WorldWideScience

Sample records for large biological sample

  1. Biological sample collector

    Science.gov (United States)

    Murphy, Gloria A.

    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.

  2. Large Pelagics Biological Survey

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Large Pelagics Biological Survey (LPBS) collects additional length and weight information and body parts such as otoliths, caudal vertebrae, dorsal spines, and...

  3. Enhanced Biological Sampling Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This is a database of a variety of biological, reproductive, and energetic data collected from fish on the continental shelf in the northwest Atlantic Ocean. Species...

  4. A Feedfordward Adaptive Controller to Reduce the Imaging Time of Large-Sized Biological Samples with a SPM-Based Multiprobe Station

    Directory of Open Access Journals (Sweden)

    Manel Puig-Vidal

    2012-01-01

    Full Text Available The time required to image large samples is an important limiting factor in SPM-based systems. In multiprobe setups, especially when working with biological samples, this drawback can make impossible to conduct certain experiments. In this work, we present a feedfordward controller based on bang-bang and adaptive controls. The controls are based in the difference between the maximum speeds that can be used for imaging depending on the flatness of the sample zone. Topographic images of Escherichia coli bacteria samples were acquired using the implemented controllers. Results show that to go faster in the flat zones, rather than using a constant scanning speed for the whole image, speeds up the imaging process of large samples by up to a 4x factor.

  5. Biological Sampling Variability Study

    Energy Technology Data Exchange (ETDEWEB)

    Amidan, Brett G. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Hutchison, Janine R. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2016-11-08

    There are many sources of variability that exist in the sample collection and analysis process. This paper addresses many, but not all, sources of variability. The main focus of this paper was to better understand and estimate variability due to differences between samplers. Variability between days was also studied, as well as random variability within each sampler. Experiments were performed using multiple surface materials (ceramic and stainless steel), multiple contaminant concentrations (10 spores and 100 spores), and with and without the presence of interfering material. All testing was done with sponge sticks using 10-inch by 10-inch coupons. Bacillus atrophaeus was used as the BA surrogate. Spores were deposited using wet deposition. Grime was coated on the coupons which were planned to include the interfering material (Section 3.3). Samples were prepared and analyzed at PNNL using CDC protocol (Section 3.4) and then cultured and counted. Five samplers were trained so that samples were taken using the same protocol. Each sampler randomly sampled eight coupons each day, four coupons with 10 spores deposited and four coupons with 100 spores deposited. Each day consisted of one material being tested. The clean samples (no interfering materials) were run first, followed by the dirty samples (coated with interfering material). There was a significant difference in recovery efficiency between the coupons with 10 spores deposited (mean of 48.9%) and those with 100 spores deposited (mean of 59.8%). There was no general significant difference between the clean and dirty (containing interfering material) coupons or between the two surface materials; however, there was a significant interaction between concentration amount and presence of interfering material. The recovery efficiency was close to the same for coupons with 10 spores deposited, but for the coupons with 100 spores deposited, the recovery efficiency for the dirty samples was significantly larger (65

  6. Querying Large Biological Network Datasets

    Science.gov (United States)

    Gulsoy, Gunhan

    2013-01-01

    New experimental methods has resulted in increasing amount of genetic interaction data to be generated every day. Biological networks are used to store genetic interaction data gathered. Increasing amount of data available requires fast large scale analysis methods. Therefore, we address the problem of querying large biological network datasets.…

  7. Evaluation of the programmed temperature vaporiser for large-volume injection of biological samples in gas chromatography

    NARCIS (Netherlands)

    van Hout, M.W J; de Zeeuw, R.A; Franke, J.P.; de Jong, G.J.

    1999-01-01

    The use of a programmed temperature vaporiser (PTV) with a packed liner was evaluated for the injection of large volumes (up to 100 mu l) of plasma extracts in a gas chromatograph. Solvent purity, which is essential when large volumes are injected into the GC system, was determined. Special attentio

  8. Biological Sample Monitoring Database (BSMDBS)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Biological Sample Monitoring Database System (BSMDBS) was developed for the Northeast Fisheries Regional Office and Science Center (NER/NEFSC) to record and...

  9. A Review of Biological Agent Sampling Methods and ...

    Science.gov (United States)

    Report This study was conducted to evaluate current sampling and analytical capabilities, from a time and resource perspective, for a large-scale biological contamination incident. The analysis will be useful for strategically directing future research investment.

  10. Biological Environmental Sampling Technologies Assessment

    Science.gov (United States)

    2015-12-01

    with many identifier platforms, including PCR, immunoassay, LFI, other immunoassays, gene sequencing, culturing , flow cytometry, and many other...Aquila 1000 instrument. Figure 7. Q-linea Aquila 1000 instrument. Vendor: Q-linea AB; Uppsala, Sweden Phone: +46.0.18.444.36.10 Website...and methods: Polymerase Chain Reaction (PCR), immunoassay, gene sequencing, culturing , etc... There must be enough collected sample remaining after

  11. Sample preparation in biological mass spectrometry

    CERN Document Server

    Ivanov, Alexander R

    2011-01-01

    The aim of this book is to provide the researcher with important sample preparation strategies in a wide variety of analyte molecules, specimens, methods, and biological applications requiring mass spectrometric analysis as a detection end-point.

  12. Fluorine ion transmission through thin biological samples

    Institute of Scientific and Technical Information of China (English)

    XueJian-Ming; WangYu-Gang; 等

    1998-01-01

    F2+ beam with 3MeV is used to irradiate thin biological samples(onion inner suface membrane and kidney bean coat)in the transmission measurement ,its current density is 400-800nA/cm2,Results show that the onion samples can be broken up quickly under ion irradiating;as to kidney bean samples,about 60% of the implanted ions penetrate the samples,most of them lose part of their eneregy,fewer ions are found to be able to transmit through the sample without energy loss.SEM experiments are carried out to study sample's damage induced by the ions irradiation.

  13. Modular microfluidic system for biological sample preparation

    Energy Technology Data Exchange (ETDEWEB)

    Rose, Klint A.; Mariella, Jr., Raymond P.; Bailey, Christopher G.; Ness, Kevin Dean

    2015-09-29

    A reconfigurable modular microfluidic system for preparation of a biological sample including a series of reconfigurable modules for automated sample preparation adapted to selectively include a) a microfluidic acoustic focusing filter module, b) a dielectrophoresis bacteria filter module, c) a dielectrophoresis virus filter module, d) an isotachophoresis nucleic acid filter module, e) a lyses module, and f) an isotachophoresis-based nucleic acid filter.

  14. Discovering biological progression underlying microarray samples.

    Directory of Open Access Journals (Sweden)

    Peng Qiu

    2011-04-01

    Full Text Available In biological systems that undergo processes such as differentiation, a clear concept of progression exists. We present a novel computational approach, called Sample Progression Discovery (SPD, to discover patterns of biological progression underlying microarray gene expression data. SPD assumes that individual samples of a microarray dataset are related by an unknown biological process (i.e., differentiation, development, cell cycle, disease progression, and that each sample represents one unknown point along the progression of that process. SPD aims to organize the samples in a manner that reveals the underlying progression and to simultaneously identify subsets of genes that are responsible for that progression. We demonstrate the performance of SPD on a variety of microarray datasets that were generated by sampling a biological process at different points along its progression, without providing SPD any information of the underlying process. When applied to a cell cycle time series microarray dataset, SPD was not provided any prior knowledge of samples' time order or of which genes are cell-cycle regulated, yet SPD recovered the correct time order and identified many genes that have been associated with the cell cycle. When applied to B-cell differentiation data, SPD recovered the correct order of stages of normal B-cell differentiation and the linkage between preB-ALL tumor cells with their cell origin preB. When applied to mouse embryonic stem cell differentiation data, SPD uncovered a landscape of ESC differentiation into various lineages and genes that represent both generic and lineage specific processes. When applied to a prostate cancer microarray dataset, SPD identified gene modules that reflect a progression consistent with disease stages. SPD may be best viewed as a novel tool for synthesizing biological hypotheses because it provides a likely biological progression underlying a microarray dataset and, perhaps more importantly, the

  15. LOGISTICS OF ECOLOGICAL SAMPLING ON LARGE RIVERS

    Science.gov (United States)

    The objectives of this document are to provide an overview of the logistical problems associated with the ecological sampling of boatable rivers and to suggest solutions to those problems. It is intended to be used as a resource for individuals preparing to collect biological dat...

  16. LOGISTICS OF ECOLOGICAL SAMPLING ON LARGE RIVERS

    Science.gov (United States)

    The objectives of this document are to provide an overview of the logistical problems associated with the ecological sampling of boatable rivers and to suggest solutions to those problems. It is intended to be used as a resource for individuals preparing to collect biological dat...

  17. [The ethical implications of conserving biological samples].

    Science.gov (United States)

    Tazzite, A; Roky, R; Avard, D

    2009-09-01

    The conservation and use of biological samples become more and more frequent all around the world. Biobanks of human body substances (blood, urine, DNA, tissues, cells, etc.), and personal data associated with them are created. They have a double character as they are collections of both human biological samples and personal data. In some cases, the gametes, reproductive tissues, embryos, foetal tissue after abortion or even specimens of dead donors are collected and conserved. Although biobanks raise hopes in both the development of new therapies, new drugs and their integration into clinical medicine, they also point to concerns related to ethical questions such as: the principles of information, the consent of the persons concerned, the confidentiality about the personal data, and in some cases discrimination and stigmatisation. Other ethical aspects could raise gradually as research advance. Research being carried out on human sample requires informed free consent from the person who should be able to consent. The donor must be sufficiently informed about the process of research, the purpose, benefits and the risks involved in participating in this research. In the case of persons unable to give consent such minors or persons with mental disabilities, special measures are undertaken. Once the consent was given, the right of withdrawal has been consistently supported by the various declarations and regulations, but some oppose this right for a number of reasons particularly in the case of research on the samples without risk of physical exposure. In this case the notion of human body integrity is different than in research involving therapeutic or clinical intervention. In the case of withdrawal of consent, the samples should be destroyed, but the anonymous results arising from them and their analysis are not affected. What is the case for future uses? Should the researcher obtain again the consent from the donor for a secondary use of the samples? This is a

  18. Atomic force microscopy of biological samples

    Energy Technology Data Exchange (ETDEWEB)

    Doktycz, Mitchel John [ORNL

    2010-01-01

    The ability to evaluate structural-functional relationships in real time has allowed scanning probe microscopy (SPM) to assume a prominent role in post genomic biological research. In this mini-review, we highlight the development of imaging and ancillary techniques that have allowed SPM to permeate many key areas of contemporary research. We begin by examining the invention of the scanning tunneling microscope (STM) by Binnig and Rohrer in 1982 and discuss how it served to team biologists with physicists to integrate high-resolution microscopy into biological science. We point to the problems of imaging nonconductive biological samples with the STM and relate how this led to the evolution of the atomic force microscope (AFM) developed by Binnig, Quate, and Gerber, in 1986. Commercialization in the late 1980s established SPM as a powerful research tool in the biological research community. Contact mode AFM imaging was soon complemented by the development of non-contact imaging modes. These non-contact modes eventually became the primary focus for further new applications including the development of fast scanning methods. The extreme sensitivity of the AFM cantilever was recognized and has been developed into applications for measuring forces required for indenting biological surfaces and breaking bonds between biomolecules. Further functional augmentation to the cantilever tip allowed development of new and emerging techniques including scanning ion-conductance microscopy (SICM), scanning electrochemical microscope (SECM), Kelvin force microscopy (KFM) and scanning near field ultrasonic holography (SNFUH).

  19. Atomic force microscopy of biological samples.

    Science.gov (United States)

    Allison, David P; Mortensen, Ninell P; Sullivan, Claretta J; Doktycz, Mitchel J

    2010-01-01

    The ability to evaluate structural-functional relationships in real time has allowed scanning probe microscopy (SPM) to assume a prominent role in post genomic biological research. In this mini-review, we highlight the development of imaging and ancillary techniques that have allowed SPM to permeate many key areas of contemporary research. We begin by examining the invention of the scanning tunneling microscope (STM) by Binnig and Rohrer in 1982 and discuss how it served to team biologists with physicists to integrate high-resolution microscopy into biological science. We point to the problems of imaging nonconductive biological samples with the STM and relate how this led to the evolution of the atomic force microscope (AFM) developed by Binnig, Quate, and Gerber, in 1986. Commercialization in the late 1980s established SPM as a powerful research tool in the biological research community. Contact mode AFM imaging was soon complemented by the development of non-contact imaging modes. These non-contact modes eventually became the primary focus for further new applications including the development of fast scanning methods. The extreme sensitivity of the AFM cantilever was recognized and has been developed into applications for measuring forces required for indenting biological surfaces and breaking bonds between biomolecules. Further functional augmentation to the cantilever tip allowed development of new and emerging techniques including scanning ion-conductance microscopy (SICM), scanning electrochemical microscope (SECM), Kelvin force microscopy (KFM) and scanning near field ultrasonic holography (SNFUH). © 2010 John Wiley & Sons, Inc.

  20. The application of ESEM to biological samples

    Energy Technology Data Exchange (ETDEWEB)

    McGregor, J E; Donald, A M, E-mail: jem60@cam.ac.u [Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 OHE (United Kingdom)

    2010-07-01

    The Environmental Scanning Electron Microscope (ESEM) differs from a conventional SEM in that a differential pumping system maintains a pressure of gas (typically H{sub 2}O) in the specimen chamber whilst the gun remains at high vacuum. Ionizing collisions between electrons and these gas molecules create positive ions which drift down onto the sample neutralising specimen charge. It is therefore possible to image insulating samples without the need for metallic coating. The presence of water vapour in the chamber also means that a high relative humidity can be maintained and samples can be imaged in a hydrated state without the need for dehydration and fixation. These features suggest that ESEM could be well suited to imaging biological samples undergoing natural biological processes. We present a proof of principle study on the closure of stomatal pores in Tradescantia andersonia leaf tissue. An imaging protocol is developed and the advantages and limitations of this technique are discussed. Images of Vicia fabaleaf tissue are also presented. Challenges include minimising beam damage and reconciling the need for an adequate physiological temperature and a low gas pressure favourable for imaging, with the thermodynamic constraints on achieving a high relative humidity.

  1. Accelerator mass spectrometry of small biological samples.

    Science.gov (United States)

    Salehpour, Mehran; Forsgard, Niklas; Possnert, Göran

    2008-12-01

    Accelerator mass spectrometry (AMS) is an ultra-sensitive technique for isotopic ratio measurements. In the biomedical field, AMS can be used to measure femtomolar concentrations of labeled drugs in body fluids, with direct applications in early drug development such as Microdosing. Likewise, the regenerative properties of cells which are of fundamental significance in stem-cell research can be determined with an accuracy of a few years by AMS analysis of human DNA. However, AMS nominally requires about 1 mg of carbon per sample which is not always available when dealing with specific body substances such as localized, organ-specific DNA samples. Consequently, it is of analytical interest to develop methods for the routine analysis of small samples in the range of a few tens of microg. We have used a 5 MV Pelletron tandem accelerator to study small biological samples using AMS. Different methods are presented and compared. A (12)C-carrier sample preparation method is described which is potentially more sensitive and less susceptible to contamination than the standard procedures.

  2. Measurement of NO in biological samples.

    Science.gov (United States)

    Csonka, C; Páli, T; Bencsik, P; Görbe, A; Ferdinandy, P; Csont, T

    2015-03-01

    Although the physiological regulatory function of the gasotransmitter NO (a diatomic free radical) was discovered decades ago, NO is still in the frontline research in biomedicine. NO has been implicated in a variety of physiological and pathological processes; therefore, pharmacological modulation of NO levels in various tissues may have significant therapeutic value. NO is generated by NOS in most of cell types and by non-enzymatic reactions. Measurement of NO is technically difficult due to its rapid chemical reactions with a wide range of molecules, such as, for example, free radicals, metals, thiols, etc. Therefore, there are still several contradictory findings on the role of NO in different biological processes. In this review, we briefly discuss the major techniques suitable for measurement of NO (electron paramagnetic resonance, electrochemistry, fluorometry) and its derivatives in biological samples (nitrite/nitrate, NOS, cGMP, nitrosothiols) and discuss the advantages and disadvantages of each method. We conclude that to obtain a meaningful insight into the role of NO and NO modulator compounds in physiological or pathological processes, concomitant assessment of NO synthesis, NO content, as well as molecular targets and reaction products of NO is recommended.

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

    Science.gov (United States)

    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.

  4. [Biological material sampling for atomic absorption analysis].

    Science.gov (United States)

    Makarenko, N P; Ganebnykh, E V

    2007-01-01

    The optimum conditions have been chosen for mineralization of biological material for the atomic absorption determination of toxic metals, by using a [Russian characters: see text]-01 laboratory furnace (Gefest) upon exposure to high temperature, pressure, and microwave field. The completeness of dissection of biological material by microwave mineralization is shown under the optimal conditions.

  5. Biological Sample Ambient Preservation (BioSAP) Device Project

    Data.gov (United States)

    National Aeronautics and Space Administration — To address NASA's need for alternative methods for ambient preservation of human biological samples collected during extended spaceflight and planetary operations,...

  6. Biological Fingerprinting of Herbal Samples by Means of Liquid Chromatography

    Directory of Open Access Journals (Sweden)

    Łukasz Cieśla

    2012-01-01

    Full Text Available Biological chromatographic fingerprinting is a relatively new concept in the quality control of herbal samples. Originally it has been developed with the application of HPLC, and recently herbal samples' biological profiles have been obtained by means of thin-layer chromatography (TLC. This paper summarizes the application of liquid chromatographic techniques for the purpose of biological fingerprint analysis (BFA of complex herbal samples. In case of biological TLC fingerprint, which is a relatively novel solution, perspectives of its further development are outlined in more detail. Apart from already published data, some novel results are also shown and briefly discussed. The paper aims at drawing scientists' attention to the unique solutions offered by biological fingerprint construction.

  7. Manipulation of biological samples using micro and nano techniques

    DEFF Research Database (Denmark)

    Castillo, Jaime; Dimaki, Maria; Svendsen, Winnie Edith

    2009-01-01

    The constant interest in handling, integrating and understanding biological systems of interest for the biomedical field, the pharmaceutical industry and the biomaterial researchers demand the use of techniques that allow the manipulation of biological samples causing minimal or no damage to thei...

  8. Micro and Nano Techniques for the Handling of Biological Samples

    DEFF Research Database (Denmark)

    Micro and Nano Techniques for the Handling of Biological Samples reviews the different techniques available to manipulate and integrate biological materials in a controlled manner, either by sliding them along a surface (2-D manipulation), or by gripping and moving them to a new position (3-D man...

  9. Micro and Nano Techniques for the Handling of Biological Samples

    DEFF Research Database (Denmark)

    Micro and Nano Techniques for the Handling of Biological Samples reviews the different techniques available to manipulate and integrate biological materials in a controlled manner, either by sliding them along a surface (2-D manipulation), or by gripping and moving them to a new position (3-D...

  10. [Biological Advisory Subcommittee Sampling Methods : Results, Resolutions, and Correspondences : 2002

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This document contains a variety of information concerning Biological Advisory Subcommittee sampling methods at the Rocky Mountain Arsenal Refuge in 2002. Multiple...

  11. Large Whale Biology Survey (DE9908, EK500)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The large whale biology survey primarily focuses on right whales in the coastal and continental shelf areas, with the following objectives: 1) Develop a better...

  12. Gene coexpression measures in large heterogeneous samples using count statistics.

    Science.gov (United States)

    Wang, Y X Rachel; Waterman, Michael S; Huang, Haiyan

    2014-11-18

    With the advent of high-throughput technologies making large-scale gene expression data readily available, developing appropriate computational tools to process these data and distill insights into systems biology has been an important part of the "big data" challenge. Gene coexpression is one of the earliest techniques developed that is still widely in use for functional annotation, pathway analysis, and, most importantly, the reconstruction of gene regulatory networks, based on gene expression data. However, most coexpression measures do not specifically account for local features in expression profiles. For example, it is very likely that the patterns of gene association may change or only exist in a subset of the samples, especially when the samples are pooled from a range of experiments. We propose two new gene coexpression statistics based on counting local patterns of gene expression ranks to take into account the potentially diverse nature of gene interactions. In particular, one of our statistics is designed for time-course data with local dependence structures, such as time series coupled over a subregion of the time domain. We provide asymptotic analysis of their distributions and power, and evaluate their performance against a wide range of existing coexpression measures on simulated and real data. Our new statistics are fast to compute, robust against outliers, and show comparable and often better general performance.

  13. Solid-phase microextraction for the analysis of biological samples

    NARCIS (Netherlands)

    Theodoridis, G; Koster, EHM; de Jong, GJ

    2000-01-01

    Solid-phase microextraction (SPME) has been introduced for the extraction of organic compounds from environmental samples. This relatively new extraction technique has now also gained a lot of interest in a broad field of analysis including food, biological and pharmaceutical samples. SPME has a num

  14. Field-Flow Fractionation Analysis of Complex Biological Samples

    Directory of Open Access Journals (Sweden)

    Mijić, I.

    2014-03-01

    Full Text Available Normal analytical methods have difficulties when analysing complex samples containing particles of different size. In the 1960s, a new analytical technique was developed, which was able to overcome those difficulties. This new, Field-Flow Fractionation (FFF technique has been primarily used in the separation of large particles such as macromolecules and colloids. The development and improvement of the FFF technique led to the coupling of the technique with other specific and sensitive analytical methods which resulted in the FFF technique becoming very useful in isolation, separation and analysis of various complex samples, such as powders, emulsions, colloids, geological sediments, biopolymers, complex proteins, polysaccharides, synthetic polymers, and many others. The separation field in the FFF technique is a thin, empty flow chamber called a channel. The structure of the ribbonlike channel with view of the parabolic flow can be seen in Fig. 1. Separation is achieved by the interaction of sample components with an externally generated field, which is applied perpendicularly to the direction of the mobile flow inside the channel. Sample components, which differ in molar mass, size or other properties are pushed by the applied perpendicular field into different velocity regions within the parabolic flow profile of the mobile phase across the channel. The flow has different velocity depending on the position within the channel; the velocity at the walls is zero and it increases towards the centre of the channel. Samples are carried downstream through the channel at different velocities and exit the channel after different retention times. The relative distribution of samples in the parabolic flow determines the separation characteristics. Different operating modes have different types of distributions. The most frequently used mechanisms of FFF separation are listed in Fig. 2. Based on the characteristics of analysed particles and applied outer

  15. Automated force volume image processing for biological samples.

    Directory of Open Access Journals (Sweden)

    Pavel Polyakov

    Full Text Available Atomic force microscopy (AFM has now become a powerful technique for investigating on a molecular level, surface forces, nanomechanical properties of deformable particles, biomolecular interactions, kinetics, and dynamic processes. This paper specifically focuses on the analysis of AFM force curves collected on biological systems, in particular, bacteria. The goal is to provide fully automated tools to achieve theoretical interpretation of force curves on the basis of adequate, available physical models. In this respect, we propose two algorithms, one for the processing of approach force curves and another for the quantitative analysis of retraction force curves. In the former, electrostatic interactions prior to contact between AFM probe and bacterium are accounted for and mechanical interactions operating after contact are described in terms of Hertz-Hooke formalism. Retraction force curves are analyzed on the basis of the Freely Jointed Chain model. For both algorithms, the quantitative reconstruction of force curves is based on the robust detection of critical points (jumps, changes of slope or changes of curvature which mark the transitions between the various relevant interactions taking place between the AFM tip and the studied sample during approach and retraction. Once the key regions of separation distance and indentation are detected, the physical parameters describing the relevant interactions operating in these regions are extracted making use of regression procedure for fitting experiments to theory. The flexibility, accuracy and strength of the algorithms are illustrated with the processing of two force-volume images, which collect a large set of approach and retraction curves measured on a single biological surface. For each force-volume image, several maps are generated, representing the spatial distribution of the searched physical parameters as estimated for each pixel of the force-volume image.

  16. Automated Force Volume Image Processing for Biological Samples

    Science.gov (United States)

    Duan, Junbo; Duval, Jérôme F. L.; Brie, David; Francius, Grégory

    2011-01-01

    Atomic force microscopy (AFM) has now become a powerful technique for investigating on a molecular level, surface forces, nanomechanical properties of deformable particles, biomolecular interactions, kinetics, and dynamic processes. This paper specifically focuses on the analysis of AFM force curves collected on biological systems, in particular, bacteria. The goal is to provide fully automated tools to achieve theoretical interpretation of force curves on the basis of adequate, available physical models. In this respect, we propose two algorithms, one for the processing of approach force curves and another for the quantitative analysis of retraction force curves. In the former, electrostatic interactions prior to contact between AFM probe and bacterium are accounted for and mechanical interactions operating after contact are described in terms of Hertz-Hooke formalism. Retraction force curves are analyzed on the basis of the Freely Jointed Chain model. For both algorithms, the quantitative reconstruction of force curves is based on the robust detection of critical points (jumps, changes of slope or changes of curvature) which mark the transitions between the various relevant interactions taking place between the AFM tip and the studied sample during approach and retraction. Once the key regions of separation distance and indentation are detected, the physical parameters describing the relevant interactions operating in these regions are extracted making use of regression procedure for fitting experiments to theory. The flexibility, accuracy and strength of the algorithms are illustrated with the processing of two force-volume images, which collect a large set of approach and retraction curves measured on a single biological surface. For each force-volume image, several maps are generated, representing the spatial distribution of the searched physical parameters as estimated for each pixel of the force-volume image. PMID:21559483

  17. Separation methods for taurine analysis in biological samples.

    Science.gov (United States)

    Mou, Shifen; Ding, Xiaojing; Liu, Yongjian

    2002-12-05

    Taurine plays an important role in a variety of physiological functions, pharmacological actions and pathological conditions. Many methods for taurine analysis, therefore, have been reported to monitor its levels in biological samples. This review discusses the following techniques: sample preparation; separation and determination methods including high-performance liquid chromatography, gas chromatography, ion chromatography, capillary electrophoresis and hyphenation procedures. It covers articles published between 1990 and 2001.

  18. Fast x-ray fluorescence microtomography of hydrated biological samples.

    Directory of Open Access Journals (Sweden)

    Enzo Lombi

    Full Text Available Metals and metalloids play a key role in plant and other biological systems as some of them are essential to living organisms and all can be toxic at high concentrations. It is therefore important to understand how they are accumulated, complexed and transported within plants. In situ imaging of metal distribution at physiological relevant concentrations in highly hydrated biological systems is technically challenging. In the case of roots, this is mainly due to the possibility of artifacts arising during sample preparation such as cross sectioning. Synchrotron x-ray fluorescence microtomography has been used to obtain virtual cross sections of elemental distributions. However, traditionally this technique requires long data acquisition times. This has prohibited its application to highly hydrated biological samples which suffer both radiation damage and dehydration during extended analysis. However, recent advances in fast detectors coupled with powerful data acquisition approaches and suitable sample preparation methods can circumvent this problem. We demonstrate the heightened potential of this technique by imaging the distribution of nickel and zinc in hydrated plant roots. Although 3D tomography was still impeded by radiation damage, we successfully collected 2D tomograms of hydrated plant roots exposed to environmentally relevant metal concentrations for short periods of time. To our knowledge, this is the first published example of the possibilities offered by a new generation of fast fluorescence detectors to investigate metal and metalloid distribution in radiation-sensitive, biological samples.

  19. Stability of glufosfamide in phosphate buffers and in biological samples.

    Science.gov (United States)

    Sun, Yuming; Chen, Xiaoyan; Xu, Haiyan; Guan, Zhongmin; Zhong, Dafang

    2006-03-07

    Glufosfamide is a new, potential chemotherapeutic agent currently under investigation. Stability of glufosfamide was investigated in sodium phosphate buffers with different pH and temperature and in biological samples. Glufosfamide and isophosphamide mustard were quantified simultaneously using a liquid chromatography-ion trap mass spectrometric method; precision and accuracy were within 15% for each analyte. Glufosfamide was stable in neutral buffers, but decomposed to form isophosphoramide mustard under acidic and basic conditions, which was pH- and temperature-dependent. The stability of glufosfamide varied in different biological samples. Results indicated that glufosfamide was unstable in some biological samples, such as the small intestine, smooth muscles, pancreas and urine, especially in the small intestine homogenate, with a half-life of 1.1 h. But the pH (<8) and beta-glucosidase of the tissue homogenate was found to have negligible contribution to the degradation of glufosfamide. The enzymatic inhibition experiment with the specific inhibitor, saccharo-1,4-lactone, demonstrated that it was glucuronidase that resulted in the degradation of glufosfamide in small intestine homogenate. Methanol was recommended to be used to homogenize the tissue in an ice water bath, and the container for urine collection should also be maintained in an ice water bath, and all the biological samples collected should be preserved in frozen condition until analysis.

  20. Study of β-NMR for Liquid Biological Samples

    CERN Document Server

    Beattie, Caitlin

    2017-01-01

    β-NMR is an exotic form of NMR spectroscopy that allows for the characterization of matter based on the anisotropic β-decay of radioactive probe nuclei. This has been shown to be an effective spectroscopic technique for many different compounds, but its use for liquid biological samples is relatively unexplored. The work at the VITO line of ISOLDE seeks to employ this technique to study such samples. Currently, preparations are being made for an experiment to characterize DNA G-quadruplexes and their interactions with stabilizing cations. More specifically, the work in which I engaged as a summer student focused on the experiment’s liquid handling system and the stability of the relevant biological samples under vacuum.

  1. Sample-path Large Deviations in Credit Risk

    CERN Document Server

    Leijdekker, Vincent; Spreij, Peter

    2009-01-01

    The event of large losses plays an important role in credit risk. As these large losses are typically rare, and portfolios usually consist of a large number of positions, large deviation theory is the natural tool to analyze the tail asymptotics of the probabilities involved. We first derive a sample-path large deviation principle (LDP) for the portfolio's loss process, which enables the computation of the logarithmic decay rate of the probabilities of interest. In addition, we derive exact asymptotic results for a number of specific rare-event probabilities, such as the probability of the loss process exceeding some given function.

  2. Evaluating noninvasive genetic sampling techniques to estimate large carnivore abundance.

    Science.gov (United States)

    Mumma, Matthew A; Zieminski, Chris; Fuller, Todd K; Mahoney, Shane P; Waits, Lisette P

    2015-09-01

    Monitoring large carnivores is difficult because of intrinsically low densities and can be dangerous if physical capture is required. Noninvasive genetic sampling (NGS) is a safe and cost-effective alternative to physical capture. We evaluated the utility of two NGS methods (scat detection dogs and hair sampling) to obtain genetic samples for abundance estimation of coyotes, black bears and Canada lynx in three areas of Newfoundland, Canada. We calculated abundance estimates using program capwire, compared sampling costs, and the cost/sample for each method relative to species and study site, and performed simulations to determine the sampling intensity necessary to achieve abundance estimates with coefficients of variation (CV) of sampling was effective for both coyotes and bears and hair snags effectively sampled bears in two of three study sites. Rub pads were ineffective in sampling coyotes and lynx. The precision of abundance estimates was dependent upon the number of captures/individual. Our simulations suggested that ~3.4 captures/individual will result in a sampling was more cost-effective for sampling multiple species, but suggest that hair sampling may be less expensive at study sites with limited road access for bears. Given the dependence of sampling scheme on species and study site, the optimal sampling scheme is likely to be study-specific warranting pilot studies in most circumstances. © 2015 John Wiley & Sons Ltd.

  3. Tight Sample Complexity of Large-Margin Learning

    CERN Document Server

    Sabato, Sivan; Tishby, Naftali

    2010-01-01

    We obtain a tight distribution-specific characterization of the sample complexity of large-margin classification with L_2 regularization: We introduce the \\gamma-adapted-dimension, which is a simple function of the spectrum of a distribution's covariance matrix, and show distribution-specific upper and lower bounds on the sample complexity, both governed by the \\gamma-adapted-dimension of the source distribution. We conclude that this new quantity tightly characterizes the true sample complexity of large-margin classification. The bounds hold for a rich family of sub-Gaussian distributions.

  4. Using electron microscopy to calculate optical properties of biological samples.

    Science.gov (United States)

    Wu, Wenli; Radosevich, Andrew J; Eshein, Adam; Nguyen, The-Quyen; Yi, Ji; Cherkezyan, Lusik; Roy, Hemant K; Szleifer, Igal; Backman, Vadim

    2016-11-01

    The microscopic structural origins of optical properties in biological media are still not fully understood. Better understanding these origins can serve to improve the utility of existing techniques and facilitate the discovery of other novel techniques. We propose a novel analysis technique using electron microscopy (EM) to calculate optical properties of specific biological structures. This method is demonstrated with images of human epithelial colon cell nuclei. The spectrum of anisotropy factor g, the phase function and the shape factor D of the nuclei are calculated. The results show strong agreement with an independent study. This method provides a new way to extract the true phase function of biological samples and provides an independent validation for optical property measurement techniques.

  5. Toxicological Analysis of Some Drugs of Abuse in Biological Samples

    Directory of Open Access Journals (Sweden)

    Anne Marie Ciobanu

    2015-10-01

    Full Text Available Consumption of drugs of abuse is a scourge of modern world. Abuse, drug addiction and their consequences are one of the major current problems of European society because of the significant repercussions in individual, family, social and economic level. In this context, toxicological analysis of the drugs of abuse in biological samples is a useful tool for: diagnosis of drug addiction, checking an auto-response, mandatory screening in some treatment programs, identification of a substance in the case of an overdose, determining compliance of the treatment. The present paper aims to address the needs of healthcare professionals involved in drugs addiction treatment through systematic presentation of information regarding their toxicological analysis. Basically, it is a tool that help you to select the suitable biological sample and the right collecting time, as well as the proper analysis technique, depending on the purpose of analysis, pharmacokinetic characteristics of the drugs of abuse, available equipment and staff expertise.

  6. Analytical methodologies for the determination of benzodiazepines in biological samples.

    Science.gov (United States)

    Persona, Karolina; Madej, Katarzyna; Knihnicki, Paweł; Piekoszewski, Wojciech

    2015-09-10

    Benzodiazepine drugs belong to important and most widely used medicaments. They demonstrate such therapeutic properties as anxiolytic, sedative, somnifacient, anticonvulsant, diastolic and muscle relaxant effects. However, despite the fact that benzodiazepines possess high therapeutic index and are considered to be relatively safe, their use can be dangerous when: (1) co-administered with alcohol, (2) co-administered with other medicaments like sedatives, antidepressants, neuroleptics or morphine like substances, (3) driving under their influence, (4) using benzodiazepines non-therapeutically as drugs of abuse or in drug-facilitated crimes. For these reasons benzodiazepines are still studied and determined in a variety of biological materials. In this article, sample preparation techniques which have been applied in analysis of benzodiazepine drugs in biological samples have been reviewed and presented. The next part of the article is focused on a review of analytical methods which have been employed for pharmacological, toxicological or forensic study of this group of drugs in the biological matrices. The review was preceded by a description of the physicochemical properties of the selected benzodiazepines and two, very often coexisting in the same analyzed samples, sedative-hypnotic drugs.

  7. Applications of large-scale density functional theory in biology

    Science.gov (United States)

    Cole, Daniel J.; Hine, Nicholas D. M.

    2016-10-01

    Density functional theory (DFT) has become a routine tool for the computation of electronic structure in the physics, materials and chemistry fields. Yet the application of traditional DFT to problems in the biological sciences is hindered, to a large extent, by the unfavourable scaling of the computational effort with system size. Here, we review some of the major software and functionality advances that enable insightful electronic structure calculations to be performed on systems comprising many thousands of atoms. We describe some of the early applications of large-scale DFT to the computation of the electronic properties and structure of biomolecules, as well as to paradigmatic problems in enzymology, metalloproteins, photosynthesis and computer-aided drug design. With this review, we hope to demonstrate that first principles modelling of biological structure-function relationships are approaching a reality.

  8. Large sample NAA work at BARC: Methodology and applications

    Science.gov (United States)

    Acharya, R.; Swain, K. K.; Sudarshan, K.; Tripathi, R.; Pujari, P. K.; Reddy, A. V. R.

    2010-10-01

    Large sample neutron activation analysis (LSNAA) was carried out using thermal column facility of Apsara reactor at Bhabha Atomic Research Centre, Mumbai, India. The k0-based internal monostandard NAA (IM-NAA) using in situ detection efficiency was used to analyze large and non-standard geometry samples of clay pottery, uranium ore and stainless steel. Elemental concentration ratios with respect to Na as a monostandard were used in the study of pottery and ore samples. For stainless steel sample of SS 304L, the absolute concentrations were calculated from concentration ratios by mass balance approach since all the major elements (Fe, Cr, Ni and Mn) were amenable to NAA. Applications of LSNAA in the above-mentioned three different areas are described in this paper.

  9. Large sample NAA work at BARC: Methodology and applications

    Energy Technology Data Exchange (ETDEWEB)

    Acharya, R., E-mail: racharya@barc.gov.i [Radiochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085 (India); Swain, K.K. [Analytical Chemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085 (India); Sudarshan, K.; Tripathi, R.; Pujari, P.K. [Radiochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085 (India); Reddy, A.V.R. [Analytical Chemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085 (India)

    2010-10-11

    Large sample neutron activation analysis (LSNAA) was carried out using thermal column facility of Apsara reactor at Bhabha Atomic Research Centre, Mumbai, India. The k{sub 0}-based internal monostandard NAA (IM-NAA) using in situ detection efficiency was used to analyze large and non-standard geometry samples of clay pottery, uranium ore and stainless steel. Elemental concentration ratios with respect to Na as a monostandard were used in the study of pottery and ore samples. For stainless steel sample of SS 304L, the absolute concentrations were calculated from concentration ratios by mass balance approach since all the major elements (Fe, Cr, Ni and Mn) were amenable to NAA. Applications of LSNAA in the above-mentioned three different areas are described in this paper.

  10. Tracking Evolutionary Processes with Large Samples of Galaxy Pairs

    CERN Document Server

    Barton, Elizabeth J; Bullock, James S; Wright, Shelley A

    2009-01-01

    Modern redshift surveys enable the identification of large samples of galaxies in pairs, taken from many different environments. Meanwhile, cosmological simulations allow a detailed understanding of the statistical properties of the selected pair samples. Using these tools in tandem leads to a quantitative understanding of the effects of galaxy-galaxy interactions and, separately, the effects quenching processes in the environments of even very small groups. In the era of the next generation of large telescopes, detailed studies of interactions will be enabled to much higher redshifts.

  11. Exploring Technostress: Results of a Large Sample Factor Analysis

    OpenAIRE

    Steponas Jonušauskas; Agota Giedre Raisiene

    2016-01-01

    With reference to the results of a large sample factor analysis, the article aims to propose the frame examining technostress in a population. The survey and principal component analysis of the sample consisting of 1013 individuals who use ICT in their everyday work was implemented in the research. 13 factors combine 68 questions and explain 59.13 per cent of the answers dispersion. Based on the factor analysis, questionnaire was reframed and prepared to reasonably analyze the respondents’ an...

  12. Standard reporting requirements for biological samples in metabolomics experiments: Microbial and in vitro biology experiments

    NARCIS (Netherlands)

    Werf, M.J. van der; Takors, R.; Smedsgaard, J.; Nielsen, J.; Ferenci, T.; Portais, J.C.; Wittmann, C.; Hooks, M.; Tomassini, A.; Oldiges, M.; Fostel, J.; Sauer, U.

    2007-01-01

    With the increasing use of metabolomics as a means to study a large number of different biological research questions, there is a need for a minimal set of reporting standards that allow the scientific community to evaluate, understand, repeat, compare and re-investigate metabolomics studies. Here w

  13. Neutron Activation Analysis of Inhomogeneous Large Samples; An Explorative Study

    NARCIS (Netherlands)

    Baas, H.W.

    2004-01-01

    Neutron activation analysis is a powerful technique for the determination of trace-element concentrations. Since both neutrons that are used for activation and gamma rays that are detected have a high penetrating power, the technique can be applied for relatively large samples (up to 13 L), as demon

  14. Measurement, Sampling, and Equating Errors in Large-Scale Assessments

    Science.gov (United States)

    Wu, Margaret

    2010-01-01

    In large-scale assessments, such as state-wide testing programs, national sample-based assessments, and international comparative studies, there are many steps involved in the measurement and reporting of student achievement. There are always sources of inaccuracies in each of the steps. It is of interest to identify the source and magnitude of…

  15. Using biological samples in epidemiological research on drugs of abuse

    Directory of Open Access Journals (Sweden)

    Hallvard Gjerde

    2011-12-01

    Full Text Available Blood, oral fluid (saliva, urine and hair are the most commonly used biological matrices for drug testing in epidemiological drug research. Other biological matrices may also be used for selected purposes. Blood reflects recent drug intake and may be used to assess impairment. Oral fluid reflects drug presence in blood and thereby also recent intake, but drug concentrations in this matrix cannot be used to accurately estimate concentrations in blood. Urine reflects drug use during the last few days and in some cases for a longer period, but does not indicate the dose size or frequency of use. Hair reflects drug use during several months, but is a poor matrix for detecting use of cannabis. If using a single drug dose, this can be detected in blood and urine if the sample is taken within the detection timeframes, in most cases also in oral fluid. Single drug use is most often insufficient for producing a positive test result in a sample of hair. For cocaine and amphetamine, weekly use may be needed, while for cannabis a positive result is not guaranteed even after daily use. Refusal rates are lowest for oral fluid and highest for blood and hair samples. The analytical costs are lowest for urine and highest for hair. Combined use of questionnaires/interviews and drug testing detects more drug use than when using only one of those methods and is therefore expected to give more accurate data.

  16. Incubation Station for the Bacterial Growth Study in Biological Samples

    Directory of Open Access Journals (Sweden)

    Carlos Rafael Duharte Rodríguez

    2015-12-01

    Full Text Available This work shows the designing and characterization of a prototype of laboratory incubator as support of Microbiology research, in particular for the research of the bacterial growth in biological samples through optic methods (Turbidimetry and electrometric measurements of bioimpedance. It shows the results of simulation and experimentation of the design proposed for the canals of measurement of the variables: temperature and humidity, with a high linearity from the adequate selection of the corresponding sensors and the analogue components of every canal, controlled with help of a microcontroller AT89C51 (ATMEL with adequate benefi ts for this type of application.

  17. Comparison of large networks with sub-sampling strategies

    Science.gov (United States)

    Ali, Waqar; Wegner, Anatol E.; Gaunt, Robert E.; Deane, Charlotte M.; Reinert, Gesine

    2016-07-01

    Networks are routinely used to represent large data sets, making the comparison of networks a tantalizing research question in many areas. Techniques for such analysis vary from simply comparing network summary statistics to sophisticated but computationally expensive alignment-based approaches. Most existing methods either do not generalize well to different types of networks or do not provide a quantitative similarity score between networks. In contrast, alignment-free topology based network similarity scores empower us to analyse large sets of networks containing different types and sizes of data. Netdis is such a score that defines network similarity through the counts of small sub-graphs in the local neighbourhood of all nodes. Here, we introduce a sub-sampling procedure based on neighbourhoods which links naturally with the framework of network comparisons through local neighbourhood comparisons. Our theoretical arguments justify basing the Netdis statistic on a sample of similar-sized neighbourhoods. Our tests on empirical and synthetic datasets indicate that often only 10% of the neighbourhoods of a network suffice for optimal performance, leading to a drastic reduction in computational requirements. The sampling procedure is applicable even when only a small sample of the network is known, and thus provides a novel tool for network comparison of very large and potentially incomplete datasets.

  18. A low temperature scanning force microscope for biological samples

    Energy Technology Data Exchange (ETDEWEB)

    Gustafsson, Mats Gustaf Lennart [Univ. of California, Berkeley, CA (United States)

    1993-05-01

    An SFM has been constructed capable of operating at 143 K. Two contributions to SFM technology are described: a new method of fabricating tips, and new designs of SFM springs that significantly lower the noise level. The SFM has been used to image several biological samples (including collagen, ferritin, RNA, purple membrane) at 143 K and room temperature. No improvement in resolution resulted from 143 K operation; several possible reasons for this are discussed. Possibly sharper tips may help. The 143 K SFM will allow the study of new categories of samples, such as those prepared by freeze-frame, single molecules (temperature dependence of mechanical properties), etc. The SFM was used to cut single collagen molecules into segments with a precision of {le} 10 nm.

  19. Assessment of the differential linear coherent scattering coefficient of biological samples

    Science.gov (United States)

    Conceição, A. L. C.; Antoniassi, M.; Poletti, M. E.

    2010-07-01

    New differential linear coherent scattering coefficient, μ CS, data for four biological tissue types (fat pork, tendon chicken, adipose and fibroglandular human breast tissues) covering a large momentum transfer interval (0.07≤ q≤70.5 nm -1), resulted from combining WAXS and SAXS data, are presented in order to emphasize the need to update the default data-base by including the molecular interference and the large-scale arrangements effect. The results showed that the differential linear coherent scattering coefficient demonstrates influence of the large-scale arrangement, mainly due to collagen fibrils for tendon chicken and fibroglandular breast samples, and triacylglycerides for fat pork and adipose breast samples at low momentum transfer region. While, at high momentum transfer, the μ CS reflects effects of molecular interference related to water for tendon chicken and fibroglandular samples and, fatty acids for fat pork and adipose samples.

  20. Microsystem strategies for sample preparation in biological detection.

    Energy Technology Data Exchange (ETDEWEB)

    James, Conrad D.; Galambos, Paul C.; Bennett, Dawn Jonita (University of Maryland Baltimore County, Baltimore, MD); Manginell, Monica; Okandan, Murat; Acrivos, Andreas (The City College of New York, NY); Brozik, Susan Marie; Khusid, Boris (New Jersey Institute of Technology, Newark, NJ)

    2005-03-01

    The objective of this LDRD was to develop microdevice strategies for dealing with samples to be examined in biological detection systems. This includes three sub-components: namely, microdevice fabrication, sample delivery to the microdevice, and sample processing within the microdevice. The first component of this work focused on utilizing Sandia's surface micromachining technology to fabricate small volume (nanoliter) fluidic systems for processing small quantities of biological samples. The next component was to develop interfaces for the surface-micromachined silicon devices. We partnered with Micronics, a commercial company, to produce fluidic manifolds for sample delivery to our silicon devices. Pressure testing was completed to examine the strength of the bond between the pressure-sensitive adhesive layer and the silicon chip. We are also pursuing several other methods, both in house and external, to develop polymer-based fluidic manifolds for packaging silicon-based microfluidic devices. The second component, sample processing, is divided into two sub-tasks: cell collection and cell lysis. Cell collection was achieved using dielectrophoresis, which employs AC fields to collect cells at energized microelectrodes, while rejecting non-cellular particles. Both live and dead Staph. aureus bacteria have been collected using RF frequency dielectrophoresis. Bacteria have been separated from polystyrene microspheres using frequency-shifting dielectrophoresis. Computational modeling was performed to optimize device separation performance, and to predict particle response to the dielectrophoretic traps. Cell lysis is continuing to be pursued using microactuators to mechanically disrupt cell membranes. Novel thermal actuators, which can generate larger forces than previously tested electrostatic actuators, have been incorporated with and tested with cell lysis devices. Significant cell membrane distortion has been observed, but more experiments need to be

  1. Workflow for large-scale analysis of melanoma tissue samples

    Directory of Open Access Journals (Sweden)

    Maria E. Yakovleva

    2015-09-01

    Full Text Available The aim of the present study was to create an optimal workflow for analysing a large cohort of malignant melanoma tissue samples. Samples were lysed with urea and enzymatically digested with trypsin or trypsin/Lys C. Buffer exchange or dilution was used to reduce urea concentration prior to digestion. The tissue digests were analysed directly or following strong cation exchange (SCX fractionation by nano LC–MS/MS. The approach which resulted in the largest number of protein IDs involved a buffer exchange step before enzymatic digestion with trypsin and chromatographic separation in 120 min gradient followed by SCX–RP separation of peptides.

  2. The use of contrast agent for imaging biological samples

    Energy Technology Data Exchange (ETDEWEB)

    Dammer, J; Sopko, V; Jakubek, J [Institute of Experimental and Applied Physics, Czech Technical University in Prague, Horska 3a/22, CZ 12800 Prague 2 (Czech Republic); Weyda, F, E-mail: jiri.dammer@utef.cvut.cz [Biological center of the Academy of Sciences of the Czech Republic, Institute of Entomology, Branisovska 31, CZ-37005 Ceske Budejovice (Czech Republic)

    2011-01-15

    The technique of X-ray transmission imaging has been available for over a century and is still among the fastest and easiest approaches to the studies of internal structure of biological samples. Recent advances in semiconductor technology have led to the development of new types of X-ray detectors with direct conversion of interacting X-ray photon to an electric signal. Semiconductor pixel detectors seem to be specially promising; compared to the film technique, they provide single-quantum and real-time digital information about the objects being studied. We describe the recently developed radiographic apparatus, equipped with Medipix2 semiconductor pixel detector. The detector is used as an imager that counts individual photons of ionizing radiation, emitted by an X-ray tube (micro- or nano-focus FeinFocus). Thanks to the wide dynamic range of the Medipix2 detector and its high spatial resolution better than 1{mu}m, the setup is particularly suitable for radiographic imaging of small biological samples, including in-vivo observations with contrast agent (Optiray). Along with the description of the apparatus we provide examples of the use iodine contrast agent as a tracer in various insects as model organisms. The motivation of our work is to develop our imaging techniques as non-destructive and non-invasive. Microradiographic imaging helps detect organisms living in a not visible environment, visualize the internal biological processes and also to resolve the details of their body (morphology). Tiny live insects are an ideal object for our studies.

  3. A course in mathematical statistics and large sample theory

    CERN Document Server

    Bhattacharya, Rabi; Patrangenaru, Victor

    2016-01-01

    This graduate-level textbook is primarily aimed at graduate students of statistics, mathematics, science, and engineering who have had an undergraduate course in statistics, an upper division course in analysis, and some acquaintance with measure theoretic probability. It provides a rigorous presentation of the core of mathematical statistics. Part I of this book constitutes a one-semester course on basic parametric mathematical statistics. Part II deals with the large sample theory of statistics — parametric and nonparametric, and its contents may be covered in one semester as well. Part III provides brief accounts of a number of topics of current interest for practitioners and other disciplines whose work involves statistical methods. Large Sample theory with many worked examples, numerical calculations, and simulations to illustrate theory Appendices provide ready access to a number of standard results, with many proofs Solutions given to a number of selected exercises from Part I Part II exercises with ...

  4. Discovering large network motifs from a complex biological network

    Energy Technology Data Exchange (ETDEWEB)

    Terada, Aika; Sese, Jun, E-mail: terada@sel.is.ocha.ac.j, E-mail: sesejun@is.ocha.ac.j [Department of Computer Science, Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo 112-8610 (Japan)

    2009-12-01

    Graph structures representing relationships between entries have been studied in statistical analysis, and the results of these studies have been applied to biological networks, whose nodes and edges represent proteins and the relationships between them, respectively. Most of the studies have focused on only graph structures such as scale-free properties and cliques, but the relationships between nodes are also important features since most of the proteins perform their functions by connecting to other proteins. In order to determine such relationships, the problem of network motif discovery has been addressed; network motifs are frequently appearing graph structures in a given graph. However, the methods for network motif discovery are highly restrictive for the application to biological network because they can only be used to find small network motifs or they do not consider noise and uncertainty in observations. In this study, we introduce a new index to measure network motifs called AR index and develop a novel algorithm called ARIANA for finding large motifs even when the network has noise. Experiments using a synthetic network verify that our method can find better network motifs than an existing algorithm. By applying ARIANA to a real complex biological network, we find network motifs associated with regulations of start time of cell functions and generation of cell energies and discover that the cell cycle proteins can be categorized into two different groups.

  5. Properties of large-scale melt-processed YBCO samples

    Science.gov (United States)

    Gauss, S.; Elschner, S.; Bestgen, H.

    Magnetic bearings and superconducting permanent magnets are some of the first possible applications of bulk high Tc superconductors. Large samples were prepared by a new melt process starting from reacted YBCO 123 and 211 powders. The addition of PtO 2 to the mixture led to reduced 211 inclusion size and better homogeneity. Simultaneously the density of microcracks dividing the a- b basal plane was reduced. For testing the overall magnetic properties of these samples magnetization and levitation force measurements were performed. In comparison to samples without PtO 2 addition a strong increase in the magnetization M and the repulsion force from a magnet were observed. The maximum in the field dependence of M increased to more than 1000 G. According to the time dependence of the trapped field after a field cooling experiment an acceptable flux creep at 77 K for a long-term application was achieved.

  6. Direct analysis of biological samples by total reflection X-ray fluorescence

    Energy Technology Data Exchange (ETDEWEB)

    Lue M, Marco P. [Unidad de Analisis Instrumental, Departamento de Quimica y Suelos, Decanato de Agronomia, Universidad Centro-occidental Lisandro Alvarado, Apartado Postal 4076, Cabudare 3023 (Venezuela)]. E-mail: luemerumarco@yahoo.es; Hernandez-Caraballo, Edwin A. [Instituto Venezolano-Andino para la Investigacion Quimica (IVAIQUIM), Facultad de Ciencias, Universidad de los Andes, Merida 5101 (Venezuela)

    2004-08-31

    The technique of total reflection X-ray fluorescence (TXRF) is well suited for the direct analysis of biological samples due to the low matrix interferences and simultaneous multi-element nature. Nevertheless, biological organic samples are frequently analysed after digestion procedures. The direct determination of analytes requires shorter analysis time, low reactive consumption and simplifies the whole analysis process. On the other hand, the biological/clinical samples are often available in minimal amounts and routine studies require the analysis of large number of samples. To overcome the difficulties associated with the analysis of organic samples, particularly of solid ones, different procedures of sample preparation and calibration to approach the direct analysis have been evaluated: (1) slurry sampling, (2) Compton peak standardization, (3) in situ microwave digestion, (4) in situ chemical modification and (5) direct analysis with internal standardization. Examples of analytical methods developed by our research group are discussed. Some of them have not been previously published, illustrating alternative strategies for coping with various problems that may be encountered in the direct analysis by total reflection X-ray fluorescence spectrometry.

  7. Comprehensive workflow for wireline fluid sampling in an unconsolidated formations utilizing new large volume sampling equipment

    Energy Technology Data Exchange (ETDEWEB)

    Kvinnsland, S.; Brun, M. [TOTAL EandP Norge (Norway); Achourov, V.; Gisolf, A. [Schlumberger (Canada)

    2011-07-01

    Precise and accurate knowledge of fluid properties is essential in unconsolidated formations to the design of production facilities. Wireline formation testers (WFT) have a wide range of applications and the latest WFT can be used to define fluid properties in the wells drilled with oil based mud (OBM) by acquiring PVT and large volume samples. To use these technologies, a comprehensive workflow has to be implemented and the aim of this paper is to present such a workflow. A sampling was conducted in highly unconsolidated sand saturated with biodegradable fluid in the Hild filed in the North Sea. Results showed the use of comprehensive workflow to be successful in obtaining large volume samples with the contamination level below 1%. Oil was precisely characterized thanks to these samples and design updates to the project were made possible. This paper highlighted that the use of the latest WFT technologies can help better characterize fluids in unconsolidated formations and thus optimize production facilities design.

  8. Micro-radiography of biological samples with medical contrast agents

    Energy Technology Data Exchange (ETDEWEB)

    Dammer, J., E-mail: jiri.dammer@lf1.cuni.cz [Charles University in Prague, First Faculty of Medicine, Salmovská 1, 120 00 Prague 2 (Czech Republic); Hospital Na Bulovce, Department of Radiological Physics, Budinova 2, 180 81 Prague 8 (Czech Republic); Institute of Experimental and Applied Physics, Czech Technical University in Prague, Horska 3a/22, 128 00 Prague 2 (Czech Republic); Weyda, F. [Faculty of Science, University of South Bohemia, Branisovska 31, 370 05 Ceske Budejovice (Czech Republic); Benes, J. [Charles University in Prague, First Faculty of Medicine, Salmovská 1, 120 00 Prague 2 (Czech Republic); Sopko, V. [Hospital Na Bulovce, Department of Radiological Physics, Budinova 2, 180 81 Prague 8 (Czech Republic); Institute of Experimental and Applied Physics, Czech Technical University in Prague, Horska 3a/22, 128 00 Prague 2 (Czech Republic); Gelbic, I. [Biology Centre, AS CR, Institute of Entomology, Department of Biochemistry and Physiology, Branisovska 31, CZ-37005 Ceske Budejovice (Czech Republic)

    2013-12-01

    Micro-radiography is an imaging technique that uses X-rays to study the internal structures of objects. This fast and easy imaging tool is based on differential X-ray attenuation by various tissues and structures within biological samples. The experimental setup described is based on the semiconductor pixel X-ray detector Medipix2 and X-ray micro-focus tube. Our micro-radiographic system has been recently used not only for the examination of internal structures of various arthropods and other biological objects but also for tracing some processes in selected model species (we used living larvae of mosquito Culex quinquefasciatus). Low concentrations of iodine, lanthanum or gold particles were used as a tracer (contrast agent). Such contrast agents increase the absorption of X-rays and allow a better visibility of internal structures of model organisms (especially the various cavities, pores, etc.). In addition, the movement of tracers in selected timing experiments demonstrates some physiological functions of digestive and excretory system.

  9. Digital holography microscopy in 3D biologic samples analysis

    Energy Technology Data Exchange (ETDEWEB)

    Ricardo, J O; Palacios, F; Palacios, G F; Sanchez, A [Department of Physics, University of Oriente (Cuba); Muramatsu, M [Department of General Physics, University of Sao Paulo - Sao Paulo (Brazil); Gesualdi, M [Engineering center, Models and Applied Social Science, UFABC - Sao Paulo (Brazil); Font, O [Department of Bio-ingeniering, University of Oriente - Santiago de Cuba (Cuba); Valin, J L [Mechanics Department, ISPJAE, Habana (Cuba); Escobedo, M; Herold, S [Department of Computation, University of Oriente (Cuba); Palacios, D F, E-mail: frpalaciosf@gmail.com [Department of Nuclear physics, University of Simon BolIva (Venezuela, Bolivarian Republic of)

    2011-01-01

    In this work it is used a setup for Digital Holography Microscopy (MHD) for 3D biologic samples reconstruction. The phase contrast image reconstruction is done by using the Double propagation Method. The system was calibrated and tested by using a micrometric scale and pure phase object respectively. It was simulated the human red blood cell (erythrocyte) and beginning from the simulated hologram the digital 3D phase image for erythrocytes it was calculated. Also there was obtained experimental holograms of human erythrocytes and its corresponding 3D phase images, being evident the correspondence qualitative and quantitative between these characteristics in the simulated erythrocyte and in the experimentally calculated by DHM in both cases.

  10. Calcium isolation from large-volume human urine samples for 41Ca analysis by accelerator mass spectrometry.

    Science.gov (United States)

    Miller, James J; Hui, Susanta K; Jackson, George S; Clark, Sara P; Einstein, Jane; Weaver, Connie M; Bhattacharyya, Maryka H

    2013-08-01

    Calcium oxalate precipitation is the first step in preparation of biological samples for (41)Ca analysis by accelerator mass spectrometry. A simplified protocol for large-volume human urine samples was characterized, with statistically significant increases in ion current and decreases in interference. This large-volume assay minimizes cost and effort and maximizes time after (41)Ca administration during which human samples, collected over a lifetime, provide (41)Ca:Ca ratios that are significantly above background.

  11. Calcium Isolation from Large-Volume Human Urine Samples for 41Ca Analysis by Accelerator Mass Spectrometry

    Science.gov (United States)

    Miller, James J; Hui, Susanta K; Jackson, George S; Clark, Sara P; Einstein, Jane; Weaver, Connie M; Bhattacharyya, Maryka H

    2013-01-01

    Calcium oxalate precipitation is the first step in preparation of biological samples for 41Ca analysis by accelerator mass spectrometry. A simplified protocol for large-volume human urine samples was characterized, with statistically significant increases in ion current and decreases in interference. This large-volume assay minimizes cost and effort and maximizes time after 41Ca administration during which human samples, collected over a lifetime, provide 41Ca:Ca ratios that are significantly above background. PMID:23672965

  12. Exploring Technostress: Results of a Large Sample Factor Analysis

    Directory of Open Access Journals (Sweden)

    Steponas Jonušauskas

    2016-06-01

    Full Text Available With reference to the results of a large sample factor analysis, the article aims to propose the frame examining technostress in a population. The survey and principal component analysis of the sample consisting of 1013 individuals who use ICT in their everyday work was implemented in the research. 13 factors combine 68 questions and explain 59.13 per cent of the answers dispersion. Based on the factor analysis, questionnaire was reframed and prepared to reasonably analyze the respondents’ answers, revealing technostress causes and consequences as well as technostress prevalence in the population in a statistically validated pattern. A key elements of technostress based on factor analysis can serve for the construction of technostress measurement scales in further research.

  13. Eigenvalue distribution of large sample covariance matrices of linear processes

    CERN Document Server

    Pfaffel, Oliver

    2012-01-01

    We derive the distribution of the eigenvalues of a large sample covariance matrix when the data is dependent in time. More precisely, the dependence for each variable $i=1,...,p$ is modelled as a linear process $(X_{i,t})_{t=1,...,n}=(\\sum_{j=0}^\\infty c_j Z_{i,t-j})_{t=1,...,n}$, where $\\{Z_{i,t}\\}$ are assumed to be independent random variables with finite fourth moments. If the sample size $n$ and the number of variables $p=p_n$ both converge to infinity such that $y=\\lim_{n\\to\\infty}{n/p_n}>0$, then the empirical spectral distribution of $p^{-1}\\X\\X^T$ converges to a non\\hyp{}random distribution which only depends on $y$ and the spectral density of $(X_{1,t})_{t\\in\\Z}$. In particular, our results apply to (fractionally integrated) ARMA processes, which we illustrate by some examples.

  14. Sampling Within k-Means Algorithm to Cluster Large Datasets

    Energy Technology Data Exchange (ETDEWEB)

    Bejarano, Jeremy [Brigham Young University; Bose, Koushiki [Brown University; Brannan, Tyler [North Carolina State University; Thomas, Anita [Illinois Institute of Technology; Adragni, Kofi [University of Maryland; Neerchal, Nagaraj [University of Maryland; Ostrouchov, George [ORNL

    2011-08-01

    Due to current data collection technology, our ability to gather data has surpassed our ability to analyze it. In particular, k-means, one of the simplest and fastest clustering algorithms, is ill-equipped to handle extremely large datasets on even the most powerful machines. Our new algorithm uses a sample from a dataset to decrease runtime by reducing the amount of data analyzed. We perform a simulation study to compare our sampling based k-means to the standard k-means algorithm by analyzing both the speed and accuracy of the two methods. Results show that our algorithm is significantly more efficient than the existing algorithm with comparable accuracy. Further work on this project might include a more comprehensive study both on more varied test datasets as well as on real weather datasets. This is especially important considering that this preliminary study was performed on rather tame datasets. Also, these datasets should analyze the performance of the algorithm on varied values of k. Lastly, this paper showed that the algorithm was accurate for relatively low sample sizes. We would like to analyze this further to see how accurate the algorithm is for even lower sample sizes. We could find the lowest sample sizes, by manipulating width and confidence level, for which the algorithm would be acceptably accurate. In order for our algorithm to be a success, it needs to meet two benchmarks: match the accuracy of the standard k-means algorithm and significantly reduce runtime. Both goals are accomplished for all six datasets analyzed. However, on datasets of three and four dimension, as the data becomes more difficult to cluster, both algorithms fail to obtain the correct classifications on some trials. Nevertheless, our algorithm consistently matches the performance of the standard algorithm while becoming remarkably more efficient with time. Therefore, we conclude that analysts can use our algorithm, expecting accurate results in considerably less time.

  15. Graph animals, subgraph sampling and motif search in large networks

    CERN Document Server

    Baskerville, Kim; Paczuski, Maya

    2007-01-01

    We generalize a sampling algorithm for lattice animals (connected clusters on a regular lattice) to a Monte Carlo algorithm for `graph animals', i.e. connected subgraphs in arbitrary networks. As with the algorithm in [N. Kashtan et al., Bioinformatics 20, 1746 (2004)], it provides a weighted sample, but the computation of the weights is much faster (linear in the size of subgraphs, instead of super-exponential). This allows subgraphs with up to ten or more nodes to be sampled with very high statistics, from arbitrarily large networks. Using this together with a heuristic algorithm for rapidly classifying isomorphic graphs, we present results for two protein interaction networks obtained using the TAP high throughput method: one of Escherichia coli with 230 nodes and 695 links, and one for yeast (Saccharomyces cerevisiae) with roughly ten times more nodes and links. We find in both cases that most connected subgraphs are strong motifs (Z-scores >10) or anti-motifs (Z-scores <-10) when the null model is the...

  16. The MWA GLEAM 4Jy Sample; a new large, bright radio source sample at 151 MHz

    CERN Document Server

    Jackson, C A; Seymour, N; White, S V; Murphy, Tara; Sadler, E M; Callingham, J R; Hunstead, R W; Hughes, J; Wall, J V; Bell, M E; Dwarakanath, K S; For, B-Q; Gaensler, B M; Hancock, P J; Hindson, L; Hurley-Walker, N; Johnston-Hollitt, M; Kapinska, A D; Lenc, E; McKinley, B; Morgan, J; Offringa, A R; Procopio, P; Staveley-Smith, L; Wayth, R B; Wu, C; Zheng, Q

    2016-01-01

    This paper outlines how the new GaLactic and Extragalactic All-sky MWA Survey (GLEAM, Wayth et al. 2015), observed by the Murchison Widefield Array covering the frequency range 72 - 231 MHz, allows identification of a new large, complete, sample of more than 2000 bright extragalactic radio sources selected at 151 MHz. With a flux density limit of 4 Jy this sample is significantly larger than the canonical fully-complete sample, 3CRR (Laing, Riley & Longair 1983). In analysing this small bright subset of the GLEAM survey we are also providing a first user check of the GLEAM catalogue ahead of its public release (Hurley-Walker et al. in prep). Whilst significant work remains to fully characterise our new bright source sample, in time it will provide important constraints to evolutionary behaviour, across a wide redshift and intrinsic radio power range, as well as being highly complementary to results from targeted, small area surveys.

  17. Inductively coupled plasma mass spectrometry in the analysis of biological samples and pharmaceutical drugs

    Science.gov (United States)

    Ossipov, K.; Seregina, I. F.; Bolshov, M. A.

    2016-04-01

    Inductively coupled plasma mass spectrometry (ICP-MS) is widely used in the analysis of biological samples (whole blood, serum, blood plasma, urine, tissues, etc.) and pharmaceutical drugs. The shortcomings of this method related to spectral and non-spectral interferences are manifested in full measure in determination of the target analytes in these complex samples strongly differing in composition. The spectral interferences are caused by similarity of masses of the target component and sample matrix components. Non-spectral interferences are related to the influence of sample matrix components on the physicochemical processes taking place during formation and transportation of liquid sample aerosols into the plasma, on the value and spatial distribution of plasma temperature and on the transmission of the ion beam from the interface to mass spectrometer detector. The review is devoted to analysis of different mechanisms of appearance of non-spectral interferences and to ways for their minimization or elimination. Special attention is paid to the techniques of biological sample preparation, which largely determine the mechanisms of the influence of sample composition on the results of element determination. The ways of lowering non-spectral interferences by instrumental parameter tuning and application of internal standards are considered. The bibliography includes 189 references.

  18. Matrix Sampling of Items in Large-Scale Assessments

    Directory of Open Access Journals (Sweden)

    Ruth A. Childs

    2003-07-01

    Full Text Available Matrix sampling of items -' that is, division of a set of items into different versions of a test form..-' is used by several large-scale testing programs. Like other test designs, matrixed designs have..both advantages and disadvantages. For example, testing time per student is less than if each..student received all the items, but the comparability of student scores may decrease. Also,..curriculum coverage is maintained, but reporting of scores becomes more complex. In this paper,..matrixed designs are compared with more traditional designs in nine categories of costs:..development costs, materials costs, administration costs, educational costs, scoring costs,..reliability costs, comparability costs, validity costs, and reporting costs. In choosing among test..designs, a testing program should examine the costs in light of its mandate(s, the content of the..tests, and the financial resources available, among other considerations.

  19. Improved FIA-ABTS method for antioxidant capacity determination in different biological samples.

    Science.gov (United States)

    Bompadre, Stefano; Leone, Luciana; Politi, Alessia; Battino, Maurizio

    2004-08-01

    In order to evaluate the actual antioxidant features of foods, beverages and also plasma from patients, a number of assays have been developed in the last few years to determine the so called total antioxidant activity (TAA), intended as the cumulative capacity of a biological sample to scavenge free radicals. Most of the assays partially failed in obtaining a good reproducibility when using plasma because it is composed of a large number of substances, some of which are present at very high concentrations and possess masking features. For these reasons we have improved the widely known ABTS method by means of a FIA system where both temperature and dispersion of sample and reagent were strictly controlled. We found that temperature may be a critical aspect in the measurement of plasma TAA whilst its influence may be less important in the assay of non-complex biological samples. We demonstrated that also the reaction time may be critical, depending on the nature of the substance employed. Data confirmed the high TAA of a methylsalicylate-containing mouthrinse as well as the negligible TAA offered by the chlorhexidine containing one. White wines (Verdicchio) also displayed interesting TAA values. The improved method was useful to screen rapidly, without dilution, with very limited handling of the sample and with high repeatability the TAA of plasma in addition to chemical products, beverages and non-complex biological mixtures.

  20. Very Large Chemical Sensor Array for Mimicking Biological Olfaction

    Science.gov (United States)

    Beccherelli, R.; Zampetti, E.; Pantalei, S.; Bernabei, M.; Persaud, K. C.

    2009-05-01

    Olfactory receptor neurons (ORN) in the mammalian olfactory system, transduce molecular properties of the odorants into electrical signals and project these into the olfactory bulb (OB). In the biological system several millions of receptor neurons of a few hundred types create redundancy and the massive convergence of the ORNs to the OB, is thought to enhance the sensitivity and selectivity of the system. To explore this concept, the NEUROCHEM project will build a polymeric chemical sensor array consisting of 216 (65536) sensors with tens of different types. To interface such a large sensor array, a topological array configuration with n rows and m columns, has been adopted, to reduce the total wiring connections to n+m. A method of addressing a single element in the array in isolation of the rest of the network has been developed. Over the array ten different conductive polymers with different sensing characteristics will be deposited by means of electrodeposition and inkjet printing. A smaller prototype of 64 elements has been investigated and the results are here reported and discussed.

  1. Amchitka Island, Alaska, Biological Monitoring Report 2011 Sampling Results

    Energy Technology Data Exchange (ETDEWEB)

    None

    2013-09-01

    The Long-Term Surveillance and Maintenance (LTS&M) Plan for the U.S. Department of Energy (DOE) Office of Legacy Management (LM) Amchitka Island sites describes how LM plans to conduct its mission to protect human health and the environment at the three nuclear test sites located on Amchitka Island, Alaska. Amchitka Island, near the western end of the Aleutian Islands, is approximately 1,340 miles west-southwest of Anchorage, Alaska. Amchitka is part of the Aleutian Island Unit of the Alaska Maritime National Wildlife Refuge, which is administered by the U.S. Fish and Wildlife Service (USFWS). Since World War II, Amchitka has been used by multiple U.S. government agencies for various military and research activities. From 1943 to 1950, it was used as a forward air base for the U.S. Armed Forces. During the middle 1960s and early 1970s, the U.S. Department of Defense (DOD) and the U.S. Atomic Energy Commission (AEC) used a portion of the island as a site for underground nuclear tests. During the late 1980s and early 1990s, the U.S. Navy constructed and operated a radar station on the island. Three underground nuclear tests were conducted on Amchitka Island. DOD, in conjunction with AEC, conducted the first nuclear test (named Long Shot) in 1965 to provide data that would improve the United States' capability of detecting underground nuclear explosions. The second nuclear test (Milrow) was a weapons-related test conducted by AEC in 1969 as a means to study the feasibility of detonating a much larger device. Cannikin, the third nuclear test on Amchitka, was a weapons-related test detonated on November 6, 1971. With the exception of small concentrations of tritium detected in surface water shortly after the Long Shot test, radioactive fission products from the tests remain in the subsurface at each test location As a continuation of the environmental monitoring that has taken place on Amchitka Island since before 1965, LM in the summer of 2011 collected biological

  2. Cosmological implications of a large complete quasar sample.

    Science.gov (United States)

    Segal, I E; Nicoll, J F

    1998-04-28

    Objective and reproducible determinations of the probabilistic significance levels of the deviations between theoretical cosmological prediction and direct model-independent observation are made for the Large Bright Quasar Sample [Foltz, C., Chaffee, F. H., Hewett, P. C., MacAlpine, G. M., Turnshek, D. A., et al. (1987) Astron. J. 94, 1423-1460]. The Expanding Universe model as represented by the Friedman-Lemaitre cosmology with parameters qo = 0, Lambda = 0 denoted as C1 and chronometric cosmology (no relevant adjustable parameters) denoted as C2 are the cosmologies considered. The mean and the dispersion of the apparent magnitudes and the slope of the apparent magnitude-redshift relation are the directly observed statistics predicted. The C1 predictions of these cosmology-independent quantities are deviant by as much as 11sigma from direct observation; none of the C2 predictions deviate by >2sigma. The C1 deviations may be reconciled with theory by the hypothesis of quasar "evolution," which, however, appears incapable of being substantiated through direct observation. The excellent quantitative agreement of the C1 deviations with those predicted by C2 without adjustable parameters for the results of analysis predicated on C1 indicates that the evolution hypothesis may well be a theoretical artifact.

  3. Developmental Risk: Evidence from Large Nonright-Handed Samples

    Directory of Open Access Journals (Sweden)

    Filippos Vlachos

    2013-01-01

    Full Text Available The aim of the present study is twofold. First, we tested the view that individuals who do not develop a typically strong behavioral laterality are distributed differentially among the two genders across age. Second, we examined whether left handedness and mixed handedness are associated with an elevated risk of some developmental or cognitive deficits. A special recruitment procedure provided norms of the Rey-Osterrieth Complex Figure (ROCF copy from large samples of left-handed ( and mixed-handed ( compared to right-handed ( schoolchildren and adults (. This graphic task was considered as reflective of the growth of visual-spatial skills and impairment at copying as a developmental risk. Subjects’ hand preference was assessed by the Edinburgh Handedness Inventory. Data analysis indicated that (1 the trend towards consistent right handedness is sex related. Girls are clearly ahead of boys in this lateralization process, and boys are overrepresented in mixed-handed subjects. The greater prevalence of mixed-handed boys compared to girls decreases with age. (2 Performance on drawing the ROCF varies according to age and handedness groups. Mixed-handed subjects scored worse in all age groups. The results are discussed in relation to the hormonal-developmental, neuropathological, and learning theories of lateralization.

  4. Using electron microscopy to calculate optical properties of biological samples

    OpenAIRE

    Wu, Wenli; Radosevich, Andrew J.; Eshein, Adam; Nguyen, The-Quyen; Yi, Ji; Cherkezyan, Lusik; Roy, Hemant K.; Szleifer, Igal; Backman, Vadim

    2016-01-01

    The microscopic structural origins of optical properties in biological media are still not fully understood. Better understanding these origins can serve to improve the utility of existing techniques and facilitate the discovery of other novel techniques. We propose a novel analysis technique using electron microscopy (EM) to calculate optical properties of specific biological structures. This method is demonstrated with images of human epithelial colon cell nuclei. The spectrum of anisotropy...

  5. Validation of Malingered Amnesia Measures with a Large Clinical Sample.

    Science.gov (United States)

    Greiffenstein, Manfred F.; And Others

    1994-01-01

    A sample of chronic postconcussive patients with and without overt malingering signs was compared with objectively brain-injured patients (total sample=106) on common episodic memory and malingered amnesia measures. Findings validate commonly cited malingering measures and new methods of classifying malingering in real-world clinical samples. (SLD)

  6. Spectroscopic analysis of bosentan in biological samples after a liquid-liquid microextraction

    Directory of Open Access Journals (Sweden)

    Sanaz Sajedi-Amin

    2015-12-01

    Conclusion: A simple, low cost, precise and accurate spectrophotometric analysis of bosentan in biological samples after liquid-liquid microextraction were developed and validated for routine analyses.

  7. Large scale sample management and data analysis via MIRACLE

    DEFF Research Database (Denmark)

    Block, Ines; List, Markus; Pedersen, Marlene Lemvig

    of staining conditions and mode of signal analysis. However, the sample management and data analysis still poses challenges because of the high number of samples, sample dilutions, customized array patterns, and various programs necessary for array construction and data processing. We developed...... evaluation. Subsequent data analysis may include correction of unequal array staining (surface normalization), estimation of protein concentration from response curves, normalization for total protein amount per sample and statistical evaluation. Established analysis methods have been integrated with MIRACLE......, offering experimental scientists a customized end-to-end solution for sample management and for data analysis. MIRACLE thus has the potential to further spread utilization of RPPAs as an emerging technology for high-throughput protein analysis....

  8. A study of diabetes mellitus within a large sample of Australian twins

    DEFF Research Database (Denmark)

    Condon, Julianne; Shaw, Joanne E; Luciano, Michelle;

    2008-01-01

    with type 2 diabetes (T2D), 41 female pairs with gestational diabetes (GD), 5 pairs with impaired glucose tolerance (IGT) and one pair with MODY. Heritabilities of T1D, T2D and GD were all high, but our samples did not have the power to detect effects of shared environment unless they were very large......Twin studies of diabetes mellitus can help elucidate genetic and environmental factors in etiology and can provide valuable biological samples for testing functional hypotheses, for example using expression and methylation studies of discordant pairs. We searched the volunteer Australian Twin...... Registry (19,387 pairs) for twins with diabetes using disease checklists from nine different surveys conducted from 1980-2000. After follow-up questionnaires to the twins and their doctors to confirm diagnoses, we eventually identified 46 pairs where one or both had type 1 diabetes (T1D), 113 pairs...

  9. Chemical, Biological, and Radiological (CBR) Contamination Survivability, Large Item Interiors

    Science.gov (United States)

    2016-08-03

    Manual (FM) 3- 11.312 and Allied Tactical Publication ( ATP ) 45C13]. f. The acronym CBR is used in this document, rather than NBC, to reflect current...Testing and Materials AT&L acquisition, technology, and logistics ATEC U.S. Army Test and Evaluation Command ATP Allied Technical Publication C...Contamination Avoidance, 2 February 2006, Change 1, 30 April 2009. 13. ATP 45C, Reporting Nuclear Detonations, Biological and Chemical Attacks, and

  10. Alteration of biological samples in speciation analysis of metalloproteins.

    Science.gov (United States)

    Wolf, Christian; Wenda, Nadine; Richter, Andrea; Kyriakopoulos, Antonios

    2007-10-01

    For investigations of metalloproteins by speciation analysis, the integrity of the protein-metal complexes before and during separation is crucial. Knowledge about potential alterations of the samples is thus essential to avoid misinterpretations of the analytical results. Chromatographic element profiles of different cytosolic samples from animal tissues were measured repeatedly to estimate the sample stability. The dependence of the signals on the dwell time of the sample in an autosampling device at 4 degrees C for a period of 10 h was observed. Alterations in the element content of different metal-containing fractions were quantified by means of recovery values. Some metalloprotein fractions (e.g. approximately 27-kDa arsenic, approximately 27-kDa iron and different zinc fractions) were stable or only minor alterations were observed and for their investigation an autosampling device is therefore suitable. However, most of the other metalloprotein fractions, especially nickel-containing proteins, showed major alterations: these samples should therefore be analysed immediately after preparation or directly after thawing.

  11. Sampling Versus Filtering in Large-Eddy Simulations

    Science.gov (United States)

    Debliquy, O.; Knaepen, B.; Carati, D.; Wray, A. A.

    2004-01-01

    A LES formalism in which the filter operator is replaced by a sampling operator is proposed. The unknown quantities that appear in the LES equations originate only from inadequate resolution (Discretization errors). The resulting viewpoint seems to make a link between finite difference approaches and finite element methods. Sampling operators are shown to commute with nonlinearities and to be purely projective. Moreover, their use allows an unambiguous definition of the LES numerical grid. The price to pay is that sampling never commutes with spatial derivatives and the commutation errors must be modeled. It is shown that models for the discretization errors may be treated using the dynamic procedure. Preliminary results, using the Smagorinsky model, are very encouraging.

  12. Censored regression analysis in large samples with many zero observations

    NARCIS (Netherlands)

    Ph.H.B.F. Franses (Philip Hans); E. Slagter (Erica); J.S. Cramer (Mars)

    1999-01-01

    textabstractWith the advent of improved data collection techniques, the applied econometrician can nowadays have access to very large data bases. Sometimes, however, these can have fairly low informational content. For example, a typical response rate in direct mailings is below 1%. Given the smal

  13. Determination of platinum, palladium, and lead in biological samples by atomic absorption spectrophotometry.

    Science.gov (United States)

    Tillery, J B; Johnson, D E

    1975-01-01

    A flameless atomic absorption method for the coextraction of platinum and palladium from biological and environmental samples by high molecular weight amine (HMWA) is given. Also, methods for lead determination in biological samples by use of extraction flameless analysis and direct aspiration-flame analysis are reported. A study of lead contamination of Vacutainer tubes is given. PMID:1227857

  14. Sample sizing of biological materials analyzed by energy dispersion X-ray fluorescence

    Energy Technology Data Exchange (ETDEWEB)

    Paiva, Jose D.S.; Franca, Elvis J.; Magalhaes, Marcelo R.L.; Almeida, Marcio E.S.; Hazin, Clovis A., E-mail: dan-paiva@hotmail.com, E-mail: ejfranca@cnen.gov.br, E-mail: marcelo_rlm@hotmail.com, E-mail: maensoal@yahoo.com.br, E-mail: chazin@cnen.gov.b [Centro Regional de Ciencias Nucleares do Nordeste (CRCN-NE/CNEN-PE), Recife, PE (Brazil)

    2013-07-01

    Analytical portions used in chemical analyses are usually less than 1g. Errors resulting from the sampling are barely evaluated, since this type of study is a time-consuming procedure, with high costs for the chemical analysis of large number of samples. The energy dispersion X-ray fluorescence - EDXRF is a non-destructive and fast analytical technique with the possibility of determining several chemical elements. Therefore, the aim of this study was to provide information on the minimum analytical portion for quantification of chemical elements in biological matrices using EDXRF. Three species were sampled in mangroves from the Pernambuco, Brazil. Tree leaves were washed with distilled water, oven-dried at 60 deg C and milled until 0.5 mm particle size. Ten test-portions of approximately 500 mg for each species were transferred to vials sealed with polypropylene film. The quality of the analytical procedure was evaluated from the reference materials IAEA V10 Hay Powder, SRM 2976 Apple Leaves. After energy calibration, all samples were analyzed under vacuum for 100 seconds for each group of chemical elements. The voltage used was 15 kV and 50 kV for chemical elements of atomic number lower than 22 and the others, respectively. For the best analytical conditions, EDXRF was capable of estimating the sample size uncertainty for further determination of chemical elements in leaves. (author)

  15. Multiple replica repulsion technique for efficient conformational sampling of biological systems.

    Science.gov (United States)

    Malevanets, Anatoly; Wodak, Shoshana J

    2011-08-17

    Here, we propose a technique for sampling complex molecular systems with many degrees of freedom. The technique, termed "multiple replica repulsion" (MRR), does not suffer from poor scaling with the number of degrees of freedom associated with common replica exchange procedures and does not require sampling at high temperatures. The algorithm involves creation of multiple copies (replicas) of the system, which interact with one another through a repulsive potential that can be applied to the system as a whole or to portions of it. The proposed scheme prevents oversampling of the most populated states and provides accurate descriptions of conformational perturbations typically associated with sampling ground-state energy wells. The performance of MRR is illustrated for three systems of increasing complexity. A two-dimensional toy potential surface is used to probe the sampling efficiency as a function of key parameters of the procedure. MRR simulations of the Met-enkephalin pentapeptide, and the 76-residue protein ubiquitin, performed in presence of explicit water molecules and totaling 32 ns each, investigate the ability of MRR to characterize the conformational landscape of the peptide, and the protein native basin, respectively. Results obtained for the enkephalin peptide reflect more closely the extensive conformational flexibility of this peptide than previously reported simulations. Those obtained for ubiquitin show that conformational ensembles sampled by MRR largely encompass structural fluctuations relevant to biological recognition, which occur on the microsecond timescale, or are observed in crystal structures of ubiquitin complexes with other proteins. MRR thus emerges as a very promising simple and versatile technique for modeling the structural plasticity of complex biological systems. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  16. Sequential Monte Carlo on large binary sampling spaces

    CERN Document Server

    Schäfer, Christian

    2011-01-01

    A Monte Carlo algorithm is said to be adaptive if it automatically calibrates its current proposal distribution using past simulations. The choice of the parametric family that defines the set of proposal distributions is critical for a good performance. In this paper, we present such a parametric family for adaptive sampling on high-dimensional binary spaces. A practical motivation for this problem is variable selection in a linear regression context. We want to sample from a Bayesian posterior distribution on the model space using an appropriate version of Sequential Monte Carlo. Raw versions of Sequential Monte Carlo are easily implemented using binary vectors with independent components. For high-dimensional problems, however, these simple proposals do not yield satisfactory results. The key to an efficient adaptive algorithm are binary parametric families which take correlations into account, analogously to the multivariate normal distribution on continuous spaces. We provide a review of models for binar...

  17. Eigenvectors of some large sample covariance matrix ensembles

    CERN Document Server

    Ledoit, Olivier

    2009-01-01

    We consider sample covariance matrices $S_N=\\frac{1}{p}\\Sigma_N^{1/2}X_NX_N^* \\Sigma_N^{1/2}$ where $X_N$ is a $N \\times p$ real or complex matrix with i.i.d. entries with finite $12^{\\rm th}$ moment and $\\Sigma_N$ is a $N \\times N$ positive definite matrix. In addition we assume that the spectral measure of $\\Sigma_N$ almost surely converges to some limiting probability distribution as $N \\to \\infty$ and $p/N \\to \\gamma >0.$ We quantify the relationship between sample and population eigenvectors by studying the asymptotics of functionals of the type $\\frac{1}{N} \\text{Tr} (g(\\Sigma_N) (S_N-zI)^{-1})),$ where $I$ is the identity matrix, $g$ is a bounded function and $z$ is a complex number. This is then used to compute the asymptotically optimal bias correction for sample eigenvalues, paving the way for a new generation of improved estimators of the covariance matrix and its inverse.

  18. Deep Penetration of Charged Particles in Biological Samples

    Institute of Scientific and Technical Information of China (English)

    WANG Rui-Jin; MU Yu-Guang; ZHAO Ming-Wen; MA Yu-Chen; XIA Yue-Yuan; LIU Xiang-Dong; LIU Ji-Tian; ZHANG Jian-Hua; YU Zeng-Liang

    2001-01-01

    Experimental evidence of abnormally deep penetration in some botanical targets by low-energy ion beams is presented. The energy spectra of 818kev He+ ions penetrating a 70μm thick seed coat of maize, fruit peel of grape and of tomato all have a common feature. The leading edges of these broad spectra indicate that some of the penetrating ions pass through the thick targets easily and only lose a small fraction of their initial incident energy. Rutherford backscattering spectrometry and electron microprobe measurements are used to determine the argon concentration in multilayer samples of the seed coat of maize implanted by 200 kev Ar+ ions. The results show that about 10% of the Ar+ ions can penetrate deeper than ~l00 μm in these samples.

  19. Deep Penetration of Charged Particles in Biological Samples

    Science.gov (United States)

    Wang, Rui-Jin; Xia, Yue-Yuan; Mu, Yu-Guang; Zhao, Ming-Wen; Ma, Yu-Chen; Liu, Xiang-Dong; Zhang, Jian-Hua; Liu, Ji-Tian; Yu, Zeng-Liang

    2001-02-01

    Experimental evidence of abnormally deep penetration in some botanical targets by low-energy ion beams is presented. The energy spectra of 818 keV He+ ions penetrating a 70 µm thick seed coat of maize, fruit peel of grape and of tomato all have a common feature. The leading edges of these broad spectra indicate that some of the penetrating ions pass through the thick targets easily and only lose a small fraction of their initial incident energy. Rutherford backscattering spectrometry and electron microprobe measurements are used to determine the argon concentration in multilayer samples of the seed coat of maize implanted by 200 keV Ar+ ions. The results show that about 10% of the Ar+ ions can penetrate deeper than ~100 µm in these samples.

  20. Micro-differential scanning calorimeter for liquid biological samples

    Science.gov (United States)

    Wang, Shuyu; Yu, Shifeng; Siedler, Michael S.; Ihnat, Peter M.; Filoti, Dana I.; Lu, Ming; Zuo, Lei

    2016-10-01

    We developed an ultrasensitive micro-DSC (differential scanning calorimeter) for liquid protein sample characterization. This design integrated vanadium oxide thermistors and flexible polymer substrates with microfluidics chambers to achieve a high sensitivity (6 V/W), low thermal conductivity (0.7 mW/K), high power resolutions (40 nW), and well-defined liquid volume (1 μl) calorimeter sensor in a compact and cost-effective way. We further demonstrated the performance of the sensor with lysozyme unfolding. The measured transition temperature and enthalpy change were in accordance with the previous literature data. This micro-DSC could potentially raise the prospect of high-throughput biochemical measurement by parallel operation with miniaturized sample consumption.

  1. Heritability of psoriasis in a large twin sample

    DEFF Research Database (Denmark)

    Lønnberg, Ann Sophie; Skov, L; Skytthe, A;

    2013-01-01

    AIM: To study the concordance of psoriasis in a population-based twin sample. METHODS: Data on psoriasis in 10,725 twin pairs, 20-71 years of age, from the Danish Twin Registry was collected via a questionnaire survey. The concordance and heritability of psoriasis were estimated. RESULTS: In total......, 4.1% of the men and 4.2% of the women had a lifetime history of psoriasis. The probandwise concordance for psoriasis was larger in monozygotic than in dizygotic twins, 0.33 vs. 0.17. Genetic factors explained 68% (60-75%) of the variation in the susceptibility to psoriasis, whereas the rest...

  2. Elemental distribution and sample integrity comparison of freeze-dried and frozen-hydrated biological tissue samples with nuclear microprobe

    Energy Technology Data Exchange (ETDEWEB)

    Vavpetič, P., E-mail: primoz.vavpetic@ijs.si [Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana (Slovenia); Vogel-Mikuš, K. [Biotechnical Faculty, Department of Biology, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana (Slovenia); Jeromel, L. [Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana (Slovenia); Ogrinc Potočnik, N. [Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana (Slovenia); FOM-Institute AMOLF, Science Park 104, 1098 XG Amsterdam (Netherlands); Pongrac, P. [Biotechnical Faculty, Department of Biology, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana (Slovenia); Department of Plant Physiology, University of Bayreuth, Universitätstr. 30, 95447 Bayreuth (Germany); Drobne, D.; Pipan Tkalec, Ž.; Novak, S.; Kos, M.; Koren, Š.; Regvar, M. [Biotechnical Faculty, Department of Biology, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana (Slovenia); Pelicon, P. [Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana (Slovenia)

    2015-04-01

    The analysis of biological samples in frozen-hydrated state with micro-PIXE technique at Jožef Stefan Institute (JSI) nuclear microprobe has matured to a point that enables us to measure and examine frozen tissue samples routinely as a standard research method. Cryotome-cut slice of frozen-hydrated biological sample is mounted between two thin foils and positioned on the sample holder. The temperature of the cold stage in the measuring chamber is kept below 130 K throughout the insertion of the samples and the proton beam exposure. Matrix composition of frozen-hydrated tissue is consisted mostly of ice. Sample deterioration during proton beam exposure is monitored during the experiment, as both Elastic Backscattering Spectrometry (EBS) and Scanning Transmission Ion Microscopy (STIM) in on–off axis geometry are recorded together with the events in two PIXE detectors and backscattered ions from the chopper in a single list-mode file. The aim of this experiment was to determine differences and similarities between two kinds of biological sample preparation techniques for micro-PIXE analysis, namely freeze-drying and frozen-hydrated sample preparation in order to evaluate the improvements in the elemental localisation of the latter technique if any. In the presented work, a standard micro-PIXE configuration for tissue mapping at JSI was used with five detection systems operating in parallel, with proton beam cross section of 1.0 × 1.0 μm{sup 2} and a beam current of 100 pA. The comparison of the resulting elemental distributions measured at the biological tissue prepared in the frozen-hydrated and in the freeze-dried state revealed differences in elemental distribution of particular elements at the cellular level due to the morphology alteration in particular tissue compartments induced either by water removal in the lyophilisation process or by unsatisfactory preparation of samples for cutting and mounting during the shock-freezing phase of sample preparation.

  3. Elemental distribution and sample integrity comparison of freeze-dried and frozen-hydrated biological tissue samples with nuclear microprobe

    Science.gov (United States)

    Vavpetič, P.; Vogel-Mikuš, K.; Jeromel, L.; Ogrinc Potočnik, N.; Pongrac, P.; Drobne, D.; Pipan Tkalec, Ž.; Novak, S.; Kos, M.; Koren, Š.; Regvar, M.; Pelicon, P.

    2015-04-01

    The analysis of biological samples in frozen-hydrated state with micro-PIXE technique at Jožef Stefan Institute (JSI) nuclear microprobe has matured to a point that enables us to measure and examine frozen tissue samples routinely as a standard research method. Cryotome-cut slice of frozen-hydrated biological sample is mounted between two thin foils and positioned on the sample holder. The temperature of the cold stage in the measuring chamber is kept below 130 K throughout the insertion of the samples and the proton beam exposure. Matrix composition of frozen-hydrated tissue is consisted mostly of ice. Sample deterioration during proton beam exposure is monitored during the experiment, as both Elastic Backscattering Spectrometry (EBS) and Scanning Transmission Ion Microscopy (STIM) in on-off axis geometry are recorded together with the events in two PIXE detectors and backscattered ions from the chopper in a single list-mode file. The aim of this experiment was to determine differences and similarities between two kinds of biological sample preparation techniques for micro-PIXE analysis, namely freeze-drying and frozen-hydrated sample preparation in order to evaluate the improvements in the elemental localisation of the latter technique if any. In the presented work, a standard micro-PIXE configuration for tissue mapping at JSI was used with five detection systems operating in parallel, with proton beam cross section of 1.0 × 1.0 μm2 and a beam current of 100 pA. The comparison of the resulting elemental distributions measured at the biological tissue prepared in the frozen-hydrated and in the freeze-dried state revealed differences in elemental distribution of particular elements at the cellular level due to the morphology alteration in particular tissue compartments induced either by water removal in the lyophilisation process or by unsatisfactory preparation of samples for cutting and mounting during the shock-freezing phase of sample preparation.

  4. Towards a methodology for large-sample prompt-gamma neutron-activation analysis

    NARCIS (Netherlands)

    Degenaar, I.H.

    2004-01-01

    Large-sample prompt-gamma neutron-activation analysis, or shortly LS PGNAA, is a method by which mass fractions of elements can be determined in large samples with a mass over 1 kg. In this method the large sample is irradiated with neutrons. Directly (prompt) after absorption of the neutrons photon

  5. Nanocharacterization of Soft Biological Samples in Shear Mode with Quartz Tuning Fork Probes

    OpenAIRE

    Manel Puig-Vidal; Laura Gonzalez; Jorge Otero

    2012-01-01

    Quartz tuning forks are extremely good resonators and their use is growing in scanning probe microscopy. Nevertheless, only a few studies on soft biological samples have been reported using these probes. In this work, we present the methodology to develop and use these nanosensors to properly work with biological samples. The working principles, fabrication and experimental setup are presented. The results in the nanocharacterization of different samples in different ambients are presented by...

  6. Multiphoton imaging of biological samples during freezing and heating

    Science.gov (United States)

    Breunig, H. G.; Uchugonova, A.; König, K.

    2014-02-01

    We applied multiphoton microscopic imaging to observe freezing and heating effects in plant- and animal cell samples. The experimental setups consisted of a multiphoton imaging system and a heating and cooling stage which allows for precise temperature control from liquid nitrogen temperature (-196°C 77 K) up to +600°C (873 K) with heating/freezing rates between 0.01 K/min and 150 K/min. Two multiphoton imaging systems were used: a system based on a modified optical microscope and a flexible mobile system. To illustrate the imaging capabilities, plant leafs as well as animal cells were microscopically imaged in vivo during freezing based on autofluorescence lifetime and intensity of intrinsic molecules. The measurements illustrate the usefulness of multiphoton imaging to investigate freezing effects on animal and plant cells.

  7. Comparative analysis of toxin detection in biological and enviromental samples

    Science.gov (United States)

    Ogert, Robert A.; Burans, James; O'Brien, Tom; Ligler, Frances S.

    1994-03-01

    The basic recognition schemes underlying the principles of standard enzyme-linked immunosorbent assay (ELISA) and radioimmunoassay (RIA) protocols are increasingly being adapted for use with new detection devices. A direct comparison was made using a fiber optic biosensor that employs evanescent wave detection and an ELISA using avidin-biotin. The assays were developed for the detection of Ricinus communis agglutinin II, also known as ricin or RCA60. Detection limits between the two methods were comparable for ricin in phosphate buffered saline (PBS), however results in complex samples differed slightly. In PBS, sensitivity for ricin was 1 ng/ml using the fiber optic device and 500 pg/ml using the ELISA. The fiber optic sensor could not detect ricin directly in urine or serum spiked with 5 ng/ml ricin, however, the ELISA showed detection but at reduced levels to the PBS control.

  8. Information Transfer With Censored Data: Some Large-Sample Results

    Science.gov (United States)

    Clarke, Robin T.

    1991-06-01

    This paper presents some new results for the transfer and extension of information at sites with short hydrological records. The results refer particularly to the transfer and extension of annual flood data. The methods described make use of incomplete or "censored" data such as may be supplied by people living near a river or from records collected for nonhydrological purposes, and they constitute extensions to methods already described in the literature. For two specific censoring configurations, the gain in information is assessed analytically; it is shown that, under certain conditions, the gain in information can be substantial, but in general the gain is small, particularly where scale parameters are estimated. For other configurations of censored data, an analytical formulation is not possible, and integrals are given from which information gain may be assessed by numerical calculation. Another result extends the use of flood peaks exceeding some threshold value ("peaks over a threshold," POTs); probabilistic models of flood frequency using POTs are, in effect, fitted using censored data. The value of the results presented in the paper is likely to be restricted by assumptions about the probabilistic structure of flood sequences: in one case that their distribution (at different sites) is bivariate lognormal, and, for the POT model, that floods occur as a Poisson process with POTs exponentially distributed. The results show, in strictly qualitative terms, the circumstances in which information might be gained by the use of censored data at two sites, and how large (or small) the gains might be.

  9. Biological Conservation of Giant Limpets: The Implications of Large Size.

    Science.gov (United States)

    Espinosa, F; Rivera-Ingraham, G A

    Patellogastropods, also known as true limpets, are distributed throughout the world and constitute key species in coastal ecosystems. Some limpet species achieve remarkable sizes, which in the most extreme cases can surpass 35cm in shell length. In this review, we focus on giant limpets, which are defined as those with a maximum shell size surpassing 10cm. According to the scientific literature, there are a total of 14 species across five genera that reach these larger sizes. Four of these species are threatened or in danger of extinction. Inhabiting the intertidal zones, limpets are frequently affected by anthropogenic impacts, namely collection by humans, pollution and habitat fragmentation. In the case of larger species, their conspicuous size has made them especially prone to human collection since prehistoric times. Size is not phylogeny-dependent among giant limpets, but is instead related to behavioural traits instead. Larger-sized species tend to be nonmigratory and territorial compared to those that are smaller. Collection by humans has been cited as the main cause behind the decline and/or extinction of giant limpet populations. Their conspicuously large size makes them the preferred target of human collection. Because they are protandric species, selectively eliminating larger specimens of a given population seriously compromises their viability and has led to local extinction events in some cases. Additionally, sustained collection over time may lead to microevolutionary responses that result in genetic changes. The growing presence of artificial structures in coastal ecosystems may cause population fragmentation and isolation, limiting the genetic flow and dispersion capacity of many limpet species. However, when they are necessitated, artificial structures could be managed to establish marine artificial microreserves and contribute to the conservation of giant limpet species that naturally settle on them. © 2017 Elsevier Ltd. All rights reserved.

  10. Robotic, MEMS-based Multi Utility Sample Preparation Instrument for ISS Biological Workstation Project

    Data.gov (United States)

    National Aeronautics and Space Administration — This project will develop a multi-functional, automated sample preparation instrument for biological wet-lab workstations on the ISS. The instrument is based on a...

  11. Detection of heavy metals in biological samples through anodic stripping voltammetry

    OpenAIRE

    Buzea, Vlad; Florescu, Monica; Badea, Mihaela

    2012-01-01

    The toxicological aspects due to the presence of heavy metals in biological samples impose to have accurate and rapid methods for their detection. This paper is aimed to review approaches to anodic stripping voltammetry (ASV) determination of several heavy metals (lead, cadmium, copper, mercury, zinc) in biological matrices (blood, urine, saliva, tissue sample). Analytical performances (LOD, data linearity range, sensitivity) of the reviewed methods were presented for several electrochemical ...

  12. Two Test Items to Explore High School Students' Beliefs of Sample Size When Sampling from Large Populations

    Science.gov (United States)

    Bill, Anthony; Henderson, Sally; Penman, John

    2010-01-01

    Two test items that examined high school students' beliefs of sample size for large populations using the context of opinion polls conducted prior to national and state elections were developed. A trial of the two items with 21 male and 33 female Year 9 students examined their naive understanding of sample size: over half of students chose a…

  13. Sample preparation strategies for food and biological samples prior to nanoparticle detection and imaging

    DEFF Research Database (Denmark)

    Larsen, Erik Huusfeldt; Löschner, Katrin

    2014-01-01

    fractionation (AFFF, or AF4) coupled on-line to various detectors including static and dynamic light scattering (LS), UV or fluorescence (FL) spectroscopies and ICP-MS have proven useful and powerful [1, 2, 3]. Furthermore, additional information obtained by an imaging method such as transmission electron...... microscopy (TEM) proved to be necessary for trouble shooting of results obtained from AFFF-LS-ICP-MS. Aqueous and enzymatic extraction strategies were tested for thorough sample preparation aiming at degrading the sample matrix and to liberate the AgNPs from chicken meat into liquid suspension. The resulting...

  14. Microfluidic devices for sample clean-up and screening of biological samples

    NARCIS (Netherlands)

    Tetala, K.K.R.

    2009-01-01

    Analytical chemistry plays an important role in the separation and identification of analytes from raw samples (e.g. plant extracts, blood), but the whole analytical process is tedious, difficult to automate and time consuming. To overcome these drawbacks, the concept of μTAS (miniaturized total ana

  15. Microfluidic devices for sample clean-up and screening of biological samples

    NARCIS (Netherlands)

    Tetala, K.K.R.

    2009-01-01

    Analytical chemistry plays an important role in the separation and identification of analytes from raw samples (e.g. plant extracts, blood), but the whole analytical process is tedious, difficult to automate and time consuming. To overcome these drawbacks, the concept of μTAS (miniaturized total ana

  16. Biospark: scalable analysis of large numerical datasets from biological simulations and experiments using Hadoop and Spark.

    Science.gov (United States)

    Klein, Max; Sharma, Rati; Bohrer, Chris H; Avelis, Cameron M; Roberts, Elijah

    2017-01-15

    Data-parallel programming techniques can dramatically decrease the time needed to analyze large datasets. While these methods have provided significant improvements for sequencing-based analyses, other areas of biological informatics have not yet adopted them. Here, we introduce Biospark, a new framework for performing data-parallel analysis on large numerical datasets. Biospark builds upon the open source Hadoop and Spark projects, bringing domain-specific features for biology.

  17. Exploring Earth's Atmospheric Biology using a Platform-Extensible Sampling Payload

    Science.gov (United States)

    Gentry, D.; Rothschild, L.

    2012-12-01

    The interactions between Earth's atmosphere and its biosphere, or aerobiology, remain a significant unknown. What few studies have been done conclusively show that Earth's atmosphere has a rich and dynamic microbial presence[Bowers et al., 2010]; that microbes suspended in air survive over long times (1-2 weeks)[Smith et al., 2010] and travel great distances (>5000 km)[Kellogg and Griffin, 2006]; that some airborne bacteria actively nucleate ice crystals, affecting meteorology[Delort et al., 2010]; and that the presence of microbes in the atmosphere has other planetary-scale effects[Delort et al., 2010]. Basic questions, however, such as the number of microbes present, their activity level and state, the different species present and their variance over time and space, remain largely unquantified. Compounding the significant physical and environmental challenges of reliable aerobiological sampling, collection and analysis of biological samples at altitudes above ~10-20 km has traditionally used ad hoc instrumentation and techniques, yielding primarily qualitative analytical results that lack a common basis for comparison[Bowers et al., 2010]. There is a strong need for broad-basis, repeatable, reliably comparable data about aerobiological basics. We describe here a high-altitude environmental and biological sampling project designed specifically to address these issues. The goal is a robust, reliable, re-usable sampling system, with open reproducibility and adaptability for multiple low-cost flight platforms (including ground-tethered systems, high-altitude balloons, and suborbital sounding rockets); by establishing a common modular payload structure for high-altitude sampling with appeal to a broad user base, we hope to encourage widespread collection of comparable aerobiological data. We are on our third prototype iteration, with demonstrated function of two sample capture modules, a support backbone (tracking, data logging, event response, etc.), a simple ground

  18. In-focus electron microscopy of frozen-hydrated biological samples with a Boersch phase plate

    Energy Technology Data Exchange (ETDEWEB)

    Barton, B.; Rhinow, D.; Walter, A.; Schroeder, R. [Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main (Germany); Benner, G.; Majorovits, E.; Matijevic, M.; Niebel, H. [Carl Zeiss NTS GmbH, D-73447 Oberkochen (Germany); Mueller, H.; Haider, M. [CEOS GmbH, Englerstr. 26, 69126 Heidleberg (Germany); Lacher, M.; Schmitz, S.; Holik, P. [Caesar Research Center, Ludwig-Erhard-Allee 2, D-53175 Bonn (Germany); Kuehlbrandt, W., E-mail: werner.kuehlbrandt@mpibp-frankfurt.mpg.de [Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main (Germany)

    2011-12-15

    We report the implementation of an electrostatic Einzel lens (Boersch) phase plate in a prototype transmission electron microscope dedicated to aberration-corrected cryo-EM. The combination of phase plate, C{sub s} corrector and Diffraction Magnification Unit (DMU) as a new electron-optical element ensures minimal information loss due to obstruction by the phase plate and enables in-focus phase contrast imaging of large macromolecular assemblies. As no defocussing is necessary and the spherical aberration is corrected, maximal, non-oscillating phase contrast transfer can be achieved up to the information limit of the instrument. A microchip produced by a scalable micro-fabrication process has 10 phase plates, which are positioned in a conjugate, magnified diffraction plane generated by the DMU. Phase plates remained fully functional for weeks or months. The large distance between phase plate and the cryo sample permits the use of an effective anti-contaminator, resulting in ice contamination rates of <0.6 nm/h at the specimen. Maximal in-focus phase contrast was obtained by applying voltages between 80 and 700 mV to the phase plate electrode. The phase plate allows for in-focus imaging of biological objects with a signal-to-noise of 5-10 at a resolution of 2-3 nm, as demonstrated for frozen-hydrated virus particles and purple membrane at liquid-nitrogen temperature. -- Highlights: Black-Right-Pointing-Pointer We implement an electrostatic Boersch phase plate into a dedicated prototypical TEM. Black-Right-Pointing-Pointer Phase contrast aberration-corrected electron microscope (PACEM) includes a diffraction magnification unit (DMU). Black-Right-Pointing-Pointer DMU minimizes obstruction of low spatial frequencies by the phase plate. Black-Right-Pointing-Pointer In-focus phase contrast generation is demonstrated for frozen-hydrated biological specimens.

  19. Development of Sampling and Preservation Techniques to Retard Chemical and Biological Changes in Water Samples

    Science.gov (United States)

    1983-06-24

    accomplishing the original scope of work (development of sampling and pres- ervation techniques). System No. I is described in Table 1. Quadruplicate SARM ...Rate: 1.0 ml/min Injection Volume: 40-100 p1 Quadruplicate SARM reference solutions were analyzed for the four munitions at the following concentration...tion of SARM Reference Solutions of DNP, RDX, TNBI DNB, 2,4-DNT, TNT, Tetryl, and DPA ...... .............. A-6 2 Statistical Evaluation of DNP in

  20. Mercury speciation and total trace element determination of low-biomass biological samples.

    Science.gov (United States)

    Taylor, Vivien F; Jackson, Brian P; Chen, Celia Y

    2008-12-01

    Current approaches to mercury speciation and total trace element analysis require separate extraction/digestions of the sample. Ecologically important aquatic organisms--notably primary consumers such as zooplankton, polychaetes and amphipods--usually yield very low biomass for analysis, even with significant compositing of multiple organisms. Individual organisms in the lower aquatic food chains (mussels, snails, oysters, silversides, killifish) can also have very low sample mass, and analysis of whole single organisms is important to metal uptake studies. A method for the determination of both methyl Hg and total heavy metal concentrations (Zn, As, Se, Cd, Hg, Pb) in a single, low-mass sample of aquatic organisms was developed. Samples (2 to 50 mg) were spiked with enriched with (201)MeHg and (199)Hg, then leached in 4 M HNO(3) at 55 degrees C for extraction of MeHg. After 16 h, an aliquot (0.05 mL) was removed to determine mercury species (methyl and inorganic Hg) by isotope dilution gas chromatography inductively coupled plasma mass spectrometry (ICP-MS). The leachate was then acidified to 9 M HNO(3) and digested in a microwave at 150 degrees C for 10 min, and total metal concentrations were determined by collision cell ICP-MS. The method was validated by analyzing five biological certified reference materials. Average percent recoveries for Zn, As, Se, Cd, MeHg, Hg(total) and Pb were 99.9%, 103.5%, 100.4%, 103.3%, 101%, 97.7%, and 97.1%, respectively. The correlation between the sum of MeHg and inorganic Hg from the speciation analysis and total Hg by conventional digestion of the sample was determined for a large sample set of aquatic invertebrates (n = 285). Excellent agreement between the two measured values was achieved. This method is advantageous in situations where sample size is limited, and where correlations between Hg species and other metals are required in the same sample. The method also provides further validation of speciation data, by

  1. Procedures for cryogenic X-ray ptychographic imaging of biological samples

    Science.gov (United States)

    Yusuf, M.; Zhang, F.; Chen, B.; Bhartiya, A.; Cunnea, K.; Wagner, U.; Cacho-Nerin, F.; Schwenke, J.; Robinson, I. K.

    2017-01-01

    Biological sample-preparation procedures have been developed for imaging human chromosomes under cryogenic conditions. A new experimental setup, developed for imaging frozen samples using beamline I13 at Diamond Light Source, is described. This manuscript describes the equipment and experimental procedures as well as the authors’ first ptychographic reconstructions using X-rays.

  2. Procedures for cryogenic X-ray ptychographic imaging of biological samples.

    Science.gov (United States)

    Yusuf, M; Zhang, F; Chen, B; Bhartiya, A; Cunnea, K; Wagner, U; Cacho-Nerin, F; Schwenke, J; Robinson, I K

    2017-03-01

    Biological sample-preparation procedures have been developed for imaging human chromosomes under cryogenic conditions. A new experimental setup, developed for imaging frozen samples using beamline I13 at Diamond Light Source, is described. This manuscript describes the equipment and experimental procedures as well as the authors' first ptychographic reconstructions using X-rays.

  3. Procedures for cryogenic X-ray ptychographic imaging of biological samples

    Directory of Open Access Journals (Sweden)

    M. Yusuf

    2017-03-01

    Full Text Available Biological sample-preparation procedures have been developed for imaging human chromosomes under cryogenic conditions. A new experimental setup, developed for imaging frozen samples using beamline I13 at Diamond Light Source, is described. This manuscript describes the equipment and experimental procedures as well as the authors' first ptychographic reconstructions using X-rays.

  4. Study of complex matrix effect on solid phase microextraction for biological sample analysis.

    Science.gov (United States)

    Jiang, Ruifen; Xu, Jianqiao; Zhu, Fang; Luan, Tiangang; Zeng, Feng; Shen, Yong; Ouyang, Gangfeng

    2015-09-11

    Solid phase microextraction (SPME) has become a useful tool for in vivo monitoring the behavior of environmental organic pollutants in biological species due to its simplicity, relatively non-invasive, and cost-effective manner. However, the complex matrices in biological samples could significantly influence the extraction kinetic, and bias the quantification result. In this study, we investigated the effect of complex matrix on the extraction kinetic of SPME for biological sample analysis. Two sample matrices, phosphate-buffered saline (PBS) with bovine serum albumin (BSA) and agarose gel with BSA were used to simulate the biological fluid and tissue. Results showed that the addition of BSA significantly enhanced the mass transfer of organic compounds onto SPME fiber in both PBS buffer and gel sample. Enhancement factors ranging from 1.3 to 27, and 2.0 to 80 were found for all selected polyaromatic hydrocarbons (PAHs) in PBS buffer and agarose gel with BSA concentration of 0.1-5%, respectively. Then, an improved theoretical model was applied to quantify the observed enhancement effect, and the result showed that the predicted sampling time constant agreed well with the experimental one in complex matrix. Furthermore, a simplified equation was proposed for the real biological sample analysis.

  5. Determination of Cu, Zn, and Se in microvolumes of liquid biological samples

    Science.gov (United States)

    Shaban, H. A.; Shaltout, A. A.; Abdou, M.; Al Ashker, E. A.; Elgohary, M.

    2011-01-01

    Cu, Zn, and Se were successfully determined in a few microliters (<100 μl) of biological samples using discrete injection atomic absorption spectrometry. Different factors were investigated in order to obtain a biological sample volume which is valid for analysis. Among them are the effect of microsampling volume variations (starting from 40 to 200 μl), nebulization efficiency, detection limits, precision, and finally the calibration and sensitivity of the proposed method. It was found that 60 μl of the biological sample was adequate for the quantitative analysis with reasonable precision. The advantages of the proposed method are not only rapidity, simplicity, sensitivity, and good precision, but also, contrary to conventional flame atomic absorption spectrometry, the capability of analyzing microvolumes of samples.

  6. Non-destructive electron microscopy imaging and analysis of biological samples with graphene coating

    Science.gov (United States)

    Park, Jong Bo; Kim, Yong-Jin; Kim, Seong-Min; Yoo, Je Min; Kim, Youngsoo; Gorbachev, Roman; Barbolina, I. I.; Kim, Sang Jin; Kang, Sangmin; Yoon, Myung-Han; Cho, Sung-Pyo; Novoselov, Konstantin S.; Hong, Byung Hee

    2016-12-01

    In electron microscopy (EM), charging of non-conductive biological samples by focused electron beams hinders their high-resolution imaging. Gold or platinum coatings have been commonly used to prevent such sample charging, but it disables further quantitative and qualitative chemical analyses such as energy dispersive spectroscopy (EDS). Here we report that graphene-coating on biological samples enables non-destructive high-resolution imaging by EM as well as chemical analysis by EDS, utilizing graphene’s transparency to electron beams, high conductivity, outstanding mechanical strength and flexibility. We believe that the graphene-coated imaging and analysis would provide us a new opportunity to explore various biological phenomena unseen before due to the limitation in sample preparation and image resolution, which will broaden our understanding on the life mechanism of various living organisms.

  7. Preparation of Biological Samples Containing Metoprolol and Bisoprolol for Applying Methods for Quantitative Analysis

    Directory of Open Access Journals (Sweden)

    Corina Mahu Ştefania

    2015-12-01

    Full Text Available Arterial hypertension is a complex disease with many serious complications, representing a leading cause of mortality. Selective beta-blockers such as metoprolol and bisoprolol are frequently used in the management of hypertension. Numerous analytical methods have been developed for the determination of these substances in biological fluids, such as liquid chromatography coupled with mass spectrometry, gas chromatography coupled with mass spectrometry, high performance liquid chromatography. Due to the complex composition of biological fluids a biological sample pre-treatment before the use of the method for quantitative determination is required in order to remove proteins and potential interferences. The most commonly used methods for processing biological samples containing metoprolol and bisoprolol were identified through a thorough literature search using PubMed, ScienceDirect, and Willey Journals databases. Articles published between years 2005-2015 were reviewed. Protein precipitation, liquid-liquid extraction and solid phase extraction are the main techniques for the extraction of these drugs from plasma, serum, whole blood and urine samples. In addition, numerous other techniques have been developed for the preparation of biological samples, such as dispersive liquid-liquid microextraction, carrier-mediated liquid phase microextraction, hollow fiber-protected liquid phase microextraction, on-line molecularly imprinted solid phase extraction. The analysis of metoprolol and bisoprolol in human plasma, urine and other biological fluids provides important information in clinical and toxicological trials, thus requiring the application of appropriate extraction techniques for the detection of these antihypertensive substances at nanogram and picogram levels.

  8. Quantitating morphological changes in biological samples during scanning electron microscopy sample preparation with correlative super-resolution microscopy.

    Science.gov (United States)

    Zhang, Ying; Huang, Tao; Jorgens, Danielle M; Nickerson, Andrew; Lin, Li-Jung; Pelz, Joshua; Gray, Joe W; López, Claudia S; Nan, Xiaolin

    2017-01-01

    Sample preparation is critical to biological electron microscopy (EM), and there have been continuous efforts on optimizing the procedures to best preserve structures of interest in the sample. However, a quantitative characterization of the morphological changes associated with each step in EM sample preparation is currently lacking. Using correlative EM and superresolution microscopy (SRM), we have examined the effects of different drying methods as well as osmium tetroxide (OsO4) post-fixation on cell morphology during scanning electron microscopy (SEM) sample preparation. Here, SRM images of the sample acquired under hydrated conditions were used as a baseline for evaluating morphological changes as the sample went through SEM sample processing. We found that both chemical drying and critical point drying lead to a mild cellular boundary retraction of ~60 nm. Post-fixation by OsO4 causes at least 40 nm additional boundary retraction. We also found that coating coverslips with adhesion molecules such as fibronectin prior to cell plating helps reduce cell distortion from OsO4 post-fixation. These quantitative measurements offer useful information for identifying causes of cell distortions in SEM sample preparation and improving current procedures.

  9. Cloning, Stem Cells, and the Current National Debate: Incorporating Ethics into a Large Introductory Biology Course

    Science.gov (United States)

    Fink, Rachel D.

    2002-01-01

    Discussing the ethical issues involved in topics such as cloning and stem cell research in a large introductory biology course is often difficult. Teachers may be wary of presenting material biased by personal beliefs, and students often feel inhibited speaking about moral issues in a large group. Yet, to ignore what is happening "out there"…

  10. Membrane materials for storing biological samples intended for comparative nanotoxicological testing

    Science.gov (United States)

    Metelkin, A.; Kuznetsov, D.; Kolesnikov, E.; Chuprunov, K.; Kondakov, S.; Osipov, A.; Samsonova, J.

    2015-11-01

    The study is aimed at identifying the samples of most promising membrane materials for storing dry specimens of biological fluids (Dried Blood Spots, DBS technology). Existing sampling systems using cellulose fiber filter paper have a number of drawbacks such as uneven distribution of the sample spot, dependence of the spot spreading area on the individual biosample properties, incomplete washing-off of the sample due to partially inconvertible sorption of blood components on cellulose fibers, etc. Samples of membrane materials based on cellulose, polymers and glass fiber with applied biosamples were studied using methods of scanning electron microscopy, FT-IR spectroscopy and surface-wetting measurement. It was discovered that cellulose-based membrane materials sorb components of biological fluids inside their structure, while membranes based on glass fiber display almost no interaction with the samples and biological fluid components dry to films in the membrane pores between the structural fibers. This characteristic, together with the fact that membrane materials based on glass fiber possess sufficient strength, high wetting properties and good storage capacity, attests them as promising material for dry samples of biological fluids storage systems.

  11. Electromembrane extraction as a rapid and selective miniaturized sample preparation technique for biological fluids

    DEFF Research Database (Denmark)

    Gjelstad, Astrid; Pedersen-Bjergaard, Stig; Seip, Knut Fredrik

    2015-01-01

    This special report discusses the sample preparation method electromembrane extraction, which was introduced in 2006 as a rapid and selective miniaturized extraction method. The extraction principle is based on isolation of charged analytes extracted from an aqueous sample, across a thin film....... Technical aspects of electromembrane extraction, important extraction parameters as well as a handful of examples of applications from different biological samples and bioanalytical areas are discussed in the paper....

  12. Chemometric and Statistical Analyses of ToF-SIMS Spectra of Increasingly Complex Biological Samples

    Energy Technology Data Exchange (ETDEWEB)

    Berman, E S; Wu, L; Fortson, S L; Nelson, D O; Kulp, K S; Wu, K J

    2007-10-24

    Characterizing and classifying molecular variation within biological samples is critical for determining fundamental mechanisms of biological processes that will lead to new insights including improved disease understanding. Towards these ends, time-of-flight secondary ion mass spectrometry (ToF-SIMS) was used to examine increasingly complex samples of biological relevance, including monosaccharide isomers, pure proteins, complex protein mixtures, and mouse embryo tissues. The complex mass spectral data sets produced were analyzed using five common statistical and chemometric multivariate analysis techniques: principal component analysis (PCA), linear discriminant analysis (LDA), partial least squares discriminant analysis (PLSDA), soft independent modeling of class analogy (SIMCA), and decision tree analysis by recursive partitioning. PCA was found to be a valuable first step in multivariate analysis, providing insight both into the relative groupings of samples and into the molecular basis for those groupings. For the monosaccharides, pure proteins and protein mixture samples, all of LDA, PLSDA, and SIMCA were found to produce excellent classification given a sufficient number of compound variables calculated. For the mouse embryo tissues, however, SIMCA did not produce as accurate a classification. The decision tree analysis was found to be the least successful for all the data sets, providing neither as accurate a classification nor chemical insight for any of the tested samples. Based on these results we conclude that as the complexity of the sample increases, so must the sophistication of the multivariate technique used to classify the samples. PCA is a preferred first step for understanding ToF-SIMS data that can be followed by either LDA or PLSDA for effective classification analysis. This study demonstrates the strength of ToF-SIMS combined with multivariate statistical and chemometric techniques to classify increasingly complex biological samples

  13. The biological traits of the large red scorpionfish, Scorpaena scrofa: Temporal and ontogenetic dynamics

    Science.gov (United States)

    Matić-Skoko, Sanja; Stagličić, Nika; Kraljević, Miro; Pallaoro, Armin; Dulčić, Jakov

    2015-01-01

    Large red scorpionfish, Scorpaena scrofa, is a prevalent, important and highly valued commercial species throughout the rocky coastal areas of the Mediterranean Sea. Despite this, there is a surprising scarcity of biological and ecological information for this species. As artisanal fisheries have a very long tradition in the whole Mediterranean, a considerable impact of continuous fishing pressure is expected on this valuable rockfish. To elucidate some biological parameters that indicate the status of S. scrofa in the Adriatic Sea and to show which consequences high fishery effort may have on its age, growth and reproduction, sampling was carried out in the middle Adriatic using trammel nets. Temporal trends in body size/weight of S. scrofa were also assessed using long-term data including specimens caught from 1960 to 2010. Temporal trends of S. scrofa in the middle Adriatic indicated significant decreases of 19% in length and 43% in total weight over time. In contrast, official landings for the last five years showed an increase of 13%. However, this increasing trend most likely reflects the continuous change in national policies for reporting the catches. Both catch data and landings statistics showed peak in catch per unit effort during summer which coincides with spawning period of S. scrofa. Length at first sexual maturity was observed at 29.0 cm for females and 24.9 cm for males. All specimens larger than 32 cm were mature. Age analysis revealed 15 age classes with a 25 year old female as the oldest specimen. However, age classes 3+ and 4+ were predominant in the total catch. The growth rate is relatively high during the first four years of life and afterwards it considerably slows down, with females growing at slightly slower rate and attaining slightly larger sizes than males. Given the identified biological implications that confirm our assumptions of inherent vulnerabilities and negative effects arising from continued artisanal fisheries practice

  14. Correlation of mRNA and protein in complex biological samples.

    Science.gov (United States)

    Maier, Tobias; Güell, Marc; Serrano, Luis

    2009-12-17

    The correlation between mRNA and protein abundances in the cell has been reported to be notoriously poor. Recent technological advances in the quantitative analysis of mRNA and protein species in complex samples allow the detailed analysis of this pathway at the center of biological systems. We give an overview of available methods for the identification and quantification of free and ribosome-bound mRNA, protein abundances and individual protein turnover rates. We review available literature on the correlation of mRNA and protein abundances and discuss biological and technical parameters influencing the correlation of these central biological molecules.

  15. Recent developments in fatty acids profile determination in biological samples - a review

    Directory of Open Access Journals (Sweden)

    Tiuca Ioana

    2015-12-01

    Full Text Available The present paper is a literature review of the recent years dealing with the most important separation techniques of fatty acids in biological samples. Our aim was to make a synthesis of the analytical methods used, to note the most used ones, but also to mention other methods that are less utilized, which can have important advantages (such as less time consuming, greener reagents, etc.. Gas-chromatographic separation methods were described and compared to liquid chromatographic separations of fatty acids in different types of biological samples. In the same time, the importance of determining fatty acids profiles in biological samples was revealed, pointing out the possible implications in diagnostics of different types of disorders or remarking different profiles compared to healthy states.

  16. JURISPRUDENTIAL EXAMINATION REGARDING BIOLOGICAL SAMPLING IN THE CASE OF CONVICTED PERSONS

    Directory of Open Access Journals (Sweden)

    Gabriela\tNEMŢOI

    2015-12-01

    Full Text Available Objectives: The research devotes particular attention to the timing of biological sampling in the case of convicted persons. The main idea of the research is the factual situation regarding the criminal case law, which is not unified; problematic that prevents the formation of the National System of Judicial Genetic Data. Materials and Methods: The study focuses on evaluating the two opinions of jurisprudence on the implementation of the text of the law (Law no. 76/2008. Results: The carried research on different cases has shown that legal text is not mandatory, but its application is arbitrary, at the discretion of the court, but, nevertheless, the biological sampling in the case of convicted persons disregards the form for penalty. Conclusions: In the context of the creation of the National System of Judicial Genetic Data is a control condition on the typology of criminal profiling, we believe that biological sampling should be a priority to ensure safety of the individual.

  17. Energy-filtered transmission electron microscopy of biological samples on highly transparent carbon nanomembranes

    CERN Document Server

    Rhinow, Daniel; Weber, Nils-Eike; Beyer, André; Gölzhäuser, Armin; Kühlbrandt, Werner; Hampp, Norbert; Turchanin, Andrey; 10.1016/j.ultramic.2011.01.028

    2011-01-01

    Ultrathin carbon nanomembranes (CNM) comprising crosslinked biphenyl precursors have been tested as support films for energy-filtered transmission electron microscopy (EFTEM) of biological specimens. Due to their high transparency CNM are ideal substrates for electron energy loss spectroscopy (EELS) and electron spectroscopic imaging (ESI) of stained and unstained biological samples. Virtually background-free elemental maps of tobacco mosaic virus (TMV) and ferritin have been obtained from samples supported by ~ 1 nm thin CNM. Furthermore, we have tested conductive carbon nanomembranes (cCNM) comprising nanocrystalline graphene, obtained by thermal treatment of CNM, as supports for cryoEM of ice-embedded biological samples. We imaged ice-embedded TMV on cCNM and compared the results with images of ice-embedded TMV on conventional carbon film (CC), thus analyzing the gain in contrast for TMV on cCNM in a quantitative manner. In addition we have developed a method for the preparation of vitrified specimens, sus...

  18. Energy-filtered transmission electron microscopy of biological samples on highly transparent carbon nanomembranes

    Energy Technology Data Exchange (ETDEWEB)

    Rhinow, Daniel, E-mail: daniel.rhinow@biophys.mpg.de [Max-Planck-Institute of Biophysics, Department of Structural Biology, Max-von-Laue-Strasse 3, D-60439 Frankfurt (Germany); Bueenfeld, Matthias; Weber, Nils-Eike; Beyer, Andre; Goelzhaeuser, Armin [University of Bielefeld, Department of Physics, Universitaetsstrasse 25, D-33615 Bielefeld (Germany); Kuehlbrandt, Werner [Max-Planck-Institute of Biophysics, Department of Structural Biology, Max-von-Laue-Strasse 3, D-60439 Frankfurt (Germany); Hampp, Norbert [University of Marburg, Department of Chemistry, Hans-Meerwein-Strasse, D-35032 Marburg (Germany); Turchanin, Andrey [University of Bielefeld, Department of Physics, Universitaetsstrasse 25, D-33615 Bielefeld (Germany)

    2011-04-15

    Ultrathin carbon nanomembranes (CNM) comprising crosslinked biphenyl precursors have been tested as support films for energy-filtered transmission electron microscopy (EFTEM) of biological specimens. Due to their high transparency CNM are ideal substrates for electron energy loss spectroscopy (EELS) and electron spectroscopic imaging (ESI) of stained and unstained biological samples. Virtually background-free elemental maps of tobacco mosaic virus (TMV) and ferritin have been obtained from samples supported by {approx}1 nm thin CNM. Furthermore, we have tested conductive carbon nanomembranes (cCNM) comprising nanocrystalline graphene, obtained by thermal treatment of CNM, as supports for cryoEM of ice-embedded biological samples. We imaged ice-embedded TMV on cCNM and compared the results with images of ice-embedded TMV on conventional carbon film (CC), thus analyzing the gain in contrast for TMV on cCNM in a quantitative manner. In addition we have developed a method for the preparation of vitrified specimens, suspended over the holes of a conventional holey carbon film, while backed by ultrathin cCNM. -- Research highlights: {yields} We examine ultrathin carbon nanomembranes (CNM) as supports for biological TEM. {yields} CNM comprise crosslinked biphenyl precursors. {yields} CNM supports enable background-free elemental mapping of heavy and light elements. {yields} We perform cryoEM of ice-embedded biological samples on graphene-like conductive CNM.

  19. ``Standoff Biofinder'' for Fast, Noncontact, Nondestructive, Large-Area Detection of Biological Materials for Planetary Exploration

    Science.gov (United States)

    Misra, Anupam K.; Acosta-Maeda, Tayro E.; Sharma, Shiv K.; McKay, Christopher P.; Gasda, Patrick J.; Taylor, G. Jeffrey; Lucey, Paul G.; Flynn, Luke; Nurul Abedin, M.; Clegg, Samuel M.; Wiens, Roger

    2016-09-01

    We developed a prototype instrument called the Standoff Biofinder, which can quickly locate biological material in a 500 cm2 area from a 2 m standoff distance with a detection time of 0.1 s. All biogenic materials give strong fluorescence signals when excited with UV and visible lasers. In addition, the luminescence decay time of biogenic compounds is much shorter (biofluorescent materials to obtain real-time fluorescence images that show the locations of biological materials among luminescent minerals in a geological context. The Standoff Biofinder instrument will be useful for locating biological material during future NASA rover, lander, and crewed missions. Additionally, the instrument can be used for nondestructive detection of biological materials in unique samples, such as those obtained by sample return missions from the outer planets and asteroids. The Standoff Biofinder also has the capacity to detect microbes and bacteria on space instruments for planetary protection purposes.

  20. Determination of cadmium and lead in human biological samples by spectrometric techniques: a review.

    Science.gov (United States)

    Lemos, Valfredo Azevedo; de Carvalho, Anaildes Lago

    2010-12-01

    The analysis of human biological samples, such as blood, urine, nails, and hair, is generally used for the verification of human exposure to toxic metals. In this review, various spectrometric methods for the determination of cadmium and lead in biological samples are discussed and compared. Several spectrometric techniques are presented and discussed with respect to various characteristics such as sensitivity, selectivity, and cost. Special attention is drawn to the procedures for digestion prior to the determination of cadmium and lead in hair, nails, blood, and urine.

  1. Spectroscopic analysis of bosentan in biological samples after a liquid-liquid microextraction

    Science.gov (United States)

    Sajedi-Amin, Sanaz; Assadpour-Zeynali, Karim; Panahi-Azar, Vahid; Kebriaeezadeh, Abbas; Khoubnasabjafari, Maryam; Ansarin, Khalil; Jouyban-Gharamaleki, Vahid; Jouyban, Abolghasem

    2015-01-01

    Introduction:Microextraction processes with UV-Vis measurement have been developed and validated for analysis of bosentan in biological samples. Methods:In this work, liquid–liquid microextraction procedures (DLLME & USAEME) were employed for cleanup, pre-concentration, and determination of bosentan in biological samples by UV-Vis spectroscopy at 270 nm. The method was validated and applied to the determination of bosentan in spiked serum, exhaled breath condensate and urine samples. Results:Various experimental factors including type of extraction and dispersive solvents and their volumes, pH, sonication time and centrifuging time were investigated. Under the optimum conditions, the method was linear in the range of 1.0–5.0 μg.mL-1, with coefficient of determination (R2) of > 0.998. The limit of detection (LOD) was 0.07 mg.L-1. Recovery of the target analyte in biological samples was 106.2%. The method could be easily applied for higher concentration of bosentan and needs more improvement for application in the pharmacokinetic investigations where more sensitive methods are required. Conclusion:A simple, low cost, precise and accurate spectrophotometric analysis of bosentan in biological samples after liquid-liquid microextraction were developed and validated for routine analyses. PMID:26929923

  2. Association of environmental toxic elements in biological samples of myocardial infarction patients at different stages.

    Science.gov (United States)

    Afridi, Hassan Imran; Kazi, Tasneem Gul; Kazi, Naveed; Kandhro, Ghulam Abbas; Baig, Jameel Ahmed; Jamali, Mohammad Khan; Arain, Mohammad Balal; Shah, Abdul Qadir; Shah, Faheem; Khan, Sumaira; Kolachi, Nida Fatima

    2011-06-01

    The exposure of toxic elements may directly or indirectly associate with different pathogenesis of heart diseases. In the present study, the association of arsenic (As), cadmium (Cd), cobalt (Co), lead (Pb), and nickel (Ni) in biological samples (whole blood and urine) and mortality from myocardial infarction (MI) patients at first, second, and third heart attacks was carried out. Both biological samples of 130 MI patients (77 male and 53 female), with ages ranging from 45 to 60 years, and 61 healthy persons (33 male and 28 female) of the same age group were collected. The elements in biological samples were assessed by electrothermal atomic absorption spectrophotometer, prior to microwave-assisted acid digestion. The validity of methodology was checked by the biological certified reference materials. During this study, 78% of 32 patients aged above 50 years, registered after third MI attack, died. In these subjects, the levels of As, Cd, Co, Ni, and Pb in blood samples were higher in MI patients as compared with referents (p < 0.05), while increased by 11.7%, 12.2%, 5.55%, and 7.2%, respectively, in the blood samples of those patients who tolerated the third MI attack (p = 0.12). The high level of understudied toxic elements may play a role in the mortality of MI patients.

  3. Photothermal method using a pyroelectric sensor for thermophysical characterization of agricultural and biological samples

    Science.gov (United States)

    Frandas, A.; Dadarlat, Dorin; Chirtoc, Mihai; Jalink, Henk; Bicanic, Dane D.; Paris, D.; Antoniow, Jean S.; Egee, Michel; Ungureanu, Costica

    1998-07-01

    The photopyroelectric method in different experimental configurations was used for thermophysical characterization of agricultural and biological samples. The study appears important due to the relation of thermal parameters to the quality of foodstuffs (connected to their preservation, storage and adulteration), migration profiles in biodegradable packages, and the mechanism of desiccation tolerance of seeds. Results are presented on the thermal parameters measurement and their dependence on temperature and water content for samples such as: honey, starch, seeds.

  4. Tomographic imaging of transparent biological samples using the pyramid phase microscope.

    Science.gov (United States)

    Iglesias, Ignacio

    2016-08-01

    We show how a pyramid phase microscope can be used to obtain tomographic information of the spatial variation of refractive index in biological samples using the Radon transform. A method that uses the information provided by the phase microscope for axial and lateral repositioning of the sample when it rotates is also described. Its application to the reconstruction of mouse embryos in the blastocyst stage is demonstrated.

  5. Phytochemical analysis and biological evaluation of selected African propolis samples from Cameroon and Congo

    NARCIS (Netherlands)

    Papachroni, D.; Graikou, K.; Kosalec, I.; Damianakos, H.; Ingram, V.J.; Chinou, I.

    2015-01-01

    The objective of this study was the chemical analysis of four selected samples of African propolis (Congo and Cameroon) and their biological evaluation. Twenty-one secondary metabolites belonging to four different chemical groups were isolated from the 70% ethanolic extracts of propolis and their st

  6. Analysis of biopharmaceutical proteins in biological matrices by LC-MS/MS I. Sample preparation

    NARCIS (Netherlands)

    Bischoff, Rainer; Bronsema, Kees J.; van de Merbel, Nico C.

    2013-01-01

    Part I of this review discusses sample-preparation aspects of quantifying biopharmaceutical proteins in complex biological matrices by LC-MS/MS with a focus on blood-derived body fluids. We conclude Part I with a short overview over options for automating the entire analytical procedure, which is

  7. Analysis of biopharmaceutical proteins in biological matrices by LC-MS/MS I. Sample preparation

    NARCIS (Netherlands)

    Bischoff, Rainer; Bronsema, Kees J.; van de Merbel, Nico C.

    2013-01-01

    Part I of this review discusses sample-preparation aspects of quantifying biopharmaceutical proteins in complex biological matrices by LC-MS/MS with a focus on blood-derived body fluids. We conclude Part I with a short overview over options for automating the entire analytical procedure, which is in

  8. Phytochemical analysis and biological evaluation of selected African propolis samples from Cameroon and Congo

    NARCIS (Netherlands)

    Papachroni, D.; Graikou, K.; Kosalec, I.; Damianakos, H.; Ingram, V.J.; Chinou, I.

    2015-01-01

    The objective of this study was the chemical analysis of four selected samples of African propolis (Congo and Cameroon) and their biological evaluation. Twenty-one secondary metabolites belonging to four different chemical groups were isolated from the 70% ethanolic extracts of propolis and their

  9. Phytochemical analysis and biological evaluation of selected African propolis samples from Cameroon and Congo

    NARCIS (Netherlands)

    Papachroni, D.; Graikou, K.; Kosalec, I.; Damianakos, H.; Ingram, V.J.; Chinou, I.

    2015-01-01

    The objective of this study was the chemical analysis of four selected samples of African propolis (Congo and Cameroon) and their biological evaluation. Twenty-one secondary metabolites belonging to four different chemical groups were isolated from the 70% ethanolic extracts of propolis and their st

  10. Large sample neutron activation analysis: a challenge in cultural heritage studies.

    Science.gov (United States)

    Stamatelatos, Ion E; Tzika, Faidra

    2007-07-01

    Large sample neutron activation analysis compliments and significantly extends the analytical tools available for cultural heritage and authentication studies providing unique applications of non-destructive, multi-element analysis of materials that are too precious to damage for sampling purposes, representative sampling of heterogeneous materials or even analysis of whole objects. In this work, correction factors for neutron self-shielding, gamma-ray attenuation and volume distribution of the activity in large volume samples composed of iron and ceramic material were derived. Moreover, the effect of inhomogeneity on the accuracy of the technique was examined.

  11. Using Facebook Groups to Encourage Science Discussions in a Large-Enrollment Biology Class

    Science.gov (United States)

    Pai, Aditi; McGinnis, Gene; Bryant, Dana; Cole, Megan; Kovacs, Jennifer; Stovall, Kyndra; Lee, Mark

    2017-01-01

    This case study reports the instructional development, impact, and lessons learned regarding the use of Facebook as an educational tool within a large enrollment Biology class at Spelman College (Atlanta, GA). We describe the use of this social networking site to (a) engage students in active scientific discussions, (b) build community within the…

  12. Biohorizons: An eConference to Assess Human Biology in Large, First-Year Classes

    Science.gov (United States)

    Moni, Roger W.; Moni, Karen B.; Poronnik, Philip; Lluka, Lesley J.

    2007-01-01

    The authors detail the design, implementation and evaluation of an eConference entitled "Biohorizons," using a presage-process-product model to describe the development of an eLearning community. Biohorizons was a summative learning and assessment task aiming to introduce large classes of first-year Human Biology students to the practices of…

  13. Biology Faculty at Large Research Institutions: The Nature of their Pedagogical Content Knowledge

    Science.gov (United States)

    Hill, Kathleen M.

    To address the need of scientists and engineers in the United States workforce and ensure that students in higher education become scientifically literate, research and policy has called for improvements in undergraduate education in the sciences. One particular pathway for improving undergraduate education in the science fields is to reform undergraduate teaching. Only a limited number of studies have explored the pedagogical content knowledge of postsecondary level teachers. This study was conducted to characterize the PCK of biology faculty and explore the factors influencing their PCK. Data included semi-structured interviews, classroom observations, documents, and instructional artifacts. A qualitative inquiry was designed to conduct an in-depth investigation focusing on the PCK of six biology instructors, particularly the types of knowledge they used for teaching biology, their perceptions of teaching, and the social interactions and experiences that influenced their PCK. The findings of this study reveal that the PCK of the biology faculty included eight domains of knowledge: (1) content, (2) context, (3) learners and learning, (4) curriculum, (5) instructional strategies, (6) representations of biology, (7) assessment, and (8) building rapport with students. Three categories of faculty PCK emerged: (1) PCK as an expert explainer, (2) PCK as an instructional architect, and (3) a transitional PCK, which fell between the two prior categories. Based on the interpretations of the data, four social interactions and experiences were found to influence biology faculty PCK: (1) teaching experience, (2) models and mentors, (3) collaborations about teaching, and (4) science education research. The varying teaching perspectives of the faculty also influenced their PCK. This study shows that the PCK of biology faculty for teaching large introductory courses at large research institutions is heavily influenced by factors beyond simply years of teaching experience and

  14. The NYC native air sampling pilot project: using HVAC filter data for urban biological incident characterization.

    Science.gov (United States)

    Ackelsberg, Joel; Leykam, Frederic M; Hazi, Yair; Madsen, Larry C; West, Todd H; Faltesek, Anthony; Henderson, Gavin D; Henderson, Christopher L; Leighton, Terrance

    2011-09-01

    Native air sampling (NAS) is distinguished from dedicated air sampling (DAS) devices (eg, BioWatch) that are deployed to detect aerosol disseminations of biological threat agents. NAS uses filter samples from heating, ventilation, and air conditioning (HVAC) systems in commercial properties for environmental sampling after DAS detection of biological threat agent incidents. It represents an untapped, scientifically sound, efficient, widely distributed, and comparably inexpensive resource for postevent environmental sampling. Calculations predict that postevent NAS would be more efficient than environmental surface sampling by orders of magnitude. HVAC filter samples could be collected from pre-identified surrounding NAS facilities to corroborate the DAS alarm and delineate the path taken by the bioaerosol plume. The New York City (NYC) Native Air Sampling Pilot Project explored whether native air sampling would be acceptable to private sector stakeholders and could be implemented successfully in NYC. Building trade associations facilitated outreach to and discussions with property owners and managers, who expedited contact with building managers of candidate NAS properties that they managed or owned. Nominal NAS building requirements were determined; procedures to identify and evaluate candidate NAS facilities were developed; data collection tools and other resources were designed and used to expedite candidate NAS building selection and evaluation in Manhattan; and exemplar environmental sampling playbooks for emergency responders were completed. In this sample, modern buildings with single or few corporate tenants were the best NAS candidate facilities. The Pilot Project successfully demonstrated that in one urban setting a native air sampling strategy could be implemented with effective public-private collaboration.

  15. Quantitative and dynamic measurements of biological fresh samples with X-ray phase contrast tomography

    Energy Technology Data Exchange (ETDEWEB)

    Hoshino, Masato, E-mail: hoshino@spring8.or.jp; Uesugi, Kentaro [Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198 (Japan); Tsukube, Takuro [Japanese Red Cross Kobe Hospital, 1-3-1 Wakinohamakaigandori, Chuo-ku, Kobe, Hyogo 651-0073 (Japan); Yagi, Naoto [Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198 (Japan)

    2014-10-08

    Quantitative measurements of biological fresh samples based on three-dimensional densitometry using X-ray phase contrast tomography are presented. X-ray phase contrast tomography using a Talbot grating interferometer was applied to biological fresh samples which were not fixed by any fixatives. To achieve a high-throughput measurement for the fresh samples the X-ray phase contrast tomography measurement procedure was improved. The three-dimensional structure of a fresh mouse fetus was clearly depicted as a mass density map using X-ray phase contrast tomography. The mouse fetus measured in the fresh state was then fixed by formalin and measured in the fixed state. The influence of the formalin fixation on soft tissue was quantitatively evaluated by comparing the fresh and fixed samples. X-ray phase contrast tomography was also applied to the dynamic measurement of a biological fresh sample. Morphological changes of a ring-shaped fresh pig aorta were measured tomographically under different degrees of stretching.

  16. Microfluidic solutions enabling continuous processing and monitoring of biological samples: A review.

    Science.gov (United States)

    Karle, Marc; Vashist, Sandeep Kumar; Zengerle, Roland; von Stetten, Felix

    2016-07-27

    The last decade has witnessed tremendous advances in employing microfluidic solutions enabling Continuous Processing and Monitoring of Biological Samples (CPMBS), which is an essential requirement for the control of bio-processes. The microfluidic systems are superior to the traditional inline sensors due to their ability to implement complex analytical procedures, such as multi-step sample preparation, and enabling the online measurement of parameters. This manuscript provides a backgound review of microfluidic approaches employing laminar flow, hydrodynamic separation, acoustophoresis, electrophoresis, dielectrophoresis, magnetophoresis and segmented flow for the continuous processing and monitoring of biological samples. The principles, advantages and limitations of each microfluidic approach are described along with its potential applications. The challenges in the field and the future directions are also provided.

  17. Lead Assessment in Biological Samples of Children with Different Gastrointestinal Disorders.

    Science.gov (United States)

    Shah, Faheem; Ullah, Naeem; Kazi, Tasneem Gul; Khan, Ajmal; Kandhro, Ghulam Abbas; Afridi, Hassan Imran; Arain, Mohammad Balal; Khan, Zahid; Farooq, Umar

    2016-01-01

    Lead (Pb) levels have been evaluated in the biological samples of children with different gastrointestinal disorders. Blood, scalp hair, and urine samples of children (of age 4-10 years) complaining about different gastrointestinal disorders were analyzed. For comparison, age matched healthy subjects were also included in this study. Biological samples were digested in a microwave oven prior to Pb determination by graphite furnace atomic absorption spectrometry. Significant differences in Pb profile were found between the diseased and referent children. Elevated Pb contents were observed in case of diseased children than WHO permissible limit, while normal results were obtained for healthy referents. The results were compared with those of healthy children having the same age, socioeconomic status, and residential areas.

  18. A Method for Determining the Content of Glycoproteins in Biological Samples

    Directory of Open Access Journals (Sweden)

    Yang Gao

    2016-11-01

    Full Text Available The glycoprotein purified from the mycelium extract of Tremella fuciformis was marked with iodine through the iodine substitution reaction. The content of iodine, which is indicative of the amount of the marked tremella glycoprotein (ITG, was detected with Inductively coupled plasma mass spectrometry (ICP-MS. The method was found to be stable, sensitive, and accurate at detecting the content of iodine-substituted glycoprotein, and was used in the quantitative analysis of biological samples, including blood and organs. Different biological samples were collected from rats after oral administration of ITG, and were tested for iodine content by ICP-MS to calculate the amount of ITG in the samples. The results suggested that ICP-MS is a sensitive, stable, and accurate method for detection of iodinated glycoproteins in blood and organs.

  19. Toward greener analytical techniques for the absolute quantification of peptides in pharmaceutical and biological samples.

    Science.gov (United States)

    Van Eeckhaut, Ann; Mangelings, Debby

    2015-09-10

    Peptide-based biopharmaceuticals represent one of the fastest growing classes of new drug molecules. New reaction types included in the synthesis strategies to reduce the rapid metabolism of peptides, along with the availability of new formulation and delivery technologies, resulted in an increased marketing of peptide drug products. In this regard, the development of analytical methods for quantification of peptides in pharmaceutical and biological samples is of utmost importance. From the sample preparation step to their analysis by means of chromatographic or electrophoretic methods, many difficulties should be tackled to analyze them. Recent developments in analytical techniques emphasize more and more on the use of green analytical techniques. This review will discuss the progresses in and challenges observed during green analytical method development for the quantification of peptides in pharmaceutical and biological samples.

  20. Nanocharacterization of soft biological samples in shear mode with quartz tuning fork probes.

    Science.gov (United States)

    Otero, Jorge; Gonzalez, Laura; Puig-Vidal, Manel

    2012-01-01

    Quartz tuning forks are extremely good resonators and their use is growing in scanning probe microscopy. Nevertheless, only a few studies on soft biological samples have been reported using these probes. In this work, we present the methodology to develop and use these nanosensors to properly work with biological samples. The working principles, fabrication and experimental setup are presented. The results in the nanocharacterization of different samples in different ambients are presented by using different working modes: amplitude modulation with and without the use of a Phase-Locked Loop (PLL) and frequency modulation. Pseudomonas aeruginosa bacteria are imaged in nitrogen using amplitude modulation. Microcontact printed antibodies are imaged in buffer using amplitude modulation with a PLL. Finally, metastatic cells are imaged in air using frequency modulation.

  1. Nanocharacterization of Soft Biological Samples in Shear Mode with Quartz Tuning Fork Probes

    Directory of Open Access Journals (Sweden)

    Manel Puig-Vidal

    2012-04-01

    Full Text Available Quartz tuning forks are extremely good resonators and their use is growing in scanning probe microscopy. Nevertheless, only a few studies on soft biological samples have been reported using these probes. In this work, we present the methodology to develop and use these nanosensors to properly work with biological samples. The working principles, fabrication and experimental setup are presented. The results in the nanocharacterization of different samples in different ambients are presented by using different working modes: amplitude modulation with and without the use of a Phase-Locked Loop (PLL and frequency modulation. Pseudomonas aeruginosa bacteria are imaged in nitrogen using amplitude modulation. Microcontact printed antibodies are imaged in buffer using amplitude modulation with a PLL. Finally, metastatic cells are imaged in air using frequency modulation.

  2. Direct observation of unstained wet biological samples by scanning-electron generation X-ray microscopy.

    Science.gov (United States)

    Ogura, Toshihiko

    2010-01-01

    Analytical tools of nanometre-scale resolution are indispensable in the fields of biology, physics and chemistry. One suitable tool, the soft X-ray microscope, provides high spatial resolution of visible light for wet specimens. For biological specimens, X-rays of water-window wavelength between carbon (284 eV; 4.3 nm) and oxygen (540 eV; 2.3 nm) absorption edges provide high-contrast imaging of biological samples in water. Among types of X-ray microscope, the transmission X-ray microscope using a synchrotron radiation source with diffractive zone plates offers the highest spatial resolution, approaching 15-10nm. However, even higher resolution is required to measure proteins and protein complexes in biological specimens; therefore, a new type of X-ray microscope with higher resolution that uses a simple light source is desirable. Here we report a novel scanning-electron generation X-ray microscope (SGXM) that demonstrates direct imaging of unstained wet biological specimens. We deposited wet yeasts in the space between two silicon nitride (Si(3)N(4)) films. A scanning electron beam of accelerating voltage 5 keV and current 1.6 nA irradiates the titanium (Ti)-coated Si(3)N(4) film, and the soft X-ray signal from it is detected by an X-ray photodiode (PD) placed below the sample. The SGXM can theoretically achieve better than 5 nm resolution. Our method can be utilized easily for various wet biological samples of bacteria, viruses, and protein complexes.

  3. Solid Phase Microextraction and Related Techniques for Drugs in Biological Samples

    Directory of Open Access Journals (Sweden)

    Mohammad Mahdi Moein

    2014-01-01

    Full Text Available In drug discovery and development, the quantification of drugs in biological samples is an important task for the determination of the physiological performance of the investigated drugs. After sampling, the next step in the analytical process is sample preparation. Because of the low concentration levels of drug in plasma and the variety of the metabolites, the selected extraction technique should be virtually exhaustive. Recent developments of sample handling techniques are directed, from one side, toward automatization and online coupling of sample preparation units. The primary objective of this review is to present the recent developments in microextraction sample preparation methods for analysis of drugs in biological fluids. Microextraction techniques allow for less consumption of solvent, reagents, and packing materials, and small sample volumes can be used. In this review the use of solid phase microextraction (SPME, microextraction in packed sorbent (MEPS, and stir-bar sorbtive extraction (SBSE in drug analysis will be discussed. In addition, the use of new sorbents such as monoliths and molecularly imprinted polymers will be presented.

  4. Development of an improved immunoassay for detection of sorLA in cells and biological samples

    DEFF Research Database (Denmark)

    Andersen, Olav Michael; Thakurta, Ishita Guha; West, Mark J.

    , or traditional sandwich ELISA assays which are time consuming and less sensitive. Hence, the purpose of the present study is to develop a new assay called AlphaLISA which is fast and very sensitive, to measure sorLA in extremely small volumes of cells and biological samples. Methods: The Alpha...... retinopathy, and acute leukemia. Despite the overwhelming evidence regarding the role of sorLA in various diseases, there has been a lack of technologies which can precisely quantitate the levels of sorLA in various complex biological matrices. The methods are either qualitative like immunohistochemistry...

  5. Eclipsing binary stars in the Large and Small Magellanic Clouds from the MACHO project: The Sample

    Energy Technology Data Exchange (ETDEWEB)

    Faccioli, L; Alcock, C; Cook, K; Prochter, G; Protopapas, P; Syphers, D

    2007-03-29

    We present a new sample of 4634 eclipsing binary stars in the Large Magellanic Cloud (LMC), expanding on a previous sample of 611 objects and a new sample of 1509 eclipsing binary stars in the Small Magellanic Cloud (SMC), that were identified in the light curve database of the MACHO project. We perform a cross correlation with the OGLE-II LMC sample, finding 1236 matches. A cross correlation with the OGLE-II SMC sample finds 698 matches. We then compare the LMC subsamples corresponding to center and the periphery of the LMC and find only minor differences between the two populations. These samples are sufficiently large and complete that statistical studies of the binary star populations are possible.

  6. Cost-effective Sampling Design Applied to Large-scale Monitoring of Boreal Birds

    Directory of Open Access Journals (Sweden)

    Matthew Carlson

    2002-12-01

    Full Text Available Despite their important roles in biodiversity conservation, large-scale ecological monitoring programs are scarce, in large part due to the difficulty of achieving an effective design under fiscal constraints. Using long-term avian monitoring in the boreal forest of Alberta, Canada as an example, we present a methodology that uses power analysis, statistical modeling, and partial derivatives to identify cost-effective sampling strategies for ecological monitoring programs. Empirical parameter estimates were used in simulations that estimated the power of sampling designs to detect trend in a variety of species' populations and community metrics. The ability to detect trend with increased sample effort depended on the monitoring target's variability and how effort was allocated to sampling parameters. Power estimates were used to develop nonlinear models of the relationship between sample effort and power. A cost model was also developed, and partial derivatives of the power and cost models were evaluated to identify two cost-effective avian sampling strategies. For decreasing sample error, sampling multiple plots at a site is preferable to multiple within-year visits to the site, and many sites should be sampled relatively infrequently rather than sampling few sites frequently, although the importance of frequent sampling increases for variable targets. We end by stressing the need for long-term, spatially extensive data for additional taxa, and by introducing optimal design as an alternative to power analysis for the evaluation of ecological monitoring program designs.

  7. Characterizing the Sample Complexity of Large-Margin Learning With Second-Order Statistics

    CERN Document Server

    Sabato, Sivan; Tishby, Naftali

    2012-01-01

    We obtain a tight distribution-specific characterization of the sample complexity of large-margin classification with L_2 regularization: We introduce the margin-adapted dimension, which is a simple function of the second order statistics of the data distribution, and show distribution-specific upper and lower bounds on the sample complexity, both governed by the margin-adapted dimension of the data distribution. The upper bounds are universal, and the lower bounds hold for a rich family of sub-Gaussian distributions. We conclude that this new quantity tightly characterizes the true sample complexity of large-margin classification.

  8. A reconfigurable real-time compressive-sampling camera for biological applications.

    Directory of Open Access Journals (Sweden)

    Bo Fu

    Full Text Available Many applications in biology, such as long-term functional imaging of neural and cardiac systems, require continuous high-speed imaging. This is typically not possible, however, using commercially available systems. The frame rate and the recording time of high-speed cameras are limited by the digitization rate and the capacity of on-camera memory. Further restrictions are often imposed by the limited bandwidth of the data link to the host computer. Even if the system bandwidth is not a limiting factor, continuous high-speed acquisition results in very large volumes of data that are difficult to handle, particularly when real-time analysis is required. In response to this issue many cameras allow a predetermined, rectangular region of interest (ROI to be sampled, however this approach lacks flexibility and is blind to the image region outside of the ROI. We have addressed this problem by building a camera system using a randomly-addressable CMOS sensor. The camera has a low bandwidth, but is able to capture continuous high-speed images of an arbitrarily defined ROI, using most of the available bandwidth, while simultaneously acquiring low-speed, full frame images using the remaining bandwidth. In addition, the camera is able to use the full-frame information to recalculate the positions of targets and update the high-speed ROIs without interrupting acquisition. In this way the camera is capable of imaging moving targets at high-speed while simultaneously imaging the whole frame at a lower speed. We have used this camera system to monitor the heartbeat and blood cell flow of a water flea (Daphnia at frame rates in excess of 1500 fps.

  9. Flexible sampling large-scale social networks by self-adjustable random walk

    Science.gov (United States)

    Xu, Xiao-Ke; Zhu, Jonathan J. H.

    2016-12-01

    Online social networks (OSNs) have become an increasingly attractive gold mine for academic and commercial researchers. However, research on OSNs faces a number of difficult challenges. One bottleneck lies in the massive quantity and often unavailability of OSN population data. Sampling perhaps becomes the only feasible solution to the problems. How to draw samples that can represent the underlying OSNs has remained a formidable task because of a number of conceptual and methodological reasons. Especially, most of the empirically-driven studies on network sampling are confined to simulated data or sub-graph data, which are fundamentally different from real and complete-graph OSNs. In the current study, we propose a flexible sampling method, called Self-Adjustable Random Walk (SARW), and test it against with the population data of a real large-scale OSN. We evaluate the strengths of the sampling method in comparison with four prevailing methods, including uniform, breadth-first search (BFS), random walk (RW), and revised RW (i.e., MHRW) sampling. We try to mix both induced-edge and external-edge information of sampled nodes together in the same sampling process. Our results show that the SARW sampling method has been able to generate unbiased samples of OSNs with maximal precision and minimal cost. The study is helpful for the practice of OSN research by providing a highly needed sampling tools, for the methodological development of large-scale network sampling by comparative evaluations of existing sampling methods, and for the theoretical understanding of human networks by highlighting discrepancies and contradictions between existing knowledge/assumptions of large-scale real OSN data.

  10. Physicochemical characteristics and biological activities of seasonal atmospheric particulate matter sampling in two locations of Paris.

    Science.gov (United States)

    Baulig, Augustin; Poirault, Jean-Jacques; Ausset, Patrick; Schins, Roel; Shi, Tingming; Baralle, Delphine; Dorlhene, Pascal; Meyer, Martine; Lefevre, Roger; Baeza-Squiban, Armelle; Marano, Francelyne

    2004-11-15

    Fine particulate matter present in urban areas seems to be incriminated in respiratory disorders. The aim of this study was to relate physicochemical characteristics of PM2.5 (particulate matter collected with a 50% efficiency for particles with an aerodynamic diameter of 2.5 microm) to their biological activities toward a bronchial epithelial cell line 16-HBE. Two seasonal sampling campaigns of particles were realized, respectively, in a kerbside and an urban background station in Paris. Sampled-PM2.5 mainly consist of particles with a size below 1 microm and are mainly composed of soot as assessed by analytical scanning electron microscopy. The different PM2.5 samples contrasted in their PAH content, which was the highest in the kerbside station in winter, as well as in their metal content. Kerbside station samples were characterized by the highest Fe and Cu content, which appears correlated to their hydroxyl radical generating properties measured by electron paramagnetic resonance. Particles were compared by their capacity to induce cytotoxicity, intracellular ROS production, and proinflammatory cytokine release (GM-CSF and TNF-alpha). At a concentration of 10 microg/cm2, all samples induced peroxide production and cytokine release to the similar extent in the absence of cytotoxicity. In conclusion, whereas the PM2.5 samples differ by their PAH and metal composition, they induce the same biological responses likely either due to components bioavailability and/ or interactions between PM components.

  11. Improved preparation of small biological samples for mercury analysis using cold vapor atomic absorption spectroscopy.

    Science.gov (United States)

    Adair, B M; Cobb, G P

    1999-05-01

    Concentrations of mercury in biological samples collected for environmental studies are often less than 0.1 microgram/g. Low mercury concentrations and small organ sizes in many wildlife species (approximately 0.1 g) increase the difficulty of mercury determination at environmentally relevant concentrations. We have developed a digestion technique to extract mercury from small (0.1 g), biological samples at these relevant concentrations. Mean recoveries (+/- standard error) from validation trials of mercury fortified tissue samples using cold vapor atomic absorption spectroscopy for analysis ranged from 102 +/- 4.3% (2.5 micrograms/L, n = 15) to 108 +/- 1.4% (25 micrograms/L, n = 15). Recoveries of inorganic mercury were 99 +/- 5 (n = 19) for quality assurance samples analyzed during environmental evaluations conducted during a 24 month period. This technique can be used to determine total mercury concentrations of 60 ng Hg/g sample. Samples can be analyzed in standard laboratories in a short time, at minimal cost. The technique is versatile and can be used to determine mercury concentrations in several different matrices, limiting the time and expense of method development and validation.

  12. A Prototype Ice-Melting Probe for Collecting Biological Samples from Cryogenic Ice at Low Pressure

    Science.gov (United States)

    Davis, Ashley

    2017-08-01

    In the Solar System, the surface of an icy moon is composed of irregular ice formations at cryogenic temperatures (ice, must contain a device that collects samples without refreezing liquid and without sublimation of ice. In addition, if the samples are biological in nature, then precautions must be taken to ensure the samples do not overheat or mix with the oxidized layer. To achieve these conditions, the collector must maintain temperatures close to maintenance or growth conditions of the organism (ice and directs the meltwater upward into a reservoir. The force on the probe is proportional to the height of meltwater (pressure) obtained in the system and allows regulation of the melt rate and temperature of the sample. The device can collect 5-50 mL of meltwater from the surface of an ice block at 233-208 K with an environmental pressure of less than 10-2 atm while maintaining a sample temperature between 273 and 293 K. These conditions maintain most biological samples in a pristine state and maintain the integrity of most organisms' structure and function.

  13. Characterization of femtosecond laser-induced breakdown spectroscopy (fsLIBS) and applications for biological samples.

    Science.gov (United States)

    Gill, Ruby K; Knorr, Florian; Smith, Zachary J; Kahraman, Mehmet; Madsen, Dorte; Larsen, Delmar S; Wachsmann-Hogiu, Sebastian

    2014-01-01

    We characterize the femtosecond laser-induced breakdown spectroscopy (fsLIBS) signal for biological tissues as a function of different excitation parameters with femtosecond laser systems. These parameters include laser energy, depth of focus, and number of pulses per focal volume. We used femtosecond laser pulses of 800 nm and energy between 25 and 123 μJ to generate LIBS signals in biological tissues. As expected, we observed a linear increase in the fsLIBS intensity as a function of the laser energy. In addition, we show that moving the beam out of focus and the presence of overlapping pulses on the same focal area leads to a decrease in fsLIBS intensity due to changes in focal spot size. We also demonstrate that fsLIBS can distinguish between different biological tissue samples.

  14. Elemental and isotopic imaging of biological samples using NanoSIMS.

    Science.gov (United States)

    Kilburn, Matt R; Clode, Peta L

    2014-01-01

    With its low detection limits and the ability to analyze most of the elements in the periodic table, secondary ion mass spectrometry (SIMS) represents one of the most versatile in situ analytical techniques available, and recent developments have resulted in significant advantages for the use of imaging mass spectrometry in biological and biomedical research. Increases in spatial resolution and sensitivity allow detailed interrogation of samples at relevant scales and chemical concentrations. Advances in dynamic SIMS, specifically with the advent of NanoSIMS, now allow the tracking of stable isotopes within biological systems at subcellular length scales, while static SIMS combines subcellular imaging with molecular identification. In this chapter, we present an introduction to the SIMS technique, with particular reference to NanoSIMS, and discuss its application in biological and biomedical research.

  15. A novel computational approach towards the certification of large-scale boson sampling

    Science.gov (United States)

    Huh, Joonsuk

    Recent proposals of boson sampling and the corresponding experiments exhibit the possible disproof of extended Church-Turning Thesis. Furthermore, the application of boson sampling to molecular computation has been suggested theoretically. Till now, however, only small-scale experiments with a few photons have been successfully performed. The boson sampling experiments of 20-30 photons are expected to reveal the computational superiority of the quantum device. A novel theoretical proposal for the large-scale boson sampling using microwave photons is highly promising due to the deterministic photon sources and the scalability. Therefore, the certification protocol of large-scale boson sampling experiments should be presented to complete the exciting story. We propose, in this presentation, a computational protocol towards the certification of large-scale boson sampling. The correlations of paired photon modes and the time-dependent characteristic functional with its Fourier component can show the fingerprint of large-scale boson sampling. This work was supported by Basic Science Research Program through the National Research Foundation of Korea(NRF) funded by the Ministry of Education, Science and Technology(NRF-2015R1A6A3A04059773), the ICT R&D program of MSIP/IITP [2015-019, Fundamental Research Toward Secure Quantum Communication] and Mueunjae Institute for Chemistry (MIC) postdoctoral fellowship.

  16. Large-scale targeted metagenomics analysis of bacterial ecological changes in 88 kimchi samples during fermentation.

    Science.gov (United States)

    Lee, Moeun; Song, Jung Hee; Jung, Min Young; Lee, Se Hee; Chang, Ji Yoon

    2017-09-01

    The microbial communities in kimchi vary widely, but the precise effects of differences in region of origin, ingredients, and preparation method on the microbiota are unclear. We analyzed the bacterial community composition of household (n = 69) and commercial (n = 19) kimchi samples obtained from six Korean provinces between April and August 2015. Samples were analyzed by barcoded pyrosequencing targeting the V1-V3 region of the 16S ribosomal RNA gene. The initial pH of the kimchi samples was 5.00-6.39, and the salt concentration was 1.72-4.42%. Except for sampling locality, all categorical variables, i.e., salt concentration, major ingredient, fermentation period, sampling time, and manufacturing process, influenced the bacterial community composition. Particularly, samples were highly clustered by sampling time and salt concentration in non-metric multidimensional scaling plots and an analysis of similarity. These results indicated that the microbial community differed according to fermentation conditions such as salt concentration, major ingredient, fermentation period, and sampling time. Furthermore, fermentation properties, including pH, acidity, salt concentration, and microbial abundance differed between kimchi samples from household and commercial sources. Analyses of changes in bacterial ecology during fermentation will improve our understanding of the biological properties of kimchi, as well as the relationships between these properties and the microbiota of kimchi. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. 37 GHz observations of a large sample of BL Lacertae objects

    CERN Document Server

    Nieppola, E; Lähteenmäki, A; Valtaoja, E; Hakala, T; Hovatta, T; Kotiranta, M; Nummila, S; Ojala, T; Parviainen, M; Ranta, M; Saloranta, P -M; Torniainen, I; Tröller, M; 10.1086/512609

    2009-01-01

    We present 37 GHz data obtained at Metsahovi Radio Observatory in 2001 December - 2005 April for a large sample of BL Lacertae objects. We also report the mean variability indices and radio spectral indices in frequency intervals 5 - 37 GHz and 37 - 90 GHz. Approximately 34 % of the sample was detected at 37 GHz, 136 BL Lacertae objects in all. A large majority of the detected sources were low-energy BL Lacs (LBLs). The variability index values of the sample were diverse, the mean fractional variability of the sample being \\Delta S_2 = 0.31. The spectral indices also varied widely, but the average radio spectrum of the sample sources is flat. Our observations show that many of the high-energy BL Lacs (HBL), which are usually considered radio-quiet, can at times be detected at 37 GHz.

  18. Applications of PIXE to biological and biomedical samples at the university of gent

    Science.gov (United States)

    Maenhaut, W.; Vandenhaute, J.; Duflou, H.; De Reuck, J.

    1987-03-01

    The research on biological and biomedical samples, conducted at the University of Gent during the last 4-5 years and using PIXE as analytical technique, is presented. Our optimized sample/target preparation methods are described, and the accuracy and precision obtainable with them are discussed. Two comprehensive biological/biomedical research projects, initiated at Gent, are presented. The first aims at investigating possible trace element changes in tissues of experimental animals (rats) as a result of liver necrosis or cirrhosis, induced by intraperitoneal injection with CCl 4. The second project involves the determination of the regional distribution of trace elements in the human brain. Eight elements, i.e. K, Ca, Mn, Fe, Cu, Zn, Se and Rb, are being measured in up to 50 different regions of 12 normal brains, and in selected brain regions from patients with neurological disorders. Some of the results of the two projects are discussed.

  19. Axial-scanning low-coherence interferometer method for noncontact thickness measurement of biological samples.

    Science.gov (United States)

    Kim, Do-Hyun; Song, Chul-Gyu; Ilev, Ilko K; Kang, Jin U

    2011-02-20

    We investigated a high-precision optical method for measuring the thickness of biological samples regardless of their transparency. The method is based on the precise measurement of optical path length difference of the end surfaces of objects, using a dual-arm axial-scanning low-coherence interferometer. This removes any consideration of the shape, thickness, or transparency of testing objects when performing the measurement. Scanning the reference simplifies the measurement setup, resulting in unambiguous measurement. Using a 1310 nm wavelength superluminescent diode, with a 65 nm bandwidth, the measurement accuracy was as high as 11.6 μm. We tested the method by measuring the thickness of both transparent samples and nontransparent soft biological tissues.

  20. Axial-scanning low-coherence interferometer method for noncontact thickness measurement of biological samples

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Do-Hyun; Song, Chul-Gyu; Ilev, Ilko K.; Kang, Jin U.

    2011-02-20

    We investigated a high-precision optical method for measuring the thickness of biological samples regardless of their transparency. The method is based on the precise measurement of optical path length difference of the end surfaces of objects, using a dual-arm axial-scanning low-coherence interferometer. This removes any consideration of the shape, thickness, or transparency of testing objects when performing the measurement. Scanning the reference simplifies the measurement setup, resulting in unambiguous measurement. Using a 1310 nm wavelength superluminescent diode, with a 65 nm bandwidth, the measurement accuracy was as high as 11.6 {mu}m. We tested the method by measuring the thickness of both transparent samples and nontransparent soft biological tissues.

  1. Electroanalytical Determination of Danofloxacin in Biological Samples Using Square Wave Voltammetry

    Directory of Open Access Journals (Sweden)

    Chirley Vanessa Boone

    2014-10-01

    Full Text Available The voltammetric behavior of danofloxacin (DFX has been studied, in aqueous solution, on a glassy carbon electrode using square wave voltammetry (SWV as electroanalytical technique. After optimization of the experimental conditions, DFX was analyzed in spiked biologic samples using a Britton-Robinson buffer with pH = 5.0 as the supporting electrolyte. Oxidation occurs at 0.98 V vs. Ag/AgCl in a two-electron process controlled by adsorption of the electrogenerated products on the electrode surface. A acceptable recovery was obtained for assay of spiked biologic samples, with value of 98.7% for the swine urine and 95.3 % for the bovine urine.

  2. Scaling up the DBSCAN Algorithm for Clustering Large Spatial Databases Based on Sampling Technique

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Clustering, in data mining, is a useful technique for discoveringinte resting data distributions and patterns in the underlying data, and has many app lication fields, such as statistical data analysis, pattern recognition, image p rocessing, and etc. We combine sampling technique with DBSCAN alg orithm to cluster large spatial databases, and two sampling-based DBSCAN (SDBSC A N) algorithms are developed. One algorithm introduces sampling technique inside DBSCAN, and the other uses sampling procedure outside DBSCAN. Experimental resul ts demonstrate that our algorithms are effective and efficient in clustering lar ge-scale spatial databases.

  3. Sampling designs matching species biology produce accurate and affordable abundance indices

    Directory of Open Access Journals (Sweden)

    Grant Harris

    2013-12-01

    Full Text Available Wildlife biologists often use grid-based designs to sample animals and generate abundance estimates. Although sampling in grids is theoretically sound, in application, the method can be logistically difficult and expensive when sampling elusive species inhabiting extensive areas. These factors make it challenging to sample animals and meet the statistical assumption of all individuals having an equal probability of capture. Violating this assumption biases results. Does an alternative exist? Perhaps by sampling only where resources attract animals (i.e., targeted sampling, it would provide accurate abundance estimates more efficiently and affordably. However, biases from this approach would also arise if individuals have an unequal probability of capture, especially if some failed to visit the sampling area. Since most biological programs are resource limited, and acquiring abundance data drives many conservation and management applications, it becomes imperative to identify economical and informative sampling designs. Therefore, we evaluated abundance estimates generated from grid and targeted sampling designs using simulations based on geographic positioning system (GPS data from 42 Alaskan brown bears (Ursus arctos. Migratory salmon drew brown bears from the wider landscape, concentrating them at anadromous streams. This provided a scenario for testing the targeted approach. Grid and targeted sampling varied by trap amount, location (traps placed randomly, systematically or by expert opinion, and traps stationary or moved between capture sessions. We began by identifying when to sample, and if bears had equal probability of capture. We compared abundance estimates against seven criteria: bias, precision, accuracy, effort, plus encounter rates, and probabilities of capture and recapture. One grid (49 km2 cells and one targeted configuration provided the most accurate results. Both placed traps by expert opinion and moved traps between capture

  4. Sampling designs matching species biology produce accurate and affordable abundance indices

    Science.gov (United States)

    Farley, Sean; Russell, Gareth J.; Butler, Matthew J.; Selinger, Jeff

    2013-01-01

    Wildlife biologists often use grid-based designs to sample animals and generate abundance estimates. Although sampling in grids is theoretically sound, in application, the method can be logistically difficult and expensive when sampling elusive species inhabiting extensive areas. These factors make it challenging to sample animals and meet the statistical assumption of all individuals having an equal probability of capture. Violating this assumption biases results. Does an alternative exist? Perhaps by sampling only where resources attract animals (i.e., targeted sampling), it would provide accurate abundance estimates more efficiently and affordably. However, biases from this approach would also arise if individuals have an unequal probability of capture, especially if some failed to visit the sampling area. Since most biological programs are resource limited, and acquiring abundance data drives many conservation and management applications, it becomes imperative to identify economical and informative sampling designs. Therefore, we evaluated abundance estimates generated from grid and targeted sampling designs using simulations based on geographic positioning system (GPS) data from 42 Alaskan brown bears (Ursus arctos). Migratory salmon drew brown bears from the wider landscape, concentrating them at anadromous streams. This provided a scenario for testing the targeted approach. Grid and targeted sampling varied by trap amount, location (traps placed randomly, systematically or by expert opinion), and traps stationary or moved between capture sessions. We began by identifying when to sample, and if bears had equal probability of capture. We compared abundance estimates against seven criteria: bias, precision, accuracy, effort, plus encounter rates, and probabilities of capture and recapture. One grid (49 km2 cells) and one targeted configuration provided the most accurate results. Both placed traps by expert opinion and moved traps between capture sessions, which

  5. Zebrafish whole-adult-organism chemogenomics for large-scale predictive and discovery chemical biology.

    Directory of Open Access Journals (Sweden)

    Siew Hong Lam

    2008-07-01

    Full Text Available The ability to perform large-scale, expression-based chemogenomics on whole adult organisms, as in invertebrate models (worm and fly, is highly desirable for a vertebrate model but its feasibility and potential has not been demonstrated. We performed expression-based chemogenomics on the whole adult organism of a vertebrate model, the zebrafish, and demonstrated its potential for large-scale predictive and discovery chemical biology. Focusing on two classes of compounds with wide implications to human health, polycyclic (halogenated aromatic hydrocarbons [P(HAHs] and estrogenic compounds (ECs, we generated robust prediction models that can discriminate compounds of the same class from those of different classes in two large independent experiments. The robust expression signatures led to the identification of biomarkers for potent aryl hydrocarbon receptor (AHR and estrogen receptor (ER agonists, respectively, and were validated in multiple targeted tissues. Knowledge-based data mining of human homologs of zebrafish genes revealed highly conserved chemical-induced biological responses/effects, health risks, and novel biological insights associated with AHR and ER that could be inferred to humans. Thus, our study presents an effective, high-throughput strategy of capturing molecular snapshots of chemical-induced biological states of a whole adult vertebrate that provides information on biomarkers of effects, deregulated signaling pathways, and possible affected biological functions, perturbed physiological systems, and increased health risks. These findings place zebrafish in a strategic position to bridge the wide gap between cell-based and rodent models in chemogenomics research and applications, especially in preclinical drug discovery and toxicology.

  6. Biologically inspired large scale chemical sensor arrays and embedded data processing

    Science.gov (United States)

    Marco, S.; Gutiérrez-Gálvez, A.; Lansner, A.; Martinez, D.; Rospars, J. P.; Beccherelli, R.; Perera, A.; Pearce, T.; Vershure, P.; Persaud, K.

    2013-05-01

    Biological olfaction outperforms chemical instrumentation in specificity, response time, detection limit, coding capacity, time stability, robustness, size, power consumption, and portability. This biological function provides outstanding performance due, to a large extent, to the unique architecture of the olfactory pathway, which combines a high degree of redundancy, an efficient combinatorial coding along with unmatched chemical information processing mechanisms. The last decade has witnessed important advances in the understanding of the computational primitives underlying the functioning of the olfactory system. EU Funded Project NEUROCHEM (Bio-ICT-FET- 216916) has developed novel computing paradigms and biologically motivated artefacts for chemical sensing taking inspiration from the biological olfactory pathway. To demonstrate this approach, a biomimetic demonstrator has been built featuring a large scale sensor array (65K elements) in conducting polymer technology mimicking the olfactory receptor neuron layer, and abstracted biomimetic algorithms have been implemented in an embedded system that interfaces the chemical sensors. The embedded system integrates computational models of the main anatomic building blocks in the olfactory pathway: the olfactory bulb, and olfactory cortex in vertebrates (alternatively, antennal lobe and mushroom bodies in the insect). For implementation in the embedded processor an abstraction phase has been carried out in which their processing capabilities are captured by algorithmic solutions. Finally, the algorithmic models are tested with an odour robot with navigation capabilities in mixed chemical plumes

  7. Preconcentration and determination of heavy metals in water, sediment and biological samples

    Directory of Open Access Journals (Sweden)

    Shirkhanloo Hamid

    2011-01-01

    Full Text Available In this study, a simple, sensitive and accurate column preconcentration method was developed for the determination of Cd, Cu and Pb ions in river water, urine and sediment samples by flame atomic absorption spectrometry. The procedure is based on the retention of the analytes on a mixed cellulose ester membrane (MCEM column from buffered sample solutions and then their elution from the column with nitric acid. Several parameters, such as pH of the sample solution, volume of the sample and eluent and flow rates of the sample were evaluated. The effects of diverse ions on the preconcentration were also investigated. The recoveries were >95 %. The developed method was applied to the determination of trace metal ions in river water, urine and sediment samples, with satisfactory results. The 3δ detection limits for Cu, Pb and Cd were found to be 2, 3 and 0.2 μg dm−3, respectively. The presented procedure was successfully applied for determination of the copper, lead and cadmium contents in real samples, i.e., river water and biological samples.

  8. High-resolution, high-transmission soft x-ray spectrometer for the study of biological samples

    Energy Technology Data Exchange (ETDEWEB)

    Fuchs, Oliver; Weinhardt, L.; Blum, M.; Welgand, M.; Umbach, E.; Bar, M.; Heske, C.; Denlinger, J.; Chuang, Y.-D.; McKinney, W.; Hussain, Z.; Gullikson, E.; Jones, M.; Batson, P.; Nelles, B.; Follath, R.

    2009-06-11

    We present a variable line-space grating spectrometer for soft s-rays that coverst the photon energy range between 130 and 650 eV. The optical design is based on the Hettrick-Underwood principle and tailored to synchrotron-based studies of radiation-sensitive biological samples. The spectrometer is able to record the entire spectral range in one shot, i.e., without any mechanical motion, at a resolving power of 1200 or better. Despite is slitless design, such a resolving power can be achieved for a source spot as large as (30 x 3000) micrometers squared, which is important for keeping beam damage effects in radiation-sensitive samples low. The high spectrometer efficiency allows recording of comprehensive two-dimensional resonant inelastic soft x-ray scatters (RIXS) maps with good statistics within several minutes. This is exemplarily demonstrated for a RIXS map of highly oriented pyrolytic graphite, which was taken with 10 min.

  9. High-resolution, high-transmission soft x-ray spectrometer for the study of biological samples

    Energy Technology Data Exchange (ETDEWEB)

    Fuchs, Oliver; Weinhardt, L.; Blum, M.; Weigand, M.; Umbach, E.; Bar, M.; Heske, Clemens; Denlinger, Jonathan; Chuang, Y.-D.; McKinney, Wayne; Hussain, Zahid; Gullikson, Eric; Jones, M.; Batson, Phil; Nelles, B.; Follath, R.

    2009-03-09

    We present a variable line-space grating spectrometer for soft x-rays that covers the photon energy range between 130 and 650 eV. The optical design is based on the Hettrick-Underwood principle and tailored to synchrotron-based studies of radiation-sensitive biological samples. The spectrometer is able to record the entire spectral range in one shot, i.e., without any mechanical motion, at a resolving power of 1200 or better. Despite its slitless design, such a resolving power can be achieved for a source spot as large as 30x3000 mu m2, which is important for keeping beam damage effects in radiation-sensitive samples low. The high spectrometer efficiency allows recording of comprehensive two-dimensional resonant inelastic soft x-ray scattering (RIXS) maps with good statistics within several minutes. This is exemplarily demonstrated for a RIXS map of highly oriented pyrolytic graphite, which was taken within 10 min.

  10. AIS-BN: An Adaptive Importance Sampling Algorithm for Evidential Reasoning in Large Bayesian Networks

    CERN Document Server

    Cheng, J; 10.1613/jair.764

    2011-01-01

    Stochastic sampling algorithms, while an attractive alternative to exact algorithms in very large Bayesian network models, have been observed to perform poorly in evidential reasoning with extremely unlikely evidence. To address this problem, we propose an adaptive importance sampling algorithm, AIS-BN, that shows promising convergence rates even under extreme conditions and seems to outperform the existing sampling algorithms consistently. Three sources of this performance improvement are (1) two heuristics for initialization of the importance function that are based on the theoretical properties of importance sampling in finite-dimensional integrals and the structural advantages of Bayesian networks, (2) a smooth learning method for the importance function, and (3) a dynamic weighting function for combining samples from different stages of the algorithm. We tested the performance of the AIS-BN algorithm along with two state of the art general purpose sampling algorithms, likelihood weighting (Fung and Chang...

  11. Large loop conformation sampling using the activation relaxation technique, ART-nouveau method.

    Science.gov (United States)

    St-Pierre, Jean-François; Mousseau, Normand

    2012-07-01

    We present an adaptation of the ART-nouveau energy surface sampling method to the problem of loop structure prediction. This method, previously used to study protein folding pathways and peptide aggregation, is well suited to the problem of sampling the conformation space of large loops by targeting probable folding pathways instead of sampling exhaustively that space. The number of sampled conformations needed by ART nouveau to find the global energy minimum for a loop was found to scale linearly with the sequence length of the loop for loops between 8 and about 20 amino acids. Considering the linear scaling dependence of the computation cost on the loop sequence length for sampling new conformations, we estimate the total computational cost of sampling larger loops to scale quadratically compared to the exponential scaling of exhaustive search methods.

  12. RAPID SEPARATION METHOD FOR 237NP AND PU ISOTOPES IN LARGE SOIL SAMPLES

    Energy Technology Data Exchange (ETDEWEB)

    Maxwell, S.; Culligan, B.; Noyes, G.

    2010-07-26

    A new rapid method for the determination of {sup 237}Np and Pu isotopes in soil and sediment samples has been developed at the Savannah River Site Environmental Lab (Aiken, SC, USA) that can be used for large soil samples. The new soil method utilizes an acid leaching method, iron/titanium hydroxide precipitation, a lanthanum fluoride soil matrix removal step, and a rapid column separation process with TEVA Resin. The large soil matrix is removed easily and rapidly using this two simple precipitations with high chemical recoveries and effective removal of interferences. Vacuum box technology and rapid flow rates are used to reduce analytical time.

  13. The Tip-Sample Interaction in Atomic Force Microscopy and its Implications for Biological Applications.

    Science.gov (United States)

    Baselt, David Randall

    This thesis describes the construction of an atomic force microscope and its application to the study of tip -sample interactions, primarily through the use of friction and hardness (elasticity) imaging. Part one describes the atomic force microscope, which consists of a scanned-cantilever stage (chapter 2); a versatile digital signal processor-based control system with self-optimizing feedback, lock-in amplifier emulation (for hardness imaging), and macro programmability (chapter 3); and image processing software (chapter 4). Part two describes a number of results that have helped to characterize the tip-sample interaction and the contact imaging modes used for its study. Meniscus forces act laterally as well as normally, and that they vary with position (chapter 5). Friction measurements couple with scanner position and feedback, and the meniscus effects friction images (chapter 6). Sliding of the tip over the sample surface introduces slope-dependence into hardness measurements (chapter 7). Dull tips can create prominent topography artifacts even on very flat surfaces (chapter 8). In an investigation of collagen fibrils, AFM has revealed the characteristic 65 nm banding pattern, a second, minor banding pattern, and microfibrils that run along the fibril axis. The distribution of proteoglycans along the fibrils creates a characteristic pattern in friction images. Although imaging in water reduces interaction forces, water can also make biological samples more sensitive to force. However, for robust biological samples imaged in air, tip shape presents a greater obstacle than tip -sample interaction forces to obtaining high-resolution images. Tip contamination increases tip-sample friction and can occasionally improve resolution (chapter 9). For a separate project I have designed a general -purpose nearfield scanning optical microscope (chapter 10).

  14. Target and non-target screening strategies for organic contaminants, residues and illicit substances in food , environmental and human biological samples by UHPLC-QTOF-MS

    OpenAIRE

    Hernández Hernández, Félix; Díaz San Pedro, Ramón; Sancho Llopis, Juan Vicente; Ibáñez Martínez, María

    2012-01-01

    In this paper, we illustrate the potential of ultra-high performance liquid chromatography (UHPLC) coupled with hybrid quadrupole time-of-flight mass spectrometry (QTOF MS) for large scale screening of organic contaminants in different types of samples. Thanks to the full-spectrum acquisition at satisfactory sensitivity, it is feasible to apply both (post)-target and non-target approaches for the rapid qualitative screening of organic pollutants in food, biological and environmental samples. ...

  15. Potentiometric detection in UPLC as an easy alternative to determine cocaine in biological samples.

    Science.gov (United States)

    Daems, Devin; van Nuijs, Alexander L N; Covaci, Adrian; Hamidi-Asl, Ezat; Van Camp, Guy; Nagels, Luc J

    2015-07-01

    The analytical methods which are often used for the determination of cocaine in complex biological matrices are a prescreening immunoassay and confirmation by chromatography combined with mass spectrometry. We suggest an ultra-high-pressure liquid chromatography combined with a potentiometric detector, as a fast and practical method to detect and quantify cocaine in biological samples. An adsorption/desorption model was used to investigate the usefulness of the potentiometric detector to determine cocaine in complex matrices. Detection limits of 6.3 ng mL(-1) were obtained in plasma and urine, which is below the maximum residue limit (MRL) of 25 ng mL(-1). A set of seven plasma samples and 10 urine samples were classified identically by both methods as exceeding the MRL or being inferior to it. The results obtained with the UPLC/potentiometric detection method were compared with the results obtained with the UPLC/MS method for samples spiked with varying cocaine concentrations. The intraclass correlation coefficient was 0.997 for serum (n =7) and 0.977 for urine (n =8). As liquid chromatography is an established technique, and as potentiometry is very simple and cost-effective in terms of equipment, we believe that this method is potentially easy, inexpensive, fast and reliable.

  16. RNA SAMPLE PREPARATION APPLIED TO GENE EXPRESSION PROFILING FOR THE HORSE BIOLOGICAL PASSPORT.

    Science.gov (United States)

    Bailly-Chouriberry, Ludovic; Baudoin, Florent; Cormant, Florence; Glavieux, Yohan; Loup, Benoit; Garcia, Patrice; Popot, Marie-Agnès; Bonnaire, Yves

    2017-04-05

    The improvement of doping control is an on-going race. Techniques to fight against doping are usually based on the direct detection of drugs or their metabolites by analytical methods such as chromatography hyphenated to mass spectrometry after ad hoc sample preparation. Nowadays, omic methods constitute an attractive development and advances have been achieved particularly by application of molecular biology tools for detection of anabolic androgenic steroids (AAS), erythropoiesis-stimulating agent (ESA) or to control human growth hormone misuses. These interesting results across different animal species have suggested that modification of gene expression offers promising new methods of improving the window of detection of banned substances by targeting their effects on blood cell gene expression. In this context, the present study describes the possibility of using a modified version of the dedicated Human IVD (in vitro Diagnostics) PAXgene® Blood RNA Kit for horse gene expression analysis in blood collected on PAXgene® tubes applied to the Horse Biological Passport. The commercial kit was only approved for human blood samples and has required an optimization of specific technical requirements for equine blood samples. Improvements and recommendations were achieved for sample collection, storage and RNA extraction procedure. Following these developments, RNA yield and quality were demonstrated to be suitable for downstream gene expression analysis by qPCR techniques.

  17. A comparison of sample preparation strategies for biological tissues and subsequent trace element analysis using LA-ICP-MS.

    Science.gov (United States)

    Bonta, Maximilian; Török, Szilvia; Hegedus, Balazs; Döme, Balazs; Limbeck, Andreas

    2017-03-01

    Laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) is one of the most commonly applied methods for lateral trace element distribution analysis in medical studies. Many improvements of the technique regarding quantification and achievable lateral resolution have been achieved in the last years. Nevertheless, sample preparation is also of major importance and the optimal sample preparation strategy still has not been defined. While conventional histology knows a number of sample pre-treatment strategies, little is known about the effect of these approaches on the lateral distributions of elements and/or their quantities in tissues. The technique of formalin fixation and paraffin embedding (FFPE) has emerged as the gold standard in tissue preparation. However, the potential use for elemental distribution studies is questionable due to a large number of sample preparation steps. In this work, LA-ICP-MS was used to examine the applicability of the FFPE sample preparation approach for elemental distribution studies. Qualitative elemental distributions as well as quantitative concentrations in cryo-cut tissues as well as FFPE samples were compared. Results showed that some metals (especially Na and K) are severely affected by the FFPE process, whereas others (e.g., Mn, Ni) are less influenced. Based on these results, a general recommendation can be given: FFPE samples are completely unsuitable for the analysis of alkaline metals. When analyzing transition metals, FFPE samples can give comparable results to snap-frozen tissues. Graphical abstract Sample preparation strategies for biological tissues are compared with regard to the elemental distributions and average trace element concentrations.

  18. Challenges of biological sample preparation for SIMS imaging of elements and molecules at subcellular resolution

    Energy Technology Data Exchange (ETDEWEB)

    Chandra, Subhash [Cornell SIMS Laboratory, Department of Earth and Atmospheric Sciences, Snee Hall, Cornell University, Ithaca, NY 14853 (United States)], E-mail: sc40@cornell.edu

    2008-12-15

    Secondary ion mass spectrometry (SIMS) based imaging techniques capable of subcellular resolution characterization of elements and molecules are becoming valuable tools in many areas of biology and medicine. Due to high vacuum requirements of SIMS, the live cells cannot be analyzed directly in the instrument. The sample preparation, therefore, plays a critical role in preserving the native chemical composition for SIMS analysis. This work focuses on the evaluation of frozen-hydrated and frozen freeze-dried sample preparations for SIMS studies of cultured cells with a CAMECA IMS-3f dynamic SIMS ion microscope instrument capable of producing SIMS images with a spatial resolution of 500 nm. The sandwich freeze-fracture method was used for fracturing the cells. The complimentary fracture planes in the plasma membrane were characterized by field-emission secondary electron microscopy (FESEM) in the frozen-hydrated state. The cells fractured at the dorsal surface were used for SIMS analysis. The frozen-hydrated SIMS analysis of individual cells under dynamic primary ion beam (O{sub 2}{sup +}) revealed local secondary ion signal enhancements correlated with the water image signals of {sup 19}(H{sub 3}O){sup +}. A preferential removal of water from the frozen cell matrix in the Z-axis was also observed. These complications render the frozen-hydrated sample type less desirable for subcellular dynamic SIMS studies. The freeze-drying of frozen-hydrated cells, either inside the instrument or externally in a freeze-drier, allowed SIMS imaging of subcellular chemical composition. Morphological evaluations of fractured freeze-dried cells with SEM and confocal laser scanning microscopy (CLSM) revealed well-preserved mitochondria, Golgi apparatus, and stress fibers. SIMS analysis of fractured freeze-dried cells revealed well-preserved chemical composition of even the most highly diffusible ions like K{sup +} and Na{sup +} in physiologically relevant concentrations. The high K

  19. Functional results after repair of large hiatal hernia by use of a biologic mesh

    Directory of Open Access Journals (Sweden)

    Filimon eAntonakis

    2016-03-01

    Full Text Available Background: The aim of this observational study is to analyze the results of patients with large hiatal hernia and upside-down stomach after surgical closure with a biologic mesh (Permacol®, Covidien, Neustadt an der Donau, Germany. Biologic mesh is used to prevent long-term detrimental effects of artificial meshes and to reduce recurrence rates. Methods: A total of 13 patients with a large hiatal hernia and endothoracic stomach, who underwent surgery between 2010 and 2014, were included. Interviews and upper endoscopy were conducted to determine recurrence, lifestyle restrictions and current complaints. Results: After a mean follow-up of 26+18 months (range 3-58 months 10 patients (three men, mean age 73+13, range 26-81 years were evaluated. A small recurrent axial hernia was found in one patient postoperatively. Dysphagia was the most common complaint (four cases, while in one case the problem was solved after endoscopic dilatation. In three cases bloat and postprandial pain were documented. In one case explantation of the mesh was necessary due to mesh migration and painful adhesions. In one further case with gastroparesis pyloroplasty was performed without success.Conclusion: Recurrence was rare after hernia repair with the biologic mesh Permacol®. Dysphagia, gas bloat and intraabdominal pain were frequent complaints. Despite the small number of patients it can be concluded that a biologic mesh may be an alternative to synthetic meshes to reduce recurrences. Long-term results should be studied in the future in order to assess the potential of biologic meshes to preserve esophageal function as well. This is important since artificial meshes are known to erode the esophagus after 5–10 years.

  20. High-resolution monochromator for iron nuclear resonance vibrational spectroscopy of biological samples

    Science.gov (United States)

    Yoda, Yoshitaka; Okada, Kyoko; Wang, Hongxin; Cramer, Stephen P.; Seto, Makoto

    2016-12-01

    A new high-resolution monochromator for 14.4-keV X-rays has been designed and developed for the Fe nuclear resonance vibrational spectroscopy of biological samples. In addition to high resolution, higher flux and stability are especially important for measuring biological samples, because of the very weak signals produced due to the low concentrations of Fe-57. A 24% increase in flux while maintaining a high resolution better than 0.9 meV is achieved in the calculation by adopting an asymmetric reflection of Ge, which is used as the first crystal of the three-bounce high-resolution monochromator. A 20% increase of the exit beam size is acceptable to our biological applications. The higher throughput of the new design has been experimentally verified. A fine rotation mechanics that combines a weak-link hinge with a piezoelectric actuator was used for controlling the photon energy of the monochromatic beam. The resulting stability is sufficient to preserve the intrinsic resolution.

  1. A review on determination of steroids in biological samples exploiting nanobio-electroanalytical methods.

    Science.gov (United States)

    Yadav, Saurabh K; Chandra, Pranjal; Goyal, Rajendra N; Shim, Yoon-Bo

    2013-01-31

    The applications of nanomaterial modified sensors, molecularly imprinting polymer based, aptamer based, and immunosensors have been described in the determination of steroids using electroanalytical techniques. After a brief description of the steroids and assays in biological fluids, the principles of electrochemical detection with the advantages and the limitations of the various sensors are presented. The nanomaterial modified sensors catalyze the oxidation/reduction of steroids and are suitable for sensing them in environmental samples and biological fluids. The determination of steroids based on their reduction has been found more useful in comparison to oxidation as the common metabolites present in the biological fluids do not undergo reduction in the usual potential window and hence, do not interfere in the determination. The sensors based on immunosensors and aptamers were found more sensitive and selective for steroid determination. Conducting polymer modified bio-sensors and microchip devices are suggested as possible future prospects for the ultra sensitive and simultaneous determination of steroids and their metabolites in various samples.

  2. Measurement of Beryllium in Biological Samples by Accelerator Mass Spectrometry: Applications for Studying Chronic Beryllium Disease

    Energy Technology Data Exchange (ETDEWEB)

    Chiarappa-Zucca, M L; Finkel, R C; Martinelli, R E; McAninch, J E; Nelson, D O; Turtletaub, K W

    2004-04-15

    A method using accelerator mass spectrometry (AMS) has been developed for quantifying attomoles of beryllium (Be) in biological samples. This method provides the sensitivity to trace Be in biological samples at very low doses with the purpose of identifying the molecular targets involved in chronic beryllium disease. Proof of the method was tested by administering 0.001, 0.05, 0.5 and 5.0 {micro}g {sup 9}Be and {sup 10}Be by intraperitoneal injection to male mice and removing spleen, liver, femurs, blood, lung, and kidneys after 24 h exposure. These samples were prepared for AMS analysis by tissue digestion in nitric acid, followed by further organic oxidation with hydrogen peroxide and ammonium persulfate and lastly, precipitation of Be with ammonium hydroxide, and conversion to beryllium oxide at 800 C. The {sup 10}Be/{sup 9}Be ratio of the extracted beryllium oxide was measured by AMS and Be in the original sample was calculated. Results indicate that Be levels were dose-dependent in all tissues and the highest levels were measured in the spleen and liver. The measured {sup 10}Be/{sup 9}Be ratios spanned 4 orders of magnitude, from 10{sup -10} to 10{sup -14}, with a detection limit of 3.0 x 10{sup -14}, which is equivalent to 0.8 attomoles of {sup 10}Be. These results show that routine quantification of nanogram levels of Be in tissues is possible and that AMS is a sensitive method that can be used in biological studies to understand the molecular dosimetry of Be and mechanisms of toxicity.

  3. Occupational biological risk knowledge and perception: results from a large survey in Rome, Italy

    Directory of Open Access Journals (Sweden)

    Maria De Giusti

    2012-06-01

    Full Text Available BACKGROUND: A cross-sectional survey on knowledge and perception of occupational biological risk among workers in several occupations was carried out in the industrial area of Rome. METHODS: The study was carried out in the period of March-April 2010 using a questionnaire with 33 items on the following areas: a socio-demographic data; b perception of the biological risks in ordinary occupational activity; c knowledge about biological risks; d biological risks in the working environment. The questionnaire was submitted to a convenience sample of workers of an industrial area in Southern Rome. RESULTS: 729 participants entered the study from the following work activities: food, catering, service, farming and breeding, healthcare, school and research (males 57.2%; mean age 37.4 years, SD = 10.9. Significant associations were found between different activity areas with respect to the relevance of the biological risk (p = 0.044 and the perception of the biological risk (p < 0.001. With respect to vehicles of infectious agents, the highest percentages of the most common biological risk exposures were: air and physical contact for the catering and food group, 66.7% and 61.90% respectively; air and blood for the health and research group, with 73.50% and 57.00% respectively; and physical contact and blood for the service group, 63.10 % and 48.30%. Significant difference of proportions were found about the prevalent effect caused by the biological agents was the occurrence of infectious diseases (59.90% food group, 91.60% health and research and 79.30% service group (p < 0.001. The perception of knowledge resulted in a good rank (sufficient, many or complete in the food and catering group, 78.3% with significant difference compared to other professions (p < 0.001. CONCLUSIONS: All participants show good knowledge the effects induced by biological agents and it is significant that almost half of the respondents are aware of the risks concerning allergies

  4. Novel Technique for Sampling of Breast Implant-associated Seroma in Anaplastic Large Cell Lymphoma.

    Science.gov (United States)

    van Dorp, Martijn; T'Kindt, Johan; Mertens, Marianne; Colpaert, Steven D M

    2016-04-01

    We describe a novel technique for the sampling of breast implant-associated seroma. Using a blunt-tip lipofilling cannula, we have the freedom of movement to sample all fluid collections and prevent the misfortunes of damaging the implant. Also, we have demonstrated the inability of the Coleman style I lipofilling cannula to perforate a silicone breast implant. This practical and reliable technique will prove to be useful in managing the breast implant-associated seroma, especially with the rising incidence of the anaplastic large cell lymphoma, where the sampling of seroma is mandatory.

  5. Spectrochemical analysis of powdered biological samples using transversely excited atmospheric carbon dioxide laser plasma excitation

    Science.gov (United States)

    Zivkovic, Sanja; Momcilovic, Milos; Staicu, Angela; Mutic, Jelena; Trtica, Milan; Savovic, Jelena

    2017-02-01

    The aim of this study was to develop a simple laser induced breakdown spectroscopy (LIBS) method for quantitative elemental analysis of powdered biological materials based on laboratory prepared calibration samples. The analysis was done using ungated single pulse LIBS in ambient air at atmospheric pressure. Transversely-Excited Atmospheric pressure (TEA) CO2 laser was used as an energy source for plasma generation on samples. The material used for the analysis was a blue-green alga Spirulina, widely used in food and pharmaceutical industries and also in a few biotechnological applications. To demonstrate the analytical potential of this particular LIBS system the obtained spectra were compared to the spectra obtained using a commercial LIBS system based on pulsed Nd:YAG laser. A single sample of known concentration was used to estimate detection limits for Ba, Ca, Fe, Mg, Mn, Si and Sr and compare detection power of these two LIBS systems. TEA CO2 laser based LIBS was also applied for quantitative analysis of the elements in powder Spirulina samples. Analytical curves for Ba, Fe, Mg, Mn and Sr were constructed using laboratory produced matrix-matched calibration samples. Inductively coupled plasma optical emission spectroscopy (ICP-OES) was used as the reference technique for elemental quantification, and reasonably well agreement between ICP and LIBS data was obtained. Results confirm that, in respect to its sensitivity and precision, TEA CO2 laser based LIBS can be successfully applied for quantitative analysis of macro and micro-elements in algal samples. The fact that nearly all classes of materials can be prepared as powders implies that the proposed method could be easily extended to a quantitative analysis of different kinds of materials, organic, biological or inorganic.

  6. Simple Sensitive Spectrophotometric Determination of Vanadium in Biological and Environmental Samples

    Directory of Open Access Journals (Sweden)

    B. Krishna Priya

    2006-01-01

    Full Text Available Novel, rapid, highly sensitive and selective spectrophotometric method for the determination of traces of vanadium (V in environmental and biological samples, pharmaceutical and steel samples was studied. The method is based on oxidation of 2,4- dinitro phenyl hydrazine(2,4-DNPH by vanadium (V followed by coupling reaction with N-(1-naphthalene-1-ylethane-1,2-diamine-dihydrochloride (NEDA in acidic medium to give red colored derivative or on oxidation of 4-Amino Pyridine by vanadium (V followed by coupling reaction with NEDA in basic medium to give pink colored derivative. The red colored derivative having an λmax 495 nm which is stable for 8 days and the pink colored derivative with 525 nm is stable for more than 7 days at 350C. Beer's law is obeyed for vanadium (V in the concentration range of 0.02 - 3.5 μg mL–1 (red derivative and 0.03 – 4.5 μg mL–1 (pink derivative at the wave length of maximum absorption. The optimum reaction conditions and other analytical parameters were investigated to enhance the sensitivity of the present method. The detailed study of various interferences made the method more selective. The proposed method was successfully applied to the analysis of vanadium in natural water samples, plant material, soil samples, synthetic mixtures, pharmaceutical samples and biological samples. The results obtained were agreed with the reported methods at the 95 % confidence level. The performance of proposed method was evaluated in terms of Student's t-test and Variance ratio f-test which indicates the significance of proposed method over reported method.

  7. Analyses of odontometric sexual dimorphism and sex assessment accuracy on a large sample.

    Science.gov (United States)

    Angadi, Punnya V; Hemani, S; Prabhu, Sudeendra; Acharya, Ashith B

    2013-08-01

    Correct sex assessment of skeletonized human remains allows investigators to undertake a more focused search of missing persons' files to establish identity. Univariate and multivariate odontometric sex assessment has been explored in recent years on small sample sizes and have not used a test sample. Consequently, inconsistent results have been produced in terms of accuracy of sex allocation. This paper has derived data from a large sample of males and females, and applied logistic regression formulae on a test sample. Using a digital caliper, buccolingual and mesiodistal dimensions of all permanent teeth (except third molars) were measured on 600 dental casts (306 females, 294 males) of young adults (18-32 years), and the data subjected to univariate (independent samples' t-test) and multivariate statistics (stepwise logistic regression analysis, or LRA). The analyses revealed that canines were the most sexually dimorphic teeth followed by molars. All tooth variables were larger in males, with 51/56 (91.1%) being statistically larger (p contradiction to a previous report of virtually 100% sex allocation for a small heterogeneous sample. These reflect the importance of using a large sample to quantify sexual dimorphism in tooth dimensions and the application of the derived formulae on a test dataset to ascertain accuracy which, at best, is moderate in nature.

  8. Coding SNPs as intrinsic markers for sample tracking in large-scale transcriptome studies.

    Science.gov (United States)

    Xu, Weihong; Gao, Hong; Seok, Junhee; Wilhelmy, Julie; Mindrinos, Michael N; Davis, Ronald W; Xiao, Wenzhong

    2012-06-01

    Large-scale transcriptome profiling in clinical studies often involves assaying multiple samples of a patient to monitor disease progression, treatment effect, and host response in multiple tissues. Such profiling is prone to human error, which often results in mislabeled samples. Here, we present a method to detect mislabeled sample outliers using coding single nucleotide polymorphisms (cSNPs) specifically designed on the microarray and demonstrate that the mislabeled samples can be efficiently identified by either simple clustering of allele-specific expression scores or Mahalanobis distance-based outlier detection method. Based on our results, we recommend the incorporation of cSNPs into future transcriptome array designs as intrinsic markers for sample tracking.

  9. Non-target time trend screening: a data reduction strategy for detecting emerging contaminants in biological samples.

    Science.gov (United States)

    Plassmann, Merle M; Tengstrand, Erik; Åberg, K Magnus; Benskin, Jonathan P

    2016-06-01

    Non-targeted mass spectrometry-based approaches for detecting novel xenobiotics in biological samples are hampered by the occurrence of naturally fluctuating endogenous substances, which are difficult to distinguish from environmental contaminants. Here, we investigate a data reduction strategy for datasets derived from a biological time series. The objective is to flag reoccurring peaks in the time series based on increasing peak intensities, thereby reducing peak lists to only those which may be associated with emerging bioaccumulative contaminants. As a result, compounds with increasing concentrations are flagged while compounds displaying random, decreasing, or steady-state time trends are removed. As an initial proof of concept, we created artificial time trends by fortifying human whole blood samples with isotopically labelled standards. Different scenarios were investigated: eight model compounds had a continuously increasing trend in the last two to nine time points, and four model compounds had a trend that reached steady state after an initial increase. Each time series was investigated at three fortification levels and one unfortified series. Following extraction, analysis by ultra performance liquid chromatography high-resolution mass spectrometry, and data processing, a total of 21,700 aligned peaks were obtained. Peaks displaying an increasing trend were filtered from randomly fluctuating peaks using time trend ratios and Spearman's rank correlation coefficients. The first approach was successful in flagging model compounds spiked at only two to three time points, while the latter approach resulted in all model compounds ranking in the top 11 % of the peak lists. Compared to initial peak lists, a combination of both approaches reduced the size of datasets by 80-85 %. Overall, non-target time trend screening represents a promising data reduction strategy for identifying emerging bioaccumulative contaminants in biological samples. Graphical abstract

  10. Practical Guide to Using Cryoprotectants in Biological Sample Preparation at Cryogenic temperature for Electron Microscopic Studies

    Directory of Open Access Journals (Sweden)

    A-Reum Je

    2011-10-01

    Full Text Available Cryo-fixation enables the preservation of the fine structures of intracellular organelles in a condition that is as close to their native state as possible compared with chemical fixation and room temperature processing. Fixation is the initial step for biological sample preparation in electron microscopy. This step is critically important because the goals of electron microscopic observation are fundamentally dependent on well-preserved specimens resulting from this fixation. In the present work, key components of cryo-fixation, cryoprotectants, are tested with various cell types of interest. The results show that dextran can be easily adapted for use with animal cells and cyanobacteria, whereas 1-hexadecene is applicable to plant and yeast cells. The current report provides useful information on the preparation of cryo-fixed biological specimens using high pressure freezing and freeze-substitution aimed at electron microscopic observation.

  11. H2S Analysis in Biological Samples Using Gas Chromatography with Sulfur Chemiluminescence Detection

    Science.gov (United States)

    Vitvitsky, Victor; Banerjee, Ruma

    2015-01-01

    Hydrogen sulfide (H2S) is a metabolite and signaling molecule in biological tissues that regulates many physiological processes. Reliable and sensitive methods for H2S analysis are necessary for a better understanding of H2S biology and for the pharmacological modulation of H2S levels in vivo. In this chapter, we describe the use of gas chromatography coupled to sulfur chemiluminescence detection to measure the rates of H2S production and degradation by tissue homogenates at physiologically relevant concentrations of substrates. This method allows separation of H2S from other sulfur compounds and provides sensitivity of detection to ~15 pg (or 0.5 pmol) of H2S per injected sample. PMID:25725519

  12. Large-Scale Multiplexed Quantitative Discovery Proteomics Enabled by the Use of an 18O-Labeled “Universal” Reference Sample

    Science.gov (United States)

    Qian, Wei-Jun; Liu, Tao; Petyuk, Vladislav A.; Gritsenko, Marina A.; Petritis, Brianne O.; Polpitiya, Ashoka D.; Kaushal, Amit; Xiao, Wenzhong; Finnerty, Celeste C.; Jeschke, Marc G.; Jaitly, Navdeep; Monroe, Matthew E.; Moore, Ronald J.; Moldawer, Lyle L.; Davis, Ronald W.; Tompkins, Ronald G.; Herndon, David N.; Camp, David G.; Smith, Richard D.

    2009-01-01

    The quantitative comparison of protein abundances across a large number of biological or patient samples represents an important proteomics challenge that needs to be addressed for proteomics discovery applications. Herein, we describe a strategy that incorporates a stable isotope 18O-labeled ″universal″ reference sample as a comprehensive set of internal standards for analyzing large sample sets quantitatively. As a pooled sample, the 18O-labeled ″universal″ reference sample is spiked into each individually processed unlabeled biological sample and the peptide/protein abundances are quantified based on 16O/18O isotopic peptide pair abundance ratios that compare each unlabeled sample to the identical reference sample. This approach also allows for the direct application of label-free quantitation across the sample set simultaneously along with the labeling-approach (i.e., dual-quantitation) since each biological sample is unlabeled except for the labeled reference sample that is used as internal standards. The effectiveness of this approach for large-scale quantitative proteomics is demonstrated by its application to a set of 18 plasma samples from severe burn patients. When immunoaffinity depletion and cysteinyl-peptide enrichment-based fractionation with high resolution LC-MS measurements were combined, a total of 312 plasma proteins were confidently identified and quantified with a minimum of two unique peptides per protein. The isotope labeling data was directly compared with the label-free 16O-MS intensity data extracted from the same data sets. The results showed that the 18O reference-based labeling approach had significantly better quantitative precision compared to the label-free approach. The relative abundance differences determined by the two approaches also displayed strong correlation, illustrating the complementary nature of the two quantitative methods. The simplicity of including the 18O-reference for accurate quantitation makes this

  13. Slow-spinning low-sideband HR-MAS NMR spectroscopy: delicate analysis of biological samples

    Science.gov (United States)

    Renault, Marie; Shintu, Laetitia; Piotto, Martial; Caldarelli, Stefano

    2013-11-01

    High-Resolution Magic-Angle Spinning (HR-MAS) NMR spectroscopy has become an extremely versatile analytical tool to study heterogeneous systems endowed with liquid-like dynamics. Spinning frequencies of several kHz are however required to obtain NMR spectra, devoid of spinning sidebands, with a resolution approaching that of purely isotropic liquid samples. An important limitation of the method is the large centrifugal forces that can damage the structure of the sample. In this communication, we show that optimizing the sample preparation, particularly avoiding air bubbles, and the geometry of the sample chamber of the HR-MAS rotor leads to high-quality low-sideband NMR spectra even at very moderate spinning frequencies, thus allowing the use of well-established solution-state NMR procedures for the characterization of small and highly dynamic molecules in the most fragile samples, such as live cells and intact tissues.

  14. Slow-spinning low-sideband HR-MAS NMR spectroscopy: delicate analysis of biological samples

    Science.gov (United States)

    Renault, Marie; Shintu, Laetitia; Piotto, Martial; Caldarelli, Stefano

    2013-01-01

    High-Resolution Magic-Angle Spinning (HR-MAS) NMR spectroscopy has become an extremely versatile analytical tool to study heterogeneous systems endowed with liquid-like dynamics. Spinning frequencies of several kHz are however required to obtain NMR spectra, devoid of spinning sidebands, with a resolution approaching that of purely isotropic liquid samples. An important limitation of the method is the large centrifugal forces that can damage the structure of the sample. In this communication, we show that optimizing the sample preparation, particularly avoiding air bubbles, and the geometry of the sample chamber of the HR-MAS rotor leads to high-quality low-sideband NMR spectra even at very moderate spinning frequencies, thus allowing the use of well-established solution-state NMR procedures for the characterization of small and highly dynamic molecules in the most fragile samples, such as live cells and intact tissues. PMID:24284435

  15. Validation of the IPQ-R in a large, representative dutch sample.

    NARCIS (Netherlands)

    Heijmans, M.; Rijken, M.

    2003-01-01

    This paper presents a validation study of the revised version of the Illness Perception Questionnaire ( IPQ-R) in a large representative Dutch sample of 4000 chronic disease patients. All patients took part in a longitudinal study, called Panel of Patients with Chronic Diseases, which is conducted b

  16. Imitation of Tongue Protrusion in Human Neonates: Specificity of the Response in a Large Sample

    Science.gov (United States)

    Nagy, Emese; Pilling, Karen; Orvos, Hajnalka; Molnar, Peter

    2013-01-01

    Although a large body of evidence has accumulated on the young human infant's ability to imitate, the phenomenon has failed to gain unanimous acceptance. Imitation of tongue protrusion, the most tested gesture to date, was examined in a sample of 115 newborns in the first 5 days of life in 3 seating positions. An ethologically based…

  17. Prevalence of neuropsychiatric symptoms in a large sample of Dutch nursing home patients with dementia

    NARCIS (Netherlands)

    Zuidema, Sytse U; Derksen, Els; Verhey, Frans R J; Koopmans, Raymond T C M

    2007-01-01

    OBJECTIVE: To estimate the prevalence of neuropsychiatric symptoms of dementia patients in Dutch nursing homes. METHODS: Cross-sectional study in a large sample of 1322 demented patients living in 59 dementia special care units (SCUs) in The Netherlands. Symptoms were observed by licensed vocational

  18. Tonic immobility in a large community sample : Prevalence and association with PTSD symptoms

    NARCIS (Netherlands)

    Hagenaars, M.A.

    2016-01-01

    People can be paralyzed when facing threat. Such paralysis, or “peritraumatic tonic immobility” (TI), is important as it seems associated with later PTSD development. However, the prevalence of TI is not known. This study investigated its prevalence in a large representative sample as well as its as

  19. Psychometric Properties of the Penn State Worry Questionnaire for Children in a Large Clinical Sample

    Science.gov (United States)

    Pestle, Sarah L.; Chorpita, Bruce F.; Schiffman, Jason

    2008-01-01

    The Penn State Worry Questionnaire for Children (PSWQ-C; Chorpita, Tracey, Brown, Collica, & Barlow, 1997) is a 14-item self-report measure of worry in children and adolescents. Although the PSWQ-C has demonstrated favorable psychometric properties in small clinical and large community samples, this study represents the first psychometric…

  20. An off-line breath sampling and analysis method suitable for large screening studies

    NARCIS (Netherlands)

    Steeghs, M.M.L.; Cristescu, S.M.; Munnik, P.; Zanen, P.; Harren, F.J.M.

    2007-01-01

    We present a new, off-line breath collection and analysis method, suitable for large screening studies. The breath collection system is based on the guidelines of the American Thoracic Society for the sampling of exhaled NO. Breath containing volatile gases is collected in custom-made black-layered

  1. Investigating sex differences in psychological predictors of snack intake among a large representative sample

    NARCIS (Netherlands)

    Adriaanse, M.A.; Evers, C.; Verhoeven, A.A.C.; de Ridder, D.T.D.

    It is often assumed that there are substantial sex differences in eating behaviour (e.g. women are more likely to be dieters or emotional eaters than men). The present study investigates this assumption in a large representative community sample while incorporating a comprehensive set of

  2. Software engineering the mixed model for genome-wide association studies on large samples

    Science.gov (United States)

    Mixed models improve the ability to detect phenotype-genotype associations in the presence of population stratification and multiple levels of relatedness in genome-wide association studies (GWAS), but for large data sets the resource consumption becomes impractical. At the same time, the sample siz...

  3. Psychometric Properties of the Penn State Worry Questionnaire for Children in a Large Clinical Sample

    Science.gov (United States)

    Pestle, Sarah L.; Chorpita, Bruce F.; Schiffman, Jason

    2008-01-01

    The Penn State Worry Questionnaire for Children (PSWQ-C; Chorpita, Tracey, Brown, Collica, & Barlow, 1997) is a 14-item self-report measure of worry in children and adolescents. Although the PSWQ-C has demonstrated favorable psychometric properties in small clinical and large community samples, this study represents the first psychometric…

  4. Determinants of salivary evening alpha-amylase in a large sample free of psychopathology

    NARCIS (Netherlands)

    Veen, Gerthe; Giltay, Erik J.; Vreeburg, Sophie A.; Licht, Carmilla M. M.; Cobbaert, Christa M.; Zitman, Frans G.; Penninx, Brenda W. J. H.

    2012-01-01

    Objective: Recently, salivary alpha-amylase (sAA) has been proposed as a suitable index for sympathetic activity and dysregulation of the autonomic nervous system (ANS). Although determinants of sAA have been described, they have not been studied within the same study with a large sample size withou

  5. Determinants of salivary evening alpha-amylase in a large sample free of psychopathology

    NARCIS (Netherlands)

    Veen, Gerthe; Giltay, Erik J.; Vreeburg, Sophie A.; Licht, Carmilla M. M.; Cobbaert, Christa M.; Zitman, Frans G.; Penninx, Brenda W. J. H.

    Objective: Recently, salivary alpha-amylase (sAA) has been proposed as a suitable index for sympathetic activity and dysregulation of the autonomic nervous system (ANS). Although determinants of sAA have been described, they have not been studied within the same study with a large sample size

  6. No association of candidate genes with cannabis use in a large sample of Australian twin families

    NARCIS (Netherlands)

    Verweij, K.J.H.; Zietsch, B.P.; Liu, J.Z.; Medland, S.E.; Lynskey, M.T.; Madden, P.A.F.; Agrawal, A.; Montgomery, G.W.; Heath, A.C.; Martin, N.G.

    2012-01-01

    While there is solid evidence that cannabis use is heritable, attempts to identify genetic influences at the molecular level have yielded mixed results. Here, a large twin family sample (n = 7452) was used to test for association between 10 previously reported candidate genes and lifetime frequency

  7. Surface-enhanced Raman scattering detection of silver nanoparticles in environmental and biological samples.

    Science.gov (United States)

    Guo, Huiyuan; Xing, Baoshan; Hamlet, Leigh C; Chica, Andrea; He, Lili

    2016-06-01

    Growing concerns over the potential release and threat of silver nanoparticles (AgNPs) to environmental and biological systems urge researchers to investigate their fate and behavior. However, current analytical techniques cannot meet the requirements for rapidly, sensitively and reliably probing AgNPs in complex matrices. Surface-enhanced Raman spectroscopy (SERS) has shown great capability for rapid detection of AgNPs based on an indicator molecule that can bind on the AgNP surface. The objective of this study was to exploit SERS to detect AgNPs in environmental and biological samples through optimizing the Raman indicator for SERS. Seven indicator molecules were selected and determined to obtain their SERS signals at optimal concentrations. Among them, 1,2-di(4-pyridyl)ethylene (BPE), crystal violet and ferric dimethyl-dithiocarbamate (ferbam) produced the highest SERS intensities. Further experiments on binding competition between each two of the three candidates showed that ferbam had the highest AgNPs-binding ability. The underlying mechanism lies in the strong binding affinity of ferbam with AgNPs via multiple sulfur atoms. We further validated ferbam to be an effective indicator for SERS detection of as low as 0.1mg/L AgNPs in genuine surface water and 0.57 mg/L in spinach juice. Moreover, limited interference on SERS detection of AgNPs was found from environmentally relevant inorganic ions, organic matter, inorganic particles, as well as biologically relevant components, demonstrating the ferbam-assisted SERS is an effective and sensitive method to detect AgNPs in complex environmental and biological samples.

  8. In-situ sampling of a large-scale particle simulation for interactive visualization and analysis

    Energy Technology Data Exchange (ETDEWEB)

    Woodring, Jonathan L [Los Alamos National Laboratory; Ahrens, James P [Los Alamos National Laboratory; Heitmann, Katrin [Los Alamos National Laboratory

    2010-12-09

    We propose storing a random sampling of data from large scale particle simulations, such as the Roadrunner Universe MC{sup 3} cosmological simulation, to be used for interactive post-analysis and visualization. Simulation data generation rates will continue to be far greater than storage bandwidth rates and other limiting technologies by many orders of magnitude. This implies that only a very small fraction of data generated by the simulation can ever be stored and subsequently post-analyzed. The limiting technology in this situation is analogous to the problem in many population surveys: there aren't enough human resources to query a large population. To cope with the lack of resources, statistical sampling techniques are used to create a representative data set of a large population. Mirroring that situation, we propose to store a simulation-time random sampling of the particle data to cope with the bOlllenecks and support interactive, exploratory post-analysis. The particle samples are immediately stored in a level-ol-detail format for post-visualization and analysis, which amortizes the cost of post-processing for interactive visualization. Additionally, we incorporate a system for recording and visualizing sample approximation error information for confidence and importance highlighting.

  9. A flux extraction device to measure the magnetic moment of large samples; application to bulk superconductors.

    Science.gov (United States)

    Egan, R; Philippe, M; Wera, L; Fagnard, J F; Vanderheyden, B; Dennis, A; Shi, Y; Cardwell, D A; Vanderbemden, P

    2015-02-01

    We report the design and construction of a flux extraction device to measure the DC magnetic moment of large samples (i.e., several cm(3)) at cryogenic temperature. The signal is constructed by integrating the electromotive force generated by two coils wound in series-opposition that move around the sample. We show that an octupole expansion of the magnetic vector potential can be used conveniently to treat near-field effects for this geometrical configuration. The resulting expansion is tested for the case of a large, permanently magnetized, type-II superconducting sample. The dimensions of the sensing coils are determined in such a way that the measurement is influenced by the dipole magnetic moment of the sample and not by moments of higher order, within user-determined upper bounds. The device, which is able to measure magnetic moments in excess of 1 A m(2) (1000 emu), is validated by (i) a direct calibration experiment using a small coil driven by a known current and (ii) by comparison with the results of numerical calculations obtained previously using a flux measurement technique. The sensitivity of the device is demonstrated by the measurement of flux-creep relaxation of the magnetization in a large bulk superconductor sample at liquid nitrogen temperature (77 K).

  10. The scope of detector Medipix2 in micro-radiography of biological samples

    Energy Technology Data Exchange (ETDEWEB)

    Dammer, J., E-mail: jiri.dammer@utef.cvut.cz [Institute of Experimental and Applied Physics, Czech Technical University in Prague, Horska 3a/22, CZ-12800 Prague 2 (Czech Republic); Weyda, F. [Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Entomology, Branisovska 31, CZ-37005 Ceske Budejovice (Czech Republic); Faculty of Science, University of South Bohemia, Branisovska 31, CZ-37005 Ceske Budejovice (Czech Republic); Jakubek, J. [Institute of Experimental and Applied Physics, Czech Technical University in Prague, Horska 3a/22, CZ-12800 Prague 2 (Czech Republic); Skrabal, P. [Faculty of Biomedical Engineering, Czech Technical University in Prague, Nam. Sitna 3105, CZ-272 01 Kladno (Czech Republic); Sopko, V.; Vavrik, D. [Institute of Experimental and Applied Physics, Czech Technical University in Prague, Horska 3a/22, CZ-12800 Prague 2 (Czech Republic)

    2011-05-15

    We present our experimental setup devoted to high resolution X-ray micro-radiography that is suitable for imaging of small biological samples. The photon source is a FeinFocus micro-focus X-ray tube. The single photon counting pixel device Medipix2 serves as imaging area. Recently used imaging detectors as radiography films or scintillator detectors, cannot visualize required information about inner structure of scanned sample. Detectors Medipix2 do not suffer from so-called dark current noise and work in unlimited dynamic range. These features of detectors confer high quality and high contrast of final images. The radiographic imaging with detectors Medipix2 represents non-invasive and non-destructive method of investigation. Hereby, we demonstrate results of micro-radiographic study of internal structures of tiny biological samples. In addition to morphological and anatomical studies, we would like to present preliminary study of dynamic processes inside of organisms using micro-radiographic video-capturing.

  11. Applications of a DAD-HPLC method for determination of loratadine on biological samples

    Directory of Open Access Journals (Sweden)

    Pavalache Georgeta

    2015-06-01

    Full Text Available The aim of research is to assess the active substance by a HPLC method for the separation and quantitative determination of loratadine. The method has been developed and validated on the standard solutions, in previous research. The current study was undertaken to present the results obtained from loratadine determination in biological samples (human serum, urine and breast milk. These results may be applicable on patients with different physiological conditions (aging, pregnancy or recently giving birth, etc. and pathological conditions which may interfere with the metabolism of loratadine. The used HPLC method detected loratadine concentrations in human serum samples, respectively urine samples, at 2 hours after drug administration. The method detected traces of loratadine which passed into breast milk, as well. Data were statistically interpreted using MED CALC 10.2 software. These results show that the applied method can be used for quantitative analysis of loratadine in biological fluids (all permissible limits of quality specifications being in the range 95- 105%.

  12. Cellular characterization of compression induced-damage in live biological samples

    Science.gov (United States)

    Bo, Chiara; Balzer, Jens; Hahnel, Mark; Rankin, Sara M.; Brown, Katherine A.; Proud, William G.

    2011-06-01

    Understanding the dysfunctions that high-intensity compression waves induce in human tissues is critical to impact on acute-phase treatments and requires the development of experimental models of traumatic damage in biological samples. In this study we have developed an experimental system to directly assess the impact of dynamic loading conditions on cellular function at the molecular level. Here we present a confinement chamber designed to subject live cell cultures in liquid environment to compression waves in the range of tens of MPa using a split Hopkinson pressure bars system. Recording the loading history and collecting the samples post-impact without external contamination allow the definition of parameters such as pressure and duration of the stimulus that can be related to the cellular damage. The compression experiments are conducted on Mesenchymal Stem Cells from BALB/c mice and the damage analysis are compared to two control groups. Changes in Stem cell viability, phenotype and function are assessed flow cytometry and with in vitro bioassays at two different time points. Identifying the cellular and molecular mechanisms underlying the damage caused by dynamic loading in live biological samples could enable the development of new treatments for traumatic injuries.

  13. Predicting brain structure in population-based samples with biologically informed genetic scores for schizophrenia.

    Science.gov (United States)

    Van der Auwera, Sandra; Wittfeld, Katharina; Shumskaya, Elena; Bralten, Janita; Zwiers, Marcel P; Onnink, A Marten H; Usberti, Niccolo; Hertel, Johannes; Völzke, Henry; Völker, Uwe; Hosten, Norbert; Franke, Barbara; Grabe, Hans J

    2017-04-01

    Schizophrenia is associated with brain structural abnormalities including gray and white matter volume reductions. Whether these alterations are caused by genetic risk variants for schizophrenia is unclear. Previous attempts to detect associations between polygenic factors for schizophrenia and structural brain phenotypes in healthy subjects have been negative or remain non-replicated. In this study, we used genetic risk scores that were based on the accumulated effect of selected risk variants for schizophrenia belonging to specific biological systems like synaptic function, neurodevelopment, calcium signaling, and glutamatergic neurotransmission. We hypothesized that this "biologically informed" approach would provide the missing link between genetic risk for schizophrenia and brain structural phenotypes. We applied whole-brain voxel-based morphometry (VBM) analyses in two population-based target samples and subsequent regions of interest (ROIs) analyses in an independent replication sample (total N = 2725). No consistent association between the genetic scores and brain volumes were observed in the investigated samples. These results suggest that in healthy subjects with a higher genetic risk for schizophrenia additional factors apart from common genetic variants (e.g., infection, trauma, rare genetic variants, or gene-gene interactions) are required to induce structural abnormalities of the brain. Further studies are recommended to test for possible gene-gene or gene-environment effects. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  14. Sample Duplication Method for Monte Carlo Simulation of Large Reaction-Diffusion System

    Institute of Scientific and Technical Information of China (English)

    张红东; 陆建明; 杨玉良

    1994-01-01

    The sample duplication method for the Monte Carlo simulation of large reaction-diffusion system is proposed in this paper. It is proved that the sample duplication method will effectively raise the efficiency and statistical precision of the simulation without changing the kinetic behaviour of the reaction-diffusion system and the critical condition for the bifurcation of the steady-states. The method has been applied to the simulation of spatial and time dissipative structure of Brusselator under the Dirichlet boundary condition. The results presented in this paper definitely show that the sample duplication method provides a very efficient way to sol-’e the master equation of large reaction-diffusion system. For the case of two-dimensional system, it is found that the computation time is reduced at least by a factor of two orders of magnitude compared to the algorithm reported in literature.

  15. Surface-enhanced Raman scattering detection of silver nanoparticles in environmental and biological samples

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Huiyuan [Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003 (United States); Xing, Baoshan, E-mail: bx@umass.edu [Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003 (United States); Hamlet, Leigh C.; Chica, Andrea [Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003 (United States); He, Lili, E-mail: lilihe@foodsci.umass.edu [Department of Food Science, University of Massachusetts, Amherst, MA 01003 (United States)

    2016-06-01

    Growing concerns over the potential release and threat of silver nanoparticles (AgNPs) to environmental and biological systems urge researchers to investigate their fate and behavior. However, current analytical techniques cannot meet the requirements for rapidly, sensitively and reliably probing AgNPs in complex matrices. Surface-enhanced Raman spectroscopy (SERS) has shown great capability for rapid detection of AgNPs based on an indicator molecule that can bind on the AgNP surface. The objective of this study was to exploit SERS to detect AgNPs in environmental and biological samples through optimizing the Raman indicator for SERS. Seven indicator molecules were selected and determined to obtain their SERS signals at optimal concentrations. Among them, 1,2-di(4-pyridyl)ethylene (BPE), crystal violet and ferric dimethyl-dithiocarbamate (ferbam) produced the highest SERS intensities. Further experiments on binding competition between each two of the three candidates showed that ferbam had the highest AgNPs-binding ability. The underlying mechanism lies in the strong binding affinity of ferbam with AgNPs via multiple sulfur atoms. We further validated ferbam to be an effective indicator for SERS detection of as low as 0.1 mg/L AgNPs in genuine surface water and 0.57 mg/L in spinach juice. Moreover, limited interference on SERS detection of AgNPs was found from environmentally relevant inorganic ions, organic matter, inorganic particles, as well as biologically relevant components, demonstrating the ferbam-assisted SERS is an effective and sensitive method to detect AgNPs in complex environmental and biological samples. - Graphical abstract: SERS signal intensity of ferbam indicates the concentration of AgNPs. - Highlights: • Ferbam was found to be the best indicator for SERS detection of AgNPs. • SERS was able to detect AgNPs in both environmental and biological samples. • Major components in the two matrices had limited effect on AgNP detection.

  16. Scaling ice microstructures from the laboratory to nature: cryo-EBSD on large samples.

    Science.gov (United States)

    Prior, David; Craw, Lisa; Kim, Daeyeong; Peyroux, Damian; Qi, Chao; Seidemann, Meike; Tooley, Lauren; Vaughan, Matthew; Wongpan, Pat

    2017-04-01

    Electron backscatter diffraction (EBSD) has extended significantly our ability to conduct detailed quantitative microstructural investigations of rocks, metals and ceramics. EBSD on ice was first developed in 2004. Techniques have improved significantly in the last decade and EBSD is now becoming more common in the microstructural analysis of ice. This is particularly true for laboratory-deformed ice where, in some cases, the fine grain sizes exclude the possibility of using a thin section of the ice. Having the orientations of all axes (rather than just the c-axis as in an optical method) yields important new information about ice microstructure. It is important to examine natural ice samples in the same way so that we can scale laboratory observations to nature. In the case of ice deformation, higher strain rates are used in the laboratory than those seen in nature. These are achieved by increasing stress and/or temperature and it is important to assess that the microstructures produced in the laboratory are comparable with those observed in nature. Natural ice samples are coarse grained. Glacier and ice sheet ice has a grain size from a few mm up to several cm. Sea and lake ice has grain sizes of a few cm to many metres. Thus extending EBSD analysis to larger sample sizes to include representative microstructures is needed. The chief impediments to working on large ice samples are sample exchange, limitations on stage motion and temperature control. Large ice samples cannot be transferred through a typical commercial cryo-transfer system that limits sample sizes. We transfer through a nitrogen glove box that encloses the main scanning electron microscope (SEM) door. The nitrogen atmosphere prevents the cold stage and the sample from becoming covered in frost. Having a long optimal working distance for EBSD (around 30mm for the Otago cryo-EBSD facility) , by moving the camera away from the pole piece, enables the stage to move without crashing into either the

  17. High resolution x-ray microtomography of biological samples: Requirements and strategies for satisfying them

    Energy Technology Data Exchange (ETDEWEB)

    Loo, B.W. Jr. [Univ. of California, San Francisco, CA (United States)]|[Univ. of California, Davis, CA (United States)]|[Lawrence Berkeley National Lab., CA (United States); Rothman, S.S. [Univ. of California, San Francisco, CA (United States)]|[Lawrence Berkeley National Lab., CA (United States)

    1997-02-01

    High resolution x-ray microscopy has been made possible in recent years primarily by two new technologies: microfabricated diffractive lenses for soft x-rays with about 30-50 nm resolution, and high brightness synchrotron x-ray sources. X-ray microscopy occupies a special niche in the array of biological microscopic imaging methods. It extends the capabilities of existing techniques mainly in two areas: a previously unachievable combination of sub-visible resolution and multi-micrometer sample size, and new contrast mechanisms. Because of the soft x-ray wavelengths used in biological imaging (about 1-4 nm), XM is intermediate in resolution between visible light and electron microscopies. Similarly, the penetration depth of soft x-rays in biological materials is such that the ideal sample thickness for XM falls in the range of 0.25 - 10 {mu}m, between that of VLM and EM. XM is therefore valuable for imaging of intermediate level ultrastructure, requiring sub-visible resolutions, in intact cells and subcellular organelles, without artifacts produced by thin sectioning. Many of the contrast producing and sample preparation techniques developed for VLM and EM also work well with XM. These include, for example, molecule specific staining by antibodies with heavy metal or fluorescent labels attached, and sectioning of both frozen and plastic embedded tissue. However, there is also a contrast mechanism unique to XM that exists naturally because a number of elemental absorption edges lie in the wavelength range used. In particular, between the oxygen and carbon absorption edges (2.3 and 4.4 nm wavelength), organic molecules absorb photons much more strongly than does water, permitting element-specific imaging of cellular structure in aqueous media, with no artifically introduced contrast agents. For three-dimensional imaging applications requiring the capabilities of XM, an obvious extension of the technique would therefore be computerized x-ray microtomography (XMT).

  18. 3D nanoscale imaging of biological samples with laboratory-based soft X-ray sources

    Science.gov (United States)

    Dehlinger, Aurélie; Blechschmidt, Anne; Grötzsch, Daniel; Jung, Robert; Kanngießer, Birgit; Seim, Christian; Stiel, Holger

    2015-09-01

    In microscopy, where the theoretical resolution limit depends on the wavelength of the probing light, radiation in the soft X-ray regime can be used to analyze samples that cannot be resolved with visible light microscopes. In the case of soft X-ray microscopy in the water-window, the energy range of the radiation lies between the absorption edges of carbon (at 284 eV, 4.36 nm) and oxygen (543 eV, 2.34 nm). As a result, carbon-based structures, such as biological samples, posses a strong absorption, whereas e.g. water is more transparent to this radiation. Microscopy in the water-window, therefore, allows the structural investigation of aqueous samples with resolutions of a few tens of nanometers and a penetration depth of up to 10μm. The development of highly brilliant laser-produced plasma-sources has enabled the transfer of Xray microscopy, that was formerly bound to synchrotron sources, to the laboratory, which opens the access of this method to a broader scientific community. The Laboratory Transmission X-ray Microscope at the Berlin Laboratory for innovative X-ray technologies (BLiX) runs with a laser produced nitrogen plasma that emits radiation in the soft X-ray regime. The mentioned high penetration depth can be exploited to analyze biological samples in their natural state and with several projection angles. The obtained tomogram is the key to a more precise and global analysis of samples originating from various fields of life science.

  19. Magnetic induction spectroscopy: non-contact measurement of the electrical conductivity spectra of biological samples

    Science.gov (United States)

    Barai, A.; Watson, S.; Griffiths, H.; Patz, R.

    2012-08-01

    Measurement of the electrical conductivity of biological tissues as a function of frequency, often termed ‘bioelectrical impedance spectroscopy (BIS)’, provides valuable information on tissue structure and composition. In implementing BIS though, there can be significant practical difficulties arising from the electrode-sample interface which have likely limited its deployment in industrial applications. In magnetic induction spectroscopy (MIS) these difficulties are eliminated through the use of fully non-contacting inductive coupling between the sensors and sample. However, inductive coupling introduces its own set of technical difficulties, primarily related to the small magnitudes of the induced currents and their proportionality with frequency. This paper describes the design of a practical MIS system incorporating new, highly-phase-stable electronics and compares its performance with that of electrode-based BIS in measurements on biological samples including yeast suspensions in saline (concentration 50-400 g l-1) and solid samples of potato, cucumber, tomato, banana and porcine liver. The shapes of the MIS spectra were in good agreement with those for electrode-based BIS, with a residual maximum discrepancy of 28%. The measurement precision of the MIS was 0.05 S m-1 at 200 kHz, improving to 0.01 S m-1 at a frequency of 20 MHz, for a sample volume of 80 ml. The data-acquisition time for each MIS measurement was 52 s. Given the value of spectroscopic conductivity information and the many advantages of obtaining these data in a non-contacting manner, even through electrically-insulating packaging materials if necessary, it is concluded that MIS is a technique with considerable potential for monitoring bio-industrial processes and product quality.

  20. The correlation of arsenic levels in drinking water with the biological samples of skin disorders

    Energy Technology Data Exchange (ETDEWEB)

    Kazi, Tasneem Gul [Center of Excellence in Analytical Chemistry, University of Sindh, Jamshoro 76080 (Pakistan)], E-mail: tgkazi@yahoo.com; Arain, Muhammad Balal [Center of Excellence in Analytical Chemistry, University of Sindh, Jamshoro 76080 (Pakistan)], E-mail: bilal_ku2004@yahoo.com; Baig, Jameel Ahmed [Center of Excellence in Analytical Chemistry, University of Sindh, Jamshoro 76080 (Pakistan)], E-mail: jab_mughal@yahoo.com; Jamali, Muhammad Khan [Center of Excellence in Analytical Chemistry, University of Sindh, Jamshoro 76080 (Pakistan)], E-mail: mkhanjamali@yahoo.com; Afridi, Hassan Imran [Center of Excellence in Analytical Chemistry, University of Sindh, Jamshoro 76080 (Pakistan)], E-mail: hassanimranafridi@yahoo.com; Jalbani, Nusrat [Pakistan Council for Scientific and Industrial Research, University Road Karachi-75280 (Pakistan)], E-mail: nusratjalbani_21@yahoo.com; Sarfraz, Raja Adil [Center of Excellence in Analytical Chemistry, University of Sindh, Jamshoro 76080 (Pakistan)], E-mail: rajaadilsarfraz@gmail.com; Shah, Abdul Qadir [Center of Excellence in Analytical Chemistry, University of Sindh, Jamshoro 76080 (Pakistan)], E-mail: aqshah07@yahoo.com; Niaz, Abdul [Center of Excellence in Analytical Chemistry, University of Sindh, Jamshoro 76080 (Pakistan)], E-mail: niazchemist2k6@yahoo.com

    2009-01-15

    Arsenic (As) poisoning has become a worldwide public health concern. The skin is quite sensitive to As and skin lesions are the most common and earliest nonmalignant effects associated to chronic As exposure. In 2005-2007, a survey was carried out on surface and groundwater arsenic contamination and relationships between As exposure via the drinking water and related adverse health effects (melanosis and keratosis) on villagers resides on the banks of Manchar lake, southern part of Sindh, Pakistan. We screened the population from arsenic-affected villages, 61 to 73% population were identified patients suffering from chronic arsenic toxicity. The effects of As toxicity via drinking water were estimated by biological samples (scalp hair and blood) of adults (males and females), have or have not skin problem (n = 187). The referent samples of both genders were also collected from the areas having low level of As (< 10 {mu}g/L) in drinking water (n = 121). Arsenic concentration in drinking water and biological samples were analyzed using electrothermal atomic absorption spectrometry. The range of arsenic concentrations in lake surface water was 35.2-158 {mu}g/L, which is 3-15 folds higher than World Health Organization [WHO, 2004. Guidelines for drinking-water quality third ed., WHO Geneva Switzerland.]. It was observed that As concentration in the scalp hair and blood samples were above the range of permissible values 0.034-0.319 {mu}g As/g for hair and < 0.5-4.2 {mu}g/L for blood. The linear regressions showed good correlations between arsenic concentrations in water versus hair and blood samples of exposed skin diseased subjects (R{sup 2} = 0.852 and 0.718) as compared to non-diseased subjects (R{sup 2} = 0.573 and 0.351), respectively.

  1. Non-destructive high-resolution thermal imaging techniques to evaluate wildlife and delicate biological samples

    Energy Technology Data Exchange (ETDEWEB)

    Lavers, C; Franklin, P; Franklin, P; Plowman, A; Sayers, G; Bol, J; Shepard, D; Fields, D, E-mail: brnc-radarcomms1@nrta.mod.u [Sensors Team, Plymouth University at Britannia Royal Naval College, Dartmouth, Devon (United Kingdom) and Paignton Zoological Park, Paignton, Devon (United Kingdom); Thermal Wave Imaging, Inc., 845 Livernoise St, Ferndale, MI (United States); Buckfast Butterfly and Otter Sanctuary, Buckfast, Devon (United Kingdom)

    2009-07-01

    Thermal imaging cameras now allows routine monitoring of dangerous yet endangered wildlife in captivity. This study looks at the potential applications of radiometrically calibrated thermal data to wildlife, as well as providing parameters for future materials applications. We present a non-destructive active testing technique suitable for enhancing imagery contrast of thin or delicate biological specimens yielding improved thermal contrast at room temperature, for analysis of sample thermal properties. A broad spectrum of animals is studied with different textured surfaces, reflective and emissive properties in the infra red part of the electromagnetic spectrum. Some surface features offer biomimetic materials design opportunities.

  2. Selective extraction of proteins and other macromolecules from biological samples using molecular imprinted polymers.

    Science.gov (United States)

    Stevenson, Derek; El-Sharif, Hazim F; Reddy, Subrayal M

    2016-11-01

    The accurate determination of intact macromolecules in biological samples, such as blood, plasma, serum, urine, tissue and feces is a challenging problem. The increased interest in macromolecules both as candidate drugs and as biomarkers for diagnostic purposes means that new method development approaches are needed. This review charts developments in the use of molecularly imprinted polymers first for small-molecular-mass compounds then for proteins and other macromolecules. Examples of the development of molecularly imprinted polymers for macromolecules are highlighted. The two main application areas to date are sensors and separation science, particularly SPE. Examples include peptides and polypeptides, lysozyme, hemoglobin, ovalbumin, bovine serum albumin and viruses.

  3. Evaluation of Botanical Reference Materials for the Determination of Vanadium in Biological Samples

    DEFF Research Database (Denmark)

    Heydorn, Kaj; Damsgaard, Else

    1982-01-01

    Three botanical reference materials prepared by the National Bureau of Standards have been studied by neutron activation analysis to evaluate their suitability with respect to the determination of vanadium in biological samples. Various decomposition methods were applied in connection with chemic....... A reference value of 1.15 mg/kg of this material is recommended, based on results from 3 different methods. All three materials are preferable to SRM 1571 Orchard Leaves, while Bowen's Kale remains the material of choice because of its lower concentration....

  4. Biological soil crusts emit large amounts of NO and HONO affecting the nitrogen cycle in drylands

    Science.gov (United States)

    Tamm, Alexandra; Wu, Dianming; Ruckteschler, Nina; Rodríguez-Caballero, Emilio; Steinkamp, Jörg; Meusel, Hannah; Elbert, Wolfgang; Behrendt, Thomas; Sörgel, Matthias; Cheng, Yafang; Crutzen, Paul J.; Su, Hang; Pöschl, Ulrich; Weber, Bettina

    2016-04-01

    Dryland systems currently cover ˜40% of the world's land surface and are still expanding as a consequence of human impact and global change. In contrast to that, information on their role in global biochemical processes is limited, probably induced by the presumption that their sparse vegetation cover plays a negligible role in global balances. However, spaces between the sparse shrubs are not bare, but soils are mostly covered by biological soil crusts (biocrusts). These biocrust communities belong to the oldest life forms, resulting from an assembly between soil particles and cyanobacteria, lichens, bryophytes, and algae plus heterotrophic organisms in varying proportions. Depending on the dominating organism group, cyanobacteria-, lichen-, and bryophyte-dominated biocrusts are distinguished. Besides their ability to restrict soil erosion they fix atmospheric carbon and nitrogen, and by doing this they serve as a nutrient source in strongly depleted dryland ecosystems. In this study we show that a fraction of the nitrogen fixed by biocrusts is metabolized and subsequently returned to the atmosphere in the form of nitric oxide (NO) and nitrous acid (HONO). These gases affect the radical formation and oxidizing capacity within the troposphere, thus being of particular interest to atmospheric chemistry. Laboratory measurements using dynamic chamber systems showed that dark cyanobacteria-dominated crusts emitted the largest amounts of NO and HONO, being ˜20 times higher than trace gas fluxes of nearby bare soil. We showed that these nitrogen emissions have a biogenic origin, as emissions of formerly strongly emitting samples almost completely ceased after sterilization. By combining laboratory, field, and satellite measurement data we made a best estimate of global annual emissions amounting to ˜1.1 Tg of NO-N and ˜0.6 Tg of HONO-N from biocrusts. This sum of 1.7 Tg of reactive nitrogen emissions equals ˜20% of the soil release under natural vegetation according

  5. Biological and biomedical (14)C-accelerator mass spectrometry and graphitization of carbonaceous samples.

    Science.gov (United States)

    Chung, Ill-Min; Kim, Seung-Hyun

    2013-06-21

    Accelerator mass spectrometry (AMS) is the ultimate technique for measuring rare isotopes in small samples. Biological and biomedical applications of (14)C-AMS (bio-(14)C-AMS) commenced in the early 1990s and are now widely used in many research fields including pharmacology, toxicology, food, and nutrition. For accurate, precise, and reproducible bio-(14)C-AMS analysis, the graphitization step in sample preparation is the most critical step. So, various sample preparation methods for a process called graphitization have been reported for specific applications. Catalytic graphitization using either a flame-sealed borosilicate tube or a septa-sealed vial is a popular sample preparation method for bio-(14)C-AMS. In this review, we introduce the AMS system, especially for bio-(14)C-AMS. In addition, we also review the graphitization method for bio-(14)C-AMS to promote further understanding and improvement of sample preparation for this technique. Examples of catalytic graphitization methods over the past two decades are described.

  6. Data management strategies for multinational large-scale systems biology projects.

    Science.gov (United States)

    Wruck, Wasco; Peuker, Martin; Regenbrecht, Christian R A

    2014-01-01

    Good accessibility of publicly funded research data is essential to secure an open scientific system and eventually becomes mandatory [Wellcome Trust will Penalise Scientists Who Don't Embrace Open Access. The Guardian 2012]. By the use of high-throughput methods in many research areas from physics to systems biology, large data collections are increasingly important as raw material for research. Here, we present strategies worked out by international and national institutions targeting open access to publicly funded research data via incentives or obligations to share data. Funding organizations such as the British Wellcome Trust therefore have developed data sharing policies and request commitment to data management and sharing in grant applications. Increased citation rates are a profound argument for sharing publication data. Pre-publication sharing might be rewarded by a data citation credit system via digital object identifiers (DOIs) which have initially been in use for data objects. Besides policies and incentives, good practice in data management is indispensable. However, appropriate systems for data management of large-scale projects for example in systems biology are hard to find. Here, we give an overview of a selection of open-source data management systems proved to be employed successfully in large-scale projects.

  7. Large scale inference in the Infinite Relational Model: Gibbs sampling is not enough

    DEFF Research Database (Denmark)

    Albers, Kristoffer Jon; Moth, Andreas Leon Aagard; Mørup, Morten

    2013-01-01

    The stochastic block-model and its non-parametric extension, the Infinite Relational Model (IRM), have become key tools for discovering group-structure in complex networks. Identifying these groups is a combinatorial inference problem which is usually solved by Gibbs sampling. However, whether...... Gibbs sampling suffices and can be scaled to the modeling of large scale real world complex networks has not been examined sufficiently. In this paper we evaluate the performance and mixing ability of Gibbs sampling in the Infinite Relational Model (IRM) by implementing a high performance Gibbs sampler....... We find that Gibbs sampling can be computationally scaled to handle millions of nodes and billions of links. Investigating the behavior of the Gibbs sampler for different sizes of networks we find that the mixing ability decreases drastically with the network size, clearly indicating a need...

  8. Development of a novel reaction chamber for ion beam analysis of large samples

    Energy Technology Data Exchange (ETDEWEB)

    Kakuee, O.R. [Van de Graaff Laboratory, Nuclear Science Research School, Nuclear Science and Technology Research Institute (NSTRI), 14395-836 Tehran (Iran, Islamic Republic of)], E-mail: okakuee@yahoo.com; Fathollahi, V.; Agha-Aligol, D.; Farmahini-Farahani, M.; Oliaiy, P.; Lamehi-Rachti, M. [Van de Graaff Laboratory, Nuclear Science Research School, Nuclear Science and Technology Research Institute (NSTRI), 14395-836 Tehran (Iran, Islamic Republic of)

    2008-04-15

    A novel vacuum chamber for ion beam analysis of large-size industrial samples - whose analysis are not feasible in conventional ion beam analysis reaction chambers - has been designed, fabricated and successfully tested. Using the newly developed chamber, both PIXE and RBS analyses could be carried out at the same time and on the same point of the samples. Ion beam analysis using this novel chamber lacks the disadvantages of external beam analysis and benefits the advantages of in-vacuum analysis. This has been achieved by designing a tiny open port in the wall of the reaction chamber to be sealed with a small flat area of sample body where its analysis is of interest. As a case study, two samples of gas turbine blades, a corroded one at highly corrosive environment and a refurbished one after application of certain coatings are analysed using the novel chamber. Experimental results confirm the performance and capability of the reaction chamber.

  9. Monte Carlo non-local means: random sampling for large-scale image filtering.

    Science.gov (United States)

    Chan, Stanley H; Zickler, Todd; Lu, Yue M

    2014-08-01

    We propose a randomized version of the nonlocal means (NLM) algorithm for large-scale image filtering. The new algorithm, called Monte Carlo nonlocal means (MCNLM), speeds up the classical NLM by computing a small subset of image patch distances, which are randomly selected according to a designed sampling pattern. We make two contributions. First, we analyze the performance of the MCNLM algorithm and show that, for large images or large external image databases, the random outcomes of MCNLM are tightly concentrated around the deterministic full NLM result. In particular, our error probability bounds show that, at any given sampling ratio, the probability for MCNLM to have a large deviation from the original NLM solution decays exponentially as the size of the image or database grows. Second, we derive explicit formulas for optimal sampling patterns that minimize the error probability bound by exploiting partial knowledge of the pairwise similarity weights. Numerical experiments show that MCNLM is competitive with other state-of-the-art fast NLM algorithms for single-image denoising. When applied to denoising images using an external database containing ten billion patches, MCNLM returns a randomized solution that is within 0.2 dB of the full NLM solution while reducing the runtime by three orders of magnitude.

  10. Polybrominated diphenyl ethers in water, sediment, soil, and biological samples from different industrial areas in Zhejiang, China

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Junxia; Lin, Zhenkun [Zhejiang Provincial Key Lab for Technology and Application of Model Organisms, Institute of Watershed Science and Environmental Ecology, Wenzhou Medical College, Wenzhou 325035 (China); Lin, Kuangfei [School of Resources and Environmental Engineering, East China University of Science and Technology/State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, Shanghai 200237 (China); Wang, Chunyan [Zhejiang Provincial Key Lab for Technology and Application of Model Organisms, Institute of Watershed Science and Environmental Ecology, Wenzhou Medical College, Wenzhou 325035 (China); Zhang, Wei [School of Resources and Environmental Engineering, East China University of Science and Technology/State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, Shanghai 200237 (China); Cui, Changyuan [Zhejiang Provincial Key Lab for Technology and Application of Model Organisms, Institute of Watershed Science and Environmental Ecology, Wenzhou Medical College, Wenzhou 325035 (China); Lin, Junda [Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL 32901 (United States); Dong, Qiaoxiang, E-mail: dqxdong@163.com [Zhejiang Provincial Key Lab for Technology and Application of Model Organisms, Institute of Watershed Science and Environmental Ecology, Wenzhou Medical College, Wenzhou 325035 (China); Huang, Changjiang, E-mail: cjhuang5711@163.com [Zhejiang Provincial Key Lab for Technology and Application of Model Organisms, Institute of Watershed Science and Environmental Ecology, Wenzhou Medical College, Wenzhou 325035 (China)

    2011-12-15

    Highlights: Black-Right-Pointing-Pointer We examined PBDE concentrations in various matrices from different industrial areas. Black-Right-Pointing-Pointer Elevated PBDE levels were found in areas with low-voltage electrical manufactures. Black-Right-Pointing-Pointer Areas with e-waste recycling activities also had higher PBDE concentrations. Black-Right-Pointing-Pointer PBDE content and composition in water samples varied from one area to another. Black-Right-Pointing-Pointer PBDE composition in sediment/soil and biological samples was predominated by BDE-209. - Abstract: Polybrominated diphenyl ethers (PBDEs) have been used extensively in electrical and electronic products, but little is known about their distribution in the environment surrounding the manufacturing factories. This study reports PBDE contamination in various matrices from the location (Liushi, Zhejiang province) that produces more than 70% of the low-voltage electrical appliances in China. Additionally, PBDE contamination was compared with other industries such as the e-waste recycling business (Fengjiang) in the same region. Specifically, we measured seven PBDE congeners (BDEs - 47, 99, 100, 153, 154, 183, and 209) in water, sediment, soil, plant, and animal tissues from four different areas in this region. The present study revealed elevated PBDE concentrations in all matrices collected from Liushi and Fengjiang in comparison with highly industrialized areas without significant PBDE contamination sources. In water samples, there were large variations of PBDE content and composition across different areas. In sediment/soil and biological samples, BDE-209 was the predominant congener and this could be due to the abundant usage of deca-BDE mixtures in China. Our findings provide the very first data on PBDE contamination in the local environments surrounding the electronics industry, and also reveal widespread PBDE contamination in highly industrialized coastal regions of China.

  11. A round-robin determination of boron in botanical and biological samples.

    Science.gov (United States)

    Downing, R G; Strong, P L

    1998-01-01

    The accurate determination of boron (B) at trace and ultratrace concentrations is an important step toward establishing the role of B in biological functions. However, low-level B concentrations are difficult to determine accurately, especially for many botanical and biological matrices. A round-robin study was conducted to assess analytical agreement for low-level B determinations. Ten experienced research groups from analytical laboratories extending across Europe, Asia, and the US participated in this study. These groups represent a cross-section of academic, commercial, and government facilities. The researchers employed both ion-coupled plasma and neutron techniques in the study. Results from this round-robin study indicate good agreement between participating laboratories at the mg/kg level, but at the lowest levels, microg/kg, only three laboratories participated, and agreement was poor. By encouraging discussion among scientists over these data, the secondary goal of this round-robin study is to stimulate continued improvement in analytical procedures and techniques for accurate low-level B determinations. Furthermore, it is intended to encourage the development of a variety of low-level (low mg/kg and microg/kg) B certified reference samples in biological and botanical matrices. The results from the round-robin analyses were compiled and are summarized in this article.

  12. Proton Transmitting Energy Spectra and Transmission Electron Microscope Examinations of Biological Samples

    Science.gov (United States)

    Tan, Chun-yu; Xia, Yue-yuan; Zhang, Jian-hua; Mu, Yu-guang; Wang, Rui-jin; Liu, Ji-tian; Liu, Xiang-dong; Yu, Zeng-liang

    1999-02-01

    Transmission energy spectra of 530 keV H+ ion penetrating 140 μm thick seed coat of maize and fruit peel of grape with thickness of 100 μm were measured. The result indicates that these thick biological targets, as seen by the penetrating ions, are inhomogeneous, and there are open "channel like" paths along which the incident ions can transmit the targets easily. While most of the incident ions are stopped in the targets, some of the transmitting ions only lose a small fraction of their initial incident energy. The transmission energy spectra show a pure electronic stopping feature. Transmission electron microscope (TEM) micrographes taken from the samples of seed coat of maize and fruit peel of tomato with thickness of 60 μm indicate that 150 keV electron beam from the TEM can penetrate the thick samples to give very good images with clear contrasts.

  13. Analytical Methodologies for the Determination of Endocrine Disrupting Compounds in Biological and Environmental Samples

    Science.gov (United States)

    Sosa-Ferrera, Zoraida; Mahugo-Santana, Cristina; Santana-Rodríguez, José Juan

    2013-01-01

    Endocrine-disruptor compounds (EDCs) can mimic natural hormones and produce adverse effects in the endocrine functions by interacting with estrogen receptors. EDCs include both natural and synthetic chemicals, such as hormones, personal care products, surfactants, and flame retardants, among others. EDCs are characterised by their ubiquitous presence at trace-level concentrations and their wide diversity. Since the discovery of the adverse effects of these pollutants on wildlife and human health, analytical methods have been developed for their qualitative and quantitative determination. In particular, mass-based analytical methods show excellent sensitivity and precision for their quantification. This paper reviews recently published analytical methodologies for the sample preparation and for the determination of these compounds in different environmental and biological matrices by liquid chromatography coupled with mass spectrometry. The various sample preparation techniques are compared and discussed. In addition, recent developments and advances in this field are presented. PMID:23738329

  14. Analytical methodologies for the determination of endocrine disrupting compounds in biological and environmental samples.

    Science.gov (United States)

    Sosa-Ferrera, Zoraida; Mahugo-Santana, Cristina; Santana-Rodríguez, José Juan

    2013-01-01

    Endocrine-disruptor compounds (EDCs) can mimic natural hormones and produce adverse effects in the endocrine functions by interacting with estrogen receptors. EDCs include both natural and synthetic chemicals, such as hormones, personal care products, surfactants, and flame retardants, among others. EDCs are characterised by their ubiquitous presence at trace-level concentrations and their wide diversity. Since the discovery of the adverse effects of these pollutants on wildlife and human health, analytical methods have been developed for their qualitative and quantitative determination. In particular, mass-based analytical methods show excellent sensitivity and precision for their quantification. This paper reviews recently published analytical methodologies for the sample preparation and for the determination of these compounds in different environmental and biological matrices by liquid chromatography coupled with mass spectrometry. The various sample preparation techniques are compared and discussed. In addition, recent developments and advances in this field are presented.

  15. Phytochemical analysis and biological evaluation of selected African propolis samples from Cameroon and Congo.

    Science.gov (United States)

    Papachroni, Danai; Graikou, Konstantia; Kosalec, Ivan; Damianakos, Harilaos; Ingram, Verina; Chinou, Ioanna

    2015-01-01

    The objective of this study was the chemical analysis of four selected samples of African propolis (Congo and Cameroon) and their biological evaluation. Twenty-one secondary metabolites belonging to four different chemical groups were isolated from the 70% ethanolic extracts of propolis and their structures were elucidated on the basis of spectral evidence. Three triterpenes and two diprenyl-flavonoids were identified from Congo propolis, which has been investigated for the first time, while thirteen triterpenes, three diprenyl-flavonoids, two monoterpenic alcohols and one fatty acid ester have been identified from Cameroon propolis samples. To our knowledge, the identified diprenyl-flavonoids, as well as five of the isolated and determined triterpenes, are reported for the first time in propolis. Moreover, the total polyphenol content was estimated in all extracts and the antimicrobial activities of all four extracts were studied against six Gram-positive and -negative bacteria and three pathogenic fungi, showing an interesting antibacterial profile.

  16. Fiber laser-microscope system for femtosecond photodisruption of biological samples.

    Science.gov (United States)

    Yavaş, Seydi; Erdogan, Mutlu; Gürel, Kutan; Ilday, F Ömer; Eldeniz, Y Burak; Tazebay, Uygar H

    2012-03-01

    We report on the development of a ultrafast fiber laser-microscope system for femtosecond photodisruption of biological targets. A mode-locked Yb-fiber laser oscillator generates few-nJ pulses at 32.7 MHz repetition rate, amplified up to ∼125 nJ at 1030 nm. Following dechirping in a grating compressor, ∼240 fs-long pulses are delivered to the sample through a diffraction-limited microscope, which allows real-time imaging and control. The laser can generate arbitrary pulse patterns, formed by two acousto-optic modulators (AOM) controlled by a custom-developed field-programmable gate array (FPGA) controller. This capability opens the route to fine optimization of the ablation processes and management of thermal effects. Sample position, exposure time and imaging are all computerized. The capability of the system to perform femtosecond photodisruption is demonstrated through experiments on tissue and individual cells.

  17. 4D x-ray phase contrast tomography for repeatable motion of biological samples

    Science.gov (United States)

    Hoshino, Masato; Uesugi, Kentaro; Yagi, Naoto

    2016-09-01

    X-ray phase contrast tomography based on a grating interferometer was applied to fast and dynamic measurements of biological samples. To achieve this, the scanning procedure in the tomographic scan was improved. A triangle-shaped voltage signal from a waveform generator to a Piezo stage was used for the fast phase stepping in the grating interferometer. In addition, an optical fiber coupled x-ray scientific CMOS camera was used to achieve fast and highly efficient image acquisitions. These optimizations made it possible to perform an x-ray phase contrast tomographic measurement within an 8 min scan with density resolution of 2.4 mg/cm3. A maximum volume size of 13 × 13 × 6 mm3 was obtained with a single tomographic measurement with a voxel size of 6.5 μm. The scanning procedure using the triangle wave was applied to four-dimensional measurements in which highly sensitive three-dimensional x-ray imaging and a time-resolved dynamic measurement of biological samples were combined. A fresh tendon in the tail of a rat was measured under a uniaxial stretching and releasing condition. To maintain the freshness of the sample during four-dimensional phase contrast tomography, the temperature of the bathing liquid of the sample was kept below 10° using a simple cooling system. The time-resolved deformation of the tendon and each fascicle was measured with a temporal resolution of 5.7 Hz. Evaluations of cross-sectional area size, length of the axis, and mass density in the fascicle during a stretching process provided a basis for quantitative analysis of the deformation of tendon fascicle.

  18. A Simple Sampling Method for Estimating the Accuracy of Large Scale Record Linkage Projects.

    Science.gov (United States)

    Boyd, James H; Guiver, Tenniel; Randall, Sean M; Ferrante, Anna M; Semmens, James B; Anderson, Phil; Dickinson, Teresa

    2016-05-17

    Record linkage techniques allow different data collections to be brought together to provide a wider picture of the health status of individuals. Ensuring high linkage quality is important to guarantee the quality and integrity of research. Current methods for measuring linkage quality typically focus on precision (the proportion of incorrect links), given the difficulty of measuring the proportion of false negatives. The aim of this work is to introduce and evaluate a sampling based method to estimate both precision and recall following record linkage. In the sampling based method, record-pairs from each threshold (including those below the identified cut-off for acceptance) are sampled and clerically reviewed. These results are then applied to the entire set of record-pairs, providing estimates of false positives and false negatives. This method was evaluated on a synthetically generated dataset, where the true match status (which records belonged to the same person) was known. The sampled estimates of linkage quality were relatively close to actual linkage quality metrics calculated for the whole synthetic dataset. The precision and recall measures for seven reviewers were very consistent with little variation in the clerical assessment results (overall agreement using the Fleiss Kappa statistics was 0.601). This method presents as a possible means of accurately estimating matching quality and refining linkages in population level linkage studies. The sampling approach is especially important for large project linkages where the number of record pairs produced may be very large often running into millions.

  19. Contemporary models of pediatric obsessive-compulsive disorder: An evaluation with a large clinical sample.

    Science.gov (United States)

    De Nadai, Alessandro; Nagpal, Prianka S; Piacentini, John; Peris, Tara S; Geffken, Gary R; Geller, Daniel A; Murphy, Tanya K; Storch, Eric A; Lewin, Adam B

    2015-09-30

    We evaluated the construct validity of the Child Yale-Brofwn Obsessive-Compulsive Scale (CYBOCS) in a large clinical sample (N=730) using confirmatory factor analysis. Results found inadequate fit for a priori models, though a model accounting for overlapping item content displayed good fit. Parallel obsessions/compulsions items may provide largely redundant information on the CYBOCS. Findings suggest modifying the CYBOCS to reduce burden on researchers, patients, and clinicians, and to more accurately measure pediatric obsessive-compulsive disorder (OCD). Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  20. A comparison of quantitative reconstruction techniques for PIXE-tomography analysis applied to biological samples

    Energy Technology Data Exchange (ETDEWEB)

    Beasley, D.G., E-mail: dgbeasley@ctn.ist.utl.pt [IST/C2TN, Universidade de Lisboa, Campus Tecnológico e Nuclear, E.N.10, 2686-953 Sacavém (Portugal); Alves, L.C. [IST/C2TN, Universidade de Lisboa, Campus Tecnológico e Nuclear, E.N.10, 2686-953 Sacavém (Portugal); Barberet, Ph.; Bourret, S.; Devès, G.; Gordillo, N.; Michelet, C. [Univ. Bordeaux, CENBG, UMR 5797, F-33170 Gradignan (France); CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan (France); Le Trequesser, Q. [Univ. Bordeaux, CENBG, UMR 5797, F-33170 Gradignan (France); CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan (France); Institut de Chimie de la Matière Condensée de Bordeaux (ICMCB, UPR9048) CNRS, Université de Bordeaux, 87 avenue du Dr. A. Schweitzer, Pessac F-33608 (France); Marques, A.C. [IST/IPFN, Universidade de Lisboa, Campus Tecnológico e Nuclear, E.N.10, 2686-953 Sacavém (Portugal); Seznec, H. [Univ. Bordeaux, CENBG, UMR 5797, F-33170 Gradignan (France); CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan (France); Silva, R.C. da [IST/IPFN, Universidade de Lisboa, Campus Tecnológico e Nuclear, E.N.10, 2686-953 Sacavém (Portugal)

    2014-07-15

    The tomographic reconstruction of biological specimens requires robust algorithms, able to deal with low density contrast and low element concentrations. At the IST/ITN microprobe facility new GPU-accelerated reconstruction software, JPIXET, has been developed, which can significantly increase the speed of quantitative reconstruction of Proton Induced X-ray Emission Tomography (PIXE-T) data. It has a user-friendly graphical user interface for pre-processing, data analysis and reconstruction of PIXE-T and Scanning Transmission Ion Microscopy Tomography (STIM-T). The reconstruction of PIXE-T data is performed using either an algorithm based on a GPU-accelerated version of the Maximum Likelihood Expectation Maximisation (MLEM) method or a GPU-accelerated version of the Discrete Image Space Reconstruction Algorithm (DISRA) (Sakellariou (2001) [2]). The original DISRA, its accelerated version, and the MLEM algorithm, were compared for the reconstruction of a biological sample of Caenorhabditis elegans – a small worm. This sample was analysed at the microbeam line of the AIFIRA facility of CENBG, Bordeaux. A qualitative PIXE-T reconstruction was obtained using the CENBG software package TomoRebuild (Habchi et al. (2013) [6]). The effects of pre-processing and experimental conditions on the elemental concentrations are discussed.

  1. Respondent driven sampling for HIV biological and behavioral surveillance in Latin America and the Caribbean.

    Science.gov (United States)

    Montealegre, Jane R; Johnston, Lisa G; Murrill, Christopher; Monterroso, Edgar

    2013-09-01

    Since 2005, respondent driven sampling (RDS) has been widely used for HIV biological and behavioral surveillance surveys (BBSS) in Latin America and the Caribbean (LAC). In this manuscript, we provide a focused review of RDS among hard-to-reach high-risk populations in LAC and describe their principal operational, design, and analytical considerations. We reviewed published and unpublished reports, protocols, and manuscripts for RDS studies conducted in LAC between January 1, 2005 and December 31, 2011. We abstracted key operational information and generated summary statistics across all studies. Between 2005 and 2011, 87 RDS studies were conducted in 15 countries in LAC (68 % in South America, 18 % in Mexico and Central America, and 14 % in the Caribbean). The target populations were primarily men who have sex with men (43 %), sex workers (29 %), and drug users (26 %). Study considerations included establishing clear eligibility criteria, measuring social network sizes, collecting specimens for biological testing, among others. Most of the reviewed studies are the first in their respective countries to collect data on hard-to-reach populations and the first attempt to use a probability-based sampling method. These RDS studies allowed researchers and public health practitioners in LAC to access hard-to-reach HIV high-risk populations and collect valuable data on the prevalence of HIV and other infections, as well as related risk behaviors.

  2. [The biomonitoring of toxic substances in biological samples of general population].

    Science.gov (United States)

    Ibarluzea, Jesús; Aurrekoetxea, Juan José; Porta, Miquel; Sunyer, Jordi; Ballester, Ferran

    2016-11-01

    Many of the world's most developed countries have adopted biomonitoring of toxic substances in order to ascertain their levels in biological samples. These substances get into the body through different environmental exposures. Monitoring toxic substances in biological samples should allow us to ascertain their levels in vulnerable groups, assess their evolution over time, make comparisons with levels observed in other countries, identify groups at risk or with high toxic levels and promote research. The main objective of biomonitoring is to act as a policy design tool to facilitate the implementation of particular measures in various sectors: health, environmental, agricultural and livestock or food industry sectors. In Spain, information on levels of toxic substances of environmental origin is provided by specific studies on health effects from environmental sources, such as the INMA project (INfancia y Medio Ambiente [childhood and environment]). In addition, biomonitoring projects have been implemented in Catalonia and the Canary Islands, together with a national biomonitoring programme in the adult working population. However, further progress is needed to develop a system that covers the general population as well as subgroups at risk, which relies on the collaboration of the involved authorities and the participation of professionals from different sectors and citizen organisations interested in the relationship between health and the environment.

  3. Study on immunocapture-chemiluminescence assay of lipase activity in a biological sample.

    Science.gov (United States)

    Ichibangase, Tomoko; Hamabe, Chie; Ohba, Yoshihito; Kishikawa, Naoya; Nakashima, Kenichiro; Kayamori, Yuzo; Kang, Dongchon; Hamasaki, Naotaka; Kuroda, Naotaka

    2006-01-01

    A new approach for the determination of lipase (triacylglycerol lipase, EC.3.1.1.3) activity in a biological sample was investigated by combining an immunocapture technique with a chemiluminescence (CL) assay method in order to eliminate interference with CL detection. The proposed method consists of an immunocapture step to trap lipase and a subsequent step for CL detection of the activity of the captured lipase. The CL detection is based on the luminol-hydrogen peroxide (H(2)O(2))-horseradish peroxidase (HRP) reaction and utilizes a proenhancer substrate [a lauric acid ester of 2-(4-hydroxyphenyl)-4,5-diphenylimidazole (HDI)] which liberates an active enhancer, HDI, by enzymatic hydrolysis. A polyclonal antibody prepared with porcine pancreas lipase was used for the immunocapture. The proposed immunocapture-CL method effectively eliminated the interference with the CL reaction from biological components and enabled the determination of spiked porcine pancreas lipase activity in serum samples in the range 0.41-1.1 U(HDI) (1 U(HDI) corresponds to the amount which liberates 1 pmol HDI/min at 37 degrees C from the substrate). The method was further applied to the assay of the activity for human pancreas lipase in serum and the results showed good correlation (r = 0.871) with those by the conventional colorimetric method.

  4. Label-free three-dimensional reconstruction of biological samples (Conference Presentation)

    Science.gov (United States)

    Aknoun, Sherazade; Bon, Pierre; Savatier, Julien; Monneret, Serge; Wattellier, Benoit F.

    2016-03-01

    We describe the use of spatially incoherent illumination combined with quantitative phase imaging (QPI) [1] to make tridimensional reconstruction of semi-transparent biological samples. Quantitative phase imaging is commonly used with coherent illumination for the relatively simple interpretation of the phase measurement. We propose to use spatially incoherent illumination which is known to increase lateral and axial resolution compared to classical coherent illumination. The goal is to image thick samples with intracellular resolution [2]. The 3D volume is imaged by axially scanning the sample with a quadri-wave lateral shearing interferometer used as a conventional camera while using spatially incoherent white-light illumination (native microscope halogen source) or NIR light. We use a non-modified inverted microscope equipped with a Z-axis piezo stage. A z-stack is recorded by objective translation along the optical axis. The main advantages of this approach are its easy implementation, compared to the other state-of-the-art diffraction tomographic setups, and its speed which makes even label-free 3D living sample imaging possible. A deconvolution algorithm is used to compensate for the loss in contrast due to spatially incoherent illumination. This makes the tomographic volume phase values quantitative. Hence refractive index could be recovered from the optical slices. We will present tomographic reconstruction of cells, thick fixed tissue of few tens of micrometers using white light, and the use of NIR light to reach deeper planes in the tissue.

  5. Label-free three dimensional reconstruction of biological samples (Conference Presentation)

    Science.gov (United States)

    Aknoun, Sherazade; Bon, Pierre; Savatier, Julien; Monneret, Serge; Wattellier, Benoit F.

    2016-03-01

    We describe the use of spatially incoherent illumination combined with quantitative phase imaging (QPI) [1] to make tridimensional reconstruction of semi-transparent biological samples. Quantitative phase imaging is commonly used with coherent illumination for the relatively simple interpretation of the phase measurement. We propose to use spatially incoherent illumination which is known to increase lateral and axial resolution compared to classical coherent illumination. The goal is to image thick samples with intracellular resolution [2]. The 3D volume is imaged by axially scanning the sample with a quadri-wave lateral shearing interferometer used as a conventional camera while using spatially incoherent white-light illumination (native microscope halogen source) or NIR light. We use a non-modified inverted microscope equipped with a Z-axis piezo stage. A z-stack is recorded by objective translation along the optical axis. The main advantages of this approach are its easy implementation, compared to the other state-of-the-art diffraction tomographic setups, and its speed which makes even label-free 3D living sample imaging possible. A deconvolution algorithm is used to compensate for the loss in contrast due to spatially incoherent illumination. This makes the tomographic volume phase values quantitative. Hence refractive index could be recovered from the optical slices. We will present tomographic reconstruction of cells, thick fixed tissue of few tens of micrometers using white light, and the use of NIR light to reach deeper planes in the tissue.

  6. An inexpensive and portable microvolumeter for rapid evaluation of biological samples.

    Science.gov (United States)

    Douglass, John K; Wcislo, William T

    2010-08-01

    We describe an improved microvolumeter (MVM) for rapidly measuring volumes of small biological samples, including live zooplankton, embryos, and small animals and organs. Portability and low cost make this instrument suitable for widespread use, including at remote field sites. Beginning with Archimedes' principle, which states that immersing an arbitrarily shaped sample in a fluid-filled container displaces an equivalent volume, we identified procedures that maximize measurement accuracy and repeatability across a broad range of absolute volumes. Crucial steps include matching the overall configuration to the size of the sample, using reflected light to monitor fluid levels precisely, and accounting for evaporation during measurements. The resulting precision is at least 100 times higher than in previous displacement-based methods. Volumes are obtained much faster than by traditional histological or confocal methods and without shrinkage artifacts due to fixation or dehydration. Calibrations using volume standards confirmed accurate measurements of volumes as small as 0.06 microL. We validated the feasibility of evaluating soft-tissue samples by comparing volumes of freshly dissected ant brains measured with the MVM and by confocal reconstruction.

  7. Preparative divergent flow IEF without carrier ampholytes for separation of complex biological samples.

    Science.gov (United States)

    Stastna, Miroslava; Slais, Karel

    2010-01-01

    Efficient separation method is a crucial part of the process in which components of highly complex biological sample are identified and characterized. Based on the principles of recently newly established electrophoretic method called divergent flow IEF (DF IEF), we have tested the DF IEF instrument which is able to operate without the use of background carrier ampholytes. We have verified that during separation and focusing of sample consisting of high numbers of proteins (yeast lysate and wheat flour extract), the pH gradient of preparative DF IEF can be created by autofocusing of the sample components themselves without any addition of carrier ampholytes. In DF IEF, the proteins are separated, desalted and concentrated in one step. The fractions of yeast lysate sample, collected at the DF IEF output and subjected to gel IEF, contained the zones of proteins gradually covering the pI values from 3.7 to 8.5. In our experimental arrangement, the highest number of proteins has been found in fractions with pI values around 5.3 as detected by polyacrylamide gel IEF with CBB staining. During DF IEF, the selected protein bands have been concentrated up to 16.8-fold.

  8. Tracing the trajectory of skill learning with a very large sample of online game players.

    Science.gov (United States)

    Stafford, Tom; Dewar, Michael

    2014-02-01

    In the present study, we analyzed data from a very large sample (N = 854,064) of players of an online game involving rapid perception, decision making, and motor responding. Use of game data allowed us to connect, for the first time, rich details of training history with measures of performance from participants engaged for a sustained amount of time in effortful practice. We showed that lawful relations exist between practice amount and subsequent performance, and between practice spacing and subsequent performance. Our methodology allowed an in situ confirmation of results long established in the experimental literature on skill acquisition. Additionally, we showed that greater initial variation in performance is linked to higher subsequent performance, a result we link to the exploration/exploitation trade-off from the computational framework of reinforcement learning. We discuss the benefits and opportunities of behavioral data sets with very large sample sizes and suggest that this approach could be particularly fecund for studies of skill acquisition.

  9. A Novel CPU/GPU Simulation Environment for Large-Scale Biologically-Realistic Neural Modeling

    Directory of Open Access Journals (Sweden)

    Roger V Hoang

    2013-10-01

    Full Text Available Computational Neuroscience is an emerging field that provides unique opportunities to studycomplex brain structures through realistic neural simulations. However, as biological details are added tomodels, the execution time for the simulation becomes longer. Graphics Processing Units (GPUs are now being utilized to accelerate simulations due to their ability to perform computations in parallel. As such, they haveshown significant improvement in execution time compared to Central Processing Units (CPUs. Most neural simulators utilize either multiple CPUs or a single GPU for better performance, but still show limitations in execution time when biological details are not sacrificed. Therefore, we present a novel CPU/GPU simulation environment for large-scale biological networks,the NeoCortical Simulator version 6 (NCS6. NCS6 is a free, open-source, parallelizable, and scalable simula-tor, designed to run on clusters of multiple machines, potentially with high performance computing devicesin each of them. It has built-in leaky-integrate-and-fire (LIF and Izhikevich (IZH neuron models, but usersalso have the capability to design their own plug-in interface for different neuron types as desired. NCS6is currently able to simulate one million cells and 100 million synapses in quasi real time by distributing dataacross these heterogeneous clusters of CPUs and GPUs.

  10. A novel CPU/GPU simulation environment for large-scale biologically realistic neural modeling.

    Science.gov (United States)

    Hoang, Roger V; Tanna, Devyani; Jayet Bray, Laurence C; Dascalu, Sergiu M; Harris, Frederick C

    2013-01-01

    Computational Neuroscience is an emerging field that provides unique opportunities to study complex brain structures through realistic neural simulations. However, as biological details are added to models, the execution time for the simulation becomes longer. Graphics Processing Units (GPUs) are now being utilized to accelerate simulations due to their ability to perform computations in parallel. As such, they have shown significant improvement in execution time compared to Central Processing Units (CPUs). Most neural simulators utilize either multiple CPUs or a single GPU for better performance, but still show limitations in execution time when biological details are not sacrificed. Therefore, we present a novel CPU/GPU simulation environment for large-scale biological networks, the NeoCortical Simulator version 6 (NCS6). NCS6 is a free, open-source, parallelizable, and scalable simulator, designed to run on clusters of multiple machines, potentially with high performance computing devices in each of them. It has built-in leaky-integrate-and-fire (LIF) and Izhikevich (IZH) neuron models, but users also have the capability to design their own plug-in interface for different neuron types as desired. NCS6 is currently able to simulate one million cells and 100 million synapses in quasi real time by distributing data across eight machines with each having two video cards.

  11. A cooperative strategy for parameter estimation in large scale systems biology models

    Directory of Open Access Journals (Sweden)

    Villaverde Alejandro F

    2012-06-01

    Full Text Available Abstract Background Mathematical models play a key role in systems biology: they summarize the currently available knowledge in a way that allows to make experimentally verifiable predictions. Model calibration consists of finding the parameters that give the best fit to a set of experimental data, which entails minimizing a cost function that measures the goodness of this fit. Most mathematical models in systems biology present three characteristics which make this problem very difficult to solve: they are highly non-linear, they have a large number of parameters to be estimated, and the information content of the available experimental data is frequently scarce. Hence, there is a need for global optimization methods capable of solving this problem efficiently. Results A new approach for parameter estimation of large scale models, called Cooperative Enhanced Scatter Search (CeSS, is presented. Its key feature is the cooperation between different programs (“threads” that run in parallel in different processors. Each thread implements a state of the art metaheuristic, the enhanced Scatter Search algorithm (eSS. Cooperation, meaning information sharing between threads, modifies the systemic properties of the algorithm and allows to speed up performance. Two parameter estimation problems involving models related with the central carbon metabolism of E. coli which include different regulatory levels (metabolic and transcriptional are used as case studies. The performance and capabilities of the method are also evaluated using benchmark problems of large-scale global optimization, with excellent results. Conclusions The cooperative CeSS strategy is a general purpose technique that can be applied to any model calibration problem. Its capability has been demonstrated by calibrating two large-scale models of different characteristics, improving the performance of previously existing methods in both cases. The cooperative metaheuristic presented here

  12. An immunomagnetic separator for concentration of pathogenic micro-organisms from large volume samples

    Energy Technology Data Exchange (ETDEWEB)

    Rotariu, Ovidiu [School of Biological Sciences, University of Aberdeen, Cruickshank Building, St. Machar Drive, Aberdeen (United Kingdom) and National Institute of R-D for Technical Physics I.F.T. Iasi, Mangeron 47 Blvd., Iasi (Romania)]. E-mail: o.rotariu@abdn.ac.uk; Ogden, Iain D. [Department of Medical Microbiology, University of Aberdeen, Aberdeen (United Kingdom); MacRae, Marion [Department of Medical Microbiology, University of Aberdeen, Aberdeen (United Kingdom); Badescu, Vasile [National Institute of R-D for Technical Physics I.F.T. Iasi, Mangeron 47 Blvd., Iasi (Romania); Strachan, Norval J.C. [School of Biological Sciences, University of Aberdeen, Cruickshank Building, St. Machar Drive, Aberdeen (United Kingdom)

    2005-05-15

    The standard method of immunomagnetic separation of pathogenic bacteria from food and environmental matrices processes 1 ml volumes. Pathogens present at low levels (<1 pathogenic bacteria per ml) will not be consistently detected by this method. Here a flow through immunomagnetic separator (FTIMS) has been designed and tested to process large volume samples (>50 ml). Preliminary results show that between 70 and 113 times more Escherchia coli O157 are recovered compared with the standard 1 ml method.

  13. PROJECTION-PURSUIT BASED PRINCIPAL COMPONENT ANALYSIS: A LARGE SAMPLE THEORY

    Institute of Scientific and Technical Information of China (English)

    Jian ZHANG

    2006-01-01

    The principal component analysis (PCA) is one of the most celebrated methods in analysing multivariate data. An effort of extending PCA is projection pursuit (PP), a more general class of dimension-reduction techniques. However, the application of this extended procedure is often hampered by its complexity in computation and by lack of some appropriate theory. In this paper, by use of the empirical processes we established a large sample theory for the robust PP estimators of the principal components and dispersion matrix.

  14. Results from a large sample of MRPC-strip prototypes for ALICE TOF detector

    CERN Document Server

    Akindinov, A; Anselmo, F; Antonioli, P; Basile, M; Cara Romeo, G; Cifarelli, L; Cindolo, F; De Caro, A; De Pasquale, S; Di Bartolomeo, A; Fusco-Girard, M; Golovine, V; Guida, M; Hatzifotiadou, D; Kaidalov, A B; Kim, D H; Kiselev, S M; Laurenti, G; Lee, K; Lee, S C; Lioublev, E; Luvisetto, M L; Margotti, A; Martemyanov, A N; Nania, R; Otiougova, P; Pesci, A; Polozov, P A; Scapparone, E; Scioli, G; Sellito, S; Smirnitsky, A V; Tchoumakov, M M; Usenko, E; Valenti, G; Voloshin, K G; Williams, M C S; Zampolli, C; Zgreev, B V; Zichichi, Antonino

    2004-01-01

    The MRPC (multi resistive plate chamber) strip is the basic element of the ALICE time-of-flight detector. A test of a large sample of MRPC-strip prototypes corresponding to 1.2% of the full detector was carried out during the autumn of 2002 at the CERN proton synchrotron facility. This paper summarizes the main results obtained in terms of uniformity of response for all the tested channels.

  15. An enzyme-based DNA preparation method for application to forensic biological samples and degraded stains.

    Science.gov (United States)

    Lounsbury, Jenny A; Coult, Natalie; Miranian, Daniel C; Cronk, Stephen M; Haverstick, Doris M; Kinnon, Paul; Saul, David J; Landers, James P

    2012-09-01

    Extraction of DNA from forensic samples typically uses either an organic extraction protocol or solid phase extraction (SPE) and these methods generally involve numerous sample transfer, wash and centrifugation steps. Although SPE has been successfully adapted to the microdevice, it can be problematic because of lengthy load times and uneven packing of the solid phase. A closed-tube enzyme-based DNA preparation method has recently been developed which uses a neutral proteinase to lyse cells and degrade proteins and nucleases [14]. Following a 20 min incubation of the buccal or whole blood sample with this proteinase, DNA is polymerase chain reaction (PCR)-ready. This paper describes the optimization and quantitation of DNA yield using this method, and application to forensic biological samples, including UV- and heat-degraded whole blood samples on cotton or blue denim substrates. Results demonstrate that DNA yield can be increased from 1.42 (±0.21)ng/μL to 7.78 (±1.40)ng/μL by increasing the quantity of enzyme per reaction by 3-fold. Additionally, there is a linear relationship between the amount of starting cellular material added and the concentration of DNA in the solution, thereby allowing DNA yield estimations to be made. In addition, short tandem repeat (STR) profile results obtained using DNA prepared with the enzyme method were comparable to those obtained with a conventional SPE method, resulting in full STR profiles (16 of 16 loci) from liquid samples (buccal swab eluate and whole blood), dried buccal swabs and bloodstains and partial profiles from UV or heat-degraded bloodstains on cotton or blue denim substrates. Finally, the DNA preparation method is shown to be adaptable to glass or poly(methyl methacrylate) (PMMA) microdevices with little impact on STR peak height but providing a 20-fold reduction in incubation time (as little as 60 s), leading to a ≥1 h reduction in DNA preparation time.

  16. A simple method for estimating genetic diversity in large populations from finite sample sizes

    Directory of Open Access Journals (Sweden)

    Rajora Om P

    2009-12-01

    Full Text Available Abstract Background Sample size is one of the critical factors affecting the accuracy of the estimation of population genetic diversity parameters. Small sample sizes often lead to significant errors in determining the allelic richness, which is one of the most important and commonly used estimators of genetic diversity in populations. Correct estimation of allelic richness in natural populations is challenging since they often do not conform to model assumptions. Here, we introduce a simple and robust approach to estimate the genetic diversity in large natural populations based on the empirical data for finite sample sizes. Results We developed a non-linear regression model to infer genetic diversity estimates in large natural populations from finite sample sizes. The allelic richness values predicted by our model were in good agreement with those observed in the simulated data sets and the true allelic richness observed in the source populations. The model has been validated using simulated population genetic data sets with different evolutionary scenarios implied in the simulated populations, as well as large microsatellite and allozyme experimental data sets for four conifer species with contrasting patterns of inherent genetic diversity and mating systems. Our model was a better predictor for allelic richness in natural populations than the widely-used Ewens sampling formula, coalescent approach, and rarefaction algorithm. Conclusions Our regression model was capable of accurately estimating allelic richness in natural populations regardless of the species and marker system. This regression modeling approach is free from assumptions and can be widely used for population genetic and conservation applications.

  17. Investigation of resins suitable for the preparation of biological sample for 3-D electron microscopy.

    Science.gov (United States)

    Kizilyaprak, Caroline; Longo, Giovanni; Daraspe, Jean; Humbel, Bruno M

    2015-02-01

    In the last two decades, the third-dimension has become a focus of attention in electron microscopy to better understand the interactions within subcellular compartments. Initially, transmission electron tomography (TEM tomography) was introduced to image the cell volume in semi-thin sections (∼ 500 nm). With the introduction of the focused ion beam scanning electron microscope, a new tool, FIB-SEM tomography, became available to image much larger volumes. During TEM tomography and FIB-SEM tomography, the resin section is exposed to a high electron/ion dose such that the stability of the resin embedded biological sample becomes an important issue. The shrinkage of a resin section in each dimension, especially in depth, is a well-known phenomenon. To ensure the dimensional integrity of the final volume of the cell, it is important to assess the properties of the different resins and determine the formulation which has the best stability in the electron/ion beam. Here, eight different resin formulations were examined. The effects of radiation damage were evaluated after different times of TEM irradiation. To get additional information on mass-loss and the physical properties of the resins (stiffness and adhesion), the topography of the irradiated areas was analysed with atomic force microscopy (AFM). Further, the behaviour of the resins was analysed after ion milling of the surface of the sample with different ion currents. In conclusion, two resin formulations, Hard Plus and the mixture of Durcupan/Epon, emerged that were considerably less affected and reasonably stable in the electron/ion beam and thus suitable for the 3-D investigation of biological samples.

  18. Large antenna experiments aboard the space shuttle: Application of nonuniform sampling techniques

    Science.gov (United States)

    Rahmatsamii, Y.

    1988-01-01

    Future satellite communication and scientific spacecraft will utilize antennas with dimensions as large as 20 meters. In order to commercially use these large, low sidelobe and multiple beam antennas, a high level of confidence must be established as to their performance in the 0-g and space environment. Furthermore, it will be desirable to demonstrate the applicability of surface compensation techniques for slowly varying surface distortions which could result from thermal effects. An overview of recent advances in performing RF measurements on large antennas is presented with emphasis given to the application of a space based far-field range utilizing the Space Shuttle and the concept of a newly developed nonuniform sampling technique.

  19. IS THE BRAZILIAN REAL A COMMODITY CURRENCY? LARGE SAMPLE EMPIRICAL EVIDENCE

    Directory of Open Access Journals (Sweden)

    Filipe Monteiro de Castro Albert

    2014-01-01

    Full Text Available Brazil is one of the world’s largest base materials exporters, and this paper examines through large time series samples whether the Brazilian Real can be characterized as a commodity currency. The Real/US dollar real exchange rate and a real commodity prices index are found to be non-stationary and not cointegrated, while a risk premium appeared to have a large and statistically significant long term relationship with exchange rate movements. Combined first difference models showed that real exchange rate elasticity to risk premium is twice as large as to commodity prices, although both variables have considerable influence. Some specifications outperformed a random walk model with respect to root mean square forecast errors for many horizons, but the latter still better determined the exchange rate in longer terms.

  20. Spatial Clustering from GALEX-SDSS samples: Star Formation History and large-scale clustering

    CERN Document Server

    Heinis, Sebastien; Szalay, A S; Arnouts, Stephane; Aragon-Calvo, Miguel A; Wyder, Ted K; Barlow, Tom A; Foster, Karl; Friedman, Peter G; Martin, D Christopher; Morrissey, Patrick; Neff, Susan G; Schiminovich, David; Seibert, Mark; Bianchi, Luciana; Donas, Jose; Heckman, Timothy M; Lee, Young-Wook; Madore, Barry F; Milliard, Bruno; Rich, R Michael; Yi, Sukyoung K

    2009-01-01

    We measure the projected spatial correlation function w_p(r_p) from a large sample combining GALEX ultraviolet imaging with the SDSS spectroscopic sample. We study the dependence of the clustering strength for samples selected on (NUV - r)_abs color, specific star formation rate (SSFR), and stellar mass. We find that there is a smooth transition in the clustering of galaxies as a function of this color from weak clustering among blue galaxies to stronger clustering for red galaxies. The clustering of galaxies within the "green valley" has an intermediate strength, and is consistent with that expected from galaxy groups. The results are robust to the correction for dust extinction. The comparison with simple analytical modeling suggests that the halo occupation number increases with older star formation epochs. When splitting according to SSFR, we find that the SSFR is a more sensitive tracer of environment than stellar mass.

  1. Probing large-scale structure with large samples of X-ray selected AGN: I Baryonic acoustic oscillations

    CERN Document Server

    Hütsi, Gert; Kolodzig, Alexander; Sunyaev, Rashid

    2014-01-01

    We investigate the potential of large X-ray selected AGN samples for detecting baryonic acoustic oscillations (BAO). Though AGN selection in X-ray band is very clean and efficient, it does not provide us redshift information, and thus needs to be complemented with an optical follow-up. The main focus of this study is: (i) to find necessary requirements to the quality of the optical follow-up and (ii) to formulate the optimal strategy of the X-ray survey, in order to detect the BAO. We demonstrate that redshift accuracy of sigma_0=10^{-2} and the catastrophic failure rate of <~30% are sufficient for a reliable detection of BAO in future X-ray surveys. Spectroscopic quality redshifts combined with negligible fraction of catastrophic failures will boost the confidence level of the BAO detection by a factor of ~2. For the meaningful detection of BAO, X-ray surveys of moderate depth of F_lim ~ few 10^{-15} erg/s/cm^2 covering sky area from a ~few hundred to ~ten thousand square degrees are required. The optimal...

  2. Estimation of the fraction of biologically active methyl tert-butyl ether degraders in a heterogeneous biomass sample

    DEFF Research Database (Denmark)

    Waul, Christopher Kevin; Arvin, Erik; Schmidt, Jens Ejbye

    2008-01-01

    The fraction of biologically active methyl tert-butyl ether degraders in reactors is just as important for prediction of removal rates as knowledge of the kinetic parameters. The fraction of biologically active methyl tert-butyl ether degraders in a heterogeneous biomass sample, taken from a packed...

  3. Sensitive Determination of Terazosin in Pharmaceutical Formulations and Biological Samples by Ionic-Liquid Microextraction Prior to Spectrofluorimetry

    Directory of Open Access Journals (Sweden)

    Mohsen Zeeb

    2012-01-01

    Full Text Available An efficient and environmentally friendly sample preparation method based on the application of hydrophobic 1-Hexylpyridinium hexafluorophosphate [Hpy][PF6] ionic liquid (IL as a microextraction solvent was proposed to preconcentrate terazosin. The performance of the microextraction method was improved by introducing a common ion of pyridinium IL into the sample solution. Due to the presence of the common ion, the solubility of IL significantly decreased. As a result, the phase separation successfully occurred even at high ionic strength, and the volume of the settled IL-phase was not influenced by variations in the ionic strength (up to 30% w/v. After preconcentration step, the enriched phase was introduced to the spectrofluorimeter for the determination of terazosin. The obtained results revealed that this system did not suffer from the limitations of that in conventional ionic-liquid microextraction. Under optimum experimental conditions, the proposed method provided a limit of detection (LOD of 0.027 μg L−1 and a relative standard deviation (R.S.D. of 2.4%. The present method was successfully applied to terazosin determination in actual pharmaceutical formulations and biological samples. Considering the large variety of ionic liquids, the proposed microextraction method earns many merits, and will present a wide application in the future.

  4. Sensitive determination of terazosin in pharmaceutical formulations and biological samples by ionic-liquid microextraction prior to spectrofluorimetry.

    Science.gov (United States)

    Zeeb, Mohsen; Sadeghi, Mahdi

    2012-01-01

    An efficient and environmentally friendly sample preparation method based on the application of hydrophobic 1-Hexylpyridinium hexafluorophosphate [Hpy][PF(6)] ionic liquid (IL) as a microextraction solvent was proposed to preconcentrate terazosin. The performance of the microextraction method was improved by introducing a common ion of pyridinium IL into the sample solution. Due to the presence of the common ion, the solubility of IL significantly decreased. As a result, the phase separation successfully occurred even at high ionic strength, and the volume of the settled IL-phase was not influenced by variations in the ionic strength (up to 30% w/v). After preconcentration step, the enriched phase was introduced to the spectrofluorimeter for the determination of terazosin. The obtained results revealed that this system did not suffer from the limitations of that in conventional ionic-liquid microextraction. Under optimum experimental conditions, the proposed method provided a limit of detection (LOD) of 0.027 μg L(-1) and a relative standard deviation (R.S.D.) of 2.4%. The present method was successfully applied to terazosin determination in actual pharmaceutical formulations and biological samples. Considering the large variety of ionic liquids, the proposed microextraction method earns many merits, and will present a wide application in the future.

  5. The Constitutive Content of the Crime of Refusal or Evasion from Collecting Biological Samples in the Romanian Criminal Law

    National Research Council Canada - National Science Library

    Minodora-Ioana BĂLAN-RUSU

    2015-01-01

    In the paper we have examined the constitutive content of the offense of refusal or evasion from collecting biological samples, with elements of similarity and differences between the current and the old law...

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

    Science.gov (United States)

    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.

  7. [Detection and typing by molecular biology of human papillomavirus in genital samples].

    Science.gov (United States)

    Suárez Moya, A; Esquivias Gómez, J I; Vidart Aragón, J A; Picazo de la Garza, J J

    2006-06-01

    Recently, there has been a marked increase in human papillomavirus (HPV) infection, and the etiological relationship between some HPV genotypes and genital cancer has been confirmed. Therefore, we used current molecular biology techniques to evaluate the prevalence of these viruses and their genotype in genital samples. We processed 401 genital samples from 281 women and 120 men, all with a diagnosis compatible with HPV infection. Virus was detected using PCR, and positive samples were typed using an array technique which enabled us to detect the 35 most common types of mucous-associated HPV. Of the 401 patients studied, 185 (46.1%) were positive, and only one type of HPV was detected in 133 cases. We found that 41.6% of the women and 56.7% of the men were positive. A total of 260 HPVs were typed; 154 were high oncogenic risk. They infected 16 men (23.5%) and 88 women (75.2%). The difference was statistically significant (pHVP 16 in 52 cases. We found a 46% prevalence of HPV infection. More than half of these patients were infected by high-risk HPV. The presence of high-risk HPV was significantly higher in women.

  8. Troubleshooting digital macro photography for image acquisition and the analysis of biological samples.

    Science.gov (United States)

    Liepinsh, Edgars; Kuka, Janis; Dambrova, Maija

    2013-01-01

    For years, image acquisition and analysis have been an important part of life science experiments to ensure the adequate and reliable presentation of research results. Since the development of digital photography and digital planimetric methods for image analysis approximately 20 years ago, new equipment and technologies have emerged, which have increased the quality of image acquisition and analysis. Different techniques are available to measure the size of stained tissue samples in experimental animal models of disease; however, the most accurate method is digital macro photography with software that is based on planimetric analysis. In this study, we described the methodology for the preparation of infarcted rat heart and brain tissue samples before image acquisition, digital macro photography techniques and planimetric image analysis. These methods are useful in the macro photography of biological samples and subsequent image analysis. In addition, the techniques that are described in this study include the automated analysis of digital photographs to minimize user input and exclude the risk of researcher-generated errors or bias during image analysis.

  9. Ultrasensitive techniques for measurement of uranium in biological samples and the nephrotoxicity of uranium: Proceedings

    Energy Technology Data Exchange (ETDEWEB)

    Kathren, R.L.; Weber, J.R. (eds.)

    1988-04-01

    Edited transcripts are provided of two public meetings sponsored by the Division of Radiation Programs and Earth Sciences of the Nuclear Regulatory Commission, Occupational Radiation Protection Branch. The first meeting, held on December 3, 1985, included nine presentations covering ultrasensitive techniques for measurement of uranium in biological specimens. Topics included laser-spectrometric techniques for uranium bioassay, correlation of urinary uranium samples with air sampling results in industrial settings, delayed neutron counting, laser-kinetic phosphometry, isotope dilution mass spectrometry, resonance ionization spectroscopy, fission track analysis, laser-induced fluorescence, and costs of sampling and processing. The nine presentations of the second meeting dealt with the nephrotoxicity of uranium. Among the topics presented were the physiology of the kidney, the effects of heavy metals on the kidney, animal studies in uranium nephrotoxicity, comparisons of kidney histology in nine humans, renal effects in uranium mill workers, renal damage from different uranium isotopes, and Canadian studies on uranium toxicity. Discussions following the presentations are included in the edited transcripts. 30 refs., 9 figs., 9 tabs.

  10. Inalienably Yours? The new case for an inalienable property right in human biological material: Empowerment of sample donors or a recipe for a tragic Anti-Commons?

    Directory of Open Access Journals (Sweden)

    Jasper A. Bovenberg

    2004-12-01

    Full Text Available Modern biomedical research into the genetic component of common diseases calls for broad access to existing and novel collections of samples of human biological material, aka Biobanks. Groups of donors of these samples, however, increasingly claim a property right in their samples. They perceive the recognition of a personal property right in their biological material as the best means to serve two goals: to secure ongoing control over their samples after donation and to underpin their claim for a share in the proceeds that the research on their samples may yield. Given the objective of ensuring ongoing control, this property right is claimed to be inalienable. Recognition of a personal property right in one’s biological material is problematic, especially where the requirement of inalienability seems at odds with the claim for a share of the profits. Yet, property rights in human biological material may be justified in a certain context, e.g. to enable subsets of patients to negotiate the terms and conditions of the research into their specific disorders. Biobanks, however, contain so many samples, which can be used for so many research purposes, that the unrestricted exercise of personal property rights by the sample donors will lead to a proliferation of rights. This proliferation is likely to deter or slow down both the creation of de novo Biobanks and the use of existing sample collections. Thus, recognising inalienable property rights in human biological material may lead to suboptimal use of these resources and create a classic ‘anticommons property’ scenario. It would also undermine the current trend to simplify existing informed consent requirements which aims to facilitate broad and previously unanticipated research on de novo and existing Biobanks. In addition, the tradition of altruistic participation in research and the notion that large-scale collections of human biological material are global public goods are arguments against

  11. From large-eddy simulation to multi-UAVs sampling of shallow cumulus clouds

    Science.gov (United States)

    Lamraoui, Fayçal; Roberts, Greg; Burnet, Frédéric

    2016-04-01

    In-situ sampling of clouds that can provide simultaneous measurements at satisfying spatio-temporal resolutions to capture 3D small scale physical processes continues to present challenges. This project (SKYSCANNER) aims at bringing together cloud sampling strategies using a swarm of unmanned aerial vehicles (UAVs) based on Large-eddy simulation (LES). The multi-UAV-based field campaigns with a personalized sampling strategy for individual clouds and cloud fields will significantly improve the understanding of the unresolved cloud physical processes. An extensive set of LES experiments for case studies from ARM-SGP site have been performed using MesoNH model at high resolutions down to 10 m. The carried out simulations led to establishing a macroscopic model that quantifies the interrelationship between micro- and macrophysical properties of shallow convective clouds. Both the geometry and evolution of individual clouds are critical to multi-UAV cloud sampling and path planning. The preliminary findings of the current project reveal several linear relationships that associate many cloud geometric parameters to cloud related meteorological variables. In addition, the horizontal wind speed indicates a proportional impact on cloud number concentration as well as triggering and prolonging the occurrence of cumulus clouds. In the framework of the joint collaboration that involves a Multidisciplinary Team (including institutes specializing in aviation, robotics and atmospheric science), this model will be a reference point for multi-UAVs sampling strategies and path planning.

  12. Evaluation of cadmium, lead, nickel and zinc status in biological samples of smokers and nonsmokers hypertensive patients

    OpenAIRE

    H. I. Afridi; Kazi, T G; Kazi, N G; Jamali, M K; Arain, M B; Sirajuddin,; Baig, J. A.; Kandhro, G A; Wadhwa, S K; Shah, A Q

    2009-01-01

    The objective of this study was to evaluate the association between trace and toxic elements zinc (Zn), cadmium (Cd), nickel (Ni) and lead (Pb) in biological samples (scalp hair, blood and urine) of smoker and nonsmoker hypertensive patients (n=457), residents of Hyderabad, Pakistan. For the purpose of comparison, the biological samples of age-matched healthy controls were selected as referents. The concentrations of trace and toxic elements were measured by atomic absorption spectrophotomete...

  13. Determination of steroid hormones in biological and environmental samples using green microextraction techniques: an overview.

    Science.gov (United States)

    Aufartová, Jana; Mahugo-Santana, Cristina; Sosa-Ferrera, Zoraida; Santana-Rodríguez, José Juan; Nováková, Lucie; Solich, Petr

    2011-10-17

    Residues of steroid hormones have become a cause for concern because they can affect the biological activity of non-target organisms. Steroid hormones are a potential risk for wildlife and humans through the consumption of contaminated food or water. Their determination requires extraction and clean-up steps, prior to detection, to reach low concentration levels. In recent years, a great effort has been made to develop new analytical methodologies, such as microextraction techniques, that reduce environmental pollution. Researchers have modified old methods to incorporate procedures that use less-hazardous chemicals or that use smaller amounts of them. They are able to do direct analysis using miniaturised equipment and reduced amounts of solvents and wastes. These accomplishments are the main objectives of green analytical chemistry. In this overview, we focus on microextraction techniques for the determination of steroid hormones in biological (e.g., human urine, human serum, fish, shrimp and prawn tissue and milk) and environmental (e.g., wastewaters, surface waters, tap waters, river waters, sewage sludges, marine sediments and river sediments) samples. We comment on the most recent applications in sorptive-microextraction modes, such as solid phase microextraction (SPME) with molecularly imprinted polymers (MIPs), in-tube solid-phase microextraction (IT-SPME), stir-bar sorptive extraction (SBSE) and microextraction in packed sorbent (MEPS). We also describe liquid-phase microextraction (LPME) approaches reported in the literature that are applied to the determination of steroid hormones.

  14. Monitoring prion protein expression in complex biological samples by SERS for diagnostic applications

    Energy Technology Data Exchange (ETDEWEB)

    Manno, D; Filippo, E; Fiore, R; Serra, A [Dipartimento di Scienza dei Materiali, Universita del Salento, Lecce (Italy); Urso, E; Rizzello, A; Maffia, M [Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Universita del Salento, Lecce (Italy)

    2010-04-23

    Surface-enhanced Raman spectroscopy (SERS) allows a new insight into the analysis of cell physiology. In this work, the difficulty of producing suitable substrates that, besides permitting the amplification of the Raman signal, do not interact with the biological material causing alteration, has been overcome by a combined method of hydrothermal green synthesis and thermal annealing. The SERS analysis of the cell membrane has been performed with special attention to the cellular prion protein PrP{sup C}. In addition, SERS has also been used to reveal the prion protein-Cu(II) interaction in four different cell models (B104, SH-SY5Y, GN11, HeLa), expressing PrP{sup C} at different levels. A significant implication of the current work consists of the intriguing possibility of revealing and quantifying prion protein expression in complex biological samples by a cheap SERS-based method, replacing the expensive and time-consuming immuno-assay systems commonly employed.

  15. Differential scanning calorimetry as a complementary diagnostic tool for the evaluation of biological samples.

    Science.gov (United States)

    Garbett, Nichola C; Brock, Guy N

    2016-05-01

    Differential scanning calorimetry (DSC) is a tool for measuring the thermal stability profiles of complex molecular interactions in biological fluids. DSC profiles (thermograms) of biofluids provide specific signatures which are being utilized as a new diagnostic approach for characterizing disease but the development of these approaches is still in its infancy. This article evaluates several approaches for the analysis of thermograms which could increase the utility of DSC for clinical application. Thermograms were analyzed using localized thermogram features and principal components (PCs). The performance of these methods was evaluated alongside six models for the classification of a data set comprised of 300 systemic lupus erythematosus (SLE) patients and 300 control subjects obtained from the Lupus Family Registry and Repository (LFRR). Classification performance was substantially higher using the penalized algorithms relative to localized features/PCs alone. The models were grouped into two sets, the first having smoother solution vectors but lower classification accuracies than the second with seemingly noisier solution vectors. Coupling thermogram technology with modern classification algorithms provides a powerful diagnostic approach for analysis of biological samples. The solution vectors from the models may reflect important information from the thermogram profiles for discriminating between clinical groups. DSC thermograms show sensitivity to changes in the bulk plasma proteome that correlate with clinical status. To move this technology towards clinical application the development of new approaches is needed to extract discriminatory parameters from DSC profiles for the comparison and diagnostic classification of patients. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Trace Level Arsenic Quantification through Cloud Point Extraction: Application to Biological and Environmental Samples

    Directory of Open Access Journals (Sweden)

    Kempahanumakkagari Suresh Kumar

    2012-01-01

    Full Text Available A sensitive solvent-free extraction protocol for the quantification of arsenic at trace level has been described. It is based on the reaction of arsenic (V with molybdate in acidic medium in presence of antimony (III and ascorbic acid as a reducing agent to form a blue-colored arsenomolybdenum blue complex. The complex has been extracted into surfactant phase using Triton X-114, and its absorbance was measured at 690 nm. The detection limit, working range, and the relative standard deviation were found to be 1 ng mL−1, 10–200 ng mL−1, and 1.2%, respectively. The effect of common ions was studied, and the method has been applied to determine trace levels of As(III and As(V from a variety of samples like environmental, biological, and commercially procured chemicals.

  17. Determination of Sodium Cromoglycate by a New Kinetic Spectrophotometric Method in Biological Samples

    Directory of Open Access Journals (Sweden)

    Mohsen Keyvanfard

    2013-01-01

    Full Text Available A new kinetic spectrophotometric method is described for the determination of ultratrace amounts of sodium cromoglycate (SCG. The method based on catalytic action of SCG on the oxidation of amaranth with periodate in acidic and micellar medium. The reaction was monitored spectrophotometrically by measuring the decrease in absorbance of the amaranth at 518 nm, for the first 4 min from initiation of the reaction. Calibration curve was linear in the range of 4.0−36.0 ng mL−1 SCG. The limit of detection is 2.7 ng mL−1 SCG. The relative standard deviation (RSD for ten replicate analyses of 12, 20, and 28 ng mL−1 SCG was 0.40%, 0.32%, and 0.53%, respectively. The proposed method was used for the determination of SCG in biological samples.

  18. Selective spectrofluorimetric determination of zinc in biological samples by Flow Injection Analysis (FIA)

    Energy Technology Data Exchange (ETDEWEB)

    Fernandez, P.; Perez Conde, C.; Gutierrez, A.; Camara, C. (Universidad Complutense, Madrid (Spain). Dept. de Quimica Analitica)

    1992-03-01

    The automatization of a spectrofluorimetric method for the determination of zinc at trace level is described. It is based on the formation of the fluorescent complex Zn(II)-5,7-dibromo-8-quinolinol (Zn(II)-DBQ) followed by extraction into diethylether using flow injection analysis. The optimum fluorescent emission is reached in hexamethylenetetramine (H{sub 2}MTA{sup +}/HMTA) buffer pH 6.0. A membrane phase separator was used. The calibration graph is linear up to 1.5 {mu}g/ml of Zn(II). The proposed method (detection limit 3 ng/ml) is very selective and has been successfully applied to determine Zn(II) in biological samples, tap waters and various food items. (orig.).

  19. Determination of gadolinium-based MRI contrast agents in biological and environmental samples: A review

    Energy Technology Data Exchange (ETDEWEB)

    Telgmann, Lena [University of Münster, Institute of Inorganic and Analytical Chemistry, Münster (Germany); Sperling, Michael [University of Münster, Institute of Inorganic and Analytical Chemistry, Münster (Germany); European Virtual Institute for Speciation Analysis (EVISA), Münster (Germany); Karst, Uwe, E-mail: uk@uni-muenster.de [University of Münster, Institute of Inorganic and Analytical Chemistry, Münster (Germany)

    2013-02-18

    Highlights: ► All major methods for the analysis of Gd-based MRI contrast agents are discussed. ► Biological and environmental samples are covered. ► Pharmacokinetics and species transformation can be investigated. ► The figures of merit as limit of detection and analysis time are described. -- Abstract: The development of analytical methods and strategies to determine gadolinium and its complexes in biological and environmental matrices is evaluated in this review. Gadolinium (Gd) chelates are employed as contrast agents for magnetic resonance imaging (MRI) since the 1980s. In general they were considered as safe and well-tolerated, when in 2006, the disease nephrogenic systemic fibrosis (NSF) was connected to the administration of MRI contrast agents based on Gd. Pathogenesis and etiology of NSF are yet unclear and called for the development of several analytical methods to obtain elucidation in this field. Determination of Gd complex stability in vitro and in vivo, as well as the quantification of Gd in body fluids like blood and urine was carried out. Separation of the Gd chelates was achieved with high performance liquid chromatography (HPLC) and capillary electrophoresis (CE). For detection, various methods were employed, including UV–vis absorbance and fluorescence spectroscopy, electrospray ionization mass spectrometry (ESI-MS) and inductively coupled plasma mass spectrometry (ICP-MS). A second challenge for analysts was the discovery of high concentrations of anthropogenic Gd in surface waters draining populated areas. The source could soon be determined to be the increasing administration of Gd complexes during MRI examinations. Identification and quantification of the contrast agents was carried out in various surface and groundwater samples to determine the behavior and fate of the Gd chelates in the environment. The improvement of limits of detection (LOD) and limits of quantification (LOQ) was and still is the goal of past and ongoing

  20. CO2 isotope analyses using large air samples collected on intercontinental flights by the CARIBIC Boeing 767

    NARCIS (Netherlands)

    Assonov, S.S.; Brenninkmeijer, C.A.M.; Koeppel, C.; Röckmann, T.

    2009-01-01

    Analytical details for 13C and 18O isotope analyses of atmospheric CO2 in large air samples are given. The large air samples of nominally 300 L were collected during the passenger aircraft-based atmospheric chemistry research project CARIBIC and analyzed for a large number of trace gases and

  1. Gay and Bisexual Men's Perceptions of the Donation and Use of Human Biological Samples for Research: A Qualitative Study.

    Directory of Open Access Journals (Sweden)

    Chris Patterson

    Full Text Available Human biological samples (biosamples are increasingly important in diagnosing, treating and measuring the prevalence of illnesses. For the gay and bisexual population, biosample research is particularly important for measuring the prevalence of human immunodeficiency virus (HIV. By determining people's understandings of, and attitudes towards, the donation and use of biosamples, researchers can design studies to maximise acceptability and participation. In this study we examine gay and bisexual men's attitudes towards donating biosamples for HIV research. Semi-structured telephone interviews were conducted with 46 gay and bisexual men aged between 18 and 63 recruited in commercial gay scene venues in two Scottish cities. Interview transcripts were analysed thematically using the framework approach. Most men interviewed seemed to have given little prior consideration to the issues. Participants were largely supportive of donating tissue for medical research purposes, and often favourable towards samples being stored, reused and shared. Support was often conditional, with common concerns related to: informed consent; the protection of anonymity and confidentiality; the right to withdraw from research; and ownership of samples. Many participants were in favour of the storage and reuse of samples, but expressed concerns related to data security and potential misuse of samples, particularly by commercial organisations. The sensitivity of tissue collection varied between tissue types and collection contexts. Blood, urine, semen and bowel tissue were commonly identified as sensitive, and donating saliva and as unlikely to cause discomfort. To our knowledge, this is the first in-depth study of gay and bisexual men's attitudes towards donating biosamples for HIV research. While most men in this study were supportive of donating tissue for research, some clear areas of concern were identified. We suggest that these minority concerns should be accounted

  2. Software engineering the mixed model for genome-wide association studies on large samples.

    Science.gov (United States)

    Zhang, Zhiwu; Buckler, Edward S; Casstevens, Terry M; Bradbury, Peter J

    2009-11-01

    Mixed models improve the ability to detect phenotype-genotype associations in the presence of population stratification and multiple levels of relatedness in genome-wide association studies (GWAS), but for large data sets the resource consumption becomes impractical. At the same time, the sample size and number of markers used for GWAS is increasing dramatically, resulting in greater statistical power to detect those associations. The use of mixed models with increasingly large data sets depends on the availability of software for analyzing those models. While multiple software packages implement the mixed model method, no single package provides the best combination of fast computation, ability to handle large samples, flexible modeling and ease of use. Key elements of association analysis with mixed models are reviewed, including modeling phenotype-genotype associations using mixed models, population stratification, kinship and its estimation, variance component estimation, use of best linear unbiased predictors or residuals in place of raw phenotype, improving efficiency and software-user interaction. The available software packages are evaluated, and suggestions made for future software development.

  3. Estimating the Size of a Large Network and its Communities from a Random Sample

    CERN Document Server

    Chen, Lin; Crawford, Forrest W

    2016-01-01

    Most real-world networks are too large to be measured or studied directly and there is substantial interest in estimating global network properties from smaller sub-samples. One of the most important global properties is the number of vertices/nodes in the network. Estimating the number of vertices in a large network is a major challenge in computer science, epidemiology, demography, and intelligence analysis. In this paper we consider a population random graph G = (V;E) from the stochastic block model (SBM) with K communities/blocks. A sample is obtained by randomly choosing a subset W and letting G(W) be the induced subgraph in G of the vertices in W. In addition to G(W), we observe the total degree of each sampled vertex and its block membership. Given this partial information, we propose an efficient PopULation Size Estimation algorithm, called PULSE, that correctly estimates the size of the whole population as well as the size of each community. To support our theoretical analysis, we perform an exhausti...

  4. Probing large-scale structure with large samples of X-ray selected AGN. I. Baryonic acoustic oscillations

    Science.gov (United States)

    Hütsi, Gert; Gilfanov, Marat; Kolodzig, Alexander; Sunyaev, Rashid

    2014-12-01

    We investigate the potential of large X-ray-selected AGN samples for detecting baryonic acoustic oscillations (BAO). Though AGN selection in X-ray band is very clean and efficient, it does not provide redshift information, and thus needs to be complemented with an optical follow-up. The main focus of this study is (i) to find the requirements needed for the quality of the optical follow-up and (ii) to formulate the optimal strategy of the X-ray survey, in order to detect the BAO. We demonstrate that redshift accuracy of σ0 = 10-2 at z = 1 and the catastrophic failure rate of ffail ≲ 30% are sufficient for a reliable detection of BAO in future X-ray surveys. Spectroscopic quality redshifts (σ0 = 10-3 and ffail ~ 0) will boost the confidence level of the BAO detection by a factor of ~2. For meaningful detection of BAO, X-ray surveys of moderate depth of Flim ~ few 10-15 erg s-1/cm2 covering sky area from a few hundred to ~ten thousand square degrees are required. The optimal strategy for the BAO detection does not necessarily require full sky coverage. For example, in a 1000 day-long survey by an eROSITA type telescope, an optimal strategy would be to survey a sky area of ~9000 deg2, yielding a ~16σ BAO detection. A similar detection will be achieved by ATHENA+ or WFXT class telescopes in a survey with a duration of 100 days, covering a similar sky area. XMM-Newton can achieve a marginal BAO detection in a 100-day survey covering ~400 deg2. These surveys would demand a moderate-to-high cost in terms the optical follow-ups, requiring determination of redshifts of ~105 (XMM-Newton) to ~3 × 106 objects (eROSITA, ATHENA+, and WFXT) in these sky areas.

  5. Towards human-computer synergetic analysis of large-scale biological data.

    Science.gov (United States)

    Singh, Rahul; Yang, Hui; Dalziel, Ben; Asarnow, Daniel; Murad, William; Foote, David; Gormley, Matthew; Stillman, Jonathan; Fisher, Susan

    2013-01-01

    Advances in technology have led to the generation of massive amounts of complex and multifarious biological data in areas ranging from genomics to structural biology. The volume and complexity of such data leads to significant challenges in terms of its analysis, especially when one seeks to generate hypotheses or explore the underlying biological processes. At the state-of-the-art, the application of automated algorithms followed by perusal and analysis of the results by an expert continues to be the predominant paradigm for analyzing biological data. This paradigm works well in many problem domains. However, it also is limiting, since domain experts are forced to apply their instincts and expertise such as contextual reasoning, hypothesis formulation, and exploratory analysis after the algorithm has produced its results. In many areas where the organization and interaction of the biological processes is poorly understood and exploratory analysis is crucial, what is needed is to integrate domain expertise during the data analysis process and use it to drive the analysis itself. In context of the aforementioned background, the results presented in this paper describe advancements along two methodological directions. First, given the context of biological data, we utilize and extend a design approach called experiential computing from multimedia information system design. This paradigm combines information visualization and human-computer interaction with algorithms for exploratory analysis of large-scale and complex data. In the proposed approach, emphasis is laid on: (1) allowing users to directly visualize, interact, experience, and explore the data through interoperable visualization-based and algorithmic components, (2) supporting unified query and presentation spaces to facilitate experimentation and exploration, (3) providing external contextual information by assimilating relevant supplementary data, and (4) encouraging user-directed information

  6. Presence and significant determinants of cognitive impairment in a large sample of patients with multiple sclerosis.

    Directory of Open Access Journals (Sweden)

    Martina Borghi

    Full Text Available OBJECTIVES: To investigate the presence and the nature of cognitive impairment in a large sample of patients with Multiple Sclerosis (MS, and to identify clinical and demographic determinants of cognitive impairment in MS. METHODS: 303 patients with MS and 279 healthy controls were administered the Brief Repeatable Battery of Neuropsychological tests (BRB-N; measures of pre-morbid verbal competence and neuropsychiatric measures were also administered. RESULTS: Patients and healthy controls were matched for age, gender, education and pre-morbid verbal Intelligence Quotient. Patients presenting with cognitive impairment were 108/303 (35.6%. In the overall group of participants, the significant predictors of the most sensitive BRB-N scores were: presence of MS, age, education, and Vocabulary. The significant predictors when considering MS patients only were: course of MS, age, education, vocabulary, and depression. Using logistic regression analyses, significant determinants of the presence of cognitive impairment in relapsing-remitting MS patients were: duration of illness (OR = 1.053, 95% CI = 1.010-1.097, p = 0.015, Expanded Disability Status Scale score (OR = 1.247, 95% CI = 1.024-1.517, p = 0.028, and vocabulary (OR = 0.960, 95% CI = 0.936-0.984, p = 0.001, while in the smaller group of progressive MS patients these predictors did not play a significant role in determining the cognitive outcome. CONCLUSIONS: Our results corroborate the evidence about the presence and the nature of cognitive impairment in a large sample of patients with MS. Furthermore, our findings identify significant clinical and demographic determinants of cognitive impairment in a large sample of MS patients for the first time. Implications for further research and clinical practice were discussed.

  7. Large-Scale Depletion of CD25+ Regulatory T Cells from Patient Leukapheresis Samples

    Science.gov (United States)

    Powell, Daniel J.; Parker, Linda L.; Rosenberg, Steven A.

    2006-01-01

    Summary The ability to selectively enrich or deplete T lymphocytes of specific phenotype and function holds significant promise for application in adoptive immunotherapy protocols. Although CD4+ T cells can have an impact on CD8+ T-cell effector function, memory, and maintenance, a subset of CD4+ T cells, CD25+ regulatory T cells (Treg), can regulate peripheral self tolerance and possess the ability to suppress antitumor responses. The authors report the ability to selectively deplete CD25+ Treg cells from patient leukapheresis samples using a clinical-grade, large-scale immunomagnetic system. Using leukapheresis samples containing up to 1.3 × 1010 white blood cells, efficient depletion of Treg cells was measured by flow cytometric analysis of CD25 expression and FOXP3 expression on post-depletion products. Remnant CD25+ cells could not be detected in CD25-depleted products after short-term culture in IL-2 or enriched following secondary immunomagnetic selection for CD25+ cells, confirming that efficient depletion had occurred. In parallel to efficient enrichment of CD25− cells, immunomagnetic selection resulted in the recovery of Treg cells, since CD25+ lymphocytes removed during depletion were primarily composed of CD4+ T cells that expressed high levels of FOXP3 and possessed suppressive activity against autologous TCR-stimulated CD4+ CD25− T cells in vitro. These results show that selective separation of functional CD25+ Treg cells from large-scale samples can be performed in large scale under clinical-grade conditions with sufficient selection, recovery, viability, ability to expand, and function for potential use in adoptive immunotherapy. PMID:16000960

  8. Sampling large landscapes with small-scale stratification-User's Manual

    Science.gov (United States)

    Bart, Jonathan

    2011-01-01

    This manual explains procedures for partitioning a large landscape into plots, assigning the plots to strata, and selecting plots in each stratum to be surveyed. These steps are referred to as the "sampling large landscapes (SLL) process." We assume that users of the manual have a moderate knowledge of ArcGIS and Microsoft ® Excel. The manual is written for a single user but in many cases, some steps will be carried out by a biologist designing the survey and some steps will be carried out by a quantitative assistant. Thus, the manual essentially may be passed back and forth between these users. The SLL process primarily has been used to survey birds, and we refer to birds as subjects of the counts. The process, however, could be used to count any objects. ®

  9. X-Rays from Superbubbles in the Large Magellanic Cloud. VI. A Sample of Thirteen Superbubbles

    CERN Document Server

    Dunne, B C; Chu, Y H; Dunne, Bryan C.; Points, Sean D.; Chu, You-Hua

    2001-01-01

    We present ROSAT observations and analysis of thirteen superbubbles in the Large Magellanic Cloud. Eleven of these observations have not been previously reported. We have studied the X-ray morphology of the superbubbles, and have extracted and analyzed their X-ray spectra. Diffuse X-ray emission is detected from each of these superbubbles, and X-ray emission is brighter than is theoretically expected for a wind-blown bubble, suggesting that the X-ray emission from the superbubbles has been enhanced by interactions between the superbubble shell and interior SNRs. We have also found significant positive correlations between the X-ray luminosity of a superbubble and its H-alpha luminosity, expansion velocity, and OB star count. Further, we have found that a large fraction of the superbubbles in the sample show evidence of ``breakout'' regions, where hot X-ray emitting gas extends beyond the H-alpha shell.

  10. Evaluation of blade-strike models for estimating the biological performance of large Kaplan hydro turbines

    Energy Technology Data Exchange (ETDEWEB)

    Deng, Z. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Carlson, T. J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Ploskey, G. R. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Richmond, M. C. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2005-11-01

    Bio-indexing of hydro turbines has been identified as an important means to optimize passage conditions for fish by identifying operations for existing and new design turbines that minimize the probability of injury. Cost-effective implementation of bio-indexing requires the use of tools such as numerical and physical turbine models to generate hypotheses for turbine operations that can be tested at prototype scales using live fish. Blade strike has been proposed as an index variable for the biological performance of turbines. Report reviews an evaluation of the use of numerical blade-strike models as a means with which to predict the probability of blade strike and injury of juvenile salmon smolt passing through large Kaplan turbines on the mainstem Columbia River.

  11. Large sample inference for a win ratio analysis of a composite outcome based on prioritized components.

    Science.gov (United States)

    Bebu, Ionut; Lachin, John M

    2016-01-01

    Composite outcomes are common in clinical trials, especially for multiple time-to-event outcomes (endpoints). The standard approach that uses the time to the first outcome event has important limitations. Several alternative approaches have been proposed to compare treatment versus control, including the proportion in favor of treatment and the win ratio. Herein, we construct tests of significance and confidence intervals in the context of composite outcomes based on prioritized components using the large sample distribution of certain multivariate multi-sample U-statistics. This non-parametric approach provides a general inference for both the proportion in favor of treatment and the win ratio, and can be extended to stratified analyses and the comparison of more than two groups. The proposed methods are illustrated with time-to-event outcomes data from a clinical trial.

  12. Determination of the efficiency of a detector in gamma spectrometry of large-volume samples

    CERN Document Server

    Tertyshnik, E G

    2012-01-01

    The experimental - calculated method is proposed to determine the full energy peak efficiency (FEPE) of detectors {\\epsilon}(E) in case a measurement of the large-volume samples. Water is used as standard absorber in which the linear attenuation coefficients for photons {\\mu}0 (E) is well known. The value {\\mu} (E) in sample material (matrix of the sample) is determined experimentally by means of spectrometer. The formulas are given for calculation of the ratio {\\epsilon}(E)/ {\\epsilon}0(E), where {\\epsilon}0(E) is FEPE of the detector for photons those are arising in the container filled with water (it is found by adding in the container of the Reference radioactive solutions). To prove the validity of the method ethanol (density 0,8 g/cm3) and water solutions of salts (density 1,2 and 1,5 g/cm3) were used for simulation of the samples with different attenuation coefficients. Standard deviation between experimental and calculated efficiencies has been about 5 %.

  13. Large-sample study of the kernel density estimators under multiplicative censoring

    CERN Document Server

    Asgharian, Masoud; Fakoor, Vahid; 10.1214/11-AOS954

    2012-01-01

    The multiplicative censoring model introduced in Vardi [Biometrika 76 (1989) 751--761] is an incomplete data problem whereby two independent samples from the lifetime distribution $G$, $\\mathcal{X}_m=(X_1,...,X_m)$ and $\\mathcal{Z}_n=(Z_1,...,Z_n)$, are observed subject to a form of coarsening. Specifically, sample $\\mathcal{X}_m$ is fully observed while $\\mathcal{Y}_n=(Y_1,...,Y_n)$ is observed instead of $\\mathcal{Z}_n$, where $Y_i=U_iZ_i$ and $(U_1,...,U_n)$ is an independent sample from the standard uniform distribution. Vardi [Biometrika 76 (1989) 751--761] showed that this model unifies several important statistical problems, such as the deconvolution of an exponential random variable, estimation under a decreasing density constraint and an estimation problem in renewal processes. In this paper, we establish the large-sample properties of kernel density estimators under the multiplicative censoring model. We first construct a strong approximation for the process $\\sqrt{k}(\\hat{G}-G)$, where $\\hat{G}$ is...

  14. A Pipeline for Large Data Processing Using Regular Sampling for Unstructured Grids

    Energy Technology Data Exchange (ETDEWEB)

    Berres, Anne Sabine [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Adhinarayanan, Vignesh [Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States); Turton, Terece [Univ. of Texas, Austin, TX (United States); Feng, Wu [Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States); Rogers, David Honegger [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-05-12

    Large simulation data requires a lot of time and computational resources to compute, store, analyze, visualize, and run user studies. Today, the largest cost of a supercomputer is not hardware but maintenance, in particular energy consumption. Our goal is to balance energy consumption and cognitive value of visualizations of resulting data. This requires us to go through the entire processing pipeline, from simulation to user studies. To reduce the amount of resources, data can be sampled or compressed. While this adds more computation time, the computational overhead is negligible compared to the simulation time. We built a processing pipeline at the example of regular sampling. The reasons for this choice are two-fold: using a simple example reduces unnecessary complexity as we know what to expect from the results. Furthermore, it provides a good baseline for future, more elaborate sampling methods. We measured time and energy for each test we did, and we conducted user studies in Amazon Mechanical Turk (AMT) for a range of different results we produced through sampling.

  15. Formalin-induced fluorescence reveals cell shape and morphology in biological tissue samples.

    Directory of Open Access Journals (Sweden)

    Ulrich Leischner

    Full Text Available Ultramicroscopy is a powerful tool to reveal detailed three-dimensional structures of large microscopical objects. Using high magnification, we observed that formalin induces fluorescence more in extra-cellular space and stains cellular structures negatively, rendering cells as dark objects in front of a bright background. Here, we show this effect on a three-dimensional image stack of a hippocampus sample, focusing on the CA1 region. This method, called FIF-Ultramicroscopy, allows for the three-dimensional observation of cellular structures in various tissue types without complicated staining techniques.

  16. Synchrotron-based X-ray fluorescence, imaging and elemental mapping from biological samples

    Indian Academy of Sciences (India)

    D V Rao; M Swapna; R Cesareo; A Brunetti; T Akatsuka; T Yuasa; T Takeda; G E Gigante

    2011-02-01

    The present study utilized the new hard X-ray microspectroscopy beamline facility, X27A, available at NSLS, BNL, USA, for elemental mapping. This facility provided the primary beam in a small spot of the order of ∼ 10 m, for focussing. With this spatial resolution and high flux throughput, the synchrotron-based X-ray fluorescent intensities for Mn, Fe, Zn, Cr, Ti and Cu were measured using a liquid-nitrogen-cooled 13-element energy-dispersive high-purity germanium detector. The sample is scanned in a `step-and-repeat’ mode for fast elemental mapping measurements and generated elemental maps at 8, 10 and 12 keV, from a small animal shell (snail). The accumulated trace elements, from these biological samples, in small areas have been identified. Analysis of the small areas will be better suited to establish the physiology of metals in specific structures like small animal shell and the distribution of other elements.

  17. Application of ion mobility spectrometry for the determination of tramadol in biological samples

    Directory of Open Access Journals (Sweden)

    Ali Sheibani

    2014-12-01

    Full Text Available In this study, a simple and rapid ion mobility spectrometry (IMS method has been described for the determination of tramadol. The operating instrumental parameters that could influence IMS were investigated and optimized (temperature; injection: 220 and IMS cell: 190°C, flow rate; carrier: 300 and drift: 600 mL/minute, voltage; corona: 2300 and drift: 7000 V, pulse width: 100 μs. Under optimum conditions, the calibration curves were linear within two orders of magnitude with R2 ≥ 0.998 for the determination of tramadol in human plasma, saliva, serum, and urine samples. The limits of detection and the limits of quantitation were between 0.1 and 0.3 and 0.3 and 1 ng/mL, respectively. The relative standard deviations were between 7.5 and 8.8%. The recovery results (90–103.9% indicate that the proposed method can be applied for tramadol analysis in different biological samples.

  18. A new HPLC method for the direct analysis of triglycerides of dicarboxylic acids in biological samples.

    Science.gov (United States)

    Capristo, E; Mingrone, G; De Gaetano, A; Addolorato, G; Greco, A V; Gasbarrini, G

    1999-11-01

    Dicarboxylic acids (DA) are alternate lipid substrates recently proposed in parenteral nutrition. Two new derivatives of DA, a triglyceride of sebacic (TGC10) and one of dodecanedioic (TGC12) acid have been synthesised in order to reduce the amount of sodium given with the unesterified forms. The present paper describes a rapid and direct high-performance liquid chromatographic method (HPLC) for the analysis of these substances in both plasma and urine. Thirty-six male Wistar rats were rapidly injected with 64 mg of TGC10 or 53 mg of TGC12. The triglycerides and their products of hydrolysis were measured in plasma samples taken at different times. For the dose of 500 ng the intra-assay variations ranged from 6. 80+/-0.35% for TGC10 to 18.6+/-3.20% for TGC12 and the inter-assay variations were from 4.44+/-2.21% for TGC10 to 15.0+/-6.72% for TGC12. The detection limit for both triglycerides was 5 ng. This rapid and direct HPLC method could have practical implications in monitoring the concentration of both triglycerides and free forms of DA in biological samples of patients who might benefit from the administration of these substances during parenteral nutrition regimens.

  19. Assessment of DDT levels in selected environmental media and biological samples from Mexico and Central America.

    Science.gov (United States)

    Pérez-Maldonado, Iván N; Trejo, Antonio; Ruepert, Clemens; Jovel, Reyna del Carmen; Méndez, Mónica Patricia; Ferrari, Mirtha; Saballos-Sobalvarro, Emilio; Alexander, Carlos; Yáñez-Estrada, Leticia; Lopez, Dania; Henao, Samuel; Pinto, Emilio R; Díaz-Barriga, Fernando

    2010-03-01

    Taking into account the environmental persistence and the toxicity of DDT, the Pan American Health Organization (PAHO) organized a surveillance program in Mesoamerica which included the detection of residual DDT in environmental (soil) and biological samples (fish tissue and children's blood). This program was carried out in communities from Mexico, Guatemala, El Salvador, Honduras, Nicaragua, Costa Rica and Panama. This paper presents the first report of that program. As expected, the results show that the levels for [summation operator] DDT in soil (outdoor or indoor) and fish samples in the majority of the locations studied are below guidelines. However, in some locations, we found children with high concentrations of DDT as in Mexico (mean level 50.2 ng/mL). Furthermore, in some communities and for some matrices, the DDT/DDE quotient is higher than one and this may reflect a recent DDT exposure. Therefore, more efforts are needed to avoid exposure and to prevent the reintroduction of DDT into the region. In this regard it is important to know that under the surveillance of PAHO and with the support of UNEP, a regional program in Mesoamerica for the collection and disposal of DDT and other POPs stockpiles is in progress. Copyright (c) 2009 Elsevier Ltd. All rights reserved.

  20. Synchrotron-based X-ray fluorescence imaging and elemental mapping from biological samples

    Energy Technology Data Exchange (ETDEWEB)

    D Rao; M Swapna; R Cesareo; A Brunetti; T Akatsuka; T Yuasa; T Takeda; G Gigante

    2011-12-31

    The present study utilized the new hard X-ray microspectroscopy beamline facility, X27A, available at NSLS, BNL, USA, for elemental mapping. This facility provided the primary beam in a small spot of the order of {approx}10 {mu}m, for focussing. With this spatial resolution and high flux throughput, the synchrotron-based X-ray fluorescent intensities for Mn, Fe, Zn, Cr, Ti and Cu were measured using a liquid-nitrogen-cooled 13-element energy-dispersive high-purity germanium detector. The sample is scanned in a 'step-and-repeat' mode for fast elemental mapping measurements and generated elemental maps at 8, 10 and 12 keV, from a small animal shell (snail). The accumulated trace elements, from these biological samples, in small areas have been identified. Analysis of the small areas will be better suited to establish the physiology of metals in specific structures like small animal shell and the distribution of other elements.

  1. Copper, chromium, manganese, iron, nickel, and zinc levels in biological samples of diabetes mellitus patients.

    Science.gov (United States)

    Kazi, Tasneem Gul; Afridi, Hassan Imran; Kazi, Naveed; Jamali, Mohammad Khan; Arain, Mohammad Bilal; Jalbani, Nussarat; Kandhro, Ghulam Abbas

    2008-04-01

    There is accumulating evidence that the metabolism of several trace elements is altered in diabetes mellitus and that these nutrients might have specific roles in the pathogenesis and progress of this disease. The aim of present study was to compare the level of essential trace elements, chromium (Cr), copper (Cu), iron (Fe), manganese (Mn), nickel (Ni), and zinc (Zn) in biological samples (whole blood, urine, and scalp hair) of patients who have diabetes mellitus type 2 (n = 257), with those of nondiabetic control subjects (n = 166), age ranged (45-75) of both genders. The element concentrations were measured by means of an atomic absorption spectrophotometer after microwave-induced acid digestion. The validity and accuracy was checked by conventional wet-acid-digestion method and using certified reference materials. The overall recoveries of all elements were found in the range of (97.60-99.49%) of certified values. The results of this study showed that the mean values of Zn, Mn, and Cr were significantly reduced in blood and scalp-hair samples of diabetic patients as compared to control subjects of both genders (p < 0.001). The urinary levels of these elements were found to be higher in the diabetic patients than in the age-matched healthy controls. In contrast, high mean values of Cu and Fe were detected in scalp hair and blood from patients versus the nondiabetic subjects, but the differences found in blood samples was not significant (p < 0.05). These results are consistent with those obtained in other studies, confirming that deficiency and efficiency of some essential trace metals may play a role in the development of diabetes mellitus.

  2. Psychopathic traits and reactive-proactive aggression in a large community sample of Polish adolescents.

    Science.gov (United States)

    Perenc, Lidia; Radochonski, Mieczyslaw

    2014-08-01

    This paper presents results of the only large-scale study carried-out in Poland to date on the prevalence of psychopathic traits and their relationship with aggressive behaviour in mainstream adolescents. The sample consists of 9,415 students (4,808 boys, 4,607 girls) in the first to third grades at 142 public secondary schools. Psychopathic traits were measured by teacher-report ratings with the antisocial process screening device (APSD), while aggressive behaviours were assessed using the Reactive-Proactive Aggression Questionnaire. Analysis of results revealed that boys scored much higher than girls in total APSD scale measuring psychopathic traits. Only 2.68% of assessed adolescents scored above the cut-off of 25 points. Results also showed significant correlations between psychopathic traits and both proactive and reactive aggression. The authors concluded that screening a large sample to identify children and youths with psychopathic traits has some important advantages but, on the other hand, it is a sensitive undertaking because of the label 'psychopath' can have negative consequences for the subjects.

  3. A large sample of binary quasars: Does quasar bias tracks from Mpc scale to kpc scales?

    Science.gov (United States)

    Eftekharzadeh, Sarah; Myers, Adam D.; Djorgovski, Stanislav G.; Graham, Matthew J.

    2017-01-01

    We present the most precise estimate to date of the bias of quasars on very small scales, based on a measurement of the clustering of 47 spectroscopically confirmed binary quasars with proper transverse separations of ~25 h^{-1} kpc. The quasars in our sample, which is an order-of-magnitude larger than previous samples, are targeted using a Kernel Density Estimation technique (KDE) applied to Sloan Digital Sky Survey (SDSS) imaging over most of the SDSS area. Our sample is "complete," in that all possible pairs of binary quasars across our area of interest have been spectroscopically confirmed from a combination of previous surveys and our own long-slit observational campaign. We determine the projected correlation function of quasars (\\bar W_p) in four bins of proper transverse scale over the range 17.0 \\lesssim R_{prop} \\lesssim 36.2 h^{-1} kpc. Due to our large sample size, our measured projected correlation function in each of these four bins of scale is more than twice as precise as any previous measurement made over our {\\em full} range of scales. We also measure the bias of our quasar sample in four slices of redshift across the range 0.43 \\le z \\le 2.26 and compare our results to similar measurements of how quasar bias evolves on Mpc-scales. This measurement addresses the question of whether it is reasonable to assume that quasar bias evolves with redshift in a similar fashion on both Mpc and kpc scales. Our results can meaningfully constrain the one-halo term of the Halo Occupation Distribution (HOD) of quasars and how it evolves with redshift. This work was partially supported by NSF grant 1515404.

  4. Evaluation of arsenic, cobalt, copper and manganese in biological Samples of Steel mill workers by electrothermal atomic absorption Spectrometry.

    Science.gov (United States)

    Afridi, H I; Kazi, T G; Kazi, N G; Jamali, M K; Arain, M B; Sirajuddin; Kandhro, G A; Shah, A Q; Baig, J A

    2009-02-01

    The determination of trace and toxic elements in biological samples (blood, urine and scalp hair samples) of human beings is an important clinical test. The aim of our present study was to determine the concentration of arsenic (As), copper (Cu), cobalt (Co) and manganese (Mn), in biological samples of male production workers (PW) and quality control workers (QW) of steel mill, with aged 25-55 years, to assess the possible influence of environmental exposure. For comparison purpose, the same biological samples of unexposed healthy males of same age group were collected as control subjects. The determination of all elements in biological samples was carried out by electrothermal atomic absorption spectrometry, prior to microwave assisted acid digestion. The accuracy of the As, Cu, Co and Mn measurements was tested by simultaneously analyzing certified reference materials (CRMs) and for comparative purposes conventional wet acid digestion method was used on the same CRMs. No significant differences were observed between the analytical results and the certified values, using both methods (paired t-test at P > 0.05). The results indicate that concentrations of As, Cu, Co and Mn in all three biological samples of the exposed workers (QW and PW) were significantly higher than those of the controls. The possible correlation of these elements with the etiology of different physiological disorders is discussed. The results were also demonstrated the need of attention for improvements in workplace, ventilation and industrial hygiene practices.

  5. The Nature of Discourse throughout 5E Lessons in a Large Enrolment College Biology Course

    Science.gov (United States)

    Sickel, Aaron J.; Witzig, Stephen B.; Vanmali, Binaben H.; Abell, Sandra K.

    2013-04-01

    Large enrolment science courses play a significant role in educating undergraduate students. The discourse in these classes usually involves an instructor lecturing with little or no student participation, despite calls from current science education reform documents to elicit and utilize students' ideas in teaching. In this study, we used the 5E instructional model to develop and implement four lessons in a large enrolment introductory biology course with multiple opportunities for teacher-student and student-student interaction. Data consisted of video and audio recordings of whole-class and small-group discussions that took place throughout the study. We then used a science classroom discourse framework developed by Mortimer and Scott (2003) to characterize the discursive interactions in each 5E lesson phase. Analysis of the data resulted in two assertions. First, the purpose, communicative approach, patterns of discourse, and teaching interventions were unique to each 5E lesson phase. Second, the type of lesson topic influenced the content of the discourse. We discuss how the findings help characterize the discourse of each phase in a 5E college science lesson and propose a model to understand internalization through discursive interaction using this reform-based approach. We conclude with implications for facilitating discourse in college science lessons and future research. This study provides support for using the discourse framework to characterize discursive interaction in college science courses.

  6. Recent excitements in protein NMR: Large proteins and biologically relevant dynamics

    Indian Academy of Sciences (India)

    SAI CHAITANYA CHILIVERI; MANDAR V DESHMUKH

    2016-12-01

    The advent of Transverse Relaxation Optimized SpectroscopY (TROSY) and perdeuteration allowed biomolecularNMR spectroscopists to overcome the size limitation barrier (~20 kDa) in de novo structure determination of proteins.The utility of these techniques was immediately demonstrated on large proteins and protein complexes (e.g. GroELGroES,ClpP protease, Hsp90-p53, 20S proteasome, etc.). Further, recent methodological developments such asResidual Dipolar Couplings and Paramagnetic Relaxation Enhancement allowed accurate measurement of long-rangestructural restraints. Additionally, Carr-Purcell-Meiboom-Gill (CPMG), rotating frame relaxation experiments (R1ρ)and saturation transfer experiments (CEST and DEST) created never-before accessibility to the μs–ms timescaledynamic parameters that led to the deeper understanding of biological processes. Meanwhile, the excitement in thefield continued with a series of developments in the fast data acquisition methods allowing rapid structural studies onless stable proteins. This review aims to discuss important developments in the field of biomolecular NMRspectroscopy in the recent past, i.e., in the post TROSY era. These developments not only gave access to the structuralstudies of large protein assemblies, but also revolutionized tools in the arsenal of today’s biomolecular NMR and pointto a bright future of biomolecular NMR spectroscopy.

  7. Decommissioning samples from the Ft. Lewis, WA, solvent refined coal pilot plant: chemical analysis and biological testing

    Energy Technology Data Exchange (ETDEWEB)

    Weimer, W.C.; Wright, C.W.

    1985-10-01

    This report presents the results from chemical analyses and limited biological assays of three sets of samples from the Ft. Lewis, WA solvent refined coal (SRC) pilot plant. The samples were collected during the process of decommissioning this facility. Chemical composition was determined for chemical class fractions of the samples by using high-resolution gas chromatography (GC), high-resolution GC/mass spectrometry (MS) and high-resolution MS. Biological activity was measuring using both the histidine reversion microbial mutagenicity assay with Salmonella typhimurium, TA98 and an initiation/promotion mouse-skin tumorigenicity assay. 19 refs., 7 figs., 27 tabs.

  8. Characterising resting-state functional connectivity in a large sample of adults with ADHD.

    Science.gov (United States)

    Mostert, Jeanette C; Shumskaya, Elena; Mennes, Maarten; Onnink, A Marten H; Hoogman, Martine; Kan, Cornelis C; Arias Vasquez, Alejandro; Buitelaar, Jan; Franke, Barbara; Norris, David G

    2016-06-03

    Attention-deficit/hyperactivity disorder (ADHD) is a common childhood psychiatric disorder that often persists into adulthood. While several studies have identified altered functional connectivity in brain networks during rest in children with ADHD, few studies have been performed on adults with ADHD. Existing studies have generally investigated small samples. We therefore investigated aberrant functional connectivity in a large sample of adult patients with childhood-onset ADHD, using a data-driven, whole-brain approach. Adults with a clinical ADHD diagnosis (N=99) and healthy, adult comparison subjects (N=113) underwent a 9-minute resting-state fMRI session in a 1.5T MRI scanner. After elaborate preprocessing including a thorough head-motion correction procedure, group independent component analysis (ICA) was applied from which we identified six networks of interest: cerebellum, executive control, left and right frontoparietal and two default-mode networks. Participant-level network maps were obtained using dual-regression and tested for differences between patients with ADHD and controls using permutation testing. Patients showed significantly stronger connectivity in the anterior cingulate gyrus of the executive control network. Trends were also observed for stronger connectivity in the cerebellum network in ADHD patients compared to controls. However, there was considerable overlap in connectivity values between patients and controls, leading to relatively low effect sizes despite the large sample size. These effect sizes were slightly larger when testing for correlations between hyperactivity/impulsivity symptoms and connectivity strength in the executive control and cerebellum networks. This study provides important insights for studies on the neurobiology of adult ADHD; it shows that resting-state functional connectivity differences between adult patients and controls exist, but have smaller effect sizes than existing literature suggested.

  9. Reconstruction of large, irregularly sampled multidimensional images. A tensor-based approach.

    Science.gov (United States)

    Morozov, Oleksii Vyacheslav; Unser, Michael; Hunziker, Patrick

    2011-02-01

    Many practical applications require the reconstruction of images from irregularly sampled data. The spline formalism offers an attractive framework for solving this problem; the currently available methods, however, are hard to deploy for large-scale interpolation problems in dimensions greater than two (3-D, 3-D+time) because of an exponential increase of their computational cost (curse of dimensionality). Here, we revisit the standard regularized least-squares formulation of the interpolation problem, and propose to perform the reconstruction in a uniform tensor-product B-spline basis as an alternative to the classical solution involving radial basis functions. Our analysis reveals that the underlying multilinear system of equations admits a tensor decomposition with an extreme sparsity of its one dimensional components. We exploit this property for implementing a parallel, memory-efficient system solver. We show that the computational complexity of the proposed algorithm is essentially linear in the number of measurements and that its dependency on the number of dimensions is significantly less than that of the original sparse matrix-based implementation. The net benefit is a substantial reduction in memory requirement and operation count when compared to standard matrix-based algorithms, so that even 4-D problems with millions of samples become computationally feasible on desktop PCs in reasonable time. After validating the proposed algorithm in 3-D and 4-D, we apply it to a concrete imaging problem: the reconstruction of medical ultrasound images (3-D+time) from a large set of irregularly sampled measurements, acquired by a fast rotating ultrasound transducer.

  10. Prevalence and correlates of problematic smartphone use in a large random sample of Chinese undergraduates.

    Science.gov (United States)

    Long, Jiang; Liu, Tie-Qiao; Liao, Yan-Hui; Qi, Chang; He, Hao-Yu; Chen, Shu-Bao; Billieux, Joël

    2016-11-17

    Smartphones are becoming a daily necessity for most undergraduates in Mainland China. Because the present scenario of problematic smartphone use (PSU) is largely unexplored, in the current study we aimed to estimate the prevalence of PSU and to screen suitable predictors for PSU among Chinese undergraduates in the framework of the stress-coping theory. A sample of 1062 undergraduate smartphone users was recruited by means of the stratified cluster random sampling strategy between April and May 2015. The Problematic Cellular Phone Use Questionnaire was used to identify PSU. We evaluated five candidate risk factors for PSU by using logistic regression analysis while controlling for demographic characteristics and specific features of smartphone use. The prevalence of PSU among Chinese undergraduates was estimated to be 21.3%. The risk factors for PSU were majoring in the humanities, high monthly income from the family (≥1500 RMB), serious emotional symptoms, high perceived stress, and perfectionism-related factors (high doubts about actions, high parental expectations). PSU among undergraduates appears to be ubiquitous and thus constitutes a public health issue in Mainland China. Although further longitudinal studies are required to test whether PSU is a transient phenomenon or a chronic and progressive condition, our study successfully identified socio-demographic and psychological risk factors for PSU. These results, obtained from a random and thus representative sample of undergraduates, opens up new avenues in terms of prevention and regulation policies.

  11. Determination of As, Cd, Cu, Hg and Pb in biological samples by modern electrothermal atomic absorption spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Sardans, Jordi, E-mail: j.sardans@creaf.uab.ca [Ecophysiological and Global Change Unit CSIC-CREAF, Edifici C, Universitat Autonoma de Barcelona, Bellaterra 08193, Barcelona (Spain); Montes, Fernando [Departamento de Ciencias Analiticas, Facultad de Ciencias, Universidad Nacional de Educacion a Distancia (UNED), C/ Senda del Rey 9. 28040 Madrid (Spain); Penuelas, Josep [Ecophysiological and Global Change Unit CSIC-CREAF, Edifici C, Universitat Autonoma de Barcelona, Bellaterra 08193, Barcelona (Spain)

    2010-02-15

    Pollution from heavy metals has increased in recent decades and has become an important concern for environmental agencies. Arsenic, cadmium, copper, mercury and lead are among the trace elements that have the greatest impact and carry the highest risk to human health. Electrothermal atomic absorption spectrometry (ETAAS) has long been used for trace element analyses and over the past few years, the main constraints of atomic absorption spectrometry (AAS) methods, namely matrix interferences that provoked high background absorption and interferences, have been reduced. The use of new, more efficient modifiers and in situ trapping methods for stabilization and pre-concentration of these analytes, progress in control of atomization temperatures, new designs of atomizers and advances in methods to correct background spectral interferences have permitted an improvement in sensitivity, an increase in detection power, reduction in sample manipulation, and increase in the reproducibility of the results. These advances have enhanced the utility of Electrothermal atomic absorption spectrometry (ETAAS) for trace element determination at mug L{sup -1} levels, especially in difficult matrices, giving rise to greater reproducibility, lower economic cost and ease of sample pre-treatment compared to other methods. Moreover, the recent introduction of high resolution continuum source Electrothermal atomic absorption spectrometry (HR-CS-ETAAS) has facilitated direct solid sampling, reducing background noise and opening the possibility of achieving even more rapid quantitation of some elements. The incorporation of flow injection analysis (FIA) systems for automation of sample pre-treatment, as well as chemical vapor generation renders (ETAAS) into a feasible option for detection of As and Hg in environmental and food control studies wherein large numbers of samples can be rapidly analyzed. A relatively inexpensive approach with low sample consumption provide additional advantages

  12. The large universal Pantoea plasmid LPP-1 plays a major role in biological and ecological diversification.

    Science.gov (United States)

    De Maayer, Pieter; Chan, Wai-Yin; Blom, Jochen; Venter, Stephanus N; Duffy, Brion; Smits, Theo H M; Coutinho, Teresa A

    2012-11-15

    Pantoea spp. are frequently isolated from a wide range of ecological niches and have various biological roles, as plant epi- or endophytes, biocontrol agents, plant-growth promoters or as pathogens of both plant and animal hosts. This suggests that members of this genus have undergone extensive genotypic diversification. One means by which this occurs among bacteria is through the acquisition and maintenance of plasmids. Here, we have analyzed and compared the sequences of a large plasmid common to all sequenced Pantoea spp. The Large PantoeaPlasmids (LPP-1) of twenty strains encompassing seven different Pantoea species, including pathogens and endo-/epiphytes of a wide range of plant hosts as well as insect-associated strains, were compared. The LPP-1 plasmid sequences range in size from ~281 to 794 kb and carry between 238 and 750 protein coding sequences (CDS). A core set of 46 proteins, encompassing 2.2% of the total pan-plasmid (2,095 CDS), conserved among all LPP-1 plasmid sequences, includes those required for thiamine and pigment biosynthesis. Phylogenetic analysis reveals that these plasmids have arisen from an ancestral plasmid, which has undergone extensive diversification. Analysis of the proteins encoded on LPP-1 also showed that these plasmids contribute to a wide range of Pantoea phenotypes, including the transport and catabolism of various substrates, inorganic ion assimilation, resistance to antibiotics and heavy metals, colonization and persistence in the host and environment, pathogenesis and antibiosis. LPP-1 is universal to all Pantoea spp. whose genomes have been sequenced to date and is derived from an ancestral plasmid. LPP-1 encodes a large array of proteins that have played a major role in the adaptation of the different Pantoea spp. to their various ecological niches and their specialization as pathogens, biocontrol agents or benign saprophytes found in many diverse environments.

  13. The large universal Pantoea plasmid LPP-1 plays a major role in biological and ecological diversification

    Directory of Open Access Journals (Sweden)

    De Maayer Pieter

    2012-11-01

    Full Text Available Abstract Background Pantoea spp. are frequently isolated from a wide range of ecological niches and have various biological roles, as plant epi- or endophytes, biocontrol agents, plant-growth promoters or as pathogens of both plant and animal hosts. This suggests that members of this genus have undergone extensive genotypic diversification. One means by which this occurs among bacteria is through the acquisition and maintenance of plasmids. Here, we have analyzed and compared the sequences of a large plasmid common to all sequenced Pantoea spp. Results and discussion The Large PantoeaPlasmids (LPP-1 of twenty strains encompassing seven different Pantoea species, including pathogens and endo-/epiphytes of a wide range of plant hosts as well as insect-associated strains, were compared. The LPP-1 plasmid sequences range in size from ~281 to 794 kb and carry between 238 and 750 protein coding sequences (CDS. A core set of 46 proteins, encompassing 2.2% of the total pan-plasmid (2,095 CDS, conserved among all LPP-1 plasmid sequences, includes those required for thiamine and pigment biosynthesis. Phylogenetic analysis reveals that these plasmids have arisen from an ancestral plasmid, which has undergone extensive diversification. Analysis of the proteins encoded on LPP-1 also showed that these plasmids contribute to a wide range of Pantoea phenotypes, including the transport and catabolism of various substrates, inorganic ion assimilation, resistance to antibiotics and heavy metals, colonization and persistence in the host and environment, pathogenesis and antibiosis. Conclusions LPP-1 is universal to all Pantoea spp. whose genomes have been sequenced to date and is derived from an ancestral plasmid. LPP-1 encodes a large array of proteins that have played a major role in the adaptation of the different Pantoea spp. to their various ecological niches and their specialization as pathogens, biocontrol agents or benign saprophytes found in many diverse

  14. Rapid Preparation Methods of Biological Samples for Ionic Compounds Using Ion Exchange Type Monolithic Silica Spin Column

    OpenAIRE

    宮崎, 将太; 山田, 智子; 太田, 茂徳; 斉藤, 剛; 奈女良, 昭; 大平, 真義

    2010-01-01

    We developed a device comprising a spin column packed with ion exchange type (SCX and SAX) monolithic silica for extracting ionic compounds from biological samples. The methods involving the use of these spin column are not useful for the extraction of ionic analytes, but are highly reproducible for the analysis in serum and urine. This spin column enabled sample preparation in less than 10 min. Handling such as sample loading, washing, and elution of analytes, was exhibited by the centrifuga...

  15. Nanoparticle sensor for label free detection of swine DNA in mixed biological samples

    Energy Technology Data Exchange (ETDEWEB)

    Ali, M E; Hashim, U [Institute of Nano Electronic Engineering (INNE), Universiti Malaysia Perlis, Lot 104-108, Tingkat 1, Block A, Taman Pertiwi Indah, Jalan Kangar-Alor Star, Seriab, 01000 Kangar, Perlis (Malaysia); Mustafa, S; Che Man, Y B; Yusop, M H M [Halal Products Research Institute, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor (Malaysia); Bari, M F [School of Materials Engineering, University Malaysia Perlis, Seriab 01000, Kangar, Perlis (Malaysia); Islam, Kh N [Department of Preclinical Sciences, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor (Malaysia); Hasan, M F, E-mail: uda@unimap.edu.my [Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor (Malaysia)

    2011-05-13

    We used 40 {+-} 5 nm gold nanoparticles (GNPs) as colorimetric sensor to visually detect swine-specific conserved sequence and nucleotide mismatch in PCR-amplified and non-amplified mitochondrial DNA mixtures to authenticate species. Colloidal GNPs changed color from pinkish-red to gray-purple in 2 mM PBS. Visually observed results were clearly reflected by the dramatic reduction of surface plasmon resonance peak at 530 nm and the appearance of new features in the 620-800 nm regions in their absorption spectra. The particles were stabilized against salt-induced aggregation upon the adsorption of single-stranded DNA. The PCR products, without any additional processing, were hybridized with a 17-base probe prior to exposure to GNPs. At a critical annealing temperature (55 {sup 0}C) that differentiated matched and mismatched base pairing, the probe was hybridized to pig PCR product and dehybridized from the deer product. The dehybridized probe stuck to GNPs to prevent them from salt-induced aggregation and retained their characteristic red color. Hybridization of a 27-nucleotide probe to swine mitochondrial DNA identified them in pork-venison, pork-shad and venison-shad binary admixtures, eliminating the need of PCR amplification. Thus the assay was applied to authenticate species both in PCR-amplified and non-amplified heterogeneous biological samples. The results were determined visually and validated by absorption spectroscopy. The entire assay (hybridization plus visual detection) was performed in less than 10 min. The LOD (for genomic DNA) of the assay was 6 {mu}g ml{sup -1} swine DNA in mixed meat samples. We believe the assay can be applied for species assignment in food analysis, mismatch detection in genetic screening and homology studies between closely related species.

  16. Fast screening of ketamine in biological samples based on molecularly imprinted photonic hydrogels

    Energy Technology Data Exchange (ETDEWEB)

    Meng, Liang [Department of Forensic Science, People' s Public Security University of China, Beijing (China); Meng, Pinjia, E-mail: mengpinjia@163.com [Department of Forensic Science, People' s Public Security University of China, Beijing (China); Zhang, Qingqing; Wang, Yanji [Department of Forensic Science, People' s Public Security University of China, Beijing (China)

    2013-04-10

    Graphical abstract: A novel label-free colorimetric chemosensor: with the increase in the concentration of ketamine, the Bragg diffraction peak of MIPHs gradually shifted to the longer wavelength region. Accompanying the peak shift, the color change of MIPHs was also observed obviously: from green to red. Highlights: ► We developed the label-free colorimetric MIPHs for handy and fast screening of ketamine. ► The obvious color change of MIPHs was observed upon ketamine. ► The MIPHs exhibited good sensing abilities in an aqueous environment. ► The sensing mechanisms of the water-compatible MIPHs were investigated. ► The MIPHs were employed to screening ketamine in real biological samples. -- Abstract: A novel label-free colorimetric chemosensor was developed for handy and fast screening of ketamine with high sensitivity and specificity based on molecularly imprinted photonic hydrogels (MIPHs) that combined the colloidal-crystal with molecular imprinting technique. The unique inverse opal arrays with a thin polymer wall in which the imprinted nanocavities of ketamine moleculars distributed allowed high sensitive, quick responsive, specific detection of the target analyte, and good regenerating ability in an aqueous environment. Due to the hierarchical inverse opal structural characteristics, the specific ketamine molecular recognition process can induce obvious swelling of the MIPHs to be directly transferred into visually perceptible optical signal (change in color) which can be detected by the naked eye through Bragg diffractive shifts of ordered macroporous arrays. In order to enhance the recognition ability in aqueous environments, the MIPHs were designed as water-compatible and synthesized in a water–methanol system. The molecular recognition mechanisms were investigated. The proposed MIPHs were successfully employed to screen trace level ketamine in human urine and saliva samples, exhibiting high sensitivity, rapid response, and specificity in the

  17. Nanoparticle sensor for label free detection of swine DNA in mixed biological samples

    Science.gov (United States)

    Ali, M. E.; Hashim, U.; Mustafa, S.; Che Man, Y. B.; Yusop, M. H. M.; Bari, M. F.; Islam, Kh N.; Hasan, M. F.

    2011-05-01

    We used 40 ± 5 nm gold nanoparticles (GNPs) as colorimetric sensor to visually detect swine-specific conserved sequence and nucleotide mismatch in PCR-amplified and non-amplified mitochondrial DNA mixtures to authenticate species. Colloidal GNPs changed color from pinkish-red to gray-purple in 2 mM PBS. Visually observed results were clearly reflected by the dramatic reduction of surface plasmon resonance peak at 530 nm and the appearance of new features in the 620-800 nm regions in their absorption spectra. The particles were stabilized against salt-induced aggregation upon the adsorption of single-stranded DNA. The PCR products, without any additional processing, were hybridized with a 17-base probe prior to exposure to GNPs. At a critical annealing temperature (55 °C) that differentiated matched and mismatched base pairing, the probe was hybridized to pig PCR product and dehybridized from the deer product. The dehybridized probe stuck to GNPs to prevent them from salt-induced aggregation and retained their characteristic red color. Hybridization of a 27-nucleotide probe to swine mitochondrial DNA identified them in pork-venison, pork-shad and venison-shad binary admixtures, eliminating the need of PCR amplification. Thus the assay was applied to authenticate species both in PCR-amplified and non-amplified heterogeneous biological samples. The results were determined visually and validated by absorption spectroscopy. The entire assay (hybridization plus visual detection) was performed in less than 10 min. The LOD (for genomic DNA) of the assay was 6 µg ml - 1 swine DNA in mixed meat samples. We believe the assay can be applied for species assignment in food analysis, mismatch detection in genetic screening and homology studies between closely related species.

  18. Electronic noses for monitoring benzene occupational exposure in biological samples of Egyptian workers

    Directory of Open Access Journals (Sweden)

    Ehab I. Mohamed

    2013-02-01

    Full Text Available Objectives: Benzene is commonly emitted in several industries, leading to widespread environmental and occupational exposure hazards. While less toxic solvents have been substituted for benzene, it is still a component of petroleum products and is a trace impurity in industrial products resulting in continued higher occupational exposures in industrial settings in developing countries. Materials and Methods: We investigated the potential use of an electronic nose (e-nose to monitor the headspace volatiles in biological samples from benzene-exposed Egyptian workers and non-exposed controls. The study population comprised 150 non-smoking male workers exposed to benzene and an equal number of matching non-exposed controls. We determined biomarkers of benzene used to estimate exposure and risk including: benzene in exhaled air and blood; and its urinary metabolites such as phenol and muconic acid using gas chromatography technique and a portable e-nose. Results: The average benzene concentration measured in the ambient air of the workplace of all studied industrial settings in Alexandria, Egypt; was 97.56±88.12 μg/m3 (range: 4.69–260.86 μg/m3. Levels of phenol and muconic acid were signifi cantly (p < 0.001 higher in both blood and urine of benzene-exposed workers as compared to non-exposed controls. Conclusions: The e-nose technology has successfully classifi ed and distinguished benzene-exposed workers from non-exposed controls for all measured samples of blood, urine and the exhaled air with a very high degree of precision. Thus, it will be a very useful tool for the low-cost mass screening and early detection of health hazards associated with the exposure to benzene in the industry.

  19. Nanoparticle sensor for label free detection of swine DNA in mixed biological samples.

    Science.gov (United States)

    Ali, M E; Hashim, U; Mustafa, S; Man, Y B Che; Yusop, M H M; Bari, M F; Islam, Kh N; Hasan, M F

    2011-05-13

    We used 40 ± 5 nm gold nanoparticles (GNPs) as colorimetric sensor to visually detect swine-specific conserved sequence and nucleotide mismatch in PCR-amplified and non-amplified mitochondrial DNA mixtures to authenticate species. Colloidal GNPs changed color from pinkish-red to gray-purple in 2 mM PBS. Visually observed results were clearly reflected by the dramatic reduction of surface plasmon resonance peak at 530 nm and the appearance of new features in the 620-800 nm regions in their absorption spectra. The particles were stabilized against salt-induced aggregation upon the adsorption of single-stranded DNA. The PCR products, without any additional processing, were hybridized with a 17-base probe prior to exposure to GNPs. At a critical annealing temperature (55 °C) that differentiated matched and mismatched base pairing, the probe was hybridized to pig PCR product and dehybridized from the deer product. The dehybridized probe stuck to GNPs to prevent them from salt-induced aggregation and retained their characteristic red color. Hybridization of a 27-nucleotide probe to swine mitochondrial DNA identified them in pork-venison, pork-shad and venison-shad binary admixtures, eliminating the need of PCR amplification. Thus the assay was applied to authenticate species both in PCR-amplified and non-amplified heterogeneous biological samples. The results were determined visually and validated by absorption spectroscopy. The entire assay (hybridization plus visual detection) was performed in less than 10 min. The LOD (for genomic DNA) of the assay was 6 µg ml(-1) swine DNA in mixed meat samples. We believe the assay can be applied for species assignment in food analysis, mismatch detection in genetic screening and homology studies between closely related species.

  20. BORRELIA BURGDORFERI DNA IN BIOLOGICAL SAMPLES FROM PATIENTS WITH SARCOIDOSIS USING THE POLYMERASE CHAIN REACTION TECHNIQUE

    Institute of Scientific and Technical Information of China (English)

    连伟; 罗慰慈

    1995-01-01

    Polymerase chain reaction (PCR) was used to detect the presence of Borretia burgdoferi DNA in biological samples from patients with sarcoidcsis. The target DNA sequence was of chromosomal origin. The amplified DNA sequence was analyzed by agarose gel electrophoresis, PAGE with silver staining, and the identity of amplified DNA was confirmed by restriction enzyme cleavage and DNA-DNA hybridlzation with a 32P-labelled probe. The assay was sensitive to fewer than two copies of B. burgdor feri genome, even in the presence of a 104-fold excess of human eukaryotic DNA, and was also specific to different B. burgdorferl strains tested. Sera seroiogieally positive to B. burgdorferi (n=26), broncbemlveolar lavage fluid and supematant of BALF (n=26) and peripheral blood (n=9) from sarcoidosis patients were tested. The positive rate was low (4/26, 2/26, and 0/9, respectively). It was considered that DNA from B. bur gdor feri may be identified in a minority of patients with s,arcoidosis, and it may play a pathogenetic rote in such cases. More studies need to be done before advancing the hypothesis of an etiologic role of B. burgdorferi in sarcoidosis.

  1. Development of novel separation techniques for biological samples in capillary electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Huan -Tsung [Iowa State Univ., Ames, IA (United States)

    1994-07-27

    This dissertation includes three different topics: general introduction of capillary electrophoresis (CE); gradient in CE and CE in biological separations; and capillary gel electrophoresis (CGE) for DNA separation. Factors such as temperature, viscosity, pH, and the surface of capillary walls affecting the separation performance are demonstrated. A pH gradient between 3.0 and 5.2 is useful to improve the resolution among eight different organic acids. A flow gradient due to the change in the concentration of surfactant, which is able to coat to the capillary wall to change the flow rate and its direction, is also shown as a good way to improve the resolution for organic compounds. A temperature gradient caused by joule heat is shown by voltage programming to enhance the resolution and shorten the separation time for several phenolic compounds. The author also shows that self-regulating dynamic control of electroosmotic flow in CE by simply running separation in different concentrations of surfactant has less matrix effect on the separation performance. One of the most important demonstrations in this dissertation is that the author proposes on-column reaction which gives several advantages including the use of a small amount of sample, low risk of contamination, and time saving and kinetic features. The author uses this idea with laser induced fluorescence (LIF) as a detection mode to detect an on-column digestion of sub-ng of protein. This technique also is applied to single cell analysis in the group.

  2. Analytical procedure for the determination of zearalenone in environmental and biological samples.

    Science.gov (United States)

    Kwaśniewska, Katarzyna; Gadzała-Kopciuch, Renata; Cendrowski, Krzysztof

    2015-01-01

    The metabolism of zearalenone (ZEA) and analytical methods for determining the presence of ZEA and its metabolites are discussed in this study. Similar to phytoestrogens, solid metaloestrogens, pharmaceuticals, and selected pesticides, ZEA is a substance that displays endocrine activity. ZEA is accumulated in living organisms, and it is capable of contaminating all trophic levels of the food chain, from grain, maize, and other crop plants to human consumers. Zearalenone has a structure similar to that of estrogen (the presence of a macrocyclic lactone ring), it has an affinity for estrogen receptors, and it competes with 17β-estradiol for binding the estrogen receptor in natural pathways. As endocrine disruptors, zearalenone and its metabolites can also contribute to carcinogenic mutations associated with female secondary sex characteristics. The determination of zearalenone and its metabolites in various matrices, first of all biological and environmental samples, poses significant problems. A variety ways of extracting and purifying zearalenone, including liquid-liquid extraction and solid-phase extraction, are described. Furthermore, it describes the possibility of applying a plurality of sensitive and specific instrumental methods, chromatographic techniques (TLC, HPLC, GC) as well as other methods (immunoaffinity chromatography).

  3. Analysis of six relevant toxaphene congeners in biological samples using ion trap MS/MS.

    Science.gov (United States)

    Gouteux, Bruno; Lebeuf, Michel; Trottier, Steve; Gagné, Jean-Pierre

    2002-10-01

    The quantification of six polychlorinated bornanes (CHBs) was studied using ion trap MS/MS. The significance of the selection of parent ions (Ip) and daughter ions (Id) on the detection of these toxaphene congeners was assessed in standard solution and biological samples. Our results indicate that different Ip and Id, selected at either low or high mass-to-charge (m/z) ratios, influence drastically the response factor of the CHBs and the chemical noise observed. For the octachlorinated toxaphene congeners (Parlar-26 (P-26), Parlar-40/41 (P-40/41), Parlar-44 (P-44)), the detection performance of the ion trap MS/MS is similar whether Ip and Id were chosen at low or high m/z ratios. However, the selection of Ip and Id at high m/z ratios clearly enhances the detection of the nonachlorinated toxaphene congeners (Parlar-50 (P-50), Parlar-62 (P-62)). The improved method, which selects Ip and Id at low m/z ratios for P-26, P-40/41 and P-44 and at high m/z ratios for P-50 and P-62, permitted to obtain low detection limits as well as repeatable and accurate results.

  4. Development of a new catalase activity assay for biological samples using optical CUPRAC sensor

    Science.gov (United States)

    Bekdeşer, Burcu; Özyürek, Mustafa; Güçlü, Kubilay; Alkan, Fulya Üstün; Apak, Reşat

    2014-11-01

    A novel catalase activity assay was developed for biological samples (liver and kidney tissue homogenates) using a rapid and low-cost optical sensor-based ‘cupric reducing antioxidant capacity' (CUPRAC) method. The reagent, copper(II)-neocuproine (Cu(II)-Nc) complex, was immobilized onto a cation-exchanger film of Nafion, and the absorbance changes associated with the formation of the highly-colored Cu(I)-Nc chelate as a result of reaction with hydrogen peroxide (H2O2) was measured at 450 nm. When catalase was absent, H2O2 produced the CUPRAC chromophore, whereas catalase, being an effective H2O2 scavenger, completely annihilated the CUPRAC signal due to H2O2. Thus, the CUPRAC absorbance due to H2O2 oxidation concomitant with Cu(I)-Nc formation decreased proportionally with catalase. The developed sensor gave a linear response over a wide concentration range of H2O2 (0.68-78.6 μM). This optical sensor-based method applicable to tissue homogenates proved to be efficient for low hydrogen peroxide concentrations (physiological and nontoxic levels) to which the widely used UV method is not accurately responsive. Thus, conventional problems of the UV method arising from relatively low sensitivity and selectivity, and absorbance disturbance due to gaseous oxygen evolution were overcome. The catalase findings of the proposed method for tissue homogenates were statistically alike with those of HPLC.

  5. Microwave-accelerated bioassay technique for rapid and quantitative detection of biological and environmental samples.

    Science.gov (United States)

    Mohammed, Muzaffer; Syed, Maleeha F; Aslan, Kadir

    2016-01-15

    Quantitative detection of molecules of interest from biological and environmental samples in a rapid manner, particularly with a relevant concentration range, is imperative to the timely assessment of human diseases and environmental issues. In this work, we employed the microwave-accelerated bioassay (MAB) technique, which is based on the combined use of circular bioassay platforms and microwave heating, for rapid and quantitative detection of Glial Fibrillary Acidic Protein (GFAP) and Shiga like toxin (STX 1). The proof-of-principle use of the MAB technique with the circular bioassay platforms for the rapid detection of GFAP in buffer based on colorimetric and fluorescence readouts was demonstrated with a 900W kitchen microwave. We also employed the MAB technique with a new microwave system (called the iCrystal system) for the detection of GFAP from mice with brain injuries and STX 1 from a city water stream. Control bioassays included the commercially available gold standard bioassay kits run at room temperature. Our results show that the lower limit of detection (LLOD) of the colorimetric and fluorescence based bioassays for GFAP was decreased by ~1000 times using the MAB technique and our circular bioassay platforms as compared to the commercially available bioassay kits. The overall bioassay time for GFAP and STX 1 was reduced from 4h using commercially available bioassay kits to 10min using the MAB technique.

  6. Substrate-zymography: a still worthwhile method for gelatinases analysis in biological samples.

    Science.gov (United States)

    Ricci, Serena; D'Esposito, Vittoria; Oriente, Francesco; Formisano, Pietro; Di Carlo, Angelina

    2016-08-01

    Matrix metallo-proteinases (MMPs) are a family of zinc-dependent endopeptidases, capable of degrading all the molecular components of extracellular matrix. A class of MMPs is gelatinases which includes gelatinase A or MMP-2 (72 kDa) and gelatinase B or MMP-9 (92 kDa), which have been shown to play critical roles in pathophysiology of many human disease and, in particular, cancer progression. For these reasons they obtained a great interest as potential non-invasive biomarker in providing useful clinical information in cancer diagnosis and therapy. A sensitive and unexpensive method for analysis of gelatinases is the gelatine zymography, which allows to measure the relative amounts of active and inactive enzymes in body fluids and tissue extracts. The procedure involves the electrophoretic separation of proteins under denaturing but non reducing conditions through a polyacrylamide gel containing a synthetic substrate (gelatin). The aim of this mini-review has been to describe the general principles of gelatine zymography technique, underling the main advantages and disadvantages. Even though an improvement of this method is necessary for a better applicability in laboratory medicine, gelatine zymography represents the most convenient method to detect the activity of the different gelatinases from a wide range of biological samples.

  7. Cyclopentanone thiosemicarbazone, a new complexing agent for copper determination in biological samples by adsorptive stripping voltammetry.

    Science.gov (United States)

    Mahajan, Rakesh Kumar; Walia, T P S; Sumanjit; Lobana, T S

    2006-03-01

    A selective and sensitive stripping voltammetric method for the determination of trace amounts of copper(II) with cyclopentanone thiosemicarbazone (CPTSC) is presented. The method is based on the adsorptive accumulation of the resulting copper-CPTSC complex on a hanging mercury drop electrode, followed by the stripping voltammetric measurements at the reduction current of the adsorbed complex at -0.37 V vs. Ag/AgCl. The optimal conditions for the stripping analysis of copper include pH 9.3, deposition time of 120 s, and a deposition potential of -0.1 V (vs. Ag/AgCl). The peak current is linearly proportional to the copper concentration over a range 3.14 x 10(-9) M to 1.57 x 10(-6) M with a limit of detection of 1.57 x 10(-9) M. The technique has been applied to the determination of copper in biological samples, like urine and whole blood.

  8. An "Electronic Fluorescent Pictograph" browser for exploring and analyzing large-scale biological data sets.

    Directory of Open Access Journals (Sweden)

    Debbie Winter

    Full Text Available BACKGROUND: The exploration of microarray data and data from other high-throughput projects for hypothesis generation has become a vital aspect of post-genomic research. For the non-bioinformatics specialist, however, many of the currently available tools provide overwhelming amounts of data that are presented in a non-intuitive way. METHODOLOGY/PRINCIPAL FINDINGS: In order to facilitate the interpretation and analysis of microarray data and data from other large-scale data sets, we have developed a tool, which we have dubbed the electronic Fluorescent Pictograph - or eFP - Browser, available at http://www.bar.utoronto.ca/, for exploring microarray and other data for hypothesis generation. This eFP Browser engine paints data from large-scale data sets onto pictographic representations of the experimental samples used to generate the data sets. We give examples of using the tool to present Arabidopsis gene expression data from the AtGenExpress Consortium (Arabidopsis eFP Browser, data for subcellular localization of Arabidopsis proteins (Cell eFP Browser, and mouse tissue atlas microarray data (Mouse eFP Browser. CONCLUSIONS/SIGNIFICANCE: The eFP Browser software is easily adaptable to microarray or other large-scale data sets from any organism and thus should prove useful to a wide community for visualizing and interpreting these data sets for hypothesis generation.

  9. State of the art of environmentally friendly sample preparation approaches for determination of PBDEs and metabolites in environmental and biological samples: A critical review.

    Science.gov (United States)

    Berton, Paula; Lana, Nerina B; Ríos, Juan M; García-Reyes, Juan F; Altamirano, Jorgelina C

    2016-01-28

    Green chemistry principles for developing methodologies have gained attention in analytical chemistry in recent decades. A growing number of analytical techniques have been proposed for determination of organic persistent pollutants in environmental and biological samples. In this light, the current review aims to present state-of-the-art sample preparation approaches based on green analytical principles proposed for the determination of polybrominated diphenyl ethers (PBDEs) and metabolites (OH-PBDEs and MeO-PBDEs) in environmental and biological samples. Approaches to lower the solvent consumption and accelerate the extraction, such as pressurized liquid extraction, microwave-assisted extraction, and ultrasound-assisted extraction, are discussed in this review. Special attention is paid to miniaturized sample preparation methodologies and strategies proposed to reduce organic solvent consumption. Additionally, extraction techniques based on alternative solvents (surfactants, supercritical fluids, or ionic liquids) are also commented in this work, even though these are scarcely used for determination of PBDEs. In addition to liquid-based extraction techniques, solid-based analytical techniques are also addressed. The development of greener, faster and simpler sample preparation approaches has increased in recent years (2003-2013). Among green extraction techniques, those based on the liquid phase predominate over those based on the solid phase (71% vs. 29%, respectively). For solid samples, solvent assisted extraction techniques are preferred for leaching of PBDEs, and liquid phase microextraction techniques are mostly used for liquid samples. Likewise, green characteristics of the instrumental analysis used after the extraction and clean-up steps are briefly discussed.

  10. NO RELATIONSHIP BETWEEN INTELLIGENCE AND FACIAL ATTRACTIVENESS IN A LARGE, GENETICALLY INFORMATIVE SAMPLE.

    Science.gov (United States)

    Mitchem, Dorian G; Zietsch, Brendan P; Wright, Margaret J; Martin, Nicholas G; Hewitt, John K; Keller, Matthew C

    2015-05-01

    Theories in both evolutionary and social psychology suggest that a positive correlation should exist between facial attractiveness and general intelligence, and several empirical observations appear to corroborate this expectation. Using highly reliable measures of facial attractiveness and IQ in a large sample of identical and fraternal twins and their siblings, we found no evidence for a phenotypic correlation between these traits. Likewise, neither the genetic nor the environmental latent factor correlations were statistically significant. We supplemented our analyses of new data with a simple meta-analysis that found evidence of publication bias among past studies of the relationship between facial attractiveness and intelligence. In view of these results, we suggest that previously published reports may have overestimated the strength of the relationship and that the theoretical bases for the predicted attractiveness-intelligence correlation may need to be reconsidered.

  11. Parallelism, Uniqueness, and Large-Sample Asymptotics for the Dantzig Selector

    CERN Document Server

    Dicker, Lee

    2012-01-01

    The Dantzig selector (Candes and Tao, 2007) is a popular l1-regularization method for variable selection and estimation in linear regression. We present a very weak geometric condition on the observed predictors which is related to parallelism and, when satisfied, ensures the uniqueness of Dantzig selector estimators. The condition holds with probability 1, if the predictors are drawn from a continuous distribution. We discuss the necessity of this condition for uniqueness and also provide a closely related condition which ensures uniqueness of lasso estimators (Tibshirani, 1996). Large sample asymptotics for the Dantzig selector, i.e. almost sure convergence and the asymptotic distribution, follow directly from our uniqueness results and a continuity argument. The limiting distribution of the Dantzig selector is generally non-normal. Though our asymptotic results require that the number of predictors is fixed (similar to (Knight and Fu, 2000)), our uniqueness results are valid for an arbitrary number of pred...

  12. Ultrasensitive multiplex optical quantification of bacteria in large samples of biofluids

    Science.gov (United States)

    Pazos-Perez, Nicolas; Pazos, Elena; Catala, Carme; Mir-Simon, Bernat; Gómez-de Pedro, Sara; Sagales, Juan; Villanueva, Carlos; Vila, Jordi; Soriano, Alex; García de Abajo, F. Javier; Alvarez-Puebla, Ramon A.

    2016-07-01

    Efficient treatments in bacterial infections require the fast and accurate recognition of pathogens, with concentrations as low as one per milliliter in the case of septicemia. Detecting and quantifying bacteria in such low concentrations is challenging and typically demands cultures of large samples of blood (~1 milliliter) extending over 24–72 hours. This delay seriously compromises the health of patients. Here we demonstrate a fast microorganism optical detection system for the exhaustive identification and quantification of pathogens in volumes of biofluids with clinical relevance (~1 milliliter) in minutes. We drive each type of bacteria to accumulate antibody functionalized SERS-labelled silver nanoparticles. Particle aggregation on the bacteria membranes renders dense arrays of inter-particle gaps in which the Raman signal is exponentially amplified by several orders of magnitude relative to the dispersed particles. This enables a multiplex identification of the microorganisms through the molecule-specific spectral fingerprints.

  13. On the Spectral Index-Flux Density Relation for Large Samples of Radio Sources

    Institute of Scientific and Technical Information of China (English)

    Xi-Zhen Zhang; W. Reich; P. Reich; R. Wielebinski

    2003-01-01

    We present new statistical results on the spectral index-flux densityrelation for large samples of radio sources using archival data of the most sensitivesurveys, such as 6C, Miyun, WENSS, B3, NVSS, GB87. Instrumental selectioneffects and the completeness of the catalogs are discussed. Based on the spec-tral indices calculated for about 200 000 sources from the WENSS (327 MHz) andNVSS (1.4 GHz) catalogs, we obtained (1) The median spectral index increases fromαmed ~ -0.9 to αmed ~ -0.8 (Sν∝να), while S327 flux densities decrease from0.1 Jy down to 25 mJy. The median spectral indices nearly show no variation withinthe error bars when the flux density is larger than 0.1 Jy. (2) A dependence of thefraction of ultra-steep spectrum sources (USS, -1.5 ≤α<-1.0), steep spectrumsources (SSS, -1.0 ≤α< -0.5) and flat spectrum sources (FSS, -0.5 ≤α≤ 0.0) ispartly responsible for the spectral flattening. Another contribution to the spectralflattening comes from the variation of αmed of steep spectrum sources (α<-0.5)themselves which increases with decreasing flux densities. (3) The spectral flatteningfor faint sources (down to S327 ~ 20 mJy) with steep spectra (α<-0.5) suggeststhat αmed is correlated with luminosity rather than redshift according to the Con-don' model. (4) A strong spectral selection effect occurs when spectral indices arecalculated from samples with a large frequency separation.

  14. SLEPR: a sample-level enrichment-based pathway ranking method -- seeking biological themes through pathway-level consistency.

    Science.gov (United States)

    Yi, Ming; Stephens, Robert M

    2008-09-26

    Analysis of microarray and other high throughput data often involves identification of genes consistently up or down-regulated across samples as the first step in extraction of biological meaning. This gene-level paradigm can be limited as a result of valid sample fluctuations and biological complexities. In this report, we describe a novel method, SLEPR, which eliminates this limitation by relying on pathway-level consistencies. Our method first selects the sample-level differentiated genes from each individual sample, capturing genes missed by other analysis methods, ascertains the enrichment levels of associated pathways from each of those lists, and then ranks annotated pathways based on the consistency of enrichment levels of individual samples from both sample classes. As a proof of concept, we have used this method to analyze three public microarray datasets with a direct comparison with the GSEA method, one of the most popular pathway-level analysis methods in the field. We found that our method was able to reproduce the earlier observations with significant improvements in depth of coverage for validated or expected biological themes, but also produced additional insights that make biological sense. This new method extends existing analyses approaches and facilitates integration of different types of HTP data.

  15. SLEPR: a sample-level enrichment-based pathway ranking method -- seeking biological themes through pathway-level consistency.

    Directory of Open Access Journals (Sweden)

    Ming Yi

    Full Text Available Analysis of microarray and other high throughput data often involves identification of genes consistently up or down-regulated across samples as the first step in extraction of biological meaning. This gene-level paradigm can be limited as a result of valid sample fluctuations and biological complexities. In this report, we describe a novel method, SLEPR, which eliminates this limitation by relying on pathway-level consistencies. Our method first selects the sample-level differentiated genes from each individual sample, capturing genes missed by other analysis methods, ascertains the enrichment levels of associated pathways from each of those lists, and then ranks annotated pathways based on the consistency of enrichment levels of individual samples from both sample classes. As a proof of concept, we have used this method to analyze three public microarray datasets with a direct comparison with the GSEA method, one of the most popular pathway-level analysis methods in the field. We found that our method was able to reproduce the earlier observations with significant improvements in depth of coverage for validated or expected biological themes, but also produced additional insights that make biological sense. This new method extends existing analyses approaches and facilitates integration of different types of HTP data.

  16. Dimensional comparison between amplitude-modulation atomic force microscopy and scanning ion conductance microscopy of biological samples

    Science.gov (United States)

    Kim, Joonhui; Choi, MyungHoon; Jung, Goo-Eun; Rahim Ferhan, Abdul; Cho, Nam-Joon; Cho, Sang-Joon

    2016-08-01

    The range of scanning probe microscopy (SPM) applications for atomic force microscopy (AFM) is expanding in the biological sciences field, reflecting an increasing demand for tools that can improve our fundamental understanding of the physics behind biological systems. However, the complexity associated with applying SPM techniques in biomedical research hampers the full exploitation of its capabilities. Recently, the development of scanning ion conductance microscopy (SICM) has overcome these limitations and enabled contact-free, high resolution imaging of live biological specimens. In this work, we demonstrate the limitation of AFM for imaging biological samples in liquid due to artifacts arising from AFM tip-sample interaction, and how SICM imaging is able to overcome those limitations with contact-free scanning. We also demonstrate that SICM measurements, when compared to AFM, show better fit to the actual dimensions of the biological samples. Our results highlight the superiority of SICM imaging, enabling it to be widely adopted as a general and versatile research tool for biological studies in the nanoscale.

  17. Insights on antioxidant assays for biological samples based on the reduction of copper complexes-the importance of analytical conditions.

    Science.gov (United States)

    Marques, Sara S; Magalhães, Luís M; Tóth, Ildikó V; Segundo, Marcela A

    2014-06-25

    Total antioxidant capacity assays are recognized as instrumental to establish antioxidant status of biological samples, however the varying experimental conditions result in conclusions that may not be transposable to other settings. After selection of the complexing agent, reagent addition order, buffer type and concentration, copper reducing assays were adapted to a high-throughput scheme and validated using model biological antioxidant compounds of ascorbic acid, Trolox (a soluble analogue of vitamin E), uric acid and glutathione. A critical comparison was made based on real samples including NIST-909c human serum certified sample, and five study samples. The validated method provided linear range up to 100 µM Trolox, (limit of detection 2.3 µM; limit of quantification 7.7 µM) with recovery results above 85% and precision <5%. The validated developed method with an increased sensitivity is a sound choice for assessment of TAC in serum samples.

  18. Insights on Antioxidant Assays for Biological Samples Based on the Reduction of Copper Complexes—The Importance of Analytical Conditions

    Directory of Open Access Journals (Sweden)

    Sara S. Marques

    2014-06-01

    Full Text Available Total antioxidant capacity assays are recognized as instrumental to establish antioxidant status of biological samples, however the varying experimental conditions result in conclusions that may not be transposable to other settings. After selection of the complexing agent, reagent addition order, buffer type and concentration, copper reducing assays were adapted to a high-throughput scheme and validated using model biological antioxidant compounds of ascorbic acid, Trolox (a soluble analogue of vitamin E, uric acid and glutathione. A critical comparison was made based on real samples including NIST-909c human serum certified sample, and five study samples. The validated method provided linear range up to 100 µM Trolox, (limit of detection 2.3 µM; limit of quantification 7.7 µM with recovery results above 85% and precision <5%. The validated developed method with an increased sensitivity is a sound choice for assessment of TAC in serum samples.

  19. Development of high-efficiency passive counters (HEPC) for the verification of large LEU samples

    Energy Technology Data Exchange (ETDEWEB)

    Peerani, P. [European Commission, DG-JRC, IPSC, Ispra (Italy)], E-mail: paolo.peerani@jrc.it; Canadell, V.; Garijo, J.; Jackson, K. [European Commission, DG-TREN/I, Nuclear Inspections (Luxembourg); Jaime, R.; Looman, M.; Ravazzani, A. [European Commission, DG-JRC, IPSC, Ispra (Italy); Schwalbach, P. [European Commission, DG-TREN/I, Nuclear Inspections (Luxembourg); Swinhoe, M. [Los Alamos National Laboratory, Los Alamos, NM (United States)

    2009-04-01

    A paper describing the conceptual idea of using passive neutron assay for the verification of large size uranium samples in fuel fabrication plants was first presented at the 2001 ESARDA conference. The advantages of this technique, as a replacement of active interrogation using the PHOto-Neutron Interrogation Device (PHONID) device, were evident provided that a suitable detector with higher efficiency than those commercially available would be realised. The previous paper also included a feasibility study based on the experimental data. To implement this technique, a high-efficiency passive counter (HEPC) has been designed by the JRC, Ispra. JRC has also built a first smaller-scale prototype. This paper will describe the tests made in the PERLA laboratory and report the performance of the prototype. In parallel, the design of the large HEPC has been finalised for Euratom safeguards. Two units for the fuel fabrication plants in Dessel (B) and Juzbado (E) have been produced by a commercial manufacturer under JRC specifications. The two detectors have been installed in the two sites in summer 2004 after an extensive test campaign in PERLA. Since then they are in use and some feedback on the experience gained is reported at the end of this paper.

  20. Pattern transfer on large samples using a sub-aperture reactive ion beam

    Energy Technology Data Exchange (ETDEWEB)

    Miessler, Andre; Mill, Agnes; Gerlach, Juergen W.; Arnold, Thomas [Leibniz-Institut fuer Oberflaechenmodifizierung (IOM), Permoserstrasse 15, D-04318 Leipzig (Germany)

    2011-07-01

    In comparison to sole Ar ion beam sputtering Reactive Ion Beam Etching (RIBE) reveals the main advantage of increasing the selectivity for different kind of materials due to chemical contributions during the material removal. Therefore RIBE is qualified to be an excellent candidate for pattern transfer applications. The goal of the present study is to apply a sub-aperture reactive ion beam for pattern transfer on large fused silica samples. Concerning this matter, the etching behavior in the ion beam periphery plays a decisive role. Using CF{sub 4} as reactive gas, XPS measurements of the modified surface exposes impurities like Ni, Fe and Cr, which belongs to chemically eroded material of the plasma pot as well as an accumulation of carbon (up to 40 atomic percent) in the beam periphery, respectively. The substitution of CF{sub 4} by NF{sub 3} as reactive gas reveals a lot of benefits: more stable ion beam conditions in combination with a reduction of the beam size down to a diameter of 5 mm and a reduced amount of the Ni, Fe and Cr contaminations. However, a layer formation of silicon nitride handicaps the chemical contribution of the etching process. These negative side effects influence the transfer of trench structures on quartz by changing the selectivity due to altered chemical reaction of the modified resist layer. Concerning this we investigate the pattern transfer on large fused silica plates using NF{sub 3}-sub-aperture RIBE.

  1. The Sub-Surface Structure of a Large Sample of Active Regions

    CERN Document Server

    Baldner, Charles S; Basu, Sarbani

    2012-01-01

    We employ ring-diagram analysis to study the sub-surface thermal structure of active regions. We present results using a large number of active regions over the course of Solar Cycle 23. We present both traditional inversions of ring-diagram frequency differences, with a total sample size of 264, and a statistical study using Principal Component Analysis. We confirm earlier results on smaller samples that sound speed and adiabatic index are changed below regions of strong magnetic field. We find that sound speed is decreased in the region between approximately r=0.99R_sun and r=0.995R_sun (depths of 3Mm to 7Mm), and increased in the region between r=0.97R_sun and r=0.985R_sun (depths of 11Mm to 21Mm). The adiabatic index is enhanced in the same deeper layers that sound-speed enhancement is seen. A weak decrease in adiabatic index is seen in the shallower layers in many active regions. We find that the magnitudes of these perturbations depend on the strength of the surface magnetic field, but we find a great d...

  2. Facial width-to-height ratio in a large sample of Commonwealth Games athletes.

    Science.gov (United States)

    Kramer, Robin S S

    2015-02-25

    Evidence that facial width-to-height ratio (FWHR) is a sexually dimorphic morphological measure is mixed. Research has also linked FWHR with aggression and other behavioral tendencies, at least in men. Again, other research has found no such relationship. Here, I tested for both possible relationships using a sample of 2,075 male and 1,406 female athletes from the Glasgow 2014 Commonwealth Games. Men showed significantly greater FWHRs than women, but this difference could be attributed to differences in body size. In addition, I found greater FWHRs in men who competed in sports involving physical contact and those stereotyped as more masculine. Again, these results could be attributed to differences in body size between categories. For women, no differences in FWHR were found regarding the amount of contact involved in a sport and how that sport was stereotyped. Finally, the FWHRs of athletes showed no relationship with the amount of aggression and related traits that were judged as required for success in those sports, although FWHRs did correlate with perceived endurance demands in women. Therefore, in a large sample of athletes, the sex difference in FWHR could be attributed to body size, and little support was found for the predicted links between this facial measure and behavior.

  3. A Large Sample of Am Candidates from LAMOST Data Release 1

    CERN Document Server

    Hou, Wen; Yang, Haifeng; Wei, Peng; Zhao, Yongheng; Zuo, Fang; Song, Yihan; Du, Bing; Bai, Zhongrui; Zhang, Yong; Hou, Yonghui; Liu, Xiaowei

    2015-01-01

    We present a sample of metallic-line star (Am) candidates from the Large sky Area Multi-Object fiber Spectroscopic Telescope Data Release one (LAMOST DR1). According to the characteristic of under-abundance of calcium and overabundance of iron element of Am stars, we propose an empirical separation curve derived from line indices of Ca II K-line and iron lines we choose for low resolution spectra. 3537 Am candidates are ultimately selected from more than 30,000 stars which are classified as A-type or early-F stars by both LAMOST pipeline and visual inspection. Then we make some analysis on this sample and finally provide a list of these Am candidates with 10 relevant parameters. Comparing with other catalogues, Am candidates selected from LAMOST DR1 are much fainter on the whole. Obviously, our list is an important complementary to already known bright Am catalogues, and it offers valuable material for the research on this type of chemically peculiar stars.

  4. Prevalence of learned grapheme-color pairings in a large online sample of synesthetes.

    Directory of Open Access Journals (Sweden)

    Nathan Witthoft

    Full Text Available In this paper we estimate the minimum prevalence of grapheme-color synesthetes with letter-color matches learned from an external stimulus, by analyzing a large sample of English-speaking grapheme-color synesthetes. We find that at least 6% (400/6588 participants of the total sample learned many of their matches from a widely available colored letter toy. Among those born in the decade after the toy began to be manufactured, the proportion of synesthetes with learned letter-color pairings approaches 15% for some 5-year periods. Among those born 5 years or more before it was manufactured, none have colors learned from the toy. Analysis of the letter-color matching data suggests the only difference between synesthetes with matches to the toy and those without is exposure to the stimulus. These data indicate learning of letter-color pairings from external contingencies can occur in a substantial fraction of synesthetes, and are consistent with the hypothesis that grapheme-color synesthesia is a kind of conditioned mental imagery.

  5. Intelligence, academic achievement, and pediatric injury among a large sample of kindergartners

    Directory of Open Access Journals (Sweden)

    David C. Schwebel

    2010-06-01

    Full Text Available

    Objectives: Previous work reports mixed results on the roles of intelligence and academic achievement on child injury risk. Some early research offered evidence of links between lower levels of intelligence and higher rates of pediatric injury, but other work has suggested there is no relation between the variables. This study investigated the matter further, in the context of a large sample and with strong statistical power.

    Methods: Data from a national sample of 8002 kindergartners in the United States, all from low-income families, were analyzed. Intelligence was estimated using the Peabody Picture Vocabulary Test-Revised and academic achievement with the Reading and Mathematics scales of the Woodcock Johnson Psycho- Educational Battery-Revised. Mothers reported whether children had experienced an injury in the previous year that required professional medical attention.

    Results: Results of both bivariate and multivariate ordinal logistic regression models suggest higher levels of reading achievement and of mathematics achievement were associated with slightly reduced risk of pediatric injury. Intelligence was not related to injury history.

    Conclusions: Academic achievement, but not intelligence, appears to relate in a small but statistically significant inverse manner with risk for pediatric injury among kindergartners from a low-income background. Possible mediators include children’s ability to learn and remember safety-related rules or the fact that parents who encourage learning in the household might also safeguard children more effectively.

  6. Minimizing uncertainty of daily rainfall interpolation over large catchments through realistic sampling of anisotropic correlogram parameters

    Science.gov (United States)

    Gyasi-Agyei, Yeboah

    2016-04-01

    It has been established that daily rainfall gauged network density is not adequate for the level of hydrological modelling required of large catchments involving pollutant and sediment transport, such as the catchments draining the coastal regions of Queensland, Australia, to the sensitive Great Barrier Reef. This paper seeks to establish a link between the spatial structure of radar and gauge rainfall for improved interpolation of the limited gauged data over a grid or functional units of catchments in regions with or without radar records. The study area is within Mt. Stapylton weather radar station range, a 128 km square region for calibration and validation, and the Brisbane river catchment for validation only. Two time periods (2000-01-01 to 2008-12-31 and 2009-01-01 to 2015-06-30) were considered, the later period for calibration when radar records were available and both time periods for validation without regard to radar information. Anisotropic correlograms of both the gauged and radar data were developed and used to establish the linkage required for areas without radar records. The maximum daily temperature significantly influenced the distributional parameters of the linkage. While the gauged, radar and sampled correlogram parameters reproduced the mean estimates similarly using leave-one-out cross-validation of Ordinary Kriging, the gauged parameters overestimated the standard deviation (SD) which reflects uncertainty by over 91% of cases compared with the radar or the sampled parameter sets. However, the distribution of the SD generated by the radar and the sampled correlogram parameters could not be distinguished, with a Kolmogorov-Smirnov test p-value of 0.52. For the validation case with the catchment, the percentage overestimation of SD by the gauged parameter sets decreased to 81.2% and 87.1% for the earlier and later time periods, respectively. It is observed that the extreme wet days' parameters and statistics were fairly widely distributed

  7. Assessing the validity of single-item life satisfaction measures: results from three large samples.

    Science.gov (United States)

    Cheung, Felix; Lucas, Richard E

    2014-12-01

    The present paper assessed the validity of single-item life satisfaction measures by comparing single-item measures to the Satisfaction with Life Scale (SWLS)-a more psychometrically established measure. Two large samples from Washington (N = 13,064) and Oregon (N = 2,277) recruited by the Behavioral Risk Factor Surveillance System and a representative German sample (N = 1,312) recruited by the Germany Socio-Economic Panel were included in the present analyses. Single-item life satisfaction measures and the SWLS were correlated with theoretically relevant variables, such as demographics, subjective health, domain satisfaction, and affect. The correlations between the two life satisfaction measures and these variables were examined to assess the construct validity of single-item life satisfaction measures. Consistent across three samples, single-item life satisfaction measures demonstrated substantial degree of criterion validity with the SWLS (zero-order r = 0.62-0.64; disattenuated r = 0.78-0.80). Patterns of statistical significance for correlations with theoretically relevant variables were the same across single-item measures and the SWLS. Single-item measures did not produce systematically different correlations compared to the SWLS (average difference = 0.001-0.005). The average absolute difference in the magnitudes of the correlations produced by single-item measures and the SWLS was very small (average absolute difference = 0.015-0.042). Single-item life satisfaction measures performed very similarly compared to the multiple-item SWLS. Social scientists would get virtually identical answer to substantive questions regardless of which measure they use.

  8. Off flavours in large waterbodies: physics, chemistry and biology in synchrony.

    Science.gov (United States)

    Watson, S B; Charlton, M; Rao, Y R; Howell, T; Ridal, J; Brownlee, B; Marvin, C; Millard, S

    2007-01-01

    The Laurentian Great Lakes of North America are a drinking water source for millions of Canadian and US consumers. These waterbodies have undergone extensive change over the past century as a result of widespread degradation and remediation. Many of the Lakes are prone to taste and odour (T&O), and although these outbreaks have been poorly monitored, evidence suggests that they are increasing in frequency. Tracing and controlling T&O in such large systems presents a challenging task, due to their physical size and complexity. This paper presents an overview of recent investigative and management approaches to T&O in Lake Ontario and its outflow, the St. Lawrence River. We have identified three distinct patterns of T&O in these source-waters, caused by geosmin and 2-methylisoborneol and differing in their planktonic and benthic sources, and temporal and spatial dynamics. Each pattern has required a different approach by scientists and management, in partnership with the water industry. We have shown these T&O outbreaks are caused and moderated by physical, chemical and biological mechanisms over a spectrum of spatial and temporal scales. Canadian municipalities affected by these outbreaks have been key to the investigation of the links between T&O and ecosystem processes with the aim to develop more proactive water treatment and long-term management.

  9. A unique large-scale undergraduate research experience in molecular systems biology for non-mathematics majors.

    Science.gov (United States)

    Kappler, Ulrike; Rowland, Susan L; Pedwell, Rhianna K

    2016-12-28

    Systems biology is frequently taught with an emphasis on mathematical modeling approaches. This focus effectively excludes most biology, biochemistry, and molecular biology students, who are not mathematics majors. The mathematical focus can also present a misleading picture of systems biology, which is a multi-disciplinary pursuit requiring collaboration between biochemists, bioinformaticians, and mathematicians. This article describes an authentic large-scale undergraduate research experience (ALURE) in systems biology that incorporates proteomics, bacterial genomics, and bioinformatics in the one exercise. This project is designed to engage students who have a basic grounding in protein chemistry and metabolism and no mathematical modeling skills. The pedagogy around the research experience is designed to help students attack complex datasets and use their emergent metabolic knowledge to make meaning from large amounts of raw data. On completing the ALURE, participants reported a significant increase in their confidence around analyzing large datasets, while the majority of the cohort reported good or great gains in a variety of skills including "analysing data for patterns" and "conducting database or internet searches." An environmental scan shows that this ALURE is the only undergraduate-level system-biology research project offered on a large-scale in Australia; this speaks to the perceived difficulty of implementing such an opportunity for students. We argue however, that based on the student feedback, allowing undergraduate students to complete a systems-biology project is both feasible and desirable, even if the students are not maths and computing majors. © 2016 by The International Union of Biochemistry and Molecular Biology, 2016.

  10. Large Scale Computing and Storage Requirements for Biological and Environmental Research

    Energy Technology Data Exchange (ETDEWEB)

    DOE Office of Science, Biological and Environmental Research Program Office (BER),

    2009-09-30

    In May 2009, NERSC, DOE's Office of Advanced Scientific Computing Research (ASCR), and DOE's Office of Biological and Environmental Research (BER) held a workshop to characterize HPC requirements for BER-funded research over the subsequent three to five years. The workshop revealed several key points, in addition to achieving its goal of collecting and characterizing computing requirements. Chief among them: scientific progress in BER-funded research is limited by current allocations of computational resources. Additionally, growth in mission-critical computing -- combined with new requirements for collaborative data manipulation and analysis -- will demand ever increasing computing, storage, network, visualization, reliability and service richness from NERSC. This report expands upon these key points and adds others. It also presents a number of"case studies" as significant representative samples of the needs of science teams within BER. Workshop participants were asked to codify their requirements in this"case study" format, summarizing their science goals, methods of solution, current and 3-5 year computing requirements, and special software and support needs. Participants were also asked to describe their strategy for computing in the highly parallel,"multi-core" environment that is expected to dominate HPC architectures over the next few years.

  11. 33S nuclear magnetic resonance spectroscopy of biological samples obtained with a laboratory model 33S cryogenic probe.

    Science.gov (United States)

    Hobo, Fumio; Takahashi, Masato; Saito, Yuta; Sato, Naoki; Takao, Tomoaki; Koshiba, Seizo; Maeda, Hideaki

    2010-05-01

    (33)S nuclear magnetic resonance (NMR) spectroscopy is limited by inherently low NMR sensitivity because of the quadrupolar moment and low gyromagnetic ratio of the (33)S nucleus. We have developed a 10 mm (33)S cryogenic NMR probe, which is operated at 9-26 K with a cold preamplifier and a cold rf switch operated at 60 K. The (33)S NMR sensitivity of the cryogenic probe is as large as 9.8 times that of a conventional 5 mm broadband NMR probe. The (33)S cryogenic probe was applied to biological samples such as human urine, bile, chondroitin sulfate, and scallop tissue. We demonstrated that the system can detect and determine sulfur compounds having SO(4)(2-) anions and -SO(3)(-) groups using the (33)S cryogenic probe, as the (33)S nuclei in these groups are in highly symmetric environments. The NMR signals for other common sulfur compounds such as cysteine are still undetectable by the (33)S cryogenic probe, as the (33)S nuclei in these compounds are in asymmetric environments. If we shorten the rf pulse width or decrease the rf coil diameter, we should be able to detect the NMR signals for these compounds.

  12. Humidity-controlled preparation of frozen-hydrated biological samples for cryogenic coherent x-ray diffraction microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Takayama, Yuki; Nakasako, Masayoshi [Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Kanagawa 223-8522 (Japan); RIKEN Harima Institute/SPring-8, 1-1-1 Kouto, Mikaduki, Sayo, Hyogo 679-5148 (Japan)

    2012-05-15

    Coherent x-ray diffraction microscopy (CXDM) has the potential to visualize the structures of micro- to sub-micrometer-sized biological particles, such as cells and organelles, at high resolution. Toward advancing structural studies on the functional states of such particles, here, we developed a system for the preparation of frozen-hydrated biological samples for cryogenic CXDM experiments. The system, which comprised a moist air generator, microscope, micro-injector mounted on a micromanipulator, custom-made sample preparation chamber, and flash-cooling device, allowed for the manipulation of sample particles in the relative humidity range of 20%-94%rh at 293 K to maintain their hydrated and functional states. Here, we report the details of the system and the operation procedure, including its application to the preparation of a frozen-hydrated chloroplast sample. Sample quality was evaluated through a cryogenic CXDM experiment conducted at BL29XUL of SPring-8. Taking the performance of the system and the quality of the sample, the system was suitable to prepare frozen-hydrated biological samples for cryogenic CXDM experiments.

  13. Biological communities in San Francisco Bay track large-scale climate forcing over the North Pacific

    Science.gov (United States)

    Cloern, James E.; Hieb, Kathryn A.; Jacobson, Teresa; Sansó, Bruno; Di Lorenzo, Emanuele; Stacey, Mark T.; Largier, John L.; Meiring, Wendy; Peterson, William T.; Powell, Thomas M.; Winder, Monika; Jassby, Alan D.

    2010-11-01

    Long-term observations show that fish and plankton populations in the ocean fluctuate in synchrony with large-scale climate patterns, but similar evidence is lacking for estuaries because of shorter observational records. Marine fish and invertebrates have been sampled in San Francisco Bay since 1980 and exhibit large, unexplained population changes including record-high abundances of common species after 1999. Our analysis shows that populations of demersal fish, crabs and shrimp covary with the Pacific Decadal Oscillation (PDO) and North Pacific Gyre Oscillation (NPGO), both of which reversed signs in 1999. A time series model forced by the atmospheric driver of NPGO accounts for two-thirds of the variability in the first principal component of species abundances, and generalized linear models forced by PDO and NPGO account for most of the annual variability of individual species. We infer that synchronous shifts in climate patterns and community variability in San Francisco Bay are related to changes in oceanic wind forcing that modify coastal currents, upwelling intensity, surface temperature, and their influence on recruitment of marine species that utilize estuaries as nursery habitat. Ecological forecasts of estuarine responses to climate change must therefore consider how altered patterns of atmospheric forcing across ocean basins influence coastal oceanography as well as watershed hydrology.

  14. Accelerator mass spectrometry analysis of 14C-oxaliplatin concentrations in biological samples and 14C contents in biological samples and antineoplastic agents

    Science.gov (United States)

    Toyoguchi, Teiko; Kobayashi, Takeshi; Konno, Noboru; Shiraishi, Tadashi; Kato, Kazuhiro; Tokanai, Fuyuki

    2015-10-01

    Accelerator mass spectrometry (AMS) is expected to play an important role in microdose trials. In this study, we measured the 14C concentration in 14C-oxaliplatin-spiked serum, urine and supernatant of fecal homogenate samples in our Yamagata University (YU) - AMS system. The calibration curves of 14C concentration in serum, urine and supernatant of fecal homogenate were linear (the correlation coefficients were ⩾0.9893), and the precision and accuracy was within the acceptance criteria. To examine a 14C content of water in three vacuum blood collection tubes and a syringe were measured. 14C was not detected from water in these devices. The mean 14C content in urine samples of 6 healthy Japanese volunteers was 0.144 dpm/mL, and the intra-day fluctuation of 14C content in urine from a volunteer was little. The antineoplastic agents are administered to the patients in combination. Then, 14C contents of the antineoplastic agents were quantitated. 14C contents were different among 10 antineoplastic agents; 14C contents of paclitaxel injection and docetaxel hydrate injection were higher than those of the other injections. These results indicate that our quantitation method using YU-AMS system is suited for microdosing studies and that measurement of baseline and co-administered drugs might be necessary for the studies in low concentrations.

  15. Accelerator mass spectrometry analysis of {sup 14}C-oxaliplatin concentrations in biological samples and {sup 14}C contents in biological samples and antineoplastic agents

    Energy Technology Data Exchange (ETDEWEB)

    Toyoguchi, Teiko, E-mail: tteiko@med.id.yamagata-u.ac.jp [Department of Pharmacy, Yamagata University Hospital, 2-2-2 Iida-Nishi, Yamagata-shi, Yamagata 990-9585 (Japan); Kobayashi, Takeshi; Konno, Noboru; Shiraishi, Tadashi [Department of Pharmacy, Yamagata University Hospital, 2-2-2 Iida-Nishi, Yamagata-shi, Yamagata 990-9585 (Japan); Kato, Kazuhiro; Tokanai, Fuyuki [Department of Physics, Faculty of Science, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata-shi, Yamagata 990-8560 (Japan)

    2015-10-15

    Accelerator mass spectrometry (AMS) is expected to play an important role in microdose trials. In this study, we measured the {sup 14}C concentration in {sup 14}C-oxaliplatin-spiked serum, urine and supernatant of fecal homogenate samples in our Yamagata University (YU) – AMS system. The calibration curves of {sup 14}C concentration in serum, urine and supernatant of fecal homogenate were linear (the correlation coefficients were ⩾0.9893), and the precision and accuracy was within the acceptance criteria. To examine a {sup 14}C content of water in three vacuum blood collection tubes and a syringe were measured. {sup 14}C was not detected from water in these devices. The mean {sup 14}C content in urine samples of 6 healthy Japanese volunteers was 0.144 dpm/mL, and the intra-day fluctuation of {sup 14}C content in urine from a volunteer was little. The antineoplastic agents are administered to the patients in combination. Then, {sup 14}C contents of the antineoplastic agents were quantitated. {sup 14}C contents were different among 10 antineoplastic agents; {sup 14}C contents of paclitaxel injection and docetaxel hydrate injection were higher than those of the other injections. These results indicate that our quantitation method using YU-AMS system is suited for microdosing studies and that measurement of baseline and co-administered drugs might be necessary for the studies in low concentrations.

  16. Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights.

    Science.gov (United States)

    Pasolli, Edoardo; Truong, Duy Tin; Malik, Faizan; Waldron, Levi; Segata, Nicola

    2016-07-01

    Shotgun metagenomic analysis of the human associated microbiome provides a rich set of microbial features for prediction and biomarker discovery in the context of human diseases and health conditions. However, the use of such high-resolution microbial features presents new challenges, and validated computational tools for learning tasks are lacking. Moreover, classification rules have scarcely been validated in independent studies, posing questions about the generality and generalization of disease-predictive models across cohorts. In this paper, we comprehensively assess approaches to metagenomics-based prediction tasks and for quantitative assessment of the strength of potential microbiome-phenotype associations. We develop a computational framework for prediction tasks using quantitative microbiome profiles, including species-level relative abundances and presence of strain-specific markers. A comprehensive meta-analysis, with particular emphasis on generalization across cohorts, was performed in a collection of 2424 publicly available metagenomic samples from eight large-scale studies. Cross-validation revealed good disease-prediction capabilities, which were in general improved by feature selection and use of strain-specific markers instead of species-level taxonomic abundance. In cross-study analysis, models transferred between studies were in some cases less accurate than models tested by within-study cross-validation. Interestingly, the addition of healthy (control) samples from other studies to training sets improved disease prediction capabilities. Some microbial species (most notably Streptococcus anginosus) seem to characterize general dysbiotic states of the microbiome rather than connections with a specific disease. Our results in modelling features of the "healthy" microbiome can be considered a first step toward defining general microbial dysbiosis. The software framework, microbiome profiles, and metadata for thousands of samples are publicly

  17. Mapping the Snow Line Altitude for Large Glacier Samples from Multitemporal Landsat Imagery

    Science.gov (United States)

    Rastner, P.; Nicholson, L. I.; Notarnicola, C.; Prinz, R.; Sailer, R.

    2015-12-01

    The cryosphere of mountain regions is fastly changing in response to climate change. This is particularly evident in global-scale glacier retreat. Trends in snow cover, however, are more difficult to determine, as annual fluctuations can be very large. Snow is an important parameter in the energy and mass balance of glaciers and the snow line altitude (SLA) at the end of the melting period can be considered as a proxy for the equilibrium line altitude (ELA). By frequently observing the SLA from satellite, region-wide monitoring of glaciers and improved calibration and validation of transient glacier (mass balance) models is possible. In the near future, frequent mapping of the SLA will be strongly facilitated by satellite missions like Sentinel 2A/B, where the same region will be covered every 5 days with 10 m spatial resolution. For this study we have developed an automated tool to derive the SLA for large glacier samples from remote sensing data. The method is first applied in the Ötztal Alps (Austria) where reliable in-situ data of mass balance and ELA are available for several glaciers over a 30-years period. The algorithm currently works with multi-temporal Landsat imagery (1972-2015), digital glacier outlines and a high-quality national DEM. All input datasets are atmospherically and topographically pre-processed before the SLA is automatically retrieved for each glacier. The remote-sensing derived SLA is generally about 200 m lower than the ELA, however, a clear trend in the altitude of the end of summer snow line is detectable (~ 200 m), which is in agreement with the ELA trend observed in the field. After bias correction and conversion to mass balance, the variability in observed mass balance can be well reproduced from the satellite-derived SLA time series. This is promising for application of the approach in other regions.

  18. Horvitz-Thompson survey sample methods for estimating large-scale animal abundance

    Science.gov (United States)

    Samuel, M.D.; Garton, E.O.

    1994-01-01

    Large-scale surveys to estimate animal abundance can be useful for monitoring population status and trends, for measuring responses to management or environmental alterations, and for testing ecological hypotheses about abundance. However, large-scale surveys may be expensive and logistically complex. To ensure resources are not wasted on unattainable targets, the goals and uses of each survey should be specified carefully and alternative methods for addressing these objectives always should be considered. During survey design, the impoflance of each survey error component (spatial design, propofiion of detected animals, precision in detection) should be considered carefully to produce a complete statistically based survey. Failure to address these three survey components may produce population estimates that are inaccurate (biased low), have unrealistic precision (too precise) and do not satisfactorily meet the survey objectives. Optimum survey design requires trade-offs in these sources of error relative to the costs of sampling plots and detecting animals on plots, considerations that are specific to the spatial logistics and survey methods. The Horvitz-Thompson estimators provide a comprehensive framework for considering all three survey components during the design and analysis of large-scale wildlife surveys. Problems of spatial and temporal (especially survey to survey) heterogeneity in detection probabilities have received little consideration, but failure to account for heterogeneity produces biased population estimates. The goal of producing unbiased population estimates is in conflict with the increased variation from heterogeneous detection in the population estimate. One solution to this conflict is to use an MSE-based approach to achieve a balance between bias reduction and increased variation. Further research is needed to develop methods that address spatial heterogeneity in detection, evaluate the effects of temporal heterogeneity on survey

  19. Critical tests for determination of microbiological quality and biological activity in commercial vermicompost samples of different origins.

    Science.gov (United States)

    Grantina-Ievina, Lelde; Andersone, Una; Berkolde-Pīre, Dace; Nikolajeva, Vizma; Ievinsh, Gederts

    2013-12-01

    The aim of the present paper was to show that differences in biological activity among commercially produced vermicompost samples can be found by using a relatively simple test system consisting of microorganism tests on six microbiological media and soilless seedling growth tests with four vegetable crop species. Significant differences in biological properties among analyzed samples were evident both at the level of microbial load as well as plant growth-affecting activity. These differences were mostly manufacturer- and feedstock-associated, but also resulted from storage conditions of vermicompost samples. A mature vermicompost sample that was produced from sewage sludge still contained considerable number of Escherichia coli. Samples from all producers contained several potentially pathogenic fungal species such as Aspergillus fumigatus, Pseudallescheria boidii, Pseudallescheria fimeti, Pseudallescheria minutispora, Scedosporium apiospermum, Scedosporium prolificans, Scopulariopsis brevicaulis, Stachybotrys chartarum, Geotrichum spp., Aphanoascus terreus, and Doratomyces columnaris. In addition, samples from all producers contained plant growth-promoting fungi from the genera Trichoderma and Mortierella. The described system can be useful both for functional studies aiming at understanding of factors affecting quality characteristics of vermicompost preparations and for routine testing of microbiological quality and biological activity of organic waste-derived composts and vermicomposts.

  20. Using a Module-Based Laboratory to Incorporate Inquiry into a Large Cell Biology Course

    Science.gov (United States)

    Howard, David R.; Miskowski, Jennifer A.

    2005-01-01

    Because cell biology has rapidly increased in breadth and depth, instructors are challenged not only to provide undergraduate science students with a strong, up-to-date foundation of knowledge, but also to engage them in the scientific process. To these ends, revision of the Cell Biology Lab course at the University of Wisconsin-La Crosse was…

  1. Using a Module-Based Laboratory to Incorporate Inquiry into a Large Cell Biology Course

    Science.gov (United States)

    Howard, David R.; Miskowski, Jennifer A.

    2005-01-01

    Because cell biology has rapidly increased in breadth and depth, instructors are challenged not only to provide undergraduate science students with a strong, up-to-date foundation of knowledge, but also to engage them in the scientific process. To these ends, revision of the Cell Biology Lab course at the University of Wisconsin-La Crosse was…

  2. Orbital Monitoring of the AstraLux Large M-dwarf Multiplicity Sample

    CERN Document Server

    Janson, Markus; Brandner, Wolfgang; Bonnefoy, Mickael; Schlieder, Joshua; Kohler, Rainer; Hormuth, Felix; Henning, Thomas; Hippler, Stefan

    2014-01-01

    Orbital monitoring of M-type binaries is essential for constraining their fundamental properties. This is particularly useful in young systems, where the extended pre-main sequence evolution can allow for precise isochronal dating. Here, we present the continued astrometric monitoring of the more than 200 binaries of the AstraLux Large Multiplicity Survey, building both on our previous work, archival data, and new astrometric data spanning the range of 2010-2012. The sample is very young overall -- all included stars have known X-ray emission, and a significant fraction (18%) of them have recently also been identified as members of young moving groups in the Solar neighborhood. We identify ~30 targets that both have indications of being young and for which an orbit either has been closed or appears possible to close in a reasonable timeframe (a few years to a few decades). One of these cases, GJ 4326, is however identified as probably being substantially older than has been implied from its apparent moving gr...

  3. Evaluation of Inflammatory Markers in a Large Sample of Obstructive Sleep Apnea Patients without Comorbidities

    Directory of Open Access Journals (Sweden)

    Izolde Bouloukaki

    2017-01-01

    Full Text Available Systemic inflammation is important in obstructive sleep apnea (OSA pathophysiology and its comorbidity. We aimed to assess the levels of inflammatory biomarkers in a large sample of OSA patients and to investigate any correlation between these biomarkers with clinical and polysomnographic (PSG parameters. This was a cross-sectional study in which 2983 patients who had undergone a polysomnography for OSA diagnosis were recruited. Patients with known comorbidities were excluded. Included patients (n=1053 were grouped according to apnea-hypopnea index (AHI as mild, moderate, and severe. Patients with AHI < 5 served as controls. Demographics, PSG data, and levels of high-sensitivity C-reactive protein (hs-CRP, fibrinogen, erythrocyte sedimentation rate (ESR, and uric acid (UA were measured and compared between groups. A significant difference was found between groups in hs-CRP, fibrinogen, and UA. All biomarkers were independently associated with OSA severity and gender (p<0.05. Females had increased levels of hs-CRP, fibrinogen, and ESR (p<0.001 compared to men. In contrast, UA levels were higher in men (p<0.001. Our results suggest that inflammatory markers significantly increase in patients with OSA without known comorbidities and correlate with OSA severity. These findings may have important implications regarding OSA diagnosis, monitoring, treatment, and prognosis. This trial is registered with ClinicalTrials.gov number NCT03070769.

  4. Using co-occurrence to evaluate belief coherence in a large non clinical sample.

    Directory of Open Access Journals (Sweden)

    Rachel Pechey

    Full Text Available Much of the recent neuropsychological literature on false beliefs (delusions has tended to focus on individual or single beliefs, with few studies actually investigating the relationship or co-occurrence between different types of co-existing beliefs. Quine and Ullian proposed the hypothesis that our beliefs form an interconnected web in which the beliefs that make up that system must somehow "cohere" with one another and avoid cognitive dissonance. As such beliefs are unlikely to be encapsulated (i.e., exist in isolation from other beliefs. The aim of this preliminary study was to empirically evaluate the probability of belief co-occurrence as one indicator of coherence in a large sample of subjects involving three different thematic sets of beliefs (delusion-like, paranormal & religious, and societal/cultural. Results showed that the degree of belief co-endorsement between beliefs within thematic groupings was greater than random occurrence, lending support to Quine and Ullian's coherentist account. Some associations, however, were relatively weak, providing for well-established examples of cognitive dissonance.

  5. Large-sample hydrology: a need to balance depth with breadth

    Science.gov (United States)

    Gupta, H. V.; Perrin, C.; Blöschl, G.; Montanari, A.; Kumar, R.; Clark, M.; Andréassian, V.

    2014-02-01

    A holy grail of hydrology is to understand catchment processes well enough that models can provide detailed simulations across a variety of hydrologic settings at multiple spatiotemporal scales, and under changing environmental conditions. Clearly, this cannot be achieved only through intensive place-based investigation at a small number of heavily instrumented catchments, or by empirical methods that do not fully exploit our understanding of hydrology. In this opinion paper, we discuss the need to actively promote and pursue the use of a "large catchment sample" approach to modeling the rainfall-runoff process, thereby balancing depth with breadth. We examine the history of such investigations, discuss the benefits (improved process understanding resulting in robustness of prediction at ungauged locations and under change), examine some practical challenges to implementation and, finally, provide perspectives on issues that need to be taken into account as we move forward. Ultimately, our objective is to provoke further discussion and participation, and to promote a potentially important theme for the upcoming Scientific Decade of the International Association of Hydrological Sciences entitled Panta Rhei.

  6. BROAD ABSORPTION LINE DISAPPEARANCE ON MULTI-YEAR TIMESCALES IN A LARGE QUASAR SAMPLE

    Energy Technology Data Exchange (ETDEWEB)

    Filiz Ak, N.; Brandt, W. N.; Schneider, D. P. [Department of Astronomy and Astrophysics, Pennsylvania State University, University Park, PA 16802 (United States); Hall, P. B. [Department of Physics and Astronomy, York University, 4700 Keele St., Toronto, Ontario M3J 1P3 (Canada); Anderson, S. F.; Gibson, R. R. [Astronomy Department, University of Washington, Seattle, WA 98195 (United States); Lundgren, B. F. [Department of Physics, Yale University, New Haven, CT 06511 (United States); Myers, A. D. [Department of Physics and Astronomy, University of Wyoming, Laramie, WY 82071 (United States); Petitjean, P. [Institut d' Astrophysique de Paris, Universite Paris 6, F-75014, Paris (France); Ross, Nicholas P. [Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 92420 (United States); Shen Yue [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, MS-51, Cambridge, MA 02138 (United States); York, D. G. [Department of Astronomy and Astrophysics, and Enrico Fermi Institute, University of Chicago, 5640 S. Ellis Ave., Chicago, IL 60637 (United States); Bizyaev, D.; Brinkmann, J.; Malanushenko, E.; Oravetz, D. J.; Pan, K.; Simmons, A. E. [Apache Point Observatory, P.O. Box 59, Sunspot, NM 88349-0059 (United States); Weaver, B. A., E-mail: nfilizak@astro.psu.edu [Center for Cosmology and Particle Physics, New York University, New York, NY 10003 (United States)

    2012-10-01

    We present 21 examples of C IV broad absorption line (BAL) trough disappearance in 19 quasars selected from systematic multi-epoch observations of 582 bright BAL quasars (1.9 < z < 4.5) by the Sloan Digital Sky Survey-I/II (SDSS-I/II) and SDSS-III. The observations span 1.1-3.9 yr rest-frame timescales, longer than have been sampled in many previous BAL variability studies. On these timescales, Almost-Equal-To 2.3% of C IV BAL troughs disappear and Almost-Equal-To 3.3% of BAL quasars show a disappearing trough. These observed frequencies suggest that many C IV BAL absorbers spend on average at most a century along our line of sight to their quasar. Ten of the 19 BAL quasars showing C IV BAL disappearance have apparently transformed from BAL to non-BAL quasars; these are the first reported examples of such transformations. The BAL troughs that disappear tend to be those with small-to-moderate equivalent widths, relatively shallow depths, and high outflow velocities. Other non-disappearing C IV BALs in those nine objects having multiple troughs tend to weaken when one of them disappears, indicating a connection between the disappearing and non-disappearing troughs, even for velocity separations as large as 10,000-15,000 km s{sup -1}. We discuss possible origins of this connection including disk-wind rotation and changes in shielding gas.

  7. Molecular dynamics computer simulations of sputtering of benzene sample by large mixed Lennard-Jones clusters

    Energy Technology Data Exchange (ETDEWEB)

    Rzeznik, L., E-mail: rzeznik@lippmann.lu [University of Information Technology and Management, Sucharskiego 2, 35-225 Rzeszów (Poland); Postawa, Z. [Institute of Physics, Jagiellonian University, Reymonta 4, 30-059 Kraków (Poland)

    2014-05-01

    Molecular dynamics computer simulations have been used to probe the role of the projectile composition on the emission efficiency and the sample damage. A benzene crystal was bombarded by 15 keV large heterogeneous noble gas clusters containing 2953 atoms. The projectiles used in this study are two-component clusters composed of Ne, Ar, and Kr atoms directed at 0° and 60° relative to the surface normal. It has been found that for normal incidence the total sputtering yield decreases with the projectile mass, whereas for 60° impact angle the yield increases with this quantity. For both 0° and 60° impact angles the observed sputtering yield for heterogeneous clusters cannot be calculated as a sum of sputtering yields obtained for homogeneous projectiles multiplied by the concentration of each component in the multi-component cluster. The difference in deposition scenarios of the primary kinetic energy is shown to be responsible for the observed behavior of the total sputtering yield.

  8. Continuum and Emission Line Strength Relations for a large Active Galactic Nuclei Sample

    CERN Document Server

    Dietrich, M; Shields, J C; Constantin, A; Junkkarinen, V T; Chaffee, F; Foltz, C B

    2002-01-01

    We report on the analysis of a large sample of 744 type 1 Active Galactic Nuclei, including quasars and Seyfert 1 galaxies across the redshift range from 0 < z < 5 and spanning nearly 6 orders of magnitude in continuum luminosity. We discuss correlations of continuum and emission line properties in the rest-frame ultraviolet and optical spectral ranges. The well established Baldwin Effect is detected for almost all emission lines from OVI1034 to [OIII]5007. Their equivalent widths are significantly anti-correlated with the continuum strength, while they are nearly independent of redshift. This is the well known Baldwin Effect. Its slope beta, measured as log W_lambda ~ beta * log lambda * L_lambda (1450A), shows a tendency to become steeper towards higher luminosity. The slope of the Baldwin Effect also increases with the ionization energy needed to create the individual lines. In contrast to this general trend, the NV1240 equivalent width is nearly independent of continuum luminosity and remains nearly...

  9. Patterns of intimate partner violence in a large, epidemiological sample of divorcing couples.

    Science.gov (United States)

    Beck, Connie J A; Anderson, Edward R; O'Hara, Karey L; Benjamin, G Andrew H

    2013-10-01

    In many jurisdictions divorcing couples are court-ordered to participate in divorce mediation to resolve parenting plan disputes prior to a court allowing a case to proceed to trial. Historically, a significant number (40-80%) of these divorcing couples enter this highly stressful legal process having experienced violence and abuse within the relationship (Pearson, 1997). Several researchers have developed typologies that describe couple-level patterns of Intimate Partner Violence and Abuse (IPV/A) behaviors; one research team suggested their typology could apply specifically to such divorcing people (Kelly & Johnson, 2008). In this context, identification and accurate classification of IPV/A can lead to better decisions as long-term, difficult to modify custody orders concerning the children are made during divorce mediation. Accurate identification and classification of IPV/A can also assist clinical researchers designing specialized interventions for couples and individuals experiencing IPV/A, mental health practitioners who may treat these families, and custody evaluators who may make recommendations to the courts. The current study includes a large epidemiological sample of divorcing couples and provides a robust statistical solution with five distinct categories of IPV/A. Two of the five categories were similar to those proposed by Johnson (2006c). The current study also provides descriptions and frequencies of each type of IPV/A, and discusses implications for court personnel, researchers and practitioners.

  10. A test of the interpersonal theory of suicide in a large sample of current firefighters.

    Science.gov (United States)

    Chu, Carol; Buchman-Schmitt, Jennifer M; Hom, Melanie A; Stanley, Ian H; Joiner, Thomas E

    2016-06-30

    Recent research suggests that firefighters experience elevated rates of suicidal ideation and behaviors. The interpersonal theory of suicide may shed light on this finding. This theory postulates that suicidal desire is strongest among individuals experiencing perceived burdensomeness and thwarted belongingness, and that the combination of suicide desire and acquired capability for suicide is necessary for the development of suicidal behaviors. We tested the propositions of the interpersonal theory in a large sample of current United States firefighters (N=863). Participants completed self-report measures of perceived burdensomeness, thwarted belongingness, fearlessness about death (FAD; a component of acquired capability), and career suicidal ideation and suicide attempt history. Regression models were used to examine the association between interpersonal theory constructs, career suicidal ideation severity, and the presence of career suicide attempts. In line with theory predictions, the three-way interaction between perceived burdensomeness, thwarted belongingness, and FAD was significantly associated with career suicide attempts, beyond participant sex. However, findings were no longer significant after accounting for years of firefighter service or age. Contrary to predictions, the two-way interaction between perceived burdensomeness and thwarted belongingness was not significantly related to career suicidal ideation severity. Applications of the theory to firefighters and future research are discussed.

  11. Osteoporosis Self-Assessment Tool Performance in a Large Sample of Postmenopausal Women of Mendoza, Argentina

    Directory of Open Access Journals (Sweden)

    Fernando D. Saraví

    2013-01-01

    Full Text Available The Osteoporosis Self-assessment Tool (OST is a clinical instrument designed to select patients at risk of osteoporosis, who would benefit from a bone mineral density measurement. The OST only takes into account the age and weight of the subject. It was developed for Asian women and later validated for European and North American white women. The performance of the OST in a sample of 4343 women from Greater Mendoza, a large metropolitan area of Argentina, was assessed. Dual X-ray absorptiometry (DXA scans of lumbar spine and hip were obtained. Patients were classified as either osteoporotic (N=1830 or nonosteoporotic (n=2513 according to their lowest T-score at any site. Osteoporotic patients had lower OST scores (P<0.0001. A receiver operating characteristic (ROC curve showed an area under the curve of 71% (P<0.0001, with a sensitivity of 83.7% and a specificity of 44% for a cut-off value of 2. Positive predictive value was 52% and negative predictive value was 79%. The odds ratio for the diagnosis of osteoporosis was 4.06 (CI95 3.51 to 4.71; P<0.0001. It is concluded that the OST is useful for selecting postmenopausal women for DXA testing in the studied population.

  12. Large sample area and size are needed for forest soil seed bank studies to ensure low discrepancy with standing vegetation.

    Directory of Open Access Journals (Sweden)

    You-xin Shen

    Full Text Available A large number of small-sized samples invariably shows that woody species are absent from forest soil seed banks, leading to a large discrepancy with the seedling bank on the forest floor. We ask: 1 Does this conventional sampling strategy limit the detection of seeds of woody species? 2 Are large sample areas and sample sizes needed for higher recovery of seeds of woody species? We collected 100 samples that were 10 cm (length × 10 cm (width × 10 cm (depth, referred to as larger number of small-sized samples (LNSS in a 1 ha forest plot, and placed them to germinate in a greenhouse, and collected 30 samples that were 1 m × 1 m × 10 cm, referred to as small number of large-sized samples (SNLS and placed them (10 each in a nearby secondary forest, shrub land and grass land. Only 15.7% of woody plant species of the forest stand were detected by the 100 LNSS, contrasting with 22.9%, 37.3% and 20.5% woody plant species being detected by SNLS in the secondary forest, shrub land and grassland, respectively. The increased number of species vs. sampled areas confirmed power-law relationships for forest stand, the LNSS and SNLS at all three recipient sites. Our results, although based on one forest, indicate that conventional LNSS did not yield a high percentage of detection for woody species, but SNLS strategy yielded a higher percentage of detection for woody species in the seed bank if samples were exposed to a better field germination environment. A 4 m2 minimum sample area derived from power equations is larger than the sampled area in most studies in the literature. Increased sample size also is needed to obtain an increased sample area if the number of samples is to remain relatively low.

  13. H2S Analysis in Biological Samples Using Gas Chromatography with Sulfur Chemiluminescence Detection

    OpenAIRE

    Vitvitsky, Victor; Banerjee, Ruma

    2015-01-01

    Hydrogen sulfide (H2S) is a metabolite and signaling molecule in biological tissues that regulates many physiological processes. Reliable and sensitive methods for H2S analysis are necessary for a better understanding of H2S biology and for the pharmacological modulation of H2S levels in vivo. In this chapter, we describe the use of gas chromatography coupled to sulfur chemiluminescence detection to measure the rates of H2S production and degradation by tissue homogenates at physiologically r...

  14. Quantitative Modeling of Membrane Transport and Anisogamy by Small Groups Within a Large-Enrollment Organismal Biology Course

    Directory of Open Access Journals (Sweden)

    Eric S. Haag

    2016-12-01

    Full Text Available Quantitative modeling is not a standard part of undergraduate biology education, yet is routine in the physical sciences. Because of the obvious biophysical aspects, classes in anatomy and physiology offer an opportunity to introduce modeling approaches to the introductory curriculum. Here, we describe two in-class exercises for small groups working within a large-enrollment introductory course in organismal biology. Both build and derive biological insights from quantitative models, implemented using spreadsheets. One exercise models the evolution of anisogamy (i.e., small sperm and large eggs from an initial state of isogamy. Groups of four students work on Excel spreadsheets (from one to four laptops per group. The other exercise uses an online simulator to generate data related to membrane transport of a solute, and a cloud-based spreadsheet to analyze them. We provide tips for implementing these exercises gleaned from two years of experience.

  15. Papers presented to the Conference on Large Body Impacts and Terrestrial Evolution: Geological, Climatological, and Biological Implications

    Science.gov (United States)

    1981-01-01

    The effects of large impacts on the environment are discussed and include thermal effects, atmospheric effects, changes in ocean temperatures, and geomagnetic anomalies. Biological factors such as extinction and increases in mutation development were investigated. Geological anomalies studied include stratigraphic gaps, extinction of entire boundary layers from the geological record, and geochemical oddities. Evidence was examined for impact cratering throughout the world.

  16. [Physical, chemical and biological study of dust from large-scale pig farms].

    Science.gov (United States)

    Raszyk, J

    1986-04-01

    Dust deposition in 16 halls of two large pig-fattening farms with dry or wet feeding systems was analyzed. In the halls with wet feeding the samples contained maximally 28 dust particles up to 10 micron and 17 particles up to 5 micron per cm3 of air, in the halls with dry feeding 220 particles smaller than 10 micron and 205 particles smaller than 5 micron per cm3 of air. The total amino acid content in the dust deposition was 17.440 +/- 1.820 g per 100 g of sample and the content of nitrogen compounds (N X X 6.25, %), was 24.170 +/- 2.910. The contents of chemical elements were as follows (mg per kg): zinc 448 +/- 151; manganese 109.9 +/- 49.5; copper 40.5 +/- 12.1; lead 4.77 +/- +/- 4.79; chromium 1.64 +/- 1.47; cadmium 1.61 +/- 1.62; mercury 0.36 +/- 0.39. Chlorinated carbohydrates and triazine and diazine herbicides were present in the following amounts (mg per kg): HCB 0.0023 +/- 0.0021; Lindane 0.0058 +/- 0.0079; DDE 0.0048 +/- +/- 0.0024; DDT 0.0065 +/- 0.0015; Simazine 0.060 +/- 0.020; Atrazine 0.083 +/- 0.059; Prometryn 0.093 +/- 0.040; Chloridazon 0.036 +/- 0.008; Terbutryn 0.085 +/- 0.029. The content of aflatoxin B1 was 12.89 +/- 9.31 micrograms per kg and the maximum amount of polychlorinated biphenyls was 8 mg per kg. Nitrovin was found out only in the dust of two halls: 4.0 and 7.9 mg per kg. The dust deposition also contained 21 genera and species of moulds, six species of mites, numerous saprophytic bacteria and, in some cases, Staphylococcus aureus. For the time being, no viruses have been detected in the dust samples.

  17. Estimation of calcium, magnesium, cadmium, and lead in biological samples from paralyzed quality control and production steel mill workers.

    Science.gov (United States)

    Afridi, Hassan Imran; Talpur, Farah Naz; Kazi, Tasneem Gul; Kazi, Naveed; Arain, Sadaf Sadia; Shah, Faheem

    2015-06-01

    The determination of trace and toxic metals in the biological samples of human beings is an important clinical screening procedure. The aim of the present study was to compare the level of essential trace and toxic elements cadmium (Cd), calcium (Ca), lead (Pb), and magnesium (Mg) in biological samples (whole blood, urine, and scalp hair) of male paralyzed production (PPW) and quality control workers (PQW) of a steel mill, age ranged (35-55 years). For comparison purposes, healthy age-matched exposed referent subjects (EC), working in steel mill and control subjects (NEC), who were not working in industries and lived far away from the industrial areas, were selected as control subjects. The concentrations of electrolytes and toxic elements in biological samples were measured by atomic absorption spectrometry after microwave-assisted acid digestion. The validity and accuracy of the methodology were checked using certified reference materials. The results of this study showed that the mean values of Cd and Pb were significantly higher in scalp hair, blood, and urine samples of PPW and PQW as compared to NEC and EC (p urine samples of PPW and PQW. The results show the need for immediate improvements in workplace, ventilation, and industrial hygiene practices.

  18. The large universal Pantoea plasmid LPP-1 plays a major role in biological and ecological diversification

    National Research Council Canada - National Science Library

    De Maayer, Pieter; Chan, Wai-Yin; Blom, Jochen; Venter, Stephanus N; Duffy, Brion; Smits, Theo H M; Coutinho, Teresa A

    2012-01-01

    Pantoea spp. are frequently isolated from a wide range of ecological niches and have various biological roles, as plant epi- or endophytes, biocontrol agents, plant-growth promoters or as pathogens of both plant and animal hosts...

  19. Note: Design and development of wireless controlled aerosol sampling network for large scale aerosol dispersion experiments

    Science.gov (United States)

    Gopalakrishnan, V.; Subramanian, V.; Baskaran, R.; Venkatraman, B.

    2015-07-01

    Wireless based custom built aerosol sampling network is designed, developed, and implemented for environmental aerosol sampling. These aerosol sampling systems are used in field measurement campaign, in which sodium aerosol dispersion experiments have been conducted as a part of environmental impact studies related to sodium cooled fast reactor. The sampling network contains 40 aerosol sampling units and each contains custom built sampling head and the wireless control networking designed with Programmable System on Chip (PSoC™) and Xbee Pro RF modules. The base station control is designed using graphical programming language LabView. The sampling network is programmed to operate in a preset time and the running status of the samplers in the network is visualized from the base station. The system is developed in such a way that it can be used for any other environment sampling system deployed in wide area and uneven terrain where manual operation is difficult due to the requirement of simultaneous operation and status logging.

  20. Investigating probabilistic sampling approaches for large-scale surveys in software engineering

    National Research Council Canada - National Science Library

    de Mello, Rafael Maiani; da Silva, Pedro Corrêa; Travassos, Guilherme Horta

    2015-01-01

    .... Specialized literature often presents limitations on interpreting surveys’ results, mainly due to the use of sampling frames established by convenience and non-probabilistic criteria for sampling from them...

  1. Note: Design and development of wireless controlled aerosol sampling network for large scale aerosol dispersion experiments.

    Science.gov (United States)

    Gopalakrishnan, V; Subramanian, V; Baskaran, R; Venkatraman, B

    2015-07-01

    Wireless based custom built aerosol sampling network is designed, developed, and implemented for environmental aerosol sampling. These aerosol sampling systems are used in field measurement campaign, in which sodium aerosol dispersion experiments have been conducted as a part of environmental impact studies related to sodium cooled fast reactor. The sampling network contains 40 aerosol sampling units and each contains custom built sampling head and the wireless control networking designed with Programmable System on Chip (PSoC™) and Xbee Pro RF modules. The base station control is designed using graphical programming language LabView. The sampling network is programmed to operate in a preset time and the running status of the samplers in the network is visualized from the base station. The system is developed in such a way that it can be used for any other environment sampling system deployed in wide area and uneven terrain where manual operation is difficult due to the requirement of simultaneous operation and status logging.

  2. Note: Design and development of wireless controlled aerosol sampling network for large scale aerosol dispersion experiments

    Energy Technology Data Exchange (ETDEWEB)

    Gopalakrishnan, V.; Subramanian, V.; Baskaran, R.; Venkatraman, B. [Radiation Impact Assessment Section, Radiological Safety Division, Indira Gandhi Centre for Atomic Research, Kalpakkam 603 102 (India)

    2015-07-15

    Wireless based custom built aerosol sampling network is designed, developed, and implemented for environmental aerosol sampling. These aerosol sampling systems are used in field measurement campaign, in which sodium aerosol dispersion experiments have been conducted as a part of environmental impact studies related to sodium cooled fast reactor. The sampling network contains 40 aerosol sampling units and each contains custom built sampling head and the wireless control networking designed with Programmable System on Chip (PSoC™) and Xbee Pro RF modules. The base station control is designed using graphical programming language LabView. The sampling network is programmed to operate in a preset time and the running status of the samplers in the network is visualized from the base station. The system is developed in such a way that it can be used for any other environment sampling system deployed in wide area and uneven terrain where manual operation is difficult due to the requirement of simultaneous operation and status logging.

  3. Religion and the Unmaking of Prejudice toward Muslims: Evidence from a Large National Sample

    Science.gov (United States)

    Shaver, John H.; Troughton, Geoffrey; Sibley, Chris G.; Bulbulia, Joseph A.

    2016-01-01

    In the West, anti-Muslim sentiments are widespread. It has been theorized that inter-religious tensions fuel anti-Muslim prejudice, yet previous attempts to isolate sectarian motives have been inconclusive. Factors contributing to ambiguous results are: (1) failures to assess and adjust for multi-level denomination effects; (2) inattention to demographic covariates; (3) inadequate methods for comparing anti-Muslim prejudice relative to other minority group prejudices; and (4) ad hoc theories for the mechanisms that underpin prejudice and tolerance. Here we investigate anti-Muslim prejudice using a large national sample of non-Muslim New Zealanders (N = 13,955) who responded to the 2013 New Zealand Attitudes and Values Study. We address previous shortcomings by: (1) building Bayesian multivariate, multi-level regression models with denominations modeled as random effects; (2) including high-resolution demographic information that adjusts for factors known to influence prejudice; (3) simultaneously evaluating the relative strength of anti-Muslim prejudice by comparing it to anti-Arab prejudice and anti-immigrant prejudice within the same statistical model; and (4) testing predictions derived from the Evolutionary Lag Theory of religious prejudice and tolerance. This theory predicts that in countries such as New Zealand, with historically low levels of conflict, religion will tend to increase tolerance generally, and extend to minority religious groups. Results show that anti-Muslim and anti-Arab sentiments are confounded, widespread, and substantially higher than anti-immigrant sentiments. In support of the theory, the intensity of religious commitments was associated with a general increase in tolerance toward minority groups, including a poorly tolerated religious minority group: Muslims. Results clarify religion’s power to enhance tolerance in peaceful societies that are nevertheless afflicted by prejudice. PMID:26959976

  4. Utilization of professional psychological care in a large German sample of cancer patients.

    Science.gov (United States)

    Faller, Hermann; Weis, Joachim; Koch, Uwe; Brähler, Elmar; Härter, Martin; Keller, Monika; Schulz, Holger; Wegscheider, Karl; Boehncke, Anna; Hund, Bianca; Reuter, Katrin; Richard, Matthias; Sehner, Susanne; Wittchen, Hans-Ulrich; Mehnert, Anja

    2017-04-01

    Although one-third of cancer patients are perceived to have a need for psychological support based on the percentage of mental disorders, little is known about the actual utilization of psychological care in cancer. We aimed to assess cancer patients' reported use of psychological care and its correlates in a large, representative sample. In a multicenter, cross-sectional study in Germany, 4020 cancer patients (mean age 58 years, 51% women) were evaluated. We obtained self-reports of use of psychotherapy and psychological counseling. We measured distress with the Distress Thermometer, symptoms of depression with the Patient Health Questionnaire, anxiety with the Generalized Anxiety Disorder Scale, and social support with the Illness-specific Social Support Scale. In a subsample of 2141, we evaluated the presence of a mental disorder using the Composite International Diagnostic Interview. In total, 28.9% (95% confidence interval 27.4%-30.4%) reported having used psychotherapy or psychological counseling or both because of distress due to cancer. Independent correlates of utilization included age (odds ratio [OR] = 0.97 per year], sex (male, OR = 0.55), social support (OR = 0.96), symptoms of depression (OR = 1.04) and anxiety (OR = 1.08), the diagnosis of a mental disorder (OR = 1.68), and a positive attitude toward psychosocial support (OR = 1.27). Less than half of those currently diagnosed with a mental disorder reported having taken up psychological support offers. Special efforts should be made to reach populations that report low utilization of psychological care in spite of having a need for support. Copyright © 2016 John Wiley & Sons, Ltd.

  5. Religion and the Unmaking of Prejudice toward Muslims: Evidence from a Large National Sample.

    Science.gov (United States)

    Shaver, John H; Troughton, Geoffrey; Sibley, Chris G; Bulbulia, Joseph A

    2016-01-01

    In the West, anti-Muslim sentiments are widespread. It has been theorized that inter-religious tensions fuel anti-Muslim prejudice, yet previous attempts to isolate sectarian motives have been inconclusive. Factors contributing to ambiguous results are: (1) failures to assess and adjust for multi-level denomination effects; (2) inattention to demographic covariates; (3) inadequate methods for comparing anti-Muslim prejudice relative to other minority group prejudices; and (4) ad hoc theories for the mechanisms that underpin prejudice and tolerance. Here we investigate anti-Muslim prejudice using a large national sample of non-Muslim New Zealanders (N = 13,955) who responded to the 2013 New Zealand Attitudes and Values Study. We address previous shortcomings by: (1) building Bayesian multivariate, multi-level regression models with denominations modeled as random effects; (2) including high-resolution demographic information that adjusts for factors known to influence prejudice; (3) simultaneously evaluating the relative strength of anti-Muslim prejudice by comparing it to anti-Arab prejudice and anti-immigrant prejudice within the same statistical model; and (4) testing predictions derived from the Evolutionary Lag Theory of religious prejudice and tolerance. This theory predicts that in countries such as New Zealand, with historically low levels of conflict, religion will tend to increase tolerance generally, and extend to minority religious groups. Results show that anti-Muslim and anti-Arab sentiments are confounded, widespread, and substantially higher than anti-immigrant sentiments. In support of the theory, the intensity of religious commitments was associated with a general increase in tolerance toward minority groups, including a poorly tolerated religious minority group: Muslims. Results clarify religion's power to enhance tolerance in peaceful societies that are nevertheless afflicted by prejudice.

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

    Science.gov (United States)

    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.

  7. Characterization of mitochondrial haplogroups in a large population-based sample from the United States.

    Science.gov (United States)

    Mitchell, Sabrina L; Goodloe, Robert; Brown-Gentry, Kristin; Pendergrass, Sarah A; Murdock, Deborah G; Crawford, Dana C

    2014-07-01

    Mitochondrial DNA (mtDNA) haplogroups are valuable for investigations in forensic science, molecular anthropology, and human genetics. In this study, we developed a custom panel of 61 mtDNA markers for high-throughput classification of European, African, and Native American/Asian mitochondrial haplogroup lineages. Using these mtDNA markers, we constructed a mitochondrial haplogroup classification tree and classified 18,832 participants from the National Health and Nutrition Examination Surveys (NHANES). To our knowledge, this is the largest study to date characterizing mitochondrial haplogroups in a population-based sample from the United States, and the first study characterizing mitochondrial haplogroup distributions in self-identified Mexican Americans separately from Hispanic Americans of other descent. We observed clear differences in the distribution of maternal genetic ancestry consistent with proposed admixture models for these subpopulations, underscoring the genetic heterogeneity of the United States Hispanic population. The mitochondrial haplogroup distributions in the other self-identified racial/ethnic groups within NHANES were largely comparable to previous studies. Mitochondrial haplogroup classification was highly concordant with self-identified race/ethnicity (SIRE) in non-Hispanic whites (94.8 %), but was considerably lower in admixed populations including non-Hispanic blacks (88.3 %), Mexican Americans (81.8 %), and other Hispanics (61.6 %), suggesting SIRE does not accurately reflect maternal genetic ancestry, particularly in populations with greater proportions of admixture. Thus, it is important to consider inconsistencies between SIRE and genetic ancestry when performing genetic association studies. The mitochondrial haplogroup data that we have generated, coupled with the epidemiologic variables in NHANES, is a valuable resource for future studies investigating the contribution of mtDNA variation to human health and disease.

  8. Orbital Monitoring of the AstraLux Large M-dwarf Multiplicity Sample

    Science.gov (United States)

    Janson, Markus; Bergfors, Carolina; Brandner, Wolfgang; Bonnefoy, Mickaël; Schlieder, Joshua; Köhler, Rainer; Hormuth, Felix; Henning, Thomas; Hippler, Stefan

    2014-10-01

    Orbital monitoring of M-type binaries is essential for constraining their fundamental properties. This is particularly useful in young systems, where the extended pre-main-sequence evolution can allow for precise isochronal dating. Here, we present the continued astrometric monitoring of the more than 200 binaries of the AstraLux Large Multiplicity Survey, building both on our previous work, archival data, and new astrometric data spanning the range of 2010-2012. The sample is very young overall—all included stars have known X-ray emission, and a significant fraction (18%) of them have recently also been identified as members of young moving groups in the solar neighborhood. We identify ~30 targets that both have indications of being young and for which an orbit either has been closed or appears possible to close in a reasonable time frame (a few years to a few decades). One of these cases, GJ 4326, is, however, identified as probably being substantially older than has been implied from its apparent moving group membership, based on astrometric and isochronal arguments. With further astrometric monitoring, these targets will provide a set of empirical isochrones, against which theoretical isochrones can be calibrated, and which can be used to evaluate the precise ages of nearby young moving groups. Based on observations collected at the European Southern Observatory, Chile, under observing programs 081.C-0314(A), 082.C-0053(A), and 084.C-0812(A), and on observations collected at the Centro Astronómico Hispano Alemán (CAHA) at Calar Alto, operated jointly by the Max-Planck Institute for Astronomy and the Instituto de Astrofísica de Andalucía (CSIC).

  9. Preconcentration and determination of heavy metals in water, sediment and biological samples

    OpenAIRE

    Shirkhanloo Hamid; Mousavi Zavvar Hassan; Rouhollahi Ahmad

    2011-01-01

    In this study, a simple, sensitive and accurate column preconcentration method was developed for the determination of Cd, Cu and Pb ions in river water, urine and sediment samples by flame atomic absorption spectrometry. The procedure is based on the retention of the analytes on a mixed cellulose ester membrane (MCEM) column from buffered sample solutions and then their elution from the column with nitric acid. Several parameters, such as pH of the sample solution, volume of the sample ...

  10. Chiral analysis of amphetamines, methadone and metabolites in biological samples by electrodriven methods.

    Science.gov (United States)

    Mandrioli, Roberto; Mercolini, Laura; Raggi, Maria A

    2011-10-01

    Amphetamines and methadone are synthetic chiral drugs with a high potential for abuse. As such, several analytical methods have been developed for their enantioseparation and analysis in biological tissues, and some of these are based on electrodriven techniques. In this review, the most important and recent of these latter methods are reviewed and their main advantages and disadvantages are discussed. Particular attention is paid to the suitability of each method for the application to the biological matrix of interest: while all methods have been successfully applied for one or more biological tissues, to reach this goal they must overcome the sensitivity problem that is common to almost all capillary electrophoretic techniques. Most methods use one or more cyclodextrin derivatives as the chiral selector, thus the separation mechanism is not particularly complicated or unusual.

  11. The European Large Area ISO Survey - IX. The 90-mu m luminosity function from the Final Analysis sample

    NARCIS (Netherlands)

    Serjeant, S; Carraminana, A; Gonzales-Solares, E; Heraudeau, P; Mujica, R; Perez-Fournon, [No Value; Sedgwick, N; Rowan-Robinson, M; Franceschini, A; Babbedge, T; del Burgo, C; Ciliegi, P; Efstathiou, A; La Franca, F; Gruppioni, C; Hughes, D; Lari, C; Oliver, S; Pozzi, F; Stickel, M; Vaccari, M

    2004-01-01

    We present the 90-mum luminosity function of the Final Analysis of the European Large Area ISO Survey (ELAIS), extending the sample size of our previous analysis (Paper IV) by about a factor of 4. Our sample extends to z = 1.1, similar to50 times the comoving volume of Paper IV, and 10(7.7)

  12. Sampling

    CERN Document Server

    Thompson, Steven K

    2012-01-01

    Praise for the Second Edition "This book has never had a competitor. It is the only book that takes a broad approach to sampling . . . any good personal statistics library should include a copy of this book." —Technometrics "Well-written . . . an excellent book on an important subject. Highly recommended." —Choice "An ideal reference for scientific researchers and other professionals who use sampling." —Zentralblatt Math Features new developments in the field combined with all aspects of obtaining, interpreting, and using sample data Sampling provides an up-to-date treat

  13. Automatic instrument for chemical processing to detect microorganism in biological samples by measuring light reactions

    Science.gov (United States)

    Kelbaugh, B. N.; Picciolo, G. L.; Chappelle, E. W.; Colburn, M. E. (Inventor)

    1973-01-01

    An automated apparatus is reported for sequentially assaying urine samples for the presence of bacterial adenosine triphosphate (ATP) that comprises a rotary table which carries a plurality of sample containing vials and automatically dispenses fluid reagents into the vials preparatory to injecting a light producing luciferase-luciferin mixture into the samples. The device automatically measures the light produced in each urine sample by a bioluminescence reaction of the free bacterial adenosine triphosphate with the luciferase-luciferin mixture. The light measured is proportional to the concentration of bacterial adenosine triphosphate which, in turn, is proportional to the number of bacteria present in the respective urine sample.

  14. Remaining Sites Verification Package for the 141-C Large Animal Barn and Biology Laboratory (Hog Barn), Waste Site Reclassification Form 2006-027

    Energy Technology Data Exchange (ETDEWEB)

    R. A. Carlson

    2006-05-24

    The 141-C waste site is a former large animal barn and biology laboratory within the 100-F Area experimental animal farm. Strontium-90, arsenic, and multiple polycyclic aromatic hydrocarbons were detected within residual demolition debris at concentrations exceeding cleanup criteria. The site has been remediated by removing approximately 900 bank cubic meters of soil and debris within the former building footprint to the Environmental Restoration Disposal Facility. The results of verification sampling demonstrated that residual contaminant concentrations do not preclude any future uses and allow for unrestricted use of shallow zone soils. The results also showed that residual contaminant concentrations are protective of groundwater and the Columbia River.

  15. Constant-Distance Mode Nanospray Desorption Electrospray Ionization Mass Spectrometry Imaging of Biological Samples with Complex Topography

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, Son N.; Liyu, Andrey V.; Chu, Rosalie K.; Anderton, Christopher R.; Laskin, Julia

    2017-01-17

    A new approach for constant distance mode mass spectrometry imaging of biological samples using nanospray desorption electrospray ionization (nano-DESI MSI) was developed by integrating a shear-force probe with nano-DESI probe. The technical concept and basic instrumental setup as well as general operation of the system are described. Mechanical dampening of resonant oscillations due to the presence of shear forces between the probe and the sample surface enables constant-distance imaging mode via a computer controlled closed feedback loop. The capability of simultaneous chemical and topographic imaging of complex biological samples is demonstrated using living Bacillus Subtilis ATCC 49760 colonies on agar plates. The constant-distance mode nano-DESI MSI enabled imaging of many metabolites including non-ribosomal peptides (surfactin, plipastatin and iturin) and iron-bound heme on the surface of living bacterial colonies ranging in diameter from 10 mm to 13 mm with height variations of up to 0.8 mm above the agar plate. Co-registration of ion images to topographic images provided higher-contrast images. Constant-mode nano-DESI MSI is ideally suited for imaging biological samples of complex topography in their native state.

  16. Nitrous oxide determination in postmortem biological samples: a case of serial fatal poisoning in a public hospital.

    Science.gov (United States)

    Poli, Diana; Gagliano-Candela, Roberto; Strisciullo, Giuseppe; Colucci, Anna P; Strada, Luigi; Laviola, Domenica; Goldoni, Matteo; Mutti, Antonio

    2010-01-01

    In a public hospital, eight cases of fatal poisoning by nitrous oxide (N(2)O) occurred under oxygen administration, due to an erroneous swapping of the lines in the gas system. The aim of the study was to clarify the factors involved in asphyxia by characterizing gases from different lines and measuring N(2)O concentrations in postmortem biological samples from bodies exhumed. Analyses carried out on the gas system confirmed the erroneous substitution of O(2) line with N(2)O and air line with O(2). Consequently, high N(2)O amounts were revealed in several tissues and gaseous biological samples. All specimens were analyzed by headspace gas chromatography technique. A rigorous quantitative analysis was possible only in blood (11.29-2152.04 mg/L) and urine (95.11 mg/L) and in air samples from stomach and trachea (from 5.28 to 83.63 g/m(3)). This study demonstrates that N(2)O can be detected in biological samples even 1 month after death.

  17. Constant-Distance Mode Nanospray Desorption Electrospray Ionization Mass Spectrometry Imaging of Biological Samples with Complex Topography.

    Science.gov (United States)

    Nguyen, Son N; Liyu, Andrey V; Chu, Rosalie K; Anderton, Christopher R; Laskin, Julia

    2017-01-17

    A new approach for constant-distance mode mass spectrometry imaging (MSI) of biological samples using nanospray desorption electrospray ionization (nano-DESI) was developed by integrating a shear-force probe with the nano-DESI probe. The technical concept and basic instrumental setup, as well as the general operation of the system are described. Mechanical dampening of resonant oscillations due to the presence of shear forces between the probe and the sample surface enabled the constant-distance imaging mode via a computer-controlled closed-feedback loop. The capability of simultaneous chemical and topographic imaging of complex biological samples is demonstrated using living Bacillus subtilis ATCC 49760 colonies on agar plates. The constant-distance mode nano-DESI MSI enabled imaging of many metabolites, including nonribosomal peptides (surfactin, plipastatin, and iturin) on the surface of living bacterial colonies, ranging in diameter from 10 to 13 mm, with height variations up to 0.8 mm above the agar plate. Co-registration of ion images to topographic images provided higher-contrast images. Based on this effort, constant-mode nano-DESI MSI proved to be ideally suited for imaging biological samples of complex topography in their native states.

  18. Estimation of copper and iron burden in biological samples of various stages of hepatitis C and liver cirrhosis patients.

    Science.gov (United States)

    Arain, Salma Aslam; Kazi, Tasneem G; Afridi, Hassan Imran; Talpur, Farah Naz; Mughal, Moina Akhtar; Shah, Faheem; Arain, Sadaf Sadia; Panhwar, Abdul Haleem

    2014-08-01

    There is accumulative evidence that the metabolism of iron (Fe) and copper (Cu) is altered in human due to infections, indicating that both elements have roles in pathogenesis and progress of viral diseases. In the present study, the correlation of Cu and Fe was evaluate in biological samples (serum and scalp hair) of hepatitis C (hepatitis C virus (HCV)) patients of both genders at different stages. For comparative study, the scalp hair and serum samples of healthy individuals of same age group (30-50 years) and socioeconomic status were collected. The biological samples were analyzed for Fe and Cu by atomic absorption spectroscopy after microwave-assisted acid digestion. The validity and accuracy of methodology were checked by certified reference materials of same matrixes. The levels of Cu and Fe in biological samples were enhanced in hepatic disorder patients, including acute (after diagnosis test, anti-HCV sero-positive) hepatic fibrosis and liver cirrhosis as compared to healthy referents. The difference was significant (p  0.1) except in the first stage of HCV (p human body seems to contribute to the development of cirrhosis in patients with viral hepatitis C.

  19. How Parents Influence School Grades: Hints from a Sample of Adoptive and Biological Families

    Science.gov (United States)

    Johnson, Wendy; McGue, Matt; Iacono, William G.

    2007-01-01

    Using the biological and adoptive families in the Minnesota-based Sibling Interaction and Behavior Study, we investigated the associations among genetic and environmental influences on IQ, parenting, parental expectations for offspring educational attainment, engagement in school, and school grades. All variables showed substantial genetic…

  20. Microwave-ultrasound combined reactor suitable for atmospheric sample preparation procedure of biological and chemical products

    NARCIS (Netherlands)

    Lagha, A.; Chemat, S.; Bartels, P.V.; Chemat, F.

    1999-01-01

    A compact apparatus in which a specific position can be irradiated by microwaves (MW) and ultrasound (US) simultaneously has been developed. The MW-US reactor has been designed for atmospheric pressure digestion and dissolution of biological and chemical products. The reactor can treat a range of th

  1. AutoMate Express™ forensic DNA extraction system for the extraction of genomic DNA from biological samples.

    Science.gov (United States)

    Liu, Jason Y; Zhong, Chang; Holt, Allison; Lagace, Robert; Harrold, Michael; Dixon, Alan B; Brevnov, Maxim G; Shewale, Jaiprakash G; Hennessy, Lori K

    2012-07-01

    The AutoMate Express™ Forensic DNA Extraction System was developed for automatic isolation of DNA from a variety of forensic biological samples. The performance of the system was investigated using a wide range of biological samples. Depending on the sample type, either PrepFiler™ lysis buffer or PrepFiler BTA™ lysis buffer was used to lyse the samples. After lysis and removal of the substrate using LySep™ column, the lysate in the sample tubes were loaded onto AutoMate Express™ instrument and DNA was extracted using one of the two instrument extraction protocols. Our study showed that DNA was recovered from as little as 0.025 μL of blood. DNA extracted from casework-type samples was free of detectable PCR inhibitors and the short tandem repeat profiles were complete, conclusive, and devoid of any PCR artifacts. The system also showed consistent performance from day-to-day operation. 2012 American Academy of Forensic Sciences. Published 2012. This article is a U.S. Government work and is in the public domain in the U.S.A.

  2. A comparison of two sampling designs for fish assemblage assessment in a large river

    Science.gov (United States)

    Kiraly, Ian A.; Coghlan Jr., Stephen M.; Zydlewski, Joseph; Hayes, Daniel

    2014-01-01

    We compared the efficiency of stratified random and fixed-station sampling designs to characterize fish assemblages in anticipation of dam removal on the Penobscot River, the largest river in Maine. We used boat electrofishing methods in both sampling designs. Multiple 500-m transects were selected randomly and electrofished in each of nine strata within the stratified random sampling design. Within the fixed-station design, up to 11 transects (1,000 m) were electrofished, all of which had been sampled previously. In total, 88 km of shoreline were electrofished during summer and fall in 2010 and 2011, and 45,874 individuals of 34 fish species were captured. Species-accumulation and dissimilarity curve analyses indicated that all sampling effort, other than fall 2011 under the fixed-station design, provided repeatable estimates of total species richness and proportional abundances. Overall, our sampling designs were similar in precision and efficiency for sampling fish assemblages. The fixed-station design was negatively biased for estimating the abundance of species such as Common Shiner Luxilus cornutus and Fallfish Semotilus corporalis and was positively biased for estimating biomass for species such as White Sucker Catostomus commersonii and Atlantic Salmon Salmo salar. However, we found no significant differences between the designs for proportional catch and biomass per unit effort, except in fall 2011. The difference observed in fall 2011 was due to limitations on the number and location of fixed sites that could be sampled, rather than an inherent bias within the design. Given the results from sampling in the Penobscot River, application of the stratified random design is preferable to the fixed-station design due to less potential for bias caused by varying sampling effort, such as what occurred in the fall 2011 fixed-station sample or due to purposeful site selection.

  3. Biologic

    CERN Document Server

    Kauffman, L H

    2002-01-01

    In this paper we explore the boundary between biology and the study of formal systems (logic). In the end, we arrive at a summary formalism, a chapter in "boundary mathematics" where there are not only containers but also extainers ><, entities open to interaction and distinguishing the space that they are not. The boundary algebra of containers and extainers is to biologic what boolean algebra is to classical logic. We show how this formalism encompasses significant parts of the logic of DNA replication, the Dirac formalism for quantum mechanics, formalisms for protein folding and the basic structure of the Temperley Lieb algebra at the foundations of topological invariants of knots and links.

  4. Psychopathic Traits in a Large Community Sample: Links to Violence, Alcohol Use, and Intelligence

    Science.gov (United States)

    Neumann, Craig S.; Hare, Robert D.

    2008-01-01

    Numerous studies conducted with offender or forensic psychiatric samples have revealed that individuals with psychopathic traits are at risk for violence and other externalizing psychopathology. These traits appear to be continuously distributed in these samples, leading investigators to speculate on the presence of such traits in the general…

  5. A high performance liquid chromatographic method of analysis of 4'-O-tetrahydropyranyladriamycin and their metabolites in biological samples.

    Science.gov (United States)

    Matsushita, Y; Iguchi, H; Kiyosaki, T; Tone, H; Ishikura, T; Takeuchi, T; Umezawa, H

    1983-07-01

    A method for measuring 4'-O-tetrahydropyranyladriamycin (THP) and its metabolites in biological samples are described. By reversed-phase high performance liquid chromatography using fluorescence detection, THP and its metabolites were all separated on a single chromatogram within 18 minutes. A linear calibration curve was obtained up to 2,000 ng/ml of THP in plasma. The recovery of THP in the analysis was more than 95% above 5 ng/ml and 87.1% even at 1.25 ng/ml. Thus the lower limit was 1.25 ng/ml in biological samples. Blood levels and urinary excretion in mice and dogs were satisfactory measured by this analytical method.

  6. Environmental Sampling Procedures and Methods to Respond to Biological Contamination (White Powder)

    Energy Technology Data Exchange (ETDEWEB)

    Piepel, Gregory F.; Amidan, Brett G.; Matzke, Brett D.

    2008-11-01

    This is a contribution to the annual report for the DHS Standards Office. It summarizes statistics-focused work associated with developing validated sampling procedures and methods. The main focus is on the experimental and sampling design constructed for contamination and decontamination field tests conducted during September 2007 in a remote, unused office building on the Idaho National Laboratory site.

  7. An Activity To Demonstrate the Concept of Sampling Error for the Introductory Biology Classroom.

    Science.gov (United States)

    Rutledge, Michael L.

    2001-01-01

    This activity makes students a part of an investigation that determines the frequency of a particular plant variety in a simulated population. Provides an opportunity for students to observe the inherent variability of estimates, observe the relationship between sample size and sampling error, and consider aspects of research design. (Author/SAH)

  8. A 96-well screen filter plate for high-throughput biological sample preparation and LC-MS/MS analysis.

    Science.gov (United States)

    Peng, Sean X; Cousineau, Martin; Juzwin, Stephen J; Ritchie, David M

    2006-01-01

    A novel 96-well screen filter plate (patent pending) has been invented to eliminate a time-consuming and labor-intensive step in preparation of in vivo study samples--to remove blood or plasma clots. These clots plug the pipet tips during a manual or automated sample-transfer step causing inaccurate pipetting or total pipetting failure. Traditionally, these blood and plasma clots are removed by picking them out manually one by one from each sample tube before any sample transfer can be made. This has significantly slowed the sample preparation process and has become a bottleneck for automated high-throughput sample preparation using robotic liquid handlers. Our novel screen filter plate was developed to solve this problem. The 96-well screen filter plate consists of 96 stainless steel wire-mesh screen tubes connected to the 96 openings of a top plate so that the screen filter plate can be readily inserted into a 96-well sample storage plate. Upon insertion, the blood and plasma clots are excluded from entering the screen tube while clear sample solutions flow freely into it. In this way, sample transfer can be easily completed by either manual or automated pipetting methods. In this report, three structurally diverse compounds were selected to evaluate and validate the use of the screen filter plate. The plasma samples of these compounds were transferred and processed in the presence and absence of the screen filter plate and then analyzed by LC-MS/MS methods. Our results showed a good agreement between the samples prepared with and without the screen filter plate, demonstrating the utility and efficiency of this novel device for preparation of blood and plasma samples. The device is simple, easy to use, and reusable. It can be employed for sample preparation of other biological fluids that contain floating particulates or aggregates.

  9. Prospects of use of cobalt nitrate as a contrast medium in electron microscopy of biological samples

    Directory of Open Access Journals (Sweden)

    I. O. Tikhankov

    2008-01-01

    Full Text Available The method of cobalt nitrate impregnation of ultrathin sections of plant and animal tissues, which are embedded in epoxy resin, has been worked out. Various aspects of such handling of specimens have been examined. Best conditions for the sections staining were determined. The advantage of this method was analyzed. The estimation of the possibilities to implicate this method for the morphological and histochemical study of various biological specimens has been made.

  10. The Constitutive Content of the Crime of Refusal or Evasion from Collecting Biological Samples According to the New Criminal Code

    OpenAIRE

    Minodora-Ioana BALAN-RUSU

    2014-01-01

    The purpose and the objectives of the research consist of examining the constitutive content of the crime of refusal or evasion from collecting biological samples according to the New Criminal Code, thus presenting some recent examples of judicial practice that may be applied in terms of new regulations imposed by the entry into force of the New Romanian Criminal Code. The research results consist of examining the constitutive content referring to judicial practice, and highlig...

  11. Active learning not associated with student learning in a random sample of college biology courses.

    Science.gov (United States)

    Andrews, T M; Leonard, M J; Colgrove, C A; Kalinowski, S T

    2011-01-01

    Previous research has suggested that adding active learning to traditional college science lectures substantially improves student learning. However, this research predominantly studied courses taught by science education researchers, who are likely to have exceptional teaching expertise. The present study investigated introductory biology courses randomly selected from a list of prominent colleges and universities to include instructors representing a broader population. We examined the relationship between active learning and student learning in the subject area of natural selection. We found no association between student learning gains and the use of active-learning instruction. Although active learning has the potential to substantially improve student learning, this research suggests that active learning, as used by typical college biology instructors, is not associated with greater learning gains. We contend that most instructors lack the rich and nuanced understanding of teaching and learning that science education researchers have developed. Therefore, active learning as designed and implemented by typical college biology instructors may superficially resemble active learning used by education researchers, but lacks the constructivist elements necessary for improving learning.

  12. Metabolomics identifies a biological response to chronic low-dose natural uranium contamination in urine samples.

    Science.gov (United States)

    Grison, Stéphane; Favé, Gaëlle; Maillot, Matthieu; Manens, Line; Delissen, Olivia; Blanchardon, Eric; Banzet, Nathalie; Defoort, Catherine; Bott, Romain; Dublineau, Isabelle; Aigueperse, Jocelyne; Gourmelon, Patrick; Martin, Jean-Charles; Souidi, Maâmar

    2013-01-01

    Because uranium is a natural element present in the earth's crust, the population may be chronically exposed to low doses of it through drinking water. Additionally, the military and civil uses of uranium can also lead to environmental dispersion that can result in high or low doses of acute or chronic exposure. Recent experimental data suggest this might lead to relatively innocuous biological reactions. The aim of this study was to assess the biological changes in rats caused by ingestion of natural uranium in drinking water with a mean daily intake of 2.7 mg/kg for 9 months and to identify potential biomarkers related to such a contamination. Subsequently, we observed no pathology and standard clinical tests were unable to distinguish between treated and untreated animals. Conversely, LC-MS metabolomics identified urine as an appropriate biofluid for discriminating the experimental groups. Of the 1,376 features detected in urine, the most discriminant were metabolites involved in tryptophan, nicotinate, and nicotinamide metabolic pathways. In particular, N-methylnicotinamide, which was found at a level seven times higher in untreated than in contaminated rats, had the greatest discriminating power. These novel results establish a proof of principle for using metabolomics to address chronic low-dose uranium contamination. They open interesting perspectives for understanding the underlying biological mechanisms and designing a diagnostic test of exposure.

  13. A high-performance direct transmethylation method for total fatty acids assessment in biological and foodstuff samples.

    Science.gov (United States)

    Castro-Gómez, Pilar; Fontecha, Javier; Rodríguez-Alcalá, Luis M

    2014-10-01

    Isolation is the main bottleneck in the analysis of fatty acids in biological samples and foods. In the last few decades some methods described direct derivatization procedures bypassing these steps. They involve the utilization of methanolic HCL or BF3 as catalysts, but several evidences from previous works suggest these reagents are unstable, lead to the formation of artifacts and alter the distribution of specific compounds as hydroxy fatty acids or CLA. However, the main issue is that they are excellent esterification reagents but poor in transterification, being not suitable for the analysis of all lipid classes and leading to erroneous composition quantitations. The present research work is a comprehensive comparison of six general methylation protocols using base, acid or base/acid catalysts plus a proposed method in the analysis of total fatty acids in lipid standards mixtures, foodstuff and biological samples. The addition of aprotic solvents to the reaction mixture to avoid alterations was also tested. Results confirmed that procedures solely involving acid catalyst resulted in incomplete derivatizations and alteration of the fatty acid profile, partially corrected by addition of the aprotic solvent. The proposed method combining sodium methoxyde and sulfuric acid showed absence of alteration of the FAME profile and the best values for response factors (short chain fatty acids to PUFA), accuracy in the determination of total cholesterol and derivatization performance, thus showing a high reliability in the determination of the total fatty acid composition in biological samples and foods.

  14. Capillary zone electrophoresis for analysis of phytochelatins and other thiol peptides in complex biological samples derivatized with monobromobimane.

    Science.gov (United States)

    Perez-Rama, Mónica; Torres Vaamonde, Enrique; Abalde Alonso, Julio

    2005-02-01

    A new method to improve the analysis of phytochelatins and their precursors (cysteine, gamma-Glu-Cys, and glutathione) derivatized with monobromobimane (mBrB) in complex biological samples by capillary zone electrophoresis is described. The effects of the background electrolyte pH, concentration, and different organic additives (acetonitrile, methanol, and trifluoroethanol) on the separation were studied to achieve optimum resolution and number of theoretical plates of the analyzed compounds in the electropherograms. Optimum separation of the thiol peptides was obtained with 150 mM phosphate buffer at pH 1.60. Separation efficiency was improved when 2.5% v/v methanol was added to the background electrolyte. The electrophoretic conditions were 13 kV and capillary dimensions with 30 cm length from the inlet to the detector (38 cm total length) and 50 microm inner diameter. The injection was by pressure at 50 mbar for 17 s. Under these conditions, the separation between desglycyl-peptides and phytochelatins was also achieved. We also describe the optimum conditions for the derivatization of biological samples with mBrB to increase electrophoretic sensitivity and number of theoretical plates. The improved method was shown to be simple, reproducible, selective, and accurate in measuring thiol peptides in complex biological samples, the detection limit being 2.5 microM glutathione at a wavelength of 390 nm.

  15. Evaluation of cadmium, lead, nickel and zinc status in biological samples of smokers and nonsmokers hypertensive patients.

    Science.gov (United States)

    Afridi, H I; Kazi, T G; Kazi, N G; Jamali, M K; Arain, M B; Sirajuddin; Baig, J A; Kandhro, G A; Wadhwa, S K; Shah, A Q

    2010-01-01

    The objective of this study was to evaluate the association between trace and toxic elements zinc (Zn), cadmium (Cd), nickel (Ni) and lead (Pb) in biological samples (scalp hair, blood and urine) of smoker and nonsmoker hypertensive patients (n=457), residents of Hyderabad, Pakistan. For the purpose of comparison, the biological samples of age-matched healthy controls were selected as referents. The concentrations of trace and toxic elements were measured by atomic absorption spectrophotometer prior to microwave-assisted acid digestion. The validity and accuracy of the methodology were checked using certified reference materials and by the conventional wet acid digestion method on the same certified reference materials and real samples. The recovery of all the studied elements was found to be in the range of 97.8-99.3% in certified reference materials. The results of this study showed that the mean values of Cd, Ni and Pb were significantly higher in scalp hair, blood and urine samples of both smoker and nonsmoker patients than in referents (P<0.001), whereas the concentration of Zn was lower in the scalp hair and blood, but higher in the urine samples of hypertensive patients. The deficiency of Zn and the high exposure of toxic metals as a result of tobacco smoking may be synergistic with risk factors associated with hypertension.

  16. Quantifying microplastic pollution on sandy beaches: the conundrum of large sample variability and spatial heterogeneity.

    Science.gov (United States)

    Fisner, Mara; Majer, Alessandra P; Balthazar-Silva, Danilo; Gorman, Daniel; Turra, Alexander

    2017-05-01

    Despite the environmental risks posed by microplastic pollution, there are presently few standardized protocols for monitoring these materials within marine and coastal habitats. We provide a robust comparison of methods for sampling microplastics on sandy beaches using pellets as a model and attempt to define a framework for reliable standing stock estimation. We performed multiple comparisons to determine: (1) the optimal size of sampling equipment, (2) the depth to which samples should be obtained, (3) the optimal sample resolution for cross-shore transects, and (4) the number of transects required to yield reproducible along-shore estimates across the entire sections of a beach. Results affirmed that the use of a manual auger with a 20-cm diameter yielded the best compromise between reproducibility (i.e., standard deviation) and sampling/processing time. Secondly, we suggest that sediments should be profiled to a depth of at least 1 m to fully assess the depth distribution of pellets. Thirdly, although sample resolution did not have major consequence for overall density estimates, using 7-m intervals provides an optimal balance between precision (SD) and effort (total sampling time). Finally, and perhaps most importantly, comparing the minimum detectable difference yielded by different numbers of transects along a given section of beach suggests that estimating absolute particle density is probably unviable for most systems and that monitoring might be better accomplished through hierarchical or time series sampling efforts. Overall, while our study provides practical information that can improve sampling efforts, the heterogeneous nature of microplastic pollution poses a major conundrum to reproducible monitoring and management of this significant and growing problem.

  17. Automatic sampling for unbiased and efficient stereological estimation using the proportionator in biological studies

    DEFF Research Database (Denmark)

    Gardi, Jonathan Eyal; Nyengaard, Jens Randel; Gundersen, Hans Jørgen Gottlieb

    2008-01-01

    cerebellum, total number of orexin positive neurons in transgenic mice brain, and estimating the absolute area and the areal fraction of β islet cells in dog pancreas.  The proportionator was at least eight times more efficient (precision and time combined) than traditional computer controlled sampling.......Quantification of tissue properties is improved using the general proportionator sampling and estimation procedure: automatic image analysis and non-uniform sampling with probability proportional to size (PPS). The complete region of interest is partitioned into fields of view, and every field...

  18. Fluorometric quantification of protoporphyrin IX in biological skin samples from in vitro penetration/permeation studies

    Directory of Open Access Journals (Sweden)

    Fábia Cristina Rossetti

    2010-12-01

    Full Text Available A fluorometric analytical method was developed for quantification of protoporphyrin IX (PpIX in skin samples and receptor phase solution after in vitro cutaneous penetration/permeation studies. Analytical conditions used were: excitation and emission wavelengths: 400 nm and 632 nm; bandwidth: 0.5 nm; excitation and emission slits: 10/10. PpIX was recovered from two different layers of skin, the stratum corneum (SC and the epidermis plus dermis ([E+D], by vortex homogenization, probe and bath sonication, using DMSO as an extraction solvent. The detection and quantification limits were 0.002 and 0.005 μg/mL, respectively. The assay was linear from 0.005 - 0.5 μg/mL. The within-day and between-day assay precision and accuracy in DMSO and receptor phase solution were each studied at the two concentration levels 0.04 and 0.2 μg/mL, and 0.01 and 0.08 μg/mL, respectively. The coefficients of variation and deviation from the theoretical values were lower than 5%. The skin recovery of PpIX from SC and [E+D] layers using two different concentrations (0.5 and 1.0 μg/mL were all above 90.0%. The method described has potential application to in vitro penetration/permeation studies of PpIX using porcine skin as a biological membrane model.Um método analítico por espectrofluorimetria foi desenvolvido para quantificar a protoporfirina IX (Pp IX em amostras de pele e fase receptora após a realização de testes in vitro de penetração/permeação cutâneas. As condições analíticas utilizadas foram: comprimentos de onda de excitação e emissão: 400 nm e 632 nm; largura de banda: 0,5 nm; fendas de excitação e emissão: 10/10. A PpIX foi extraída de amostras de estrato córneo (EC e da epiderme sem estrato córneo + derme ([E+D] através da agitação em vórtex e sonicação por haste e banho, utilizando-se o DMSO como solvente extrator. O limite de detecção e quantificação foram, respectivamente, de 0,002 e 0,005 μg/mL. O método mostrou

  19. Ultrasound-assisted extraction followed by disposable pipette purification for the determination of polychlorinated biphenyls in small-size biological tissue samples.

    Science.gov (United States)

    Pena-Abaurrea, M; García de la Torre, V S; Ramos, L

    2013-11-22

    The use of solid-phase extraction pipette tip (also called disposable pipette extraction, DPX) has been evaluated for the purification of environmentally relevant polychlorinated biphenyls (PCBs) in fatty extracts obtained by ultrasound-assisted extraction with a sonication probe from small-size biological tissues. Complete sample treatment involved only 50 mg of sample and was completed in ca. 15 min with minimal sample manipulation and reagents consumption (i.e., 1.5 mL of n-hexane and 0.8 g of acidic silica). The performance of the proposed methodology for the intended determination was firstly evaluated by determination of the endogenous PCB levels in a naturally contaminated internal reference material. The determined concentrations showed a good agreement with those obtained using a more conventional sample preparation procedure previously validated in our laboratory (recoveries, as compared to levels determined using the latter method, were in the 85-123% range for a large majority of the studied congeners, and the relative standard deviations were in general lower than 14%). Results obtained for the analysis of reference food samples and certified reference materials NIST 1945 and 1947 demonstrated that, when combined with gas chromatography coupled to ion trap mass spectrometry working in the tandem mode, GC-ITD(MS/MS), the proposed methodology allowed accurate determination of most of the investigated PCBs and that 50 mg of sample sufficed for the screening of less abundant toxic congeners. Copyright © 2013 Elsevier B.V. All rights reserved.

  20. Large-scale mapping of transposable element insertion sites using digital encoding of sample identity.

    Science.gov (United States)

    Gohl, Daryl M; Freifeld, Limor; Silies, Marion; Hwa, Jennifer J; Horowitz, Mark; Clandinin, Thomas R

    2014-03-01

    Determining the genomic locations of transposable elements is a common experimental goal. When mapping large collections of transposon insertions, individualized amplification and sequencing is both time consuming and costly. We describe an approach in which large numbers of insertion lines can be simultaneously mapped in a single DNA sequencing reaction by using digital error-correcting codes to encode line identity in a unique set of barcoded pools.

  1. Significance of stromal-1 and stromal-2 signatures and biologic prognostic model in diffuse large B-cell lymphoma

    Science.gov (United States)

    Abdou, Asmaa Gaber; Asaad, Nancy; Kandil, Mona; Shabaan, Mohammed; Shams, Asmaa

    2017-01-01

    Objective : Diffuse Large B Cell Lymphoma (DLBCL) is a heterogeneous group of tumors with different biological and clinical characteristics that have diverse clinical outcomes and response to therapy. Stromal-1 signature of tumor microenvironment of DLBCL represents extracellular matrix deposition and histiocytic infiltrate, whereas stromal-2 represents angiogenesis that could affect tumor progression. Methods : The aim of the present study is to assess the significance of stromal-1 signature using SPARC-1 and stromal-2 signature using CD31 expression and then finally to construct biologic prognostic model (BPM) in 60 cases of DLBCL via immunohistochemistry. Results : Microvessel density (PBPM showed that 42 cases (70%) were of low biologic score (0–1) and 18 cases (30%) were of high biologic score (2–3). Low BPM cases showed less probability for splenic involvement (P=0.04) and a higher rate of complete response to therapy compared with high score cases (P=0.08). Conclusions : The DLBCL microenvironment could modulate tumor progression behavior since angiogenesis and SPARC positive stromal cells promote dissemination by association with spleen involvement and capsular invasion. Biologic prognostic models, including modified BPM, which considered cell origin of DLBCL and stromal signature pathways, could determine DLBCL progression and response to therapy. PMID:28607806

  2. Environmental contaminants in water, sediment and biological samples from Playa Lakes in southeastern New Mexico - 1992

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Sediment, water, bird tissue, and invertebrates were collected from 10 playa lakes in Southeastern New Mexico in 1991 and 1992. These samples were analyzed for a...

  3. Oxygen bomb combustion of biological samples for inductively coupled plasma optical emission spectrometry

    Science.gov (United States)

    Souza, Gilberto B.; Carrilho, Elma Neide V. M.; Oliveira, Camila V.; Nogueira, Ana Rita A.; Nóbrega, Joaquim A.

    2002-12-01

    A rapid sample preparation method is proposed for decomposition of milk powder, corn bran, bovine and fish tissues, containing certified contents of the analytes. The procedure involves sample combustion in a commercial stainless steel oxygen bomb operating at 25 bar. Most of the samples were decomposed within 5 min. Diluted nitric acid or water-soluble tertiary amines 10% v/v were used as absorption solutions. Calcium, Cu, K, Mg, Na, P, S and Zn were recovered with the bomb washings and determined by inductively coupled plasma optical emission spectrometry (ICP-OES). Ethanol mixed with paraffin was used as a combustion aid to allow complete combustion. A cooling step prior releasing of the bomb valve was employed to increase the efficiency of sample combustion. Iodine was also determined in milk samples spiked with potassium iodide to evaluate the volatilization and collection of iodine in amine CFA-C medium and the feasibility of its determination by ICP-OES with axial view configuration. Most of the element recoveries in the samples were between 91 and 105% and the certified and found contents exhibited a fair agreement at a 95% confidence level.

  4. Accelerating Computation of Large Biological Datasets using MapReduce Framework.

    Science.gov (United States)

    Wang, Chao; Dai, Dong; Li, Xi; Wang, Aili; Zhou, Xuehai

    2016-04-05

    The maximal information coefficient (MIC) has been proposed to discover relationships and associations between pairs of variables. It poses significant challenges for bioinformatics scientists to accelerate the MIC calculation, especially in genome sequencing and biological annotations. In this paper we explore a parallel approach which uses MapReduce framework to improve the computing efficiency and throughput of the MIC computation. The acceleration system includes biological data storage on HDFS, preprocessing algorithms, distributed memory cache mechanism, and the partition of MapReduce jobs. Based on the acceleration approach, we extend the traditional two-variable algorithm to multiple variables algorithm. The experimental results show that our parallel solution provides a linear speedup comparing with original algorithm without affecting the correctness and sensitivity.

  5. The Sum of the Parts: Large-scale Modeling in Systems Biology

    DEFF Research Database (Denmark)

    Fridolin, Gross; Green, Sara

    2017-01-01

    these questions, we distinguish between two types of reductionism, namely 'modular reductionism' and 'bottom-up reductionism'. Much knowledge in molecular biology has been gained by decomposing living systems into functional modules or through detailed studies of molecular processes. We ask whether systems...... biology provides novel ways to ​ ​recompose these findings in the context of the system as a whole via computational simulations. As an example of computational integration of modules, we analyze the first whole-cell model of the bacterium ​ ​M. genitalium. Secondly, we examine the attempt to recompose...... processes across different spatial scales via multi-scale cardiac models. Although these models also rely on a number of idealizations and simplifying assumptions, we argue that they provide insight into the limitations of reductionist approaches. Whole-cell models can be used to discover properties arising...

  6. Computation of the effective mechanical response of biological networks accounting for large configuration changes.

    Science.gov (United States)

    El Nady, K; Ganghoffer, J F

    2016-05-01

    The asymptotic homogenization technique is involved to derive the effective elastic response of biological membranes viewed as repetitive beam networks. Thereby, a systematic methodology is established, allowing the prediction of the overall mechanical properties of biological membranes in the nonlinear regime, reflecting the influence of the geometrical and mechanical micro-parameters of the network structure on the overall response of the equivalent continuum. Biomembranes networks are classified based on nodal connectivity, so that we analyze in this work 3, 4 and 6-connectivity networks, which are representative of most biological networks. The individual filaments of the network are described as undulated beams prone to entropic elasticity, with tensile moduli determined from their persistence length. The effective micropolar continuum evaluated as a continuum substitute of the biological network has a kinematics reflecting the discrete network deformation modes, involving a nodal displacement and a microrotation. The statics involves the classical Cauchy stress and internal moments encapsulated into couple stresses, which develop internal work in duality to microcurvatures reflecting local network undulations. The relative ratio of the characteristic bending length of the effective micropolar continuum to the unit cell size determines the relevant choice of the equivalent medium. In most cases, the Cauchy continuum is sufficient to model biomembranes. The peptidoglycan network may exhibit a re-entrant hexagonal configuration due to thermal or pressure fluctuations, for which micropolar effects become important. The homogenized responses are in good agreement with FE simulations performed over the whole network. The predictive nature of the employed homogenization technique allows the identification of a strain energy density of a hyperelastic model, for the purpose of performing structural calculations of the shape evolutions of biomembranes.

  7. The latest advancements in proteomic two-dimensional gel electrophoresis analysis applied to biological samples.

    Science.gov (United States)

    Santucci, Laura; Bruschi, Maurizio; Ghiggeri, Gian Marco; Candiano, Giovanni

    2015-01-01

    Two-dimensional gel electrophoresis (2DE) is one of the fundamental approaches in proteomics for the separation and visualization of complex protein mixtures. Proteins can be analyzed by 2DE using isoelectric focusing (IEF) in the first dimension, combined to sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) in the second dimension, gel staining (silver and Coomassie), image analysis, and 2DE gel database. High-resolution 2DE can resolve up to 5,000 different proteins simultaneously (∼2,000 proteins routinely), and detect and quantify <1 ng of protein per spot. Here, we describe the latest developments for a more complete analysis of biological fluids.

  8. Performance of the goulden large-sample extractor in multiclass pesticide isolation and preconcentration from stream water

    Science.gov (United States)

    Foster, G.D.; Foreman, W.T.; Gates, Paul M.

    1991-01-01

    The reliability of the Goulden large-sample extractor in preconcentrating pesticides from water was evaluated from the recoveries of 35 pesticides amended to filtered stream waters. Recoveries greater than 90% were observed for many of the pesticides in each major chemical class, but recoveries for some of the individual pesticides varied in seemingly unpredictable ways. Corrections cannot yet be factored into liquid-liquid extraction theory to account for matrix effects, which were apparent between the two stream waters tested. The Goulden large-sample extractor appears to be well suited for rapid chemical screening applications, with quantitative analysis requiring special quality control considerations. ?? 1991 American Chemical Society.

  9. The Role of Family Environment in Depressive Symptoms among University Students: A Large Sample Survey in China

    OpenAIRE

    Yunmiao Yu; Xiuxian Yang; Yanjie Yang; Lu Chen; Xiaohui Qiu; Zhengxue Qiao; Jiawei Zhou; Hui Pan; Bo Ban; Xiongzhao Zhu; Jincai He; Yongqing Ding; Bing Bai

    2015-01-01

    Objective To explore the relationship between family environment and depressive symptoms and to evaluate the influence of hard and soft family environmental factors on depression levels in a large sample of university students in China. Methods A multi-stage stratified sampling procedure was used to select 6,000 participants. The response rate was 88.8%, with 5,329 students completing the Beck Depression Inventory (BDI) and the Family Environment Scale Chinese Version (FES-CV), which was adap...

  10. Development of a radioimmunoassay for the determination of buprenorphine in biological samples

    Energy Technology Data Exchange (ETDEWEB)

    Debrabandere, L.; Boven, M. Van; Daenens, P. (Louvain Univ. (Belgium))

    1993-02-01

    The development of a specific and sensitive radioimmunoassay for the detection of buprenorphine in urine samples is described. With minor adjustments, the assay was also applied to the analysis for buprenorphine in plasma samples. The 2-diazobenzoic acid derivative of buprenorphine has been prepared as a hapten. The immunization of rabbits with the hapten-bovine serum albumin conjugate resulted in the production of antibodies, which cross-reacted with N-dealkylbuprenophine up to about the 90% level. The antibodies showed very low cross-reactivities with the 3-O-glucuronides and with the structural analogue etorphine. The assay was mainly used to prescreen for buprenorphine in urine samples of persons suspected of Temgesic misuse and to determine buprenorphine in plasma samples. A linear calibration graph for buprenorphine was obtained after logit-log regression. The spiking recovery study showed a linear regression. Intra-and inter-assay relative standard deviations were < 4.35 and < 6.36%, respectively. A comparison study of the high-performance liquid chromatographic determination (X) to the radioimmunoassay (Y) resulted in the following regression equation for the urine samples: Y = 1.44 + 1.64 X (n = 32; r 0.910) and Y = 0.007 + 1.58 X (n = 10; r = 0.930) for plasma specimens. The minimum detectable dose of the immunoassay was calculated to be 10 pg ml[sup -1] (Student's t-distribution, p 0.01, degrees of freedom = 8). (Author).

  11. Enrichment of diluted cell populations from large sample volumes using 3D carbon-electrode dielectrophoresis.

    Science.gov (United States)

    Islam, Monsur; Natu, Rucha; Larraga-Martinez, Maria Fernanda; Martinez-Duarte, Rodrigo

    2016-05-01

    Here, we report on an enrichment protocol using carbon electrode dielectrophoresis to isolate and purify a targeted cell population from sample volumes up to 4 ml. We aim at trapping, washing, and recovering an enriched cell fraction that will facilitate downstream analysis. We used an increasingly diluted sample of yeast, 10(6)-10(2) cells/ml, to demonstrate the isolation and enrichment of few cells at increasing flow rates. A maximum average enrichment of 154.2 ± 23.7 times was achieved when the sample flow rate was 10 μl/min and yeast cells were suspended in low electrically conductive media that maximizes dielectrophoresis trapping. A COMSOL Multiphysics model allowed for the comparison between experimental and simulation results. Discussion is conducted on the discrepancies between such results and how the model can be further improved.

  12. A Large, First-Year, Introductory, Multi-Sectional Biological Concepts of Health Course Designed to Develop Skills and Enhance Deeper Learning

    Science.gov (United States)

    Murrant, Coral L.; Dyck, David J.; Kirkland, James B.; Newton, Genevieve S.; Ritchie, Kerry L.; Tishinsky, Justine M.; Bettger, William J.; Richardson, Nicolette S.

    2015-01-01

    Large first-year biology classes, with their heavy emphasis on factual content, contribute to low student engagement and misrepresent the dynamic, interdisciplinary nature of biological science. We sought to redesign a course to deliver fundamental biology curriculum through the study of health, promote skills development, and encourage a deeper…

  13. Supercritical Fluid Extraction and Ultra Performance Liquid Chromatography of Respiratory Quinones for Microbial Community Analysis in Environmental and Biological Samples

    Directory of Open Access Journals (Sweden)

    Koichi Fujie

    2012-03-01

    Full Text Available Microbial community structure plays a significant role in environmental assessment and animal health management. The development of a superior analytical strategy for the characterization of microbial community structure is an ongoing challenge. In this study, we developed an effective supercritical fluid extraction (SFE and ultra performance liquid chromatography (UPLC method for the analysis of bacterial respiratory quinones (RQ in environmental and biological samples. RQ profile analysis is one of the most widely used culture-independent tools for characterizing microbial community structure. A UPLC equipped with a photo diode array (PDA detector was successfully applied to the simultaneous determination of ubiquinones (UQ and menaquinones (MK without tedious pretreatment. Supercritical carbon dioxide (scCO2 extraction with the solid-phase cartridge trap proved to be a more effective and rapid method for extracting respiratory quinones, compared to a conventional organic solvent extraction method. This methodology leads to a successful analytical procedure that involves a significant reduction in the complexity and sample preparation time. Application of the optimized methodology to characterize microbial communities based on the RQ profile was demonstrated for a variety of environmental samples (activated sludge, digested sludge, and compost and biological samples (swine and Japanese quail feces.

  14. Supercritical fluid extraction and ultra performance liquid chromatography of respiratory quinones for microbial community analysis in environmental and biological samples.

    Science.gov (United States)

    Hanif, Muhammad; Atsuta, Yoichi; Fujie, Koichi; Daimon, Hiroyuki

    2012-03-05

    Microbial community structure plays a significant role in environmental assessment and animal health management. The development of a superior analytical strategy for the characterization of microbial community structure is an ongoing challenge. In this study, we developed an effective supercritical fluid extraction (SFE) and ultra performance liquid chromatography (UPLC) method for the analysis of bacterial respiratory quinones (RQ) in environmental and biological samples. RQ profile analysis is one of the most widely used culture-independent tools for characterizing microbial community structure. A UPLC equipped with a photo diode array (PDA) detector was successfully applied to the simultaneous determination of ubiquinones (UQ) and menaquinones (MK) without tedious pretreatment. Supercritical carbon dioxide (scCO(2)) extraction with the solid-phase cartridge trap proved to be a more effective and rapid method for extracting respiratory quinones, compared to a conventional organic solvent extraction method. This methodology leads to a successful analytical procedure that involves a significant reduction in the complexity and sample preparation time. Application of the optimized methodology to characterize microbial communities based on the RQ profile was demonstrated for a variety of environmental samples (activated sludge, digested sludge, and compost) and biological samples (swine and Japanese quail feces).

  15. Measurement of the unstained biological sample by a novel scanning electron generation X-ray microscope based on SEM.

    Science.gov (United States)

    Ogura, Toshihiko

    2009-08-01

    We introduced a novel X-ray microscope system based on scanning electron microscopy using thin film, which enables the measurement of unstained biological samples without damage. An unstained yeast sample was adsorbed under a titanium (Ti)-coated silicon nitride (Si3N4) film 90 nm thick. The X-ray signal from the film was detected by an X-ray photodiode (PD) placed below the sample. With an electron beam at 2.6 kV acceleration and 6.75 nA current, the yeast image is obtained using the X-ray PD. The image is created by soft X-rays from the Ti layer. The Ti layer is effective in generating the characteristic 2.7-nm wavelength X-rays by the irradiation of electrons. Furthermore, we investigated the electron trajectory and the generation of the characteristic X-rays within the Ti-coated Si3N4 film by Monte Carlo simulation. Our system can be easily utilized to observe various unstained biological samples of cells, bacteria, and viruses.

  16. Optical multiband surface photometry of a sample of Seyfert galaxies. I. Large-scale morphology and local environment analysis of matched Seyfert and inactive galaxy samples

    CERN Document Server

    Slavcheva-Mihova, L; 10.1051/0004-6361/200913243

    2010-01-01

    Parallel analysis of the large-scale morphology and local environment of matched active and control galaxy samples plays an important role in studies of the fueling of active galactic nuclei. We carry out a detailed morphological characterization of a sample of 35 Seyfert galaxies and a matched sample of inactive galaxies in order to compare the evidence of non-axisymmetric perturbation of the potential and, in the second part of this paper, to be able to perform a multicomponent photometric decomposition of the Seyfert galaxies. We constructed contour maps, BVRcIc profiles of the surface brightness, ellipticity, and position angle, as well as colour index profiles. We further used colour index images, residual images, and structure maps, which helped clarify the morphology of the galaxies. We studied the presence of close companions using literature data. By straightening out the morphological status of some of the objects, we derived an improved morphological classification and built a solid basis for a fur...

  17. Diffraction enhanced imaging and x-ray fluorescence microtomography for analyzing biological samples

    Energy Technology Data Exchange (ETDEWEB)

    Rocha, H.S.; Pereira, G.R.; Lopes, R.T. [Laboratorio de Instrumentacao Nuclear-COPPE/UFRJ-RJ (Brazil); Anjos, M.J. [Instituto de Fisica-UERJ-RJ (Brazil); Faria, P. [Instituto Nacional do Cancer-INCa-RJ (Brazil); Kellermann, G.; Perez, C.A. [Laboratorio Nacional de Luz Sincrotron-Campinas-SP (Brazil); Tirao, G. [Faculdad de Mat. Astronomia y Fisica (FAMAF), UNC. Cordoba (Argentina); Mazzaro, I. [Laboratorio de Optica de Raios X e Instrumentacao-UFPR-Curitiba-PR (Brazil); Giles, C. [Laboratorio de Cristalografia Aplicada e Raios X-UNICAMP-Campinas-SP (Brazil)

    2007-07-15

    In this work, breast tissue samples were investigated in order to verify the distribution of certain elements by x-ray fluorescence computed tomography (XRFCT) correlated with the characteristics and pathology of each tissue observed by diffraction enhanced imaging (DEI). The DEI system can show details in low attenuation tissues. It is based on the contrast imaging obtained by extinction, diffraction and refraction characteristics and can improve reduction in false positive and false negative diagnoses. XRFCT allows mapping of all elements within the sample, since even a minute fluorescence signal can be detected. DEI imaging techniques revealed the complex structure of the disease, confirmed by the histological section, and showed microstructures in all planes of the sample. The XRFCT showed the distribution of Zn, Cu and Fe at higher concentration. (authors)

  18. A combined method for correlative 3D imaging of biological samples from macro to nano scale

    Science.gov (United States)

    Kellner, Manuela; Heidrich, Marko; Lorbeer, Raoul-Amadeus; Antonopoulos, Georgios C.; Knudsen, Lars; Wrede, Christoph; Izykowski, Nicole; Grothausmann, Roman; Jonigk, Danny; Ochs, Matthias; Ripken, Tammo; Kühnel, Mark P.; Meyer, Heiko

    2016-10-01

    Correlative analysis requires examination of a specimen from macro to nano scale as well as applicability of analytical methods ranging from morphological to molecular. Accomplishing this with one and the same sample is laborious at best, due to deformation and biodegradation during measurements or intermediary preparation steps. Furthermore, data alignment using differing imaging techniques turns out to be a complex task, which considerably complicates the interconnection of results. We present correlative imaging of the accessory rat lung lobe by combining a modified Scanning Laser Optical Tomography (SLOT) setup with a specially developed sample preparation method (CRISTAL). CRISTAL is a resin-based embedding method that optically clears the specimen while allowing sectioning and preventing degradation. We applied and correlated SLOT with Multi Photon Microscopy, histological and immunofluorescence analysis as well as Transmission Electron Microscopy, all in the same sample. Thus, combining CRISTAL with SLOT enables the correlative utilization of a vast variety of imaging techniques.

  19. Development of a Solid Phase Extraction Method for Agricultural Pesticides in Large-Volume Water Samples

    Science.gov (United States)

    An analytical method using solid phase extraction (SPE) and analysis by gas chromatography/mass spectrometry (GC/MS) was developed for the trace determination of a variety of agricultural pesticides and selected transformation products in large-volume high-elevation lake water sa...

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

    Science.gov (United States)

    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.

  1. Gender Differences in Achievement in a Large, Nationally Representative Sample of Children and Adolescents

    Science.gov (United States)

    Scheiber, Caroline; Reynolds, Matthew R.; Hajovsky, Daniel B.; Kaufman, Alan S.

    2015-01-01

    The purpose of this study was to investigate developmental gender differences in academic achievement areas, with the primary focus on writing, using the child and adolescent portion (ages 6-21 years) of the "Kaufman Test of Educational Achievement-Second Edition, Brief Form," norming sample (N = 1,574). Path analytic models with gender,…

  2. Homogenization of sample absorption for the imaging of large and dense fossils with synchrotron microtomography.

    Science.gov (United States)

    Sanchez, Sophie; Fernandez, Vincent; Pierce, Stephanie E; Tafforeau, Paul

    2013-09-01

    Propagation phase-contrast synchrotron radiation microtomography (PPC-SRμCT) has proved to be very successful for examining fossils. Because fossils range widely in taphonomic preservation, size, shape and density, X-ray computed tomography protocols are constantly being developed and refined. Here we present a 1-h procedure that combines a filtered high-energy polychromatic beam with long-distance PPC-SRμCT (sample to detector: 4-16 m) and an attenuation protocol normalizing the absorption profile (tested on 13-cm-thick and 5.242 g cm(-3) locally dense samples but applicable to 20-cm-thick samples). This approach provides high-quality imaging results, which show marked improvement relative to results from images obtained without the attenuation protocol in apparent transmission, contrast and signal-to-noise ratio. The attenuation protocol involves immersing samples in a tube filled with aluminum or glass balls in association with a U-shaped aluminum profiler. This technique therefore provides access to a larger dynamic range of the detector used for tomographic reconstruction. This protocol homogenizes beam-hardening artifacts, thereby rendering it effective for use with conventional μCT scanners.

  3. Autosomal STR allele frequencies for the CODIS system from a large random population sample in Chile.

    Science.gov (United States)

    Vergara, Ismael A; Villouta, Pamela; Herrera, Sandra; Melo, Francisco

    2012-05-01

    The thirteen autosomal STR loci of the CODIS system were typed from DNA of 732 unrelated male individuals sampled from different locations in Chile. This is the first report of allele frequencies for the thirteen STRs loci defined in the CODIS system from the Chilean population.

  4. Moderators of implicit and explicit drinking identity in a large US adult sample.

    Science.gov (United States)

    Lindgren, Kristen P; Gasser, Melissa L; Werntz, Alexandra; Namaky, Nauder; Baldwin, Scott A; Teachman, Bethany A

    2016-09-01

    Drinking identity (viewing oneself as a drinker) is a potential risk factor for problematic drinking in US undergraduate samples. Whether that risk extends to a broader, more general US sample is unknown. Additionally, there are critical, unanswered questions with respect to moderators of the drinking identity-problematic drinking relationship; an important issue for designing prevention efforts. Study aims were to assess the unique associations and interactive effects of implicit and explicit measures of drinking identity on problematic drinking, and to evaluate age and sex as potential moderators of the drinking identity-problematic drinking relationship. A sample of 11,320 adults aged 18-98 completed measures of implicit and explicit drinking identity and problematic drinking (the Alcohol Use Disorder Identification Test; AUDIT). Implicit and explicit drinking identity had positive, significant associations with AUDIT scores, as expected. Moderation analyses indicated small, but significant, interactions. There was an implicit by explicit identity interaction consistent with a synergistic effect: lower implicit and explicit identity was linked to a greater probability of being a non-drinker. Age moderated explicit but not implicit identity: lower drinking identity appeared to be more protective for younger individuals. Sex moderated implicit but not explicit identity: a weaker positive association with implicit identity and AUDIT scores was observed among men, potentially reflecting stigma against women's drinking. Findings suggest that drinking identity's potential as a risk factor for problematic drinking extends to a more general US sample and that both implicit and explicit identity should be targeted in prevention efforts.

  5. Effect of Comorbidity on Treatment of Anxious Children and Adolescents: Results from a Large, Combined Sample

    Science.gov (United States)

    Rapee, Ronald M.; Lyneham, Heidi J.; Hudson, Jennifer L.; Kangas, Maria; Wuthrich, Viviana M.; Schniering, Carolyn A.

    2013-01-01

    Objective: The purpose of the present study was to evaluate the influence of comorbid disorders on the degree of change and the endpoint of cognitive-behavioral treatment in anxious young people. Method: Data on 750 children 6 to 18 years old were compiled from different samples within one clinic. All children had a primary anxiety disorder and…

  6. Set-up and calibration of a method to measure 10B concentration in biological samples by neutron autoradiography

    Science.gov (United States)

    Gadan, M. A.; Bortolussi, S.; Postuma, I.; Ballarini, F.; Bruschi, P.; Protti, N.; Santoro, D.; Stella, S.; Cansolino, L.; Clerici, A.; Ferrari, C.; Zonta, A.; Zonta, C.; Altieri, S.

    2012-03-01

    A selective uptake of boron in the tumor is the base of Boron Neutron Capture Therapy, which can destroy the tumor substantially sparing the normal tissue. In order to deliver a lethal dose to the tumor, keeping the dose absorbed by normal tissues below the tolerance level, it is mandatory to know the 10B concentration present in each kind of tissue at the moment of irradiation. This work presents the calibration procedure adopted for a boron concentration measurement method based on neutron autoradiography, where biological samples are deposited on sensitive films and irradiated in the thermal column of the TRIGA reactor (University of Pavia). The latent tracks produced in the film by the charged particles coming from the neutron capture in 10B are made visible by a proper etching, allowing the measurement of the track density. A calibration procedure with standard samples provides curves of track density as a function of boron concentration, to be used in the measurement of biological samples. In this paper, the bulk etch rate parameter and the calibration curves obtained for both liquid samples and biological tissues with known boron concentration are presented. A bulk etch rate value of (1.64 ± 0.02) μm/h and a linear dependence with etching time were found. The plots representing the track density versus the boron concentration in a range between 5 and 50 μg/g (ppm) are linear, with an angular coefficient of (1.614 ± 0.169)·10-3 tracks/(μm2 ppm) for liquids and (1.598 ± 0.097)·10-2 tracks/(μm2 ppm) for tissues.

  7. Parallel workflow manager for non-parallel bioinformatic applications to solve large-scale biological problems on a supercomputer.

    Science.gov (United States)

    Suplatov, Dmitry; Popova, Nina; Zhumatiy, Sergey; Voevodin, Vladimir; Švedas, Vytas

    2016-04-01

    Rapid expansion of online resources providing access to genomic, structural, and functional information associated with biological macromolecules opens an opportunity to gain a deeper understanding of the mechanisms of biological processes due to systematic analysis of large datasets. This, however, requires novel strategies to optimally utilize computer processing power. Some methods in bioinformatics and molecular modeling require extensive computational resources. Other algorithms have fast implementations which take at most several hours to analyze a common input on a modern desktop station, however, due to multiple invocations for a large number of subtasks the full task requires a significant computing power. Therefore, an efficient computational solution to large-scale biological problems requires both a wise parallel implementation of resource-hungry methods as well as a smart workflow to manage multiple invocations of relatively fast algorithms. In this work, a new computer software mpiWrapper has been developed to accommodate non-parallel implementations of scientific algorithms within the parallel supercomputing environment. The Message Passing Interface has been implemented to exchange information between nodes. Two specialized threads - one for task management and communication, and another for subtask execution - are invoked on each processing unit to avoid deadlock while using blocking calls to MPI. The mpiWrapper can be used to launch all conventional Linux applications without the need to modify their original source codes and supports resubmission of subtasks on node failure. We show that this approach can be used to process huge amounts of biological data efficiently by running non-parallel programs in parallel mode on a supercomputer. The C++ source code and documentation are available from http://biokinet.belozersky.msu.ru/mpiWrapper .

  8. CASP10-BCL::Fold efficiently samples topologies of large proteins.

    Science.gov (United States)

    Heinze, Sten; Putnam, Daniel K; Fischer, Axel W; Kohlmann, Tim; Weiner, Brian E; Meiler, Jens

    2015-03-01

    During CASP10 in summer 2012, we tested BCL::Fold for prediction of free modeling (FM) and template-based modeling (TBM) targets. BCL::Fold assembles the tertiary structure of a protein from predicted secondary structure elements (SSEs) omitting more flexible loop regions early on. This approach enables the sampling of conformational space for larger proteins with more complex topologies. In preparation of CASP11, we analyzed the quality of CASP10 models throughout the prediction pipeline to understand BCL::Fold's ability to sample the native topology, identify native-like models by scoring and/or clustering approaches, and our ability to add loop regions and side chains to initial SSE-only models. The standout observation is that BCL::Fold sampled topologies with a GDT_TS score > 33% for 12 of 18 and with a topology score > 0.8 for 11 of 18 test cases de novo. Despite the sampling success of BCL::Fold, significant challenges still exist in clustering and loop generation stages of the pipeline. The clustering approach employed for model selection often failed to identify the most native-like assembly of SSEs for further refinement and submission. It was also observed that for some β-strand proteins model refinement failed as β-strands were not properly aligned to form hydrogen bonds removing otherwise accurate models from the pool. Further, BCL::Fold samples frequently non-natural topologies that require loop regions to pass through the center of the protein. © 2015 Wiley Periodicals, Inc.

  9. Comparative quantification of Campylobacter jejuni from environmental samples using traditional and molecular biological techniques.

    Science.gov (United States)

    Rothrock, Michael J; Cook, Kimberly L; Bolster, Carl H

    2009-06-01

    Campylobacter jejuni is one of the most common causes of gastroenteritis in the world. Given the potential risks to human, animal, and environmental health, the development and optimization of methods to quantify this important pathogen in environmental samples is essential. Two of the most commonly used methods for quantifying C. jejuni are selective plate counting and quantitative real-time PCR (qPCR). Unfortunately, little comparative research has been performed to evaluate the accuracy of these methods for quantification of C. jejuni in aqueous and solid matricies. In this study, the limit of detection and the level of resolution obtained using these 2 methods was evaluated for C. jejuni and compared with that of the common indicator organism Escherichia coli. The use of selective plate count media for quantification of C. jejuni resulted in a 0.7-1.2 log underestimation of cell concentrations, compared with qPCR in both water and column leachate samples, whereas E. coli concentrations were found to be similar with either technique. For C. jejuni, only the qPCR assay accurately measured 2-fold changes in cell concentrations in water samples, whereas concentrations of E. coli were accurately measured regardless of method. Based on these data, qPCR assays were found to be more accurate than selective plate counts for quantification of C. jejuni from environmental samples.

  10. Phase microscopy of technical and biological samples through random phase modulation with a difuser

    DEFF Research Database (Denmark)

    Almoro, Percival; Pedrini, Giancarlo; Gundu, Phanindra Narayan

    2010-01-01

    A technique for phase microscopy using a phase diffuser and a reconstruction algorithm is proposed. A magnified specimen wavefront is projected on the diffuser plane that modulates the wavefront into a speckle field. The speckle patterns at axially displaced planes are sampled and used in an iter...

  11. Detection of mutant protein in complex biological samples: Glucocerebrosidase mutations in Gaucher’s disease

    NARCIS (Netherlands)

    Bleijlevens, B.; van Breemen, M.J.; Donker-Koopman, W.E.; de Koster, C.G.; Aerts, J.M.F.G.

    2008-01-01

    We report a sensitive method to detect point mutations in proteins from complex samples. The method is based on surface-enhanced laser desorption/ionization time-of-flight (SELDI-ToF) MS but can be extended to other MS platforms. The target protein in this study is the lysosomal enzyme glucocerebros

  12. Determination of total magnesium in biological samples using electrothermal atomic absorption spectrometry

    Science.gov (United States)

    Hulanicki, Adam; Godlewska, Beata; Brzóska, Malgorzata

    1995-11-01

    Magnesium content is an important diagnostic parameter in medicine. It is recognized that its determination in one compartment is not sufficient for reliable information about the magnesium status in the body. In addition to the common procedures of magnesium determination in blood by flame atomic absorption spectrometry, the procedure of electrothermal atomization has also been developed and applied to the analysis of blood fractions, mononuclear cells and isolated nuclei of liver cells. Electrothermal atomization is preferred in cases where the sample size is limited and the magnesium content low. The total errors are in the order of 3-4%. Various techniques of sample pretreatment have been tested and direct dilution with 0.05 mol l -1 nitric acid was optimal when the samples were not mineralized. The calibration graph based on standards containing albumin was found to give the best results, as the form of magnesium in the samples may influence the ashing and atomization processes. Good agreement was obtained for determination of magnesium in standard serum. The results are compared with those obtained by the standard flame atomization technique.

  13. Sample Preparation and Identification of Biological, Chemical and Mid-Spectrum Agents

    Science.gov (United States)

    2005-10-01

    substrate molecule is called a hydrolase. Substrates commonly used are sodium hippurate, DNA, urea, esculin, starch , casein, lecithin and polysorbate-80...processed sample are first denatured and separated by gel electrophoresis [usually sodium dodecyl polyacrylamide gel electrophoresis (SDS-PAGE)] and

  14. The Sum of the Parts: Large-scale Modeling in Systems Biology

    DEFF Research Database (Denmark)

    Fridolin, Gross; Green, Sara

    2017-01-01

    Systems biologists often distance themselves from reductionist approaches and formulate their aim as understanding living systems “as a whole”. Yet, it is often unclear what kind of reductionism they have in mind, and in what sense their methodologies offer a more comprehensive approach. To address...... at the interface of dynamically coupled processes within a biological system, thereby making more apparent what is lost through decomposition. Similarly, multi-scale modeling highlights the importance of macroscale parameters and models and challenges the view that living systems can be understood “bottom...

  15. Solid-phase extraction and liquid chromatographic quantitation of quinfamide in biological samples.

    Science.gov (United States)

    Morales, J M; Jung, C H; Alarcón, A; Barreda, A

    2000-09-15

    This paper describes a high-performance liquid chromatographic method for the assay of quinfamide and its main metabolite, 1-(dichloroacetyl)-1,2,3,4,-tetrahydro-6-quinolinol, in plasma, urine and feces. It requires 1 ml of biological fluid, an extraction using Sep-Pack cartridges and acetonitrile for drug elution. Analysis was performed on a CN column (5 microm) using water-acetonitrile-methanol (40:50:10) as a mobile phase at 269 nm. Results showed that the assay was linear in the range between 0.08 and 2.0 microg/ml. The limit of quantitation was 0.08 microg/ml. Maximum assay coefficient of variation was 14%. Recovery obtained in plasma, urine and feces ranged from 82% to 98%.

  16. Contrastive analysis of hedges in a sample of Chinese and English molecular biology papers.

    Science.gov (United States)

    Gao, Xiaofang

    2004-10-01

    Hedge is defined as the expression of provisionalness and possibility that makes scientific messages tentative, vague, and imprecise, thereby reducing the force of claims scientists make. Linguistic study of hedges began in the early 1970s in generative semantics. Since then, the focus has shifted from seeking linguistic properties in spoken discourse to analyzing its pragmatic functions in written contextual communication. The purpose of this paper was to analyze hedges in Chinese and English scientific articles from the perspective of contrastive pragmatics. Based on a contextual analysis of 5 Chinese and 5 English scientific articles, selected randomly, from two journals in molecular biology--Science in China and Proceedings of the National Academy of Sciences of the United States of America, there were significant differences between Chinese and English scientific articles in use of hedges.

  17. Electrophoresis tests on STS-3 and ground control experiments - A basis for future biological sample selections

    Science.gov (United States)

    Morrison, D. R.; Lewis, M. L.

    1982-01-01

    Static zone electrophoresis is an electrokinetic method of separating macromolecules and small particles. However, its application for the isolation of biological cells and concentrated protein solutions is limited by sedimentation and convection. Microgravity eliminates or reduces sedimentation, floatation, and density-driven convection arising from either Joule heating or concentration differences. The advantages of such an environment were first demonstrated in space during the Apollo 14 and 16 missions. In 1975 the Electrophoresis Technology Experiment (MA-011) was conducted during the Apollo-Soyuz Test Project flight. In 1979 a project was initiated to repeat the separations of human kidney cells. One of the major objectives of the Electrophoresis Equipment Verification Tests (EEVT) on STS-3 was to repeat and thereby validate the first successful electrophoretic separation of human kidney cells. Attention is given to the EEVT apparatus, the preflight electrophoresis, and inflight operational results.

  18. Atypical carcinoid and large cell neuroendocrine carcinoma of the lung: a proteomic dataset from formalin-fixed archival samples

    Directory of Open Access Journals (Sweden)

    Alessandro Tanca

    2016-06-01

    Full Text Available Here we present a dataset generated using formalin-fixed paraffin-embedded archival samples from two rare lung neuroendocrine tumor subtypes (namely, two atypical carcinoids, ACs, and two large-cell neuroendocrine carcinomas, LCNECs. Samples were subjected to a shotgun proteomics pipeline, comprising full-length protein extraction, SDS removal through spin columns, in solution trypsin digestion, long gradient liquid chromatography peptide separation and LTQ-Orbitrap mass spectrometry analysis. A total of 1260 and 2436 proteins were identified in the AC and LCNEC samples, respectively, with FDR <1%. MS data are available in the PeptideAtlas repository at http://www.peptideatlas.org/PASS/PASS00375.

  19. Atypical carcinoid and large cell neuroendocrine carcinoma of the lung: a proteomic dataset from formalin-fixed archival samples.

    Science.gov (United States)

    Tanca, Alessandro; Addis, Maria Filippa; Pisanu, Salvatore; Abbondio, Marcello; Pagnozzi, Daniela; Eccher, Albino; Rindi, Guido; Cossu-Rocca, Paolo; Uzzau, Sergio; Fanciulli, Giuseppe

    2016-06-01

    Here we present a dataset generated using formalin-fixed paraffin-embedded archival samples from two rare lung neuroendocrine tumor subtypes (namely, two atypical carcinoids, ACs, and two large-cell neuroendocrine carcinomas, LCNECs). Samples were subjected to a shotgun proteomics pipeline, comprising full-length protein extraction, SDS removal through spin columns, in solution trypsin digestion, long gradient liquid chromatography peptide separation and LTQ-Orbitrap mass spectrometry analysis. A total of 1260 and 2436 proteins were identified in the AC and LCNEC samples, respectively, with FDR <1%. MS data are available in the PeptideAtlas repository at http://www.peptideatlas.org/PASS/PASS00375.

  20. Atypical carcinoid and large cell neuroendocrine carcinoma of the lung: a proteomic dataset from formalin-fixed archival samples

    Science.gov (United States)

    Tanca, Alessandro; Addis, Maria Filippa; Pisanu, Salvatore; Abbondio, Marcello; Pagnozzi, Daniela; Eccher, Albino; Rindi, Guido; Cossu-Rocca, Paolo; Uzzau, Sergio; Fanciulli, Giuseppe

    2016-01-01

    Here we present a dataset generated using formalin-fixed paraffin-embedded archival samples from two rare lung neuroendocrine tumor subtypes (namely, two atypical carcinoids, ACs, and two large-cell neuroendocrine carcinomas, LCNECs). Samples were subjected to a shotgun proteomics pipeline, comprising full-length protein extraction, SDS removal through spin columns, in solution trypsin digestion, long gradient liquid chromatography peptide separation and LTQ-Orbitrap mass spectrometry analysis. A total of 1260 and 2436 proteins were identified in the AC and LCNEC samples, respectively, with FDR <1%. MS data are available in the PeptideAtlas repository at http://www.peptideatlas.org/PASS/PASS00375. PMID:27054153

  1. Physical descriptions of the bacterial nucleoid at large scales, and their biological implications

    Science.gov (United States)

    Benza, Vincenzo G.; Bassetti, Bruno; Dorfman, Kevin D.; Scolari, Vittore F.; Bromek, Krystyna; Cicuta, Pietro; Cosentino Lagomarsino, Marco

    2012-07-01

    Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex and dynamic protein-rich state, which is highly organized at various length scales. This has implications for modulating (when not directly enabling) the core biological processes of replication, transcription and segregation. We overview the progress in this area, driven in the last few years by new scientific ideas and new interdisciplinary experimental techniques, ranging from high space- and time-resolution microscopy to high-throughput genomics employing sequencing to map different aspects of the nucleoid-related interactome. The aim of this review is to present the wide spectrum of experimental and theoretical findings coherently, from a physics viewpoint. In particular, we highlight the role that statistical and soft condensed matter physics play in describing this system of fundamental biological importance, specifically reviewing classic and more modern tools from the theory of polymers. We also discuss some attempts toward unifying interpretations of the current results, pointing to possible directions for future investigation.

  2. Accelerating inference for diffusions observed with measurement error and large sample sizes using approximate Bayesian computation

    DEFF Research Database (Denmark)

    Picchini, Umberto; Forman, Julie Lyng

    2016-01-01

    In recent years, dynamical modelling has been provided with a range of breakthrough methods to perform exact Bayesian inference. However, it is often computationally unfeasible to apply exact statistical methodologies in the context of large data sets and complex models. This paper considers...... a nonlinear stochastic differential equation model observed with correlated measurement errors and an application to protein folding modelling. An approximate Bayesian computation (ABC)-MCMC algorithm is suggested to allow inference for model parameters within reasonable time constraints. The ABC algorithm...... applications. A simulation study is conducted to compare our strategy with exact Bayesian inference, the latter resulting two orders of magnitude slower than ABC-MCMC for the considered set-up. Finally, the ABC algorithm is applied to a large size protein data. The suggested methodology is fairly general...

  3. VizieR Online Data Catalog: VLT/NaCo Large program I. Sample (Desidera+, 2015)

    Science.gov (United States)

    Desidera, S.; Covino, E.; Messina, S.; Carson, J.; Hagelberg, J.; Schlieder, J. E.; Biazzo, K.; Alcala, J.; Chauvin, G.; Vigan, A.; Beuzit, J. L.; Bonavita, M.; Bonnefoy, M.; Delorme, P.; D'Orazi, V.; Esposito, M.; Feldt, M.; Girardi, L.; Gratton, R.; Henning, T.; Lagrange, A. M.; Lanzafame, A. C.; Launhardt, R.; Marmier, M.; Melo, C.; Meyer, M.; Mouillet, D.; Moutou, C.; Segransan, D.; Udry, S.; Zaidi, C. M.

    2014-10-01

    Stellar parameters for 86 stars observed in NaCo Large Program and their wide companions are presented. These include coordinates, magnitudes, spectral types, metallicity, mass, distance, radial velocities, proper motions, space velocities Xray luminosity, chromospheric emission, rotation period, projected rotational velocity, lithium equivalent width, effective temperature, age (Tables 9-12). Table D1 summarizes the details of the rotation period search (results for individual segments and for the whole timeseries). (13 data files).

  4. Memory-Optimized Software Synthesis from Dataflow Program Graphs with Large Size Data Samples

    Directory of Open Access Journals (Sweden)

    Hyunok Oh

    2003-05-01

    Full Text Available In multimedia and graphics applications, data samples of nonprimitive type require significant amount of buffer memory. This paper addresses the problem of minimizing the buffer memory requirement for such applications in embedded software synthesis from graphical dataflow programs based on the synchronous dataflow (SDF model with the given execution order of nodes. We propose a memory minimization technique that separates global memory buffers from local pointer buffers: the global buffers store live data samples and the local buffers store the pointers to the global buffer entries. The proposed algorithm reduces 67% memory for a JPEG encoder, 40% for an H.263 encoder compared with unshared versions, and 22% compared with the previous sharing algorithm for the H.263 encoder. Through extensive buffer sharing optimization, we believe that automatic software synthesis from dataflow program graphs achieves the comparable code quality with the manually optimized code in terms of memory requirement.

  5. Problematic Social Media Use: Results from a Large-Scale Nationally Representative Adolescent Sample.

    Science.gov (United States)

    Bányai, Fanni; Zsila, Ágnes; Király, Orsolya; Maraz, Aniko; Elekes, Zsuzsanna; Griffiths, Mark D; Andreassen, Cecilie Schou; Demetrovics, Zsolt

    2017-01-01

    Despite social media use being one of the most popular activities among adolescents, prevalence estimates among teenage samples of social media (problematic) use are lacking in the field. The present study surveyed a nationally representative Hungarian sample comprising 5,961 adolescents as part of the European School Survey Project on Alcohol and Other Drugs (ESPAD). Using the Bergen Social Media Addiction Scale (BSMAS) and based on latent profile analysis, 4.5% of the adolescents belonged to the at-risk group, and reported low self-esteem, high level of depression symptoms, and elevated social media use. Results also demonstrated that BSMAS has appropriate psychometric properties. It is concluded that adolescents at-risk of problematic social media use should be targeted by school-based prevention and intervention programs.

  6. Problematic Social Media Use: Results from a Large-Scale Nationally Representative Adolescent Sample

    Science.gov (United States)

    Bányai, Fanni; Zsila, Ágnes; Király, Orsolya; Maraz, Aniko; Elekes, Zsuzsanna; Griffiths, Mark D.; Andreassen, Cecilie Schou

    2017-01-01

    Despite social media use being one of the most popular activities among adolescents, prevalence estimates among teenage samples of social media (problematic) use are lacking in the field. The present study surveyed a nationally representative Hungarian sample comprising 5,961 adolescents as part of the European School Survey Project on Alcohol and Other Drugs (ESPAD). Using the Bergen Social Media Addiction Scale (BSMAS) and based on latent profile analysis, 4.5% of the adolescents belonged to the at-risk group, and reported low self-esteem, high level of depression symptoms, and elevated social media use. Results also demonstrated that BSMAS has appropriate psychometric properties. It is concluded that adolescents at-risk of problematic social media use should be targeted by school-based prevention and intervention programs. PMID:28068404

  7. Sampling the sound field in auditoria using large natural-scale array measurements.

    Science.gov (United States)

    Witew, Ingo B; Vorländer, Michael; Xiang, Ning

    2017-03-01

    Suitable data for spatial wave field analyses in concert halls need to satisfy the sampling theorem and hence requires densely spaced measurement positions over extended regions. The described measurement apparatus is capable of automatically sampling the sound field in auditoria over a surface of 5.30 m × 8.00 m to any appointed resolutions. In addition to discussing design features, a case study based on measured impulse responses is presented. The experimental data allow wave field animations demonstrating how sound propagating at grazing incidence over theater seating is scattered from rows of chairs (seat-dip effect). The visualized data of reflections and scattering from an auditorium's boundaries give insights and opportunities for advanced analyses.

  8. Irreducibility and efficiency of ESIP to sample marker genotypes in large pedigrees with loops

    Directory of Open Access Journals (Sweden)

    Schelling Matthias

    2002-09-01

    Full Text Available Abstract Markov chain Monte Carlo (MCMC methods have been proposed to overcome computational problems in linkage and segregation analyses. This approach involves sampling genotypes at the marker and trait loci. Among MCMC methods, scalar-Gibbs is the easiest to implement, and it is used in genetics. However, the Markov chain that corresponds to scalar-Gibbs may not be irreducible when the marker locus has more than two alleles, and even when the chain is irreducible, mixing has been observed to be slow. Joint sampling of genotypes has been proposed as a strategy to overcome these problems. An algorithm that combines the Elston-Stewart algorithm and iterative peeling (ESIP sampler to sample genotypes jointly from the entire pedigree is used in this study. Here, it is shown that the ESIP sampler yields an irreducible Markov chain, regardless of the number of alleles at a locus. Further, results obtained by ESIP sampler are compared with other methods in the literature. Of the methods that are guaranteed to be irreducible, ESIP was the most efficient.

  9. Determination of trace lead in biological and water samples with dispersive liquid-liquid microextraction preconcentration.

    Science.gov (United States)

    Liang, Pei; Sang, Hongbo

    2008-09-01

    A new method for the determination of trace lead was developed by dispersive liquid-liquid microextraction preconcentration and graphite furnace atomic absorption spectrometry. In the proposed approach, 1-phenyl-3-methyl-4-benzoyl-5-pyrazolone (PMBP) was used as a chelating agent, and carbon tetrachloride and ethanol were selected as extraction and dispersive solvents. Some factors influencing the extraction efficiency of lead and its subsequent determination, including extraction and dispersive solvent type and volume, pH of sample solution, concentration of the chelating agent, and extraction time, were studied and optimized. Under the optimum conditions, the enrichment factor of this method for lead was reached at 78. The detection limit for lead was 39 ng L(-1) (3 sigma), and the relative standard deviation (RSD) was 3.2% (n=7, c=10 ng mL(-1)). The method was successfully applied to the determination of trace amounts of lead in human urine and water samples.

  10. Biodiversity of bacteriophages: morphological and biological properties of a large group of phages isolated from urban sewage

    Science.gov (United States)

    Jurczak-Kurek, Agata; Gąsior, Tomasz; Nejman-Faleńczyk, Bożena; Bloch, Sylwia; Dydecka, Aleksandra; Topka, Gracja; Necel, Agnieszka; Jakubowska-Deredas, Magdalena; Narajczyk, Magdalena; Richert, Malwina; Mieszkowska, Agata; Wróbel, Borys; Węgrzyn, Grzegorz; Węgrzyn, Alicja

    2016-01-01

    A large scale analysis presented in this article focuses on biological and physiological variety of bacteriophages. A collection of 83 bacteriophages, isolated from urban sewage and able to propagate in cells of different bacterial hosts, has been obtained (60 infecting Escherichia coli, 10 infecting Pseudomonas aeruginosa, 4 infecting Salmonella enterica, 3 infecting Staphylococcus sciuri, and 6 infecting Enterococcus faecalis). High biological diversity of the collection is indicated by its characteristics, both morphological (electron microscopic analyses) and biological (host range, plaque size and morphology, growth at various temperatures, thermal inactivation, sensitivity to low and high pH, sensitivity to osmotic stress, survivability upon treatment with organic solvents and detergents), and further supported by hierarchical cluster analysis. By the end of the research no larger collection of phages from a single environmental source investigated by these means had been found. The finding was confirmed by whole genome analysis of 7 selected bacteriophages. Moreover, particular bacteriophages revealed unusual biological features, like the ability to form plaques at low temperature (4 °C), resist high temperature (62 °C or 95 °C) or survive in the presence of an organic solvents (ethanol, acetone, DMSO, chloroform) or detergent (SDS, CTAB, sarkosyl) making them potentially interesting in the context of biotechnological applications. PMID:27698408

  11. A rapid method for assaying thiaminase I activity in diverse biological samples.

    Directory of Open Access Journals (Sweden)

    Clifford E Kraft

    Full Text Available Vitamin B1 (thiamine deficiencies can lead to neurological disorders, reproductive failure and death in wild and domestic animal populations. In some cases, disease is brought about by the consumption of foods high in thiaminase I activity. Levels of thiaminase activity in these foods are highly variable and the factors leading to production of this enzyme are poorly understood. Here we describe improvements in a spectrophotometric thiaminase I activity assay that measures the disappearance of 4-nitrothiophenol, a favored nucleophile co-substrate that replaces the thiazole portion of thiamine during the inactivation of thiamine by the enzyme. Scalable sample processing protocols and a 96-well microtiter plate format are presented that allow the rapid evaluation of multiple, replicated samples in the course of only a few hours. Observed levels of activity in bacterial culture supernatant, fish, ferns and molluscs using this colorimetric assay were similar to previously published reports that employed a radiometric method. Organisms devoid of thiaminase I, based upon previous work, showed no activity with this assay. In addition, activity was found in a variety of fishes and one fern species from which this enzyme had not previously been reported. Overall, we demonstrate the suitability of this technique for measuring thiaminase I activity within small amounts of tissue and environmental samples with replication levels that were heretofore prohibitive. The assay provides a considerable improvement in the ability to examine and understand the properties of an enzyme that has a substantial influence on organism and ecosystem health.

  12. Electrochemical Analysis of Antichemotherapeutic Drug Zanosar in Pharmaceutical and Biological Samples by Differential Pulse Polarography

    Directory of Open Access Journals (Sweden)

    Chennupalle Nageswara Reddy

    2013-01-01

    Full Text Available The electrochemical reduction of zanosar was investigated systematically by direct current polarography, cyclic voltammetry, and differential pulse polarography (DPP. A simple DPP technique was proposed for the direct quantitative determination of anticancer drug zanosar in pharmaceutical formulation and spiked human urine samples for the first time. The reduction potential was −0.28 V versus Ag/AgCl with a hanging mercury drop electrode in Britton-Robinson buffer as supporting electrolyte. The dependence of the intensities of currents and potentials on pH, concentration, scan rate, deposition time, and nature of the supporting electrolyte was investigated. The calibration curve was found to be linear with the following equation: y=0.4041x+0.012, with a correlation coefficient of 0.992 (R2 over a concentration range from 1.0×10-7 M to 1.0×10-3 M. In the present investigation, the achieved limit of detection (LOD and limit of quantization (LQD were 7.42×10-8 M and 2.47×10-8 M; respectively. Excipients did not interfere with the determination of zanosar in pharmaceutical formulation and spiked urine samples. Precision and accuracy of the developed method were checked by recovery studies in pharmaceutical formulation and spiked human urine samples.

  13. Label-free quantification of Tacrolimus in biological samples by atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Menotta, Michele, E-mail: michele.menotta@uniurb.it [Department of Biomolecular Sciences, University of Urbino “Carlo Bo” via Saffi 2, Urbino (Italy); Biagiotti, Sara [Department of Biomolecular Sciences, University of Urbino “Carlo Bo” via Saffi 2, Urbino (Italy); Streppa, Laura [Physics Laboratory, CNRS-ENS, UMR 5672, Lyon (France); Cell and Molecular Biology Laboratory, CNRS-ENS Lyon, UMR 5239, IFR128, Lyon (France); Rossi, Luigia; Magnani, Mauro [Department of Biomolecular Sciences, University of Urbino “Carlo Bo” via Saffi 2, Urbino (Italy)

    2015-07-16

    Highlights: • Tacrolimus is a potent immunosuppressant drug that has to be continually monitored. • We present an atomic force microscope approach for quantification of Tacrolimus in blood samples. • Detection and quantification have been successfully achieved. - Abstract: In the present paper we describe an atomic force microscopy (AFM)-based method for the quantitative analysis of FK506 (Tacrolimus) in whole blood (WB) samples. Current reference methods used to quantify this immunosuppressive drug are based on mass spectrometry. In addition, an immunoenzymatic assay (ELISA) has been developed and is widely used in clinic, even though it shows a small but consistent overestimation of the actual drug concentration when compared with the mass spectrometry method. The AFM biosensor presented herein utilises the endogen drug receptor, FKBP12, to quantify Tacrolimus levels. The biosensor was first assayed to detect the free drug in solution, and subsequently used for the detection of Tacrolimus in blood samples. The sensor was suitable to generate a dose–response curve in the full range of clinical drug monitoring. A comparison with the clinically tested ELISA assay is also reported.

  14. Evaluation of an ultrasonic acid digestion procedure for total heavy metals determination in environmental and biological samples

    Energy Technology Data Exchange (ETDEWEB)

    Kazi, Tasneem G. [Center of Excellence in Analytical Chemistry, University of Sindh, Jamshoro 76080 (Pakistan)], E-mail: tgkazi@yahoo.com; Jamali, Mohammad K. [Center of Excellence in Analytical Chemistry, University of Sindh, Jamshoro 76080 (Pakistan)], E-mail: mkhanjamali@yahoo.com; Arain, Mohammad B. [Center of Excellence in Analytical Chemistry, University of Sindh, Jamshoro 76080 (Pakistan)], E-mail: bilal_ku2004@yahoo.com; Afridi, Hassan I. [Center of Excellence in Analytical Chemistry, University of Sindh, Jamshoro 76080 (Pakistan)], E-mail: hassanimranafridi@yahoo.com; Jalbani, Nusrat [Pakistan Council for Scientific and Industrial Research, University Road, Karachi 75280 (Pakistan)], E-mail: nusratjalbani_21@yahoo.com; Sarfraz, Raja A. [Center of Excellence in Analytical Chemistry, University of Sindh, Jamshoro 76080 (Pakistan)], E-mail: rajaadilsarfraz@gmail.com; Ansari, Rehana [Center of Excellence in Analytical Chemistry, University of Sindh, Jamshoro 76080 (Pakistan)], E-mail: rehana_ansari_57@yahoo.com

    2009-01-30

    In this study, a sample preparation method based on ultrasonic assisted acid digestion (UAD) has been evaluated for total heavy metals (Cd, Cr, Ni and Pb) determination in different environmental (soil, sediment and sewage sludge), and biological (fish muscles, vegetables and grains) samples, using electrothermal atomic absorption spectrometry (ETAAS). The investigated parameters influencing UAD such as presonication time, sonication time, temperature of ultrasonic bath, and different acid mixtures were fully optimized, whereas power was maintained constant at 100% of nominal power of ultrasonic bath. Six different sets of above parameters were applied on six certified reference materials (CRMs) having different matrices. The accuracy of the method was also tested by comparing the results with those obtained from conventional hot plate assisted acid digestion method on same CRMs. Analytical results for HMs by both methods showed no significant difference at 95% confidence limit (p < 0.05). Recoveries of HMs ranging from 96.2% to 102% and 96.3% to 98.6% were obtained from biological and environmental samples, respectively. The average relative standard deviation of UAD method varied between 3.5% and 8.2%, depending on the analyte.

  15. A signature-based method to distinguish time-of-flight secondary-ion mass spectra from biological samples.

    Science.gov (United States)

    Quong, Judy N; Quong, Andrew A; Wu, Kuang Jen; Kercher, James R

    2005-11-01

    Time-Of-Flight Mass Spectrometry (TOF-SIMS) was used to determine elemental and biomolecular ions from isolated protein samples. We identified a set of 23 mass-to-charge ratio (m/z) peaks that represent signatures for distinguishing biological samples. The 23 peaks were identified by Singular Value Decomposition (SVD) and Canonical Analysis (CA) to find the underlying structure in the complex mass-spectra data sets. From this modified data, SVD was used to identify sets of m/z peaks, and we used these patterns from the TOF-SIMS data to predict the biological source from which individual mass spectra were generated. The signatures were validated using an additional data set different from the initial training set used to identify the signatures. We present a simple method to identify multiple variables required for sample classification based on mass spectra that avoids overfit. This is important in a variety of studies using mass spectrometry, including the ability to identify proteins in complex mixtures and for the identification of new biomarkers.

  16. Determination of lead in biological samples of children with different physiological consequences using cloud point extraction method.

    Science.gov (United States)

    Shah, Faheem; Kazi, Tasneem Gul; Ullah, Naeem; Afridi, Hassan Imran

    2013-06-01

    In present study, lead (Pb) level in biological samples of children with physiological disorders (liver, bone, and gastrointestinal; age ranged 1-10 years) have been assessed. For comparison purpose, age-matched healthy children were also selected. Cloud point extraction (CPE) was employed for preconcentration of Pb in acid-digested biological samples prior to its determination by flame atomic absorption spectrometry (FAAS). Dithizone (diphenylthiocarbazone) and nonionic surfactant Triton X-114 (TX-114) were used as complexing reagent and extractant, respectively. The effects of several experimental variables on proposed CPE were evaluated. Under the optimum experimental conditions, the observed detection limit (LOD) and the enhancement factor (EF) were 0.08 μg L(-1) and 53, respectively. Relative standard deviation (RSD) of 10 μg L(-1) Pb was 3.4 %. It was observed that children with liver-, bone-, and gastrointestinal-related disorders had three- to fourfold higher Pb level in blood and scalp hair samples.

  17. Correlation of Arsenic Levels in Smokeless Tobacco Products and Biological Samples of Oral Cancer Patients and Control Consumers.

    Science.gov (United States)

    Arain, Sadaf S; Kazi, Tasneem G; Afridi, Hassan I; Talpur, Farah N; Kazi, Atif G; Brahman, Kapil D; Naeemullah; Panhwar, Abdul H; Kamboh, Muhammad A

    2015-12-01

    It has been extensively reported that chewing of smokeless tobacco (SLT) can lead to cancers of oral cavity. In present study, the relationship between arsenic (As) exposure via chewing/inhaling different SLT products in oral cancer patients have or/not consumed SLT products was studied. The As in different types of SLT products (gutkha, mainpuri, and snuff) and biological (scalp hair and blood) samples of different types of oral cancer patients and controls were analyzed. Both controls and oral cancer patients have same age group (ranged 30-60 years), socio-economic status, localities, and dietary habits. The concentrations of As in SLT products and biological samples were measured by electrothermal atomic absorption spectrophotometer after microwave-assisted acid digestion. The validity and accuracy of the methodology were checked by certified reference materials. The resulted data of present study indicates that the concentration of As was significantly higher in scalp hair and blood samples of oral cancer patients than those of controls (p0.01). The intake of As via consuming different SLT may have synergistic effects, in addition to other risk factors associated with oral cancer.

  18. Physical descriptions of the bacterial nucleoid at large scales, and their biological implications

    CERN Document Server

    Benza, Vincenzo G; Dorfman, Kevin D; Scolari, Vittore F; Bromek, Krystyna; Cicuta, Pietro; Lagomarsino, Marco Cosentino

    2012-01-01

    Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex and dynamic protein-rich state, which is highly organised at various length scales. This has implications on modulating (when not enabling) the core biological processes of replication, transcription, segregation. We overview the progress in this area, driven in the last few years by new scientific ideas and new interdisciplinary experimental techniques, ranging from high space- and time-resolution microscopy to high-throughput genomics employing sequencing to map different aspects of the nucleoid-related interactome. The aim of this review is to present the wide spectrum of experimental and theoretical findings coherently, from a physics viewpoint. We also discuss some attempts of interpretation that unify different results, highlighting the role that statistical and soft co...

  19. Applications of High Resolution Laser Induced Breakdown Spectroscopy for Environmental and Biological Samples

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Madhavi Z [ORNL; Labbe, Nicole [ORNL; Wagner, Rebekah J. [Pennsylvania State University, University Park, PA

    2013-01-01

    This chapter details the application of LIBS in a number of environmental areas of research such as carbon sequestration and climate change. LIBS has also been shown to be useful in other high resolution environmental applications for example, elemental mapping and detection of metals in plant materials. LIBS has also been used in phytoremediation applications. Other biological research involves a detailed understanding of wood chemistry response to precipitation variations and also to forest fires. A cross-section of Mountain pine (pinceae Pinus pungen Lamb.) was scanned using a translational stage to determine the differences in the chemical features both before and after a fire event. Consequently, by monitoring the elemental composition pattern of a tree and by looking for abrupt changes, one can reconstruct the disturbance history of a tree and a forest. Lastly we have shown that multivariate analysis of the LIBS data is necessary to standardize the analysis and correlate to other standard laboratory techniques. LIBS along with multivariate statistical analysis makes it a very powerful technology that can be transferred from laboratory to field applications with ease.

  20. Maternal bereavement and childhood asthma-analyses in two large samples of Swedish children.

    Directory of Open Access Journals (Sweden)

    Fang Fang

    Full Text Available BACKGROUND: Prenatal factors such as prenatal psychological stress might influence the development of childhood asthma. METHODOLOGY AND PRINCIPAL FINDINGS: We assessed the association between maternal bereavement shortly before and during pregnancy, as a proxy for prenatal stress, and the risk of childhood asthma in the offspring, based on two samples of children 1-4 (n = 426,334 and 7-12 (n = 493,813 years assembled from the Swedish Medical Birth Register. Exposure was maternal bereavement of a close relative from one year before pregnancy to child birth. Asthma event was defined by a hospital contact for asthma or at least two dispenses of inhaled corticosteroids or montelukast. In the younger sample we calculated hazards ratios (HRs of a first-ever asthma event using Cox models and in the older sample odds ratio (ORs of an asthma attack during 12 months using logistic regression. Compared to unexposed boys, exposed boys seemed to have a weakly higher risk of first-ever asthma event at 1-4 years (HR: 1.09; 95% confidence interval [CI]: 0.98, 1.22 as well as an asthma attack during 12 months at 7-12 years (OR: 1.10; 95% CI: 0.96, 1.24. No association was suggested for girls. Boys exposed during the second trimester had a significantly higher risk of asthma event at 1-4 years (HR: 1.55; 95% CI: 1.19, 2.02 and asthma attack at 7-12 years if the bereavement was an older child (OR: 1.58; 95% CI: 1.11, 2.25. The associations tended to be stronger if the bereavement was due to a traumatic death compared to natural death, but the difference was not statistically significant. CONCLUSIONS/SIGNIFICANCE: Our results showed some evidence for a positive association between prenatal stress and childhood asthma among boys but not girls.