selectivity and stability of this system were evaluated. Selected phenolic compounds (PCs), such as quercetin (QRC), catechin (CAT), rutin (RUT), gallic acid (GA), caffeic acid (CA) and syringic acid (SA), produced analytically useful chemiluminescence signals with low detection limits ranging from 0.35 nmol L(-1) for QRC to 11.31 nmol L(-1) for SA. The mixing sequence and the chip design were crucial, as the sensitivity and reproducibility could be substantially affected by these two factors. In addition, the anionic surfactant (i.e., sodium dodecyl sulfate (SDS)) can significantly enhance the CL signal intensity by as much as 300% for the QRC solution. Spectroscopic studies indicated that the enhancement was due to a strong guest-host interaction between the cationic R6G molecules and the anionic amphiphilic environment. Other parameters that could affect the CL intensities of the PCs were carefully optimized. Finally, the method was successfully applied to tea and sweetener samples. Six different tea samples exhibited total phenolic/antioxidant levels from 7.32 to 13.5 g per 100g of sample with respect to GA. Four different sweetener samples were also analyzed and exhibited total phenolic/antioxidant levels from 500.9 to 3422.9 mg kg(-1) with respect to GA. The method was selective, rapid and sensitive when used to estimate the total phenolic/antioxidant level, and the results were in good agreement with those reported for honey and tea samples. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Lunar Sample Quarantine & Sample Curation

    NASA Technical Reports Server (NTRS)

    Allton, Judith H.

    2000-01-01

    The main goal of this presentation is to discuss some of the responsibility of the lunar sample quarantine project. The responsibilities are: flying the mission safely, and on schedule, protect the Earth from biohazard, and preserve scientific integrity of samples.

  5. Enhanced sampling of 2D interference patterns.

    PubMed

    Schwartz, Eyal; Ribak, Erez N

    2017-03-01

    We propose a simple analysis to improve the resolution of interference patterns which consist of straight fringes. As the pattern is rotated with respect to the detector, each row or column in the camera perceives it in a slightly shifted manner. We support this proposed method by analyzing both simulated and experimental interference patterns, and verify it using an interferogram obtained from a spectrally complex light source. The results imply that this technique could be implemented in different aspects of image analysis common in many fields in physics.

  6. Comparison of ultrasound-enhanced air-assisted liquid-liquid microextraction and low-density solvent-based dispersive liquid-liquid microextraction methods for determination of nonsteroidal anti-inflammatory drugs in human urine samples.

    PubMed

    Barfi, Behruz; Asghari, Alireza; Rajabi, Maryam; Goochani Moghadam, Ahmad; Mirkhani, Nasim; Ahmadi, Farhad

    2015-01-01

    Two dispersive-based liquid-liquid microextraction methods including ultrasound-enhanced air-assisted liquid-liquid microextraction (USE-AALLME) and low-density solvent-based dispersive liquid-liquid microextraction (LDS-DLLME) were compared for the extraction of salicylic acid (the hydrolysis product of acetylsalicylic acid), diclofenac and ibuprofen, as instances of the most commonly used nonsteroidal anti-inflammatory drugs (NSAIDs), in human urine prior to their determination by gas chromatography with flame ionization detection (GC-FID). The influence of different parameters affecting the USE-AALLME (including type and volume of the extraction solvent, sample pH, ionic strength, and simultaneous sonication and number of extraction cycles) and the LDS-DLLME (including type and volume of the extraction and disperser solvents, sample pH, and ionic strength) were investigated to optimize their extraction efficiencies. Both methods are fast, simple and convenient with organic solvent consumption at μL level. However, the best results were obtained using the USE-AALLME method, applying 30 μL of 1-octanol as extraction solvent, 5.0 mL of sample at pH 3.0, without salt addition, and 5 extraction cycles during 20s of sonication. This method was validated based on linearities (r(2) >0 .971), limits of detection (0.1-1.0 μg L(-1)), linear dynamic ranges (0.4-1000.0 μg L(-1)), enrichment factors (115 ± 3-135 ± 3), consumptive indices (0.043-0.037), inter- and intra-day precisions (4.3-4.8 and 5.6-6.1, respectively), and relative recoveries (94-103%). The USE-AALLME in combination with GC-FID, and with no need to derivatization step, was demonstrated to be a simple, inexpensive, sensitive and efficient method to determine NSAIDs in human urine samples.

  7. Sampling Development

    ERIC Educational Resources Information Center

    Adolph, Karen E.; Robinson, Scott R.

    2011-01-01

    Research in developmental psychology requires sampling at different time points. Accurate depictions of developmental change provide a foundation for further empirical studies and theories about developmental mechanisms. However, overreliance on widely spaced sampling intervals in cross-sectional and longitudinal designs threatens the validity of…

  8. Sampling Development

    ERIC Educational Resources Information Center

    Adolph, Karen E.; Robinson, Scott R.

    2011-01-01

    Research in developmental psychology requires sampling at different time points. Accurate depictions of developmental change provide a foundation for further empirical studies and theories about developmental mechanisms. However, overreliance on widely spaced sampling intervals in cross-sectional and longitudinal designs threatens the validity of…

  9. Polyol-enhanced dispersive liquid-liquid microextraction coupled with gas chromatography and nitrogen phosphorous detection for the determination of organophosphorus pesticides from aqueous samples, fruit juices, and vegetables.

    PubMed

    Farajzadeh, Mir Ali; Afshar Mogaddam, Mohammad Reza; Alizadeh Nabil, Ali Akbar

    2015-12-01

    Polyol-enhanced dispersive liquid-liquid microextraction has been proposed for the extraction and preconcentration of some organophosphorus pesticides from different samples. In the present study, a high volume of an aqueous phase containing a polyol (sorbitol) is prepared and then a disperser solvent along with an extraction solvent is rapidly injected into it. Sorbitol showed the best results and it was more effective on the extraction recoveries of the analytes than inorganic salts such as sodium chloride, potassium chloride, and sodium sulfate. Under the optimum extraction conditions, the method showed low limits of detection and quantification within the ranges of 12-56 and 44-162 pg/mL, respectively. Enrichment factors and extraction recoveries were in the ranges of 2799-3033 and 84-92%, respectively. The method precision was evaluated at a concentration of 10 ng/mL of each analyte, and relative standard deviations were found to be less than 5.9% for intraday (n = 6) and less than 7.8% for interday (n = 4). Finally, some aqueous samples were successfully analyzed using the proposed method and four analytes (diazinon, dimethoate, chlorpyrifos, and phosalone) were determined, some of them at ng/mL level. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Solvent-assisted stir bar sorptive extraction by using swollen polydimethylsiloxane for enhanced recovery of polar solutes in aqueous samples: Application to aroma compounds in beer and pesticides in wine.

    PubMed

    Ochiai, Nobuo; Sasamoto, Kikuo; David, Frank; Sandra, Pat

    2016-07-15

    A novel solvent-assisted stir bar sorptive extraction (SA-SBSE) technique was developed for enhanced recovery of polar solutes in aqueous samples. A conventional PDMS stir bar was swollen in several solvents with log Kow ranging from 1.0 to 3.5 while stirring for 30min prior to extraction. After extraction, thermal desorption - gas chromatography - (tandem) mass spectrometry (TD-GC-(MS/)MS) or liquid desorption - large volume injection (LD-LVI)-GC-MS were performed. An initial study involved investigation of potential solvents for SA-SBSE by weighing of the residual solvent in the swollen PDMS stir bar before and after extraction. Compared to conventional SBSE, SA-SBSE using diethyl ether, methyl isobutyl ketone, dichloromethane, diisopropyl ether and toluene provided higher recoveries from water samples for test solutes with log Kow<2.5. For SA-SBSE using dichloromethane, recoveries were improved by factors of 1.4-4.1, while maintaining or even improving the recoveries for test solutes with log Kow>2.5. The performance of the SA-SBSE method using dichloromethane, diisopropyl ether, and cyclohexane is illustrated with analyses of aroma compounds in beer and of pesticides in wine.

  11. Ab initio molecular dynamics with enhanced sampling for surface reaction kinetics at finite temperatures: CH2 ⇌ CH + H on Ni(111) as a case study

    NASA Astrophysics Data System (ADS)

    Sun, Geng; Jiang, Hong

    2015-12-01

    A comprehensive understanding of surface thermodynamics and kinetics based on first-principles approaches is crucial for rational design of novel heterogeneous catalysts, and requires combining accurate electronic structure theory and statistical mechanics modeling. In this work, ab initio molecular dynamics (AIMD) combined with the integrated tempering sampling (ITS) method has been explored to study thermodynamic and kinetic properties of elementary processes on surfaces, using a simple reaction CH 2 ⇌ CH + H on the Ni(111) surface as an example. By a careful comparison between the results from ITS-AIMD simulation and those evaluated in terms of the harmonic oscillator (HO) approximation, it is found that the reaction free energy and entropy from the HO approximation are qualitatively consistent with the results from ITS-AIMD simulation, but there are also quantitatively significant discrepancies. In particular, the HO model misses the entropy effects related to the existence of multiple adsorption configurations arising from the frustrated translation and rotation motion of adsorbed species, which are different in the reactant and product states. The rate constants are evaluated from two ITS-enhanced approaches, one using the transition state theory (TST) formulated in terms of the potential of mean force (PMF) and the other one combining ITS with the transition path sampling (TPS) technique, and are further compared to those based on harmonic TST. It is found that the rate constants from the PMF-based TST are significantly smaller than those from the harmonic TST, and that the results from PMF-TST and ITS-TPS are in a surprisingly good agreement. These findings indicate that the basic assumptions of transition state theory are valid in such elementary surface reactions, but the consideration of statistical averaging of all important adsorption configurations and reaction pathways, which are missing in the harmonic TST, are critical for

  12. Elevating sampling

    PubMed Central

    Labuz, Joseph M.; Takayama, Shuichi

    2014-01-01

    Sampling – the process of collecting, preparing, and introducing an appropriate volume element (voxel) into a system – is often under appreciated and pushed behind the scenes in lab-on-a-chip research. What often stands in the way between proof-of-principle demonstrations of potentially exciting technology and its broader dissemination and actual use, however, is the effectiveness of sample collection and preparation. The power of micro- and nanofluidics to improve reactions, sensing, separation, and cell culture cannot be accessed if sampling is not equally efficient and reliable. This perspective will highlight recent successes as well as assess current challenges and opportunities in this area. PMID:24781100

  13. SAMPLING SYSTEM

    DOEpatents

    Hannaford, B.A.; Rosenberg, R.; Segaser, C.L.; Terry, C.L.

    1961-01-17

    An apparatus is given for the batch sampling of radioactive liquids such as slurries from a system by remote control, while providing shielding for protection of operating personnel from the harmful effects of radiation.

  14. Magnetooptic sampling

    NASA Astrophysics Data System (ADS)

    Riordan, Jennifer Ann

    1999-10-01

    The magneto-optic sampling (MO) technique provides an alternate and complementary method for detection of freely-propagating electromagnetic pulses. With the Faraday effect as the basis for the sampling technique, coupling between the optical sampling pulses and the terahertz (THz) electromagnetic waves is simplified strict orthogonal propagation. Optimal Faraday rotation occurs when the propagation direction of the optical pulses are parallel to the magnetic component THz waves. Several materials were experimentally investigated. These materials include glasses (SF-59, Tb:glass), crystals (TGG, KTb3F10) and semiconductors (GaP, ZnTe). Several of the materials possess unknowns at the GHz and THz frequencies of interest. As such, time- domain spectroscopic experiments determined refractive index and absorption coefficient data for these samples. Theoretical descriptions and author-developed simulations are contrasted with experimental data throughout this work. A minimum temporal response of 1.3 ps followed theoretical predictions for the orthogonal propagation of the THz and probe beams in a sample of TGG. The minimum detectable magnetic field was 10-8T/ Hz , with shot-noise limited detection. Time-resolved measurements of electromagnetic pulses in liquids via MO sampling propel this technique beyond that possible with electro-optically based experiments. Both polar (water, acetone, methanol) and nonpolar (carbon tetrachloride, carbon disulfide) liquids were investigated and provided frequency bandwidth responses up to 20 GHz. The nonpolar liquids demonstrated shorter temporal responses than the polar liquids. This is attributable to the dielectric responses of the liquids, as the polar liquids have much higher absorption and dispersion at GHz frequencies. Comparisons between these liquids are developed with theoretical explanations. Direct probing of an electromagnetic pulse inside a liquid is discussed and demonstrated. Finally, a

  15. SAMPLING OSCILLOSCOPE

    DOEpatents

    Sugarman, R.M.

    1960-08-30

    An oscilloscope is designed for displaying transient signal waveforms having random time and amplitude distributions. The oscilloscopc is a sampling device that selects for display a portion of only those waveforms having a particular range of amplitudes. For this purpose a pulse-height analyzer is provided to screen the pulses. A variable voltage-level shifter and a time-scale rampvoltage generator take the pulse height relative to the start of the waveform. The variable voltage shifter produces a voltage level raised one step for each sequential signal waveform to be sampled and this results in an unsmeared record of input signal waveforms. Appropriate delay devices permit each sample waveform to pass its peak amplitude before the circuit selects it for display.

  16. Sampling apparatus

    DOEpatents

    Gordon, Norman R.; King, Lloyd L.; Jackson, Peter O.; Zulich, Alan W.

    1989-01-01

    A sampling apparatus is provided for sampling substances from solid surfaces. The apparatus includes first and second elongated tubular bodies which telescopically and sealingly join relative to one another. An absorbent pad is mounted to the end of a rod which is slidably received through a passageway in the end of one of the joined bodies. The rod is preferably slidably and rotatably received through the passageway, yet provides a selective fluid tight seal relative thereto. A recess is formed in the rod. When the recess and passageway are positioned to be coincident, fluid is permitted to flow through the passageway and around the rod. The pad is preferably laterally orientable relative to the rod and foldably retractable to within one of the bodies. A solvent is provided for wetting of the pad and solubilizing or suspending the material being sampled from a particular surface.

  17. Sampling apparatus

    DOEpatents

    Gordon, N.R.; King, L.L.; Jackson, P.O.; Zulich, A.W.

    1989-07-18

    A sampling apparatus is provided for sampling substances from solid surfaces. The apparatus includes first and second elongated tubular bodies which telescopically and sealingly join relative to one another. An absorbent pad is mounted to the end of a rod which is slidably received through a passageway in the end of one of the joined bodies. The rod is preferably slidably and rotatably received through the passageway, yet provides a selective fluid tight seal relative thereto. A recess is formed in the rod. When the recess and passageway are positioned to be coincident, fluid is permitted to flow through the passageway and around the rod. The pad is preferably laterally orientable relative to the rod and foldably retractable to within one of the bodies. A solvent is provided for wetting of the pad and solubilizing or suspending the material being sampled from a particular surface. 15 figs.

  18. A new method for the enhancement of electromembrane extraction efficiency using carbon nanotube reinforced hollow fiber for the determination of acidic drugs in spiked plasma, urine, breast milk and wastewater samples.

    PubMed

    Hasheminasab, Kobra Sadat; Fakhari, Ali Reza; Shahsavani, Abolfath; Ahmar, Hamid

    2013-04-12

    A new design of low voltage electromembrane extraction (EME) using carbon nanotube reinforced hollow fiber was developed for the determination of acidic drugs in biological and wastewater samples. The supported liquid membrane (SLM) with carbon nanotubes as the sorbent interface was used in this research. CNTs have large surface area and high adsorption capacity for a wide range of organic and inorganic species. Therefore, the presence of CNTs in SLM increased the overall analyte partition coefficient in the membrane and lead to enhancement in analyte transport. Optimization of the variables affecting this method was carried out in order to achieve the best extraction efficiency. Ibuprofen and naproxen, nonsteroid anti-inflammatory drugs (NSAIDs), were selected as model acidic drugs. Optimal extractions were accomplished with 1-octanol with 3.0 mg mL(-1) CNTs as the SLM, with 5V as the driving force, and with pH 7.4 in donor and pH 12 in acceptor solutions. Equilibrium extraction conditions were obtained after 10 min of operation with the whole assembly agitated at 500 rpm. Under the optimized extraction conditions, the proposed EME technique provided good linearity (>0.998), repeatability (RSD=2.7-3.2), low limits of detection (1-3 ng mL(-1)), excellent preconcentration (PF=180-188) and high recoveries (90-94%). In comparison with the conventional EME method, this method showed better results (lower voltage, higher preconcentration factors and higher recoveries). Finally, the developed method was successfully used for the determination of ibuprofen and naproxen in different spiked matrices including plasma, urine, breast milk and wastewater samples. Copyright © 2013 Elsevier B.V. All rights reserved.

  19. Chain Sampling

    DTIC Science & Technology

    1972-08-01

    35609 Advanced Techniques Branch Plans and Programs Analysis Division Directorate for Product Assurance U. S. Army Missile Command Redstone Arsenal...Ray Heathcock Advanced Techniques Branch Plans and Programs Analysis Division Directorate for Product Assurance U. S. Army Missile Command...for Product Assurance has established a rather unique computer program for handling a variety of chain sampling schemes and is available for

  20. β-Cyclodextrin enhanced on-line organic solvent field-amplified sample stacking in capillary zone electrophoresis for analysis of ambroxol in human plasma, following liquid-liquid extraction in the 96-well format.

    PubMed

    Li, Ji; Bi, Youwei; Wang, Li; Sun, Fanlu; Chen, Zhao; Xu, Guili; Fan, Guorong

    2012-07-01

    A field-amplified sample stacking (FASS) and capillary zone electrophoresis (CZE) method is described for the quantification of ambroxol hydrochloride in human plasma, following liquid-liquid extraction in the 96-well format. The separation was carried out at 25 °C in a 31.2 cm × 75 μm fused-silica capillary with an applied voltage of 15 kV. The background electrolyte (BGE) was composed of 6.25 mM borate-25 mM phosphate (pH 3.0) and 1mM β-cyclodextrin. The detection wavelength was 210 nm. Clean-up and preconcentration of plasma biosamples were developed by 96-well format liquid-liquid extraction (LLE). In this study, FASS in combination with β-cyclodextrin enhanced the sensitivity about 60-70 fold in total. The method was suitably validated with respect to stability, specificity, linearity, lower limit of quantitation, accuracy, precision, extraction recovery and robustness. The calibration graph was linear for ambroxol hydrochloride from 2 to 500 ng/ml. The lower limit of quantification was 2 ng/ml. The intra- and inter-day precisions of lowest limit of quantification (LLOQ) were 9.61 and 11.80%, respectively. The method developed was successfully applied to the evaluation of clinical pharmacokinetic study of ambroxol hydrochloride tablet after oral administration to 12 healthy volunteers. Copyright © 2012. Published by Elsevier B.V.

  1. Ultrasound-assisted surfactant-enhanced emulsification microextraction with solidification of floating organic droplet followed by high performance liquid chromatography for the determination of strobilurin fungicides in fruit juice samples.

    PubMed

    Liang, Pei; Liu, Guojiao; Wang, Fang; Wang, Wanting

    2013-05-01

    A novel method, ultrasound-assisted surfactant-enhanced emulsification microextraction with solidification of floating organic droplet (UASEME-SFOD), has been developed for the extraction of four strobilurin fungicides (kresoxim-methyl, picoxystrobin, pyraclostrobin and trifloxystrobin) in fruit juices. In the UASEME-SFOD technique, Tween 80 was used as emulsifier, and 1-undecanol was used as extraction solvent without using any organic dispersive solvent. Several parameters that affect the extraction efficiency, such as the kind and volume of extraction solvent, the type and concentration of the surfactant, extraction time, extraction temperature and salt addition were investigated and optimized. Under the optimum extraction condition, the method yields a linear calibration curve in the concentration range from 5 to 10,000 ng mL(-1) for the targeted analytes with the correlation coefficient ranging from 0.9991 to 0.9998. The enrichment factors were in the range between 95 and 135, and the limits of detection of the method were 2-4 ng mL(-1). The fruit juice samples were successfully analyzed using the proposed method, and the relative recoveries at fortified levels of 50 and 100 ng mL(-1) were in the range of 82.6-97.5%. Copyright © 2013 Elsevier B.V. All rights reserved.

  2. Sampling Strategy

    NASA Technical Reports Server (NTRS)

    2008-01-01

    Three locations to the right of the test dig area are identified for the first samples to be delivered to the Thermal and Evolved Gas Analyzer (TEGA), the Wet Chemistry Lab (WCL), and the Optical Microscope (OM) on NASA's Phoenix Mars Lander. These sampling areas are informally labeled 'Baby Bear', 'Mama Bear', and 'Papa Bear' respectively. This image was taken on the seventh day of the Mars mission, or Sol 7 (June 1, 2008) by the Surface Stereo Imager aboard NASA's Phoenix Mars Lander.

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  3. Sampling Strategy

    NASA Technical Reports Server (NTRS)

    2008-01-01

    Three locations to the right of the test dig area are identified for the first samples to be delivered to the Thermal and Evolved Gas Analyzer (TEGA), the Wet Chemistry Lab (WCL), and the Optical Microscope (OM) on NASA's Phoenix Mars Lander. These sampling areas are informally labeled 'Baby Bear', 'Mama Bear', and 'Papa Bear' respectively. This image was taken on the seventh day of the Mars mission, or Sol 7 (June 1, 2008) by the Surface Stereo Imager aboard NASA's Phoenix Mars Lander.

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  4. Biorack - samples

    NASA Image and Video Library

    1997-01-13

    STS081-E-05145 (13 Jan. 1997) --- Astronaut John M. Grunsfeld, mission specialist, works with a Passive Thermal Conditioning Unit (PTCU), the cylindrical device suspended between the mission specialist and the nearby biorack glovebox onboard the Spacehab Double Module (DM). He holds a container of experiment samples in his left hand. This image was recorded with an Electronic Still Camera (ESC) and was later downlinked to flight controllers in Houston, Texas. Grunsfeld and five astronaut crew mates are preparing for a scheduled mid-week docking with Russia's Mir Space Station.

  5. Sample sequencing

    SciTech Connect

    Prange, C.

    1994-04-01

    The goal of the Human Genome Project is to sequence all 3 billion basepairs of human DNA. At Lawrence Livermore Lab, attention is focused on Chromosome 19, which has been estimated to contain approximately 2000 genes. So far, only 200 have been mapped to specific areas on the chromosome. For this reason, a simple method is needed to predict the most likely locations of the coding regions in the DNA. In addition, there is also a need for unique market sites (STS`s) along the chromosome. Sample sequencing uses standard cloning techniques to prepare DNA for sequencing. Once sequence is obtained, it is analyzed using databases to predict the regions most likely to contain genes. All sequences may also be used to generate STS`s. So far, 21 fragments from five different clones have been completely sequenced, with fragments from eight more clones in progress. Constant improvement of methods to increase efficiency and accuracy combined with utilization of the most current databases available make sample sequencing a useful tool for reaching the goals of the Human Genome Project.

  6. High Temporospatial Resolution Dynamic Contrast Enhanced (DCE) Wrist MRI with Variable-Density Pseudo-Random CIRcular Cartesian UnderSampling (CIRCUS) Acquisition: Evaluation of Perfusion in Rheumatoid Arthritis Patients

    PubMed Central

    Liu, Jing; Pedoia, Valentina; Heilmeier, Ursula; Ku, Eric; Su, Favian; Khanna, Sameer; Imboden, John; Graf, Jonathan; Link, Thomas; Li, Xiaojuan

    2016-01-01

    This study is to evaluate highly accelerated 3D dynamic contrast-enhanced (DCE) wrist MRI for assessment of perfusion in rheumatoid arthritis (RA) patients. A pseudo-random variable-density undersampling strategy, CIRcular Cartesian UnderSampling (CIRCUS), was combined with k-t SPARSE-SENSE reconstruction to achieve a highly accelerated 3D DCE wrist MRI. Two healthy volunteers and ten RA patients were studied. Two patients were on methotrexate (MTX) only (Group I) and the other eight were treated with a combination therapy of MTX and Anti-Tumour Necrosis Factor (TNF) therapy (Group II). Patients were scanned at baseline and 3-month follow-up. DCE MR images were used to evaluate perfusion in synovitis and bone marrow edema pattern in the RA wrist joints. A series of perfusion parameters were derived and compared with clinical disease activity scores of 28 joints (DAS28). 3D DCE wrist MR images were obtained with a spatial resolution of 0.3×0.3×1.5mm3 and temporal resolution of 5 s (with an acceleration factor of 20). The derived perfusion parameters, most notably, transition time (dT) of synovitis, showed significant negative correlations with DAS28-ESR (r=-0.80, p<0.05) and DAS28-CRP (r=-0.87, p<0.05) at baseline and also correlated significantly with treatment responses evaluated by clinical score changes between baseline and 3-month follow-up (with DAS28-ESR: r=-0.79, p<0.05, and DAS28-CRP: r=-0.82, p<0.05). Highly accelerated 3D DCE wrist MRI with improved temporospatial resolution has been achieved in RA patients and provides accurate assessment of neovascularization and perfusion in RA joints, showing promise as a potential tool for evaluating treatment responses. PMID:26608949

  7. Clinical Feasibility of Free-Breathing Dynamic T1-Weighted Imaging With Gadoxetic Acid-Enhanced Liver Magnetic Resonance Imaging Using a Combination of Variable Density Sampling and Compressed Sensing.

    PubMed

    Yoon, Jeong Hee; Yu, Mi Hye; Chang, Won; Park, Jin-Young; Nickel, Marcel Dominik; Son, Yohan; Kiefer, Berthold; Lee, Jeong Min

    2017-10-01

    The purpose of the study was to investigate the clinical feasibility of free-breathing dynamic T1-weighted imaging (T1WI) using Cartesian sampling, compressed sensing, and iterative reconstruction in gadoxetic acid-enhanced liver magnetic resonance imaging (MRI). This retrospective study was approved by our institutional review board, and the requirement for informed consent was waived. A total of 51 patients at high risk of breath-holding failure underwent dynamic T1WI in a free-breathing manner using volumetric interpolated breath-hold (BH) examination with compressed sensing reconstruction (CS-VIBE) and hard gating. Timing, motion artifacts, and image quality were evaluated by 4 radiologists on a 4-point scale. For patients with low image quality scores (<3) on the late arterial phase, respiratory motion-resolved (extradimension [XD]) reconstruction was additionally performed and reviewed in the same manner. In addition, in 68.6% (35/51) patients who had previously undergone liver MRI, image quality and motion artifacts on dynamic phases using CS-VIBE were compared with previous BH-T1WIs. In all patients, adequate arterial-phase timing was obtained at least once. Overall image quality of free-breathing T1WI was 3.30 ± 0.59 on precontrast and 2.68 ± 0.70, 2.93 ± 0.65, and 3.30 ± 0.49 on early arterial, late arterial, and portal venous phases, respectively. In 13 patients with lower than average image quality (<3) on the late arterial phase, motion-resolved reconstructed T1WI (XD-reconstructed CS-VIBE) significantly reduced motion artifacts (P < 0.002-0.021) and improved image quality (P < 0.0001-0.002). In comparison with previous BH-T1WI, CS-VIBE with hard gating or XD reconstruction showed less motion artifacts and better image quality on precontrast, arterial, and portal venous phases (P < 0.0001-0.013). Volumetric interpolated breath-hold examination with compressed sensing has the potential to provide consistent, motion-corrected free-breathing dynamic T

  8. Computer Graphics Simulations of Sampling Distributions.

    ERIC Educational Resources Information Center

    Gordon, Florence S.; Gordon, Sheldon P.

    1989-01-01

    Describes the use of computer graphics simulations to enhance student understanding of sampling distributions that arise in introductory statistics. Highlights include the distribution of sample proportions, the distribution of the difference of sample means, the distribution of the difference of sample proportions, and the distribution of sample…

  9. Driven Boson Sampling

    NASA Astrophysics Data System (ADS)

    Barkhofen, Sonja; Bartley, Tim J.; Sansoni, Linda; Kruse, Regina; Hamilton, Craig S.; Jex, Igor; Silberhorn, Christine

    2017-01-01

    Sampling the distribution of bosons that have undergone a random unitary evolution is strongly believed to be a computationally hard problem. Key to outperforming classical simulations of this task is to increase both the number of input photons and the size of the network. We propose driven boson sampling, in which photons are input within the network itself, as a means to approach this goal. We show that the mean number of photons entering a boson sampling experiment can exceed one photon per input mode, while maintaining the required complexity, potentially leading to less stringent requirements on the input states for such experiments. When using heralded single-photon sources based on parametric down-conversion, this approach offers an ˜e -fold enhancement in the input state generation rate over scattershot boson sampling, reaching the scaling limit for such sources. This approach also offers a dramatic increase in the signal-to-noise ratio with respect to higher-order photon generation from such probabilistic sources, which removes the need for photon number resolution during the heralding process as the size of the system increases.

  10. Dissolver Off-gas Hot Operations Authorization (AFCI CETE Milestone Report)

    SciTech Connect

    Jubin, Robert Thomas

    2009-06-01

    The head-end processing of the Coupled-End-to-End (CETE) Demonstration includes fuel receipt, fuel disassembly, exposure of fuel (e.g., by segmenting the fuel pins), voloxidation of the fuel to separate tritium, and fuel dissolution. All of these processing steps with the exception of the dissolution step will be accomplished in the Irradiated Fuels Examination Laboratory (IFEL) (Building 3525). The final headend step will be performed in the Radiochemical Engineering Development Center (Building 7920). The primary purpose of the fuel dissolution step is to prepare the solid fuel for subsequent liquid separations steps. This is accomplished by dissolving the fuel solids using nitric acid. During the dissolution process gases are evolved. Oxides of nitrogen are the primary off-gas components generated by the reactions of nitric acid and the fuel oxides however, during the dissolution and sparging of the resulting solution, iodine, C-14 as carbon dioxide, xenon, and krypton gasses are also released to the off-gas stream. The Dissolver Off-gas treatment rack provides a means of trapping these volatile fission products and other gases via various trapping media. Specifically the rack will recover iodine on a solid sorbent bed, scrub NOx in a water/acid column, scrub CO{sub 2} in a caustic scrubber column, remove moisture with solid sorbent drier beds and recover Xe and Kr using solid absorbent beds. The primary purpose of this experimental rack and the off-gas rack associated with the voloxidation equipment located at IFEL is to close the material balances around the volatile gases and to provide an understanding of the impacts of specific processing conditions on the fractions of the volatile components released from the various head-end processing steps.

  11. A Comparative Study of Welded ODS Cladding materials for AFCI/GNEP Applications

    SciTech Connect

    Indrajit Charit; Megan Frary; Darryl Butt; K.L. Murty; Larry Zirker; James Cole; Mitchell Meyer; Rajiv S. Mishra; Mark Woltz

    2011-03-31

    This research project involved working on the pressure resistance welding of oxide dispersion strengthened (ODS) alloys which will have a large role to play in advanced nuclear reactors. The project also demonstrated the research collaboration between four universities and one nation laboratory (Idaho National Laboratory) with participation from an industry for developing for ODS alloys. These alloys contain a high number density of very fine oxide particles that can impart high temperature strength and radiation damage resistance suitable for in-core applications in advanced reactors. The conventional fusion welding techniques tend to produce porosity-laden microstructure in the weld region and lead to the agglomeration and non-uniform distribution of the neededoxide particles. That is why two solid state welding methods - pressure resistance welding (PRW) and friction stir welding (FSW) - were chosen to be evaluated in this project. The proposal is expected to support the development of Advanced Burner Reactors (ABR) under the GNEP program (now incorporated in Fuel Cycle R&D program). The outcomes of the concluded research include training of graduate and undergraduate students and get them interested in nuclear related research.

  12. Moral Enhancement

    PubMed Central

    Douglas, Thomas

    2008-01-01

    Opponents of biomedical enhancement often claim that, even if such enhancement would benefit the enhanced, it would harm others. But this objection looks unpersuasive when the enhancement in question is a moral enhancement — an enhancement that will expectably leave the enhanced person with morally better motives than she had previously. In this article I (1) describe one type of psychological alteration that would plausibly qualify as a moral enhancement, (2) argue that we will, in the medium-term future, probably be able to induce such alterations via biomedical intervention, and (3) defend future engagement in such moral enhancements against possible objections. My aim is to present this kind of moral enhancement as a counter-example to the view that biomedical enhancement is always morally impermissible. PMID:19132138

  13. Comparative analysis of cell morphology in sputum samples homogenized with dithiothreitol, N-acetyl-L cysteine, Cytorich(®) red preservative and in cellblock preparations to enhance the sensitivity of sputum cytology for the diagnosis of lung cancer.

    PubMed

    Saraswathy Veena, Vamadevan; Sara George, Preethi; Jayasree, Kattoor; Sujathan, Kunjuraman

    2015-07-01

    Lung cancer claims highest rate of cancer related mortality worldwide, mainly due to late diagnosis and distant metastasis. Sputum cytology is the simplest, non-invasive and cost effective technique but it has low sensitivity due to lack of robust processing methods to retrieve all the diagnostic materials clogged in mucus, inflammatory exudates and blood. This study have compared conventional pick and smear method of sputum processing with samples prepared by homogenization methods using N-acetyl-l-cysteine, Dithiothreitol (DTT), CytoRich red solution and cell blocks (CBs) with respect to screening time, quality of staining, cellularity, smear background, nuclear and cytoplasmic morphology preservation, and diagnostic efficacy. The significance of CB prepared from homogenised samples for immunocytochemistry, protein extraction, Genomic DNA and RNA extraction were also evaluated on a cohort 3,185 samples. The significance of the morphological features in each of the techniques was statistically analysed using SPSS 11 software. The smear background clarity, staining quality and diagnostic efficacy of samples processed in red solution was found to be superior to the conventional method (P < 0.0001), where as samples homogenized in DTT showed a better cellularity (P < 0.0001). CBs prepared from samples homogenized in red solution were found to be very significant (P < 0.0001) in increasing the diagnostic efficacy compared to other two methods. Immunocytochemistry and DNA extraction were found possible in CBs as well as from the cell suspension. A combined analysis of smears and CBs found to improve the sensitivity of sputum cytology. The study suggests homogenization of sputum in CytoRich ® red solution and cellblock preparations routinely for all samples to improve the sensitivity of sputum cytology. IHC and DNA extraction can be performed in sputum samples suggesting the role of sputum samples for ancillary techniques. © 2015 Wiley Periodicals, Inc.

  14. Equilibrium Sampling in Biomolecular Simulation

    PubMed Central

    2015-01-01

    Equilibrium sampling of biomolecules remains an unmet challenge after more than 30 years of atomistic simulation. Efforts to enhance sampling capability, which are reviewed here, range from the development of new algorithms to parallelization to novel uses of hardware. Special focus is placed on classifying algorithms — most of which are underpinned by a few key ideas — in order to understand their fundamental strengths and limitations. Although algorithms have proliferated, progress resulting from novel hardware use appears to be more clear-cut than from algorithms alone, partly due to the lack of widely used sampling measures. PMID:21370970

  15. Sample frequency and sample duration as sources of stimulus control in delayed matching to sample.

    PubMed

    Parr, W V; Hunt, M; Williams, W A

    1999-05-03

    Three experiments examined sample duration and sample presentation frequency (SPF) on choice in a two-alternative, delayed matching-to-sample task. In Experiment 1, using a behavioural-detection approach, we demonstrated bias toward the more frequent sample, despite the conditional probability of reinforcement for a correct match on any particular trial remaining at 1.0 for both stimuli. Although retention-interval duration influenced both discriminability and bias in Experiment 1, bias was independent of retention interval in two subsequent experiments. Experiments 2 and 3 replicated the effects of SPF on bias, and demonstrated that discriminability of the stimuli was not influenced by the SPF manipulation. Experiment 2 also investigated the effect of a within-session variation in sample duration on discriminability and bias measures, both with and without unequal SPFs. Discriminability was enhanced to both the short and long samples of the unequal sample-durations' condition relative to discrimination in conditions where samples were presented for equal durations. Bias generated by varying SPF was independent of sample-duration effects and of retention-interval duration. Taken together, these data suggest independent and qualitatively different effects of sample frequency and sample duration on matching behaviour: Sample frequency has its effect on bias measures, while sample duration influences discriminability. We suggest that sample frequency is a global task factor influencing reference memory, and sample duration is a trial-specific, conditional discrimination factor, involving short-term or working memory processing. Copyright © 1999 Elsevier Science B.V. All rights reserved.

  16. Conformational sampling techniques.

    PubMed

    Hatfield, Marcus P D; Lovas, Sándor

    2014-01-01

    The potential energy hyper-surface of a protein relates the potential energy of the protein to its conformational space. This surface is useful in determining the native conformation of a protein or in examining a statistical-mechanical ensemble of structures (canonical ensemble). In determining the potential energy hyper-surface of a protein three aspects must be considered; reducing the degrees of freedom, a method to determine the energy of each conformation and a method to sample the conformational space. For reducing the degrees of freedom the choice of solvent, coarse graining, constraining degrees of freedom and periodic boundary conditions are discussed. The use of quantum mechanics versus molecular mechanics and the choice of force fields are also discussed, as well as the sampling of the conformational space through deterministic and heuristic approaches. Deterministic methods include knowledge-based statistical methods, rotamer libraries, homology modeling, the build-up method, self-consistent electrostatic field, deformation methods, tree-based elimination and eigenvector following routines. The heuristic methods include Monte Carlo chain growing, energy minimizations, metropolis monte carlo and molecular dynamics. In addition, various methods to enhance the conformational search including the deformation or smoothing of the surface, scaling of system parameters, and multi copy searching are also discussed.

  17. Enhanced methods for conditioning, storage, and extraction of liquid and solid samples of manure for determination of steroid hormones by solid-phase extraction and gas chromatography-mass spectrometry.

    PubMed

    Combalbert, Sarah; Pype, Marie-Laure; Bernet, Nicolas; Hernandez-Raquet, Guillermina

    2010-09-01

    Hormones are among the highest-impact endocrine disrupters affecting living organisms in aquatic environments. These molecules have been measured in both wastewater and sewage sludge. Analytical techniques for such matrices are well described in the literature. In contrast, there is little information about the analysis of hormones in animal waste. The objectives of this study were, first, to propose a method for conditioning swine manure samples (addition of formaldehyde, separation of the solid and liquid phases, and duration of storage) in order to determine hormones in the liquid fraction of manure by solid-phase extraction (SPE) coupled with gas chromatography-mass spectrometry (GC-MS). Our results showed that analysis of hormones was affected by matrix changes which occurred during freezing and thawing and after addition of formaldehyde, an additive frequently used to preserve environmental samples. Thus, our results argue for the conditioning of samples without formaldehyde and for separating the solid and liquid fractions of manure before freezing. Second, this study reports on the use of a liquid extraction method coupled with SPE and GC-MS analysis for determination of hormones in the solid fraction of manure. Under the conditions selected, hormone recoveries were between 80 and 100%. Finally, the optimized method was used to quantify hormones in both liquid and solid fractions of swine manure from different breeding units. High levels of estrone and α-estradiol were found in samples whereas β-estradiol was detected in smaller amounts. Estriol and progesterone were mainly found in manure from the gestating sow building whereas testosterone was detected in manure from male breeding buildings.

  18. Microwave sample preparation for analysis of metals in environmental samples

    SciTech Connect

    Collins, L.W.

    1996-10-01

    The unique nature of microwave energy enhances heating efficiency and improves acid digestion sample preparation. Faster sample preparation and improved precision of the analysis occur. These results will be illustrated in this presentation using various standard reference materials and environmentally important samples. The analytical microwave system used offers accurate temperature and pressure feedback control through the use of a hand-held controller or PC-based control. Digestions are performed in patented, user-friendly microwave vessels. USEPA Method 3015, {open_quotes}Microwave-Assisted Acid Digestion of Aqueous Samples and Extracts,{close_quotes} is properly performed when the sample is heated to 170{degrees}C within 10 minutes, and maintained for an additional 10 minutes. USEPA Method 3051, {open_quotes}Microwave-Assisted Acid Digestion of Sediments, Sludges, Soils, and Oils,{close_quotes} is properly performed when the sample is heated to 175{degrees}C within 5.5 minutes, and maintained at 175{degrees}C for an additional 4.5 minutes. After the timesaving microwave digestion period, the samples were analyzed for metals by ICP-AES. Excellent accuracy and precision were obtained, in addition to 90% time reduction when using microwave sample preparation.

  19. 40 CFR 141.702 - Sampling schedules.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 141.702 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS Enhanced Treatment for Cryptosporidium Source Water Monitoring Requirements § 141.702 Sampling schedules. (a) Systems required to conduct source water...

  20. 40 CFR 141.702 - Sampling schedules.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 141.702 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS Enhanced Treatment for Cryptosporidium Source Water Monitoring Requirements § 141.702 Sampling schedules. (a) Systems required to conduct source water monitoring...

  1. 40 CFR 141.702 - Sampling schedules.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 141.702 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS Enhanced Treatment for Cryptosporidium Source Water Monitoring Requirements § 141.702 Sampling schedules. (a) Systems required to conduct source water monitoring...

  2. 40 CFR 141.702 - Sampling schedules.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 141.702 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS Enhanced Treatment for Cryptosporidium Source Water Monitoring Requirements § 141.702 Sampling schedules. (a) Systems required to conduct source water monitoring...

  3. 40 CFR 141.702 - Sampling schedules.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 141.702 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS Enhanced Treatment for Cryptosporidium Source Water Monitoring Requirements § 141.702 Sampling schedules. (a) Systems required to conduct source water monitoring...

  4. Self-reported oral health among a community sample of people experiencing social and health inequities: cross-sectional findings from a study to enhance equity in primary healthcare settings

    PubMed Central

    Wallace, Bruce; Browne, Annette J; Varcoe, Colleen; Ford-Gilboe, Marilyn; Wathen, Nadine; Long, Phoebe M; Parker, Joanne

    2015-01-01

    Objective To describe the self-reported oral health issues among a community sample of primary care clients experiencing socioeconomic disadvantages. Methods As part of a larger mixed-methods, multiple case study evaluating an equity-oriented primary healthcare intervention, we examined the oral health of a sample of 567 people receiving care at four clinics that serve marginalised populations in two Canadian provinces. Data collected included self-rated oral health and experiences accessing and receiving healthcare, standard self-report measures of health and quality of life, and sociodemographic information. Results The prevalence of self-rated poor oral health was high, with almost half (46.3%) of the participants reporting poor or fair oral health. Significant relationships were observed between poor oral health and vulnerabilities related to mental health, trauma and housing instability. Our findings suggest that the oral health of some Canadian populations may be dramatically worse than what is reported in existing population health surveys. Conclusions Our findings reinforce the importance of addressing oral health as part of health equity strategies. The health and oral health issues experienced by this client cohort highlight the need for interdisciplinary, team-based care that can address the intersections among people's health status, oral health and social issues. PMID:26700285

  5. Self-reported oral health among a community sample of people experiencing social and health inequities: cross-sectional findings from a study to enhance equity in primary healthcare settings.

    PubMed

    Wallace, Bruce; Browne, Annette J; Varcoe, Colleen; Ford-Gilboe, Marilyn; Wathen, Nadine; Long, Phoebe M; Parker, Joanne

    2015-12-23

    To describe the self-reported oral health issues among a community sample of primary care clients experiencing socioeconomic disadvantages. As part of a larger mixed-methods, multiple case study evaluating an equity-oriented primary healthcare intervention, we examined the oral health of a sample of 567 people receiving care at four clinics that serve marginalised populations in two Canadian provinces. Data collected included self-rated oral health and experiences accessing and receiving healthcare, standard self-report measures of health and quality of life, and sociodemographic information. The prevalence of self-rated poor oral health was high, with almost half (46.3%) of the participants reporting poor or fair oral health. Significant relationships were observed between poor oral health and vulnerabilities related to mental health, trauma and housing instability. Our findings suggest that the oral health of some Canadian populations may be dramatically worse than what is reported in existing population health surveys. Our findings reinforce the importance of addressing oral health as part of health equity strategies. The health and oral health issues experienced by this client cohort highlight the need for interdisciplinary, team-based care that can address the intersections among people's health status, oral health and social issues. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  6. Enhanced extraction of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) and hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in the presence of sodium dodecyl sulphate and its application to environmental samples.

    PubMed

    Guarav; Malik, Ashok Kumar; Rai, Pramod Kumar

    2008-08-01

    A method for enhanced extraction of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) and hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) from environmental samples is developed with the assistance of sodium dodecyl sulphate (SDS) surfactant. In this study, the concentration of SDS surfactant and other analytical parameters are optimized on a high-performance liquid chromatography-UV system. An isocratic flow of 1.0 mL/min with mobile phase acetonitrile-water; 70:30 (v/v) at 230 nm wavelength on a reverse-phase amide column is used for baseline separation of explosives and making calibration curves. The amount of recovered explosives from spiked soil and water samples are calculated. The limits of detection obtained for HMX and RDX standards are 1.5 and 3.8 ppb (S/N=3), respectively, which are much better than obtained by the Environmental Protection Agency method 8330. The recoveries are found to be enhanced by 1.7 and 1.6-fold with SDS solution as compared to water for HMX and RDX, respectively, from soil samples.

  7. Coring Sample Acquisition Tool

    NASA Technical Reports Server (NTRS)

    Haddad, Nicolas E.; Murray, Saben D.; Walkemeyer, Phillip E.; Badescu, Mircea; Sherrit, Stewart; Bao, Xiaoqi; Kriechbaum, Kristopher L.; Richardson, Megan; Klein, Kerry J.

    2012-01-01

    A sample acquisition tool (SAT) has been developed that can be used autonomously to sample drill and capture rock cores. The tool is designed to accommodate core transfer using a sample tube to the IMSAH (integrated Mars sample acquisition and handling) SHEC (sample handling, encapsulation, and containerization) without ever touching the pristine core sample in the transfer process.

  8. Sampling by Length.

    ERIC Educational Resources Information Center

    Handley, John C.

    1991-01-01

    Discussion of sampling methods used in information science research focuses on Fussler's method for sampling catalog cards and on sampling by length. Highlights include simple random sampling, sampling with probability equal to size without replacement, sampling with replacement, and examples of estimating the number of books on shelves in certain…

  9. Acceptance sampling methods for sample results verification

    SciTech Connect

    Jesse, C.A.

    1993-06-01

    This report proposes a statistical sampling method for use during the sample results verification portion of the validation of data packages. In particular, this method was derived specifically for the validation of data packages for metals target analyte analysis performed under United States Environmental Protection Agency Contract Laboratory Program protocols, where sample results verification can be quite time consuming. The purpose of such a statistical method is to provide options in addition to the ``all or nothing`` options that currently exist for sample results verification. The proposed method allows the amount of data validated during the sample results verification process to be based on a balance between risks and the cost of inspection.

  10. Enhancing Employee Skills.

    ERIC Educational Resources Information Center

    1999

    This document contains four symposium papers on enhancing employee skills. "The Effect of Study Skills Training Intervention on United States Air Force Aeromedical Apprentices" (John C. Griffith) demonstrates how study skills intervention resulted in a significant increase in the end-of-course scores of a sample of 90 randomly selected Air Force…

  11. Enhancing Employee Skills.

    ERIC Educational Resources Information Center

    1999

    This document contains four symposium papers on enhancing employee skills. "The Effect of Study Skills Training Intervention on United States Air Force Aeromedical Apprentices" (John C. Griffith) demonstrates how study skills intervention resulted in a significant increase in the end-of-course scores of a sample of 90 randomly selected Air Force…

  12. Information sampling behavior with explicit sampling costs.

    PubMed

    Juni, Mordechai Z; Gureckis, Todd M; Maloney, Laurence T

    2016-07-01

    The decision to gather information should take into account both the value of information and its accrual costs in time, energy and money. Here we explore how people balance the monetary costs and benefits of gathering additional information in a perceptual-motor estimation task. Participants were rewarded for touching a hidden circular target on a touch-screen display. The target's center coincided with the mean of a circular Gaussian distribution from which participants could sample repeatedly. Each "cue" - sampled one at a time - was plotted as a dot on the display. Participants had to repeatedly decide, after sampling each cue, whether to stop sampling and attempt to touch the hidden target or continue sampling. Each additional cue increased the participants' probability of successfully touching the hidden target but reduced their potential reward. Two experimental conditions differed in the initial reward associated with touching the hidden target and the fixed cost per cue. For each condition we computed the optimal number of cues that participants should sample, before taking action, to maximize expected gain. Contrary to recent claims that people gather less information than they objectively should before taking action, we found that participants over-sampled in one experimental condition, and did not significantly under- or over-sample in the other. Additionally, while the ideal observer model ignores the current sample dispersion, we found that participants used it to decide whether to stop sampling and take action or continue sampling, a possible consequence of imperfect learning of the underlying population dispersion across trials.

  13. A Mars Sample Return Sample Handling System

    NASA Technical Reports Server (NTRS)

    Wilson, David; Stroker, Carol

    2013-01-01

    We present a sample handling system, a subsystem of the proposed Dragon landed Mars Sample Return (MSR) mission [1], that can return to Earth orbit a significant mass of frozen Mars samples potentially consisting of: rock cores, subsurface drilled rock and ice cuttings, pebble sized rocks, and soil scoops. The sample collection, storage, retrieval and packaging assumptions and concepts in this study are applicable for the NASA's MPPG MSR mission architecture options [2]. Our study assumes a predecessor rover mission collects samples for return to Earth to address questions on: past life, climate change, water history, age dating, understanding Mars interior evolution [3], and, human safety and in-situ resource utilization. Hence the rover will have "integrated priorities for rock sampling" [3] that cover collection of subaqueous or hydrothermal sediments, low-temperature fluidaltered rocks, unaltered igneous rocks, regolith and atmosphere samples. Samples could include: drilled rock cores, alluvial and fluvial deposits, subsurface ice and soils, clays, sulfates, salts including perchlorates, aeolian deposits, and concretions. Thus samples will have a broad range of bulk densities, and require for Earth based analysis where practical: in-situ characterization, management of degradation such as perchlorate deliquescence and volatile release, and contamination management. We propose to adopt a sample container with a set of cups each with a sample from a specific location. We considered two sample cups sizes: (1) a small cup sized for samples matching those submitted to in-situ characterization instruments, and, (2) a larger cup for 100 mm rock cores [4] and pebble sized rocks, thus providing diverse samples and optimizing the MSR sample mass payload fraction for a given payload volume. We minimize sample degradation by keeping them frozen in the MSR payload sample canister using Peltier chip cooling. The cups are sealed by interference fitted heat activated memory

  14. Ranked set sampling with unequal samples.

    PubMed

    Bhoj, D S

    2001-09-01

    A ranked set sampling procedure with unequal samples (RSSU) is proposed and used to estimate the population mean. This estimator is then compared with the estimators based on the ranked set sampling (RSS) and median ranked set sampling (MRSS) procedures. It is shown that the relative precisions of the estimator based on RSSU are higher than those of the estimators based on RSS and MRSS. An example of estimating the mean diameter at breast height of longleaf-pine trees on the Wade Tract in Thomas County, Georgia, is presented.

  15. Force-Control Algorithm for Surface Sampling

    NASA Technical Reports Server (NTRS)

    Acikmese, Behcet; Quadrelli, Marco B.; Phan, Linh

    2008-01-01

    A G-FCON algorithm is designed for small-body surface sampling. It has a linearization component and a feedback component to enhance performance. The algorithm regulates the contact force between the tip of a robotic arm attached to a spacecraft and a surface during sampling.

  16. Information sampling behavior with explicit sampling costs

    PubMed Central

    Juni, Mordechai Z.; Gureckis, Todd M.; Maloney, Laurence T.

    2015-01-01

    The decision to gather information should take into account both the value of information and its accrual costs in time, energy and money. Here we explore how people balance the monetary costs and benefits of gathering additional information in a perceptual-motor estimation task. Participants were rewarded for touching a hidden circular target on a touch-screen display. The target’s center coincided with the mean of a circular Gaussian distribution from which participants could sample repeatedly. Each “cue” — sampled one at a time — was plotted as a dot on the display. Participants had to repeatedly decide, after sampling each cue, whether to stop sampling and attempt to touch the hidden target or continue sampling. Each additional cue increased the participants’ probability of successfully touching the hidden target but reduced their potential reward. Two experimental conditions differed in the initial reward associated with touching the hidden target and the fixed cost per cue. For each condition we computed the optimal number of cues that participants should sample, before taking action, to maximize expected gain. Contrary to recent claims that people gather less information than they objectively should before taking action, we found that participants over-sampled in one experimental condition, and did not significantly under- or over-sample in the other. Additionally, while the ideal observer model ignores the current sample dispersion, we found that participants used it to decide whether to stop sampling and take action or continue sampling, a possible consequence of imperfect learning of the underlying population dispersion across trials. PMID:27429991

  17. How Sample Size Affects a Sampling Distribution

    ERIC Educational Resources Information Center

    Mulekar, Madhuri S.; Siegel, Murray H.

    2009-01-01

    If students are to understand inferential statistics successfully, they must have a profound understanding of the nature of the sampling distribution. Specifically, they must comprehend the determination of the expected value and standard error of a sampling distribution as well as the meaning of the central limit theorem. Many students in a high…

  18. How Sample Size Affects a Sampling Distribution

    ERIC Educational Resources Information Center

    Mulekar, Madhuri S.; Siegel, Murray H.

    2009-01-01

    If students are to understand inferential statistics successfully, they must have a profound understanding of the nature of the sampling distribution. Specifically, they must comprehend the determination of the expected value and standard error of a sampling distribution as well as the meaning of the central limit theorem. Many students in a high…

  19. Comet Surface Sampling Technologies

    NASA Astrophysics Data System (ADS)

    Zacny, K.; Chu, P.; Paulsen, G.; Indyk, S.

    2014-06-01

    The goal of the Comet Surface Sample Return (CSSR) is to acquire and return to Earth a ≥500 cc) sample. Honeybee developed several sampling technologies including a standalone CSSR Probe (CSSRP) and Pyramid Comet Sampler (PyCoS).

  20. Chorionic Villus Sampling (CVS)

    MedlinePlus

    ... Pregnancy > Prenatal care > Chorionic villus sampling Chorionic villus sampling E-mail to a friend Please fill in ... It's been added to your dashboard . Chorionic villus sampling (CVS) is a prenatal test . It’s used to ...

  1. Biocatalyst Enhancement

    EPA Science Inventory

    The increasing availability of enzyme collections has assisted attempts by pharmaceutical producers to adopt green chemistry approaches to manufacturing. A joint effort between an enzyme producer and a pharmaceutical manufacturer has been enhanced over the past three years by ena...

  2. Biocatalyst Enhancement

    EPA Science Inventory

    The increasing availability of enzyme collections has assisted attempts by pharmaceutical producers to adopt green chemistry approaches to manufacturing. A joint effort between an enzyme producer and a pharmaceutical manufacturer has been enhanced over the past three years by ena...

  3. Selecting a Sample

    ERIC Educational Resources Information Center

    Ritter, Lois A., Ed.; Sue, Valerie M., Ed.

    2007-01-01

    This chapter provides an overview of sampling methods that are appropriate for conducting online surveys. The authors review some of the basic concepts relevant to online survey sampling, present some probability and nonprobability techniques for selecting a sample, and briefly discuss sample size determination and nonresponse bias. Although some…

  4. Fluid sampling tool

    DOEpatents

    Garcia, Anthony R.; Johnston, Roger G.; Martinez, Ronald K.

    2000-01-01

    A fluid-sampling tool for obtaining a fluid sample from a container. When used in combination with a rotatable drill, the tool bores a hole into a container wall, withdraws a fluid sample from the container, and seals the borehole. The tool collects fluid sample without exposing the operator or the environment to the fluid or to wall shavings from the container.

  5. Sample Vial Secure Container

    SciTech Connect

    Baumann, M.J.

    1993-07-01

    International Atomic Energy Agency (IAEA) inspectors must maintain continuity of knowledge on all safeguard samples and, in particular, on those samples drawn from plutonium product and spent fuel input tanks at a nuclear reprocessing plant`s blister sampling station. Integrity of safeguard samples must be guaranteed from the sampling point to the moment of sample analysis at an accepted local laboratory or at the IAEA`s Safeguards Analytical Laboratory (SAL) in Seibersdorf, Austria. The safeguard samples are drawn at a blister sampling station with inspector participation and then transferred via a pneumatic post system to the facility`s analytical laboratory. Transfer of the sample by the pneumatic post system, arrival of the sample in the operator`s analytical laboratory, and storage of the sample awaiting analysis are very time consuming activities for an inspector, particularly if continuous human surveillance is required for all these activities. These activities could be observed by ordinary surveillance methods, such as a video monitoring system, but this would be cumbersome and time consuming for both the inspector and the operator. This paper describes a secure container designed to assure sample vial integrity from the point the sample is drawn to treatment of the sample at a facility`s analytical laboratory.

  6. Apollo 14 rock samples

    NASA Technical Reports Server (NTRS)

    Carlson, I. C.

    1978-01-01

    Petrographic descriptions of all Apollo 14 samples larger than 1 cm in any dimension are presented. The sample description format consists of: (1) an introductory section which includes information on lunar sample location, orientation, and return containers, (2) a section on physical characteristics, which contains the sample mass, dimensions, and a brief description; (3) surface features, including zap pits, cavities, and fractures as seen in binocular view; (4) petrographic description, consisting of a binocular description and, if possible, a thin section description; and (5) a discussion of literature relevant to sample petrology is included for samples which have previously been examined by the scientific community.

  7. Rain sampling device

    DOEpatents

    Nelson, Danny A.; Tomich, Stanley D.; Glover, Donald W.; Allen, Errol V.; Hales, Jeremy M.; Dana, Marshall T.

    1991-01-01

    The present invention constitutes a rain sampling device adapted for independent operation at locations remote from the user which allows rainfall to be sampled in accordance with any schedule desired by the user. The rain sampling device includes a mechanism for directing wet precipitation into a chamber, a chamber for temporarily holding the precipitation during the process of collection, a valve mechanism for controllably releasing samples of said precipitation from said chamber, a means for distributing the samples released from the holding chamber into vessels adapted for permanently retaining these samples, and an electrical mechanism for regulating the operation of the device.

  8. Stardust Sample: Investigator's Guidebook

    NASA Technical Reports Server (NTRS)

    Allen, Carl

    2006-01-01

    In January 2006, the Stardust spacecraft returned the first in situ collection of samples from a comet, and the first samples of contemporary interstellar dust. Stardust is the first US sample return mission from a planetary body since Apollo, and the first ever from beyond the moon. This handbook is a basic reference source for allocation procedures and policies for Stardust samples. These samples consist of particles and particle residues in aerogel collectors, in aluminum foil, and in spacecraft components. Contamination control samples and unflown collection media are also available for allocation.

  9. Rain sampling device

    DOEpatents

    Nelson, D.A.; Tomich, S.D.; Glover, D.W.; Allen, E.V.; Hales, J.M.; Dana, M.T.

    1991-05-14

    The present invention constitutes a rain sampling device adapted for independent operation at locations remote from the user which allows rainfall to be sampled in accordance with any schedule desired by the user. The rain sampling device includes a mechanism for directing wet precipitation into a chamber, a chamber for temporarily holding the precipitation during the process of collection, a valve mechanism for controllably releasing samples of the precipitation from the chamber, a means for distributing the samples released from the holding chamber into vessels adapted for permanently retaining these samples, and an electrical mechanism for regulating the operation of the device. 11 figures.

  10. Improved Sampling Method Reduces Isokinetic Sampling Errors.

    ERIC Educational Resources Information Center

    Karels, Gale G.

    The particulate sampling system currently in use by the Bay Area Air Pollution Control District, San Francisco, California is described in this presentation for the 12th Conference on Methods in Air Pollution and Industrial Hygiene Studies, University of Southern California, April, 1971. The method represents a practical, inexpensive tool that can…

  11. Improved Sampling Method Reduces Isokinetic Sampling Errors.

    ERIC Educational Resources Information Center

    Karels, Gale G.

    The particulate sampling system currently in use by the Bay Area Air Pollution Control District, San Francisco, California is described in this presentation for the 12th Conference on Methods in Air Pollution and Industrial Hygiene Studies, University of Southern California, April, 1971. The method represents a practical, inexpensive tool that can…

  12. GROUND WATER SAMPLING ISSUES

    EPA Science Inventory

    Obtaining representative ground water samples is important for site assessment and
    remedial performance monitoring objectives. Issues which must be considered prior to initiating a ground-water monitoring program include defining monitoring goals and objectives, sampling point...

  13. GROUND WATER SAMPLING ISSUES

    EPA Science Inventory

    Obtaining representative ground water samples is important for site assessment and
    remedial performance monitoring objectives. Issues which must be considered prior to initiating a ground-water monitoring program include defining monitoring goals and objectives, sampling point...

  14. Mold Testing or Sampling

    EPA Pesticide Factsheets

    In most cases, if visible mold growth is present, sampling is unnecessary. Since no EPA or other federal limits have been set for mold or mold spores, sampling cannot be used to check a building's compliance with federal mold standards.

  15. Developing Water Sampling Standards

    ERIC Educational Resources Information Center

    Environmental Science and Technology, 1974

    1974-01-01

    Participants in the D-19 symposium on aquatic sampling and measurement for water pollution assessment were informed that determining the extent of waste water stream pollution is not a cut and dry procedure. Topics discussed include field sampling, representative sampling from storm sewers, suggested sampler features and application of improved…

  16. Decision by Sampling

    ERIC Educational Resources Information Center

    Stewart, Neil; Chater, Nick; Brown, Gordon D. A.

    2006-01-01

    We present a theory of decision by sampling (DbS) in which, in contrast with traditional models, there are no underlying psychoeconomic scales. Instead, we assume that an attribute's subjective value is constructed from a series of binary, ordinal comparisons to a sample of attribute values drawn from memory and is its rank within the sample. We…

  17. Randomized branch sampling

    Treesearch

    Harry T. Valentine

    2002-01-01

    Randomized branch sampling (RBS) is a special application of multistage probability sampling (see Sampling, environmental), which was developed originally by Jessen [3] to estimate fruit counts on individual orchard trees. In general, the method can be used to obtain estimates of many different attributes of trees or other branched plants. The usual objective of RBS is...

  18. SAMPLING OF CONTAMINATED SITES

    EPA Science Inventory

    A critical aspect of characterization of the amount and species of contamination of a hazardous waste site is the sampling plan developed for that site. f the sampling plan is not thoroughly conceptualized before sampling takes place, then certain critical aspects of the limits o...

  19. SAMPLING OF CONTAMINATED SITES

    EPA Science Inventory

    A critical aspect of characterization of the amount and species of contamination of a hazardous waste site is the sampling plan developed for that site. f the sampling plan is not thoroughly conceptualized before sampling takes place, then certain critical aspects of the limits o...

  20. Fluid sampling pump

    SciTech Connect

    Allen, P.V.; Nimberger, M.; Ward, R.L.

    1991-12-24

    This patent describes a fluid sampling pump for withdrawing pressurized sample fluid from a flow line and for pumping a preselected quantity of sample fluid with each pump driving stroke from the pump to a sample vessel, the sampling pump including a pump body defining a pump bore therein having a central axis, a piston slideably moveable within the pump bore and having a fluid inlet end and an opposing operator end, a fluid sample inlet port open to sample fluid in the flow line, a fluid sample outlet port for transmitting fluid from the pump bore to the sample vessel, and a line pressure port in fluid pressure sample fluid in the flow line, an inlet valve for selectively controlling sample fluid flow from the flow line through the fluid sample inlet port, an operator unit for periodically reciprocating the piston within the pump bore, and a controller for regulating the stroke of the piston within the pump bore, and thereby the quantity of fluid pumped with each pump driving stroke. It comprises a balanced check valve seat; a balanced check valve seal; a compression member; and a central plunger.

  1. Developing Water Sampling Standards

    ERIC Educational Resources Information Center

    Environmental Science and Technology, 1974

    1974-01-01

    Participants in the D-19 symposium on aquatic sampling and measurement for water pollution assessment were informed that determining the extent of waste water stream pollution is not a cut and dry procedure. Topics discussed include field sampling, representative sampling from storm sewers, suggested sampler features and application of improved…

  2. Instructions for Sampling Particulates.

    ERIC Educational Resources Information Center

    Ekman, Frank

    This technical report presents detailed instructions for sampling particulates. The table of contents includes sections on Introduction, Volume Determinations, Apparatus - Assembly and Operation, Sampling Techniques, and Acknowledgment. Six charts, 24 graphs, and one diagram are appended to facilitate sampling, as well as sections on Isokinetic…

  3. Aerosol sampling system

    DOEpatents

    Masquelier, Donald A.

    2004-02-10

    A system for sampling air and collecting particulate of a predetermined particle size range. A low pass section has an opening of a preselected size for gathering the air but excluding particles larger than the sample particles. An impactor section is connected to the low pass section and separates the air flow into a bypass air flow that does not contain the sample particles and a product air flow that does contain the sample particles. A wetted-wall cyclone collector, connected to the impactor section, receives the product air flow and traps the sample particles in a liquid.

  4. Rockballer Sample Acquisition Tool

    NASA Technical Reports Server (NTRS)

    Giersch, Louis R.; Cook, Brant T.

    2013-01-01

    It would be desirable to acquire rock and/or ice samples that extend below the surface of the parent rock or ice in extraterrestrial environments such as the Moon, Mars, comets, and asteroids. Such samples would allow measurements to be made further back into the geologic history of the rock, providing critical insight into the history of the local environment and the solar system. Such samples could also be necessary for sample return mission architectures that would acquire samples from extraterrestrial environments for return to Earth for more detailed scientific investigation.

  5. DIY Tomography sample holder

    NASA Astrophysics Data System (ADS)

    Lari, L.; Wright, I.; Boyes, E. D.

    2015-10-01

    A very simple tomography sample holder at minimal cost was developed in-house. The holder is based on a JEOL single tilt fast exchange sample holder where its exchangeable tip was modified to allow high angle degree tilt. The shape of the tip was designed to retain mechanical stability while minimising the lateral size of the tip. The sample can be mounted on as for a standard 3mm Cu grids as well as semi-circular grids from FIB sample preparation. Applications of the holder on different sample systems are shown.

  6. Venus Sample Return Mission

    NASA Astrophysics Data System (ADS)

    Whitcomb, G.; Lebreton, J.; Scoon, G.

    The Venus Sample Return (VSR) mission was performed as an in-house activity within the European Space Agency's Science Directorate during a 4-month period. The selected baseline mission scenario involves two launches of the presently available Ariane 5 configuration. The first launch would inject a composite spacecraft consisting of an orbiter and a return capsule into a parking orbit around Venus. The second launch would deliver at Venus a lander composite, consisting of the entry, descent, sampling and ascent modules. The sampling strategy includes returning a surface (with possibly a core) sample and three atmospheric samples at high altitudes. This paper presents the design concept for the mission.

  7. Sample Caching Subsystem

    NASA Technical Reports Server (NTRS)

    Backes, Paul G.; Collins, Curtis L.

    2007-01-01

    A paper describes the Sample Caching Subsystem (SCS), a method for storing planetary core and soil samples in a container that seals the samples away from the environment to protect the integrity of the samples and any organics they might contain. This process places samples in individual sleeves that are sealed within a container for use by either the current mission or by following missions. A sample container is stored with its sleeves partially inserted. When a sample is ready to be contained, a transfer arm rotates over and grasps a sleeve, pulls it out of the container from below, rotates over and inserts the sleeve into a funnel where it is passively locked into place and then released from the arm. An external sampling tool deposits the sample into the sleeve, which is aligned with the tool via passive compliance of the funnel. After the sampling tool leaves the funnel, the arm retrieves the sleeve and inserts it all the way into the sample container. This action engages the seal. Full containers can be left behind for pick-up by subsequent science missions, and container dimensions are compatible for placement in a Mars Ascent Vehicle for later return to Earth.

  8. Curation of Frozen Samples

    NASA Technical Reports Server (NTRS)

    Fletcher, L. A.; Allen, C. C.; Bastien, R.

    2008-01-01

    NASA's Johnson Space Center (JSC) and the Astromaterials Curator are charged by NPD 7100.10D with the curation of all of NASA s extraterrestrial samples, including those from future missions. This responsibility includes the development of new sample handling and preparation techniques; therefore, the Astromaterials Curator must begin developing procedures to preserve, prepare and ship samples at sub-freezing temperatures in order to enable future sample return missions. Such missions might include the return of future frozen samples from permanently-shadowed lunar craters, the nuclei of comets, the surface of Mars, etc. We are demonstrating the ability to curate samples under cold conditions by designing, installing and testing a cold curation glovebox. This glovebox will allow us to store, document, manipulate and subdivide frozen samples while quantifying and minimizing contamination throughout the curation process.

  9. Sample Proficiency Test exercise

    SciTech Connect

    Alcaraz, A; Gregg, H; Koester, C

    2006-02-05

    The current format of the OPCW proficiency tests has multiple sets of 2 samples sent to an analysis laboratory. In each sample set, one is identified as a sample, the other as a blank. This method of conducting proficiency tests differs from how an OPCW designated laboratory would receive authentic samples (a set of three containers, each not identified, consisting of the authentic sample, a control sample, and a blank sample). This exercise was designed to test the reporting if the proficiency tests were to be conducted. As such, this is not an official OPCW proficiency test, and the attached report is one method by which LLNL might report their analyses under a more realistic testing scheme. Therefore, the title on the report ''Report of the Umpteenth Official OPCW Proficiency Test'' is meaningless, and provides a bit of whimsy for the analyses and readers of the report.

  10. Sample size calculations.

    PubMed

    Noordzij, Marlies; Dekker, Friedo W; Zoccali, Carmine; Jager, Kitty J

    2011-01-01

    The sample size is the number of patients or other experimental units that need to be included in a study to answer the research question. Pre-study calculation of the sample size is important; if a sample size is too small, one will not be able to detect an effect, while a sample that is too large may be a waste of time and money. Methods to calculate the sample size are explained in statistical textbooks, but because there are many different formulas available, it can be difficult for investigators to decide which method to use. Moreover, these calculations are prone to errors, because small changes in the selected parameters can lead to large differences in the sample size. This paper explains the basic principles of sample size calculations and demonstrates how to perform such a calculation for a simple study design.

  11. The Lunar Sample Compendium

    NASA Technical Reports Server (NTRS)

    Meyer, Charles

    2009-01-01

    The Lunar Sample Compendium is a succinct summary of the data obtained from 40 years of study of Apollo and Luna samples of the Moon. Basic petrographic, chemical and age information is compiled, sample-by-sample, in the form of an advanced catalog in order to provide a basic description of each sample. The LSC can be found online using Google. The initial allocation of lunar samples was done sparingly, because it was realized that scientific techniques would improve over the years and new questions would be formulated. The LSC is important because it enables scientists to select samples within the context of the work that has already been done and facilitates better review of proposed allocations. It also provides back up material for public displays, captures information found only in abstracts, grey literature and curatorial databases and serves as a ready access to the now-vast scientific literature.

  12. The Lunar Sample Compendium

    NASA Technical Reports Server (NTRS)

    Meyer, Charles

    2009-01-01

    The Lunar Sample Compendium is a succinct summary of the data obtained from 40 years of study of Apollo and Luna samples of the Moon. Basic petrographic, chemical and age information is compiled, sample-by-sample, in the form of an advanced catalog in order to provide a basic description of each sample. The LSC can be found online using Google. The initial allocation of lunar samples was done sparingly, because it was realized that scientific techniques would improve over the years and new questions would be formulated. The LSC is important because it enables scientists to select samples within the context of the work that has already been done and facilitates better review of proposed allocations. It also provides back up material for public displays, captures information found only in abstracts, grey literature and curatorial databases and serves as a ready access to the now-vast scientific literature.

  13. Lunar Sample Compendium

    NASA Technical Reports Server (NTRS)

    Meyer, C.

    2009-01-01

    The Lunar Sample Compendium is a succinct summary of what has been learned from the study of Apollo and Luna samples of the Moon. Basic information is compiled, sample-by-sample, in the form of an advanced catalog in order to provide a basic description of each sample. Information presented is carefully attributed to the original source publication, thus the Compendium also serves as a ready access to the now vast scientific literature pertaining to lunar smples. The Lunar Sample Compendium is a work in progress (and may always be). Future plans include: adding sections on additional samples, adding new thin section photomicrographs, replacing the faded photographs with newly digitized photos from the original negatives, attempting to correct the age data using modern decay constants, adding references to each section, and adding an internal search engine.

  14. Urine sample collection protocols for bioassay samples

    SciTech Connect

    MacLellan, J.A.; McFadden, K.M.

    1992-11-01

    In vitro radiobioassay analyses are used to measure the amount of radioactive material excreted by personnel exposed to the potential intake of radioactive material. The analytical results are then used with various metabolic models to estimate the amount of radioactive material in the subject`s body and the original intake of radioactive material. Proper application of these metabolic models requires knowledge of the excretion period. It is normal practice to design the bioassay program based on a 24-hour excretion sample. The Hanford bioassay program simulates a total 24-hour urine excretion sample with urine collection periods lasting from one-half hour before retiring to one-half hour after rising on two consecutive days. Urine passed during the specified periods is collected in three 1-L bottles. Because the daily excretion volume given in Publication 23 of the International Commission on Radiological Protection (ICRP 1975, p. 354) for Reference Man is 1.4 L, it was proposed to use only two 1-L bottles as a cost-saving measure. This raised the broader question of what should be the design capacity of a 24-hour urine sample kit.

  15. Urine sample collection protocols for bioassay samples

    SciTech Connect

    MacLellan, J.A.; McFadden, K.M.

    1992-11-01

    In vitro radiobioassay analyses are used to measure the amount of radioactive material excreted by personnel exposed to the potential intake of radioactive material. The analytical results are then used with various metabolic models to estimate the amount of radioactive material in the subject's body and the original intake of radioactive material. Proper application of these metabolic models requires knowledge of the excretion period. It is normal practice to design the bioassay program based on a 24-hour excretion sample. The Hanford bioassay program simulates a total 24-hour urine excretion sample with urine collection periods lasting from one-half hour before retiring to one-half hour after rising on two consecutive days. Urine passed during the specified periods is collected in three 1-L bottles. Because the daily excretion volume given in Publication 23 of the International Commission on Radiological Protection (ICRP 1975, p. 354) for Reference Man is 1.4 L, it was proposed to use only two 1-L bottles as a cost-saving measure. This raised the broader question of what should be the design capacity of a 24-hour urine sample kit.

  16. Sampling diffusive transition paths

    SciTech Connect

    F. Miller III, Thomas; Predescu, Cristian

    2006-10-12

    We address the problem of sampling double-ended diffusive paths. The ensemble of paths is expressed using a symmetric version of the Onsager-Machlup formula, which only requires evaluation of the force field and which, upon direct time discretization, gives rise to a symmetric integrator that is accurate to second order. Efficiently sampling this ensemble requires avoiding the well-known stiffness problem associated with sampling infinitesimal Brownian increments of the path, as well as a different type of stiffness associated with sampling the coarse features of long paths. The fine-features sampling stiffness is eliminated with the use of the fast sampling algorithm (FSA), and the coarse-feature sampling stiffness is avoided by introducing the sliding and sampling (S&S) algorithm. A key feature of the S&S algorithm is that it enables massively parallel computers to sample diffusive trajectories that are long in time. We use the algorithm to sample the transition path ensemble for the structural interconversion of the 38-atom Lennard-Jones cluster at low temperature.

  17. Sampling in Qualitative Research

    PubMed Central

    LUBORSKY, MARK R.; RUBINSTEIN, ROBERT L.

    2011-01-01

    In gerontology the most recognized and elaborate discourse about sampling is generally thought to be in quantitative research associated with survey research and medical research. But sampling has long been a central concern in the social and humanistic inquiry, albeit in a different guise suited to the different goals. There is a need for more explicit discussion of qualitative sampling issues. This article will outline the guiding principles and rationales, features, and practices of sampling in qualitative research. It then describes common questions about sampling in qualitative research. In conclusion it proposes the concept of qualitative clarity as a set of principles (analogous to statistical power) to guide assessments of qualitative sampling in a particular study or proposal. PMID:22058580

  18. Sampling functions for geophysics

    NASA Technical Reports Server (NTRS)

    Giacaglia, G. E. O.; Lunquist, C. A.

    1972-01-01

    A set of spherical sampling functions is defined such that they are related to spherical-harmonic functions in the same way that the sampling functions of information theory are related to sine and cosine functions. An orderly distribution of (N + 1) squared sampling points on a sphere is given, for which the (N + 1) squared spherical sampling functions span the same linear manifold as do the spherical-harmonic functions through degree N. The transformations between the spherical sampling functions and the spherical-harmonic functions are given by recurrence relations. The spherical sampling functions of two arguments are extended to three arguments and to nonspherical reference surfaces. Typical applications of this formalism to geophysical topics are sketched.

  19. Drug sampling in dermatology.

    PubMed

    Reid, Erika E; Alikhan, Ali; Brodell, Robert T

    2012-01-01

    The use of drug samples in a dermatology clinic is controversial. Drug samples are associated with influencing physician prescribing patterns often toward costlier drugs, increasing health care costs, increasing waste, inducing potential conflicts of interest, and decreasing the quality of patient education. On the other hand, they have the potential to help those in financial need, to improve adherence and convenience, and to expose patients to better drugs. Although some academic centers have banned drug samples altogether, many academic and private practices continue to distribute drug samples. Given the controversy of the topic, physicians who wish to distribute drug samples must do so in an ethical manner. We believe, when handled properly, drug sampling can be used in an ethical manner. Copyright © 2012 Elsevier Inc. All rights reserved.

  20. Fluid sampling device

    NASA Technical Reports Server (NTRS)

    Studenick, D. K. (Inventor)

    1977-01-01

    An inlet leak is described for sampling gases, more specifically, for selectively sampling multiple fluids. This fluid sampling device includes a support frame. A plurality of fluid inlet devices extend through the support frame and each of the fluid inlet devices include a longitudinal aperture. An opening device that is responsive to a control signal selectively opens the aperture to allow fluid passage. A closing device that is responsive to another control signal selectively closes the aperture for terminating further fluid flow.

  1. Sample positioning in microgravity

    NASA Technical Reports Server (NTRS)

    Sridharan, Govind (Inventor)

    1991-01-01

    Repulsion forces arising from laser beams are provided to produce mild positioning forces on a sample in microgravity vacuum environments. The system of the preferred embodiment positions samples using a plurality of pulsed lasers providing opposing repulsion forces. The lasers are positioned around the periphery of a confinement area and expanded to create a confinement zone. The grouped laser configuration, in coordination with position sensing devices, creates a feedback servo whereby stable position control of a sample within microgravity environment can be achieved.

  2. Immune Blood Sample Draw

    NASA Image and Video Library

    2012-04-26

    ISS030-E-257690 (26 April 2012) --- European Space Agency astronaut Andre Kuipers, Expedition 30 flight engineer, prepares for IMMUNE venous blood sample draws in the Columbus laboratory of the International Space Station. Following the blood draws, the samples were temporarily stowed in the Minus Eighty Laboratory Freezer for ISS 1 (MELFI-1) and later packed together with saliva samples on the Soyuz TMA-22 for return to Earth for analysis.

  3. Aerosol Sampling Models Survey

    DTIC Science & Technology

    1993-03-01

    Particle Sizes ) for Inlet Region of Aerosol Sampling Train .......... ................ .. 49 8 Model Efficiency Calculations (Polydispersed Particle ...0 As the MMAD particle size increases, the sampling efficiency decreases. As the flow rate increases, the sampling efficiency decreases. However, the...70 93.9 88.0 N/A 7. 5 900 130 99.5 99.2 N/A 8 . 15 900 130 94.4 93.2 N/A Table 10. Model Efficiency Calculations (Polydispersed Particle Sizes ) for

  4. LUNAR SAMPLES - APOLLO 11

    NASA Image and Video Library

    1969-08-03

    S69-40749 (July 1969) --- Dr. Grant Heikan, MSC and a Lunar Sample Preliminary Examination Team member, examines lunar material in a sieve from the bulk sample container which was opened in the Biopreparation Laboratory of the Lunar Receiving Laboratory. The samples were collected by astronauts Neil A. Armstrong and Edwin E. Aldrin Jr. during their lunar surface extravehicular activity on July 20, 1969.

  5. Sample positioning in microgravity

    NASA Technical Reports Server (NTRS)

    Sridharan, Govind (Inventor)

    1993-01-01

    Repulsion forces arising from laser beams are provided to produce mild positioning forces on a sample in microgravity vacuum environments. The system of the preferred embodiment positions samples using a plurality of pulsed lasers providing opposing repulsion forces. The lasers are positioned around the periphery of a confinement area and expanded to create a confinement zone. The grouped laser configuration, in coordination with position sensing devices, creates a feedback servo whereby stable position control of a sample within microgravity environment can be achieved.

  6. Statistical distribution sampling

    NASA Technical Reports Server (NTRS)

    Johnson, E. S.

    1975-01-01

    Determining the distribution of statistics by sampling was investigated. Characteristic functions, the quadratic regression problem, and the differential equations for the characteristic functions are analyzed.

  7. Enhancing bioremediation

    SciTech Connect

    Koenigsberg, S.

    1997-02-01

    Oxygen is often the limiting factor in aerobic bioremediation. Without adequate oxygen, contaminant degradation will either cease or proceed by highly inefficient anaerobic processes. Researchers at Regenesis Bioremediation Products recently develope a technology to combat this problem, Oxygen Release Compound (ORC) a unique formulation of magnesium peroxide release oxygen slowly when hydrated. ORC is idea for supporting bioremediation of underground storage tank releases. ORC treatment represents a low intensity approach to remediation - simple, passive, low-cost, long term enhancement of a natural attenuation. 1 fig.

  8. Sampling in qualitative research. Purposeful and theoretical sampling; merging or clear boundaries?

    PubMed

    Coyne, I T

    1997-09-01

    Sampling is a very complex issue in qualitative research as there are many variations of qualitative sampling described in the literature and much confusion and overlapping of types of sampling, particularly in the case of purposeful and theoretical sampling. The terms purposeful and theoretical are viewed synonomously and used interchangeably in the literature. Many of the most frequent misinterpretations relate to the disparate meanings and usage of the terminology. It is important that the terminology is examined so that underlying assumptions be made more explicit. Lack of shared meanings and terminology in the nursing discourse creates confusion for the neophyte researcher and increases the production of studies with weak methodologies. This paper analyses critically purposeful and theoretical sampling and offers clarification on the use of theoretical sampling for nursing research. The aim is not to make prescriptive statements on sampling; rather, to enhance understanding of the differences between purposeful and theoretical sampling for nursing research.

  9. Urine sample (image)

    MedlinePlus

    A "clean-catch" urine sample is performed by collecting the sample of urine in midstream. Men or boys should wipe clean the head ... water and rinse well. A small amount of urine should initially fall into the toilet bowl before ...

  10. Implementing Teacher Work Sampling

    ERIC Educational Resources Information Center

    Kinne, Lenore J.; Watson, Dwight C.

    2005-01-01

    This article describes how the teacher work sample methodology of the Renaissance Partnership for Improving Teacher Quality was implemented within the teacher education program at a small liberal arts college. Resulting program improvements are described, as well as on-going challenges. The adapted teacher work sample prompt and scoring rubric are…

  11. Extraterrestrial Samples at JSC

    NASA Technical Reports Server (NTRS)

    Allen, Carlton C.

    2007-01-01

    A viewgraph presentation on the curation of extraterrestrial samples at NASA Johnson Space Center is shown. The topics include: 1) Apollo lunar samples; 2) Meteorites from Antarctica; 3) Cosmic dust from the stratosphere; 4) Genesis solar wind ions; 5) Stardust comet and interstellar grains; and 5) Space-Exposed Hardware.

  12. Lifting Sample Return Capsule

    NASA Technical Reports Server (NTRS)

    2006-01-01

    NASA's Stardust sample return capsule successfully landed at the U.S. Air Force Utah Test and Training Range at 2:10 a.m. Pacific time (3:10 a.m. Mountain time). The capsule contains cometary and interstellar samples gathered by the Stardust spacecraft.

    Here, the capsule is being lifted at the landing site.

  13. Sample Return Capsule

    NASA Technical Reports Server (NTRS)

    2006-01-01

    NASA's Stardust sample return capsule successfully landed at the U.S. Air Force Utah Test and Training Range at 2:10 a.m. Pacific time (3:10 a.m. Mountain time). The capsule contains cometary and interstellar samples gathered by the Stardust spacecraft.

  14. Sampling system and method

    DOEpatents

    Decker, David L.; Lyles, Brad F.; Purcell, Richard G.; Hershey, Ronald Lee

    2013-04-16

    The present disclosure provides an apparatus and method for coupling conduit segments together. A first pump obtains a sample and transmits it through a first conduit to a reservoir accessible by a second pump. The second pump further conducts the sample from the reservoir through a second conduit.

  15. Microbiological surface sampling cart

    NASA Technical Reports Server (NTRS)

    Wilkins, J. R.; Mills, S. M.

    1972-01-01

    Mobile sampling cart automatically swabs surfaces for the recovery of microorganisms. Unit operates without human involvement and provides for control of swabbing speed, rotation of cotton swab, and the pressure and angle applied to swab. Capability of reverse direction is also available. Sampling cart use is limited to flat surfaces.

  16. Simple street tree sampling

    Treesearch

    David J. Nowak; Jeffrey T. Walton; James Baldwin; Jerry. Bond

    2015-01-01

    Information on street trees is critical for management of this important resource. Sampling of street tree populations provides an efficient means to obtain street tree population information. Long-term repeat measures of street tree samples supply additional information on street tree changes and can be used to report damages from catastrophic events. Analyses of...

  17. Automotive Work Sample.

    ERIC Educational Resources Information Center

    Shawsheen Valley Regional Vocational-Technical High School, Billerica, MA.

    This manual contains a work sample intended to assess a handicapped student's interest in and potential to pass successfully a training program in automotive mechanics or in a similar automotive job. Section 1 describes the assessment, correlates the work performed and worker traits required for completing the work sample, and lists related…

  18. Electronics Assembly Work Sample.

    ERIC Educational Resources Information Center

    Shawsheen Valley Regional Vocational-Technical High School, Billerica, MA.

    This manual contains a work sample intended to assess a handicapped student's interest in and potential to enter a training program in electronics assembly or in a similar program. Section 1 describes the assessment, correlates the work performed and worker traits required for completing the work sample, and lists related occupations and DOT…

  19. SWAB Air sampling

    NASA Image and Video Library

    2006-12-08

    ISS014-E-09425 (8 Dec. 2006) --- European Space Agency (ESA) astronaut Thomas Reiter, Expedition 14 flight engineer, conducts a Surface, Water and Air Biocharacterization (SWAB) air sampling in the Destiny laboratory of the International Space Station. Reiter holds a pair of scissors and the SWAB Air Sampling Device (ASD) floats freely near him.

  20. National Sample Assessment Protocols

    ERIC Educational Resources Information Center

    Ministerial Council on Education, Employment, Training and Youth Affairs (NJ1), 2012

    2012-01-01

    These protocols represent a working guide for planning and implementing national sample assessments in connection with the national Key Performance Measures (KPMs). The protocols are intended for agencies involved in planning or conducting national sample assessments and personnel responsible for administering associated tenders or contracts,…

  1. Donor–acceptor stacking arrangements in bulk and thin-film high-mobility conjugated polymers characterized using molecular modelling and MAS and surface-enhanced solid-state NMR spectroscopy† †Electronic supplementary information (ESI) available: Additional computational and experimental details, including the DNP sample preparation. See DOI: 10.1039/c7sc00053g Click here for additional data file.

    PubMed Central

    Chaudhari, Sachin R.; Broch, Katharina; Lesage, Anne; Lemaur, Vincent; Dudenko, Dmytro; Olivier, Yoann; Sirringhaus, Henning; Emsley, Lyndon; Grey, Clare P.

    2017-01-01

    Conjugated polymers show promising properties as cheap, sustainable and solution-processable semiconductors. A key challenge in the development of these materials is to determine the polymer chain structure, conformation and packing in both the bulk polymer and in thin films typically used in devices. However, many characterisation techniques are unable to provide atomic-level structural information owing to the presence of disorder. Here, we use molecular modelling, magic-angle spinning (MAS) and dynamic nuclear polarisation surface-enhanced NMR spectroscopy (DNP SENS) to characterise the polymer backbone group conformations and packing arrangement in the high-mobility donor–acceptor copolymer diketopyrrolo-pyrrole-dithienylthieno[3,2-b]thiophene (DPP-DTT). Using conventional 1H and 13C solid-state MAS NMR coupled with density functional theory calculations and molecular dynamics simulations, we find that the bulk polymer adopts a highly planar backbone conformation with a laterally-shifted donor-on-acceptor stacking arrangement. DNP SENS enables acquisition of 13C NMR data for polymer films, where sensitivity is limiting owing to small sample volumes. The DNP signal enhancement enables a two-dimensional 1H–13C HETCOR spectrum to be recorded for a drop-cast polymer film, and a 13C CPMAS NMR spectrum to be recorded for a spin-coated thin-film with a thickness of only 400 nm. The results show that the same planar backbone structure and intermolecular stacking arrangement is preserved in the films following solution processing and annealing, thereby rationalizing the favourable device properties of DPP-DTT, and providing a protocol for the study of other thin film materials. PMID:28507688

  2. Biological sample collector

    DOEpatents

    Murphy, Gloria A [French Camp, CA

    2010-09-07

    A biological sample collector is adapted to a collect several biological samples in a plurality of filter wells. A biological sample collector may comprise a manifold plate for mounting a filter plate thereon, the filter plate having a plurality of filter wells therein; a hollow slider for engaging and positioning a tube that slides therethrough; and a slide case within which the hollow slider travels to allow the tube to be aligned with a selected filter well of the plurality of filter wells, wherein when the tube is aligned with the selected filter well, the tube is pushed through the hollow slider and into the selected filter well to sealingly engage the selected filter well and to allow the tube to deposit a biological sample onto a filter in the bottom of the selected filter well. The biological sample collector may be portable.

  3. EDITORIAL: Enhancing nanolithography Enhancing nanolithography

    NASA Astrophysics Data System (ADS)

    Demming, Anna

    2012-01-01

    Lithography was invented in late 18th century Bavaria by an ambitious young playwright named Alois Senefelder. Senefelder experimented with stone, wax, water and ink in the hope of finding a way of reproducing text so that he might financially gain from a wider distribution of his already successful scripts. His discovery not only facilitated the profitability of his plays, but also provided the world with an affordable printing press that would ultimately democratize the dissemination of art, knowledge and literature. Since Senefelder, experiments in lithography have continued with a range of innovations including the use of electron beams and UV that allow increasingly higher-resolution features [1, 2]. Applications for this have now breached the limits of paper printing into the realms of semiconductor and microelectronic mechanical systems technology. In this issue, researchers demonstrate a technique for fabricating periodic features in poly(3,4-ethylene dioxythiophene)-poly(styrenesulfonate) (PEDOT-PSS) [3]. Their method combines field enhancements from silica nanospheres with laser-interference lithography to provide a means of patterning a polymer that has the potential to open the market of low-end, high-volume microelectronics. Laser-interference lithography has already been used successfully in patterning. Researchers in Korea used laser-interference lithography to generate stamps for imprinting a two-dimensional photonic crystal structure into green light emitting diodes (LEDs) [4]. The imprinted patterns comprised depressions 100 nm deep and 180 nm wide with a periodicity of 295 nm. In comparison with unpatterned LEDs, the intensity of photoluminescence was enhanced by a factor of seven in the LEDs that had the photonic crystal structures imprinted in them. The potential of exploiting field enhancements around nanostructures for new technologies has also attracted a great deal of attention. Researchers in the USA and Australia have used the field

  4. AUTOMATING GROUNDWATER SAMPLING AT HANFORD

    SciTech Connect

    CONNELL CW; HILDEBRAND RD; CONLEY SF; CUNNINGHAM DE

    2009-01-16

    information recorded, and enhance the efficiency and sampling capacity of field personnel. The goal of the effort is to eliminate 100 percent of the manual input to the database(s) and replace the management of paperwork by the field and clerical personnel with an almost entirely electronic process. These activities will include the following: scheduling the activities of the field teams, electronically recording water-level measurements, electronically logging and filing Groundwater Sampling Reports (GSR), and transferring field forms into the site-wide Integrated Document Management System (IDMS).

  5. Rapid Active Sampling Package

    NASA Technical Reports Server (NTRS)

    Peters, Gregory

    2010-01-01

    A field-deployable, battery-powered Rapid Active Sampling Package (RASP), originally designed for sampling strong materials during lunar and planetary missions, shows strong utility for terrestrial geological use. The technology is proving to be simple and effective for sampling and processing materials of strength. Although this originally was intended for planetary and lunar applications, the RASP is very useful as a powered hand tool for geologists and the mining industry to quickly sample and process rocks in the field on Earth. The RASP allows geologists to surgically acquire samples of rock for later laboratory analysis. This tool, roughly the size of a wrench, allows the user to cut away swaths of weathering rinds, revealing pristine rock surfaces for observation and subsequent sampling with the same tool. RASPing deeper (.3.5 cm) exposes single rock strata in-situ. Where a geologist fs hammer can only expose unweathered layers of rock, the RASP can do the same, and then has the added ability to capture and process samples into powder with particle sizes less than 150 microns, making it easier for XRD/XRF (x-ray diffraction/x-ray fluorescence). The tool uses a rotating rasp bit (or two counter-rotating bits) that resides inside or above the catch container. The container has an open slot to allow the bit to extend outside the container and to allow cuttings to enter and be caught. When the slot and rasp bit are in contact with a substrate, the bit is plunged into it in a matter of seconds to reach pristine rock. A user in the field may sample a rock multiple times at multiple depths in minutes, instead of having to cut out huge, heavy rock samples for transport back to a lab for analysis. Because of the speed and accuracy of the RASP, hundreds of samples can be taken in one day. RASP-acquired samples are small and easily carried. A user can characterize more area in less time than by using conventional methods. The field-deployable RASP used a Ni

  6. PFP Wastewater Sampling Facility

    SciTech Connect

    Hirzel, D.R.

    1995-05-11

    This test report documents the results obtained while conducting operational testing of the sampling equipment in the 225-WC building, the PFP Wastewater Sampling Facility. The Wastewater Sampling Facility houses equipment to sample and monitor the PFP`s liquid effluents before discharging the stream to the 200 Area Treated Effluent Disposal Facility (TEDF). The majority of the streams are not radioactive and discharges from the PFP Heating, Ventilation, and Air Conditioning (HVAC). The streams that might be contaminated are processed through the Low Level Waste Treatment Facility (LLWTF) before discharging to TEDF. The sampling equipment consists of two flow-proportional composite samplers, an ultrasonic flowmeter, pH and conductivity monitors, chart recorder, and associated relays and current isolators to interconnect the equipment to allow proper operation. Data signals from the monitors are received in the 234-5Z Shift Office which contains a chart recorder and alarm annunciator panel. The data signals are also duplicated and sent to the TEDF control room through the Local Control Unit (LCU). Performing the OTP has verified the operability of the PFP wastewater sampling system. This Operability Test Report documents the acceptance of the sampling system for use.

  7. Waste classification sampling plan

    SciTech Connect

    Landsman, S.D.

    1998-05-27

    The purpose of this sampling is to explain the method used to collect and analyze data necessary to verify and/or determine the radionuclide content of the B-Cell decontamination and decommissioning waste stream so that the correct waste classification for the waste stream can be made, and to collect samples for studies of decontamination methods that could be used to remove fixed contamination present on the waste. The scope of this plan is to establish the technical basis for collecting samples and compiling quantitative data on the radioactive constituents present in waste generated during deactivation activities in B-Cell. Sampling and radioisotopic analysis will be performed on the fixed layers of contamination present on structural material and internal surfaces of process piping and tanks. In addition, dose rate measurements on existing waste material will be performed to determine the fraction of dose rate attributable to both removable and fixed contamination. Samples will also be collected to support studies of decontamination methods that are effective in removing the fixed contamination present on the waste. Sampling performed under this plan will meet criteria established in BNF-2596, Data Quality Objectives for the B-Cell Waste Stream Classification Sampling, J. M. Barnett, May 1998.

  8. Instructions for borehole sampling

    SciTech Connect

    Reynolds, K.D.; Lindsey, K.A.

    1994-11-11

    Geologic systems generally are complex with physical properties and trends that can be difficult to predict. Subsurface geology exerts a fundamental control on groundwater flow and contaminant transport. The primary source for direct observation of subsurface geologic information is a borehole. However, direct observations from a borehole essentially are limited to the diameter and spacing of boreholes and the quality of the information derived from the drilling. Because it is impractical to drill a borehole every few feet to obtain data, it is necessary to maximize the data gathered during limited drilling operations. A technically defensible balance between the customer`s data quality objectives and control of drilling costs through limited drilling can be achieved with proper conduct of operations. This report presents the minimum criteria for geologic and hydrologic characterization and sampling that must be met during drilling. It outlines the sampling goals that need to be addressed when drilling boreholes, and the types of drilling techniques that work best to achieve these goals under the geologic conditions found at Hanford. This report provides general guidelines for: (1) how sampling methods are controlled by data needs, (2) how minimum sampling requirements change as knowledge and needs change, and (3) when drilling and sampling parameters need to be closely controlled with respect to the specific data needs. Consequently, the report is divided into two sections that center on: (1) a discussion of basic categories of subsurface characterization, sampling, and sampling techniques, and (2) guidelines for determining which drilling and sampling techniques meet required characterization and sampling objectives.

  9. Sample quality criteria.

    PubMed

    Ramsey, Charles A; Wagner, Claas

    2015-01-01

    The concept of Sample Quality Criteria (SQC) is the initial step in the scientific approach to representative sampling. It includes the establishment of sampling objectives, Decision Unit (DU), and confidence. Once fully defined, these criteria serve as input, in addition to material properties, to the Theory of Sampling for developing a representative sampling protocol. The first component of the SQC establishes these questions: What is the analyte(s) of concern? What is the concentration level of interest of the analyte(s)? How will inference(s) be made from the analytical data to the DU? The second component of the SQC establishes the DU, i.e., the scale at which decisions are to be made. On a large scale, a DU could be a ship or rail car; examples for small-scale DUs are individual beans, seeds, or kernels. A well-defined DU is critical because it defines the spatial and temporal boundaries of sample collection. SQC are not limited to a single DU; they can also include multiple DUs. The third SQC component, the confidence, establishes the desired probability that a correct inference (decision) can be made. The confidence level should typically correlate to the potential consequences of an incorrect decision (e.g., health or economic). The magnitude of combined errors in the sampling, sample processing and analytical protocols determines the likelihood of an incorrect decision. Thus, controlling error to a greater extent increases the probability of a correct decision. The required confidence level directly affects the sampling effort and QC measures.

  10. GRACEnet sampling protocols

    USDA-ARS?s Scientific Manuscript database

    I. INTRODUCTION1 Ronald F. Follett (Editor) U.S. Department of Agriculture, Agricultural Research Service Soil-Plant-Nutrient Research Unit Fort Collins, CO GRACEnet is an acronym derived by contraction of the project’s title, “Greenhouse Gas Reduction through Agricultural Carbon Enhancement network...

  11. Sampling video compression system

    NASA Technical Reports Server (NTRS)

    Matsumoto, Y.; Lum, H. (Inventor)

    1977-01-01

    A system for transmitting video signal of compressed bandwidth is described. The transmitting station is provided with circuitry for dividing a picture to be transmitted into a plurality of blocks containing a checkerboard pattern of picture elements. Video signals along corresponding diagonal rows of picture elements in the respective blocks are regularly sampled. A transmitter responsive to the output of the sampling circuitry is included for transmitting the sampled video signals of one frame at a reduced bandwidth over a communication channel. The receiving station is provided with a frame memory for temporarily storing transmitted video signals of one frame at the original high bandwidth frequency.

  12. Sample - Based Material Structure Modeling

    NASA Astrophysics Data System (ADS)

    Liu, Xingchen

    The paradigm of Sample-based Material Structure Modeling is proposed to facilitate the design and manufacturing of material structures towards desired mechanical properties. By modeling material structure samples via a Markov random field, the proposed paradigm views material structure as a collection of neighborhoods. The abstraction facilitates the reconstruction of both periodic and stochastic material structures and extends to the reconstruction and design of spatially varying material structures, a principal mechanism for creating and controlling spatially varying material properties in nature and engineering. The spatially varying material properties are represented and controlled using the notion of material descriptors which include common geometric, statistical, and topological measures such as correlation functions and Minkowski functionals. The proposed method is of particular advantage in preserving the microscopic geometry and related properties of the material structure sample while achieving target macroscopic property distributions during the design of material structures. For material structures that exhibit anisotropy, properly oriented neighborhoods could greatly enhance the efficiency of the material. The expansion of the design space to include the rotation of neighborhoods is appropriate when the properties that need to be preserved can be safely regarded as rotation invariant. With the assumption of orthotropic symmetry, an automatic way to determine the principal axes of neighborhoods for material structure samples with stochastic orientations is proposed. A Green's function based homogenization method is investigated for the efficient evaluation of the mechanical properties of neighborhoods. The formulated integral equation is converted into a system of linear equations which is shown to be symmetric and positive definite with the appropriate reference material properties and can be solved efficiently using the conjugate gradient method

  13. Microcavity Enhanced Raman Scattering

    NASA Astrophysics Data System (ADS)

    Petrak, Benjamin J.

    Raman scattering can accurately identify molecules by their intrinsic vibrational frequencies, but its notoriously weak scattering efficiency for gases presents a major obstacle to its practical application in gas sensing and analysis. This work explores the use of high finesse (≈50 000) Fabry-Perot microcavities as a means to enhance Raman scattering from gases. A recently demonstrated laser ablation method, which carves out a micromirror template on fused silica--either on a fiber tip or bulk substrates-- was implemented, characterized, and optimized to fabricate concave micromirror templates ˜10 mum diameter and radius of curvature. The fabricated templates were coated with a high-reflectivity dielectric coating by ion-beam sputtering and were assembled into microcavities ˜10 mum long and with a mode volume ˜100 mum 3. A novel gas sensing technique that we refer to as Purcell enhanced Raman scattering (PERS) was demonstrated using the assembled microcavities. PERS works by enhancing the pump laser's intensity through resonant recirculation at one longitudinal mode, while simultaneously, at a second mode at the Stokes frequency, the Purcell effect increases the rate of spontaneous Raman scattering by a change to the intra-cavity photon density of states. PERS was shown to enhance the rate of spontaneous Raman scattering by a factor of 107 compared to the same volume of sample gas in free space scattered into the same solid angle subtended by the cavity. PERS was also shown capable of resolving several Raman bands from different isotopes of CO2 gas for application to isotopic analysis. Finally, the use of the microcavity to enhance coherent anti-Stokes Raman scattering (CARS) from CO2 gas was demonstrated.

  14. Soil Gas Sampling

    EPA Pesticide Factsheets

    Field Branches Quality System and Technical Procedures: This document describes general and specific procedures, methods and considerations to be used and observed when collecting soil gas samples for field screening or laboratory analysis.

  15. FIR ACE samples

    NASA Image and Video Library

    2014-06-04

    ISS040-E-007368 (5 June 2014) --- NASA astronaut Reid Wiseman, Expedition 40 flight engineer, works with Advanced Colloids Experiment (ACE) samples in the Destiny laboratory of the International Space Station.

  16. Water Sample Concentrator

    ScienceCinema

    Idaho National Laboratory

    2016-07-12

    Automated portable device that concentrates and packages a sample of suspected contaminated water for safe, efficient transport to a qualified analytical laboratory. This technology will help safeguard against pathogen contamination or chemical and biolog

  17. Sample EPA Biotech Form

    EPA Pesticide Factsheets

    This sample “EPA Biotech Form” is a header sheet that will accompany all biotechnology submission choices, including MCANs, TERAs, Tier I and Tier II exemption, and biotechnology Test Market Exemption Applications (TMEAs).

  18. Preparing Samples on Mars

    NASA Image and Video Library

    2013-02-20

    This figure shows the location of CHIMRA on the turret of NASA Curiosity rover, together with a cutaway view of the device. CHIMRA processes samples from the rover scoop or drill and delivers them to science instruments.

  19. Waste tank sample transport

    SciTech Connect

    Field, J.G.; Mercado, M.S.; Smith, R.J.; Thornton, J.W.

    1994-08-01

    Since 1943, radioactive liquid waste has been stored in underground storage tanks at the Hanford Site in Richland, Washington. The waste was the result of chemical separation processes for the production of fissile defense materials. Associated with the current environmental cleanup mission, waste characterization and processing programs are requiring the extraction of samples from the tanks. Approved onsite packaging are in place and in use for transfers of samples from the tanks to onsite laboratories. Initiatives are under way to develop and procure packaging for sample shipments to offsite laboratories. This paper will provide a current status of the tank sample packaging used at the Hanford Site, as well as the project status for new packaging to be used for offsite shipments.

  20. Water Sample Concentrator

    SciTech Connect

    Idaho National Laboratory

    2009-07-21

    Automated portable device that concentrates and packages a sample of suspected contaminated water for safe, efficient transport to a qualified analytical laboratory. This technology will help safeguard against pathogen contamination or chemical and biolog

  1. Liquid sample processor

    NASA Technical Reports Server (NTRS)

    Jahnsen, V. J.; Campen, C. F., Jr.

    1975-01-01

    Processor is automatic and includes series of extraction tubes packed with fibrous absorbent material of large surface area. When introduced into these tubes, liquid test samples become completely absorbed by packing material as thin film.

  2. Lunar sample contracts

    NASA Technical Reports Server (NTRS)

    Walker, R. M.

    1974-01-01

    The major scientific accomplishments through 1971 are reported for the particle track studies of lunar samples. Results are discussed of nuclear track measurements by optical and electron microscopy, thermoluminescence, X-ray diffraction, and differential thermal analysis.

  3. LACIE sampling design

    NASA Technical Reports Server (NTRS)

    Feiveson, A. H.; Chhikara, R. S.; Hallum, C. R. (Principal Investigator)

    1979-01-01

    The sampling design in LACIE consisted of two major components, one for wheat acreage estimation and one for wheat yield prediction. The acreage design was basically a classical survey for which the sampling unit was a 5- by 6-nautical mile segment; however, there were complications caused by measurement errors and loss of data. Yield was predicted by sampling meteorological data from weather stations within a region and then using those data as input to previously fitted regression equations. Wheat production was not estimated directly, but was computed by multiplying yield and acreage estimates. The allocation of samples to countries is discussed as well as the allocation and selection of segments in strata/substrata.

  4. SWAB Air sampling

    NASA Image and Video Library

    2006-12-08

    ISS014-E-09422 (8 Dec. 2006) --- European Space Agency (ESA) astronaut Thomas Reiter, Expedition 14 flight engineer, conducts a Surface, Water and Air Biocharacterization (SWAB) air sampling in the Destiny laboratory of the International Space Station.

  5. [Foetal sampling techniques].

    PubMed

    Levy, R; Arfi, J-S; Daffos, F

    2003-06-01

    This article describes the current techniques of foetal sampling. All of them are actually ultrasound guided, and therefore generally very safe. Nevertheless, an elaborate learning process remains indispensable, in addition to a particular attention to the quality of the physician-patient dialogue. The choice of a technique depends on the indication and on the term of the pregnancy. The most frequently used technique is amniocentesis which presents a low risk of foetal loss, estimated between 0.2 and 0.5 percent. The interest of chorionic villus sampling is the possibility to obtain results at an earlier stage of pregnancy, with a lower risk taking when compared to early amniocentesis. We prefer the transabdominal chorionic villus sampling to the transvaginal. Foetal blood sampling is still required in some cases, but the risk of complications is higher--around 1 percent.

  6. Sealed container sampling device

    NASA Technical Reports Server (NTRS)

    Hennigan, T. J.

    1969-01-01

    Sampling device, by means of a tapered needle, pierces a sealed container while maintaining the seal and either evacuates or pressurizes the container. This device has many applications in the chemical, preservative and battery-manufacturing industries.

  7. Open port sampling interface

    DOEpatents

    Van Berkel, Gary J

    2017-04-25

    A system for sampling a sample material includes a probe which can have an outer probe housing with an open end. A liquid supply conduit within the housing has an outlet positioned to deliver liquid to the open end of the housing. The liquid supply conduit can be connectable to a liquid supply for delivering liquid at a first volumetric flow rate to the open end of the housing. A liquid exhaust conduit within the housing is provided for removing liquid from the open end of the housing. A liquid exhaust system can be provided for removing liquid from the liquid exhaust conduit at a second volumetric flow rate, the first volumetric flow rate exceeding the second volumetric flow rate, wherein liquid at the open end will receive sample, liquid containing sample material will be drawn into and through the liquid exhaust conduit, and liquid will overflow from the open end.

  8. Sample positioning apparatus

    DOEpatents

    Bell, Thomas H.; Johnson, Jr., Charles H.; Lane, Robert L.; Martin, Bradley E.; Tyree, William H.

    1976-01-06

    Apparatus for use in alpha particle counting with such as photomultiplier tubes, comprising a platform and linkage mechanism whereby samples are moved in linear manner toward and away from ends of the photomultiplier tubes.

  9. SAMPLING AND ANALYSIS PROTOCOLS

    SciTech Connect

    Jannik, T; P Fledderman, P

    2007-02-09

    Radiological sampling and analyses are performed to collect data for a variety of specific reasons covering a wide range of projects. These activities include: Effluent monitoring; Environmental surveillance; Emergency response; Routine ambient monitoring; Background assessments; Nuclear license termination; Remediation; Deactivation and decommissioning (D&D); and Waste management. In this chapter, effluent monitoring and environmental surveillance programs at nuclear operating facilities and radiological sampling and analysis plans for remediation and D&D activities will be discussed.

  10. TANK 5 SAMPLING

    SciTech Connect

    Vrettos, N; William Cheng, W; Thomas Nance, T

    2007-11-26

    Tank 5 at the Savannah River Site has been used to store high level waste and is currently undergoing waste removal processes in preparation for tank closure. Samples were taken from two locations to determine the contents in support of Documented Safety Analysis (DSA) development for chemical cleaning. These samples were obtained through the use of the Drop Core Sampler and the Snowbank Sampler developed by the Engineered Equipment & Systems (EES) group of the Savannah River National Laboratory (SRNL).

  11. Dissolution actuated sample container

    SciTech Connect

    Nance, Thomas A.; McCoy, Frank T.

    2013-03-26

    A sample collection vial and process of using a vial is provided. The sample collection vial has an opening secured by a dissolvable plug. When dissolved, liquids may enter into the interior of the collection vial passing along one or more edges of a dissolvable blocking member. As the blocking member is dissolved, a spring actuated closure is directed towards the opening of the vial which, when engaged, secures the vial contents against loss or contamination.

  12. Lunar Sample Compendium

    NASA Technical Reports Server (NTRS)

    Meyer, Charles

    2005-01-01

    The purpose of the Lunar Sample Compendium will be to inform scientists, astronauts and the public about the various lunar samples that have been returned from the Moon. This Compendium will be organized rock by rock in the manor of a catalog, but will not be as comprehensive, nor as complete, as the various lunar sample catalogs that are available. Likewise, this Compendium will not duplicate the various excellent books and reviews on the subject of lunar samples (Cadogen 1981, Heiken et al. 1991, Papike et al. 1998, Warren 2003, Eugster 2003). However, it is thought that an online Compendium, such as this, will prove useful to scientists proposing to study individual lunar samples and should help provide backup information for lunar sample displays. This Compendium will allow easy access to the scientific literature by briefly summarizing the significant findings of each rock along with the documentation of where the detailed scientific data are to be found. In general, discussion and interpretation of the results is left to the formal reviews found in the scientific literature. An advantage of this Compendium will be that it can be updated, expanded and corrected as need be.

  13. Lunar Samples - Apollo 17

    NASA Image and Video Library

    1972-12-27

    S72-56362 (27 Dec. 1972) --- Scientist-astronaut Harrison H. "Jack" Schmitt (facing camera), Apollo 17 lunar module pilot, was one of the first to look at the sample of "orange" soil which was brought back from the Taurus-Littrow landing site by the Apollo 17 crewmen. Schmitt discovered the material at Shorty Crater during the second Apollo 17 extravehicular activity (EVA). The "orange" sample, which was opened Wednesday, Dec. 27, 1972, is in the bag on a weighing platform in the sealed nitrogen cabinet in the upstairs processing line in the Lunar Receiving Laboratory at the Manned Spacecraft Center. Just before, the sample was removed from one of the bolt-top cans visible to the left in the cabinet. The first reaction of Schmitt was "It doesn't look the same." Most of the geologists and staff viewing the sample agreed that it was more tan and brown than orange. Closer comparison with color charts showed that the sample had a definite orange cast, according the MSC geology branch Chief William Phinney. After closer investigation and sieving, it was discovered that the orange color was caused by very fine spheres and fragments of orange glass in the midst of darker colored, larger grain material. Earlier in the day the "orange" soil was taken from the Apollo Lunar Sample Return Container No. 2 and placed in the bolt-top can (as was all the material in the ALSRC "rock box").

  14. Liquid sampling system

    DOEpatents

    Larson, Loren L.

    1987-01-01

    A conduit extends from a reservoir through a sampling station and back to the reservoir in a closed loop. A jet ejector in the conduit establishes suction for withdrawing liquid from the reservoir. The conduit has a self-healing septum therein upstream of the jet ejector for receiving one end of a double-ended cannula, the other end of which is received in a serum bottle for sample collection. Gas is introduced into the conduit at a gas bleed between the sample collection bottle and the reservoir. The jet ejector evacuates gas from the conduit and the bottle and aspirates a column of liquid from the reservoir at a high rate. When the withdrawn liquid reaches the jet ejector the rate of flow therethrough reduces substantially and the gas bleed increases the pressure in the conduit for driving liquid into the sample bottle, the gas bleed forming a column of gas behind the withdrawn liquid column and interrupting the withdrawal of liquid from the reservoir. In the case of hazardous and toxic liquids, the sample bottle and the jet ejector may be isolated from the reservoir and may be further isolated from a control station containing remote manipulation means for the sample bottle and control valves for the jet ejector and gas bleed.

  15. Liquid sampling system

    DOEpatents

    Larson, L.L.

    1984-09-17

    A conduit extends from a reservoir through a sampling station and back to the reservoir in a closed loop. A jet ejector in the conduit establishes suction for withdrawing liquid from the reservoir. The conduit has a self-healing septum therein upstream of the jet ejector for receiving one end of a double-ended cannula, the other end of which is received in a serum bottle for sample collection. Gas is introduced into the conduit at a gas bleed between the sample collection bottle and the reservoir. The jet ejector evacuates gas from the conduit and the bottle and aspirates a column of liquid from the reservoir at a high rate. When the withdrawn liquid reaches the jet ejector the rate of flow therethrough reduces substantially and the gas bleed increases the pressure in the conduit for driving liquid into the sample bottle, the gas bleed forming a column of gas behind the withdrawn liquid column and interrupting the withdrawal of liquid from the reservoir. In the case of hazardous and toxic liquids, the sample bottle and the jet ejector may be isolated from the reservoir and may be further isolated from a control station containing remote manipulation means for the sample bottle and control valves for the jet ejector and gas bleed. 5 figs.

  16. Recommended protocols for sampling macrofungi

    Treesearch

    Gregory M. Mueller; John Paul Schmit; Sabine M. Hubndorf Leif Ryvarden; Thomas E. O' Dell; D. Jean Lodge; Patrick R. Leacock; Milagro Mata; Loengrin Umania; Qiuxin (Florence) Wu; Daniel L. Czederpiltz

    2004-01-01

    This chapter discusses several issues regarding reommended protocols for sampling macrofungi: Opportunistic sampling of macrofungi, sampling conspicuous macrofungi using fixed-size, sampling small Ascomycetes using microplots, and sampling a fixed number of downed logs.

  17. Sample Return Science

    NASA Astrophysics Data System (ADS)

    Williford, K. H.; Allwood, A.; Beegle, L. W.; Bhartia, R.; Flannery, D.; Hoffmann, A.; Mora, M. F.; Orbay, J.; Petrizzo, D. A.; Tuite, M. L., Jr.; Willis, P. A.

    2014-12-01

    The first clear identification of an ancient habitable environment on Mars by the Mars Science Laboratory (MSL) rover mission relied on a synthetic analytical approach combining orbital and surface imagery and spectroscopy with sophisticated sample acquisition and handling technology including a rotary percussive drill that provided powdered rock for bulk geochemical analysis [1]. The recent announcement of the instrument package for the proposed NASA Mars2020 rover mission, including micro x-ray fluorescence (PIXL) for elemental mapping as well as scanning ultraviolet laser fluorescence and Raman (SHERLOC) suggests a shift in emphasis of Mars surface science towards spatially resolved geochemical analysis that will support the selection and acquisition of samples for coring, caching, and possible return to Earth for further analysis. During a recent field expedition to investigate Archean and Proterozoic biosignatures in the Pilbara region of Western Australia, we deployed a dry, rotary percussive coring drill with a bit assembly analogous to that being considered for Mars2020. Six targets of varying age and lithology were sampled with the coring drill, and surrounding and adjacent rock samples were collected simultaneously. These samples were subsequently prepared and subsampled for bulk and in situ, spatially resolved analysis using conventional laboratory methods as well as the existing PIXL and SHERLOC platforms currently in development. Here we present new approaches and data from this integrated and ongoing program of "sample return science" designed to simulate, and eventually reduce risk associated with a long-term effort towards Mars sample return. [1] Grotzinger, J.P. et al. 2014. Science 343 DOI: 10.1126/science.1242777.

  18. Equilibrium molecular thermodynamics from Kirkwood sampling.

    PubMed

    Somani, Sandeep; Okamoto, Yuko; Ballard, Andrew J; Wales, David J

    2015-05-21

    We present two methods for barrierless equilibrium sampling of molecular systems based on the recently proposed Kirkwood method (J. Chem. Phys. 2009, 130, 134102). Kirkwood sampling employs low-order correlations among internal coordinates of a molecule for random (or non-Markovian) sampling of the high dimensional conformational space. This is a geometrical sampling method independent of the potential energy surface. The first method is a variant of biased Monte Carlo, where Kirkwood sampling is used for generating trial Monte Carlo moves. Using this method, equilibrium distributions corresponding to different temperatures and potential energy functions can be generated from a given set of low-order correlations. Since Kirkwood samples are generated independently, this method is ideally suited for massively parallel distributed computing. The second approach is a variant of reservoir replica exchange, where Kirkwood sampling is used to construct a reservoir of conformations, which exchanges conformations with the replicas performing equilibrium sampling corresponding to different thermodynamic states. Coupling with the Kirkwood reservoir enhances sampling by facilitating global jumps in the conformational space. The efficiency of both methods depends on the overlap of the Kirkwood distribution with the target equilibrium distribution. We present proof-of-concept results for a model nine-atom linear molecule and alanine dipeptide.

  19. Equilibrium Molecular Thermodynamics from Kirkwood Sampling

    PubMed Central

    2015-01-01

    We present two methods for barrierless equilibrium sampling of molecular systems based on the recently proposed Kirkwood method (J. Chem. Phys.2009, 130, 134102). Kirkwood sampling employs low-order correlations among internal coordinates of a molecule for random (or non-Markovian) sampling of the high dimensional conformational space. This is a geometrical sampling method independent of the potential energy surface. The first method is a variant of biased Monte Carlo, where Kirkwood sampling is used for generating trial Monte Carlo moves. Using this method, equilibrium distributions corresponding to different temperatures and potential energy functions can be generated from a given set of low-order correlations. Since Kirkwood samples are generated independently, this method is ideally suited for massively parallel distributed computing. The second approach is a variant of reservoir replica exchange, where Kirkwood sampling is used to construct a reservoir of conformations, which exchanges conformations with the replicas performing equilibrium sampling corresponding to different thermodynamic states. Coupling with the Kirkwood reservoir enhances sampling by facilitating global jumps in the conformational space. The efficiency of both methods depends on the overlap of the Kirkwood distribution with the target equilibrium distribution. We present proof-of-concept results for a model nine-atom linear molecule and alanine dipeptide. PMID:25915525

  20. Deconvolution with Correct Sampling

    NASA Astrophysics Data System (ADS)

    Magain, P.; Courbin, F.; Sohy, S.

    1998-02-01

    A new method for improving the resolution of astronomical images is presented. It is based on the principle that sampled data cannot be fully deconvolved without violating the sampling theorem. Thus, the sampled image should be deconvolved not by the total point-spread function but by a narrower function chosen so that the resolution of the deconvolved image is compatible with the adopted sampling. Our deconvolution method gives results that are, in at least some cases, superior to those of other commonly used techniques: in particular, it does not produce ringing around point sources superposed on a smooth background. Moreover, it allows researchers to perform accurate astrometry and photometry of crowded fields. These improvements are a consequence of both the correct treatment of sampling and the recognition that the most probable astronomical image is not a flat one. The method is also well adapted to the optimal combination of different images of the same object, as can be obtained, e.g., from infrared observations or via adaptive optics techniques.

  1. Fluid sampling system

    DOEpatents

    Houck, E.D.

    1994-10-11

    An fluid sampling system allows sampling of radioactive liquid without spillage. A feed tank is connected to a liquid transfer jet powered by a pumping chamber pressurized by compressed air. The liquid is pumped upwardly into a sampling jet of a venturi design having a lumen with an inlet, an outlet, a constricted middle portion, and a port located above the constricted middle portion. The liquid is passed under pressure through the constricted portion causing its velocity to increase and its pressure to be decreased, thereby preventing liquid from escaping. A septum sealing the port can be pierced by a two pointed hollow needle leading into a sample bottle also sealed by a pierceable septum affixed to one end. The bottle is evacuated by flow through the sample jet, cyclic variation in the sampler jet pressure periodically leaves the evacuated bottle with lower pressure than that of the port, thus causing solution to pass into the bottle. The remaining solution in the system is returned to the feed tank via a holding tank. 4 figs.

  2. Fluid sampling system

    DOEpatents

    Houck, Edward D.

    1994-01-01

    An fluid sampling system allows sampling of radioactive liquid without spillage. A feed tank is connected to a liquid transfer jet powered by a pumping chamber pressurized by compressed air. The liquid is pumped upwardly into a sampling jet of a venturi design having a lumen with an inlet, an outlet, a constricted middle portion, and a port located above the constricted middle portion. The liquid is passed under pressure through the constricted portion causing its velocity to increase and its pressure to decreased, thereby preventing liquid from escaping. A septum sealing the port can be pierced by a two pointed hollow needle leading into a sample bottle also sealed by a pierceable septum affixed to one end. The bottle is evacuated by flow through the sample jet, cyclic variation in the sampler jet pressure periodically leaves the evacuated bottle with lower pressure than that of the port, thus causing solution to pass into the bottle. The remaining solution in the system is returned to the feed tank via a holding tank.

  3. Fluid sampling system

    SciTech Connect

    Houck, E.D.

    1993-12-31

    This invention comprises a fluid sampling system which allows sampling of radioactive liquid without spillage. A feed tank is connected to a liquid transfer jet powered by a pumping chamber pressurized by compressed air. The liquid is pumped up into a sampling jet of venturi design having a lumen with an inlet, an outlet, a constricted middle portion, and a port located above the constricted middle portion. The liquid is passed under pressure through the constricted portion causing its velocity to increase and its pressure to decrease, thereby preventing liquid from escaping. A septum sealing the port can be pierced by a two pointed hollow needle leading into a sample bottle also sealed by a pierceable septum affixed to one end. The bottle is evacuated by flow through the sample jet, cyclic variation in the sampler jet pressure periodicially leaves the evacuated bottle with lower pressure than that of the port, thus causing solution to pass into the bottle. The remaining solution in the system is returned to the feed tank via a holding tank.

  4. Rapid determination of actinides in seawater samples

    DOE PAGES

    Maxwell, Sherrod L.; Culligan, Brian K.; Hutchison, Jay B.; ...

    2014-03-09

    A new rapid method for the determination of actinides in seawater samples has been developed at the Savannah River National Laboratory. The actinides can be measured by alpha spectrometry or inductively-coupled plasma mass spectrometry. The new method employs novel pre-concentration steps to collect the actinide isotopes quickly from 80 L or more of seawater. Actinides are co-precipitated using an iron hydroxide co-precipitation step enhanced with Ti+3 reductant, followed by lanthanum fluoride co-precipitation. Stacked TEVA Resin and TRU Resin cartridges are used to rapidly separate Pu, U, and Np isotopes from seawater samples. TEVA Resin and DGA Resin were used tomore » separate and measure Pu, Am and Cm isotopes in seawater volumes up to 80 L. This robust method is ideal for emergency seawater samples following a radiological incident. It can also be used, however, for the routine analysis of seawater samples for oceanographic studies to enhance efficiency and productivity. In contrast, many current methods to determine actinides in seawater can take 1–2 weeks and provide chemical yields of ~30–60 %. This new sample preparation method can be performed in 4–8 h with tracer yields of ~85–95 %. By employing a rapid, robust sample preparation method with high chemical yields, less seawater is needed to achieve lower or comparable detection limits for actinide isotopes with less time and effort.« less

  5. Rapid determination of actinides in seawater samples

    SciTech Connect

    Maxwell, Sherrod L.; Culligan, Brian K.; Hutchison, Jay B.; Utsey, Robin C.; McAlister, Daniel R.

    2014-03-09

    A new rapid method for the determination of actinides in seawater samples has been developed at the Savannah River National Laboratory. The actinides can be measured by alpha spectrometry or inductively-coupled plasma mass spectrometry. The new method employs novel pre-concentration steps to collect the actinide isotopes quickly from 80 L or more of seawater. Actinides are co-precipitated using an iron hydroxide co-precipitation step enhanced with Ti+3 reductant, followed by lanthanum fluoride co-precipitation. Stacked TEVA Resin and TRU Resin cartridges are used to rapidly separate Pu, U, and Np isotopes from seawater samples. TEVA Resin and DGA Resin were used to separate and measure Pu, Am and Cm isotopes in seawater volumes up to 80 L. This robust method is ideal for emergency seawater samples following a radiological incident. It can also be used, however, for the routine analysis of seawater samples for oceanographic studies to enhance efficiency and productivity. In contrast, many current methods to determine actinides in seawater can take 1–2 weeks and provide chemical yields of ~30–60 %. This new sample preparation method can be performed in 4–8 h with tracer yields of ~85–95 %. By employing a rapid, robust sample preparation method with high chemical yields, less seawater is needed to achieve lower or comparable detection limits for actinide isotopes with less time and effort.

  6. Thermoluminescence of lunar samples

    USGS Publications Warehouse

    Dalrymple, G.B.; Doell, Richard R.

    1970-01-01

    Appreciable natural thermoluminescence with glow curve peaks at about 350 degrees centigrade for lunar fines and breccias and above 400 degrees centigrade for crystalline rocks has been recognized in lunar samples. Plagioclase has been identified as the principal carrier of thermoluminescence, and the difference in peak temperatures indicates compositional or structural differences between the feldspars of the different rock types. The present thermoluminescence in the lunar samples is probably the result of a dynamic equilibrium between acquisition from radiation and loss in the lunar thermal environment. A progressive change in the glow curves of core samples with depth below the surface suggests the use of thermoluminescence disequilibrium to detect surfaces buried by recent surface activity, and it also indicates that the lunar diurnal temperature variation penetrates to at least 10.5 centimeters.

  7. Sampling inhomogeneous turbulent fields

    NASA Technical Reports Server (NTRS)

    Adrian, R. J.; Moin, P.; Moser, R. D.

    1988-01-01

    The reconstruction of an inhomogeneous random process from a finite number of discrete samples can be performed in terms of the Karhunen-Loeve (KL) expansion for that process. The n(th) eigenfunction has n - 1 zero crossings which are the sampling points for the inhomogeneous process. The rapid variation of the KL eigenfunctions makes it unnecessary to have a high density of sampling (or grid points) near the wall. However, this result should not be construed to indicate that with spectral simulations significantly fewer grid points are required with the KL expansion as compared to other orthogonal expansions. Moin and Moser (1989) have shown that the advantage of the KL expansion over Chebychev expansion rapidly diminishes when high percentage (say 90 percent) energy recovery is demanded.

  8. INEL Sample Management Office

    SciTech Connect

    Watkins, C.

    1994-12-31

    The Idaho National Engineering Laboratory (INEL) Sample Management Office (SMO) was formed as part of the EG&G Idaho Environmental Restoration Program (ERP) in June, 1990. Since then, the SMO has been recognized and sought out by other prime contractors and programs at the INEL. Since December 1991, the DOE-ID Division Directors for the Environmental Restoration Division and Waste Management Division supported the expansion of the INEL ERP SMO into the INEL site wide SMO. The INEL SMO serves as a point of contact for multiple environmental analytical chemistry and laboratory issues (e.g., capacity, capability). The SMO chemists work with project managers during planning to help develop data quality objectives, select appropriate analytical methods, identify special analytical services needs, identify a source for the services, and ensure that requirements for sampling and analysis (e.g., preservations, sample volumes) are clear and technically accurate. The SMO chemists also prepare work scope statements for the laboratories performing the analyses.

  9. Viscous sludge sample collector

    DOEpatents

    Beitel, George A [Richland, WA

    1983-01-01

    A vertical core sample collection system for viscous sludge. A sample tube's upper end has a flange and is attached to a piston. The tube and piston are located in the upper end of a bore in a housing. The bore's lower end leads outside the housing and has an inwardly extending rim. Compressed gas, from a storage cylinder, is quickly introduced into the bore's upper end to rapidly accelerate the piston and tube down the bore. The lower end of the tube has a high sludge entering velocity to obtain a full-length sludge sample without disturbing strata detail. The tube's downward motion is stopped when its upper end flange impacts against the bore's lower end inwardly extending rim.

  10. Experimental scattershot boson sampling

    PubMed Central

    Bentivegna, Marco; Spagnolo, Nicolò; Vitelli, Chiara; Flamini, Fulvio; Viggianiello, Niko; Latmiral, Ludovico; Mataloni, Paolo; Brod, Daniel J.; Galvão, Ernesto F.; Crespi, Andrea; Ramponi, Roberta; Osellame, Roberto; Sciarrino, Fabio

    2015-01-01

    Boson sampling is a computational task strongly believed to be hard for classical computers, but efficiently solvable by orchestrated bosonic interference in a specialized quantum computer. Current experimental schemes, however, are still insufficient for a convincing demonstration of the advantage of quantum over classical computation. A new variation of this task, scattershot boson sampling, leads to an exponential increase in speed of the quantum device, using a larger number of photon sources based on parametric down-conversion. This is achieved by having multiple heralded single photons being sent, shot by shot, into different random input ports of the interferometer. We report the first scattershot boson sampling experiments, where six different photon-pair sources are coupled to integrated photonic circuits. We use recently proposed statistical tools to analyze our experimental data, providing strong evidence that our photonic quantum simulator works as expected. This approach represents an important leap toward a convincing experimental demonstration of the quantum computational supremacy. PMID:26601164

  11. Core sample extractor

    NASA Technical Reports Server (NTRS)

    Akins, James; Cobb, Billy; Hart, Steve; Leaptrotte, Jeff; Milhollin, James; Pernik, Mark

    1989-01-01

    The problem of retrieving and storing core samples from a hole drilled on the lunar surface is addressed. The total depth of the hole in question is 50 meters with a maximum diameter of 100 millimeters. The core sample itself has a diameter of 60 millimeters and will be two meters in length. It is therefore necessary to retrieve and store 25 core samples per hole. The design utilizes a control system that will stop the mechanism at a certain depth, a cam-linkage system that will fracture the core, and a storage system that will save and catalogue the cores to be extracted. The Rod Changer and Storage Design Group will provide the necessary tooling to get into the hole as well as to the core. The mechanical design for the cam-linkage system as well as the conceptual design of the storage device are described.

  12. [INSEE's permanent demographic sample].

    PubMed

    Sautory, O

    1987-01-01

    This article discusses the permanent demographic sample survey developed by France's Institut National de la Statistique et des Etudes Economiques (INSEE), which has been in use in that country since the census of 1968. Approximately one percent of the metropolitan population of France was chosen for inclusion by birthdate. By adding data on marriage, births of children, change of residence, schooling, employment status, and death to each person's file, longitudinal studies of fertility, nuptiality, and mortality can be conducted. Two such studies are included as examples of how the permanent sample survey can be best put to use.

  13. Contamination sampling device

    NASA Technical Reports Server (NTRS)

    Delgado, Felix A. (Inventor); Stern, Susan M. (Inventor)

    1998-01-01

    A contamination sample collection device has a wooden dowel with a cotton swab at one end, the cotton being covered by a nylon cloth and the wooden dowel being encapsulated by plastic tubing which is heat shrunk onto the dowel and onto a portion of the cotton swab to secure the cotton in place. Another plastic tube is heat shrunk onto the plastic that encapsulates the dowel and a portion of the nylon cloth to secure the nylon cloth in place. The device may thereafter be covered with aluminum foil protector. The device may be used for obtaining samples of contamination in clean room environments.

  14. diamond-sampling

    SciTech Connect

    Ballard, Grey; Kolda, Tamara; Pinar, Ali

    2016-01-26

    This software provides a means for computing only the largest few entries of the product of two matrices, both exactly and approximately (using randomized sampling techniques). The purpose of the code is to demonstrate both the time it takes to solve the problem as well as the accuracy of the approximate approach. It is also meant to serve as a foundation to test the applicability of the sampling technique to related problems in data mining, including maximum inner product search, nearest neighbor search, and maximum cosine similarity.

  15. Lunar Samples - Apollo 12

    NASA Image and Video Library

    1969-11-28

    S69-60354 (29 Nov. 1969) --- A scientist's gloved hand holds one of the numerous rock samples brought back to Earth from the Apollo 12 lunar landing mission. The rocks are under thorough examination in the Manned Spacecraft Center's (MSC) Lunar Receiving Laboratory (LRL). This sample is a highly shattered basaltic rock with a thin black-glass coating on five of its six sides. Glass fills fractures and cements the rock together. The rock appears to have been shattered and thrown out by a meteorite impact explosion and coated with molten rock material before the rock fell to the surface.

  16. Lunar Samples - Apollo 12

    NASA Image and Video Library

    1969-12-02

    S69-60580 (November 1969) --- Close-up view of Apollo 12 sample 12,065 under observation in the Manned Spacecraft Center's (MSC) Lunar Receiving Laboratory (LRL). This sample, collected during the second Apollo 12 extravehicular activity (EVA) of astronauts Charles Conrad Jr. and Alan L. Bean, is a fine-grained rock. Note the glass-lined pits. Viewer can gain an idea of the size of the rock by reference to the gauge on the bottom portion of the number meter.

  17. Returning Samples from Enceladus

    NASA Astrophysics Data System (ADS)

    Tsou, P.; Kanik, I.; Brownlee, D.; McKay, C.; Anbar, A.; Glavin, D.; Yano, H.

    2012-12-01

    From the first half century of space exploration, we have obtained samples only from the Moon, comet Wild 2, the Solar Wind and the asteroid Itokawa. The in-depth analyses of these samples in terrestrial laboratories have yielded profound knowledge that could not have been obtained without the returned samples. While obtaining samples from Solar System bodies is crucial science, it is rarely done due to cost and complexity. Cassini's discovery of geysers on Enceladus and organic materials, indicate that there is an exceptional opportunity and science rational to do a low-cost flyby sample return mission, similar to what was done by the Stardust. The earliest low cost possible flight opportunity is the next Discovery Mission [Tsou et al 2012]. Enceladus Plume Discovery - While Voyager provided evidence for young surfaces on Enceladus, the existence of Enceladus plumes was discovered by Cassini. Enceladus and comets are the only known solar system bodies that have jets enabling sample collection without landing or surface contact. Cassini in situ Findings -Cassini's made many discoveries at Saturn, including the break up of large organics in the plumes of Enceladus. Four prime criteria for habitability are liquid water, a heat source, organics and nitrogen [McKay et al. 2008, Waite et al. 2009, Postberg et al. 2011]. Out of all the NASA designated habitability targets, Enceladus is the single body that presents evidence for all four criteria. Significant advancement in the exploration of the biological potential of Enceladus can be made on returned samples in terrestrial laboratories where the full power of state-of-the-art laboratory instrumentation and procedures can be used. Without serious limits on power, mass or even cost, terrestrial laboratories provide the ultimate in analytical capability, adaptability, reproducibility and reliability. What Questions can Samples Address? - Samples collected from the Enceladus plume will enable a thorough and replicated

  18. Lunar sample analysis

    NASA Technical Reports Server (NTRS)

    Housley, R. M.

    1978-01-01

    Flameless atomic abosrption, X-ray photoemission spectroscopy, ferromagnetic resonance, scanning electron microscopy, and Moessbauer spectroscopy were used to investigate the evolution of the lunar regolith, the transport of volatile trace metals, and the surface composition of lunar samples. The development of a model for lunar volcanic eruptions is also discussed.

  19. Randomization and sampling issues

    USGS Publications Warehouse

    Geissler, P.H.

    1996-01-01

    The need for randomly selected routes and other sampling issues have been debated by the Amphibian electronic discussion group. Many excellent comments have been made, pro and con, but we have not reached consensus yet. This paper brings those comments together and attempts a synthesis. I hope that the resulting discussion will bring us closer to a consensus.

  20. Sampling for Chemical Analysis.

    ERIC Educational Resources Information Center

    Kratochvil, Byron; And Others

    1984-01-01

    This review, designed to make analysts aware of uncertainties introduced into analytical measurements during sampling, is organized under these headings: general considerations; theory; standards; and applications related to mineralogy, soils, sediments, metallurgy, atmosphere, water, biology, agriculture and food, medical and clinical areas, oil…