A technique to obtain a multiparameter radar rainfall algorithm using the probability matching procedure

International Nuclear Information System (INIS)

Gorgucci, E.; Scarchilli, G.

1997-01-01

The natural cumulative distributions of rainfall observed by a network of rain gauges and a multiparameter radar are matched to derive multiparameter radar algorithms for rainfall estimation. The use of multiparameter radar measurements in a statistical framework to estimate rainfall is resented in this paper, The techniques developed in this paper are applied to the radar and rain gauge measurement of rainfall observed in central Florida and central Italy. Conventional pointwise estimates of rainfall are also compared. The probability matching procedure, when applied to the radar and surface measurements, shows that multiparameter radar algorithms can match the probability distribution function better than the reflectivity-based algorithms. It is also shown that the multiparameter radar algorithm derived matching the cumulative distribution function of rainfall provides more accurate estimates of rainfall on the ground in comparison to any conventional reflectivity-based algorithm

Multiparameter extrapolation and deflation methods for solving equation systems

Directory of Open Access Journals (Sweden)

A. J. Hughes Hallett

1984-01-01

Full Text Available Most models in economics and the applied sciences are solved by first order iterative techniques, usually those based on the Gauss-Seidel algorithm. This paper examines the convergence of multiparameter extrapolations (accelerations of first order iterations, as an improved approximation to the Newton method for solving arbitrary nonlinear equation systems. It generalises my earlier results on single parameter extrapolations. Richardson's generalised method and the deflation method for detecting successive solutions in nonlinear equation systems are also presented as multiparameter extrapolations of first order iterations. New convergence results are obtained for those methods.

Multiparameter data acquisition and analysis system for capture gamma-ray studies

International Nuclear Information System (INIS)

Hejja, I.; Belgya, T.; Molnar, G.L.; Szepesvary, A.

1997-01-01

A PC-based multiparameter data acquisition system has been built for the Budapest neutron capture gamma-ray spectrometer. The hardware consists of a homemade multiplexer accommodating up to ten ADC inputs, a 64 kword histogram memory board and a National Instruments 32-bit DIO card, used for data acquisition and control, as well as a timer/scaler TIO card of the same company. The multiplexer inputs can be flexibly configured by means of programmable XILINX logic chips. The system is driven by a Pentium PC connected to the local Ethernet. (author)

Multi-parameter CAMAC compatible ADC scanner

Energy Technology Data Exchange (ETDEWEB)

Midttun, G J; Ingebretsen, F [Oslo Univ. (Norway). Fysisk Inst.; Johnsen, P J [Norsk Data A.S., Box 163, Oekern, Oslo 5, Norway

1979-02-15

A fast ADC scanner for multi-parameter nuclear physics experiments is described. The scanner is based on a standard CAMAC crate, and data from several different experiments can be handled simultaneously through a direct memory access (DMA) channel. The implementation on a PDP-7 computer is outlined.

Depth analysis of mechanically machined flaws on steam generator tubings using multi-parameter algorithm

International Nuclear Information System (INIS)

Nam Gung, Chan; Lee, Yoon Sang; Hwang, Seong Sik; Kim, Hong Pyo

2004-01-01

The eddy current testing (ECT) is a nondestructive technique. It is used for evaluation of material's integrity, especially, steam generator (SG) tubing in nuclear plants, due to their rapid inspection, safe and easy operation. For depth measurement of defects, we prepared Electro Discharge Machined (EDM) notches that have several of defects and applied multi-parameter (MP) algorithm. It is a crack shape estimation program developed in Argonne National Laboratory (ANL). To evaluate the MP algorithm, we compared defect profile with fractography of the defects. In the following sections, we described the basic structure of a computer-aided data analysis algorithm used as means of more accurate and efficient processing of ECT data, and explained the specification of a standard calibration. Finally, we discussed the accuracy of estimated depth profile compared with conventional ECT method

Density reconstruction in multiparameter elastic full-waveform inversion

Science.gov (United States)

Sun, Min'ao; Yang, Jizhong; Dong, Liangguo; Liu, Yuzhu; Huang, Chao

2017-12-01

Elastic full-waveform inversion (EFWI) is a quantitative data fitting procedure that recovers multiple subsurface parameters from multicomponent seismic data. As density is involved in addition to P- and S-wave velocities, the multiparameter EFWI suffers from more serious tradeoffs. In addition, compared with P- and S-wave velocities, the misfit function is less sensitive to density perturbation. Thus, a robust density reconstruction remains a difficult problem in multiparameter EFWI. In this paper, we develop an improved scattering-integral-based truncated Gauss-Newton method to simultaneously recover P- and S-wave velocities and density in EFWI. In this method, the inverse Gauss-Newton Hessian has been estimated by iteratively solving the Gauss-Newton equation with a matrix-free conjugate gradient algorithm. Therefore, it is able to properly handle the parameter tradeoffs. To give a detailed illustration of the tradeoffs between P- and S-wave velocities and density in EFWI, wavefield-separated sensitivity kernels and the Gauss-Newton Hessian are numerically computed, and their distribution characteristics are analyzed. Numerical experiments on a canonical inclusion model and a modified SEG/EAGE Overthrust model have demonstrated that the proposed method can effectively mitigate the tradeoff effects, and improve multiparameter gradients. Thus, a high convergence rate and an accurate density reconstruction can be achieved.

Multiparameter Inversion: Cramer's Rule for Pseudodifferential Operators

Directory of Open Access Journals (Sweden)

Rami Nammour

2011-01-01

a matrix. The approximate solution of the linearized multiparameter problem so produced involves no ray theory computations. It may be sufficiently accurate for some purposes; for others, it can serve as a preconditioner to enhance the convergence of standard iterative methods.

New technique for determination of long-lived radioisotopes, Iodine-129, using multiparameter coincidence spectrometry

International Nuclear Information System (INIS)

Hatsukawa, Yuichi; Oshima, Masumi; Toh, Yosuke; Shinohara, Nobuo; Kushita, Kosuke; Ueno, Takashi

2003-01-01

Multiparameter coincidence γ-ray spectrometry based on g-g coincidence is widely used in the field of nuclear structure studies, and has produced many successful results. In this study, feasibility of the method for neutron activation analysis of long lived iodine isotope, 129 I, was investigated. (author)

The generalized fracture criteria based on the multi-parameter representation of the crack tip stress field

Science.gov (United States)

Stepanova, L. V.

2017-12-01

The paper is devoted to the multi-parameter asymptotic description of the stress field near the crack tip of a finite crack in an infinite isotropic elastic plane medium subject to 1) tensile stress; 2) in-plane shear; 3) mixed mode loading for a wide range of mode-mixity situations (Mode I and Mode II). The multi-parameter series expansion of stress tensor components containing higher-order terms is obtained. All the coefficients of the multiparameter series expansion of the stress field are given. The main focus is on the discussion of the influence of considering the higher-order terms of the Williams expansion. The analysis of the higher-order terms in the stress field is performed. It is shown that the larger the distance from the crack tip, the more terms it is necessary to keep in the asymptotic series expansion. Therefore, it can be concluded that several more higher-order terms of the Williams expansion should be used for the stress field description when the distance from the crack tip is not small enough. The crack propagation direction angle is calculated. Two fracture criteria, the maximum tangential stress criterion and the strain energy density criterion, are used. The multi-parameter form of the two commonly used fracture criteria is introduced and tested. Thirty and more terms of the Williams series expansion for the near-crack-tip stress field enable the angle to be calculated more precisely.

Estimation of the crack propagation direction in a mixed-mode geometry via multi-parameter fracture criteria

Czech Academy of Sciences Publication Activity Database

Malíková, L.; Veselý, V.; Seitl, Stanislav

2015-01-01

Roč. 9, č. 33 (2015), s. 25-32 ISSN 1971-8993 Institutional support: RVO:68081723 Keywords : Near-crack-tip fields * Williams expansion * Crack propagation direction * Multi-parameter fracture criteria * Finite element analysis Subject RIV: JL - Materials Fatigue, Friction Mechanics

Methods and apparatus for multi-parameter acoustic signature inspection

Energy Technology Data Exchange (ETDEWEB)

Diaz, Aaron A [Richland, WA; Samuel, Todd J [Pasco, WA; Valencia, Juan D [Kennewick, WA; Gervais, Kevin L [Richland, WA; Tucker, Brian J [Pasco, WA; Kirihara, Leslie J [Richland, WA; Skorpik, James R [Kennewick, WA; Reid, Larry D [Benton City, WA; Munley, John T [Benton City, WA; Pappas, Richard A [Richland, WA; Wright, Bob W [West Richland, WA; Panetta, Paul D [Richland, WA; Thompson, Jason S [Richland, WA

2007-07-24

A multiparameter acoustic signature inspection device and method are described for non-invasive inspection of containers. Dual acoustic signatures discriminate between various fluids and materials for identification of the same.

BioMEMS for multiparameter clinical monitoring

Science.gov (United States)

Moser, Isabella

2003-01-01

For diabetes patients glucose monitoring means an important improvement of their life quality and additionally it is a $3-billion-a-year business. Continuous glucose monitoring provides gapless glucose level control, an early warning of hypoglycemia, and is intended to control insulin pumps. An upgrading to multi-parameter monitoring would not only benefit patients with severe metabolism defects but also the metabolism of diabetes patient could be better controlled by monitoring an additional parameter like lactate. Multi-parameter monitoring devices are not commercially available, one of the complications in the integration of different biosensors using the same detecting molecule for all analytes is chemical cross talk between adjacent amperometric biosensors. Recently some integrated biosensors were published but either they were not mass producible or they were realized in an expensive silicon based technology. In addition to it most of them were not tested under monitoring conditions but their integration principles will be discussed. As an example a low cost multi- parameter microsystem and some applications of it in clinical diagnosis will be presented. Also an overlook of non-invasive methods and (minimal) invasive methods will be given with a focus on microdialysis.

USE OF MULTIPARAMETER ANALYSIS OF LABORATORY BIOMARKERS TO ASSESS RHEUMATOID ARTHRITIS ACTIVITY

Directory of Open Access Journals (Sweden)

A. A. Novikov

2015-01-01

Full Text Available The key component in the management of patients with rheumatoid arthritis (RA is regular control of RA activity. The quantitative assessment of a patient’s status allows the development of standardized indications for anti-rheumatic therapy.Objective: to identify the laboratory biomarkers able to reflect RA activity.Subjects and methods. Fifty-eight patients with RA and 30 age- and sex-matched healthy donors were examined. The patients were divided into high/moderate and mild disease activity groups according to DAS28. The serum concentrations of 30 biomarkers were measured using immunonephelometric assay, enzyme immunoassay, and xMAP technology.Results and discussion. Multivariate analysis could identify the factors mostly related to high/moderate RA activity according to DAS28, such as fibroblast growth factor-2, monocyte chemoattractant protein-1, interleukins (IL 1α, 6, and 15, and tumor necrosis factor-α and could create a prognostic model for RA activity assessment. ROC analysis has shown that this model has excellent diagnostic efficiency in differentiating high/moderate versus low RA activity.Conclusion. To create a subjective assessment-independent immunological multiparameter index of greater diagnostic accuracy than the laboratory parameters routinely used in clinical practice may be a qualitatively new step in assessing and monitoring RA activity.

Multi-Parameter Measurement in Unseeded Flows using Femtosecond Lasers

Data.gov (United States)

National Aeronautics and Space Administration — Our approach is to use new turn-key femtosecond laser technology along with new high-speed CMOS camera technology to build a multi-parameter measurement system based...

A molecular informatics view on best practice in multi-parameter compound optimization.

Science.gov (United States)

Lusher, Scott J; McGuire, Ross; Azevedo, Rita; Boiten, Jan-Willem; van Schaik, Rene C; de Vlieg, Jacob

2011-07-01

The difference between biologically active molecules and drugs is that the latter balance an array of related and unrelated properties required for administration to patients. Inevitability, during optimization, some of these multiple factors will conflict. Although informatics has a crucial role in addressing the challenges of modern compound optimization, it is arguably still undervalued and underutilized. We present here some of the basic requirements of multi-parameter drug design, the crucial role of informatics and examples of favorable practice. The most crucial of these best practices are the need for informaticians to align their technologies and insights directly to discovery projects and for all scientists in drug discovery to become more proficient in the use of in silico methods. Copyright © 2011 Elsevier Ltd. All rights reserved.

Crack propagation direction in a mixed mode geometry estimated via multi-parameter fracture criteria

Czech Academy of Sciences Publication Activity Database

Malíková, L.; Veselý, V.; Seitl, Stanislav

2016-01-01

Roč. 89, AUG (2016), s. 99-107 ISSN 0142-1123. [International Conference on Characterisation of Crack Tip Fields /3./. Urbino, 20.04.2015-22.04.2015] Institutional support: RVO:68081723 Keywords : Near-crack-tip fields * Mixed mode * Crack propagation direction * Multi-parameter fracture criteria * Finite element analysis Subject RIV: JL - Materials Fatigue, Friction Mechanics Impact factor: 2.899, year: 2016

Tav4SB: integrating tools for analysis of kinetic models of biological systems.

Science.gov (United States)

Rybiński, Mikołaj; Lula, Michał; Banasik, Paweł; Lasota, Sławomir; Gambin, Anna

2012-04-05

Progress in the modeling of biological systems strongly relies on the availability of specialized computer-aided tools. To that end, the Taverna Workbench eases integration of software tools for life science research and provides a common workflow-based framework for computational experiments in Biology. The Taverna services for Systems Biology (Tav4SB) project provides a set of new Web service operations, which extend the functionality of the Taverna Workbench in a domain of systems biology. Tav4SB operations allow you to perform numerical simulations or model checking of, respectively, deterministic or stochastic semantics of biological models. On top of this functionality, Tav4SB enables the construction of high-level experiments. As an illustration of possibilities offered by our project we apply the multi-parameter sensitivity analysis. To visualize the results of model analysis a flexible plotting operation is provided as well. Tav4SB operations are executed in a simple grid environment, integrating heterogeneous software such as Mathematica, PRISM and SBML ODE Solver. The user guide, contact information, full documentation of available Web service operations, workflows and other additional resources can be found at the Tav4SB project's Web page: http://bioputer.mimuw.edu.pl/tav4sb/. The Tav4SB Web service provides a set of integrated tools in the domain for which Web-based applications are still not as widely available as for other areas of computational biology. Moreover, we extend the dedicated hardware base for computationally expensive task of simulating cellular models. Finally, we promote the standardization of models and experiments as well as accessibility and usability of remote services.

A Smart Multi-parameter Sensor with Online Monitoring for the Aquaculture in China

OpenAIRE

Peng , Fa; Wang , Jinxing; Liu , Shuangxi; Li , Daoliang; Xu , Dan; Wang , Yang

2013-01-01

International audience; PH, DO,ORP, EC and water-level are important parameters of the aquaculture monitoring. But the high cost of foreign sensors and high-energy consumption of Chinese sensors make it impossible for wide use in China. This paper uses MCU STM8L152 to realize the ultralow power design. With simple hardware structure design, the cost of the multi-parameter sensor can be reduced .The experiment data of the multi-parameter sensor contrasting with the results obtained by Hach mul...

Accelerated whole-brain multi-parameter mapping using blind compressed sensing.

Science.gov (United States)

Bhave, Sampada; Lingala, Sajan Goud; Johnson, Casey P; Magnotta, Vincent A; Jacob, Mathews

2016-03-01

To introduce a blind compressed sensing (BCS) framework to accelerate multi-parameter MR mapping, and demonstrate its feasibility in high-resolution, whole-brain T1ρ and T2 mapping. BCS models the evolution of magnetization at every pixel as a sparse linear combination of bases in a dictionary. Unlike compressed sensing, the dictionary and the sparse coefficients are jointly estimated from undersampled data. Large number of non-orthogonal bases in BCS accounts for more complex signals than low rank representations. The low degree of freedom of BCS, attributed to sparse coefficients, translates to fewer artifacts at high acceleration factors (R). From 2D retrospective undersampling experiments, the mean square errors in T1ρ and T2 maps were observed to be within 0.1% up to R = 10. BCS was observed to be more robust to patient-specific motion as compared to other compressed sensing schemes and resulted in minimal degradation of parameter maps in the presence of motion. Our results suggested that BCS can provide an acceleration factor of 8 in prospective 3D imaging with reasonable reconstructions. BCS considerably reduces scan time for multiparameter mapping of the whole brain with minimal artifacts, and is more robust to motion-induced signal changes compared to current compressed sensing and principal component analysis-based techniques. © 2015 Wiley Periodicals, Inc.

Realization of multi-parameter and multi-state in fault tree computer-aided building software

International Nuclear Information System (INIS)

Guo Xiaoli; Tong Jiejuan; Xue Dazhi

2004-01-01

More than one parameter and more than one failed state of a parameter are often involved in building fault tree, so it is necessary for fault tree computer-aided building software to deal with multi-parameter and multi-state. Fault Tree Expert System (FTES) has the target of aiding the FT-building work of hydraulic systems. This paper expatiates on how to realize multi-parameter and multi-state in FTES with focus on Knowledge Base and Illation Engine. (author)

Ultra-Weak Fiber Bragg Grating Sensing Network Coated with Sensitive Material for Multi-Parameter Measurements

Directory of Open Access Journals (Sweden)

Wei Bai

2017-06-01

Full Text Available A multi-parameter measurement system based on ultra-weak fiber Bragg grating (UFBG array with sensitive material was proposed and experimentally demonstrated. The UFBG array interrogation principle is time division multiplex technology with two semiconductor optical amplifiers as timing units. Experimental results showed that the performance of the proposed UFBG system is almost equal to that of traditional FBG, while the UFBG array system has obvious superiority with potential multiplexing ability for multi-point and multi-parameter measurement. The system experimented on a 144 UFBG array with the reflectivity of UFBG ~0.04% for the four target parameters: hydrogen, humidity, temperature and salinity. Moreover, a uniform solution was customized to divide the cross-sensitivity between temperature and other target parameters. It is expected that this scheme will be capable of handling thousands of multi-parameter sensors in a single fiber.

Ultra-Weak Fiber Bragg Grating Sensing Network Coated with Sensitive Material for Multi-Parameter Measurements.

Science.gov (United States)

Bai, Wei; Yang, Minghong; Hu, Chenyuan; Dai, Jixiang; Zhong, Xuexiang; Huang, Shuai; Wang, Gaopeng

2017-06-26

A multi-parameter measurement system based on ultra-weak fiber Bragg grating (UFBG) array with sensitive material was proposed and experimentally demonstrated. The UFBG array interrogation principle is time division multiplex technology with two semiconductor optical amplifiers as timing units. Experimental results showed that the performance of the proposed UFBG system is almost equal to that of traditional FBG, while the UFBG array system has obvious superiority with potential multiplexing ability for multi-point and multi-parameter measurement. The system experimented on a 144 UFBG array with the reflectivity of UFBG ~0.04% for the four target parameters: hydrogen, humidity, temperature and salinity. Moreover, a uniform solution was customized to divide the cross-sensitivity between temperature and other target parameters. It is expected that this scheme will be capable of handling thousands of multi-parameter sensors in a single fiber.

Multiparameter Stochastic Dynamics of Ecological Tourism System with Continuous Visitor Education Interventions

Directory of Open Access Journals (Sweden)

Dongping Wei

2015-01-01

Full Text Available Management of ecological tourism in protected areas faces many challenges, with visitation-related resource degradations and cultural impacts being two of them. To address those issues, several strategies including regulations, site managements, and visitor education programs have been commonly used in China and other countries. This paper presents a multiparameter stochastic differential equation model of an Ecological Tourism System to study how the populations of stakeholders vary in a finite time. The solution of Ordinary Differential Equation of Ecological Tourism System reveals that the system collapses when there is a lack of visitor educational intervention. Hence, the Stochastic Dynamic of Ecological Tourism System is introduced to suppress the explosion of the system. But the simulation results of the Stochastic Dynamic of Ecological Tourism System show that the system is still unstable and chaos in some small time interval. The Multiparameters Stochastic Dynamics of Ecological Tourism System is proposed to improve the performance in this paper. The Multiparameters Stochastic Dynamics of Ecological Tourism System not only suppresses the explosion of the system in a finite time, but also keeps the populations of stakeholders in an acceptable level. In conclusion, the Ecological Tourism System develops steadily and sustainably when land managers employ effective visitor education intervention programs to deal with recreation impacts.

Multi-parameter analysis for the technical and economic assessment of photovoltaic systems in the main European Union countries

International Nuclear Information System (INIS)

Bortolini, Marco; Gamberi, Mauro; Graziani, Alessandro; Mora, Cristina; Regattieri, Alberto

2013-01-01

Highlights: • Performance cost model assesses the feasibility and profitability of PV systems. • Multi-country and multi-parameter analysis of PV systems in the European Union area. • The impact of key technical, environmental, economic and financial data is assessed. • Germany, Italy and Spain present the most effective PV sector support strategies. • The rated power and energy self-consumption ratio affect PV plant profitability. - Abstract: In the last decades, the attention to solar energy as a renewable and nonpolluting energy source increased a lot through scientists, private and public institutions. Several efforts are made to increase the diffusion of such a source and to create the conditions making it competitive for the energy market. Particularly, for the photovoltaic (PV) sector, the module efficiency increase, manufacturing cost reduction and a strong public support, through favorable incentive schemes, generates a significant rise in the installed power, exceeding 40 GWp in 2010. Although the global trend of the PV sector is positive, differences among countries arise out of local peculiarities and evolutions in the national support policies. This paper investigates such issues focusing on the feasibility analysis of PV solar systems for eight relevant countries in the European Union area, i.e. France, Germany, Greece, Italy, Spain, The Netherlands, Turkey and United Kingdom. A multi-country and multi-parameter comparative analysis, based on the net present value and payback capital budget indices, allows to highlight the conditions most affecting the economic feasibility of PV systems. The national support strategies, along with the most relevant technical, environmental, economic and financial parameters, are the key features included and compared in the analysis. The major results deal with the conditions which make PV systems potentially profitable for each country and installation feature. The national support strategies to the PV

Multi-parameter full waveform inversion using Poisson

KAUST Repository

Oh, Juwon

2016-07-21

In multi-parameter full waveform inversion (FWI), the success of recovering each parameter is dependent on characteristics of the partial derivative wavefields (or virtual sources), which differ according to parameterisation. Elastic FWIs based on the two conventional parameterisations (one uses Lame constants and density; the other employs P- and S-wave velocities and density) have low resolution of gradients for P-wave velocities (or ). Limitations occur because the virtual sources for P-wave velocity or (one of the Lame constants) are related only to P-P diffracted waves, and generate isotropic explosions, which reduce the spatial resolution of the FWI for these parameters. To increase the spatial resolution, we propose a new parameterisation using P-wave velocity, Poisson\\'s ratio, and density for frequency-domain multi-parameter FWI for isotropic elastic media. By introducing Poisson\\'s ratio instead of S-wave velocity, the virtual source for the P-wave velocity generates P-S and S-S diffracted waves as well as P-P diffracted waves in the partial derivative wavefields for the P-wave velocity. Numerical examples of the cross-triangle-square (CTS) model indicate that the new parameterisation provides highly resolved descent directions for the P-wave velocity. Numerical examples of noise-free and noisy data synthesised for the elastic Marmousi-II model support the fact that the new parameterisation is more robust for noise than the two conventional parameterisations.

Frequency Domain Multi-parameter Full Waveform Inversion for Acoustic VTI Media

KAUST Repository

Djebbi, Ramzi; Alkhalifah, Tariq Ali

2017-01-01

Multi-parameter full waveform inversion (FWI) for transversely isotropic (TI) media with vertical axis of symmetry (VTI) suffers from the trade-off between the parameters. The trade-off results in the leakage of one parameter's update into the other

Multi-parameters scanning in HTI media

KAUST Repository

Masmoudi, Nabil

2014-08-05

Building credible anisotropy models is crucial in imaging. One way to estimate anisotropy parameters is to relate them analytically to traveltime, which is challenging in inhomogeneous media. Using perturbation theory, we develop traveltime approximations for transversely isotropic media with horizontal symmetry axis (HTI) as explicit functions of the anellipticity parameter η and the symmetry axis azimuth ϕ in inhomogeneous background media. Specifically, our expansion assumes an inhomogeneous elliptically anisotropic background medium, which may be obtained from well information and stacking velocity analysis in HTI media. This formulation has advantages on two fronts: on one hand, it alleviates the computational complexity associated with solving the HTI eikonal equation, and on the other hand, it provides a mechanism to scan for the best fitting parameters η and ϕ without the need for repetitive modeling of traveltimes, because the traveltime coefficients of the expansion are independent of the perturbed parameters η and ϕ. The accuracy of our expansion is further enhanced by the use of shanks transform. We show the effectiveness of our scheme with tests on a 3D model and we propose an approach for multi-parameters scanning in TI media.

Multi-parameters scanning in HTI media

KAUST Repository

Masmoudi, Nabil; Alkhalifah, Tariq Ali

2014-01-01

Building credible anisotropy models is crucial in imaging. One way to estimate anisotropy parameters is to relate them analytically to traveltime, which is challenging in inhomogeneous media. Using perturbation theory, we develop traveltime approximations for transversely isotropic media with horizontal symmetry axis (HTI) as explicit functions of the anellipticity parameter η and the symmetry axis azimuth ϕ in inhomogeneous background media. Specifically, our expansion assumes an inhomogeneous elliptically anisotropic background medium, which may be obtained from well information and stacking velocity analysis in HTI media. This formulation has advantages on two fronts: on one hand, it alleviates the computational complexity associated with solving the HTI eikonal equation, and on the other hand, it provides a mechanism to scan for the best fitting parameters η and ϕ without the need for repetitive modeling of traveltimes, because the traveltime coefficients of the expansion are independent of the perturbed parameters η and ϕ. The accuracy of our expansion is further enhanced by the use of shanks transform. We show the effectiveness of our scheme with tests on a 3D model and we propose an approach for multi-parameters scanning in TI media.

A multi-parameter, acquisition system positron annihilation lifetime spectrometer

International Nuclear Information System (INIS)

Sharshar, T.

2004-01-01

A positron annihilation lifetime spectrometer employing a multi-parameter acquisition system has been prepared for various purposes such as the investigation and characterization of solid-state materials. The fast-fast coincidence technique was used in the present spectrometer with a pair of plastic scintillation detectors. The acquisition system is based on the Kmax software and on CAMAC modules. The data are acquired in event-by-event list mode. The time spectrum for the desired energy windows can be obtained by off-line data sorting and analysis. The spectrometer for event-by-event data acquisition is an important step to construct a positron age-momentum correlation (AMOC) spectrometer. The AMOC technique is especially suited for the observation of positron transitions between different states during their lifetime. The system performance was tested and the results were presented and discussed

Equilibrium radionuclide ventriculography: Comparison with echo-ventriculography and digital subtraction angiocardiography, evaluation of multiparameters

Energy Technology Data Exchange (ETDEWEB)

Hoer, G; Standke, R; Klepzig, H Jr; Maul, F D; Tuengerthal, S; Tezak, S; Reifarth, N; Kanemoto, N; Happ, J; Baum, R P

1986-09-01

Subsequent to the discussion of technical prerequisites (fully-automated, reproducible multiparameter-analysis (MPA), rest, exercise) which is followed by remarks concerning the pathophysiology of ischemic left ventricular functional disorders in diastole and systole, the following points are considered: 1) comparative results of RNV, cineventriculoangiography, echo-ventriculography and intraveneous digital subtraction angiocardiography; 2) 'normal' values of RNV in MPA; 3) heart and pulmonary diseases (coronary artery disease with sensitivity and specificity of MPA), chronic obstructive pulmonary disease, chronic aortic insufficiency, hypertension; 4) summary of, and prospects for future potentialities (software, clinical indications).

Multi-parameter Analysis and Inversion for Anisotropic Media Using the Scattering Integral Method

KAUST Repository

Djebbi, Ramzi

2017-10-24

The main goal in seismic exploration is to identify locations of hydrocarbons reservoirs and give insights on where to drill new wells. Therefore, estimating an Earth model that represents the right physics of the Earth\\'s subsurface is crucial in identifying these targets. Recent seismic data, with long offsets and wide azimuth features, are more sensitive to anisotropy. Accordingly, multiple anisotropic parameters need to be extracted from the recorded data on the surface to properly describe the model. I study the prospect of applying a scattering integral approach for multi-parameter inversion for a transversely isotropic model with a vertical axis of symmetry. I mainly analyze the sensitivity kernels to understand the sensitivity of seismic data to anisotropy parameters. Then, I use a frequency domain scattering integral approach to invert for the optimal parameterization. The scattering integral approach is based on the explicit computation of the sensitivity kernels. I present a new method to compute the traveltime sensitivity kernels for wave equation tomography using the unwrapped phase. I show that the new kernels are a better alternative to conventional cross-correlation/Rytov kernels. I also derive and analyze the sensitivity kernels for a transversely isotropic model with a vertical axis of symmetry. The kernels structure, for various opening/scattering angles, highlights the trade-off regions between the parameters. For a surface recorded data, I show that the normal move-out velocity vn, ƞ and δ parameterization is suitable for a simultaneous inversion of diving waves and reflections. Moreover, when seismic data is inverted hierarchically, the horizontal velocity vh, ƞ and ϵ is the parameterization with the least trade-off. In the frequency domain, the hierarchical inversion approach is naturally implemented using frequency continuation, which makes vh, ƞ and ϵ parameterization attractive. I formulate the multi-parameter inversion using the

Multi-parameter optimization design of parabolic trough solar receiver

International Nuclear Information System (INIS)

Guo, Jiangfeng; Huai, Xiulan

2016-01-01

Highlights: • The optimal condition can be obtained by multi-parameter optimization. • Exergy and thermal efficiencies are employed as objective function. • Exergy efficiency increases at the expense of heat losses. • The heat obtained by working fluid increases as thermal efficiency grows. - Abstract: The design parameters of parabolic trough solar receiver are interrelated and interact with one another, so the optimal performance of solar receiver cannot be obtained by the convectional single-parameter optimization. To overcome the shortcoming of single-parameter optimization, a multi-parameter optimization of parabolic trough solar receiver is employed based on genetic algorithm in the present work. When the thermal efficiency is taken as the objective function, the heat obtained by working fluid increases while the average temperature of working fluid and wall temperatures of solar receiver decrease. The average temperature of working fluid and the wall temperatures of solar receiver increase while the heat obtained by working fluid decreases generally by taking the exergy efficiency as an objective function. Assuming that the solar radiation intensity remains constant, the exergy obtained by working fluid increases by taking exergy efficiency as the objective function, which comes at the expense of heat losses of solar receiver.

Rational function systems and electrical networks with multiparameters

CERN Document Server

Lu, KaiSheng

2012-01-01

To overcome the problems of system theory and network theory over real field, this book uses matrices over the field F(z) of rational functions in multiparameters describing coefficient matrices of systems and networks and makes systems and network description over F(z) and researches their structural properties: reducible condition of a class of matrices over F(z) and their characteristic polynomial; type1 matrix and two basic properties; variable replacement conditions for independent parameters; structural controllability and observability of linear systems over F(z); separability, reducibi

Representations of Urbanik's classes and multiparameter Ornstein-Uhlenbeck processes

DEFF Research Database (Denmark)

Graversen, Svend-Erik; Pedersen, Jan

2011-01-01

A class of integrals with respect to homogeneous Lévy bases on Rk is considered. In the one-dimensional case k=1 this class corresponds to the selfdecomposable distributions. Necessary and sufficient conditions for existence as well as some representations of the integrals are given. Generalizing...... the one-dimensional case it is shown that the class of integrals corresponds to Urbanik's class Lk-1(R). Finally, multiparameter Ornstein-Uhlenbeck processes are defined and studied....

Multi-Parameter Estimation for Orthorhombic Media

KAUST Repository

Masmoudi, Nabil

2015-08-19

Building reliable anisotropy models is crucial in seismic modeling, imaging and full waveform inversion. However, estimating anisotropy parameters is often hampered by the trade off between inhomogeneity and anisotropy. For instance, one way to estimate the anisotropy parameters is to relate them analytically to traveltimes, which is challenging in inhomogeneous media. Using perturbation theory, we develop travel-time approximations for orthorhombic media as explicit functions of the anellipticity parameters η1, η2 and a parameter Δγ in inhomogeneous background media. Specifically, our expansion assumes inhomogeneous ellipsoidal anisotropic background model, which can be obtained from well information and stacking velocity analysis. This approach has two main advantages: in one hand, it provides a computationally efficient tool to solve the orthorhombic eikonal equation, on the other hand, it provides a mechanism to scan for the best fitting anisotropy parameters without the need for repetitive modeling of traveltimes, because the coefficients of the traveltime expansion are independent of the perturbed parameters. Furthermore, the coefficients of the traveltime expansion provide insights on the sensitivity of the traveltime with respect to the perturbed parameters. We show the accuracy of the traveltime approximations as well as an approach for multi-parameter scanning in orthorhombic media.

Multi-Parameter Estimation for Orthorhombic Media

KAUST Repository

Masmoudi, Nabil; Alkhalifah, Tariq Ali

2015-01-01

Building reliable anisotropy models is crucial in seismic modeling, imaging and full waveform inversion. However, estimating anisotropy parameters is often hampered by the trade off between inhomogeneity and anisotropy. For instance, one way to estimate the anisotropy parameters is to relate them analytically to traveltimes, which is challenging in inhomogeneous media. Using perturbation theory, we develop travel-time approximations for orthorhombic media as explicit functions of the anellipticity parameters η1, η2 and a parameter Δγ in inhomogeneous background media. Specifically, our expansion assumes inhomogeneous ellipsoidal anisotropic background model, which can be obtained from well information and stacking velocity analysis. This approach has two main advantages: in one hand, it provides a computationally efficient tool to solve the orthorhombic eikonal equation, on the other hand, it provides a mechanism to scan for the best fitting anisotropy parameters without the need for repetitive modeling of traveltimes, because the coefficients of the traveltime expansion are independent of the perturbed parameters. Furthermore, the coefficients of the traveltime expansion provide insights on the sensitivity of the traveltime with respect to the perturbed parameters. We show the accuracy of the traveltime approximations as well as an approach for multi-parameter scanning in orthorhombic media.

Readout Distance Enhancement of the Passive Wireless Multi-Parameter Sensing System Using a Repeater Coil

Directory of Open Access Journals (Sweden)

Lifeng Wang

2018-01-01

Full Text Available A repeater coil is used to extend the detection distance of a passive wireless multi-parameter sensing system. The passive wireless sensing system has the ability of simultaneously monitoring three parameters by using backscatter modulation together with channel multiplexing. Two different repeater coils are designed and fabricated for readout distance enhancement of the sensing system: one is a PCB (printed circuit board repeater coil, and the other is a copper wire repeater coil. Under the conditions of fixed voltage and adjustable voltage, the maximum readout distance of the sensing system with and without a repeater coil is measured. Experimental results show that larger power supply voltage can help further increase the readout distance. The maximum readout distance of the sensing system with a PCB repeater coil has been extended 2.3 times, and the one with a copper wire repeater coil has been extended 3 times. Theoretical analysis and experimental results both indicate that the high Q factor repeater coil can extend the readout distance more. With the copper wire repeater coil as well as a higher power supply voltage, the passive wireless multi-parameter sensing system finally achieves a maximum readout distance of 13.5 cm.

Quantized planes and multiparameter deformations of Heisenberg and GL(N) algebras

International Nuclear Information System (INIS)

Fairlie, D.B.; Zachos, C.

1991-01-01

We summarize our work on explicitly deforming classical oscillators to multiparameter quantum oscillators which do not commute with each other. These ''anyonic'' oscillators lead to the construction of a consistent quantum algebra GL q (N) with (N - 1)(N - 2)/2 independent parameters, some of whose features and applications we shall discuss. 22 refs

Frequency Domain Multi-parameter Full Waveform Inversion for Acoustic VTI Media

KAUST Repository

Djebbi, Ramzi

2017-05-26

Multi-parameter full waveform inversion (FWI) for transversely isotropic (TI) media with vertical axis of symmetry (VTI) suffers from the trade-off between the parameters. The trade-off results in the leakage of one parameter\\'s update into the other during the inversion. It affects the accuracy and convergence of the inversion. The sensitivity analyses suggested a parameterisation using the horizontal velocity vh, epsilon and eta to reduce the trade-off for surface recorded seismic data.We test the (vh, epsilon, eta) parameterisation for acoustic VTI media using a scattering integral (SI) based inversion. The data is modeled in frequency domain and the model is updated using a preconditioned conjugate gradient method. We applied the method to the VTI Marmousi II model and in the inversion, we keep eta parameter fixed as the background initial model and we invert simultaneously for both vh and epsilon. The results show the suitability of the parameterisation for multi-parameter VTI acoustic inversion as well as the accuracy of the inversion approach.

Discrimination of land cover from a multiparameter SAR data set

International Nuclear Information System (INIS)

Pierdicca, N.; Castracane, P.; Basili, P.; Ciotti, P.; Marzano, F.S.

2001-01-01

The identification of the most valuable radar observation parameters (e.g., frequency, polarisation, incidence angle) is important both for designing non-redundant high-performance sensors (i.e. selection of frequency bands and polarizations) and for specifying mission operation requirements (i.e. temporal sampling, incidence angle). Moreover, the task of classifying multiparameter SAR images may require to adopt a strategy that implies the selection of a number of features among those available from this kind of sensors. In this paper it has performed this kind of analysis in a specific area of interest to account for the particular conditions in which remotely sensed data are going to be used. The paper summarises the results of the analysis of the radar data acquired during the MAC Europe '91 and X-SAR/SIR-C campaigns over the Montespertoli test site in Italy. The analysis is based mainly on a statistical approach aiming at demonstrating what is the contribution of different measurements performed by the polarimetric SAR for discriminating the surface coverage. The work is intended to furnish a guideline to develop an optimal strategy for acquiring and processing polarimetric data to be used for land classification

Multiparameter Sensor Chip with Barium Strontium Titanate as Multipurpose Material

OpenAIRE

Huck, Christina; Poghossian, Arshak; Kerroumi, Iman; Schusser, Sebastian; Backer, Matthias; Zander, Willi; Schubert, Juergen; Buniatyan, Vahe V; Martirosyan, Norayr W; Wagner, Patrick Hermann; Schoning, Michael J

2014-01-01

It is well known that biochemical and biotechnological processes are strongly dependent and affected by a variety of physico-chemical parameters such as pH value, temperature, pressure and electrolyte conductivity. Therefore, these quantities have to be monitored or controlled in order to guarantee a stable process operation, optimization and high yield. In this work, a sensor chip for the multiparameter detection of three physico-chemical parameters such as electrolyte conductivity, pH and t...

Spectral collocation for multiparameter eigenvalue problems arising from separable boundary value problems

Science.gov (United States)

Plestenjak, Bor; Gheorghiu, Călin I.; Hochstenbach, Michiel E.

2015-10-01

In numerous science and engineering applications a partial differential equation has to be solved on some fairly regular domain that allows the use of the method of separation of variables. In several orthogonal coordinate systems separation of variables applied to the Helmholtz, Laplace, or Schrödinger equation leads to a multiparameter eigenvalue problem (MEP); important cases include Mathieu's system, Lamé's system, and a system of spheroidal wave functions. Although multiparameter approaches are exploited occasionally to solve such equations numerically, MEPs remain less well known, and the variety of available numerical methods is not wide. The classical approach of discretizing the equations using standard finite differences leads to algebraic MEPs with large matrices, which are difficult to solve efficiently. The aim of this paper is to change this perspective. We show that by combining spectral collocation methods and new efficient numerical methods for algebraic MEPs it is possible to solve such problems both very efficiently and accurately. We improve on several previous results available in the literature, and also present a MATLAB toolbox for solving a wide range of problems.

Multiparameter cytometric analysis of complex cellular response

Czech Academy of Sciences Publication Activity Database

Šimečková, Šárka; Fedr, Radek; Remšík, Jan; Kahounová, Z.; Slabáková, Eva; Souček, Karel

2018-01-01

Roč. 93A, č. 2 (2018), s. 239-248 ISSN 1552-4922 R&D Projects: GA MZd(CZ) NV15-28628A; GA MZd(CZ) NV15-33999A; GA MZd(CZ) NV17-28518A Institutional support: RVO:68081707 Keywords : flow-cytometry * permeabilization * apoptosis * fixation Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Cell biology Impact factor: 3.222, year: 2016

High speed acquisition of multiparameter data using a Macintosh IIcx

Science.gov (United States)

Berno, Anthony; Vogel, John S.; Caffee, Marc

1991-05-01

Accelerator mass spectrometry systems based on > 3 MV tandem accelerators often use multianode ionization detectors and/or time-of-flight detectors to identify individual isotopes through multiparameter analysis. A Macintosh IIcx has been programmed to collect AMS data from a CAMAC-implemented analyzer and to display the histogrammed individual parameters and a doubleparameter array. The computer-CAMAC connection is through a NuBus to CAMAC dataway interface which allows direct addressing to all functions and registers in the crate. Asynchronous data from the rare isotope are sorted into a CAMAC memory module by a list sequence controller. Isotope switching is controlled by a one-cycle timing generator. A rate-dependent amount of time is used to transfer the data from the memory module at the end of each timing cycle. The present configuration uses 10-75 ms for rates of 500-10000 cps. Parameter analysis occurs during the rest of the 520 ms data collection cycle. Completed measurements of the isotope concentrations of each sample are written to files which are compatible with standard Macintosh databases or other processing programs. The system is inexpensive and operates at speeds comparable to those obtainable using larger computers.

Induction studies with Escherichia coli expressing recombinant interleukin-13 using multi-parameter flow cytometry

DEFF Research Database (Denmark)

Shitu, J. O.; Woodley, John; Wnek, R.

2009-01-01

The expression of interleukin-13 (IL13) following induction with IPTG in Escherichia coli results in metabolic changes as indicated by multi-parameter flow cytometry and traditional methods of fermentation profiling (O-2 uptake rate, CO2 evolution rate and optical density measurements). Induction...

Model-based dynamic multi-parameter method for peak power estimation of lithium-ion batteries

NARCIS (Netherlands)

Sun, F.; Xiong, R.; He, H.; Li, W.; Aussems, J.E.E.

2012-01-01

A model-based dynamic multi-parameter method for peak power estimation is proposed for batteries and battery management systems (BMSs) used in hybrid electric vehicles (HEVs). The available power must be accurately calculated in order to not damage the battery by over charging or over discharging or

CIMI simulations with recently developed multi-parameter chorus and plasmaspheric hiss models

Science.gov (United States)

Aryan, Homayon; Sibeck, David; Kang, Suk-bin; Balikhin, Michael; Fok, Mei-ching

2017-04-01

Simulation studies of the Earth's radiation belts are very useful in understanding the acceleration and loss of energetic particles. The Comprehensive Inner Magnetosphere-Ionosphere (CIMI) model considers the effects of the ring current and plasmasphere on the radiation belts. CIMI was formed by merging the Comprehensive Ring Current Model (CRCM) and the Radiation Belt Environment (RBE) model to solves for many essential quantities in the inner magnetosphere, including radiation belt enhancements and dropouts. It incorporates chorus and plasmaspheric hiss wave diffusion of energetic electrons in energy, pitch angle, and cross terms. Usually the chorus and plasmaspheric hiss models used in CIMI are based on single-parameter geomagnetic index (AE). Here we integrate recently developed multi-parameter chorus and plasmaspheric hiss wave models based on geomagnetic index and solar wind parameters. We then perform CIMI simulations for different storms and compare the results with data from the Van Allen Probes and the Two Wide-angle Imaging Neutral-atom Spectrometers and Akebono satellites. We find that the CIMI simulations with multi-parameter chorus and plasmaspheric hiss wave models are more comparable to data than the single-parameter wave models.

Active hydrothermal and non-active massive sulfide mound investigation using a new multiparameter chemical sensor

Science.gov (United States)

Han, C.; Wu, G.; Qin, H.; Wang, Z.

2012-12-01

Investigation of active hydrothermal mound as well as non-active massive sulfide mound are studied recently. However, there is still lack of in-situ detection method for the non-active massive sulfide mound. Even though Transient ElectroMagnetic (TEM) and Electric Self-potential (SP) methods are good, they both are labour, time and money cost work. We proposed a new multiparameter chemical sensor method to study the seafloor active hydrothermal mound as well as non-active massive sulfide mound. This sensor integrates Eh, S2- ions concentration and pH electrochemical electrodes together, and could found chemical change caused by the active hydrothermal vent, even weak chemical abnormalities by non-active massive sulfide hydrothermal mound which MARP and CTD sometimes cannot detect. In 2012, the 1st Leg of the Chinese 26th cruise, the multiparameter chemical sensor was carried out with the deepsea camera system over the Carlsberg Ridge in Indian Ocean by R/V DAYANGYIHAO. It was shown small Eh and S2- ions concentration abnormal around a site at Northwest Indian ridge. This site was also evidenced by the TV grab. In the 2nd Leg of the same cruise in June, this chemical sensor was carried out with TEM and SP survey system. The chemical abnormalities are matched very well with both TEM and SP survey results. The results show that the multiparameter chemical sensor method not only can detect active hydrothermal mound, but also can find the non-active massive sulfide hydrothermal mound.

Monitoring the Dead Sea Region by Multi-Parameter Stations

Science.gov (United States)

Mohsen, A.; Weber, M. H.; Kottmeier, C.; Asch, G.

2015-12-01

The Dead Sea Region is an exceptional ecosystem whose seismic activity has influenced all facets of the development, from ground water availability to human evolution. Israelis, Palestinians and Jordanians living in the Dead Sea region are exposed to severe earthquake hazard. Repeatedly large earthquakes (e.g. 1927, magnitude 6.0; (Ambraseys, 2009)) shook the whole Dead Sea region proving that earthquake hazard knows no borders and damaging seismic events can strike anytime. Combined with the high vulnerability of cities in the region and with the enormous concentration of historical values this natural hazard results in an extreme earthquake risk. Thus, an integration of earthquake parameters at all scales (size and time) and their combination with data of infrastructure are needed with the specific aim of providing a state-of-the-art seismic hazard assessment for the Dead Sea region as well as a first quantitative estimate of vulnerability and risk. A strong motivation for our research is the lack of reliable multi-parameter ground-based geophysical information on earthquakes in the Dead Sea region. The proposed set up of a number of observatories with on-line data access will enable to derive the present-day seismicity and deformation pattern in the Dead Sea region. The first multi-parameter stations were installed in Jordan, Israel and Palestine for long-time monitoring. All partners will jointly use these locations. All stations will have an open data policy, with the Deutsches GeoForschungsZentrum (GFZ, Potsdam, Germany) providing the hard and software for real-time data transmission via satellite to Germany, where all partners can access the data via standard data protocols.

CIMI simulations with newly developed multiparameter chorus and plasmaspheric hiss wave models

Science.gov (United States)

Aryan, Homayon; Sibeck, David G.; Kang, Suk-Bin; Balikhin, Michael A.; Fok, Mei-Ching; Agapitov, Oleksiy; Komar, Colin M.; Kanekal, Shrikanth G.; Nagai, Tsugunobu

2017-09-01

Numerical simulation studies of the Earth's radiation belts are important to understand the acceleration and loss of energetic electrons. The Comprehensive Inner Magnetosphere-Ionosphere (CIMI) model considers the effects of the ring current and plasmasphere on the radiation belts to obtain plausible results. The CIMI model incorporates pitch angle, energy, and cross diffusion of electrons, due to chorus and plasmaspheric hiss waves. These parameters are calculated using statistical wave distribution models of chorus and plasmaspheric hiss amplitudes. However, currently, these wave distribution models are based only on a single-parameter, geomagnetic index (AE) and could potentially underestimate the wave amplitudes. Here we incorporate recently developed multiparameter chorus and plasmaspheric hiss wave models based on geomagnetic index and solar wind parameters. We then perform CIMI simulations for two geomagnetic storms and compare the flux enhancement of MeV electrons with data from the Van Allen Probes and Akebono satellites. We show that the relativistic electron fluxes calculated with multiparameter wave models resemble the observations more accurately than the relativistic electron fluxes calculated with single-parameter wave models. This indicates that wave models based on a combination of geomagnetic index and solar wind parameters are more effective as inputs to radiation belt models.

Estimating reliability of degraded system based on the probability density evolution with multi-parameter

Directory of Open Access Journals (Sweden)

Jiang Ge

2017-01-01

Full Text Available System degradation was usually caused by multiple-parameter degradation. The assessment result of system reliability by universal generating function was low accurate when compared with the Monte Carlo simulation. And the probability density function of the system output performance cannot be got. So the reliability assessment method based on the probability density evolution with multi-parameter was presented for complexly degraded system. Firstly, the system output function was founded according to the transitive relation between component parameters and the system output performance. Then, the probability density evolution equation based on the probability conservation principle and the system output function was established. Furthermore, probability distribution characteristics of the system output performance was obtained by solving differential equation. Finally, the reliability of the degraded system was estimated. This method did not need to discrete the performance parameters and can establish continuous probability density function of the system output performance with high calculation efficiency and low cost. Numerical example shows that this method is applicable to evaluate the reliability of multi-parameter degraded system.

Application of multi-parameter chorus and plasmaspheric hiss wave models in radiation belt modeling

Science.gov (United States)

Aryan, H.; Kang, S. B.; Balikhin, M. A.; Fok, M. C. H.; Agapitov, O. V.; Komar, C. M.; Kanekal, S. G.; Nagai, T.; Sibeck, D. G.

2017-12-01

Numerical simulation studies of the Earth's radiation belts are important to understand the acceleration and loss of energetic electrons. The Comprehensive Inner Magnetosphere-Ionosphere (CIMI) model along with many other radiation belt models require inputs for pitch angle, energy, and cross diffusion of electrons, due to chorus and plasmaspheric hiss waves. These parameters are calculated using statistical wave distribution models of chorus and plasmaspheric hiss amplitudes. In this study we incorporate recently developed multi-parameter chorus and plasmaspheric hiss wave models based on geomagnetic index and solar wind parameters. We perform CIMI simulations for two geomagnetic storms and compare the flux enhancement of MeV electrons with data from the Van Allen Probes and Akebono satellites. We show that the relativistic electron fluxes calculated with multi-parameter wave models resembles the observations more accurately than the relativistic electron fluxes calculated with single-parameter wave models. This indicates that wave models based on a combination of geomagnetic index and solar wind parameters are more effective as inputs to radiation belt models.

Multiparameter Cell Cycle Analysis.

Science.gov (United States)

Jacobberger, James W; Sramkoski, R Michael; Stefan, Tammy; Woost, Philip G

2018-01-01

Cell cycle cytometry and analysis are essential tools for studying cells of model organisms and natural populations (e.g., bone marrow). Methods have not changed much for many years. The simplest and most common protocol is DNA content analysis, which is extensively published and reviewed. The next most common protocol, 5-bromo-2-deoxyuridine S phase labeling detected by specific antibodies, is also well published and reviewed. More recently, S phase labeling using 5'-ethynyl-2'-deoxyuridine incorporation and a chemical reaction to label substituted DNA has been established as a basic, reliable protocol. Multiple antibody labeling to detect epitopes on cell cycle regulated proteins, which is what this chapter is about, is the most complex of these cytometric cell cycle assays, requiring knowledge of the chemistry of fixation, the biochemistry of antibody-antigen reactions, and spectral compensation. However, because this knowledge is relatively well presented methodologically in many papers and reviews, this chapter will present a minimal Methods section for one mammalian cell type and an extended Notes section, focusing on aspects that are problematic or not well described in the literature. Most of the presented work involves how to segment the data to produce a complete, progressive, and compartmentalized cell cycle analysis from early G1 to late mitosis (telophase). A more recent development, using fluorescent proteins fused with proteins or peptides that are degraded by ubiquitination during specific periods of the cell cycle, termed "Fucci" (fluorescent, ubiquitination-based cell cycle indicators) provide an analysis similar in concept to multiple antibody labeling, except in this case cells can be analyzed while living and transgenic organisms can be created to perform cell cycle analysis ex or in vivo (Sakaue-Sawano et al., Cell 132:487-498, 2007). This technology will not be discussed.

Hydrometeor discrimination in melting layer using multiparameter airborne radar measurement

Science.gov (United States)

Kumagai, H.; Meneghini, R.; Kozu, T.

1992-01-01

Results from a multiparameter airborne radar/radiometer experiment (the Typhoon experiment) are presented. The experiment was conducted in the western Pacific with the NASA DC-8 aircraft, in which a dual-wavelength at X-band and Ka-band and dual-polarization at X-band radar was installed. The signatures of dBZ(X), dBZ(Ka), LDR (linear depolarization ratio) at X-band and DZ=dBZ(X)-dBZ(Ka) are discussed for the data obtained in the penetration of the typhoon Flo. With emphasis on discrimination of hydrometeor particles, some statistical features of the brightband in stratiform rain are discussed.

Piezoelectric microelectromechanical resonant sensors for chemical and biological detection.

Science.gov (United States)

Pang, Wei; Zhao, Hongyuan; Kim, Eun Sok; Zhang, Hao; Yu, Hongyu; Hu, Xiaotang

2012-01-07

Piezoelectric microelectromechanical systems (MEMS) resonant sensors, known for their excellent mass resolution, have been studied for many applications, including DNA hybridization, protein-ligand interactions, and immunosensor development. They have also been explored for detecting antigens, organic gas, toxic ions, and explosives. Most piezoelectric MEMS resonant sensors are acoustic sensors (with specific coating layers) that enable selective and label-free detection of biological events in real time. These label-free technologies have recently garnered significant attention for their sensitive and quantitative multi-parameter analysis of biological systems. Since piezoelectric MEMS resonant sensors do more than transform analyte mass or thickness into an electrical signal (e.g., frequency and impedance), special attention must be paid to their potential beyond microweighing, such as measuring elastic and viscous properties, and several types of sensors currently under development operate at different resonant modes (i.e., thickness extensional mode, thickness shear mode, lateral extensional mode, flexural mode, etc.). In this review, we provide an overview of recent developments in micromachined resonant sensors and activities relating to biochemical interfaces for acoustic sensors.

Multiparameter probability distributions for heavy rainfall modeling in extreme southern Brazil

Directory of Open Access Journals (Sweden)

Samuel Beskow

2015-09-01

New hydrological insights for the region: The Anderson–Darling and Filliben tests were the most restrictive in this study. Based on the Anderson–Darling test, it was found that the Kappa distribution presented the best performance, followed by the GEV. This finding provides evidence that these multiparameter distributions result, for the region of study, in greater accuracy for the generation of intensity–duration–frequency curves and the prediction of peak streamflows and design hydrographs. As a result, this finding can support the design of hydraulic structures and flood management in river basins.

Probabilistic teleportation via multi-parameter measurements and partially entangled states

Science.gov (United States)

Wei, Jiahua; Shi, Lei; Han, Chen; Xu, Zhiyan; Zhu, Yu; Wang, Gang; Wu, Hao

2018-04-01

In this paper, a novel scheme for probabilistic teleportation is presented with multi-parameter measurements via a non-maximally entangled state. This is in contrast to the fact that the measurement kinds for quantum teleportation are usually particular in most previous schemes. The detail implementation producers for our proposal are given by using of appropriate local unitary operations. Moreover, the total success probability and classical information of this proposal are calculated. It is demonstrated that the success probability and classical cost would be changed with the multi-measurement parameters and the entanglement factor of quantum channel. Our scheme could enlarge the research range of probabilistic teleportation.

Investigating the fatigue behavior of grain-oriented Fe-3%Si steel sheets using magnet-optical Kerr microscopy and micromagnetic multiparameter, microstructure and stress analysis

Directory of Open Access Journals (Sweden)

Deldar Shayan

2018-01-01

Full Text Available Fatigue is considered as a reason for a significant number of mechanical failures of engineering materials. Conventionally, microstructural investigations along with stress-strain hysteresis measurements are performed to understand and characterize the fatigue behavior of metallic materials. Moreover, further physical data like temperature, electrical resistance and, in the case of ferromagnetic materials, magnetic properties can be used for a comprehensive characterization of fatigue process. The present work has employed Magneto-Optical Kerr Effect (MOKE microscope and Micromagnetic Multiparameter, Microstructure and stress Analysis (3MA system to illustrate magnetic domain structure and various intrinsic magnetic properties including magnetic Barkhausen noise (MBN of the investigated material. In order to investigate the influence of the mechanical deformation processes on the magnetic parameters, samples were produced out of the grain-oriented electrical steel sheets and were subjected to a tensile test as well as a cyclic strain increase load test with R = 0 at ambient temperature.

Concept for a solid-state multi-parameter sensor system for cell-culture monitoring

International Nuclear Information System (INIS)

Baecker, M.; Beging, S.; Biselli, M.; Poghossian, A.; Wang, J.; Zang, W.; Wagner, P.; Schoening, M.J.

2009-01-01

In this study, a concept for a silicon-based modular solid-state sensor system for inline multi-parameter monitoring of cell-culture fermentation processes is presented. The envisaged multi-parameter sensor system consists of two identical sensor modules and is intended for continuous quantification of up to five (bio-)chemical and physical parameters, namely, glucose and glutamine concentration, pH value, electrolyte conductivity and temperature by applying different transducer principles and/or different operation modes. Experimental results for the field-effect electrolyte-insulator-semiconductor (EIS) sterilisable pH sensor and electrolyte conductivity sensor based on interdigitated electrodes are presented. The ongoing autoclaving does not have any significant impact on the pH-sensitive properties of a Ta 2 O 5 -gate EIS sensor. Even after 30 autoclaving cycles, the pH sensors show a clear pH response and nearly linear calibration curve with a slope of 57 ± 1 mV/pH. Additional scanning electron microscopy and ellipsometric investigations do not show any visible surface degradation or changes in the thickness of the pH-sensitive Ta 2 O 5 layer. The preliminary results demonstrate the suitability of the developed EIS sensor for an inline pH measurement during a fermentation process. In addition, interdigitated electrodes of different geometries serving as electrolyte conductivity sensor have been tested for measurements in relatively high ionic-strength solutions.

Logical analysis of biological systems

DEFF Research Database (Denmark)

Mardare, Radu Iulian

2005-01-01

R. Mardare, Logical analysis of biological systems. Fundamenta Informaticae, N 64:271-285, 2005.......R. Mardare, Logical analysis of biological systems. Fundamenta Informaticae, N 64:271-285, 2005....

High speed acquisition of multi-parameter data using a Macintosh II CX

International Nuclear Information System (INIS)

Berno, A.; Vogel, J.S.; Caffee, M.

1990-08-01

Accelerator mass spectrometry systems based on >3MV tandem accelerators often use multi-anode ionization detectors and/or time-of-flight detectors to identify individual isotopes through multi-parameter analysis. A Macintosh llcx has been programmed to collect AMS data from a CAMAC-implemented analyzer and to display the histogrammed individual parameters and a double-parameter array. The computer-CAMAC connection is through a Nu-Bus to CAMAC dataway interface which allows direct addressing to all functions and locations in the crate. The asynchronous data from counting the rare isotope is sorted into a CAMAC memory module by a list sequence controller. Isotope switching is controlled by a one-cycle timing generator. A rate-dependent amount of time is used to transfer the data from the memory module at the end of each timing cycle. The present configuration uses 10 to 75 ms for rates of 500--10000 cps. Parameter analysis occurs during the rest of the 520 ms data collection cycle. Completed measurements of the isotope concentrations of each sample are written to files which are compatible with standard Macintosh databases or other processing programs. The system is inexpensive and operates at speeds comparable to those obtainable using larger computers

Fast ADC interface with data reduction facilities for multi-parameter experiments in nuclear physics

Energy Technology Data Exchange (ETDEWEB)

Liebl, W; Franz, N; Ziegler, G [Technische Univ. Muenchen, Garching (Germany, F.R.). Fakultaet Physik; Hegewisch, S; Kunz, D; Maier, D; Lutter, R; Schoeffel, K; Stanzel, B [Muenchen Univ. (Germany, F.R.). Sektion Physik; Drescher, B [Hahn-Meitner-Institut fuer Kernforschung Berlin G.m.b.H. (Germany, F.R.)

1982-03-01

A modular ADC interface system for multi-parameter experiments with single NIM ADCs is described. 16 fast ADCs are handled by CAMAC modules and data buses in order to build up a sophisticated hardware system which is able to take coincidence data and singles spectra in parallel. The coincidence logic is handled by one of the interface modules; the interface allows online data reduction. The further expansion of the system will be discussed.

Comparative analysis of minimal residual disease detection by multiparameter flow cytometry and enhanced ASO RQ-PCR in multiple myeloma

International Nuclear Information System (INIS)

Silvennoinen, R; Lundan, T; Kairisto, V; Pelliniemi, T-T; Putkonen, M; Anttila, P; Huotari, V; Mäntymaa, P; Siitonen, S; Uotila, L; Penttilä, T-L; Juvonen, V; Selander, T; Remes, K

2014-01-01

Multiparameter flow cytometry (MFC) and allele-specific oligonucleotide real-time quantitative PCR (ASO RQ-PCR) are the two most sensitive methods to detect minimal residual disease (MRD) in multiple myeloma (MM). We compared these methods in 129 paired post-therapy samples from 22 unselected, consecutive MM patients in complete/near complete remission. Appropriate immunophenotypic and ASO RQ-PCR-MRD targets could be detected and MRD analyses constructed for all patients. The high PCR coverage could be achieved by gradual widening of the primer sets used for clonality detection. In addition, for 13 (55%) of the patients, reverse orientation of the ASO primer and individual design of the TaqMan probe improved the sensitivity and specificity of ASO RQ-PCR analysis. A significant nonlinear correlation prevailed between MFC-MRD and PCR-MRD when both were positive. Discordance between the methods was found in 32 (35%) paired samples, which were negative by MFC-MRD, but positive by ASO RQ-PCR. The findings suggest that with the described technique, ASO RQ-PCR can be constructed for all patients with MM. ASO RQ-PCR is slightly more sensitive in MRD detection than 6−10-color flow cytometry. Owing to technical demands ASO RQ-PCR could be reserved for patients in immunophenotypic remission, especially in efficacy comparisons between different drugs and treatment modalities

Generalized synchronization-based multiparameter estimation in modulated time-delayed systems

Science.gov (United States)

Ghosh, Dibakar; Bhattacharyya, Bidyut K.

2011-09-01

We propose a nonlinear active observer based generalized synchronization scheme for multiparameter estimation in time-delayed systems with periodic time delay. A sufficient condition for parameter estimation is derived using Krasovskii-Lyapunov theory. The suggested tool proves to be globally and asymptotically stable by means of Krasovskii-Lyapunov method. With this effective method, parameter identification and generalized synchronization of modulated time-delayed systems with all the system parameters unknown, can be achieved simultaneously. We restrict our study for multiple parameter estimation in modulated time-delayed systems with single state variable only. Theoretical proof and numerical simulation demonstrate the effectiveness and feasibility of the proposed technique. The block diagram of electronic circuit for multiple time delay system shows that the method is easily applicable in practical communication problems.

Ultra-Weak Fiber Bragg Grating Sensing Network Coated with Sensitive Material for Multi-Parameter Measurements

OpenAIRE

Bai, Wei; Yang, Minghong; Hu, Chenyuan; Dai, Jixiang; Zhong, Xuexiang; Huang, Shuai; Wang, Gaopeng

2017-01-01

A multi-parameter measurement system based on ultra-weak fiber Bragg grating (UFBG) array with sensitive material was proposed and experimentally demonstrated. The UFBG array interrogation principle is time division multiplex technology with two semiconductor optical amplifiers as timing units. Experimental results showed that the performance of the proposed UFBG system is almost equal to that of traditional FBG, while the UFBG array system has obvious superiority with potential multiplexing ...

TeraTools: Multiparameter data acquisition software for the Windows 95/NT OS

International Nuclear Information System (INIS)

Piercey, R.B.

1997-01-01

TeraTools, a general purpose, multiparameter, data acquisition application for Windows 95NT is described. It is based on the Kmax architecture which has been used since 1986 on the Macintosh computer at numerous industrial, education, and research sites world-wide. TeraTools includes high-level support for industry-standard modular instrumentation; a built-in scripting language; drivers for commercially available interfaces; hooks for external code extensions; event file sorting and replay; and a full set of histogramming and display tools. The environment is scalable and may be applied to problems involving a few parameters or many parameters

Multiparameter optimization of mammography: an update

Science.gov (United States)

Jafroudi, Hamid; Muntz, E. P.; Jennings, Robert J.

1994-05-01

Previously in this forum we have reported the application of multiparameter optimization techniques to the design of a minimum dose mammography system. The approach used a reference system to define the physical imaging performance required and the dose to which the dose for the optimized system should be compared. During the course of implementing the resulting design in hardware suitable for laboratory testing, the state of the art in mammographic imaging changed, so that the original reference system, which did not have a grid, was no longer appropriate. A reference system with a grid was selected in response to this change, and at the same time the optimization procedure was modified, to make it more general and to facilitate study of the optimized design under a variety of conditions. We report the changes in the procedure, and the results obtained using the revised procedure and the up- to-date reference system. Our results, which are supported by laboratory measurements, indicate that the optimized design can image small objects as well as the reference system using only about 30% of the dose required by the reference system. Hardware meeting the specification produced by the optimization procedure and suitable for clinical use is currently under evaluation in the Diagnostic Radiology Department at the Clinical Center, NH.

Multiparameter data acquisition system for spectroscopy

International Nuclear Information System (INIS)

Beiersdorfer, P.; Brown, G. V.; Hildebrandt, L.; Wong, K. L.; Ali, R.

2001-01-01

A powerful and versatile, simple to use multiparameter data acquisition system has been implemented for use in spectroscopy. In its standard configuration, the system can acquire signal from 16 time-to-digital converter channels, 16 analog-to-digital converter channels, and 12 scaler inputs. The system was put to use on the electron beam ion trap experiment to record the output from four position-sensitive proportional counters in two soft x-ray spectrometers together with the signal from an x-ray pulse height analyzer. Also recorded are the electron beam energy and the pulse height distribution of the proportional counters. All data are recorded as a function of time. Because the relevant parameters are recorded simultaneously, software gates instead of hardware gates are used to select the data of interest. This has led to a substantial cost saving over earlier data acquisition systems. Data are stored in binary or in ascii format for system-independent processing. The operation of the system is demonstrated in a measurement of the M-shell soft x-ray spectrum of gold. We used the system to record the 3--4 and 3--5 transitions of gold (Au 44+ --Au 51+ ) excited with a simulated Maxwellian with electron temperature of 2.5 keV

A Nonlinear Multiparameters Temperature Error Modeling and Compensation of POS Applied in Airborne Remote Sensing System

Directory of Open Access Journals (Sweden)

Jianli Li

2014-01-01

Full Text Available The position and orientation system (POS is a key equipment for airborne remote sensing systems, which provides high-precision position, velocity, and attitude information for various imaging payloads. Temperature error is the main source that affects the precision of POS. Traditional temperature error model is single temperature parameter linear function, which is not sufficient for the higher accuracy requirement of POS. The traditional compensation method based on neural network faces great problem in the repeatability error under different temperature conditions. In order to improve the precision and generalization ability of the temperature error compensation for POS, a nonlinear multiparameters temperature error modeling and compensation method based on Bayesian regularization neural network was proposed. The temperature error of POS was analyzed and a nonlinear multiparameters model was established. Bayesian regularization method was used as the evaluation criterion, which further optimized the coefficients of the temperature error. The experimental results show that the proposed method can improve temperature environmental adaptability and precision. The developed POS had been successfully applied in airborne TSMFTIS remote sensing system for the first time, which improved the accuracy of the reconstructed spectrum by 47.99%.

A fast ADC interface with data reduction facilities for multi-parameter experiments in nuclear physics

International Nuclear Information System (INIS)

Liebl, W.; Franz, N.; Ziegler, G.

1982-01-01

A modular ADC interface system for multi-parameter experiments with single NIM ADCs is described. 16 fast ADCs are handled by CAMAC modules and data buses in order to build up a sophisticated hardware system which is able to take coincidence data and singles spectra in parallel. The coincidence logic is handled by one of the interface modules; the interface allows online data reduction. The further expansion of the system will be discussed. (orig.)

Combining wood anatomy and stable isotope variations in a 600-year multi-parameter climate reconstruction from Corsican black pine

Science.gov (United States)

Szymczak, Sonja; Hetzer, Timo; Bräuning, Achim; Joachimski, Michael M.; Leuschner, Hanns-Hubert; Kuhlemann, Joachim

2014-10-01

We present a new multi-parameter dataset from Corsican black pine growing on the island of Corsica in the Western Mediterranean basin covering the period AD 1410-2008. Wood parameters measured include tree-ring width, latewood width, earlywood width, cell lumen area, cell width, cell wall thickness, modelled wood density, as well as stable carbon and oxygen isotopes. We evaluated the relationships between different parameters and determined the value of the dataset for climate reconstructions. Correlation analyses revealed that carbon isotope ratios are influenced by cell parameters determining cell size, whereas oxygen isotope ratios are influenced by cell parameters determining the amount of transportable water in the xylem. A summer (June to August) precipitation reconstruction dating back to AD 1185 was established based on tree-ring width. No long-term trends or pronounced periods with extreme high/low precipitation are recorded in our reconstruction, indicating relatively stable moisture conditions over the entire time period. By comparing the precipitation reconstruction with a summer temperature reconstruction derived from the carbon isotope chronologies, we identified summers with extreme climate conditions, i.e. warm-dry, warm-wet, cold-dry and cold-wet. Extreme climate conditions during summer months were found to influence cell parameter characteristics. Cold-wet summers promote the production of broad latewood composed of wide and thin-walled tracheids, while warm-wet summers promote the production of latewood with small thick-walled cells. The presented dataset emphasizes the potential of multi-parameter wood analysis from one tree species over long time scales.

Updating Parameters for Volcanic Hazard Assessment Using Multi-parameter Monitoring Data Streams And Bayesian Belief Networks

Science.gov (United States)

Odbert, Henry; Aspinall, Willy

2014-05-01

the uncertainty of inferences, and how our method provides a route to formal propagation of uncertainties in hazard models. Such approaches provide an attractive route to developing an interface between volcano monitoring analyses and probabilistic hazard scenario analysis. We discuss the use of BBNs in hazard analysis as a tractable and traceable tool for fast, rational assimilation of complex, multi-parameter data sets in the context of timely volcanic crisis decision support.

On the performance of bioanalytical fluorescence correlation spectroscopy measurements in a multiparameter photon-counting microscope

Energy Technology Data Exchange (ETDEWEB)

Mazouchi, Amir; Liu Baoxu; Bahram, Abdullah [Department of Physics, Institute for Optical Sciences, University of Toronto, Toronto (Canada); Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Rd. N., Mississauga, ON, L5L 1C6 (Canada); Gradinaru, Claudiu C., E-mail: claudiu.gradinaru@utoronto.ca [Department of Physics, Institute for Optical Sciences, University of Toronto, Toronto (Canada); Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Rd. N., Mississauga, ON, L5L 1C6 (Canada)

2011-02-28

Fluorescence correlation spectroscopy (FCS) data acquisition and analysis routines were developed and implemented in a home-built, multiparameter photon-counting microscope. Laser excitation conditions were investigated for two representative fluorescent probes, Rhodamine110 and enhanced green fluorescent protein (EGFP). Reliable local concentrations and diffusion constants were obtained by fitting measured FCS curves, provided that the excitation intensity did not exceed 20% of the saturation level for each fluorophore. Accurate results were obtained from FCS measurements for sample concentrations varying from pM to {mu}M range, as well as for conditions of high background signals. These experimental constraints were found to be determined by characteristics of the detection system and by the saturation behavior of the fluorescent probes. These factors actually limit the average number of photons that can be collected from a single fluorophore passing through the detection volume. The versatility of our setup and the data analysis capabilities were tested by measuring the mobility of EGFP in the nucleus of Drosophila cells under conditions of high concentration and molecular crowding. As a bioanalytical application, we studied by FCS the binding affinity of a novel peptide-based drug to the cancer-regulating STAT3 protein and corroborated the results with fluorescence polarization analysis derived from the same photon data.

Sensitivity analysis approaches applied to systems biology models.

Science.gov (United States)

Zi, Z

2011-11-01

With the rising application of systems biology, sensitivity analysis methods have been widely applied to study the biological systems, including metabolic networks, signalling pathways and genetic circuits. Sensitivity analysis can provide valuable insights about how robust the biological responses are with respect to the changes of biological parameters and which model inputs are the key factors that affect the model outputs. In addition, sensitivity analysis is valuable for guiding experimental analysis, model reduction and parameter estimation. Local and global sensitivity analysis approaches are the two types of sensitivity analysis that are commonly applied in systems biology. Local sensitivity analysis is a classic method that studies the impact of small perturbations on the model outputs. On the other hand, global sensitivity analysis approaches have been applied to understand how the model outputs are affected by large variations of the model input parameters. In this review, the author introduces the basic concepts of sensitivity analysis approaches applied to systems biology models. Moreover, the author discusses the advantages and disadvantages of different sensitivity analysis methods, how to choose a proper sensitivity analysis approach, the available sensitivity analysis tools for systems biology models and the caveats in the interpretation of sensitivity analysis results.

Quantitative ultrasound assessment of breast tumor response to chemotherapy using a multi-parameter approach.

Science.gov (United States)

Tadayyon, Hadi; Sannachi, Lakshmanan; Gangeh, Mehrdad; Sadeghi-Naini, Ali; Tran, William; Trudeau, Maureen E; Pritchard, Kathleen; Ghandi, Sonal; Verma, Sunil; Czarnota, Gregory J

2016-07-19

This study demonstrated the ability of quantitative ultrasound (QUS) parameters in providing an early prediction of tumor response to neoadjuvant chemotherapy (NAC) in patients with locally advanced breast cancer (LABC). Using a 6-MHz array transducer, ultrasound radiofrequency (RF) data were collected from 58 LABC patients prior to NAC treatment and at weeks 1, 4, and 8 of their treatment, and prior to surgery. QUS parameters including midband fit (MBF), spectral slope (SS), spectral intercept (SI), spacing among scatterers (SAS), attenuation coefficient estimate (ACE), average scatterer diameter (ASD), and average acoustic concentration (AAC) were determined from the tumor region of interest. Ultrasound data were compared with the ultimate clinical and pathological response of the patient's tumor to treatment and patient recurrence-free survival. Multi-parameter discriminant analysis using the κ-nearest-neighbor classifier demonstrated that the best response classification could be achieved using the combination of MBF, SS, and SAS, with an accuracy of 60 ± 10% at week 1, 77 ± 8% at week 4 and 75 ± 6% at week 8. Furthermore, when the QUS measurements at each time (week) were combined with pre-treatment (week 0) QUS values, the classification accuracies improved (70 ± 9% at week 1, 80 ± 5% at week 4, and 81 ± 6% at week 8). Finally, the multi-parameter QUS model demonstrated a significant difference in survival rates of responding and non-responding patients at weeks 1 and 4 (p=0.035, and 0.027, respectively). This study demonstrated for the first time, using new parameters tested on relatively large patient cohort and leave-one-out classifier evaluation, that a hybrid QUS biomarker including MBF, SS, and SAS could, with relatively high sensitivity and specificity, detect the response of LABC tumors to NAC as early as after 4 weeks of therapy. The findings of this study also suggested that incorporating pre-treatment QUS parameters of a tumor improved the

Truncated Gauss-Newton Implementation for Multi-Parameter Full Waveform Inversion

Science.gov (United States)

Liu, Y.; Yang, J.; Dong, L.; Wang, Y.

2014-12-01

Full waveform inversion (FWI) is a numerical optimization method which aims at minimizing the difference between the synthetic and recorded seismic data to obtain high resolution subsurface images. A practical implementation for FWI is the adjoint-state method (AD), in which the data residuals at receiver locations are simultaneously back-propagated to form the gradient. Scattering-integral method (SI) is an alternative way which is based on the explicit building of the sensitivity kernel (Fréchet derivative matrix). Although it is more memory-consuming, SI is more efficient than AD when the number of the sources is larger than the number of the receivers. To improve the convergence of FWI, the information carried out by the inverse Hessian operator is crucial. Taking account accurately of the effect of this operator in FWI can correct illumination deficits, reserve the amplitude of the subsurface parameters, and remove artifacts generated by multiple reflections. In multi-parameter FWI, the off-diagonal blocks of the Hessian operator reflect the coupling between different parameter classes. Therefore, incorporating its inverse could help to mitigate the trade-off effects. In this study, we focus on the truncated Gauss-Newton implementation for multi-parameter FWI. The model update is computed through a matrix-free conjugate gradient solution of the Newton linear system. Both the gradient and the Hessian-vector product are calculated using the SI approach instead of the first- and second-order AD. However, the gradient expressed by kernel-vector product is calculated through the accumulation of the decomposed vector-scalar products. Thus, it's not necessary to store the huge sensitivity matrix beforehand. We call this method the matrix decomposition approach (MD). And the Hessian-vector product is replaced by two kernel-vector products which are then calculated by the above MD. By this way, we don't need to solve two additional wave propagation problems as in the

Static Analysis for Systems Biology

DEFF Research Database (Denmark)

Nielson, Flemming; Nielson, Hanne Riis; Rosa, D. Schuch da

2004-01-01

This paper shows how static analysis techniques can help understanding biological systems. Based on a simple example we illustrate the outcome of performing three different analyses extracting information of increasing precision. We conclude by reporting on the potential impact and exploitation o...... of these techniques in systems biology....

Modular analysis of biological networks.

Science.gov (United States)

Kaltenbach, Hans-Michael; Stelling, Jörg

2012-01-01

The analysis of complex biological networks has traditionally relied on decomposition into smaller, semi-autonomous units such as individual signaling pathways. With the increased scope of systems biology (models), rational approaches to modularization have become an important topic. With increasing acceptance of de facto modularity in biology, widely different definitions of what constitutes a module have sparked controversies. Here, we therefore review prominent classes of modular approaches based on formal network representations. Despite some promising research directions, several important theoretical challenges remain open on the way to formal, function-centered modular decompositions for dynamic biological networks.

An Integrated Environment Monitoring System for Underground Coal Mines—Wireless Sensor Network Subsystem with Multi-Parameter Monitoring

OpenAIRE

Zhang, Yu; Yang, Wei; Han, Dongsheng; Kim, Young-Il

2014-01-01

Environment monitoring is important for the safety of underground coal mine production, and it is also an important application of Wireless Sensor Networks (WSNs). We put forward an integrated environment monitoring system for underground coal mine, which uses the existing Cable Monitoring System (CMS) as the main body and the WSN with multi-parameter monitoring as the supplementary technique. As CMS techniques are mature, this paper mainly focuses on the WSN and the interconnection between t...

Multiparameter estimation with single photons—linearly-optically generated quantum entanglement beats the shotnoise limit

Science.gov (United States)

You, Chenglong; Adhikari, Sushovit; Chi, Yuxi; LaBorde, Margarite L.; Matyas, Corey T.; Zhang, Chenyu; Su, Zuen; Byrnes, Tim; Lu, Chaoyang; Dowling, Jonathan P.; Olson, Jonathan P.

2017-12-01

It was suggested in (Motes et al 2015 Phys. Rev. Lett. 114 170802) that optical networks with relatively inexpensive overheads—single photon Fock states, passive optical elements, and single photon detection—can show significant improvements over classical strategies for single-parameter estimation, when the number of modes in the network is small (ncompute the quantum Cramér-Rao bound to show these networks can have a constant-factor quantum advantage in multi-parameter estimation for even large number of modes. Additionally, we provide a simplified measurement scheme using only single-photon (on-off) detectors that is capable of approximately obtaining this sensitivity for a small number of modes.

Multi-parameter approximation of the stress field in a cracked body in the more distant surroundings of the crack tip

Czech Academy of Sciences Publication Activity Database

Veselý, V.; Sobek, J.; Frantík, P.; Seitl, Stanislav

2016-01-01

Roč. 89, AUG (2016), s. 20-35 ISSN 0142-1123. [International Conference on Characterisation of Crack Tip Fields /3./. Urbino, 20.04.2015-22.04.2015] Institutional support: RVO:68081723 Keywords : Crack-tip fields * Williams power series * Higher order terms * Stress field reconstruction * Multi-parameter approximation accuracy Subject RIV: JL - Materials Fatigue, Friction Mechanics Impact factor: 2.899, year: 2016

A multiparameter wearable physiologic monitoring system for space and terrestrial applications

Science.gov (United States)

Mundt, Carsten W.; Montgomery, Kevin N.; Udoh, Usen E.; Barker, Valerie N.; Thonier, Guillaume C.; Tellier, Arnaud M.; Ricks, Robert D.; Darling, Robert B.; Cagle, Yvonne D.; Cabrol, Nathalie A.;

Multi-parameter Full-waveform Inversion for Acoustic VTI Medium with Surface Seismic Data

Science.gov (United States)

Cheng, X.; Jiao, K.; Sun, D.; Huang, W.; Vigh, D.

2013-12-01

Full-waveform Inversion (FWI) attracts wide attention recently in oil and gas industry as a new promising tool for high resolution subsurface velocity model building. While the traditional common image point gather based tomography method aims to focus post-migrated data in depth domain, FWI aims to directly fit the observed seismic waveform in either time or frequency domain. The inversion is performed iteratively by updating the velocity fields to reduce the difference between the observed and the simulated data. It has been shown the inversion is very sensitive to the starting velocity fields, and data with long offsets and low frequencies is crucial for the success of FWI to overcome this sensitivity. Considering the importance of data with long offsets and low frequencies, in most geologic environment, anisotropy is an unavoidable topic for FWI especially at long offsets, since anisotropy tends to have more pronounced effects on waves traveled for a great distance. In VTI medium, this means more horizontal velocity will be registered in middle-to-long offset data, while more vertical velocity will be registered in near-to-middle offset data. Up to date, most of real world applications of FWI still remain in isotropic medium, and only a few studies have been shown to account for anisotropy. And most of those studies only account for anisotropy in waveform simulation, but not invert for those anisotropy fields. Multi-parameter inversion for anisotropy fields, even in VTI medium, remains as a hot topic in the field. In this study, we develop a strategy for multi-parameter FWI for acoustic VTI medium with surface seismic data. Because surface seismic data is insensitivity to the delta fields, we decide to hold the delta fields unchanged during our inversion, and invert only for vertical velocity and epsilon fields. Through parameterization analysis and synthetic tests, we find that it is more feasible to invert for the parameterization as vertical and horizontal

Multiparameter models in the management of the development of territories, taking into account the influence of hydrometeorological factors

Science.gov (United States)

Istomin, E. P.; Popov, N. N.; Sokolov, A. G.; Fokicheva, A. A.

2018-01-01

The article considers the geoinformation management of the territory as a way to manage the organizational and technical systems and territories distributed in space. The article describes the main factors for the development and implementation of management decisions, requirements for the territorial management system and the structure of knowledge and data. Mathematical one-parameter and multiparameter models of risk assessment of management decisions applied to the natural and climatic potential of the development of the territory were considered.

Multiparameter Monitoring and Prevention of Fault-Slip Rock Burst

Directory of Open Access Journals (Sweden)

Shan-chao Hu

2017-01-01

Full Text Available Fault-slip rock burst is one type of the tectonic rock burst during mining. A detailed understanding of the precursory information of fault-slip rock burst and implementation of monitoring and early warning systems, as well as pressure relief measures, are essential to safety production in deep mines. This paper first establishes a mechanical model of stick-slip instability in fault-slip rock bursts and then reveals the failure characteristics of the instability. Then, change rule of mining-induced stress and microseismic signals before the occurrence of fault-slip rock burst are proposed, and multiparameter integrated early warning methods including mining-induced stress and energy are established. Finally, pressure relief methods targeting large-diameter boreholes and coal seam infusion are presented in accordance with the occurrence mechanism of fault-slip rock burst. The research results have been successfully applied in working faces 2310 of the Suncun Coal Mine, and the safety of the mine has been enhanced. These research results improve the theory of fault-slip rock burst mechanisms and provide the basis for prediction and forecasting, as well as pressure relief, of fault-slip rock bursts.

Evaluation of hierarchical agglomerative cluster analysis methods for discrimination of primary biological aerosol

Directory of Open Access Journals (Sweden)

I. Crawford

2015-11-01

Full Text Available In this paper we present improved methods for discriminating and quantifying primary biological aerosol particles (PBAPs by applying hierarchical agglomerative cluster analysis to multi-parameter ultraviolet-light-induced fluorescence (UV-LIF spectrometer data. The methods employed in this study can be applied to data sets in excess of 1 × 106 points on a desktop computer, allowing for each fluorescent particle in a data set to be explicitly clustered. This reduces the potential for misattribution found in subsampling and comparative attribution methods used in previous approaches, improving our capacity to discriminate and quantify PBAP meta-classes. We evaluate the performance of several hierarchical agglomerative cluster analysis linkages and data normalisation methods using laboratory samples of known particle types and an ambient data set. Fluorescent and non-fluorescent polystyrene latex spheres were sampled with a Wideband Integrated Bioaerosol Spectrometer (WIBS-4 where the optical size, asymmetry factor and fluorescent measurements were used as inputs to the analysis package. It was found that the Ward linkage with z-score or range normalisation performed best, correctly attributing 98 and 98.1 % of the data points respectively. The best-performing methods were applied to the BEACHON-RoMBAS (Bio–hydro–atmosphere interactions of Energy, Aerosols, Carbon, H2O, Organics and Nitrogen–Rocky Mountain Biogenic Aerosol Study ambient data set, where it was found that the z-score and range normalisation methods yield similar results, with each method producing clusters representative of fungal spores and bacterial aerosol, consistent with previous results. The z-score result was compared to clusters generated with previous approaches (WIBS AnalysiS Program, WASP where we observe that the subsampling and comparative attribution method employed by WASP results in the overestimation of the fungal spore concentration by a factor of 1.5 and the

Numerical Identification of Multiparameters in the Space Fractional Advection Dispersion Equation by Final Observations

Directory of Open Access Journals (Sweden)

Dali Zhang

2012-01-01

Full Text Available This paper deals with an inverse problem for identifying multiparameters in 1D space fractional advection dispersion equation (FADE on a finite domain with final observations. The parameters to be identified are the fractional order, the diffusion coefficient, and the average velocity in the FADE. The forward problem is solved by a finite difference scheme, and then an optimal perturbation regularization algorithm is introduced to determine the three parameters simultaneously. Numerical inversions are performed both with the accurate data and noisy data, and several factors having influences on realization of the algorithm are discussed. The inversion solutions are in good approximations to the exact solutions demonstrating the efficiency of the proposed algorithm.

Effective Kratzer and Coulomb potentials as limit cases of a multiparameter exponential-type potential

Energy Technology Data Exchange (ETDEWEB)

García-Ravelo, J., E-mail: g.ravelo@hotmail.com [Departamento de Física, Escuela Superior de Física y Matemáticas, Instituto Politécnico Nacional, Edificio 9, Unidad Profesional Adolfo López Mateos, México D.F., 07738 (Mexico); Menéndez, A.; García-Martínez, J. [Departamento de Física, Escuela Superior de Física y Matemáticas, Instituto Politécnico Nacional, Edificio 9, Unidad Profesional Adolfo López Mateos, México D.F., 07738 (Mexico); Schulze-Halberg, A. [Department of Mathematics and Actuarial Science and Department of Physics, Indiana University Northwest, 3400 Broadway, Gary, IN 46408 (United States)

2014-06-13

We show that the effective Kratzer and Coulomb potentials can be obtained by taking particular limits of a multiparameter exponential potential that was studied recently. Moreover, we demonstrate that the bound state solutions of the exponential potential reduce correctly to their well-known counterparts associated with the Kratzer and Coulomb potentials. As a byproduct, we obtain a new limit relation for the hypergeometric function. - Highlights: • Kratzer and Coulomb potentials are limit cases of an exponential-type potential. • From exact s-waves, approximate solutions for l-waves are obtained. • l-waves of the potential tend to the solutions of the Kratzer and Coulomb potentials. • A non-evident identity between hypergeometric functions is demonstrated.

Effective Kratzer and Coulomb potentials as limit cases of a multiparameter exponential-type potential

International Nuclear Information System (INIS)

García-Ravelo, J.; Menéndez, A.; García-Martínez, J.; Schulze-Halberg, A.

2014-01-01

We show that the effective Kratzer and Coulomb potentials can be obtained by taking particular limits of a multiparameter exponential potential that was studied recently. Moreover, we demonstrate that the bound state solutions of the exponential potential reduce correctly to their well-known counterparts associated with the Kratzer and Coulomb potentials. As a byproduct, we obtain a new limit relation for the hypergeometric function. - Highlights: • Kratzer and Coulomb potentials are limit cases of an exponential-type potential. • From exact s-waves, approximate solutions for l-waves are obtained. • l-waves of the potential tend to the solutions of the Kratzer and Coulomb potentials. • A non-evident identity between hypergeometric functions is demonstrated

Biological reference materials and analysis of toxic elements

Energy Technology Data Exchange (ETDEWEB)

Subramanian, R; Sukumar, A

1988-12-01

Biological monitoring of toxic metal pollution in the environment requires quality control analysis with use of standard reference materials. A variety of biological tissues are increasingly used for analysis of element bioaccumulation, but the available Certified Reference Materials (CRMs) are insufficient. An attempt is made to review the studies made using biological reference materials for animal and human tissues. The need to have inter-laboratory studies and CRM in the field of biological monitoring of toxic metals is also discussed.

Study of ocean red tide multi-parameter monitoring technology based on double-wavelength airborne lidar system

Science.gov (United States)

Lin, Hong; Wang, Xinming; Liang, Kun

2010-10-01

For monitoring and forecasting of the ocean red tide in real time, a marine environment monitoring technology based on the double-wavelength airborne lidar system is proposed. An airborne lidar is father more efficient than the traditional measure technology by the boat. At the same time, this technology can detect multi-parameter about the ocean red tide by using the double-wavelength lidar.It not only can use the infrared laser to detect the scattering signal under the water and gain the information about the red tise's density and size, but also can use the blue-green laser to detect the Brillouin scattering signal and deduce the temperature and salinity of the seawater.The red tide's density detecting model is firstly established by introducing the concept about the red tide scattering coefficient based on the Mie scattering theory. From the Brillouin scattering theory, the relationship about the blue-green laser's Brillouin scattering frequency shift value and power value with the seawater temperature and salinity is found. Then, the detecting mode1 of the saewater temperature and salinity can be established. The value of the red tide infrared scattering signal is evaluated by the simulation, and therefore the red tide particles' density can be known. At the same time, the blue-green laser's Brillouin scattering frequency shift value and power value are evaluated by simulating, and the temperature and salinity of the seawater can be known. Baed on the multi-parameters, the ocean red tide's growth can be monitored and forecasted.

Fitter. The package for fitting a chosen theoretical multi-parameter function through a set of data points. Application to experimental data of the YuMO spectrometer. Version 2.1.0. Long write-up and user's guide

International Nuclear Information System (INIS)

Solov'ev, A.G.; Stadnik, A.V.; Islamov, A.N.; Kuklin, A.I.

2008-01-01

Fitter is a C++ program aimed to fit a chosen theoretical multi-parameter function through a set of data points. The method of fitting is chi-square minimization. Moreover, the robust fitting method can be applied to Fitter. Fitter was designed to be used for a small-angle neutron scattering data analysis. Respective theoretical models are implemented in it. Some commonly used models (Gaussian and polynomials) are also implemented for wider applicability

[Multiparameter magnetic resonance imaging in the diagnosis of cancer of the cervix uteri].

Science.gov (United States)

Tarachkova, E V; Strel'tsova, O N; Panov, V O; Bazaeva, I Ya; Tyurin, I E

2015-01-01

Cancer of the cervix uteri (CCU) ranks third in the incidence of malignancies in women. The choice of CCU treatment mainly depends on the extent of the tumor process, i.e., the stage of the disease. Determining the stage of CCU is based on the clinical classification of the International Federation of Gynecology and Obstetrics (FIGO) (2009) and has a number of substantial limitations in evaluating parametrial invasion, tumor spread to the pelvic wall, and involvement of regional lymph nodes and in determining the true tumor sizes. Magnetic resonance imaging (MRI) is now the method of choice in staging invasive CCU. Multiparameter MRI will be able to enhance the efficiency of diagnosing microinvasive CCU as well (FIGO 2009), to plan surgical and/or chemoradiation treatment, to evaluate its efficiency, and to diagnose locally recurrent CCU.

Surface analysis and techniques in biology

CERN Document Server

Smentkowski, Vincent S

2014-01-01

This book highlights state-of-the-art surface analytical instrumentation, advanced data analysis tools, and the use of complimentary surface analytical instrumentation to perform a complete analysis of biological systems.

A novel staining protocol for multiparameter assessment of cell heterogeneity in Phormidium populations (cyanobacteria employing fluorescent dyes.

Directory of Open Access Journals (Sweden)

Daria Tashyreva

Full Text Available Bacterial populations display high heterogeneity in viability and physiological activity at the single-cell level, especially under stressful conditions. We demonstrate a novel staining protocol for multiparameter assessment of individual cells in physiologically heterogeneous populations of cyanobacteria. The protocol employs fluorescent probes, i.e., redox dye 5-cyano-2,3-ditolyl tetrazolium chloride, 'dead cell' nucleic acid stain SYTOX Green, and DNA-specific fluorochrome 4',6-diamidino-2-phenylindole, combined with microscopy image analysis. Our method allows simultaneous estimates of cellular respiration activity, membrane and nucleoid integrity, and allows the detection of photosynthetic pigments fluorescence along with morphological observations. The staining protocol has been adjusted for, both, laboratory and natural populations of the genus Phormidium (Oscillatoriales, and tested on 4 field-collected samples and 12 laboratory strains of cyanobacteria. Based on the mentioned cellular functions we suggest classification of cells in cyanobacterial populations into four categories: (i active and intact; (ii injured but active; (iii metabolically inactive but intact; (iv inactive and injured, or dead.

Complexity, Analysis and Control of Singular Biological Systems

CERN Document Server

Zhang, Qingling; Zhang, Xue

2012-01-01

Complexity, Analysis and Control of Singular Biological Systems follows the control of real-world biological systems at both ecological and phyisological levels concentrating on the application of now-extensively-investigated singular system theory. Much effort has recently been dedicated to the modelling and analysis of developing bioeconomic systems and the text establishes singular examples of these, showing how proper control can help to maintain sustainable economic development of biological resources. The book begins from the essentials of singular systems theory and bifurcations before tackling  the use of various forms of control in singular biological systems using examples including predator-prey relationships and viral vaccination and quarantine control. Researchers and graduate students studying the control of complex biological systems are shown how a variety of methods can be brought to bear and practitioners working with the economics of biological systems and their control will also find the ...

Minicomputer system for radiochemical analysis by coincidence spectrometry

International Nuclear Information System (INIS)

Brauer, F.P.; Fager, J.E.

1979-01-01

Minicomputer-based coincidence analysis methods have been developed for use in performing radiochemical analysis by high-resolution x- and gamma-ray coincidence spectrometry. This paper describes the data-acquisition and analysis methods develolped for qualitative and quantitative analyses of coincidence spectrometric data. Data-acquisition capabilities include both direct multiparameter pulse-height analysis and buffered list-mode acquisition

Prediction uncertainty assessment of a systems biology model requires a sample of the full probability distribution of its parameters

Directory of Open Access Journals (Sweden)

Simon van Mourik

2014-06-01

Full Text Available Multi-parameter models in systems biology are typically ‘sloppy’: some parameters or combinations of parameters may be hard to estimate from data, whereas others are not. One might expect that parameter uncertainty automatically leads to uncertain predictions, but this is not the case. We illustrate this by showing that the prediction uncertainty of each of six sloppy models varies enormously among different predictions. Statistical approximations of parameter uncertainty may lead to dramatic errors in prediction uncertainty estimation. We argue that prediction uncertainty assessment must therefore be performed on a per-prediction basis using a full computational uncertainty analysis. In practice this is feasible by providing a model with a sample or ensemble representing the distribution of its parameters. Within a Bayesian framework, such a sample may be generated by a Markov Chain Monte Carlo (MCMC algorithm that infers the parameter distribution based on experimental data. Matlab code for generating the sample (with the Differential Evolution Markov Chain sampler and the subsequent uncertainty analysis using such a sample, is supplied as Supplemental Information.

Analysis of biological spectrum of Divčibare flora

Directory of Open Access Journals (Sweden)

Popović Ivana

2006-01-01

Full Text Available One of the essential analyses which is performed during the floristic study of a region is the analysis of the biological spectrum. The analysis of the biological spectrum of the flora includes the determination of the type of life form for each taxon described in the flora of the study region. If it is considered that life form is a specific structural-functional response to the environmental effects and the result of the adaptation during the species evolution, it is clear that the basic characteristics of the site are more or less reflected in any life form. This fact is confirmed by the analysis of the biological spectrum of Divčibare flora. The study results are in correlation with the results of the analysis of the biological spectrum of the flora of Serbia and the Balkan Peninsula.

A multiparameter chaos control method based on OGY approach

International Nuclear Information System (INIS)

Souza de Paula, Aline; Amorim Savi, Marcelo

2009-01-01

Chaos control is based on the richness of responses of chaotic behavior and may be understood as the use of tiny perturbations for the stabilization of a UPO embedded in a chaotic attractor. Since one of these UPO can provide better performance than others in a particular situation the use of chaos control can make this kind of behavior to be desirable in a variety of applications. The OGY method is a discrete technique that considers small perturbations promoted in the neighborhood of the desired orbit when the trajectory crosses a specific surface, such as a Poincare section. This contribution proposes a multiparameter semi-continuous method based on OGY approach in order to control chaotic behavior. Two different approaches are possible with this method: coupled approach, where all control parameters influences system dynamics although they are not active; and uncoupled approach that is a particular case where control parameters return to the reference value when they become passive parameters. As an application of the general formulation, it is investigated a two-parameter actuation of a nonlinear pendulum control employing coupled and uncoupled approaches. Analyses are carried out considering signals that are generated by numerical integration of the mathematical model using experimentally identified parameters. Results show that the procedure can be a good alternative for chaos control since it provides a more effective UPO stabilization than the classical single-parameter approach.

[Cluster analysis in biomedical researches].

Science.gov (United States)

Akopov, A S; Moskovtsev, A A; Dolenko, S A; Savina, G D

2013-01-01

Cluster analysis is one of the most popular methods for the analysis of multi-parameter data. The cluster analysis reveals the internal structure of the data, group the separate observations on the degree of their similarity. The review provides a definition of the basic concepts of cluster analysis, and discusses the most popular clustering algorithms: k-means, hierarchical algorithms, Kohonen networks algorithms. Examples are the use of these algorithms in biomedical research.

Biological analysis with a nuclear microprobe

International Nuclear Information System (INIS)

Cookson, J.A.; Legge, G.J.F.

1975-01-01

Most low-energy nuclear accelerators are now partly used on analytical studies in support of sciences other than nuclear physics. This paper gives a short review of such analytical techniques (X-ray analysis, elastic scattering analysis, nuclear reaction analysis, and the nuclear microprobe) with particular reference to biological applications and also emphasizes the role of the positional analysis that can be performed with a focused beam of ions - the nuclear microprobe. (author)

Multi-parameter in vitro toxicity testing of crizotinib, sunitinib, erlotinib, and nilotinib in human cardiomyocytes

International Nuclear Information System (INIS)

Doherty, Kimberly R.; Wappel, Robert L.; Talbert, Dominique R.; Trusk, Patricia B.; Moran, Diarmuid M.; Kramer, James W.; Brown, Arthur M.; Shell, Scott A.; Bacus, Sarah

2013-01-01

Tyrosine kinase inhibitors (TKi) have greatly improved the treatment and prognosis of multiple cancer types. However, unexpected cardiotoxicity has arisen in a subset of patients treated with these agents that was not wholly predicted by pre-clinical testing, which centers around animal toxicity studies and inhibition of the human Ether-à-go-go-Related Gene (hERG) channel. Therefore, we sought to determine whether a multi-parameter test panel assessing the effect of drug treatment on cellular, molecular, and electrophysiological endpoints could accurately predict cardiotoxicity. We examined how 4 FDA-approved TKi agents impacted cell viability, apoptosis, reactive oxygen species (ROS) generation, metabolic status, impedance, and ion channel function in human cardiomyocytes. The 3 drugs clinically associated with severe cardiac adverse events (crizotinib, sunitinib, nilotinib) all proved to be cardiotoxic in our in vitro tests while the relatively cardiac-safe drug erlotinib showed only minor changes in cardiac cell health. Crizotinib, an ALK/MET inhibitor, led to increased ROS production, caspase activation, cholesterol accumulation, disruption in cardiac cell beat rate, and blockage of ion channels. The multi-targeted TKi sunitinib showed decreased cardiomyocyte viability, AMPK inhibition, increased lipid accumulation, disrupted beat pattern, and hERG block. Nilotinib, a second generation Bcr-Abl inhibitor, led to increased ROS generation, caspase activation, hERG block, and an arrhythmic beat pattern. Thus, each drug showed a unique toxicity profile that may reflect the multiple mechanisms leading to cardiotoxicity. This study demonstrates that a multi-parameter approach can provide a robust characterization of drug-induced cardiomyocyte damage that can be leveraged to improve drug safety during early phase development. - Highlights: • TKi with known adverse effects show unique cardiotoxicity profiles in this panel. • Crizotinib increases ROS, apoptosis, and

Seismo-Geochemical Variations in SW Taiwan: Multi-Parameter Automatic Gas Monitoring Results

Science.gov (United States)

Yang, T. F.; Fu, C.-C.; Walia, V.; Chen, C.-H.; Chyi, L. L.; Liu, T.-K.; Song, S.-R.; Lee, M.; Lin, C.-W.; Lin, C.-C.

2006-04-01

Gas variations of many mud volcanoes and hot springs distributed along the tectonic sutures in southwestern Taiwan are considered to be sensitive to the earthquake activity. Therefore, a multi-parameter automatic gas station was built on the bank of one of the largest mud-pools at an active fault zone of southwestern Taiwan, for continuous monitoring of CO2, CH4, N2 and H2O, the major constituents of its bubbling gases. During the year round monitoring from October 2001 to October 2002, the gas composition, especially, CH4 and CO2, of the mud pool showed significant variations. Taking the CO2/CH4 ratio as the main indicator, anomalous variations can be recognized from a few days to a few weeks before earthquakes and correlated well with those with a local magnitude >4.0 and local intensities >2. It is concluded that the gas composition in the area is sensitive to the local crustal stress/strain and is worthy to conduct real-time monitoring for the seismo-geochemical precursors.

Analysis of accuracy of Williams series approximation of stress field in cracked body – influence of area of interest around crack-tip on multi-parameter regression performance

Directory of Open Access Journals (Sweden)

J. Sobek

2017-01-01

Full Text Available A study on the accuracy of an approximation of the stress field in a cracked body is presented. Crack-tip stress tensor is expressed using the linear elastic fracture mechanics (LEFM theory in this work, more precisely via its multi-parameter formulation, i.e. by Williams power series (WPS. Determination of coefficients of terms of this series is performed using a least squares-based regression technique known as over-deterministic method (ODM for which results from finite element (FE method computation are usually taken as inputs. Main attention is paid to a detailed analysis of a suitable selection of FE nodes whose results serve as the inputs to the employed method. Two different ways of FE nodal selection are compared – nodes selected from the crack tip vicinity lying at a ring of a certain radius versus nodes selected more or less uniformly from a specified part of the test specimen body. Comparison of these approaches is made with the help of procedures developed by the authors which enable both the determination of the coefficients of terms of the analytical WPS approximation of the stress field based on the FE results and the backward reconstruction of the field (again using WPS from those determined terms’ coefficients/functions. The wedge-splitting test (WST specimen with a crack is taken as example for the study.

Multi-parameter decoupling and slope tracking control strategy of a large-scale high altitude environment simulation test cabin

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Li Ke

2014-12-01

Full Text Available A large-scale high altitude environment simulation test cabin was developed to accurately control temperatures and pressures encountered at high altitudes. The system was developed to provide slope-tracking dynamic control of the temperature–pressure two-parameter and overcome the control difficulties inherent to a large inertia lag link with a complex control system which is composed of turbine refrigeration device, vacuum device and liquid nitrogen cooling device. The system includes multi-parameter decoupling of the cabin itself to avoid equipment damage of air refrigeration turbine caused by improper operation. Based on analysis of the dynamic characteristics and modeling for variations in temperature, pressure and rotation speed, an intelligent controller was implemented that includes decoupling and fuzzy arithmetic combined with an expert PID controller to control test parameters by decoupling and slope tracking control strategy. The control system employed centralized management in an open industrial ethernet architecture with an industrial computer at the core. The simulation and field debugging and running results show that this method can solve the problems of a poor anti-interference performance typical for a conventional PID and overshooting that can readily damage equipment. The steady-state characteristics meet the system requirements.

Interactive analysis of systems biology molecular expression data

Directory of Open Access Journals (Sweden)

Prabhakar Sunil

2008-02-01

Full Text Available Abstract Background Systems biology aims to understand biological systems on a comprehensive scale, such that the components that make up the whole are connected to one another and work through dependent interactions. Molecular correlations and comparative studies of molecular expression are crucial to establishing interdependent connections in systems biology. The existing software packages provide limited data mining capability. The user must first generate visualization data with a preferred data mining algorithm and then upload the resulting data into the visualization package for graphic visualization of molecular relations. Results Presented is a novel interactive visual data mining application, SysNet that provides an interactive environment for the analysis of high data volume molecular expression information of most any type from biological systems. It integrates interactive graphic visualization and statistical data mining into a single package. SysNet interactively presents intermolecular correlation information with circular and heatmap layouts. It is also applicable to comparative analysis of molecular expression data, such as time course data. Conclusion The SysNet program has been utilized to analyze elemental profile changes in response to an increasing concentration of iron (Fe in growth media (an ionomics dataset. This study case demonstrates that the SysNet software is an effective platform for interactive analysis of molecular expression information in systems biology.

Multi-parameter variational calculations for the (2+1)-dimensional U(1) lattice gauge theory and the XY model

International Nuclear Information System (INIS)

Heys, D.W.; Stump, D.R.

1987-01-01

Variational calculations are described that use multi-parameter trial wave functions for the U(1) lattice gauge theory in two space dimensions, and for the XY model. The trial functions are constructed as the exponential of a linear combination of states from the strong-coupling basis of the model, with the coefficients treated as variational parameters. The expectation of the hamiltonian is computed by the Monte Carlo method, using a reweighting technique to evaluate expectation values in finite patches of the parameter space. The trial function for the U(1) gauge theory involves six variational parameters, and its weak-coupling behaviour is in reasonable agreement with theoretical expectations. (orig.)

Multiparameter flow cytometric remission is the most relevant prognostic factor for multiple myeloma patients who undergo autologous stem cell transplantation

Science.gov (United States)

Paiva, Bruno; Vidriales, Maria-Belén; Cerveró, Jorge; Mateo, Gema; Pérez, Jose J.; Montalbán, Maria A.; Sureda, Anna; Montejano, Laura; Gutiérrez, Norma C.; de Coca, Alfonso García; de las Heras, Natalia; Mateos, Maria V.; López-Berges, Maria C.; García-Boyero, Raimundo; Galende, Josefina; Hernández, Jose; Palomera, Luis; Carrera, Dolores; Martínez, Rafael; de la Rubia, Javier; Martín, Alejandro; Bladé, Joan; Lahuerta, Juan J.; Orfao, Alberto

2008-01-01

Minimal residual disease (MRD) assessment is standard in many hematologic malignancies but is considered investigational in multiple myeloma (MM). We report a prospective analysis of the prognostic importance of MRD detection by multiparameter flow cytometry (MFC) in 295 newly diagnosed MM patients uniformly treated in the GEM2000 protocol VBMCP/VBAD induction plus autologous stem cell transplantation [ASCT]). MRD status by MFC was determined at day 100 after ASCT. Progression-free survival (PFS; median 71 vs 37 months, P < .001) and overall survival (OS; median not reached vs 89 months, P = .002) were longer in patients who were MRD negative versus MRD positive at day 100 after ASCT. Similar prognostic differentiation was seen in 147 patients who achieved immunofixation-negative complete response after ASCT. Moreover, MRD− immunofixation-negative (IFx−) patients and MRD− IFx+ patients had significantly longer PFS than MRD+ IFx− patients. Multivariate analysis identified MRD status by MFC at day 100 after ASCT as the most important independent prognostic factor for PFS (HR = 3.64, P = .002) and OS (HR = 2.02, P = .02). Our findings demonstrate the clinical importance of MRD evaluation by MFC, and illustrate the need for further refinement of MM re-sponse criteria. This trial is registered at http://clinicaltrials.gov under identifier NCT00560053. PMID:18669875

Multiparametric amplitude analysis with on-line compression using adaptive orthogonal transform

Energy Technology Data Exchange (ETDEWEB)

Morhac, M; Matousek, V; Turzo, I

1996-12-31

The new method of multiparameter amplitude analysis with on-line compression is developed. The proposed method decreases the memory needed to store multidimensional histograms. Examples of employing the algorithms for three-dimensional spectra are presented. 5 refs.

Statistical analysis of joint toxicity in biological growth experiments

DEFF Research Database (Denmark)

Spliid, Henrik; Tørslev, J.

1994-01-01

The authors formulate a model for the analysis of designed biological growth experiments where a mixture of toxicants is applied to biological target organisms. The purpose of such experiments is to assess the toxicity of the mixture in comparison with the toxicity observed when the toxicants are...... is applied on data from an experiment where inhibition of the growth of the bacteria Pseudomonas fluorescens caused by different mixtures of pentachlorophenol and aniline was studied.......The authors formulate a model for the analysis of designed biological growth experiments where a mixture of toxicants is applied to biological target organisms. The purpose of such experiments is to assess the toxicity of the mixture in comparison with the toxicity observed when the toxicants...

Composite multi-parameter ranking of real and virtual compounds for design of MC4R agonists: renaissance of the Free-Wilson methodology.

Science.gov (United States)

Nilsson, Ingemar; Polla, Magnus O

2012-10-01

Drug design is a multi-parameter task present in the analysis of experimental data for synthesized compounds and in the prediction of new compounds with desired properties. This article describes the implementation of a binned scoring and composite ranking scheme for 11 experimental parameters that were identified as key drivers in the MC4R project. The composite ranking scheme was implemented in an AstraZeneca tool for analysis of project data, thereby providing an immediate re-ranking as new experimental data was added. The automated ranking also highlighted compounds overlooked by the project team. The successful implementation of a composite ranking on experimental data led to the development of an equivalent virtual score, which was based on Free-Wilson models of the parameters from the experimental ranking. The individual Free-Wilson models showed good to high predictive power with a correlation coefficient between 0.45 and 0.97 based on the external test set. The virtual ranking adds value to the selection of compounds for synthesis but error propagation must be controlled. The experimental ranking approach adds significant value, is parameter independent and can be tuned and applied to any drug discovery project.

Neutron activation analysis of biological substances

International Nuclear Information System (INIS)

Ordogh, M.

1978-08-01

A Bowen cabbage sample was used as a reference material for the neutron activation studies, and the method was checked by the analysis of other biological substances (blood or serum etc.). For nondestructive measurements also some non-trace elements were determined in order to decide whether the activation analysis is a useful means for such measurements. The new activation analysis procedure was used for biomedical studies as, e.g., for trace element determination in body fluids, and for the analysis of inorganic components in air samples. (R.P.)

International Conference on Recent Advances in Mathematical Biology, Analysis and Applications

CERN Document Server

Saleem, M; Srivastava, H; Khan, Mumtaz; Merajuddin, M

2016-01-01

The book contains recent developments and contemporary research in mathematical analysis and in its application to problems arising from the biological and physical sciences. The book is of interest to readers who wish to learn of new research in such topics as linear and nonlinear analysis, mathematical biology and ecology, dynamical systems, graph theory, variational analysis and inequalities, functional analysis, differential and difference equations, partial differential equations, approximation theory, and chaos. All papers were prepared by participants at the International Conference on Recent Advances in Mathematical Biology, Analysis and Applications (ICMBAA-2015) held during 4–6 June 2015 in Aligarh, India. A focal theme of the conference was the application of mathematics to the biological sciences and on current research in areas of theoretical mathematical analysis that can be used as sophisticated tools for the study of scientific problems. The conference provided researchers, academicians and ...

Prediction of chemotherapy outcome in patients with metastatic soft tissue sarcomas based on dynamic FDG PET (dPET) and a multiparameter analysis

International Nuclear Information System (INIS)

Dimitrakopoulou-Strauss, Antonia; Strauss, Ludwig G.; Vasamiliette, Julie; Egerer, Gerlinde; Schmitt, Thomas; Kasper, Bernd; Haberkorn, Uwe

2010-01-01

Dynamic PET studies with 18 F-FDG were performed in patients with metastatic soft tissue sarcomas who received conventional chemotherapy with doxorubicin hydrochloride (Adriamycin) and ifosfamide (AI-G). The goal of the study was to evaluate the impact of full kinetic analysis and assess its value with regard to the therapy outcome based on survival data. The evaluation included 17 patients with 29 metastatic lesions of soft tissue sarcomas, who were treated with chemotherapy consisting of an AI-G regimen prior to high-dose chemotherapy and peripheral blood stem cell transplantation where applicable. Patients were examined prior to onset of therapy and after completion of the first cycle of AI-G. Restaging data (n = 17) based on Response Evaluation Criteria in Solid Tumors were available. Survival data (n = 14) served for reference. The following parameters were retrieved from the dynamic PET studies: standardized uptake value (SUV), fractal dimension, two-compartment model with computation of k1, k2, k3, k4 (unit: 1/min), the fractional blood volume and the FDG influx calculated according to Patlak. The mean SUV was 6.9 prior to therapy and 4.7 after one cycle. The mean influx was 0.066 prior to therapy in comparison to 0.058 after one cycle. We dichotomized the patients according to the median survival time of 320 days into response (n = 6) and non-response (n = 8). The mean SUV was 7.6 in the group of responders and 5.4 in the group of non-responders prior to therapy. Responders revealed a mean SUV of 3.8 after therapy as compared to 5.0 SUV for non-responders. We used discriminant analysis to classify the patients into the two response groups. The classification of the non-responders was generally higher (negative predictive value > 61%) than for the responders. Finally, the combined use of the four predictor variables, namely mean SUV and k1 of both studies led to the highest accuracy of 90% for both groups. The data demonstrate that only a multiparameter

Neutron scattering for the analysis of biological structures. Brookhaven symposia in biology. Number 27

Energy Technology Data Exchange (ETDEWEB)

Schoenborn, B P [ed.

1976-01-01

Sessions were included on neutron scattering and biological structure analysis, protein crystallography, neutron scattering from oriented systems, solution scattering, preparation of deuterated specimens, inelastic scattering, data analysis, experimental techniques, and instrumentation. Separate entries were made for the individual papers.

Chemometric and biological validation of a capillary electrophoresis metabolomic experiment of Schistosoma mansoni infection in mice.

Science.gov (United States)

Garcia-Perez, Isabel; Angulo, Santiago; Utzinger, Jürg; Holmes, Elaine; Legido-Quigley, Cristina; Barbas, Coral

2010-07-01

Metabonomic and metabolomic studies are increasingly utilized for biomarker identification in different fields, including biology of infection. The confluence of improved analytical platforms and the availability of powerful multivariate analysis software have rendered the multiparameter profiles generated by these omics platforms a user-friendly alternative to the established analysis methods where the quality and practice of a procedure is well defined. However, unlike traditional assays, validation methods for these new multivariate profiling tools have yet to be established. We propose a validation for models obtained by CE fingerprinting of urine from mice infected with the blood fluke Schistosoma mansoni. We have analysed urine samples from two sets of mice infected in an inter-laboratory experiment where different infection methods and animal husbandry procedures were employed in order to establish the core biological response to a S. mansoni infection. CE data were analysed using principal component analysis. Validation of the scores consisted of permutation scrambling (100 repetitions) and a manual validation method, using a third of the samples (not included in the model) as a test or prediction set. The validation yielded 100% specificity and 100% sensitivity, demonstrating the robustness of these models with respect to deciphering metabolic perturbations in the mouse due to a S. mansoni infection. A total of 20 metabolites across the two experiments were identified that significantly discriminated between S. mansoni-infected and noninfected control samples. Only one of these metabolites, allantoin, was identified as manifesting different behaviour in the two experiments. This study shows the reproducibility of CE-based metabolic profiling methods for disease characterization and screening and highlights the importance of much needed validation strategies in the emerging field of metabolomics.

A Multiparameter Thermal Conductivity Equation for 1,1-Difluoroethane (R152a) with an Optimized Functional Form

Science.gov (United States)

Scalabrin, G.; Marchi, P.; Finezzo, F.

2006-11-01

The application of an optimization technique to the available experimental data has led to the development of a new multiparameter equation λ = λ ( T,ρ ) for the representation of the thermal conductivity of 1,1-difluoroethane (R152a). The region of validity of the proposed equation covers the temperature range from 220 to 460 K and pressures up to 55 MPa, including the near-critical region. The average absolute deviation of the equation with respect to the selected 939 primary data points is 1.32%. The proposed equation represents therefore a significant improvement with respect to the literature conventional equation. The density value required by the equation is calculated at the chosen temperature and pressure conditions using a high accuracy equation of state for the fluid.

Amino acid analysis in biological fluids by GC-MS

OpenAIRE

Kaspar, Hannelore

2009-01-01

Amino acids are intermediates in cellular metabolism and their quantitative analysis plays an important role in disease diagnostics. A gas chromatography-mass spectrometry (GC-MS) based method was developed for the quantitative analysis of free amino acids as their propyl chloroformate derivatives in biological fluids. Derivatization with propyl chloroformate could be carried out directly in the biological samples without prior protein precipitation or solid-phase extraction of the amino acid...

Multiparameter flow cytometry reveals myelodysplasia-related aberrant antigen expression in myelodysplastic/myeloproliferative neoplasms.

Science.gov (United States)

Kern, Wolfgang; Bacher, Ulrike; Schnittger, Susanne; Alpermann, Tamara; Haferlach, Claudia; Haferlach, Torsten

2013-05-01

Within the myelodysplastic/myeloproliferative neoplasm (MDS/MPN) category of the WHO (2008), only chronic myelomonocytic leukemia was so far evaluated by multiparameter flow cytometry (MFC). To investigate the potential of MFC for MDS/MPNs, unclassifiable (MDS/MPNu), and refractory anemia associated with ring sideroblasts and marked thrombocytosis (RARS-T), we studied 91 patients with these entities (60 males/31 females; 35.3-87.4 years) for MDS-related aberrant immunophenotypes (≥ 2 different cell lineages with ≥ 3 aberrantly expressed antigens). Data were correlated with cytomorphology and cytogenetics. MFC identified MDS-related immunophenotypes in 54/91 (59.3%) of patients. Patients with or without MDS-related immunophenotype did not differ significantly by demographic characteristics, blood values, or median overall survival. MDS-related immunophenotype cases showed a higher number of aberrantly expressed antigens (mean ± SD, 4.9 ± 2.4 vs. 2.0 ± 1.4; P MPNu and RARS-T. MFC therefore may be helpful to separate cases into more "MDS-like" or "MPN-like" subgroups. Copyright © 2012 International Clinical Cytometry Society.

Stability Analysis for Multi-Parameter Linear Periodic Systems

DEFF Research Database (Denmark)

Seyranian, A.P.; Solem, Frederik; Pedersen, Pauli

1999-01-01

This paper is devoted to stability analysis of general linear periodic systems depending on real parameters. The Floquet method and perturbation technique are the basis of the development. We start out with the first and higher-order derivatives of the Floquet matrix with respect to problem...

Bioinformatics approaches to single-cell analysis in developmental biology.

Science.gov (United States)

Yalcin, Dicle; Hakguder, Zeynep M; Otu, Hasan H

2016-03-01

Individual cells within the same population show various degrees of heterogeneity, which may be better handled with single-cell analysis to address biological and clinical questions. Single-cell analysis is especially important in developmental biology as subtle spatial and temporal differences in cells have significant associations with cell fate decisions during differentiation and with the description of a particular state of a cell exhibiting an aberrant phenotype. Biotechnological advances, especially in the area of microfluidics, have led to a robust, massively parallel and multi-dimensional capturing, sorting, and lysis of single-cells and amplification of related macromolecules, which have enabled the use of imaging and omics techniques on single cells. There have been improvements in computational single-cell image analysis in developmental biology regarding feature extraction, segmentation, image enhancement and machine learning, handling limitations of optical resolution to gain new perspectives from the raw microscopy images. Omics approaches, such as transcriptomics, genomics and epigenomics, targeting gene and small RNA expression, single nucleotide and structural variations and methylation and histone modifications, rely heavily on high-throughput sequencing technologies. Although there are well-established bioinformatics methods for analysis of sequence data, there are limited bioinformatics approaches which address experimental design, sample size considerations, amplification bias, normalization, differential expression, coverage, clustering and classification issues, specifically applied at the single-cell level. In this review, we summarize biological and technological advancements, discuss challenges faced in the aforementioned data acquisition and analysis issues and present future prospects for application of single-cell analyses to developmental biology. © The Author 2015. Published by Oxford University Press on behalf of the European

o-TOF ICPMS analysis of environmental, food and biological samples

International Nuclear Information System (INIS)

Krejcova, A.; Cernohorsky, T.; Ludvikova, I.; Pouzar, M.; Capova, L.

2009-01-01

Full text: o-TOF ICPMS was used for inorganic analysis of environmental, food and biological samples. The method validity was proved by analysis of spiked samples, reference materials, by determination without/with internal standards and the standard addition technique. The technique was shown to be powerful, and reliable for analysis of the samples mentioned, and high sample throughput enables environmental or biological screening studies. Independent of the number of elements analyzed, complete analysis and whole mass spectra are gained from a small sample amount in a very short time. (author)

Creation of Novel Cores for β-Secretase (BACE-1) Inhibitors: A Multiparameter Lead Generation Strategy.

Science.gov (United States)

Viklund, Jenny; Kolmodin, Karin; Nordvall, Gunnar; Swahn, Britt-Marie; Svensson, Mats; Gravenfors, Ylva; Rahm, Fredrik

2014-04-10

In order to find optimal core structures as starting points for lead optimization, a multiparameter lead generation workflow was designed with the goal of finding BACE-1 inhibitors as a treatment for Alzheimer's disease. De novo design of core fragments was connected with three predictive in silico models addressing target affinity, permeability, and hERG activity, in order to guide synthesis. Taking advantage of an additive SAR, the prioritized cores were decorated with a few, well-characterized substituents from known BACE-1 inhibitors in order to allow for core-to-core comparisons. Prediction methods and analyses of how physicochemical properties of the core structures correlate to in vitro data are described. The syntheses and in vitro data of the test compounds are reported in a separate paper by Ginman et al. [J. Med. Chem. 2013, 56, 4181-4205]. The affinity predictions are described in detail by Roos et al. [J. Chem. Inf. 2014, DOI: 10.1021/ci400374z].

Magnetic separation techniques in sample preparation for biological analysis: a review.

Science.gov (United States)

He, Jincan; Huang, Meiying; Wang, Dongmei; Zhang, Zhuomin; Li, Gongke

2014-12-01

Sample preparation is a fundamental and essential step in almost all the analytical procedures, especially for the analysis of complex samples like biological and environmental samples. In past decades, with advantages of superparamagnetic property, good biocompatibility and high binding capacity, functionalized magnetic materials have been widely applied in various processes of sample preparation for biological analysis. In this paper, the recent advancements of magnetic separation techniques based on magnetic materials in the field of sample preparation for biological analysis were reviewed. The strategy of magnetic separation techniques was summarized. The synthesis, stabilization and bio-functionalization of magnetic nanoparticles were reviewed in detail. Characterization of magnetic materials was also summarized. Moreover, the applications of magnetic separation techniques for the enrichment of protein, nucleic acid, cell, bioactive compound and immobilization of enzyme were described. Finally, the existed problems and possible trends of magnetic separation techniques for biological analysis in the future were proposed. Copyright © 2014 Elsevier B.V. All rights reserved.

Biological signals classification and analysis

CERN Document Server

Kiasaleh, Kamran

2015-01-01

This authored monograph presents key aspects of signal processing analysis in the biomedical arena. Unlike wireless communication systems, biological entities produce signals with underlying nonlinear, chaotic nature that elude classification using the standard signal processing techniques, which have been developed over the past several decades for dealing primarily with standard communication systems. This book separates what is random from that which appears to be random, and yet is truly deterministic with random appearance. At its core, this work gives the reader a perspective on biomedical signals and the means to classify and process such signals. In particular, a review of random processes along with means to assess the behavior of random signals is also provided. The book also includes a general discussion of biological signals in order to demonstrate the inefficacy of the well-known techniques to correctly extract meaningful information from such signals. Finally, a thorough discussion of recently ...

High spatial resolution distributed fiber system for multi-parameter sensing based on modulated pulses.

Science.gov (United States)

Zhang, Jingdong; Zhu, Tao; Zhou, Huan; Huang, Shihong; Liu, Min; Huang, Wei

2016-11-28

We demonstrate a cost-effective distributed fiber sensing system for the multi-parameter detection of the vibration, the temperature, and the strain by integrating phase-sensitive optical time domain reflectometry (φ-OTDR) and Brillouin optical time domain reflectometry (B-OTDR). Taking advantage of the fast changing property of the vibration and the static properties of the temperature and the strain, both the width and intensity of the laser pulses are modulated and injected into the single-mode sensing fiber proportionally, so that three concerned parameters can be extracted simultaneously by only one photo-detector and one data acquisition channel. A data processing method based on Gaussian window short time Fourier transform (G-STFT) is capable of achieving high spatial resolution in B-OTDR. The experimental results show that up to 4.8kHz vibration sensing with 3m spatial resolution at 10km standard single-mode fiber can be realized, as well as the distributed temperature and stress profiles along the same fiber with 80cm spatial resolution.

[Mass spectrometry technology and its application in analysis of biological samples].

Science.gov (United States)

Zhao, Long-Shan; Li, Qing; Guo, Chao-Wei; Chen, Xiao-Hui; Bi, Kai-Shun

2012-02-01

With the excellent merits of wide analytical range, high sensitivity, small sample size, fast analysis speed, good repeatability, simple operation, low mobile phase consumption, as well as its capability of simultaneous isolation and identification, etc, mass spectrometry techniques have become widely used in the area of environmental science, energy chemical industry, biological medicine, and so on. This article reviews the application of mass spectrometry technology in biological sample analysis in the latest three years with the focus on the new applications in pharmacokinetics and bioequivalence, toxicokinetics, pharmacokinetic-pharmacodynamic, population pharmacokinetics, identification and fragmentation pathways of drugs and their metabolites and metabonomics to provide references for further study of biological sample analysis.

Multi-parameter actuation of a neutrally stable shell: a flexible gear-less motor.

Science.gov (United States)

Hamouche, W; Maurini, C; Vidoli, S; Vincenti, A

2017-08-01

We have designed and tested experimentally a morphing structure consisting of a neutrally stable thin cylindrical shell driven by a multi-parameter piezoelectric actuation. The shell is obtained by plastically deforming an initially flat copper disc, so as to induce large isotropic and almost uniform inelastic curvatures. Following the plastic deformation, in a perfectly isotropic system, the shell is theoretically neutrally stable, having a continuous set of stable cylindrical shapes corresponding to the rotation of the axis of maximal curvature. Small imperfections render the actual structure bistable, giving preferred orientations. A three-parameter piezoelectric actuation, exerted through micro-fibre-composite actuators, allows us to add a small perturbation to the plastic inelastic curvature and to control the direction of maximal curvature. This actuation law is designed through a geometrical analogy based on a fully nonlinear inextensible uniform-curvature shell model. We report on the fabrication, identification and experimental testing of a prototype and demonstrate the effectiveness of the piezoelectric actuators in controlling its shape. The resulting motion is an apparent rotation of the shell, controlled by the voltages as in a 'gear-less motor', which is, in reality, a precession of the axis of principal curvature.

Multiparameter telemetry as a sensitive screening method to detect vaccine reactogenicity in mice.

Directory of Open Access Journals (Sweden)

Margarete Arras

Full Text Available Refined vaccines and adjuvants are urgently needed to advance immunization against global infectious challenges such as HIV, hepatitis C, tuberculosis and malaria. Large-scale screening efforts are ongoing to identify adjuvants with improved efficacy profiles. Reactogenicity often represents a major hurdle to the clinical use of new substances. Yet, irrespective of its importance, this parameter has remained difficult to screen for, owing to a lack of sensitive small animal models with a capacity for high throughput testing. Here we report that continuous telemetric measurements of heart rate, heart rate variability, body core temperature and locomotor activity in laboratory mice readily unmasked systemic side-effects of vaccination, which went undetected by conventional observational assessment and clinical scoring. Even minor aberrations in homeostasis were readily detected, ranging from sympathetic activation over transient pyrogenic effects to reduced physical activity and apathy. Results in real-time combined with the potential of scalability and partial automation in the industrial context suggest multiparameter telemetry in laboratory mice as a first-line screen for vaccine reactogenicity. This may accelerate vaccine discovery in general and may further the success of vaccines in combating infectious disease and cancer.

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

International Nuclear Information System (INIS)

Lue M, Marco P.; Hernandez-Caraballo, Edwin A.

2004-01-01

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

Biological dosimetry: chromosomal aberration analysis for dose assessment

International Nuclear Information System (INIS)

1986-01-01

In view of the growing importance of chromosomal aberration analysis as a biological dosimeter, the present report provides a concise summary of the scientific background of the subject and a comprehensive source of information at the technical level. After a review of the basic principles of radiation dosimetry and radiation biology basic information on the biology of lymphocytes, the structure of chromosomes and the classification of chromosomal aberrations are presented. This is followed by a presentation of techniques for collecting blood, storing, transporting, culturing, making chromosomal preparations and scaring of aberrations. The physical and statistical parameters involved in dose assessment are discussed and examples of actual dose assessments taken from the scientific literature are given

Evaluation of Measurements Collected with Multi-Parameter Continuous Water-Quality Monitors in Selected Illinois Streams, 2001-03

Science.gov (United States)

Groschen, George E.; King, Robin B.

2005-01-01

Eight streams, representing a wide range of environmental and water-quality conditions across Illinois, were monitored from July 2001 to October 2003 for five water-quality parameters as part of a pilot study by the U.S. Geological Survey (USGS) in cooperation with the Illinois Environmental Protection Agency (IEPA). Continuous recording multi-parameter water-quality monitors were installed to collect data on water temperature, dissolved-oxygen concentrations, specific conductivity, pH, and turbidity. The monitors were near USGS streamflow-gaging stations where stage and streamflow are continuously recorded. During the study period, the data collected for these five parameters generally met the data-quality objectives established by the USGS and IEPA at all eight stations. A similar pilot study during this period for measurement of chlorophyll concentrations failed to achieve the data-quality objectives. Of all the sensors used, the temperature sensors provided the most accurate and reliable measurements (generally within ?5 percent of a calibrated thermometer reading). Signal adjustments and calibration of all other sensors are dependent upon an accurate and precise temperature measurement. The dissolved-oxygen sensors were the next most reliable during the study and were responsive to changing conditions and accurate at all eight stations. Specific conductivity was the third most accurate and reliable measurement collected from the multi-parameter monitors. Specific conductivity at the eight stations varied widely-from less than 40 microsiemens (?S) at Rayse Creek near Waltonville to greater than 3,500 ?S at Salt Creek at Western Springs. In individual streams, specific conductivity often changed quickly (greater than 25 percent in less than 3 hours) and the sensors generally provided good to excellent record of these variations at all stations. The widest range of specific-conductivity measurements was in Salt Creek at Western Springs in the Greater Chicago

Application of secondary ion mass spectrometry (SIMS) to biological sample analysis

International Nuclear Information System (INIS)

Tamura, Hifumi

1990-01-01

Some major issues and problems related with the analysis of biological samples are discussed, focusing on demonstrated and possible solutions and the application of secondary ion mass spectrometry (SIMS) to investigation of the composition of biological samples. The effective use of secondary electrons in combination with negative ions is most practical for the analysis of biological samples. Regardless of whether positive or negative ions are used, the electric potential at the surface of a sample stays around a constant value because of the absense of the accumulation of electric charges at the surface, leading to almost complete avoidance of the charging of the biological sample. A soft tissue sample can suffer damage to the tissue or migration of atoms in removing water from the sample. Some processes including fixation and freeze drying are available to prevent this. The application of SIMS to biological analysis is still in the basic research stage and further studies will be required to develop practical methods. Possible areas of its application include medicine, pathology, toxicology, pharmacology, plant physiology and other areas related with marine life and marine contamination. (N.K.)

Application of activation techniques to biological analysis

International Nuclear Information System (INIS)

Bowen, H.J.M.

1981-01-01

Applications of activation analysis in the biological sciences are reviewed for the period of 1970 to 1979. The stages and characteristics of activation analysis are described, and its advantages and disadvantages enumerated. Most applications involve activation by thermal neutrons followed by either radiochemical or instrumental determination. Relatively little use has been made of activation by fast neutrons, photons, or charged particles. In vivo analyses are included, but those based on prompt gamma or x-ray emission are not. Major applications include studies of reference materials, and the elemental analysis of plants, marine biota, animal and human tissues, diets, and excreta. Relatively little use of it has been made in biochemistry, microbiology, and entomology, but it has become important in toxicology and environmental science. The elements most often determined are Ag, As, Au, Br, Ca, Cd, Cl, Co, Cr, Cs, Cu, Fe, Hg, I, K, Mn, Mo, Na, Rb, Sb, Sc, Se, and Zn, while few or no determinations of B, Be, Bi, Ga, Gd, Ge, H, In, Ir, Li, Nd, Os, Pd, Pr, Pt, Re, Rh, Ru, Te, Tl, or Y have been made in biological materials

Topic modeling for cluster analysis of large biological and medical datasets.

Science.gov (United States)

Zhao, Weizhong; Zou, Wen; Chen, James J

2014-01-01

The big data moniker is nowhere better deserved than to describe the ever-increasing prodigiousness and complexity of biological and medical datasets. New methods are needed to generate and test hypotheses, foster biological interpretation, and build validated predictors. Although multivariate techniques such as cluster analysis may allow researchers to identify groups, or clusters, of related variables, the accuracies and effectiveness of traditional clustering methods diminish for large and hyper dimensional datasets. Topic modeling is an active research field in machine learning and has been mainly used as an analytical tool to structure large textual corpora for data mining. Its ability to reduce high dimensionality to a small number of latent variables makes it suitable as a means for clustering or overcoming clustering difficulties in large biological and medical datasets. In this study, three topic model-derived clustering methods, highest probable topic assignment, feature selection and feature extraction, are proposed and tested on the cluster analysis of three large datasets: Salmonella pulsed-field gel electrophoresis (PFGE) dataset, lung cancer dataset, and breast cancer dataset, which represent various types of large biological or medical datasets. All three various methods are shown to improve the efficacy/effectiveness of clustering results on the three datasets in comparison to traditional methods. A preferable cluster analysis method emerged for each of the three datasets on the basis of replicating known biological truths. Topic modeling could be advantageously applied to the large datasets of biological or medical research. The three proposed topic model-derived clustering methods, highest probable topic assignment, feature selection and feature extraction, yield clustering improvements for the three different data types. Clusters more efficaciously represent truthful groupings and subgroupings in the data than traditional methods, suggesting

Multiway modeling and analysis in stem cell systems biology

Directory of Open Access Journals (Sweden)

Vandenberg Scott L

2008-07-01

Full Text Available Abstract Background Systems biology refers to multidisciplinary approaches designed to uncover emergent properties of biological systems. Stem cells are an attractive target for this analysis, due to their broad therapeutic potential. A central theme of systems biology is the use of computational modeling to reconstruct complex systems from a wealth of reductionist, molecular data (e.g., gene/protein expression, signal transduction activity, metabolic activity, etc.. A number of deterministic, probabilistic, and statistical learning models are used to understand sophisticated cellular behaviors such as protein expression during cellular differentiation and the activity of signaling networks. However, many of these models are bimodal i.e., they only consider row-column relationships. In contrast, multiway modeling techniques (also known as tensor models can analyze multimodal data, which capture much more information about complex behaviors such as cell differentiation. In particular, tensors can be very powerful tools for modeling the dynamic activity of biological networks over time. Here, we review the application of systems biology to stem cells and illustrate application of tensor analysis to model collagen-induced osteogenic differentiation of human mesenchymal stem cells. Results We applied Tucker1, Tucker3, and Parallel Factor Analysis (PARAFAC models to identify protein/gene expression patterns during extracellular matrix-induced osteogenic differentiation of human mesenchymal stem cells. In one case, we organized our data into a tensor of type protein/gene locus link × gene ontology category × osteogenic stimulant, and found that our cells expressed two distinct, stimulus-dependent sets of functionally related genes as they underwent osteogenic differentiation. In a second case, we organized DNA microarray data in a three-way tensor of gene IDs × osteogenic stimulus × replicates, and found that application of tensile strain to a

Biological Evidence Management for DNA Analysis in Cases of Sexual Assault

Science.gov (United States)

Magalhães, Teresa; Dinis-Oliveira, Ricardo Jorge; Silva, Benedita; Corte-Real, Francisco; Nuno Vieira, Duarte

2015-01-01

Biological evidence with forensic interest may be found in several cases of assault, being particularly relevant if sexually related. Sexual assault cases are characterized by low rates of disclosure, reporting, prosecution, and conviction. Biological evidence is sometimes the only way to prove the occurrence of sexual contact and to identify the perpetrator. The major focus of this review is to propose practical approaches and guidelines to help health, forensic, and law enforcement professionals to deal with biological evidence for DNA analysis. Attention should be devoted to avoiding contamination, degradation, and loss of biological evidence, as well as respecting specific measures to properly handle evidence (i.e., selection, collection, packing, sealing, labeling, storage, preservation, transport, and guarantee of the chain custody). Biological evidence must be carefully managed since the relevance of any finding in Forensic Genetics is determined, in the first instance, by the integrity and quantity of the samples submitted for analysis. PMID:26587562

Biological Evidence Management for DNA Analysis in Cases of Sexual Assault

Directory of Open Access Journals (Sweden)

Teresa Magalhães

2015-01-01

Full Text Available Biological evidence with forensic interest may be found in several cases of assault, being particularly relevant if sexually related. Sexual assault cases are characterized by low rates of disclosure, reporting, prosecution, and conviction. Biological evidence is sometimes the only way to prove the occurrence of sexual contact and to identify the perpetrator. The major focus of this review is to propose practical approaches and guidelines to help health, forensic, and law enforcement professionals to deal with biological evidence for DNA analysis. Attention should be devoted to avoiding contamination, degradation, and loss of biological evidence, as well as respecting specific measures to properly handle evidence (i.e., selection, collection, packing, sealing, labeling, storage, preservation, transport, and guarantee of the chain custody. Biological evidence must be carefully managed since the relevance of any finding in Forensic Genetics is determined, in the first instance, by the integrity and quantity of the samples submitted for analysis.

Multi-parameters monitoring during traditional Chinese medicine concentration process with near infrared spectroscopy and chemometrics

Science.gov (United States)

Liu, Ronghua; Sun, Qiaofeng; Hu, Tian; Li, Lian; Nie, Lei; Wang, Jiayue; Zhou, Wanhui; Zang, Hengchang

2018-03-01

As a powerful process analytical technology (PAT) tool, near infrared (NIR) spectroscopy has been widely used in real-time monitoring. In this study, NIR spectroscopy was applied to monitor multi-parameters of traditional Chinese medicine (TCM) Shenzhiling oral liquid during the concentration process to guarantee the quality of products. Five lab scale batches were employed to construct quantitative models to determine five chemical ingredients and physical change (samples density) during concentration process. The paeoniflorin, albiflorin, liquiritin and samples density were modeled by partial least square regression (PLSR), while the content of the glycyrrhizic acid and cinnamic acid were modeled by support vector machine regression (SVMR). Standard normal variate (SNV) and/or Savitzkye-Golay (SG) smoothing with derivative methods were adopted for spectra pretreatment. Variable selection methods including correlation coefficient (CC), competitive adaptive reweighted sampling (CARS) and interval partial least squares regression (iPLS) were performed for optimizing the models. The results indicated that NIR spectroscopy was an effective tool to successfully monitoring the concentration process of Shenzhiling oral liquid.

Knowledge Enrichment Analysis for Human Tissue- Specific Genes Uncover New Biological Insights

Directory of Open Access Journals (Sweden)

Gong Xiu-Jun

2012-06-01

Full Text Available The expression and regulation of genes in different tissues are fundamental questions to be answered in biology. Knowledge enrichment analysis for tissue specific (TS and housekeeping (HK genes may help identify their roles in biological process or diseases and gain new biological insights.In this paper, we performed the knowledge enrichment analysis for 17,343 genes in 84 human tissues using Gene Set Enrichment Analysis (GSEA and Hypergeometric Analysis (HA against three biological ontologies: Gene Ontology (GO, KEGG pathways and Disease Ontology (DO respectively.The analyses results demonstrated that the functions of most gene groups are consistent with their tissue origins. Meanwhile three interesting new associations for HK genes and the skeletal muscle tissuegenes are found. Firstly, Hypergeometric analysis against KEGG database for HK genes disclosed that three disease terms (Parkinson’s disease, Huntington’s disease, Alzheimer’s disease are intensively enriched.Secondly, Hypergeometric analysis against the KEGG database for Skeletal Muscle tissue genes shows that two cardiac diseases of “Hypertrophic cardiomyopathy (HCM” and “Arrhythmogenic right ventricular cardiomyopathy (ARVC” are heavily enriched, which are also considered as no relationship with skeletal functions.Thirdly, “Prostate cancer” is intensively enriched in Hypergeometric analysis against the disease ontology (DO for the Skeletal Muscle tissue genes, which is a much unexpected phenomenon.

A comparative analysis of South African Life Sciences and Biology ...

African Journals Online (AJOL)

This study reports on the analysis of South African Life Sciences and Biology textbooks for the inclusion of the nature of science using a conceptual framework developed by Chiappetta, Fillman and Sethna (1991). In particular, we investigated the differences between the representation of the nature of science in Biology ...

Analysis of undergraduate cell biology contents in Brazilian public universities.

Science.gov (United States)

Mermelstein, Claudia; Costa, Manoel Luis

2017-04-01

The enormous amount of information available in cell biology has created a challenge in selecting the core concepts we should be teaching our undergraduates. One way to define a set of essential core ideas in cell biology is to analyze what a specific cell biology community is teaching their students. Our main objective was to analyze the cell biology content currently being taught in Brazilian universities. We collected the syllabi of cell biology courses from public universities in Brazil and analyzed the frequency of cell biology topics in each course. We also compared the Brazilian data with the contents of a major cell biology textbook. Our analysis showed that while some cell biology topics such as plasma membrane and cytoskeleton was present in ∼100% of the Brazilian curricula analyzed others such as cell signaling and cell differentiation were present in only ∼35%. The average cell biology content taught in the Brazilian universities is quite different from what is presented in the textbook. We discuss several possible explanations for these observations. We also suggest a list with essential cell biology topics for any biological or biomedical undergraduate course. The comparative discussion of cell biology topics presented here could be valuable in other educational contexts. © 2017 The Authors. Cell Biology International Published by John Wiley & Sons Ltd on behalf of International Federation of Cell Biology.

Multi-parameter fibre Bragg grating sensor-array for thermal vacuum cycling test

Science.gov (United States)

Cheng, L.; Ahlers, B.; Toet, P.; Casarosa, G.; Appolloni, M.

2017-11-01

Fibre Bragg Grating (FBG) sensor systems based on optical fibres are gaining interest in space applications. Studies on Structural Health Monitoring (SHM) of the reusable launchers using FBG sensors have been carried out in the Future European Space Transportation Investigations Programme (FESTIP). Increasing investment in the development on FBG sensor applications is foreseen for the Future Launchers Preparatory Programme (FLPP). TNO has performed different SHM measurements with FBGs including on the VEGA interstage [1, 2] in 2006. Within the current project, a multi-parameter FBG sensor array demonstrator system for temperature and strain measurements is designed, fabricated and tested under ambient as well as Thermal Vacuum (TV) conditions in a TV chamber of the European Space Agency (ESA), ESTEC site. The aim is the development of a multi-parameters measuring system based on FBG technology for space applications. During the TV tests of a Space Craft (S/C) or its subsystems, thermal measurements, as well as strain measurements are needed by the engineers in order to verify their prediction and to validate their models. Because of the dimensions of the test specimen and the accuracy requested to the measurement, a large number of observation/measuring points are needed. Conventional sensor systems require a complex routing of the cables connecting the sensors to their acquisition unit. This will add extra weight to the construction under test. FBG sensors are potentially light-weight and can easily be multiplexed in an array configuration. The different tasks comply of a demonstrator system design; its component selection, procurement, manufacturing and finally its assembly. The temperature FBG sensor is calibrated in a dedicated laboratory setup down to liquid nitrogen (LN2) temperature at TNO. A temperature-wavelength calibration curve is generated. After a test programme definition a setup in thermal vacuum is realised at ESA premises including a mechanical

Multiparameter Flowfield Measurements in High-Pressure, Cryogenic Environments Using Femtosecond Lasers

Science.gov (United States)

Burns, Ross A.; Danehy, Paul M.; Peters, Christopher J.

2016-01-01

Femtosecond laser electronic excitation tagging (FLEET) and Rayleigh scattering (RS) from a femtosecond laser are demonstrated in the NASA Langley 0.3-m Transonic Cryogenic Tunnel (TCT). The measured signals from these techniques are examined for their thermodynamic dependencies in pure nitrogen. The FLEET signal intensity and signal lifetimes are found to scale primarily with the gas density, as does the RS signal. Several models are developed, which capture these physical behaviors. Notably, the FLEET and Rayleigh scattering intensities scale linearly with the flow density, while the FLEET signal decay rates are a more complex function of the thermodynamic state of the gas. The measurement of various flow properties are demonstrated using these techniques. While density was directly measured from the signal intensities and FLEET signal lifetime, temperature and pressure were measured using the simultaneous FLEET velocity measurements while assuming the flow had a constant total enthalpy. Measurements of density, temperature, and pressure from the FLEET signal are made with accuracies as high as 5.3 percent, 0.62 percent, and 6.2 percent, respectively, while precisions were approximately 10 percent, 0.26 percent, and 11 percent for these same quantities. Similar measurements of density from Rayleigh scattering showed an overall accuracy of 3.5 percent and a precision of 10.2 percent over a limited temperature range (T greater than 195 K). These measurements suggest a high degree of utility at using the femtosecond-laser based diagnostics for making multiparameter measurements in high-pressure, cryogenic environments such as large-scale TCT facilities.

Application of fast procedures for the real-time processing of multi-parameter events in the γ-spectroscopy

International Nuclear Information System (INIS)

Hanewinkel, H.

1984-01-01

The construction of a new structurated data acquisition system at the Cologne tandem accelerator should contribute to the further development of the experimental methods in nuclear physics. For this fast procedures for the real-time processing and on-line data reduction of multi-parameter events were development and applied. These procedures allowed in connection with the whole analyzer system an effective processing of the occurring many-parametric data. By this work an important condition for the experimental application of the high-resolution γγ anti-Compton coincidence spectrometer OSIRIS, which is constructed in an collaboration with goups in Berlin, Bonn, and Julich, was created at the Cologne accelerator. The ensued analyzer system offers however also to all other users an extension of their experimental possibilities. The requirements and the structure of the analyzer system as well as the procedures developed and applied for this are described and compared with other procedures proposed in literature. (orig./HSI) [de

High sensitivity neutron activation analysis of environmental and biological standard reference materials

International Nuclear Information System (INIS)

Greenberg, R.R.; Fleming, R.F.; Zeisler, R.

1984-01-01

Neutron activation analysis is a sensitive method with unique capabilities for the analysis of environmental and biological samples. Since it is based upon the nuclear properties of the elements, it does not suffer from many of the chemical effects that plague other methods of analysis. Analyses can be performed either with no chemical treatment of the sample (instrumentally), or with separations of the elements of interest after neutron irradiation (radiochemically). Typical examples of both types of analysis are discussed, and data obtained for a number of environmental and biological SRMs are presented. (author)

Engagement and Skill Development in Biology Students through Analysis of Art

Science.gov (United States)

Milkova, Liliana; Crossman, Colette; Wiles, Stephanie; Allen, Taylor

2013-01-01

An activity involving analysis of art in biology courses was designed with the goals of piquing undergraduates’ curiosity, broadening the ways in which college students meaningfully engage with course content and concepts, and developing aspects of students’ higher-level thinking skills, such as analysis, synthesis, and evaluation. To meet these learning outcomes, the activity had three key components: preparatory readings, firsthand visual analysis of art during a visit to an art museum, and communication of the analysis. Following a presentation on the methodology of visual analysis, students worked in small groups to examine through the disciplinary lens of biology a selection of approximately 12 original artworks related in some manner to love. The groups then developed and presented for class members a mini-exhibition of several pieces addressing one of two questions: 1) whether portrayals of love in art align with the growing understanding of the biology of love or 2) whether the bodily experience of love is universal or, alternatively, is culturally influenced, as is the experience of depression. Evaluation of quantitative and qualitative assessment data revealed that the assignment engaged students, supported development of higher-level thinking skills, and prompted meaningful engagement with course material. PMID:24297295

Engagement and skill development in biology students through analysis of art.

Science.gov (United States)

Milkova, Liliana; Crossman, Colette; Wiles, Stephanie; Allen, Taylor

2013-01-01

An activity involving analysis of art in biology courses was designed with the goals of piquing undergraduates' curiosity, broadening the ways in which college students meaningfully engage with course content and concepts, and developing aspects of students' higher-level thinking skills, such as analysis, synthesis, and evaluation. To meet these learning outcomes, the activity had three key components: preparatory readings, first-hand visual analysis of art during a visit to an art museum, and communication of the analysis. Following a presentation on the methodology of visual analysis, students worked in small groups to examine through the disciplinary lens of biology a selection of approximately 12 original artworks related in some manner to love. The groups then developed and presented for class members a mini-exhibition of several pieces addressing one of two questions: 1) whether portrayals of love in art align with the growing understanding of the biology of love or 2) whether the bodily experience of love is universal or, alternatively, is culturally influenced, as is the experience of depression. Evaluation of quantitative and qualitative assessment data revealed that the assignment engaged students, supported development of higher-level thinking skills, and prompted meaningful engagement with course material.

PyPathway: Python Package for Biological Network Analysis and Visualization.

Science.gov (United States)

Xu, Yang; Luo, Xiao-Chun

2018-05-01

Life science studies represent one of the biggest generators of large data sets, mainly because of rapid sequencing technological advances. Biological networks including interactive networks and human curated pathways are essential to understand these high-throughput data sets. Biological network analysis offers a method to explore systematically not only the molecular complexity of a particular disease but also the molecular relationships among apparently distinct phenotypes. Currently, several packages for Python community have been developed, such as BioPython and Goatools. However, tools to perform comprehensive network analysis and visualization are still needed. Here, we have developed PyPathway, an extensible free and open source Python package for functional enrichment analysis, network modeling, and network visualization. The network process module supports various interaction network and pathway databases such as Reactome, WikiPathway, STRING, and BioGRID. The network analysis module implements overrepresentation analysis, gene set enrichment analysis, network-based enrichment, and de novo network modeling. Finally, the visualization and data publishing modules enable users to share their analysis by using an easy web application. For package availability, see the first Reference.

Stability, performance and sensitivity analysis of I.I.D. jump linear systems

Science.gov (United States)

Chávez Fuentes, Jorge R.; González, Oscar R.; Gray, W. Steven

2018-06-01

This paper presents a symmetric Kronecker product analysis of independent and identically distributed jump linear systems to develop new, lower dimensional equations for the stability and performance analysis of this type of systems than what is currently available. In addition, new closed form expressions characterising multi-parameter relative sensitivity functions for performance metrics are introduced. The analysis technique is illustrated with a distributed fault-tolerant flight control example where the communication links are allowed to fail randomly.

Continuum analysis of biological systems conserved quantities, fluxes and forces

CERN Document Server

Suraishkumar, G K

2014-01-01

This book addresses the analysis, in the continuum regime, of biological systems at various scales, from the cellular level to the industrial one. It presents both fundamental conservation principles (mass, charge, momentum and energy) and relevant fluxes resulting from appropriate driving forces, which are important for the analysis, design and operation of biological systems. It includes the concept of charge conservation, an important principle for biological systems that is not explicitly covered in any other book of this kind. The book is organized in five parts: mass conservation; charge conservation; momentum conservation; energy conservation; and multiple conservations simultaneously applied. All mathematical aspects are presented step by step, allowing any reader with a basic mathematical background (calculus, differential equations, linear algebra, etc.) to follow the text with ease. The book promotes an intuitive understanding of all the relevant principles and in so doing facilitates their applica...

ADAM: analysis of discrete models of biological systems using computer algebra.

Science.gov (United States)

Hinkelmann, Franziska; Brandon, Madison; Guang, Bonny; McNeill, Rustin; Blekherman, Grigoriy; Veliz-Cuba, Alan; Laubenbacher, Reinhard

2011-07-20

Many biological systems are modeled qualitatively with discrete models, such as probabilistic Boolean networks, logical models, Petri nets, and agent-based models, to gain a better understanding of them. The computational complexity to analyze the complete dynamics of these models grows exponentially in the number of variables, which impedes working with complex models. There exist software tools to analyze discrete models, but they either lack the algorithmic functionality to analyze complex models deterministically or they are inaccessible to many users as they require understanding the underlying algorithm and implementation, do not have a graphical user interface, or are hard to install. Efficient analysis methods that are accessible to modelers and easy to use are needed. We propose a method for efficiently identifying attractors and introduce the web-based tool Analysis of Dynamic Algebraic Models (ADAM), which provides this and other analysis methods for discrete models. ADAM converts several discrete model types automatically into polynomial dynamical systems and analyzes their dynamics using tools from computer algebra. Specifically, we propose a method to identify attractors of a discrete model that is equivalent to solving a system of polynomial equations, a long-studied problem in computer algebra. Based on extensive experimentation with both discrete models arising in systems biology and randomly generated networks, we found that the algebraic algorithms presented in this manuscript are fast for systems with the structure maintained by most biological systems, namely sparseness and robustness. For a large set of published complex discrete models, ADAM identified the attractors in less than one second. Discrete modeling techniques are a useful tool for analyzing complex biological systems and there is a need in the biological community for accessible efficient analysis tools. ADAM provides analysis methods based on mathematical algorithms as a web

Multiparameter monitoring of short-term earthquake precursors and its physical basis. Implementation in the Kamchatka region

Directory of Open Access Journals (Sweden)

Pulinets Sergey

2016-01-01

Full Text Available We apply experimental approach of the multiparameter monitoring of short-term earthquake precursors which reliability was confirmed by the Lithosphere-Atmosphere-Ionosphere Coupling (LAIC model created recently [1]. A key element of the model is the process of Ion induced Nucleation (IIN and formation of cluster ions occurring as a result of the ionization of near surface air layer by radon emanating from the Earth's crust within the earthquake preparation zone. This process is similar to the formation of droplet’s embryos for cloud formation under action of galactic cosmic rays. The consequence of this process is the generation of a number of precursors that can be divided into two groups: a thermal and meteorological, and b electromagnetic and ionospheric. We demonstrate elements of prospective monitoring of some strong earthquakes in Kamchatka region and statistical results for the Chemical potential correction parameter for more than 10 years of observations for earthquakes with M≥6. As some experimental attempt, the data of Kamchatka volcanoes monitoring will be demonstrated.

A systems biology approach for pathway level analysis

OpenAIRE

Draghici, Sorin; Khatri, Purvesh; Tarca, Adi Laurentiu; Amin, Kashyap; Done, Arina; Voichita, Calin; Georgescu, Constantin; Romero, Roberto

2007-01-01

A common challenge in the analysis of genomics data is trying to understand the underlying phenomenon in the context of all complex interactions taking place on various signaling pathways. A statistical approach using various models is universally used to identify the most relevant pathways in a given experiment. Here, we show that the existing pathway analysis methods fail to take into consideration important biological aspects and may provide incorrect results in certain situations. By usin...

Fiji: an open-source platform for biological-image analysis.

Science.gov (United States)

Schindelin, Johannes; Arganda-Carreras, Ignacio; Frise, Erwin; Kaynig, Verena; Longair, Mark; Pietzsch, Tobias; Preibisch, Stephan; Rueden, Curtis; Saalfeld, Stephan; Schmid, Benjamin; Tinevez, Jean-Yves; White, Daniel James; Hartenstein, Volker; Eliceiri, Kevin; Tomancak, Pavel; Cardona, Albert

2012-06-28

Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.

SBEToolbox: A Matlab Toolbox for Biological Network Analysis.

Science.gov (United States)

Konganti, Kranti; Wang, Gang; Yang, Ence; Cai, James J

2013-01-01

We present SBEToolbox (Systems Biology and Evolution Toolbox), an open-source Matlab toolbox for biological network analysis. It takes a network file as input, calculates a variety of centralities and topological metrics, clusters nodes into modules, and displays the network using different graph layout algorithms. Straightforward implementation and the inclusion of high-level functions allow the functionality to be easily extended or tailored through developing custom plugins. SBEGUI, a menu-driven graphical user interface (GUI) of SBEToolbox, enables easy access to various network and graph algorithms for programmers and non-programmers alike. All source code and sample data are freely available at https://github.com/biocoder/SBEToolbox/releases.

Power capability evaluation for lithium iron phosphate batteries based on multi-parameter constraints estimation

Science.gov (United States)

Wang, Yujie; Pan, Rui; Liu, Chang; Chen, Zonghai; Ling, Qiang

2018-01-01

The battery power capability is intimately correlated with the climbing, braking and accelerating performance of the electric vehicles. Accurate power capability prediction can not only guarantee the safety but also regulate driving behavior and optimize battery energy usage. However, the nonlinearity of the battery model is very complex especially for the lithium iron phosphate batteries. Besides, the hysteresis loop in the open-circuit voltage curve is easy to cause large error in model prediction. In this work, a multi-parameter constraints dynamic estimation method is proposed to predict the battery continuous period power capability. A high-fidelity battery model which considers the battery polarization and hysteresis phenomenon is presented to approximate the high nonlinearity of the lithium iron phosphate battery. Explicit analyses of power capability with multiple constraints are elaborated, specifically the state-of-energy is considered in power capability assessment. Furthermore, to solve the problem of nonlinear system state estimation, and suppress noise interference, the UKF based state observer is employed for power capability prediction. The performance of the proposed methodology is demonstrated by experiments under different dynamic characterization schedules. The charge and discharge power capabilities of the lithium iron phosphate batteries are quantitatively assessed under different time scales and temperatures.

Human · mouse genome analysis and radiation biology. Proceedings

International Nuclear Information System (INIS)

Hori, Tada-aki

1994-03-01

This issue is the collection of the papers presented at the 25th NIRS symposium on Human, Mouse Genome Analysis and Radiation Biology. The 14 of the presented papers are indexed individually. (J.P.N.)

Information-theoretic analysis of the dynamics of an executable biological model.

Directory of Open Access Journals (Sweden)

Avital Sadot

Full Text Available To facilitate analysis and understanding of biological systems, large-scale data are often integrated into models using a variety of mathematical and computational approaches. Such models describe the dynamics of the biological system and can be used to study the changes in the state of the system over time. For many model classes, such as discrete or continuous dynamical systems, there exist appropriate frameworks and tools for analyzing system dynamics. However, the heterogeneous information that encodes and bridges molecular and cellular dynamics, inherent to fine-grained molecular simulation models, presents significant challenges to the study of system dynamics. In this paper, we present an algorithmic information theory based approach for the analysis and interpretation of the dynamics of such executable models of biological systems. We apply a normalized compression distance (NCD analysis to the state representations of a model that simulates the immune decision making and immune cell behavior. We show that this analysis successfully captures the essential information in the dynamics of the system, which results from a variety of events including proliferation, differentiation, or perturbations such as gene knock-outs. We demonstrate that this approach can be used for the analysis of executable models, regardless of the modeling framework, and for making experimentally quantifiable predictions.

Network Expansion and Pathway Enrichment Analysis towards Biologically Significant Findings from Microarrays

Directory of Open Access Journals (Sweden)

Wu Xiaogang

2012-06-01

Full Text Available In many cases, crucial genes show relatively slight changes between groups of samples (e.g. normal vs. disease, and many genes selected from microarray differential analysis by measuring the expression level statistically are also poorly annotated and lack of biological significance. In this paper, we present an innovative approach - network expansion and pathway enrichment analysis (NEPEA for integrative microarray analysis. We assume that organized knowledge will help microarray data analysis in significant ways, and the organized knowledge could be represented as molecular interaction networks or biological pathways. Based on this hypothesis, we develop the NEPEA framework based on network expansion from the human annotated and predicted protein interaction (HAPPI database, and pathway enrichment from the human pathway database (HPD. We use a recently-published microarray dataset (GSE24215 related to insulin resistance and type 2 diabetes (T2D as case study, since this study provided a thorough experimental validation for both genes and pathways identified computationally from classical microarray analysis and pathway analysis. We perform our NEPEA analysis for this dataset based on the results from the classical microarray analysis to identify biologically significant genes and pathways. Our findings are not only consistent with the original findings mostly, but also obtained more supports from other literatures.

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.

A strain-hardening bi-power law for the nonlinear behaviour of biological soft tissues.

Science.gov (United States)

Nicolle, S; Vezin, P; Palierne, J-F

2010-03-22

Biological soft tissues exhibit a strongly nonlinear viscoelastic behaviour. Among parenchymous tissues, kidney and liver remain less studied than brain, and a first goal of this study is to report additional material properties of kidney and liver tissues in oscillatory shear and constant shear rate tests. Results show that the liver tissue is more compliant but more strain hardening than kidney. A wealth of multi-parameter mathematical models has been proposed for describing the mechanical behaviour of soft tissues. A second purpose of this work is to develop a new constitutive law capable of predicting our experimental data in the both linear and nonlinear viscoelastic regime with as few parameters as possible. We propose a nonlinear strain-hardening fractional derivative model in which six parameters allow fitting the viscoelastic behaviour of kidney and liver tissues for strains ranging from 0.01 to 1 and strain rates from 0.0151 s(-1) to 0.7s(-1). Copyright (c) 2009 Elsevier Ltd. All rights reserved.

Charged particle activation analysis of phosphorus in biological materials

International Nuclear Information System (INIS)

Masumoto, K.; Yagi, M.

1983-01-01

Charged particle activation analysis of phosphorus in biological materials using the 31 P(α,n) sup(34m)Cl reaction has been studied. Since sup(34m)Cl is also produced by the 32 S(α,pn) and the 35 Cl(α,α'n) reactions, the thick-target yield curves on phosphorus, sulfur and chlorine were determined in order to choose the optimum irradiation conditions. As a result, it was found that the activation analysis for phosphorus without interferences from sulfur and chlorine is possible by bombarding with less than 17 MeV alphas. The applicability of this method to biological samples was then examined by irradiating several standard reference materials. It was confirmed that phosphorus can readily be determined at the detection limit of 1μg free from interferences due to the matrix elements. (author)

Analysis of the biological spectrum of vascular flora of Ravni Srem flood forests

Directory of Open Access Journals (Sweden)

Jurišić Branislav

2011-01-01

Full Text Available One of the essential analyses performed during the floristic study of a region is the analysis of the biological spectrum. The analysis of the biological spectrum of the flora includes the determination of the type of life form for each taxon described in the flora of the study region. If it is considered that life form is a specific structural-functional response to the environmental effects and the result of the adaptation during the species evolution, it is clear that the basic characteristics of the site are more or less reflected in any life form. This fact is confirmed by the analysis of the biological spectrum of the flora of Ravni Srem. The analysis of the Ravni Srem flora shows the domination of the hemicryptophytes and the subdomination of the phanerophytes with a considerable participation of the therophytes.

An Error Analysis of Structured Light Scanning of Biological Tissue

DEFF Research Database (Denmark)

Jensen, Sebastian Hoppe Nesgaard; Wilm, Jakob; Aanæs, Henrik

2017-01-01

This paper presents an error analysis and correction model for four structured light methods applied to three common types of biological tissue; skin, fat and muscle. Despite its many advantages, structured light is based on the assumption of direct reflection at the object surface only......, statistical linear model based on the scan geometry. As such, scans can be corrected without introducing any specially designed pattern strategy or hardware. We can effectively reduce the error in a structured light scanner applied to biological tissue by as much as factor of two or three........ This assumption is violated by most biological material e.g. human skin, which exhibits subsurface scattering. In this study, we find that in general, structured light scans of biological tissue deviate significantly from the ground truth. We show that a large portion of this error can be predicted with a simple...

Multi-element analysis of small biological samples

International Nuclear Information System (INIS)

Rokita, E.; Cafmeyer, J.; Maenhaut, W.

1983-01-01

A method combining PIXE and INAA was developed to determine the elemental composition of small biological samples. The method needs virtually no sample preparation and less than 1 mg is sufficient for the analysis. The method was used for determining up to 18 elements in leaves taken from Cracow Herbaceous. The factors which influence the elemental composition of leaves and the possible use of leaves as an environmental pollution indicator are discussed

Consistent robustness analysis (CRA) identifies biologically relevant properties of regulatory network models.

Science.gov (United States)

Saithong, Treenut; Painter, Kevin J; Millar, Andrew J

2010-12-16

A number of studies have previously demonstrated that "goodness of fit" is insufficient in reliably classifying the credibility of a biological model. Robustness and/or sensitivity analysis is commonly employed as a secondary method for evaluating the suitability of a particular model. The results of such analyses invariably depend on the particular parameter set tested, yet many parameter values for biological models are uncertain. Here, we propose a novel robustness analysis that aims to determine the "common robustness" of the model with multiple, biologically plausible parameter sets, rather than the local robustness for a particular parameter set. Our method is applied to two published models of the Arabidopsis circadian clock (the one-loop [1] and two-loop [2] models). The results reinforce current findings suggesting the greater reliability of the two-loop model and pinpoint the crucial role of TOC1 in the circadian network. Consistent Robustness Analysis can indicate both the relative plausibility of different models and also the critical components and processes controlling each model.

The multi-parameter borehole system and high resolution seismic studies in the western part of the main Marmara Fault in the frame of MARSITE Project.

Science.gov (United States)

Ozel, Oguz; Guralp, Cansun; Tunc, Suleyman; Yalcinkaya, Esref

2016-04-01

The main objective of this study is to install a multi-parameter borehole system and surface array as close to the main Marmara Fault (MMF) in the western Marmara Sea as possible, and measure continuously the evolution of the state of the fault zone surrounding the MMF and to detect any anomaly or change, which may occur before earthquakes by making use of the data from the arrays already running in the eastern part of the Marmara Sea. The multi-parameter borehole system is composed of very wide dynamic range and stable borehole (VBB) broad band seismic sensor, and incorporate strain meter, tilt meter, and temperature and local hydrostatic pressure measuring devices. The borehole seismic station uses the latest update technologies and design ideas to record "Earth tides" signals to the smallest magnitude -3 events. Additionally, a surface microearthquake observation array, consisting of 8-10 seismometers around the borehole is established to obtain continuous high resolution locations of micro-seismicity and to better understand the existing seismically active structures and their roles in local tectonic settings.Bringing face to face the seismograms of microearthquakes recorded by borehole and surface instruments portrays quite different contents. The shorter recording duration and nearly flat frequency spectrum up to the Nyquist frequencies of borehole records are faced with longer recording duration and rapid decay of spectral amplitudes at higher frequencies of a surface seismogram. The main causative of the observed differences are near surface geology effects that mask most of the source related information the seismograms include, and that give rise to scattering, generating longer duration seismograms. In view of these circumstances, studies on microearthquakes employing surface seismograms may bring on misleading results. Particularly, the works on earthquake physics and nucleation process of earthquakes requires elaborate analysis of tiny events. It is

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

BicPAMS: software for biological data analysis with pattern-based biclustering.

Science.gov (United States)

Henriques, Rui; Ferreira, Francisco L; Madeira, Sara C

2017-02-02

Biclustering has been largely applied for the unsupervised analysis of biological data, being recognised today as a key technique to discover putative modules in both expression data (subsets of genes correlated in subsets of conditions) and network data (groups of coherently interconnected biological entities). However, given its computational complexity, only recent breakthroughs on pattern-based biclustering enabled efficient searches without the restrictions that state-of-the-art biclustering algorithms place on the structure and homogeneity of biclusters. As a result, pattern-based biclustering provides the unprecedented opportunity to discover non-trivial yet meaningful biological modules with putative functions, whose coherency and tolerance to noise can be tuned and made problem-specific. To enable the effective use of pattern-based biclustering by the scientific community, we developed BicPAMS (Biclustering based on PAttern Mining Software), a software that: 1) makes available state-of-the-art pattern-based biclustering algorithms (BicPAM (Henriques and Madeira, Alg Mol Biol 9:27, 2014), BicNET (Henriques and Madeira, Alg Mol Biol 11:23, 2016), BicSPAM (Henriques and Madeira, BMC Bioinforma 15:130, 2014), BiC2PAM (Henriques and Madeira, Alg Mol Biol 11:1-30, 2016), BiP (Henriques and Madeira, IEEE/ACM Trans Comput Biol Bioinforma, 2015), DeBi (Serin and Vingron, AMB 6:1-12, 2011) and BiModule (Okada et al., IPSJ Trans Bioinf 48(SIG5):39-48, 2007)); 2) consistently integrates their dispersed contributions; 3) further explores additional accuracy and efficiency gains; and 4) makes available graphical and application programming interfaces. Results on both synthetic and real data confirm the relevance of BicPAMS for biological data analysis, highlighting its essential role for the discovery of putative modules with non-trivial yet biologically significant functions from expression and network data. BicPAMS is the first biclustering tool offering the

Automated GC-MS analysis of free amino acids in biological fluids.

Science.gov (United States)

Kaspar, Hannelore; Dettmer, Katja; Gronwald, Wolfram; Oefner, Peter J

2008-07-15

A gas chromatography-mass spectrometry (GC-MS) method was developed for the quantitative analysis of free amino acids as their propyl chloroformate derivatives in biological fluids. Derivatization with propyl chloroformate is carried out directly in the biological samples without prior protein precipitation or solid-phase extraction of the amino acids, thereby allowing automation of the entire procedure, including addition of reagents, extraction and injection into the GC-MS. The total analysis time was 30 min and 30 amino acids could be reliably quantified using 19 stable isotope-labeled amino acids as internal standards. Limits of detection (LOD) and lower limits of quantification (LLOQ) were in the range of 0.03-12 microM and 0.3-30 microM, respectively. The method was validated using a certified amino acid standard and reference plasma, and its applicability to different biological fluids was shown. Intra-day precision for the analysis of human urine, blood plasma, and cell culture medium was 2.0-8.8%, 0.9-8.3%, and 2.0-14.3%, respectively, while the inter-day precision for human urine was 1.5-14.1%.

Smartphones for distributed multimode sensing: biological and environmental sensing and analysis

Science.gov (United States)

Feitshans, Tyler; Williams, Robert

2013-05-01

Active and Agile Environmental and Biological sensing are becoming obligatory to generate prompt warnings for the troops and law enforcements conducting missions in hostile environments. The traditional static sensing mesh networks which provide a coarse-grained (far-field) measurement of the environmental conditions like air quality, radiation , CO2, etc … would not serve the dynamic and localized changes in the environment, which requires a fine-grained (near-field) sensing solutions. Further, sensing the biological conditions of (healthy and injured) personnel in a contaminated environment and providing a personalized analysis of the life-threatening conditions in real-time would greatly aid the success of the mission. In this vein, under SATE and YATE programs, the research team at AFRL Tec^Edge Discovery labs had demonstrated the feasibility of developing Smartphone applications , that employ a suite of external environmental and biological sensors, which provide fine-grained and customized sensing in real-time fashion. In its current state, these smartphone applications leverage a custom designed modular standalone embedded platform (with external sensors) that can be integrated seamlessly with Smartphones for sensing and further provides connectivity to a back-end data architecture for archiving, analysis and dissemination of real-time alerts. Additionally, the developed smartphone applications have been successfully tested in the field with varied environmental sensors to sense humidity, CO2/CO, wind, etc…, ; and with varied biological sensors to sense body temperature and pulse with apt real-time analysis

Microfabricated Electrochemical Cell-Based Biosensors for Analysis of Living Cells In Vitro

Directory of Open Access Journals (Sweden)

Jun Wang

2012-04-01

Full Text Available Cellular biochemical parameters can be used to reveal the physiological and functional information of various cells. Due to demonstrated high accuracy and non-invasiveness, electrochemical detection methods have been used for cell-based investigation. When combined with improved biosensor design and advanced measurement systems, the on-line biochemical analysis of living cells in vitro has been applied for biological mechanism study, drug screening and even environmental monitoring. In recent decades, new types of miniaturized electrochemical biosensor are emerging with the development of microfabrication technology. This review aims to give an overview of the microfabricated electrochemical cell-based biosensors, such as microelectrode arrays (MEA, the electric cell-substrate impedance sensing (ECIS technique, and the light addressable potentiometric sensor (LAPS. The details in their working principles, measurement systems, and applications in cell monitoring are covered. Driven by the need for high throughput and multi-parameter detection proposed by biomedicine, the development trends of electrochemical cell-based biosensors are also introduced, including newly developed integrated biosensors, and the application of nanotechnology and microfluidic technology.

Design and implementation of atmospheric multi-parameter sensor for UAVs

Science.gov (United States)

Yu, F.; Zhao, Y.; Chen, G.; Liu, Y.; Han, Y.

2017-12-01

With the rapid development of industry and the increase of cars in developing countries, air pollutants have caused a series of environmental issues such as haze and smog. However, air pollution is a process of surface-to-air mass exchange, and various kinds of atmospheric factors have close association with aerosol concentration, such as temperature, humidity, etc. Vertical distributions of aerosol in the region provide an important clue to reveal the exchange mechanism in the atmosphere between atmospheric boundary layer and troposphere. Among the various kinds of flying platforms, unmanned aerial vehicles (UAVs) shows more advantages in vertical measurement of aerosol owned to its flexibility and low cost. However, only few sensors could be mounted on the UAVs because of the limited size and power requirement. Here, a light-weight, low-power atmospheric multi-parameter sensor (AMPS) is proposed and could be mounted on several kinds of UAV platforms. The AMPS integrates multi-sensors, which are the laser aerosol particle sensor, the temperature probe, the humidity probe and the pressure probe, in order to simultaneously sample the vertical distribution characters of aerosol particle concentration, temperature, relative humidity and atmospheric pressure. The data from the sensors are synchronized by a proposed communication mechanism based on GPS. Several kinds of housing are designed to accommodate the different payload requirements of UAVs in size and weight. The experiments were carried out with AMPS mounted on three kinds of flying platforms. The results shows that the power consumption is less than 1.3 W, with relatively high accuracy in temperature (±0.1°C), relative humidity (±0.8%RH), PM2.5 (<20%) and PM10 (<20%). Vertical profiles of PM2.5 and PM10 concentrations were observed simultaneously by the AMPS three times every day in five days. The results revealed the significant correlation between the aerosol particle concentration and atmospheric

Biological Nanopores: Confined Spaces for Electrochemical Single-Molecule Analysis.

Science.gov (United States)

Cao, Chan; Long, Yi-Tao

2018-02-20

Nanopore sensing is developing into a powerful single-molecule approach to investigate the features of biomolecules that are not accessible by studying ensemble systems. When a target molecule is transported through a nanopore, the ions occupying the pore are excluded, resulting in an electrical signal from the intermittent ionic blockade event. By statistical analysis of the amplitudes, duration, frequencies, and shapes of the blockade events, many properties of the target molecule can be obtained in real time at the single-molecule level, including its size, conformation, structure, charge, geometry, and interactions with other molecules. With the development of the use of α-hemolysin to characterize individual polynucleotides, nanopore technology has attracted a wide range of research interest in the fields of biology, physics, chemistry, and nanoscience. As a powerful single-molecule analytical method, nanopore technology has been applied for the detection of various biomolecules, including oligonucleotides, peptides, oligosaccharides, organic molecules, and disease-related proteins. In this Account, we highlight recent developments of biological nanopores in DNA-based sensing and in studying the conformational structures of DNA and RNA. Furthermore, we introduce the application of biological nanopores to investigate the conformations of peptides affected by charge, length, and dipole moment and to study disease-related proteins' structures and aggregation transitions influenced by an inhibitor, a promoter, or an applied voltage. To improve the sensing ability of biological nanopores and further extend their application to a wider range of molecular sensing, we focus on exploring novel biological nanopores, such as aerolysin and Stable Protein 1. Aerolysin exhibits an especially high sensitivity for the detection of single oligonucleotides both in current separation and duration. Finally, to facilitate the use of nanopore measurements and statistical analysis

Integrated, multi-parameter, investigation of eruptive dynamics at Santiaguito lava dome, Guatemala

Science.gov (United States)

Lavallée, Yan; De Angelis, Silvio; Rietbrock, Andreas; Lamb, Oliver; Hornby, Adrian; Lamur, Anthony; Kendrick, Jackie E.; von Aulock, Felix W.; Chigna, Gustavo

2016-04-01

Understanding the nature of the signals generated at volcanoes is central to hazard mitigation efforts. Systematic identification and understanding of the processes responsible for the signals associated with volcanic activity are only possible when high-resolution data are available over relatively long periods of time. For this reason, in November 2014, the Liverpool Earth Observatory (LEO), UK, in collaboration with colleagues of the Instituto Nacional de Sismologia, Meteorologia e Hidrologia (INSIVUMEH), Guatemala, installed a large multi-parameter geophysical monitoring network at Santiaguito - the most active volcano in Guatemala. The network, which is to date the largest temporary deployment on Santiaguito, includes nine three-component broadband seismometers, three tiltmeters, and five infrasound microphones. Further, during the initial installation campaign we conducted visual and thermal infrared measurements of surface explosive activity and collected numerous rock samples for geochemical, geophysical and rheological characterisation. Activity at Santiaguito began in 1922, with the extrusion of a series of lava domes. In recent years, persistent dome extrusion has yielded spectacularly episodic piston-like motion displayed by characteristic tilt/seismic patterns (Johnson et al, 2014). This cyclicity episodically concludes with gas emissions or gas-and-ash explosions, observed to progress along a complex fault system in the dome. The explosive activity is associated with distinct geophysical signals characterised by the presence of very-long period earthquakes as well as more rapid inflation/deflation cycles; the erupted ash further evidences partial melting and thermal vesiculation resulting from fault processes (Lavallée et al., 2015). One year of data demonstrates the regularity of the periodicity and intensity of the explosions; analysis of infrasound data suggests that each explosion expulses on the order of 10,000-100,000 kg of gas and ash. We

Certification of biological reference materials by instrumental neutron activation analysis

International Nuclear Information System (INIS)

Lanjewar, Mamata R.; Lanjewar, R.B.

2014-01-01

A multielemental instrumental neutron activation analysis (INAA) method by short and long irradiation has been employed for the determination of 21 minor and trace elements in two standard Reference Materials P-RBF and P-WBF from Institute of Radioecology and Applied Nuclear Techniques ,Czechoslovakia. Also some biological standards such as Bowen's kale, cabbage leaves (Poland) including wheat and rice flour samples of local origin were analysed. It is suggested that INAA is an ideal method for the certification of Reference Materials of Biological Matrices. (author)

Micro and nano-platforms for biological cell analysis

DEFF Research Database (Denmark)

Svendsen, Winnie Edith; Castillo, Jaime; Moresco, Jacob Lange

2011-01-01

In this paper some technological platforms developed for biological cell analysis will be presented and compared to existing systems. In brief, we present a novel micro cell culture chamber based on diffusion feeding of cells, into which cells can be introduced and extracted after culturing using...... from the cells, while passive modifications involve the presence of a peptide nanotube based scaffold for the cell culturing that mimics the in vivo environment. Two applications involving fluorescent in situ hybridization (FISH) analysis and cancer cell sorting are presented, as examples of further...... analysis that can be done after cell culturing. A platform able to automate the entire process from cell culturing to cell analysis by means of simple plug and play of various self-contained, individually fabricated modules is finally described....

Cytobank: providing an analytics platform for community cytometry data analysis and collaboration.

Science.gov (United States)

Chen, Tiffany J; Kotecha, Nikesh

2014-01-01

Cytometry is used extensively in clinical and laboratory settings to diagnose and track cell subsets in blood and tissue. High-throughput, single-cell approaches leveraging cytometry are developed and applied in the computational and systems biology communities by researchers, who seek to improve the diagnosis of human diseases, map the structures of cell signaling networks, and identify new cell types. Data analysis and management present a bottleneck in the flow of knowledge from bench to clinic. Multi-parameter flow and mass cytometry enable identification of signaling profiles of patient cell samples. Currently, this process is manual, requiring hours of work to summarize multi-dimensional data and translate these data for input into other analysis programs. In addition, the increase in the number and size of collaborative cytometry studies as well as the computational complexity of analytical tools require the ability to assemble sufficient and appropriately configured computing capacity on demand. There is a critical need for platforms that can be used by both clinical and basic researchers who routinely rely on cytometry. Recent advances provide a unique opportunity to facilitate collaboration and analysis and management of cytometry data. Specifically, advances in cloud computing and virtualization are enabling efficient use of large computing resources for analysis and backup. An example is Cytobank, a platform that allows researchers to annotate, analyze, and share results along with the underlying single-cell data.

A miniaturized and integrated gel post platform for multiparameter PCR detection of herpes simplex viruses from raw genital swabs.

Science.gov (United States)

Manage, Dammika P; Lauzon, Jana; Atrazhev, Alexey; Morrissey, Yuen C; Edwards, Ann L; Stickel, Alexander J; Crabtree, H John; Pabbaraju, Kanti; Zahariadis, George; Yanow, Stephanie K; Pilarski, Linda M

2012-05-07

Herpes simplex virus (HSV) is one of the most prevalent viruses, with acute and recurrent infections in humans. The current gold standard for the diagnosis of HSV is viral culture which takes 2-14 days and has low sensitivity. In contrast, DNA amplification by polymerase chain reaction (PCR) can be performed within 1-2 h. We here describe a multiparameter PCR assay to simultaneously detect HSV-1 and HSV-2 DNA templates, together with integrated positive and negative controls, with product detection by melting curve analysis (MCA), in an array of semi-solid polyacrylamide gel posts. Each gel post is 0.67 μL in volume, and polymerized with all the components required for PCR. Both PCR and MCA can currently be performed in one hour and 20 min. Unprocessed genital swabs collected in universal transport medium were directly added to the reagents before or after polymerization, diffusing from atop the gel posts. The gel post platform detects HSV templates in as little as 2.5 nL of raw sample. In this study, 45 genital swab specimens were tested blindly as a preliminary validation of this platform. The concordance of PCR on gel posts with conventional PCR was 91%. The primer sequestration method introduced here (wherein different primers are placed in different sets of posts) enables the simultaneous detection of multiple pathogens for the same sample, together with positive and negative controls, on a single chip. This platform accepts unprocessed samples and is readily adaptable to detection of multiple different pathogens or biomarkers for point-of-care diagnostics.

Preliminary results from an integrated, multi-parameter, experiment at the Santiaguito lava dome complex, Guatemala

Science.gov (United States)

De Angelis, S.; Rietbrock, A.; Lavallée, Y.; Lamb, O. D.; Lamur, A.; Kendrick, J. E.; Hornby, A. J.; von Aulock, F. W.; Chigna, G.

2016-12-01

Understanding the complex processes that drive volcanic unrest is crucial to effective risk mitigation. Characterization of these processes, and the mechanisms of volcanic eruptions, is only possible when high-resolution geophysical and geological observations are available over comparatively long periods of time. In November 2014, the Liverpool Earth Observatory, UK, in collaboration with the Instituto Nacional de Sismologia, Meteorologia e Hidrologia (INSIVUMEH), Guatemala, established a multi-parameter geophysical network at Santiaguito, one of the most active volcanoes in Guatemala. Activity at Santiaguito throughout the past decade, until the summer of 2015, was characterized by nearly continuous lava dome extrusion accompanied by frequent and regular small-to-moderate gas or gas-and-ash explosions. Over the past two years our network collected a wealth of seismic, acoustic and deformation data, complemented by campaign visual and thermal infrared measurements, and rock and ash samples. Here we present preliminary results from the analysis of this unique dataset. Using acoustic and thermal data collected during 2014-2015 we were able to assess volume fractions of ash and gas in the eruptive plumes. The small proportion of ash inferred in the plumes confirms estimates from previous, independent, studies, and suggests that these events did not involve significant magma fragmentation in the conduit. The results also agree with the suggestion that sacrificial fragmentation along fault zones in the conduit region, due to shear-induced thermal vesiculation, may be at the origin of such events. Finally, starting in the summer of 2015, our experiment captured the transition to a new phase of activity characterized by vigorous vulcanian-style explosions producing large, ash-rich, plumes and frequent hazardous pyroclastic flows, as well as the formation a large summit crater. We present evidence of this transition in the geophysical and geological data, and discuss its

Neutron activation analysis of biological material

International Nuclear Information System (INIS)

Kucera, J.; Simkova, M.; Obrusnik, I.

1985-01-01

The possibilities are briefly summed up of usino. NAA (neutron activation analysis) for determining element traces in foodstuffs and their intake by organisms, for monitoring changes in the content of important trace elements in tissues and body fluids owing to environmental pollution, for verifying the results of other analytical techniques and for certifying the content of element traces in reference materials. Examples are given of the use of NAA, and the results are summed up of the determination of Cd, Mn and Zn in biological reference materials NBS SRM-1577, Bovine Liver, Bowen's Kale, IAEA Milk Powder A-11 and IAEA Animal Muscle H-4. (E.S.)

Biological variability in biomechanical engineering research: Significance and meta-analysis of current modeling practices.

Science.gov (United States)

Cook, Douglas; Julias, Margaret; Nauman, Eric

2014-04-11

Biological systems are characterized by high levels of variability, which can affect the results of biomechanical analyses. As a review of this topic, we first surveyed levels of variation in materials relevant to biomechanics, and compared these values to standard engineered materials. As expected, we found significantly higher levels of variation in biological materials. A meta-analysis was then performed based on thorough reviews of 60 research studies from the field of biomechanics to assess the methods and manner in which biological variation is currently handled in our field. The results of our meta-analysis revealed interesting trends in modeling practices, and suggest a need for more biomechanical studies that fully incorporate biological variation in biomechanical models and analyses. Finally, we provide some case study example of how biological variability may provide valuable insights or lead to surprising results. The purpose of this study is to promote the advancement of biomechanics research by encouraging broader treatment of biological variability in biomechanical modeling. Copyright © 2014 Elsevier Ltd. All rights reserved.

The use of reference materials in the elemental analysis of biological samples

International Nuclear Information System (INIS)

Bowen, H.J.M.

1975-01-01

Reference materials (RMs) are useful to compare the accuracy and precision of laboratories and techniques. The desirable properties of biological reference materials are listed, and the problems of production, homogenization and storage described. At present there are only 10 biological RMs available compared with 213 geological and 520 metallurgical RMs. There is a need for more biological RMs including special materials for microprobe analysis and for in vivo activation analysis. A study of 650 mean values for elements in RM Kale, analysed by many laboratories, leads to the following conclusions. 61% of the values lie within +-10% of the best mean, and 80% lie within +-20% of the best mean. Atomic absorption spectrometry gives results that are 5-30% high for seven elements, while intrumental neutron activation analysis gives low and imprecise results for K. Other techniques with poor interlaboratory precision include neutron activation for Mg, polarography for Zn and arc-spectrometry for many elements. More than half the values for elements in Kale were obtained by neutron activation, confirming the importance of this technique and the need for RMs. As a rough estimate, 6 x 10 9 elemental analyses of biological materials are carried out each year, mostly by medical, agricultural and food scientists. It seems likely that a substantial percentage of these are inaccurate, a situation that might be improved by quality control using standard RMs. (author)

Study on methods of quantitative analysis of the biological thin samples in EM X-ray microanalysis

International Nuclear Information System (INIS)

Zhang Detian; Zhang Xuemin; He Kun; Yang Yi; Zhang Sa; Wang Baozhen

2000-01-01

Objective: To study the methods of quantitative analysis of the biological thin samples. Methods: Hall theory was used to study the qualitative analysis, background subtraction, peel off overlap peaks; external radiation and aberrance of spectra. Results: The results of reliable qualitative analysis and precise quantitative analysis were achieved. Conclusion: The methods for analysis of the biological thin samples in EM X-ray microanalysis can be used in biomedical research

Supporting cognition in systems biology analysis: findings on users' processes and design implications.

Science.gov (United States)

Mirel, Barbara

2009-02-13

Current usability studies of bioinformatics tools suggest that tools for exploratory analysis support some tasks related to finding relationships of interest but not the deep causal insights necessary for formulating plausible and credible hypotheses. To better understand design requirements for gaining these causal insights in systems biology analyses a longitudinal field study of 15 biomedical researchers was conducted. Researchers interacted with the same protein-protein interaction tools to discover possible disease mechanisms for further experimentation. Findings reveal patterns in scientists' exploratory and explanatory analysis and reveal that tools positively supported a number of well-structured query and analysis tasks. But for several of scientists' more complex, higher order ways of knowing and reasoning the tools did not offer adequate support. Results show that for a better fit with scientists' cognition for exploratory analysis systems biology tools need to better match scientists' processes for validating, for making a transition from classification to model-based reasoning, and for engaging in causal mental modelling. As the next great frontier in bioinformatics usability, tool designs for exploratory systems biology analysis need to move beyond the successes already achieved in supporting formulaic query and analysis tasks and now reduce current mismatches with several of scientists' higher order analytical practices. The implications of results for tool designs are discussed.

On multielement analysis of biological samples with the aid of neutron activation

International Nuclear Information System (INIS)

Iyengar, G.V.

1980-01-01

A main objective of this study was elucidation of problems of sampling and sample preparation methods for multielement analysis of environmental and biological specimens. Another was assessment of the potentials of multielement neutron activation analysis (NAA) in environmental and biological research. In an attempt to explain the great differences in the elemental concentration ranges between biopsy and autopsy samples as reported in the literature, it was shown that post mortem changes induce great variations in the apparent elemental composition of autopsy specimens resulting in serious systematic errors. Applications of NAA to analysis of tissues of experimental animals, human tissues in health and disease, and environmental samples are illustrated with several examples. The suitability of NAA for routine analysis of elements such as Cr, Mo and Se, which are difficult to determine by other methods has been specially discussed. (author)

Analysis of antiepileptic drugs in biological fluids by means of electrokinetic chromatography.

Science.gov (United States)

Pucci, Vincenzo; Raggi, Maria Augusta

2005-02-01

An overview of the electrokinetic chromatographic methods for the analysis of antiepileptic drug levels in biological samples is presented. In particular, micellar electrokinetic capillary chromatography is a very suitable method for the determination of these drugs, because it allows a rapid, selective, and accurate analysis. In addition to the electrokinetic chromatographic studies on the determination of antiepileptic drugs, some information regarding sample pretreatment will also be reported: this is a critical step when the analysis of biological fluids is concerned. The electrokinetic chromatographic methods for the determination of recent antiepileptic drugs (e.g., lamotrigine, levetiracetam) and classical anticonvulsants (e.g., carbamazepine, phenytoin, ethosuximide, valproic acid) will be discussed in depth, and their pharmacological profiles will be briefly described as well.

Compatibility analysis of 3D printer resin for biological applications

KAUST Repository

Sivashankar, Shilpa; Agambayev, Sumeyra; Alamoudi, Kholod; Buttner, Ulrich; Khashab, Niveen M.; Salama, Khaled N.

2016-01-01

and that had the least effect on biological molecules that could be used for PCR and protein interactions and cells, whereas the others were used after treating the surface. Importance in building lab-on-chip/micrototal analysis systems and organ

Psychology and evolutionary biology; Causal analysis, evidence, and nomothetic laws

NARCIS (Netherlands)

Van Hezewijk, René

2008-01-01

Published as a chapter in Van Hezewijk, R. (2003). Psychology and evolutionary biology; Causal analysis, evidence, and nomothetic laws. In N. Stephenson, L. Radtke, R. Jorna & H. J. Stam (Eds.), Theoretical psychology; Critical contributions (pp. 405-415). Concord, Ontario: Captus Press.

The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways.

Science.gov (United States)

Beltrame, Luca; Calura, Enrica; Popovici, Razvan R; Rizzetto, Lisa; Guedez, Damariz Rivero; Donato, Michele; Romualdi, Chiara; Draghici, Sorin; Cavalieri, Duccio

2011-08-01

Many models and analysis of signaling pathways have been proposed. However, neither of them takes into account that a biological pathway is not a fixed system, but instead it depends on the organism, tissue and cell type as well as on physiological, pathological and experimental conditions. The Biological Connection Markup Language (BCML) is a format to describe, annotate and visualize pathways. BCML is able to store multiple information, permitting a selective view of the pathway as it exists and/or behave in specific organisms, tissues and cells. Furthermore, BCML can be automatically converted into data formats suitable for analysis and into a fully SBGN-compliant graphical representation, making it an important tool that can be used by both computational biologists and 'wet lab' scientists. The XML schema and the BCML software suite are freely available under the LGPL for download at http://bcml.dc-atlas.net. They are implemented in Java and supported on MS Windows, Linux and OS X.

An integrated environment monitoring system for underground coal mines--Wireless Sensor Network subsystem with multi-parameter monitoring.

Science.gov (United States)

Zhang, Yu; Yang, Wei; Han, Dongsheng; Kim, Young-Il

2014-07-21

Environment monitoring is important for the safety of underground coal mine production, and it is also an important application of Wireless Sensor Networks (WSNs). We put forward an integrated environment monitoring system for underground coal mine, which uses the existing Cable Monitoring System (CMS) as the main body and the WSN with multi-parameter monitoring as the supplementary technique. As CMS techniques are mature, this paper mainly focuses on the WSN and the interconnection between the WSN and the CMS. In order to implement the WSN for underground coal mines, two work modes are designed: periodic inspection and interrupt service; the relevant supporting technologies, such as routing mechanism, collision avoidance, data aggregation, interconnection with the CMS, etc., are proposed and analyzed. As WSN nodes are limited in energy supply, calculation and processing power, an integrated network management scheme is designed in four aspects, i.e., topology management, location management, energy management and fault management. Experiments were carried out both in a laboratory and in a real underground coal mine. The test results indicate that the proposed integrated environment monitoring system for underground coal mines is feasible and all designs performed well as expected.

An Integrated Environment Monitoring System for Underground Coal Mines—Wireless Sensor Network Subsystem with Multi-Parameter Monitoring

Science.gov (United States)

Zhang, Yu; Yang, Wei; Han, Dongsheng; Kim, Young-Il

2014-01-01

Environment monitoring is important for the safety of underground coal mine production, and it is also an important application of Wireless Sensor Networks (WSNs). We put forward an integrated environment monitoring system for underground coal mine, which uses the existing Cable Monitoring System (CMS) as the main body and the WSN with multi-parameter monitoring as the supplementary technique. As CMS techniques are mature, this paper mainly focuses on the WSN and the interconnection between the WSN and the CMS. In order to implement the WSN for underground coal mines, two work modes are designed: periodic inspection and interrupt service; the relevant supporting technologies, such as routing mechanism, collision avoidance, data aggregation, interconnection with the CMS, etc., are proposed and analyzed. As WSN nodes are limited in energy supply, calculation and processing power, an integrated network management scheme is designed in four aspects, i.e., topology management, location management, energy management and fault management. Experiments were carried out both in a laboratory and in a real underground coal mine. The test results indicate that the proposed integrated environment monitoring system for underground coal mines is feasible and all designs performed well as expected. PMID:25051037

An Integrated Environment Monitoring System for Underground Coal Mines—Wireless Sensor Network Subsystem with Multi-Parameter Monitoring

Directory of Open Access Journals (Sweden)

Yu Zhang

2014-07-01

Full Text Available Environment monitoring is important for the safety of underground coal mine production, and it is also an important application of Wireless Sensor Networks (WSNs. We put forward an integrated environment monitoring system for underground coal mine, which uses the existing Cable Monitoring System (CMS as the main body and the WSN with multi-parameter monitoring as the supplementary technique. As CMS techniques are mature, this paper mainly focuses on the WSN and the interconnection between the WSN and the CMS. In order to implement the WSN for underground coal mines, two work modes are designed: periodic inspection and interrupt service; the relevant supporting technologies, such as routing mechanism, collision avoidance, data aggregation, interconnection with the CMS, etc., are proposed and analyzed. As WSN nodes are limited in energy supply, calculation and processing power, an integrated network management scheme is designed in four aspects, i.e., topology management, location management, energy management and fault management. Experiments were carried out both in a laboratory and in a real underground coal mine. The test results indicate that the proposed integrated environment monitoring system for underground coal mines is feasible and all designs performed well as expected.

Comparison of Principal Component Analysis and Linear Discriminant Analysis applied to classification of excitation-emission matrices of the selected biological material

Directory of Open Access Journals (Sweden)

Maciej Leśkiewicz

2016-03-01

Full Text Available Quality of two linear methods (PCA and LDA applied to reduce dimensionality of feature analysis is compared and efficiency of their algorithms in classification of the selected biological materials according to their excitation-emission fluorescence matrices is examined. It has been found that LDA method reduces the dimensions (or a number of significant variables more effectively than PCA method. A relatively good discrimination within the examined biological material has been obtained with the use of LDA algorithm.[b]Keywords[/b]: Feature Analysis, Fluorescence Spectroscopy, Biological Material Classification

Activation analysis of biological materials at the Activation Analysis Centre

International Nuclear Information System (INIS)

Kukula, F.; Obrusnik, I.; Simkova, M.; Kucera, J.; Krivanek, M.

1976-01-01

A review is presented of the work of the Activation Analysis Centre of the Nuclear Research Institute for different fields of the Czechoslovak economy, aimed primarily at analyzing biological materials with the purpose of determining the contents of the so-called vital trace elements and of elements which already have a toxic effect on the organism in trace concentrations. Another important field of research is the path of trace elements from the environment to the human organism. A destructive method for the simultaneous determination of 12 trace elements in 11 kinds of human tissue has been studied. (Z.M.)

Multi-parameter vital sign database to assist in alarm optimization for general care units.

Science.gov (United States)

Welch, James; Kanter, Benjamin; Skora, Brooke; McCombie, Scott; Henry, Isaac; McCombie, Devin; Kennedy, Rosemary; Soller, Babs

2016-12-01

Continual vital sign assessment on the general care, medical-surgical floor is expected to provide early indication of patient deterioration and increase the effectiveness of rapid response teams. However, there is concern that continual, multi-parameter vital sign monitoring will produce alarm fatigue. The objective of this study was the development of a methodology to help care teams optimize alarm settings. An on-body wireless monitoring system was used to continually assess heart rate, respiratory rate, SpO 2 and noninvasive blood pressure in the general ward of ten hospitals between April 1, 2014 and January 19, 2015. These data, 94,575 h for 3430 patients are contained in a large database, accessible with cloud computing tools. Simulation scenarios assessed the total alarm rate as a function of threshold and annunciation delay (s). The total alarm rate of ten alarms/patient/day predicted from the cloud-hosted database was the same as the total alarm rate for a 10 day evaluation (1550 h for 36 patients) in an independent hospital. Plots of vital sign distributions in the cloud-hosted database were similar to other large databases published by different authors. The cloud-hosted database can be used to run simulations for various alarm thresholds and annunciation delays to predict the total alarm burden experienced by nursing staff. This methodology might, in the future, be used to help reduce alarm fatigue without sacrificing the ability to continually monitor all vital signs.

Growth Analysis of Cancer Biology Research, 2000-2011

Directory of Open Access Journals (Sweden)

Keshava,

2015-09-01

Full Text Available Methods and Material: The PubMed database was used for retrieving data on 'cancer biology.' Articles were downloaded from the years 2000 to 2011. The articles were classified chronologically and transferred to a spreadsheet application for analysis of the data as per the objectives of the study. Statistical Method: To investigate the nature of growth of articles via exponential, linear, and logistics tests. Result: The year wise analysis of the growth of articles output shows that for the years 2000 to 2005 and later there is a sudden increase in output, during the years 2006 to 2007 and 2008 to 2011. The high productivity of articles during these years may be due to their significance in cancer biology literature, having received prominence in research. Conclusion: There is an obvious need for better compilations of statistics on numbers of publications in the years from 2000 to 2011 on various disciplines on a worldwide scale, for informed critical assessments of the amount of new knowledge contributed by these publications, and for enhancements and refinements of present Scientometric techniques (citation and publication counts, so that valid measures of knowledge growth may be obtained. Only then will Scientometrics be able to provide accurate, useful descriptions and predictions of knowledge growth.

Ventilation versus biology: What is the controlling mechanism of nitrous oxide distribution in the North Atlantic?

Science.gov (United States)

Paz, Mercedes; García-Ibáñez, Maribel I.; Steinfeldt, Reiner; Ríos, Aida F.; Pérez, Fiz F.

2017-04-01

The extent to which water mass mixing and ocean ventilation contribute to nitrous oxide (N2O) distribution at the scale of oceanic basins is poorly constrained. We used novel N2O and chlorofluorocarbon measurements along with multiparameter water mass analysis to evaluate the impact of water mass mixing and Atlantic Meridional Overturning Circulation (AMOC) on N2O distribution along the Observatoire de la variabilité interannuelle et décennale en Atlantique Nord (OVIDE) section, extending from Portugal to Greenland. The biological N2O production has a stronger impact on the observed N2O concentrations in the water masses traveling northward in the upper limb of the AMOC than those in recently ventilated cold water masses in the lower limb, where N2O concentrations reflect the colder temperatures. The high N2O tongue, with concentrations as high as 16 nmol kg-1, propagates above the isopycnal surface delimiting the upper and lower AMOC limbs, which extends from the eastern North Atlantic Basin to the Iceland Basin and coincides with the maximum N2O production rates. Water mixing and basin-scale remineralization account for 72% of variation in the observed distribution of N2O. The mixing-corrected stoichiometric ratio N2O:O2 for the North Atlantic Basin of 0.06 nmol/μmol is in agreement with ratios of N2O:O2 for local N2O anomalies, suggesting than up to 28% of N2O production occurs in the temperate and subpolar Atlantic, an overlooked region for N2O cycling. Overall, our results highlight the importance of taking into account mixing, O2 undersaturation when water masses are formed and the increasing atmospheric N2O concentrations when parameterizing N2O:O2 and biological N2O production in the global oceans.

Development of in-air micro-PIXE analysis and data sharing systems in JAERI Takasaki

International Nuclear Information System (INIS)

Sakai, Takuro; Kamiya, Tomihiro; Oikawa, Masakazu

2000-01-01

An external scanning ion microbeam system has been developed for in-air micro-PIXE analysis at JAERI Takasaki. The analysis system is widely used for various researches in recent years. The system consists of the external scanning ion microbeam system, a multi-parameter data acquisition system, a file transfer protocol (FTP) server and analysis software. The software of the system provides a graphical user interface for interaction between users and an experimental setup. The server is connected to the Internet and allows remote users to access the experimental data. (author)

Analysis of complex networks from biology to linguistics

CERN Document Server

Dehmer, Matthias

2009-01-01

Mathematical problems such as graph theory problems are of increasing importance for the analysis of modelling data in biomedical research such as in systems biology, neuronal network modelling etc. This book follows a new approach of including graph theory from a mathematical perspective with specific applications of graph theory in biomedical and computational sciences. The book is written by renowned experts in the field and offers valuable background information for a wide audience.

Study on the radiation-induced biological responses based on the analysis of metabolites

International Nuclear Information System (INIS)

Jo, Sungkee; Jung, Uhee; Park, Haeran; Roh, Changhyun; Shin, Heejune; Ryu, Dongkyoung

2013-01-01

1. Objectives □ Establishment of basis of biological radiation response study by metabolite analysis 2. Project results □ Establishment of analytical basis of radiation-responsive metabolites in biological samples - Large scale collection of tissue samples from irradiated animal for radiation metabolomics research - Establishment of mass spectromety (GC MS, LC MS-MS) analysis methods of biological samples - 3 Standard Operation Protocols (SOP) for ultra high resolution mass spectrometry (FT-ICR MS, Q-TOF MS) analysis of metabolites from biological samples - Establishment of database for radiation metabolites □ Basic research on radiation-responsive metabolites and the interpretation of their functions - Validation of spermidine as a candidate biomarker of acute radiation response in mouse blood - Verification of 5 radiation-responsive steroid hormones and alteration of their metabolic enzyme activities in mouse blood - Verification of 13 radiation-responsive amino acids (related to oxidative stress, neurotransmission, energy metabolism) in regional mouse brain -Verification of 10 radiation-responsive amino acids (related to oxidative stress, neurotransmission, energy metabolism) in regional mouse brain - Verification of 74 radiation-responsive metabolites in whole rat brain by ultra high resolution FT-ICR MS and Q-TOF MS analysis 3. Expected benefits and plan of application □ Establishment of research basis of radiation metabolomics in Korea □ Provision of core technology in radiation bioscience and safety field by application of radiation metabolomics results to the technology development in radiation biodosimetry, and radiation response evaluation and modulation

Study on the radiation-induced biological responses based on the analysis of metabolites

Energy Technology Data Exchange (ETDEWEB)

Jo, Sungkee; Jung, Uhee; Park, Haeran; Roh, Changhyun; Shin, Heejune; Ryu, Dongkyoung

2013-01-15

1. Objectives □ Establishment of basis of biological radiation response study by metabolite analysis 2. Project results □ Establishment of analytical basis of radiation-responsive metabolites in biological samples - Large scale collection of tissue samples from irradiated animal for radiation metabolomics research - Establishment of mass spectromety (GC MS, LC MS-MS) analysis methods of biological samples - 3 Standard Operation Protocols (SOP) for ultra high resolution mass spectrometry (FT-ICR MS, Q-TOF MS) analysis of metabolites from biological samples - Establishment of database for radiation metabolites □ Basic research on radiation-responsive metabolites and the interpretation of their functions - Validation of spermidine as a candidate biomarker of acute radiation response in mouse blood - Verification of 5 radiation-responsive steroid hormones and alteration of their metabolic enzyme activities in mouse blood - Verification of 13 radiation-responsive amino acids (related to oxidative stress, neurotransmission, energy metabolism) in regional mouse brain -Verification of 10 radiation-responsive amino acids (related to oxidative stress, neurotransmission, energy metabolism) in regional mouse brain - Verification of 74 radiation-responsive metabolites in whole rat brain by ultra high resolution FT-ICR MS and Q-TOF MS analysis 3. Expected benefits and plan of application □ Establishment of research basis of radiation metabolomics in Korea □ Provision of core technology in radiation bioscience and safety field by application of radiation metabolomics results to the technology development in radiation biodosimetry, and radiation response evaluation and modulation.

Probing Protein Multidimensional Conformational Fluctuations by Single-Molecule Multiparameter Photon Stamping Spectroscopy

Science.gov (United States)

2015-01-01

Conformational motions of proteins are highly dynamic and intrinsically complex. To capture the temporal and spatial complexity of conformational motions and further to understand their roles in protein functions, an attempt is made to probe multidimensional conformational dynamics of proteins besides the typical one-dimensional FRET coordinate or the projected conformational motions on the one-dimensional FRET coordinate. T4 lysozyme hinge-bending motions between two domains along α-helix have been probed by single-molecule FRET. Nevertheless, the domain motions of T4 lysozyme are rather complex involving multiple coupled nuclear coordinates and most likely contain motions besides hinge-bending. It is highly likely that the multiple dimensional protein conformational motions beyond the typical enzymatic hinged-bending motions have profound impact on overall enzymatic functions. In this report, we have developed a single-molecule multiparameter photon stamping spectroscopy integrating fluorescence anisotropy, FRET, and fluorescence lifetime. This spectroscopic approach enables simultaneous observations of both FRET-related site-to-site conformational dynamics and molecular rotational (or orientational) motions of individual Cy3-Cy5 labeled T4 lysozyme molecules. We have further observed wide-distributed rotational flexibility along orientation coordinates by recording fluorescence anisotropy and simultaneously identified multiple intermediate conformational states along FRET coordinate by monitoring time-dependent donor lifetime, presenting a whole picture of multidimensional conformational dynamics in the process of T4 lysozyme open-close hinge-bending enzymatic turnover motions under enzymatic reaction conditions. By analyzing the autocorrelation functions of both lifetime and anisotropy trajectories, we have also observed the dynamic and static inhomogeneity of T4 lysozyme multidimensional conformational fluctuation dynamics, providing a fundamental

Biological and chemical removal of Cr(VI) from waste water: cost and benefit analysis.

Science.gov (United States)

Demir, Aynur; Arisoy, Münevver

2007-08-17

The objective of the present study is cost and benefit analysis of biological and chemical removal of hexavalent chromium [Cr(VI)] ions. Cost and benefit analysis were done with refer to two separate studies on removal of Cr(VI), one of heavy metals with a crucial role concerning increase in environmental pollution and disturbance of ecological balance, through biological adsorption and chemical ion-exchange. Methods of biological and chemical removal were compared with regard to their cost and percentage in chrome removal. According to the result of the comparison, cost per unit in chemical removal was calculated 0.24 euros and the ratio of chrome removal was 99.68%, whereas those of biological removal were 0.14 and 59.3% euros. Therefore, it was seen that cost per unit in chemical removal and chrome removal ratio were higher than those of biological removal method. In the current study where chrome removal is seen as immeasurable benefit in terms of human health and the environment, percentages of chrome removal were taken as measurable benefit and cost per unit of the chemicals as measurable cost.

Lab-on-a-chip for label free biological semiconductor analysis of Staphylococcal Enterotoxin B

NARCIS (Netherlands)

Yang, Minghui; Sun, Steven; Bruck, Hugh Alan; Kostov, Yordan; Rasooly, Avraham

2010-01-01

We describe a new lab-on-a-chip (LOC) which utilizes a biological semiconductor (BSC) transducer for label free analysis of Staphylococcal Enterotoxin B (SEB) (or other biological interactions) directly and electronically. BSCs are new transducers based on electrical percolation through a

Quantitative Evaluation of Biologic Therapy Options for Psoriasis: A Systematic Review and Network Meta-Analysis.

Science.gov (United States)

Jabbar-Lopez, Zarif K; Yiu, Zenas Z N; Ward, Victoria; Exton, Lesley S; Mohd Mustapa, M Firouz; Samarasekera, Eleanor; Burden, A David; Murphy, Ruth; Owen, Caroline M; Parslew, Richard; Venning, Vanessa; Warren, Richard B; Smith, Catherine H

2017-08-01

Multiple biologic treatments are licensed for psoriasis. The lack of head-to-head randomized controlled trials makes choosing between them difficult for patients, clinicians, and guideline developers. To establish their relative efficacy and tolerability, we searched MEDLINE, PubMed, Embase, and Cochrane for randomized controlled trials of licensed biologic treatments for skin psoriasis. We performed a network meta-analysis to identify direct and indirect evidence comparing biologics with one another, methotrexate, or placebo. We combined this with hierarchical cluster analysis to consider multiple outcomes related to efficacy and tolerability in combination for each treatment. Study quality, heterogeneity, and inconsistency were evaluated. Direct comparisons from 41 randomized controlled trials (20,561 participants) were included. All included biologics were efficacious compared with placebo or methotrexate at 3-4 months. Overall, cluster analysis showed adalimumab, secukinumab, and ustekinumab were comparable in terms of high efficacy and tolerability. Ixekizumab and infliximab were differentiated by very high efficacy but poorer tolerability. The lack of longer term controlled data limited our analysis to short-term outcomes. Trial performance may not equate to real-world performance, and so results need to be considered alongside real-world, long-term safety and effectiveness data. These data suggest that it is possible to discriminate between biologics to inform clinical practice and decision making (PROSPERO 2015:CRD42015017538). Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Laser apparatus and method for microscopic and spectroscopic analysis and processing of biological cells

Science.gov (United States)

Gourley, P.L.; Gourley, M.F.

1997-03-04

An apparatus and method are disclosed for microscopic and spectroscopic analysis and processing of biological cells. The apparatus comprises a laser having an analysis region within the laser cavity for containing one or more biological cells to be analyzed. The presence of a cell within the analysis region in superposition with an activated portion of a gain medium of the laser acts to encode information about the cell upon the laser beam, the cell information being recoverable by an analysis means that preferably includes an array photodetector such as a CCD camera and a spectrometer. The apparatus and method may be used to analyze biomedical cells including blood cells and the like, and may include processing means for manipulating, sorting, or eradicating cells after analysis. 20 figs.

Resolution of VTI anisotropy with elastic full-waveform inversion: theory and basic numerical examples

Science.gov (United States)

Podgornova, O.; Leaney, S.; Liang, L.

2018-03-01

Extracting medium properties from seismic data faces some limitations due to the finite frequency content of the data and restricted spatial positions of the sources and receivers. Some distributions of the medium properties make low impact on the data (including none). If these properties are used as the inversion parameters, then the inverse problem becomes over-parametrized, leading to ambiguous results. We present an analysis of multiparameter resolution for the linearized inverse problem in the framework of elastic full-waveform inversion. We show that the spatial and multiparameter sensitivities are intertwined and non-sensitive properties are spatial distributions of some non-trivial combinations of the conventional elastic parameters. The analysis accounts for the Hessian information and frequency content of the data; it is semi-analytical (in some scenarios analytical), easy to interpret, and enhances results of the widely used radiation pattern analysis. Single-type scattering is shown to have limited sensitivity, even for full-aperture data. Finite-frequency data lose multiparameter sensitivity at smooth and fine spatial scales. Also, we establish ways to quantify a spatial-multiparameter coupling and demonstrate that the theoretical predictions agree well with the numerical results.

Biological dosimetry of ionizing radiation by chromosomal aberration analysis

International Nuclear Information System (INIS)

Gonzalez-Castano, S.; Silva, A.; Navlet, J.

1990-01-01

Biological dosimetry consists of estimating absorbed doses for people exposed to radiation by mean biological methods. Several indicators used are based in haematological, biochemical, and cytogenetic data, although nowadays without doubt, the cytogenetic method is considered to be the most reliable. In this case, the study ol chromosomal aberrations, normally dicentric chromosomes, in peripheral lymphocytes can be related to absorbed dose through an experimental calibration curve. An experimental dose-response curve, using dicentric chromosomes analysis, X-rays at 300 kVp, 114 rad/min and temperature 37 degree celsius has been produced. Experimental data is fitted to model Y =α + β 1 D + β 2 D 2 , where Y is the number of dicentrics per cell and D the dose. The curve is compared with those produced elsewhere. (Author) 14 refs

Biological dosimetry of ionizing radiation by chromosomal aberration analysis

International Nuclear Information System (INIS)

Navlet Armenta, J.M.; Gonzalez, S.; Silva, A.

1990-01-01

Biological dosimetry consists of estimating absorbed doses for people exposed to radiation by mean biological methods. Several indicators used are based in haemathological, biochemical, and cytogenetic data, although nowadays without doubt, the cytogenetic method is considered to be the most reliable. In this case, the study of chromosomal aberrations, normally dicentric chromosomes, in peripheral lymphocytes can be related to absorbed dose through an experimental calibration curve. An experimental dose-response curve using dicentric chromosomes analysis, X-rays at 300 kVp, 114 rad/min and temperature 37 o C has been produced. Experimental data is fitted to model Y = α+β 1 D+β 2 D 2 , where Y is the number of dicentrics per cell and D the dose. The curve is compared with those produced elsewhere. (Author)

Application of Statistical Method of Path Analysis to Describe Soil Biological Indices

Directory of Open Access Journals (Sweden)

Y. Kooch

2016-09-01

Full Text Available Introduction: Among the collection of natural resources in the world, soil is considered as one of the most important components of the environment. Protect and improve the properties of this precious resource, requires a comprehensive and coordinated action that only through a deep understanding of quantitative (not only recognition of the quality the origin, distribution and functionality in a natural ecosystem is possible. Many researchers believe that due to the quick reactions of soil organisms to environmental changes, soil biological survey to estimate soil quality is more important than the chemical and physical properties. For this reason, in many studies the nitrogen mineralization and microbial respiration indices are regarded. The aim of the present study were to study the direct and indirect effects of soil physicochemical characteristics on the most important biological indicators (nitrogen mineralization and microbial respiration, which has not been carefully considered up to now. This research is the first study to provide evidence to the future planning and management of soil sciences. Materials and Methods: For this, a limitation of 20 ha area of Experimental Forest Station of Tarbiat Modares University was considered. Fifty five soil samples, from the top 15 cm of soil, were taken, from which bulk density, texture, organic C, total N, cation exchange capacity (CEC, nitrogen mineralization and microbial respiration were determined at the laboratory. The data stored in Excel as a database. To determine the relationship between biological indices and soil physicochemical characteristics, correlation analysis and factor analysis using principal component analysis (PCA were employed. To investigate all direct and indirect relationships between biological indices and different soil characteristics, path analysis (path analysis was used. Results and Discussion: Results showed significant positive relations between biological indices

Instrumental neutron activation analysis for the certification of biological reference materials

International Nuclear Information System (INIS)

Ambulkar, M.N.; Chutke, N.L.; Garg, A.N.

1992-01-01

A multielemental instrumental neutron activation analysis (INAA) method by short and long irradiation has been employed for the determination of 22 minor and trace constituents in two proposed Standard Reference Materials P-RBF and P-WBF from Institute of Radioecology and Applied Nuclear Techniques, Czechoslovakia. Also some biological standards such as Bowen's Kale, Cabbage leaves (Poland) including wheat and rice flour samples of local origin were analysed. It is suggested that INAA is an ideal method for the certification of reference materials of biological matrices. (author). 7 refs., 1 tab

Establishing working standards of chromosome aberrations analysis for biological dosimetry

International Nuclear Information System (INIS)

Bui Thi Kim Luyen; Tran Que; Pham Ngoc Duy; Nguyen Thi Kim Anh; Ha Thi Ngoc Lien

2015-01-01

Biological dosimetry is an dose assessment method using specify bio markers of radiation. IAEA (International Atomic Energy Agency) and ISO (International Organization for Standardization) defined that dicentric chromosome is specify for radiation, it is a gold standard for biodosimetry. Along with the documents published by IAEA, WHO, ISO and OECD, our results of study on the chromosome aberrations induced by radiation were organized systematically in nine standards that dealing with chromosome aberration test and micronucleus test in human peripheral blood lymphocytes in vitro. This standard addresses: the reference dose-effect for dose estimation, the minimum detection levels, cell culture, slide preparation, scoring procedure for chromosome aberrations use for biodosimetry, the criteria for converting aberration frequency into absorbed dose, reporting of results. Following these standards, the automatic analysis devices were calibrated for improving biological dosimetry method. This standard will be used to acquire and maintain accreditation of the Biological Dosimetry laboratory in Nuclear Research Institute. (author)

Ion beam analysis - development and application of nuclear reaction analysis methods, in particular at a nuclear microprobe

International Nuclear Information System (INIS)

Sjoeland, K.A.

1996-11-01

This thesis treats the development of Ion Beam Analysis methods, principally for the analysis of light elements at a nuclear microprobe. The light elements in this context are defined as having an atomic number less than approx. 13. The work reported is to a large extent based on multiparameter methods. Several signals are recorded simultaneously, and the data can be effectively analyzed to reveal structures that can not be observed through one-parameter collection. The different techniques are combined in a new set-up at the Lund Nuclear Microprobe. The various detectors for reaction products are arranged in such a way that they can be used for the simultaneous analysis of hydrogen, lithium, boron and fluorine together with traditional PIXE analysis and Scanning Transmission Ion Microscopy as well as photon-tagged Nuclear Reaction Analysis. 48 refs

Local Citation Analysis of Graduate Biology Theses: Collection Development Implications

Science.gov (United States)

Miller, Laura Newton

2011-01-01

This paper will focus on the citation analysis of graduate masters theses from Carleton University's Biology Department with implications for library collection management decisions. Twenty-five masters theses were studied to determine citation types and percentages, ranking of journals by frequency of citation and by number of authors citing, and…

A benchmark for statistical microarray data analysis that preserves actual biological and technical variance.

Science.gov (United States)

De Hertogh, Benoît; De Meulder, Bertrand; Berger, Fabrice; Pierre, Michael; Bareke, Eric; Gaigneaux, Anthoula; Depiereux, Eric

2010-01-11

Recent reanalysis of spike-in datasets underscored the need for new and more accurate benchmark datasets for statistical microarray analysis. We present here a fresh method using biologically-relevant data to evaluate the performance of statistical methods. Our novel method ranks the probesets from a dataset composed of publicly-available biological microarray data and extracts subset matrices with precise information/noise ratios. Our method can be used to determine the capability of different methods to better estimate variance for a given number of replicates. The mean-variance and mean-fold change relationships of the matrices revealed a closer approximation of biological reality. Performance analysis refined the results from benchmarks published previously.We show that the Shrinkage t test (close to Limma) was the best of the methods tested, except when two replicates were examined, where the Regularized t test and the Window t test performed slightly better. The R scripts used for the analysis are available at http://urbm-cluster.urbm.fundp.ac.be/~bdemeulder/.

Simulation and Analysis of Complex Biological Processes: an Organisation Modelling Perspective

NARCIS (Netherlands)

Bosse, T.; Jonker, C.M.; Treur, J.

2005-01-01

This paper explores how the dynamics of complex biological processes can be modelled and simulated as an organisation of multiple agents. This modelling perspective identifies organisational structure occurring in complex decentralised processes and handles complexity of the analysis of the dynamics

A critical analysis of the biological impacts of plasticizers on wildlife

DEFF Research Database (Denmark)

Oehlmann, J.; Schulte-Oehlmann, U.; Kloas, W.

2009-01-01

This review provides a critical analysis of the biological effects of the most widely used plasticizers, including dibutyl phthalate, diethylhexyl phthalate, dimethyl phthalate, butyl benzyl phthalate and bisphenol A (BPA), on wildlife, with a focus on annelids ( both aquatic and terrestrial...

CytoCluster: A Cytoscape Plugin for Cluster Analysis and Visualization of Biological Networks.

Science.gov (United States)

Li, Min; Li, Dongyan; Tang, Yu; Wu, Fangxiang; Wang, Jianxin

2017-08-31

Nowadays, cluster analysis of biological networks has become one of the most important approaches to identifying functional modules as well as predicting protein complexes and network biomarkers. Furthermore, the visualization of clustering results is crucial to display the structure of biological networks. Here we present CytoCluster, a cytoscape plugin integrating six clustering algorithms, HC-PIN (Hierarchical Clustering algorithm in Protein Interaction Networks), OH-PIN (identifying Overlapping and Hierarchical modules in Protein Interaction Networks), IPCA (Identifying Protein Complex Algorithm), ClusterONE (Clustering with Overlapping Neighborhood Expansion), DCU (Detecting Complexes based on Uncertain graph model), IPC-MCE (Identifying Protein Complexes based on Maximal Complex Extension), and BinGO (the Biological networks Gene Ontology) function. Users can select different clustering algorithms according to their requirements. The main function of these six clustering algorithms is to detect protein complexes or functional modules. In addition, BinGO is used to determine which Gene Ontology (GO) categories are statistically overrepresented in a set of genes or a subgraph of a biological network. CytoCluster can be easily expanded, so that more clustering algorithms and functions can be added to this plugin. Since it was created in July 2013, CytoCluster has been downloaded more than 9700 times in the Cytoscape App store and has already been applied to the analysis of different biological networks. CytoCluster is available from http://apps.cytoscape.org/apps/cytocluster.

Simulation of CNT-AFM tip based on finite element analysis for targeted probe of the biological cell

Energy Technology Data Exchange (ETDEWEB)

Yousefi, Amin Termeh, E-mail: at.tyousefi@gmail.com; Miyake, Mikio, E-mail: miyakejaist@gmail.com; Ikeda, Shoichiro, E-mail: sho16.ikeda@gmail.com [ChECA IKohza, Dept. Environmental & Green Technology (EGT), Malaysia, Japan International Institute of Technology (MJIIT), University Technology Malaysia - UTM, Kualalumpur (Malaysia); Mahmood, Mohamad Rusop, E-mail: nano@uitm.gmail.com [NANO-SciTech Centre, Institute of Science, Universiti Teknologi MARA (UiTM), Shah Alam, Selangor (Malaysia)

2016-07-06

Carbon nanotubes (CNTs) are potentially ideal tips for atomic force microscopy (AFM) due to the robust mechanical properties, nano scale diameter and also their ability to be functionalized by chemical and biological components at the tip ends. This contribution develops the idea of using CNTs as an AFM tip in computational analysis of the biological cell’s. Finite element analysis employed for each section and displacement of the nodes located in the contact area was monitored by using an output database (ODB). This reliable integration of CNT-AFM tip process provides a new class of high performance nanoprobes for single biological cell analysis.

Sampling and sample preparation methods for the analysis of trace elements in biological material

International Nuclear Information System (INIS)

Sansoni, B.; Iyengar, V.

1978-05-01

The authors attempt to give a most systamtic possible treatment of the sample taking and sample preparation of biological material (particularly in human medicine) for trace analysis (e.g. neutron activation analysis, atomic absorption spectrometry). Contamination and loss problems are discussed as well as the manifold problems of the different consistency of solid and liquid biological materials, as well as the stabilization of the sample material. The process of dry and wet ashing is particularly dealt with, where new methods are also described. (RB) [de

Stories of staying and leaving: A mixed methods analysis of biology undergraduate choice, persistence, and departure

Science.gov (United States)

Lang, Sarah Adrienne

Using a sequential, explanatory mixed methods design, this dissertation study compared students who persist in the biology major (persisters) with students who leave the biology major (switchers) in terms of how their pre-college experiences, college biology experiences, and biology performance figured into their choice of biology and their persistence in or departure from the biology major. This study combined (1) quantitative comparisons of biology persisters and switchers via a questionnaire developed for the study and survival analysis of a larger population of biology freshmen with (2) qualitative comparison of biology switchers and persisters via semi-structured life story interviews and homogenous focus groups. 319 students (207 persisters and 112 switchers) participated in the questionnaire and 36 students (20 persisters and 16 switchers) participated in life story and focus group interviews. All participants were undergraduates who entered The University of Texas at Austin as biology freshmen in the fall semesters of 2000 through 2004. Findings of this study suggest: (1) Regardless of eventual major, biology students enter college with generally the same suite of experiences, sources of personal encouragement, and reasons for choosing the biology major; (2) Despite the fact that they have also had poor experiences in the major, biology persisters do not actively decide to stay in the biology major; they simply do not leave; (3) Based upon survival analysis, biology students are most at-risk of leaving the biology major during the first two years of college and if they are African-American or Latino, women, or seeking a Bachelor of Arts degree (rather than a Bachelor of Science); (4) Biology switchers do not leave biology due to preference for other disciplines; they leave due to difficulties or dissatisfaction with aspects of the biology major, including their courses, faculty, and peers; (5) Biology performance has a differential effect on persistence in

Women are underrepresented in computational biology: An analysis of the scholarly literature in biology, computer science and computational biology.

Directory of Open Access Journals (Sweden)

Kevin S Bonham

2017-10-01

Full Text Available While women are generally underrepresented in STEM fields, there are noticeable differences between fields. For instance, the gender ratio in biology is more balanced than in computer science. We were interested in how this difference is reflected in the interdisciplinary field of computational/quantitative biology. To this end, we examined the proportion of female authors in publications from the PubMed and arXiv databases. There are fewer female authors on research papers in computational biology, as compared to biology in general. This is true across authorship position, year, and journal impact factor. A comparison with arXiv shows that quantitative biology papers have a higher ratio of female authors than computer science papers, placing computational biology in between its two parent fields in terms of gender representation. Both in biology and in computational biology, a female last author increases the probability of other authors on the paper being female, pointing to a potential role of female PIs in influencing the gender balance.

Women are underrepresented in computational biology: An analysis of the scholarly literature in biology, computer science and computational biology.

Science.gov (United States)

Bonham, Kevin S; Stefan, Melanie I

2017-10-01

While women are generally underrepresented in STEM fields, there are noticeable differences between fields. For instance, the gender ratio in biology is more balanced than in computer science. We were interested in how this difference is reflected in the interdisciplinary field of computational/quantitative biology. To this end, we examined the proportion of female authors in publications from the PubMed and arXiv databases. There are fewer female authors on research papers in computational biology, as compared to biology in general. This is true across authorship position, year, and journal impact factor. A comparison with arXiv shows that quantitative biology papers have a higher ratio of female authors than computer science papers, placing computational biology in between its two parent fields in terms of gender representation. Both in biology and in computational biology, a female last author increases the probability of other authors on the paper being female, pointing to a potential role of female PIs in influencing the gender balance.

Determination of mercury concentration in biological materials by neutron activation analysis

International Nuclear Information System (INIS)

Munoz, L.; Gras, N.; Cortes, E.; Cassorla, V.

1983-01-01

The objective of this work was to obtain a confident analytical method for measuring the mercury concentration in biological materials. Destructive neutron activation analysis was used for this purpose and a radiochemical separation method was studied to isolate the mercury from its main interferences: sodium and phosphorus, because these elements in biological materials are in high concentrations. The method developed was based on the copper amalgamation under controlled conditions. Yield and reproductibility studies were performed using 203 Hg as radioactive tracer. Finally, food samples of regular consumption were analyzed and the results were compared with those recommended by FAO/WHO. (Author)

Analysis of occupational accidents with biological material among professionals in pre-hospital services.

Science.gov (United States)

de Oliveira, Adriana Cristina; Paiva, Maria Henriqueta Rocha Siqueira

2013-02-01

To estimate the prevalence of accidents due to biological material exposure, the characteristics and post-accident conduct among professionals of pre-hospital services of the four municipalities of Minas Gerais, Brazil. A cross-sectional study, using a structured questionnaire that was developed to enable the calculation of prevalence, descriptive analysis and analytical analysis using logistic regression. The study included 228 professionals; the prevalence of accidents due to biological material exposure was 29.4%, with 49.2% percutaneous, 10.4% mucousal, 6.0% non-intact skin, and 34.4% intact skin. Among the professionals injured, those that stood out were nursing technicians (41.9%) and drivers (28.3%). Notification of the occurrence of the accident occurred in 29.8% of the cases. Percutaneous exposure was associated with time of work in the organization (OR=2.51, 95% CI: 1.18 to 5.35, paccidents with biological material should be encouraged, along with professional evaluation/monitoring.

g-PRIME: A Free, Windows Based Data Acquisition and Event Analysis Software Package for Physiology in Classrooms and Research Labs.

Science.gov (United States)

Lott, Gus K; Johnson, Bruce R; Bonow, Robert H; Land, Bruce R; Hoy, Ronald R

2009-01-01

We present g-PRIME, a software based tool for physiology data acquisition, analysis, and stimulus generation in education and research. This software was developed in an undergraduate neurophysiology course and strongly influenced by instructor and student feedback. g-PRIME is a free, stand-alone, windows application coded and "compiled" in Matlab (does not require a Matlab license). g-PRIME supports many data acquisition interfaces from the PC sound card to expensive high throughput calibrated equipment. The program is designed as a software oscilloscope with standard trigger modes, multi-channel visualization controls, and data logging features. Extensive analysis options allow real time and offline filtering of signals, multi-parameter threshold-and-window based event detection, and two-dimensional display of a variety of parameters including event time, energy density, maximum FFT frequency component, max/min amplitudes, and inter-event rate and intervals. The software also correlates detected events with another simultaneously acquired source (event triggered average) in real time or offline. g-PRIME supports parameter histogram production and a variety of elegant publication quality graphics outputs. A major goal of this software is to merge powerful engineering acquisition and analysis tools with a biological approach to studies of nervous system function.

Neutron-Activation Analysis of Biological Material with High Radiation Levels

Energy Technology Data Exchange (ETDEWEB)

Samsahl, K

1966-09-15

A method has been developed for the chemical separation and subsequent gamma-spectrometric analysis of the alkali metals, the alkaline earths, the rare earths, chromium, hafnium, lanthanum, manganese, phosphorus, scandium and silver in neutron-activated biological material. The separation steps, being fully automatic, are based on a combination of ion-exchange and partition chromatography and require 40 min.

Neutron-Activation Analysis of Biological Material with High Radiation Levels

International Nuclear Information System (INIS)

Samsahl, K.

1966-09-01

A method has been developed for the chemical separation and subsequent gamma-spectrometric analysis of the alkali metals, the alkaline earths, the rare earths, chromium, hafnium, lanthanum, manganese, phosphorus, scandium and silver in neutron-activated biological material. The separation steps, being fully automatic, are based on a combination of ion-exchange and partition chromatography and require 40 min

Thermodynamic modeling of transcription: sensitivity analysis differentiates biological mechanism from mathematical model-induced effects.

Science.gov (United States)

Dresch, Jacqueline M; Liu, Xiaozhou; Arnosti, David N; Ay, Ahmet

2010-10-24

Quantitative models of gene expression generate parameter values that can shed light on biological features such as transcription factor activity, cooperativity, and local effects of repressors. An important element in such investigations is sensitivity analysis, which determines how strongly a model's output reacts to variations in parameter values. Parameters of low sensitivity may not be accurately estimated, leading to unwarranted conclusions. Low sensitivity may reflect the nature of the biological data, or it may be a result of the model structure. Here, we focus on the analysis of thermodynamic models, which have been used extensively to analyze gene transcription. Extracted parameter values have been interpreted biologically, but until now little attention has been given to parameter sensitivity in this context. We apply local and global sensitivity analyses to two recent transcriptional models to determine the sensitivity of individual parameters. We show that in one case, values for repressor efficiencies are very sensitive, while values for protein cooperativities are not, and provide insights on why these differential sensitivities stem from both biological effects and the structure of the applied models. In a second case, we demonstrate that parameters that were thought to prove the system's dependence on activator-activator cooperativity are relatively insensitive. We show that there are numerous parameter sets that do not satisfy the relationships proferred as the optimal solutions, indicating that structural differences between the two types of transcriptional enhancers analyzed may not be as simple as altered activator cooperativity. Our results emphasize the need for sensitivity analysis to examine model construction and forms of biological data used for modeling transcriptional processes, in order to determine the significance of estimated parameter values for thermodynamic models. Knowledge of parameter sensitivities can provide the necessary

Current studies of biological materials using instrumental and radiochemical neutron activation analysis

International Nuclear Information System (INIS)

Fardy, J.J.; McOrist, G.D.; Farrar, Y.J.

1985-01-01

Instrumental neutron activation analysis still remains the preferred option when analysing the trace element distribution in a wide rage of materials by neutron activation analysis. However, when lower limits of detection are required or major interferences reduce the effectiveness of this technique, radiochemical neutron activation analysis is applied. This paper examines the current use of both methods and the development of rapid radiochemical techniques for analysis of the biological materials, hair, cow's milk, human's milk, milk powder, blood and blood serum

Nonlinear optical polarization analysis in chemistry and biology

CERN Document Server

Simpson, Garth J

2017-01-01

This rigorous yet accessible guide presents a molecular-based description of nonlinear optical polarization analysis of chemical and biological assemblies. It includes discussion of the most common nonlinear optical microscopy and interfacial measurements used for quantitative analysis, specifically second harmonic generation (SHG), two-photon excited fluorescence (2PEF), vibrational sum frequency generation (SFG), and coherent anti-Stokes Raman spectroscopy/stimulated Raman spectroscopy (CARS/SRS). A linear algebra mathematical framework is developed, allowing step-wise systematic connections to be made between the observable measurements and the molecular response. Effects considered include local field corrections, the molecular orientation distribution, rotations between the molecular frame, the local frame and the laboratory frame, and simplifications from molecular and macromolecular symmetry. Specific examples are provided throughout the book, working from the common and relatively simple case studies ...

Biologics or tofacitinib for people with rheumatoid arthritis unsuccessfully treated with biologics: a systematic review and network meta-analysis.

Science.gov (United States)

Singh, Jasvinder A; Hossain, Alomgir; Tanjong Ghogomu, Elizabeth; Mudano, Amy S; Maxwell, Lara J; Buchbinder, Rachelle; Lopez-Olivo, Maria Angeles; Suarez-Almazor, Maria E; Tugwell, Peter; Wells, George A

2017-03-10

Biologic disease-modifying anti-rheumatic drugs (DMARDs: referred to as biologics) are effective in treating rheumatoid arthritis (RA), however there are few head-to-head comparison studies. Our systematic review, standard meta-analysis and network meta-analysis (NMA) updates the 2009 Cochrane overview, 'Biologics for rheumatoid arthritis (RA)' and adds new data. This review is focused on biologic or tofacitinib therapy in people with RA who had previously been treated unsuccessfully with biologics. To compare the benefits and harms of biologics (abatacept, adalimumab, anakinra, certolizumab pegol, etanercept, golimumab, infliximab, rituximab, tocilizumab) and small molecule tofacitinib versus comparator (placebo or methotrexate (MTX)/other DMARDs) in people with RA, previously unsuccessfully treated with biologics. On 22 June 2015 we searched for randomized controlled trials (RCTs) in CENTRAL, MEDLINE, and Embase; and trials registries (WHO trials register, Clinicaltrials.gov). We carried out article selection, data extraction, and risk of bias and GRADE assessments in duplicate. We calculated direct estimates with 95% confidence intervals (CI) using standard meta-analysis. We used a Bayesian mixed treatment comparison (MTC) approach for NMA estimates with 95% credible intervals (CrI). We converted odds ratios (OR) to risk ratios (RR) for ease of understanding. We have also presented results in absolute measures as risk difference (RD) and number needed to treat for an additional beneficial outcome (NNTB). Outcomes measured included four benefits (ACR50, function measured by Health Assessment Questionnaire (HAQ) score, remission defined as DAS tofacitinib (399 participants). The majority of the trials (10/12) lasted less than 12 months.We judged 33% of the studies at low risk of bias for allocation sequence generation, allocation concealment and blinding, 25% had low risk of bias for attrition, 92% were at unclear risk for selective reporting; and 92% had low risk

Procurement of a Large Area Mapping FTIR Microscope for Organic-Inorganic Interfacial Analysis in Biological Materials

Science.gov (United States)

2015-12-31

SECURITY CLASSIFICATION OF: After acquiring the Infrared Imaging Microscope with large area mapping capabilities for structure -function research and...Inorganic Interfacial Analysis in Biological Materials The views, opinions and/or findings contained in this report are those of the author(s) and should...of a Large Area Mapping FTIR Microscope for Organic-Inorganic Interfacial Analysis in Biological Materials Report Title After acquiring the Infrared

Computational local stiffness analysis of biological cell: High aspect ratio single wall carbon nanotube tip

Energy Technology Data Exchange (ETDEWEB)

TermehYousefi, Amin, E-mail: at.tyousefi@gmail.com [Department of Human Intelligence Systems, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology (Kyutech) (Japan); Bagheri, Samira; Shahnazar, Sheida [Nanotechnology & Catalysis Research Centre (NANOCAT), IPS Building, University Malaya, 50603 Kuala Lumpur (Malaysia); Rahman, Md. Habibur [Department of Computer Science and Engineering, University of Asia Pacific, Green Road, Dhaka-1215 (Bangladesh); Kadri, Nahrizul Adib [Department of Biomedical Engineering, Faculty of Engineering, University Malaya, 50603 Kuala Lumpur (Malaysia)

2016-02-01

Carbon nanotubes (CNTs) are potentially ideal tips for atomic force microscopy (AFM) due to the robust mechanical properties, nanoscale diameter and also their ability to be functionalized by chemical and biological components at the tip ends. This contribution develops the idea of using CNTs as an AFM tip in computational analysis of the biological cells. The proposed software was ABAQUS 6.13 CAE/CEL provided by Dassault Systems, which is a powerful finite element (FE) tool to perform the numerical analysis and visualize the interactions between proposed tip and membrane of the cell. Finite element analysis employed for each section and displacement of the nodes located in the contact area was monitored by using an output database (ODB). Mooney–Rivlin hyperelastic model of the cell allows the simulation to obtain a new method for estimating the stiffness and spring constant of the cell. Stress and strain curve indicates the yield stress point which defines as a vertical stress and plan stress. Spring constant of the cell and the local stiffness was measured as well as the applied force of CNT-AFM tip on the contact area of the cell. This reliable integration of CNT-AFM tip process provides a new class of high performance nanoprobes for single biological cell analysis. - Graphical abstract: This contribution develops the idea of using CNTs as an AFM tip in computational analysis of the biological cells. The proposed software was ABAQUS 6.13 CAE/CEL provided by Dassault Systems. Finite element analysis employed for each section and displacement of the nodes located in the contact area was monitored by using an output database (ODB). Mooney–Rivlin hyperelastic model of the cell allows the simulation to obtain a new method for estimating the stiffness and spring constant of the cell. Stress and strain curve indicates the yield stress point which defines as a vertical stress and plan stress. Spring constant of the cell and the local stiffness was measured as well

Analysis of biological tissues by Moessbauer spectroscopy

International Nuclear Information System (INIS)

Bonkova, I.; Bujdos, M.; Miglierini, M.

2016-01-01

The aim of this work was to analyze of biological tissues by Moessbauer spectroscopy in terms of demonstration of the magnetic properties of iron and its structural positions. Lyophilized samples of the human brain, human and equine spleen were used for the analysis. The samples were measured with 57 Fe Moessbauer spectroscopy in transmission arrangement at room temperature (∼ 300 K) and at a temperature of liquid helium (4.2 K). The resulting Moessbauer spectra measured at room temperature had doublet character, which confirms the presence of non-magnetic particles. On the contrary, low-temperature measurements are a superposition of several sextet and one duplicate. Hyperfine parameters obtained are similar to those reported hematite, ferrihydrite or magnetite. (authors)

Building biological foundries for next-generation synthetic biology.

Science.gov (United States)

Chao, Ran; Yuan, YongBo; Zhao, HuiMin

2015-07-01

Synthetic biology is an interdisciplinary field that takes top-down approaches to understand and engineer biological systems through design-build-test cycles. A number of advances in this relatively young field have greatly accelerated such engineering cycles. Specifically, various innovative tools were developed for in silico biosystems design, DNA de novo synthesis and assembly, construct verification, as well as metabolite analysis, which have laid a solid foundation for building biological foundries for rapid prototyping of improved or novel biosystems. This review summarizes the state-of-the-art technologies for synthetic biology and discusses the challenges to establish such biological foundries.

MALDI-MS drug analysis in biological samples: opportunities and challenges.

Science.gov (United States)

Steuer, Andrea E; Poetzsch, Michael; Kraemer, Thomas

2016-09-01

Drug analysis represents a large field in different disciplines. Plasma is commonly considered to be the biosample of choice for that purpose. However, concentrations often do not represent the levels present within deeper compartments and therefore cannot sufficiently explain efficacy or toxicology of drugs. MALDI-MS in drug analysis is of great interest for high-throughput quantification and particularly spatially resolved tissue imaging. The current perspective article will deal with challenges and opportunities of MALDI-MS drug analysis in different biological samples. A particular focus will be on hair samples. Recent applications were included, reviewed for their instrumental setup and sample preparation and pros and cons as well as future perspectives are critically discussed.

Biosimilars design and analysis of follow-on biologics

CERN Document Server

2013-01-01

"This book extensively covers both statistical and regulatory considerations from design to analysis of biosimilarity. … it is well presented and comprehensively covers fundamental issues and some of the newly developed methods for biosimilarity studies. The book is very balanced between scientific aspects and regulatory requirements. In addition, the reference lists give readers helpful information. … a valuable resource for anyone interested and involved in biosimilarity studies."-Biometrics, September 2014"[Professor] Chow's book Biosimilars: Design and Analysis of Follow-On Biologics … is the first book ever written on this topic. I commend Professor Chow for his effort to introduce the topic … Overall, this is a worthwhile reference book for statisticians interested in understanding biosimilar product development and evaluation." -Yi Tsong, PhD, Center for Drug Evaluation and Research, US Food and Drug Administration, USA, in Journal of Biopharmaceutical Statistics>.

Determination of drugs in biological fluids by direct injection of samples for liquid-chromatographic analysis.

Science.gov (United States)

Mullett, Wayne M

2007-03-10

The analysis of drugs in various biological fluids is an important criterion for the determination of the physiological performance of a drug. After sampling of the biological fluid, the next step in the analytical process is sample preparation. The complexity of biological fluids adds to the challenge of direct determination of the drug by chromatographic analysis, therefore demanding a sample preparation step that is often time-consuming, tedious, and frequently overlooked. However, direct on-line injection methods offer the advantage of reducing sample preparation steps and enabling effective pre-concentration and clean-up of biological fluids. These procedures can be automated and therefore reduce the requirements for handling potentially infectious biomaterial, improve reproducibility, and minimize sample manipulations and potential contamination. The objective of this review is to present an overview of the existing literature with emphasis on advances in automated sample preparation methods for liquid-chromatographic methods. More specifically, this review concentrates on the use of direct injection techniques, such as restricted-access materials, turbulent-flow chromatography and other automated on-line solid-phase extraction (SPE) procedures. It also includes short overviews of emerging automated extraction-phase technologies, such as molecularly imprinted polymers, in-tube solid-phase micro-extraction, and micro-extraction in a packed syringe for a more selective extraction of analytes from complex samples, providing further improvements in the analysis of biological materials. Lastly, the outlook for these methods and potential new applications for these technologies are briefly discussed.

A new method of on-line multiparameter amplitude analysis with compression

International Nuclear Information System (INIS)

Morhac, M.; matousek, V.

1996-01-01

An algorithm of one-line multidimensional amplitude analysis with compression using fast adaptive orthogonal transform is presented in the paper. The method is based on a direct modification of multiplication coefficients of the signal flow graph of the fast Cooley-Tukey's algorithm. The coefficients are modified according to a reference vector representing the processed data. The method has been tested to compress three parameter experimental nuclear data. The efficiency of the derived adaptive transform is compared with classical orthogonal transforms. (orig.)

[Analysis on property of meridian supramolecules by biological evolution path].

Science.gov (United States)

Deng, Kaiwen; Tao, Yeqin; Tang, Wenhan; He, Fuyuan; Liu, Wenlong; Shi, Jilian; Yang, Yantao; Zhou, Yiqun; Chang, Xiaorong

2017-03-12

With human placed in the whole nature, by following the biologic evolution path, the property of channel structure for "imprinting template" in meridian and zang-fu was explored with supramolecular chemistry. In the history of biologic evolution, each molecule in "molecule society" gradually developed into various highly-ordered supramolecular bodies based on self-identification, self-assembly, self-organization, self-replicating of"imprinting template", and thereby the original biochemical system was established, and finally evolved into human. In the forming process of supramolecular bodies, the channel structure of"imprinting template" in guest supramolecular bodies would be kept by host supramolecular bodies, and communicate with the outside to exchange materials, energy, information, otherwise life phenomenon could not continue, for which it was the chemical nature of biolo-gical supramolecular bodies for body to develop meridian. Therefore, the human was a gigantic and complicated supramolecules body in biological nature, and possessed the supramolecules "imprinting template" at each stage of evolution, for which the meridians were formed. When meridians converged, acupoints appeared; when acupointsconverged, zang-fu appeared. With the promotion of the blood from heart, according to"imprinting template", the guest supramolecular bodies and host meridian produced qi -analysis, which was the qi -phenomenon of guest in meridian. It presented as zang-fu image of physiology and pathology as well as action regularities of medication and acupuncture tolerance, by which current various meridian viewpoints could be explained and propose the hypothesis of meridian supramolecular bodies. The meridian and its phenomenon was decide by its "imprinting template" of supramolecular bodies and self-reaction regularities, which abided through the living nature. This was the substance for meridian biology.

Elemental Analysis in Biological Matrices Using ICP-MS.

Science.gov (United States)

Hansen, Matthew N; Clogston, Jeffrey D

2018-01-01

The increasing exploration of metallic nanoparticles for use as cancer therapeutic agents necessitates a sensitive technique to track the clearance and distribution of the material once introduced into a living system. Inductively coupled plasma mass spectrometry (ICP-MS) provides a sensitive and selective tool for tracking the distribution of metal components from these nanotherapeutics. This chapter presents a standardized method for processing biological matrices, ensuring complete homogenization of tissues, and outlines the preparation of appropriate standards and controls. The method described herein utilized gold nanoparticle-treated samples; however, the method can easily be applied to the analysis of other metals.

More on the losses of dissolved CO(2) during champagne serving: toward a multiparameter modeling.

Science.gov (United States)

Liger-Belair, Gérard; Parmentier, Maryline; Cilindre, Clara

2012-11-28

Pouring champagne into a glass is far from being inconsequential with regard to the dissolved CO(2) concentration found in champagne. Three distinct bottle types, namely, a magnum bottle, a standard bottle, and a half bottle, were examined with regard to their loss of dissolved CO(2) during the service of successively poured flutes. Whatever the bottle size, a decreasing trend is clearly observed with regard to the concentration of dissolved CO(2) found within a flute (from the first to the last one of a whole service). Moreover, when it comes to champagne serving, the bottle size definitely does matter. The higher the bottle volume, the better its buffering capacity with regard to dissolved CO(2) found within champagne during the pouring process. Actually, for a given flute number in a pouring data series, the concentration of dissolved CO(2) found within the flute was found to decrease as the bottle size decreases. The impact of champagne temperature (at 4, 12, and 20 °C) on the losses of dissolved CO(2) found in successively poured flutes for a given standard 75 cL bottle was also examined. Cold temperatures were found to limit the decreasing trend of dissolved CO(2) found within the successively poured flutes (from the first to the last one of a whole service). Our experimental results were discussed on the basis of a multiparameter model that accounts for the major physical parameters that influence the loss of dissolved CO(2) during the service of a whole bottle type.

The prognosis of infective endocarditis treated with biological valves versus mechanical valves: A meta-analysis.

Science.gov (United States)

Tao, Ende; Wan, Li; Wang, WenJun; Luo, YunLong; Zeng, JinFu; Wu, Xia

2017-01-01

Surgery remains the primary form of treatment for infective endocarditis (IE). However, it is not clear what type of prosthetic valve provides a better prognosis. We conducted a meta-analysis to compare the prognosis of infective endocarditis treated with biological valves to cases treated with mechanical valves. Pubmed, Embase and Cochrane databases were searched from January 1960 to November 2016.Randomized controlled trials, retrospective cohorts and prospective studies comparing outcomes between biological valve and mechanical valve management for infective endocarditis were analyzed. The Newcastle-Ottawa Scale(NOS) was used to evaluate the quality of the literature and extracted data, and Stata 12.0 software was used for the meta-analysis. A total of 11 publications were included; 10,754 cases were selected, involving 6776 cases of biological valves and 3,978 cases of mechanical valves. The all-cause mortality risk of the biological valve group was higher than that of the mechanical valve group (HR = 1.22, 95% CI 1.03 to 1.44, P = 0.023), as was early mortality (RR = 1.21, 95% CI 1.02 to 1.43, P = 0.033). The recurrence of endocarditis (HR = 1.75, 95% CI 1.26 to 2.42, P = 0.001), as well as the risk of reoperation (HR = 1.79, 95% CI 1.15 to 2.80, P = 0.010) were more likely to occur in the biological valve group. The incidence of postoperative embolism was less in the biological valve group than in the mechanical valve group, but this difference was not statistically significant (RR = 0.90, 95% CI 0.76 to 1.07, P = 0.245). For patients with prosthetic valve endocarditis (PVE), there was no significant difference in survival rates between the biological valve group and the mechanical valve group (HR = 0.91, 95% CI 0.68 to 1.21, P = 0.520). The results of our meta-analysis suggest that mechanical valves can provide a significantly better prognosis in patients with infective endocarditis. There were significant differences in the clinical features of patients

A simple method of fabricating mask-free microfluidic devices for biological analysis.

KAUST Repository

Yi, Xin; Kodzius, Rimantas; Gong, Xiuqing; Xiao, Kang; Wen, Weijia

2010-01-01

We report a simple, low-cost, rapid, and mask-free method to fabricate two-dimensional (2D) and three-dimensional (3D) microfluidic chip for biological analysis researches. In this fabrication process, a laser system is used to cut through paper

Multi-parameter approach to evaluate the timing of memory status after 17DD-YF primary vaccination.

Science.gov (United States)

Costa-Pereira, Christiane; Campi-Azevedo, Ana Carolina; Coelho-Dos-Reis, Jordana Grazziela; Peruhype-Magalhães, Vanessa; Araújo, Márcio Sobreira Silva; do Vale Antonelli, Lis Ribeiro; Fonseca, Cristina Toscano; Lemos, Jandira Aparecida; Malaquias, Luiz Cosme Cote; de Souza Gomes, Matheus; Rodrigues Amaral, Laurence; Rios, Maria; Chancey, Caren; Persi, Harold Richard; Pereira, Jorge Marcelo; de Sousa Maia, Maria de Lourdes; Freire, Marcos da Silva; Martins, Reinaldo de Menezes; Homma, Akira; Simões, Marisol; Yamamura, Anna Yoshida; Farias, Roberto Henrique Guedes; Romano, Alessandro Pecego Martins; Domingues, Carla Magda; Tauil, Pedro Luiz; Vasconcelos, Pedro Fernando Costa; Caldas, Iramaya Rodrigues; Camacho, Luiz Antônio; Teixeira-Carvalho, Andrea; Martins-Filho, Olindo Assis

2018-06-01

In this investigation, machine-enhanced techniques were applied to bring about scientific insights to identify a minimum set of phenotypic/functional memory-related biomarkers for post-vaccination follow-up upon yellow fever (YF) vaccination. For this purpose, memory status of circulating T-cells (Naïve/early-effector/Central-Memory/Effector-Memory) and B-cells (Naïve/non-Classical-Memory/Classical-Memory) along with the cytokine profile (IFN/TNF/IL-5/IL-10) were monitored before-NV(day0) and at distinct time-points after 17DD-YF primary vaccination-PV(day30-45); PV(year1-9) and PV(year10-11). A set of biomarkers (eEfCD4; EMCD4; CMCD19; EMCD8; IFNCD4; IL-5CD8; TNFCD4; IFNCD8; TNFCD8; IL-5CD19; IL-5CD4) were observed in PV(day30-45), but not in NV(day0), with most of them still observed in PV(year1-9). Deficiencies of phenotypic/functional biomarkers were observed in NV(day0), while total lack of memory-related attributes was observed in PV(year10-11), regardless of the age at primary vaccination. Venn-diagram analysis pre-selected 10 attributes (eEfCD4, EMCD4, CMCD19, EMCD8, IFNCD4, IL-5CD8, TNFCD4, IFNCD8, TNFCD8 and IL-5CD4), of which the overall mean presented moderate accuracy to discriminate PV(day30-45)&PV(year1-9) from NV(day0)&PV(year10-11). Multi-parameter approaches and decision-tree algorithms defined the EMCD8 and IL-5CD4 attributes as the top-two predictors with moderated performance. Together with the PRNT titers, the top-two biomarkers led to a resultant memory status observed in 80% and 51% of volunteers in PV(day30-45) and PV(year1-9), contrasting with 0% and 29% found in NV(day0) and PV(year10-11), respectively. The deficiency of memory-related attributes observed at PV(year10-11) underscores the conspicuous time-dependent decrease of resultant memory following17DD-YF primary vaccination that could be useful to monitor potential correlates of protection in areas under risk of YF transmission.

Vitamin D and depression: a systematic review and meta-analysis comparing studies with and without biological flaws.

Science.gov (United States)

Spedding, Simon

2014-04-11

Efficacy of Vitamin D supplements in depression is controversial, awaiting further literature analysis. Biological flaws in primary studies is a possible reason meta-analyses of Vitamin D have failed to demonstrate efficacy. This systematic review and meta-analysis of Vitamin D and depression compared studies with and without biological flaws. The systematic review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The literature search was undertaken through four databases for randomized controlled trials (RCTs). Studies were critically appraised for methodological quality and biological flaws, in relation to the hypothesis and study design. Meta-analyses were performed for studies according to the presence of biological flaws. The 15 RCTs identified provide a more comprehensive evidence-base than previous systematic reviews; methodological quality of studies was generally good and methodology was diverse. A meta-analysis of all studies without flaws demonstrated a statistically significant improvement in depression with Vitamin D supplements (+0.78 CI +0.24, +1.27). Studies with biological flaws were mainly inconclusive, with the meta-analysis demonstrating a statistically significant worsening in depression by taking Vitamin D supplements (-1.1 CI -0.7, -1.5). Vitamin D supplementation (≥800 I.U. daily) was somewhat favorable in the management of depression in studies that demonstrate a change in vitamin levels, and the effect size was comparable to that of anti-depressant medication.

Bayesian uncertainty analysis for complex systems biology models: emulation, global parameter searches and evaluation of gene functions.

Science.gov (United States)

Vernon, Ian; Liu, Junli; Goldstein, Michael; Rowe, James; Topping, Jen; Lindsey, Keith

2018-01-02

Many mathematical models have now been employed across every area of systems biology. These models increasingly involve large numbers of unknown parameters, have complex structure which can result in substantial evaluation time relative to the needs of the analysis, and need to be compared to observed data of various forms. The correct analysis of such models usually requires a global parameter search, over a high dimensional parameter space, that incorporates and respects the most important sources of uncertainty. This can be an extremely difficult task, but it is essential for any meaningful inference or prediction to be made about any biological system. It hence represents a fundamental challenge for the whole of systems biology. Bayesian statistical methodology for the uncertainty analysis of complex models is introduced, which is designed to address the high dimensional global parameter search problem. Bayesian emulators that mimic the systems biology model but which are extremely fast to evaluate are embeded within an iterative history match: an efficient method to search high dimensional spaces within a more formal statistical setting, while incorporating major sources of uncertainty. The approach is demonstrated via application to a model of hormonal crosstalk in Arabidopsis root development, which has 32 rate parameters, for which we identify the sets of rate parameter values that lead to acceptable matches between model output and observed trend data. The multiple insights into the model's structure that this analysis provides are discussed. The methodology is applied to a second related model, and the biological consequences of the resulting comparison, including the evaluation of gene functions, are described. Bayesian uncertainty analysis for complex models using both emulators and history matching is shown to be a powerful technique that can greatly aid the study of a large class of systems biology models. It both provides insight into model behaviour

Network Analysis Tools: from biological networks to clusters and pathways.

Science.gov (United States)

Brohée, Sylvain; Faust, Karoline; Lima-Mendez, Gipsi; Vanderstocken, Gilles; van Helden, Jacques

2008-01-01

Network Analysis Tools (NeAT) is a suite of computer tools that integrate various algorithms for the analysis of biological networks: comparison between graphs, between clusters, or between graphs and clusters; network randomization; analysis of degree distribution; network-based clustering and path finding. The tools are interconnected to enable a stepwise analysis of the network through a complete analytical workflow. In this protocol, we present a typical case of utilization, where the tasks above are combined to decipher a protein-protein interaction network retrieved from the STRING database. The results returned by NeAT are typically subnetworks, networks enriched with additional information (i.e., clusters or paths) or tables displaying statistics. Typical networks comprising several thousands of nodes and arcs can be analyzed within a few minutes. The complete protocol can be read and executed in approximately 1 h.

7th Annual Systems Biology Symposium: Systems Biology and Engineering

Energy Technology Data Exchange (ETDEWEB)

Galitski, Timothy P.

2008-04-01

Systems biology recognizes the complex multi-scale organization of biological systems, from molecules to ecosystems. The International Symposium on Systems Biology has been hosted by the Institute for Systems Biology in Seattle, Washington, since 2002. The annual two-day event gathers the most influential researchers transforming biology into an integrative discipline investingating complex systems. Engineering and application of new technology is a central element of systems biology. Genome-scale, or very small-scale, biological questions drive the enigneering of new technologies, which enable new modes of experimentation and computational analysis, leading to new biological insights and questions. Concepts and analytical methods in engineering are now finding direct applications in biology. Therefore, the 2008 Symposium, funded in partnership with the Department of Energy, featured global leaders in "Systems Biology and Engineering."

[Progress on Determination and Analysis of Zopiclone in Biological Samples].

Science.gov (United States)

Shu, C X; Gong, D; Zhang, L P; Zhao, J X

2017-12-01

As a new hypnotic, zopiclone is widely used in clinical treatment. There are many methods for determination of zopiclone, including spectrophotometry, chromatography and chromatography mass spectrum, etc. Present paper reviews different kinds of biological samples associated with zopiclone, extraction and purification methods, and determination and analysis methods, which aims to provide references for the relevant research and practice. Copyright© by the Editorial Department of Journal of Forensic Medicine.

Analysis of biological materials using a nuclear microprobe

Science.gov (United States)

Mulware, Stephen Juma

The use of nuclear microprobe techniques including: Particle induced x-ray emission (PIXE) and Rutherford backscattering spectrometry (RBS) for elemental analysis and quantitative elemental imaging of biological samples is especially useful in biological and biomedical research because of its high sensitivity for physiologically important trace elements or toxic heavy metals. The nuclear microprobe of the Ion Beam Modification and Analysis Laboratory (IBMAL) has been used to study the enhancement in metal uptake of two different plants. The roots of corn (Zea mays) have been analyzed to study the enhancement of iron uptake by adding Fe (II) or Fe(III) of different concentrations to the germinating medium of the seeds. The Fe uptake enhancement effect produced by lacing the germinating medium with carbon nanotubes has also been investigated. The aim of this investigation is to ensure not only high crop yield but also Fe-rich food products especially from calcareous soil which covers 30% of world's agricultural land. The result will help reduce iron deficiency anemia, which has been identified as the leading nutritional disorder especially in developing countries by the World Health Organization. For the second plant, Mexican marigold (Tagetes erecta ), the effect of an arbuscular mycorrhizal fungi (Glomus intraradices ) for the improvement of lead phytoremediation of lead contaminated soil has been investigated. Phytoremediation provides an environmentally safe technique of removing toxic heavy metals (like lead), which can find their way into human food, from lands contaminated by human activities like mining or by natural disasters like earthquakes. The roots of Mexican marigold have been analyzed to study the role of arbuscular mycorrhizal fungi in enhancement of lead uptake from the contaminated rhizosphere.

Multi trace element analysis of dry biological materials by neutron activation analysis including a chemical group separation

International Nuclear Information System (INIS)

Weers, C.A.

1980-07-01

Multi-element analysis of dry biological material by neutron activation analysis has to include radiochemical separation. The evaporation process is described in terms of the half-volume. The pretreatment of the samples and the development of the destruction-evaporation apparatus are described. The successive adsorption steps with active charcoal, Al 2 O 3 and coprecipitation with Fe(OH) 3 are described. Results obtained for standard reference materials are summarized. (G.T.H.)

A complex neutron activation method for the analysis of biological materials

International Nuclear Information System (INIS)

Ordogh, M.

1978-01-01

The aim of the present work was to deal primarily with a few essential trace elements and to obtain reliable results of adequate accuracy and precision for the analysis of biological samples. A few other than trace elements were determined by the nondestructive technique as they can be well evaluated from the gamma-spectra. In the development of the method BOWEN's kale was chosen as model material. To confirm the reliability of the method two samples were analysed proposed by the IAEA in the frame of an international comparative analysis series. The comparative analysis shows the present method to be reliable, the precision and accuracy are good. (author)

A system for the obtention and analysis of diffuse reflection spectra from biological tissue

International Nuclear Information System (INIS)

La Cadena, A. de; La Rosa, J. de; Stolik, S.

2012-01-01

The diffuse reflection spectroscopy is a technique with is possible to study biological tissue. In the field of the biomedical applications is useful for diagnostic purposes, since is possible to analyze biological tissue in a non invasive way. also, can be used with therapeutical purposes, for example in photodynamic therapy or laser surgery because with this technique it can be determined the biological effects produced by these treatments. In this paper is shown the development of a system to obtain and analyze diffuse reflection spectra of biological tissues, using a LED as a light source, that emits light between 400-700nm. The system has an interface for the regulation of the emittance of the LED. For diffuse reflectance spectra analysis, we use an HR4000CG-UV-NIR spectrometer. (Author)

Systems theoretic analysis of the central dogma of molecular biology: some recent results.

Science.gov (United States)

Gao, Rui; Yu, Juanyi; Zhang, Mingjun; Tarn, Tzyh-Jong; Li, Jr-Shin

2010-03-01

This paper extends our early study on a mathematical formulation of the central dogma of molecular biology, and focuses discussions on recent insights obtained by employing advanced systems theoretic analysis. The goal of this paper is to mathematically represent and interpret the genetic information flow at the molecular level, and explore the fundamental principle of molecular biology at the system level. Specifically, group theory was employed to interpret concepts and properties of gene mutation, and predict backbone torsion angle along the peptide chain. Finite state machine theory was extensively applied to interpret key concepts and analyze the processes related to DNA hybridization. Using the proposed model, we have transferred the character-based model in molecular biology to a sophisticated mathematical model for calculation and interpretation.

Determination of trace elements in biological material by neutron activation analysis

International Nuclear Information System (INIS)

Tran Van, L.; Teherani, D.K.

1989-01-01

Eighteen trace elements in biological materials [grass (Imperata cylindrica), mimosa plant (Mimosa pudica), rice] by neutron activation method were determined. In the comparative analysis the content of the same element was different in each material, although they were collected at the same place and the same sampling method was applied. (author) 4 refs.; 1 fig.; 1 tab

Contextual analysis of Biology and Chemistry academic graphical abstracts

Directory of Open Access Journals (Sweden)

Cristiane Salete Florek

2016-10-01

Full Text Available http://dx.doi.org/10.5007/1984-8412.2016v13n3p1363 The Graphical Abstract (GA is a non-regular discursive practice held in the academic context, and that, when occurs, coexists with the academic abstract (AA in the table of contents of scientific journals, and in HTML versions of academic articles, materializing by the combination of the verbal and visual semiotics. In this paper, in the light of the Critical Analysis genres (MEURER, 2002; BHATIA, 2004; MOTTA-ROTH, 2006, 2008, which allow us to study a text based on the investigation of its context’s critical research, we present the results of the contextual analysis of GAs in the areas of Biology and Chemistry. This analysis was done by: i interviews with researchers of the investigated areas; and ii documentary analysis. Results show that, in general, GA: i is highlighted by presenting an advertising nature, which seeks to attract the reader’s attention; ii: summarizes the topic and the main findings of scientific research; and iii does not replace the academia abstract (AA.

NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium-scale biological networks.

Science.gov (United States)

Theodosiou, Theodosios; Efstathiou, Georgios; Papanikolaou, Nikolas; Kyrpides, Nikos C; Bagos, Pantelis G; Iliopoulos, Ioannis; Pavlopoulos, Georgios A

2017-07-14

Nowadays, due to the technological advances of high-throughput techniques, Systems Biology has seen a tremendous growth of data generation. With network analysis, looking at biological systems at a higher level in order to better understand a system, its topology and the relationships between its components is of a great importance. Gene expression, signal transduction, protein/chemical interactions, biomedical literature co-occurrences, are few of the examples captured in biological network representations where nodes represent certain bioentities and edges represent the connections between them. Today, many tools for network visualization and analysis are available. Nevertheless, most of them are standalone applications that often (i) burden users with computing and calculation time depending on the network's size and (ii) focus on handling, editing and exploring a network interactively. While such functionality is of great importance, limited efforts have been made towards the comparison of the topological analysis of multiple networks. Network Analysis Provider (NAP) is a comprehensive web tool to automate network profiling and intra/inter-network topology comparison. It is designed to bridge the gap between network analysis, statistics, graph theory and partially visualization in a user-friendly way. It is freely available and aims to become a very appealing tool for the broader community. It hosts a great plethora of topological analysis methods such as node and edge rankings. Few of its powerful characteristics are: its ability to enable easy profile comparisons across multiple networks, find their intersection and provide users with simplified, high quality plots of any of the offered topological characteristics against any other within the same network. It is written in R and Shiny, it is based on the igraph library and it is able to handle medium-scale weighted/unweighted, directed/undirected and bipartite graphs. NAP is available at http://bioinformatics.med.uoc.gr/NAP .

Vitamin D and Depression: A Systematic Review and Meta-Analysis Comparing Studies with and without Biological Flaws

Directory of Open Access Journals (Sweden)

Simon Spedding

2014-04-01

Full Text Available Efficacy of Vitamin D supplements in depression is controversial, awaiting further literature analysis. Biological flaws in primary studies is a possible reason meta-analyses of Vitamin D have failed to demonstrate efficacy. This systematic review and meta-analysis of Vitamin D and depression compared studies with and without biological flaws. The systematic review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA guidelines. The literature search was undertaken through four databases for randomized controlled trials (RCTs. Studies were critically appraised for methodological quality and biological flaws, in relation to the hypothesis and study design. Meta-analyses were performed for studies according to the presence of biological flaws. The 15 RCTs identified provide a more comprehensive evidence-base than previous systematic reviews; methodological quality of studies was generally good and methodology was diverse. A meta-analysis of all studies without flaws demonstrated a statistically significant improvement in depression with Vitamin D supplements (+0.78 CI +0.24, +1.27. Studies with biological flaws were mainly inconclusive, with the meta-analysis demonstrating a statistically significant worsening in depression by taking Vitamin D supplements (−1.1 CI −0.7, −1.5. Vitamin D supplementation (≥800 I.U. daily was somewhat favorable in the management of depression in studies that demonstrate a change in vitamin levels, and the effect size was comparable to that of anti-depressant medication.

Vitamin D and Depression: A Systematic Review and Meta-Analysis Comparing Studies with and without Biological Flaws

OpenAIRE

Simon Spedding

2014-01-01

Efficacy of Vitamin D supplements in depression is controversial, awaiting further literature analysis. Biological flaws in primary studies is a possible reason meta-analyses of Vitamin D have failed to demonstrate efficacy. This systematic review and meta-analysis of Vitamin D and depression compared studies with and without biological flaws. The systematic review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The literature search was un...

A simple method of fabricating mask-free microfluidic devices for biological analysis.

KAUST Repository

Yi, Xin

2010-09-07

We report a simple, low-cost, rapid, and mask-free method to fabricate two-dimensional (2D) and three-dimensional (3D) microfluidic chip for biological analysis researches. In this fabrication process, a laser system is used to cut through paper to form intricate patterns and differently configured channels for specific purposes. Bonded with cyanoacrylate-based resin, the prepared paper sheet is sandwiched between glass slides (hydrophilic) or polymer-based plates (hydrophobic) to obtain a multilayer structure. In order to examine the chip\\'s biocompatibility and applicability, protein concentration was measured while DNA capillary electrophoresis was carried out, and both of them show positive results. With the utilization of direct laser cutting and one-step gas-sacrificing techniques, the whole fabrication processes for complicated 2D and 3D microfluidic devices are shorten into several minutes which make it a good alternative of poly(dimethylsiloxane) microfluidic chips used in biological analysis researches.

Toxicological Analysis of Some Drugs of Abuse in Biological Samples

OpenAIRE

Anne Marie Ciobanu; Daniela Baconi; Cristian Bălălău; Carolina Negrei; Miriana Stan; Maria Bârcă

2015-01-01

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 ...

Quantitative X-ray analysis of biological fluids: the microdroplet technique

International Nuclear Information System (INIS)

Roinel, N.

1988-01-01

X-ray microanalysis can be used to quantitatively determine the elemental composition of microvolumes of biological fluids. This article describes the various steps in preparation of microdroplets for analysis: The manufacturing of micropipettes, the preparation of the specimen support, the deposition of droplets on the support, shock-freezing, and lyophilization. Examples of common artifacts (incomplete rehydration prior to freezing or partial rehydration after lyophilization) are demonstrated. Analysis can be carried out either by wavelength-dispersive analysis, which is the most sensitive method, or by energy-dispersive analysis, which is more commonly available. The minimum detectable concentration is 0.05 mmol.liter-1 for 0.1-nl samples analyzed by wavelength-dispersive spectrometry and 0.5-1 mmol.liter-1 for samples analyzed by energy-dispersive spectrometry. A major problem, especially in wavelength-dispersive analysis, where high beam currents are used, is radiation damage to the specimen; in particular chloride (but also other elements) can be lost. Quantitative analysis requires the use of standard solutions with elemental concentration in the same range as those present in the specimen

Iterative Multiparameter Elastic Waveform Inversion Using Prestack Time Imaging and Kirchhoff approximation

Science.gov (United States)

Khaniani, Hassan

boundary condition of the wave equation is set up along reflection surfaces. Hence, the surface integral Kirchhoff approximation is used as a mathematical framework instead of the volume integral of the Born approximation. In addition, I study the feasibility of iterative coupling of ray theory with the Kirchhoff approximation for inversion. For the amplitude considerations, the direct relationship between the scattering potential of the Born approximation with the reflectivity function of the asymptotic Kirchhoff approximation for elastic waves is used. Therefore, I use the linearized Zoeppritz approximation of Aki and Richards (1980) for computation of the forward modeling and migration operators as well as gradient function from Amplitude vs Offset (AVO) inversion. The multiparameter elastic inversion approach is applicable to all types of reflected wavefields such as P-to-P, P-to-S, S-to-S and S-to-P. Traveltime estimation of forward modeling and migration/inversion operators are based on the DSR equation. All operators involved in inversion, including the background model for DSR and AVO are updated at each iteration. The migration/inversion procedure maps the mode converted waves to the traveltime of incident waves which fixes the registration problem of events that travel from source to scatter point. The inversion of the reflected P-to-P and P-to-S synthetic and field data are provided for the numerical examples. This approach is applicable for complex structures however, to estimate the traveltime of scatterpoints, ray tracing can be added to the algorithm. For such a medium, the scatterpoint traveltime approximations from the PSTM, is compared to the PSDM approach using numerical analysis of ray- and FDTD-based modeling. In part of this thesis, I further improve the conventional velocity analysis of Common Scatter Point (CSP) gathers by including the tilt effects. I show that travel time response of scatter points beneath a dipping interface experiences an

BiologicalNetworks 2.0 - an integrative view of genome biology data

Directory of Open Access Journals (Sweden)

Ponomarenko Julia

2010-12-01

Full Text Available Abstract Background A significant problem in the study of mechanisms of an organism's development is the elucidation of interrelated factors which are making an impact on the different levels of the organism, such as genes, biological molecules, cells, and cell systems. Numerous sources of heterogeneous data which exist for these subsystems are still not integrated sufficiently enough to give researchers a straightforward opportunity to analyze them together in the same frame of study. Systematic application of data integration methods is also hampered by a multitude of such factors as the orthogonal nature of the integrated data and naming problems. Results Here we report on a new version of BiologicalNetworks, a research environment for the integral visualization and analysis of heterogeneous biological data. BiologicalNetworks can be queried for properties of thousands of different types of biological entities (genes/proteins, promoters, COGs, pathways, binding sites, and other and their relations (interactions, co-expression, co-citations, and other. The system includes the build-pathways infrastructure for molecular interactions/relations and module discovery in high-throughput experiments. Also implemented in BiologicalNetworks are the Integrated Genome Viewer and Comparative Genomics Browser applications, which allow for the search and analysis of gene regulatory regions and their conservation in multiple species in conjunction with molecular pathways/networks, experimental data and functional annotations. Conclusions The new release of BiologicalNetworks together with its back-end database introduces extensive functionality for a more efficient integrated multi-level analysis of microarray, sequence, regulatory, and other data. BiologicalNetworks is freely available at http://www.biologicalnetworks.org.

Sample preparation for liquid chromatographic analysis of phytochemicals in biological fluids.

Science.gov (United States)

Oh, Ju-Hee; Lee, Young-Joo

2014-01-01

Natural products have been used traditionally for the treatment and prevention of diseases for thousands of years and are nowadays consumed as dietary supplements and herbal medicine. To ensure the safe and effective use of these herbal products, information about bioavailability of active compounds in plasma or target tissues should be provided via validated analytical methods combined with appropriate sampling methods. To provide comprehensive and abridged information about sample preparation methods for the quantification of phytochemicals in biological samples using liquid chromatography analysis. Sample pre-treatment procedures used in analytical methods for in vivo pharmacokinetic studies of natural compounds or herbal medicines were reviewed. These were categorised according to the biological matrices (plasma, bile, urine, faeces and tissues) and sample clean-up processes (protein precipitation, liquid-liquid extraction and solid-phase extraction). Although various kinds of sample pre-treatment methods have been developed, liquid-liquid extraction is still widely used and solid-phase extraction is becoming increasingly popular because of its efficiency for extensive clean up of complex matrix samples. However, protein precipitation is still favoured due to its simplicity. Sample treatment for phytochemical analysis in biological fluids is an indispensable and critical step to obtain high quality results. This step could dominate the overall analytical process because both the duration of the process as well as the reliability of the data depend in large part on its efficiency. Thus, special attention should be given to the choice of a proper sample treatment method that targets analytes and their biomatrix. Copyright © 2013 John Wiley & Sons, Ltd.

Dynamic Analysis of a Phytoplankton-Fish Model with Biological and Artificial Control

OpenAIRE

Wang, Yapei; Zhao, Min; Pan, Xinhong; Dai, Chuanjun

2014-01-01

We investigate a nonlinear model of the interaction between phytoplankton and fish, which uses a pair of semicontinuous systems with biological and artificial control. First, the existence of an order-1 periodic solution to the system is analyzed using a Poincaré map and a geometric method. The stability conditions of the order-1 periodic solution are obtained by a theoretical mathematical analysis. Furthermore, based on previous analysis, we investigate the bifurcation in the order-1 periodi...

Analysis of the Threat of Genetically Modified Organisms for Biological Warfare

Science.gov (United States)

2011-05-01

biological warfare. The primary focus of the framework are those aspects of the technology directly affecting humans by inducing virulent infectious disease...applications. Simple organisms such as fruit flies have been used to study the effects of genetic changes across generations. Transgenic mice are...Analysis * Multi-cell pathogens * Toxins (Chemical products of living cells.) * Fungi (Robust organism; no genetic manipulation needed

Nonlinear multi-analysis of agent-based financial market dynamics by epidemic system

Science.gov (United States)

Lu, Yunfan; Wang, Jun; Niu, Hongli

2015-10-01

Based on the epidemic dynamical system, we construct a new agent-based financial time series model. In order to check and testify its rationality, we compare the statistical properties of the time series model with the real stock market indices, Shanghai Stock Exchange Composite Index and Shenzhen Stock Exchange Component Index. For analyzing the statistical properties, we combine the multi-parameter analysis with the tail distribution analysis, the modified rescaled range analysis, and the multifractal detrended fluctuation analysis. For a better perspective, the three-dimensional diagrams are used to present the analysis results. The empirical research in this paper indicates that the long-range dependence property and the multifractal phenomenon exist in the real returns and the proposed model. Therefore, the new agent-based financial model can recurrence some important features of real stock markets.

Derivatization reactions in the gas—liquid chromatographic analysis of drugs in biological fluids

NARCIS (Netherlands)

Hulshoff, A.; Lingeman, H.

1984-01-01

Alkylation, acylation, silylation and other derivatization reactions applied to the gas chromatographic analysis of drugs in biological matrices are reviewed. Reaction conditions are discussed in relation to reaction mechanisms. Detector-oriented labelling of drugs, and derivatization with chiral

Synthetic Biology: Putting Synthesis into Biology

Science.gov (United States)

Liang, Jing; Luo, Yunzi; Zhao, Huimin

2010-01-01

The ability to manipulate living organisms is at the heart of a range of emerging technologies that serve to address important and current problems in environment, energy, and health. However, with all its complexity and interconnectivity, biology has for many years been recalcitrant to engineering manipulations. The recent advances in synthesis, analysis, and modeling methods have finally provided the tools necessary to manipulate living systems in meaningful ways, and have led to the coining of a field named synthetic biology. The scope of synthetic biology is as complicated as life itself – encompassing many branches of science, and across many scales of application. New DNA synthesis and assembly techniques have made routine the customization of very large DNA molecules. This in turn has allowed the incorporation of multiple genes and pathways. By coupling these with techniques that allow for the modeling and design of protein functions, scientists have now gained the tools to create completely novel biological machineries. Even the ultimate biological machinery – a self-replicating organism – is being pursued at this moment. It is the purpose of this review to dissect and organize these various components of synthetic biology into a coherent picture. PMID:21064036

Potential of the PIGE method in the analysis of biological and mineral materials

International Nuclear Information System (INIS)

Havranek, V.

2006-01-01

A possible application of the PIGE method for the analysis of the biological and mineral samples has been tested using a 3.5 MeV Van de Graaff accelerator. The limits of detection of 4 mg/kg for fluorine, 10 mg/kg for aluminium and 200 mg/kg for phosphorus were achieved with a 3.15 MeV proton beam (8 mm in diameter, 20 nA current and 1000 s irradiation time). The PIGE method was found to be a suitable method for the determination of fluorine in the samples analyzed. With this technique, total fluorine in the sample can be quantitated without any chemical treatment. In the analysis of the phosphorus in thick biological samples, PIGE can compete with PIXE and is probably less sensitive to matrix effects and spectra fitting, which may bring about a higher accuracy of the results

Identifying novel glioma associated pathways based on systems biology level meta-analysis.

Science.gov (United States)

Hu, Yangfan; Li, Jinquan; Yan, Wenying; Chen, Jiajia; Li, Yin; Hu, Guang; Shen, Bairong

2013-01-01

With recent advances in microarray technology, including genomics, proteomics, and metabolomics, it brings a great challenge for integrating this "-omics" data to analysis complex disease. Glioma is an extremely aggressive and lethal form of brain tumor, and thus the study of the molecule mechanism underlying glioma remains very important. To date, most studies focus on detecting the differentially expressed genes in glioma. However, the meta-analysis for pathway analysis based on multiple microarray datasets has not been systematically pursued. In this study, we therefore developed a systems biology based approach by integrating three types of omics data to identify common pathways in glioma. Firstly, the meta-analysis has been performed to study the overlapping of signatures at different levels based on the microarray gene expression data of glioma. Among these gene expression datasets, 12 pathways were found in GeneGO database that shared by four stages. Then, microRNA expression profiles and ChIP-seq data were integrated for the further pathway enrichment analysis. As a result, we suggest 5 of these pathways could be served as putative pathways in glioma. Among them, the pathway of TGF-beta-dependent induction of EMT via SMAD is of particular importance. Our results demonstrate that the meta-analysis based on systems biology level provide a more useful approach to study the molecule mechanism of complex disease. The integration of different types of omics data, including gene expression microarrays, microRNA and ChIP-seq data, suggest some common pathways correlated with glioma. These findings will offer useful potential candidates for targeted therapeutic intervention of glioma.

Multiparameter double hole contrast detail phantom: Ability to detect image displacement due to off position anode stem

International Nuclear Information System (INIS)

Pauzi, Nur Farahana; Majid, Zafri Azran Abdul; Sapuan, Abdul Halim; Junet, Laila Kalidah; Azemin, Mohd Zulfaezal Che

2015-01-01

Contrast Detail phantom is a quality control tool to analyze the performance of imaging devices. Currently, its function is solely to evaluate the contrast detail characteristic of imaging system. It consists of drilled hole which gives effect to the penetration of x-ray beam divergence to pass through the base of each hole. This effect will lead to false appearance of image from its original location but it does not being visualized in the radiograph. In this study, a new design of Contrast Detail phantom’s hole which consists of double hole construction has been developed. It can detect the image displacement which is due to off position of anode stem from its original location. The double hole differs from previous milled hole, whereby it consists of combination of different hole diameters. Small hole diameter (3 mm) is positioned on top of larger hole diameter (10 mm). The thickness of double hole acrylic blocks is 13 mm. Result revealed that Multiparameter Double Hole Contrast Detail phantom can visualize the shifted flaw image quality produced by x-ray machine due to improper position of the anode stem which is attached to rotor and stator. The effective focal spot of x-ray beam also has been shifted from the center of collimator as a result of off-position anode stem. As a conclusion, the new design of double hole Contrast Detail phantom able to measure those parameters in a well manner

Multiparameter double hole contrast detail phantom: Ability to detect image displacement due to off position anode stem

Energy Technology Data Exchange (ETDEWEB)

Pauzi, Nur Farahana; Majid, Zafri Azran Abdul; Sapuan, Abdul Halim; Junet, Laila Kalidah [Department of Diagnostic Imaging and Radiotherapy, Kulliyyah of Allied Health Sciences, International Islamic University Malaysia, Jalan Istana, 25200, Kuantan, Pahang (Malaysia); Azemin, Mohd Zulfaezal Che [Department of Optometry and Visual Science, Kulliyyah of Allied Health Sciences, International Islamic University Malaysia, Jalan Istana, 25200, Kuantan, Pahang (Malaysia)

2015-04-24

Contrast Detail phantom is a quality control tool to analyze the performance of imaging devices. Currently, its function is solely to evaluate the contrast detail characteristic of imaging system. It consists of drilled hole which gives effect to the penetration of x-ray beam divergence to pass through the base of each hole. This effect will lead to false appearance of image from its original location but it does not being visualized in the radiograph. In this study, a new design of Contrast Detail phantom’s hole which consists of double hole construction has been developed. It can detect the image displacement which is due to off position of anode stem from its original location. The double hole differs from previous milled hole, whereby it consists of combination of different hole diameters. Small hole diameter (3 mm) is positioned on top of larger hole diameter (10 mm). The thickness of double hole acrylic blocks is 13 mm. Result revealed that Multiparameter Double Hole Contrast Detail phantom can visualize the shifted flaw image quality produced by x-ray machine due to improper position of the anode stem which is attached to rotor and stator. The effective focal spot of x-ray beam also has been shifted from the center of collimator as a result of off-position anode stem. As a conclusion, the new design of double hole Contrast Detail phantom able to measure those parameters in a well manner.

Mathematical biology

CERN Document Server

Murray, James D

1993-01-01

The book is a textbook (with many exercises) giving an in-depth account of the practical use of mathematical modelling in the biomedical sciences. The mathematical level required is generally not high and the emphasis is on what is required to solve the real biological problem. The subject matter is drawn, e.g. from population biology, reaction kinetics, biological oscillators and switches, Belousov-Zhabotinskii reaction, reaction-diffusion theory, biological wave phenomena, central pattern generators, neural models, spread of epidemics, mechanochemical theory of biological pattern formation and importance in evolution. Most of the models are based on real biological problems and the predictions and explanations offered as a direct result of mathematical analysis of the models are important aspects of the book. The aim is to provide a thorough training in practical mathematical biology and to show how exciting and novel mathematical challenges arise from a genuine interdisciplinary involvement with the biosci...

DATE analysis: A general theory of biological change applied to microarray data.

Science.gov (United States)

Rasnick, David

2009-01-01

In contrast to conventional data mining, which searches for specific subsets of genes (extensive variables) to correlate with specific phenotypes, DATE analysis correlates intensive state variables calculated from the same datasets. At the heart of DATE analysis are two biological equations of state not dependent on genetic pathways. This result distinguishes DATE analysis from other bioinformatics approaches. The dimensionless state variable F quantifies the relative overall cellular activity of test cells compared to well-chosen reference cells. The variable pi(i) is the fold-change in the expression of the ith gene of test cells relative to reference. It is the fraction phi of the genome undergoing differential expression-not the magnitude pi-that controls biological change. The state variable phi is equivalent to the control strength of metabolic control analysis. For tractability, DATE analysis assumes a linear system of enzyme-connected networks and exploits the small average contribution of each cellular component. This approach was validated by reproducible values of the state variables F, RNA index, and phi calculated from random subsets of transcript microarray data. Using published microarray data, F, RNA index, and phi were correlated with: (1) the blood-feeding cycle of the malaria parasite, (2) embryonic development of the fruit fly, (3) temperature adaptation of Killifish, (4) exponential growth of cultured S. pneumoniae, and (5) human cancers. DATE analysis was applied to aCGH data from the great apes. A good example of the power of DATE analysis is its application to genomically unstable cancers, which have been refractory to data mining strategies. 2009 American Institute of Chemical Engineers Biotechnol.

Integrating Biological Perspectives:. a Quantum Leap for Microarray Expression Analysis

Science.gov (United States)

Wanke, Dierk; Kilian, Joachim; Bloss, Ulrich; Mangelsen, Elke; Supper, Jochen; Harter, Klaus; Berendzen, Kenneth W.

2009-02-01

Biologists and bioinformatic scientists cope with the analysis of transcript abundance and the extraction of meaningful information from microarray expression data. By exploiting biological information accessible in public databases, we try to extend our current knowledge over the plant model organism Arabidopsis thaliana. Here, we give two examples of increasing the quality of information gained from large scale expression experiments by the integration of microarray-unrelated biological information: First, we utilize Arabidopsis microarray data to demonstrate that expression profiles are usually conserved between orthologous genes of different organisms. In an initial step of the analysis, orthology has to be inferred unambiguously, which then allows comparison of expression profiles between orthologs. We make use of the publicly available microarray expression data of Arabidopsis and barley, Hordeum vulgare. We found a generally positive correlation in expression trajectories between true orthologs although both organisms are only distantly related in evolutionary time scale. Second, extracting clusters of co-regulated genes implies similarities in transcriptional regulation via similar cis-regulatory elements (CREs). Vice versa approaches, where co-regulated gene clusters are found by investigating on CREs were not successful in general. Nonetheless, in some cases the presence of CREs in a defined position, orientation or CRE-combinations is positively correlated with co-regulated gene clusters. Here, we make use of genes involved in the phenylpropanoid biosynthetic pathway, to give one positive example for this approach.

Using multi-criteria analysis of simulation models to understand complex biological systems

Science.gov (United States)

Maureen C. Kennedy; E. David. Ford

2011-01-01

Scientists frequently use computer-simulation models to help solve complex biological problems. Typically, such models are highly integrated, they produce multiple outputs, and standard methods of model analysis are ill suited for evaluating them. We show how multi-criteria optimization with Pareto optimality allows for model outputs to be compared to multiple system...

Implementing an Executive-Function Syllabus: Operational Issues

Directory of Open Access Journals (Sweden)

Russell Jay Hendel

2016-08-01

Full Text Available A recent approach to pedagogic challenge, contrastive to the hierarchy approach of Bloom, Anderson, Gagne, Van Hiele, Marzano, Webb and many others, identifies pedagogic challenge with executive function: Pedagogy is defined as challenging if it addresses executive function. Executive function, in turn, is defined by the presence of multiple modalities of topic approach and a multi-parameter development of the topic. This paper discusses operational issues in implementing a teaching methodology based on multi-parameter problems. This paper advocates teaching a multi-parameter topic using a step-by-step incremental approach, introducing one parameter at a time. Examples are presented from trigonometry, actuarial mathematics, statistics and (biblical literary analysis. The paper also discusses the use of the incremental approach for problem creation and remediation.

Analysis of occupational accidents with biological material among professionals in pre-hospital services

OpenAIRE

Oliveira,Adriana Cristina de; Paiva,Maria Henriqueta Rocha Siqueira

2013-01-01

OBJECTIVE: To estimate the prevalence of accidents due to biological material exposure, the characteristics and post-accident conduct among professionals of pre-hospital services of the four municipalities of Minas Gerais, Brazil. METHOD: A cross-sectional study, using a structured questionnaire that was developed to enable the calculation of prevalence, descriptive analysis and analytical analysis using logistic regression. The study included 228 professionals; the prevalence of accidents du...

Development of silicon photonic microring resonator biosensors for multiplexed cytokine assays and in vitro diagnostics

Science.gov (United States)

Luchansky, Matthew Sam

In order to guide critical care therapies that are personalized to a patient's unique disease state, a diagnostic or theranostic medical device must quickly provide a detailed biomolecular understanding of disease onset and progression. This detailed molecular understanding of cellular processes and pathways requires the ability to measure multiple analytes in parallel. Though many traditional sensing technologies for biomarker analysis and fundamental biological studies (i.e. enzyme-linked immunosorbent assays, real-time polymerase chain reaction, etc.) rely on single-parameter measurements, it has become increasingly clear that the inherent complexity of many human illnesses and pathways necessitates quantitative and multiparameter analysis of biological samples. Currently used analytical methods are deficient in that they often provide either highly quantitative data for a single biomarker or qualitative data for many targets, but methods that simultaneously provide highly quantitative analysis of many targets have yet to be adequately developed. Fields such as medical diagnostics and cellular biology would benefit greatly from a technology that enables rapid, quantitative and reproducible assays for many targets within a single sample. In an effort to fill this unmet need, this doctoral dissertation describes the development of a clinically translational biosensing technology based on silicon photonics and developed in the chemistry research laboratory of Ryan C. Bailey. Silicon photonic microring resonators, a class of high-Q optical sensors, represent a promising platform for rapid, multiparameter in vitro measurements. The original device design utilizes 32-ring arrays for real-time biomolecular sensing without fluorescent labels, and these optical biosensors display great potential for more highly multiplexed (100s-1000s) measurements based on the impressive scalability of silicon device fabrication. Though this technology can be used to detect a variety of

PeTTSy: a computational tool for perturbation analysis of complex systems biology models.

Science.gov (United States)

Domijan, Mirela; Brown, Paul E; Shulgin, Boris V; Rand, David A

2016-03-10

Over the last decade sensitivity analysis techniques have been shown to be very useful to analyse complex and high dimensional Systems Biology models. However, many of the currently available toolboxes have either used parameter sampling, been focused on a restricted set of model observables of interest, studied optimisation of a objective function, or have not dealt with multiple simultaneous model parameter changes where the changes can be permanent or temporary. Here we introduce our new, freely downloadable toolbox, PeTTSy (Perturbation Theory Toolbox for Systems). PeTTSy is a package for MATLAB which implements a wide array of techniques for the perturbation theory and sensitivity analysis of large and complex ordinary differential equation (ODE) based models. PeTTSy is a comprehensive modelling framework that introduces a number of new approaches and that fully addresses analysis of oscillatory systems. It examines sensitivity analysis of the models to perturbations of parameters, where the perturbation timing, strength, length and overall shape can be controlled by the user. This can be done in a system-global setting, namely, the user can determine how many parameters to perturb, by how much and for how long. PeTTSy also offers the user the ability to explore the effect of the parameter perturbations on many different types of outputs: period, phase (timing of peak) and model solutions. PeTTSy can be employed on a wide range of mathematical models including free-running and forced oscillators and signalling systems. To enable experimental optimisation using the Fisher Information Matrix it efficiently allows one to combine multiple variants of a model (i.e. a model with multiple experimental conditions) in order to determine the value of new experiments. It is especially useful in the analysis of large and complex models involving many variables and parameters. PeTTSy is a comprehensive tool for analysing large and complex models of regulatory and

Elemental analysis of biological tissues of animal models in muscular dystrophies investigation

International Nuclear Information System (INIS)

Sabrina Metairon; Zamboni, C.B.; Suzuki, M.F.; Bueno, Jr.C.R.; Sant'Anna, O.A.

2012-01-01

Element concentrations in biological tissues of Dmd mdx /J and C57BL/6 J mice strains were determined using the neutron activation analysis technique. Samples of whole blood, bones and organs (heart and muscle) of these strains were irradiated in the IEA-R1 nuclear reactor at IPEN-CNEN/SP (Brazil). To perform this investigation biological samples of two-month-old adult females (n = 10) and males (n = 9) for Dmd mdx /J (dystrophic mice), and males (n 12) for C57BL/6 J (control group), originally obtained from the Jackson Laboratory (Maine, USA) and further inbred at IPEN-CNEN/SP (Sao Paulo, Brazil), were used. A significant change was observed in the analysis of the heart of dystrophic mice suggesting that this dysfunction affects severely the heart muscle. These data may, in the future, contribute to the healthcare area, in veterinary medicine and in the pharmaceutical industry allowing the evaluation of the best procedures in diagnosis, treatment and investigations of neuromuscular diseases (muscular dystrophy) of patients through the use of animal models. (author)

Analysis of working conditions focusing on biological risk: firefighters in Campo Grande, MS, Brazil.

Science.gov (United States)

Contrera-Moreno, Luciana; de Andrade, Sonia Maria Oliveira; Motta-Castro, Ana Rita Coimbra; Pinto, Alexandra Maria Almeida Carvalho; Salas, Frederico Reis Pouso; Stief, Alcione Cavalheiros Faro

2012-01-01

Firefighters are exposed to a wide range of risks, among them, biological risk. The objective was to analyze working conditions of firefighters in the city of Campo Grande, MS, Brazil, focusing on risk conditions of exposure to biological material. Three hundred and seven (307) firefighters were interviewed for data collection and observed for ergonomic job analysis (AET). 63.5% of the firefighters suffered some kind of job related accident with blood or body fluids. Statistically significant association was found between having suffered accidents at work and incomplete use of personal protective equipment (PPE). About AET regarding the biological risks, 57.1% of all patients had blood or secretions, which corresponds in average to 16.0% of the total work time, based on a working day of 24 h. Besides biological risks, other stressing factors were identified: emergency and complexity of decision, high responsibility regarding patients and environment, and conflicts. Health promotion and accident prevention actions must be emphasized as measures to minimize these risks.

Symposium on single cell analysis and genomic approaches, Experimental Biology 2017 Chicago, Illinois, April 23, 2017.

Science.gov (United States)

Coller, Hilary A

2017-09-01

Emerging technologies for the analysis of genome-wide information in single cells have the potential to transform many fields of biology, including our understanding of cell states, the response of cells to external stimuli, mosaicism, and intratumor heterogeneity. At Experimental Biology 2017 in Chicago, Physiological Genomics hosted a symposium in which five leaders in the field of single cell genomics presented their recent research. The speakers discussed emerging methodologies in single cell analysis and critical issues for the analysis of single cell data. Also discussed were applications of single cell genomics to understanding the different types of cells within an organism or tissue and the basis for cell-to-cell variability in response to stimuli. Copyright © 2017 the American Physiological Society.

SYSTEMATIC ANALYSIS OF PERSPECTIVE TRENDS IN ECOLOGICAL AND BIOLOGICAL STUDIES OF THE CASPIAN SEA

Directory of Open Access Journals (Sweden)

G. M. Abdurakhmanov

2016-01-01

Full Text Available RETRACTED ARTICLEAim. The main purpose of the ecological and biological research (EBR of the Caspian Sea is the information and technical support of decision-making to ensure the environmental management in the region taking into account the increase of anthropogenic impact and change in climatic conditions.Methods. As a basis, we have adopted the method of theoretical and mathematical generalization of a number of scientific papers and systematic analysis of the proposed solutions.Results. Analysis and mathematical processing of published literature sources has convincingly demonstrated the need for international cooperation to optimize the ecological and biological research. It has also confirmed the usefulness of the ecological and biological studies of the Caspian Sea in different directions, and the distribution of effort (cost between them requires coordinated management.Conclusion. It is shown that the data obtained by EBI have both rapid and long-term value. In the future, it is rational to develop suitable approaches to unified structuring of the EBR data, including their spatial and timing. An important task is to create a single interstate information space on the results of EBR using information and communication technologies.

Integrative biological analysis for neuropsychopharmacology.

Science.gov (United States)

Emmett, Mark R; Kroes, Roger A; Moskal, Joseph R; Conrad, Charles A; Priebe, Waldemar; Laezza, Fernanda; Meyer-Baese, Anke; Nilsson, Carol L

2014-01-01

Although advances in psychotherapy have been made in recent years, drug discovery for brain diseases such as schizophrenia and mood disorders has stagnated. The need for new biomarkers and validated therapeutic targets in the field of neuropsychopharmacology is widely unmet. The brain is the most complex part of human anatomy from the standpoint of number and types of cells, their interconnections, and circuitry. To better meet patient needs, improved methods to approach brain studies by understanding functional networks that interact with the genome are being developed. The integrated biological approaches--proteomics, transcriptomics, metabolomics, and glycomics--have a strong record in several areas of biomedicine, including neurochemistry and neuro-oncology. Published applications of an integrated approach to projects of neurological, psychiatric, and pharmacological natures are still few but show promise to provide deep biological knowledge derived from cells, animal models, and clinical materials. Future studies that yield insights based on integrated analyses promise to deliver new therapeutic targets and biomarkers for personalized medicine.

Zone analysis in biology articles as a basis for information extraction.

Science.gov (United States)

Mizuta, Yoko; Korhonen, Anna; Mullen, Tony; Collier, Nigel

2006-06-01

In the field of biomedicine, an overwhelming amount of experimental data has become available as a result of the high throughput of research in this domain. The amount of results reported has now grown beyond the limits of what can be managed by manual means. This makes it increasingly difficult for the researchers in this area to keep up with the latest developments. Information extraction (IE) in the biological domain aims to provide an effective automatic means to dynamically manage the information contained in archived journal articles and abstract collections and thus help researchers in their work. However, while considerable advances have been made in certain areas of IE, pinpointing and organizing factual information (such as experimental results) remains a challenge. In this paper we propose tackling this task by incorporating into IE information about rhetorical zones, i.e. classification of spans of text in terms of argumentation and intellectual attribution. As the first step towards this goal, we introduce a scheme for annotating biological texts for rhetorical zones and provide a qualitative and quantitative analysis of the data annotated according to this scheme. We also discuss our preliminary research on automatic zone analysis, and its incorporation into our IE framework.

An attempt to understand glioma stem cell biology through centrality analysis of a protein interaction network.

Science.gov (United States)

Mallik, Mrinmay Kumar

2018-02-07

Biological networks can be analyzed using "Centrality Analysis" to identify the more influential nodes and interactions in the network. This study was undertaken to create and visualize a biological network comprising of protein-protein interactions (PPIs) amongst proteins which are preferentially over-expressed in glioma cancer stem cell component (GCSC) of glioblastomas as compared to the glioma non-stem cancer cell (GNSC) component and then to analyze this network through centrality analyses (CA) in order to identify the essential proteins in this network and their interactions. In addition, this study proposes a new centrality analysis method pertaining exclusively to transcription factors (TFs) and interactions amongst them. Moreover the relevant molecular functions, biological processes and biochemical pathways amongst these proteins were sought through enrichment analysis. A protein interaction network was created using a list of proteins which have been shown to be preferentially expressed or over-expressed in GCSCs isolated from glioblastomas as compared to the GNSCs. This list comprising of 38 proteins, created using manual literature mining, was submitted to the Reactome FIViz tool, a web based application integrated into Cytoscape, an open source software platform for visualizing and analyzing molecular interaction networks and biological pathways to produce the network. This network was subjected to centrality analyses utilizing ranked lists of six centrality measures using the FIViz application and (for the first time) a dedicated centrality analysis plug-in ; CytoNCA. The interactions exclusively amongst the transcription factors were nalyzed through a newly proposed centrality analysis method called "Gene Expression Associated Degree Centrality Analysis (GEADCA)". Enrichment analysis was performed using the "network function analysis" tool on Reactome. The CA was able to identify a small set of proteins with consistently high centrality ranks that

Applied research and development of neutron activation analysis - The study on human health and environment by neutron activation analysis of biological samples

Energy Technology Data Exchange (ETDEWEB)

Cho, Seung Yeon; Yoo, Jong Ik; Lee, Jae Kwang; Lee, Sung Jun; Lee, Sang Sun; Jeon, Ki Hong; Na, Kyung Won; Kang, Sang Hun [Yonsei University, Seoul (Korea)

2000-04-01

With the development of the precise quantitative analytical method for the analysis of trace elements in the various biological samples such as hair and food, evaluation in view of health and environment to the trace elements in various sources which can be introduced inside human body was done. The trace elemental distribution in Korean total diet and representative food stuff was identified first. With the project the elemental distributions in supplemental healthy food and Korean and Chinese origin oriental medicine were identified. The amount of trace elements ingested with the hair analysis of oriental medicine takers were also estimated. The amounts of trace elements inhaled with the analysis of foundry air, blood and hair of foundry workers were also estimated. The basic estimation method in view of health and environment with the neutron activation analysis of biological samples such as foods and hair was established with the result. Nationwide usage system of the NAA facility in Hanaro in many different and important areas of biological area can be initiated with the results. The output of the project can support public heath, environment, and medical research area. The results can be applied for the process of micronutrients enhanced health food production and for the health safety and health status enhancement with the additional necessary data expansion and the development of various evaluation technique. 19 refs., 7 figs., 23 tabs. (Author)

Is economics becoming the Mecca of Biology?: A citation analysis of the relationship between natural and social sciences

OpenAIRE

Yalcintas, Altug

2012-01-01

This essay argues that articles in economics, especially in the fields of evolutionary and institutional economics, are as much cited in biology as in economics. The citation analysis conducted in the essay suggests that economics is now becoming the Mecca of biology.

Microfluidic Technologies for Synthetic Biology

Directory of Open Access Journals (Sweden)

Sung Kuk Lee

2011-06-01

Full Text Available Microfluidic technologies have shown powerful abilities for reducing cost, time, and labor, and at the same time, for increasing accuracy, throughput, and performance in the analysis of biological and biochemical samples compared with the conventional, macroscale instruments. Synthetic biology is an emerging field of biology and has drawn much attraction due to its potential to create novel, functional biological parts and systems for special purposes. Since it is believed that the development of synthetic biology can be accelerated through the use of microfluidic technology, in this review work we focus our discussion on the latest microfluidic technologies that can provide unprecedented means in synthetic biology for dynamic profiling of gene expression/regulation with high resolution, highly sensitive on-chip and off-chip detection of metabolites, and whole-cell analysis.

Organ-on-a-Chip: New Platform for Biological Analysis

Directory of Open Access Journals (Sweden)

Fan An

2015-01-01

Full Text Available Direct detection and analysis of biomolecules and cells in physiological microenvironment is urgently needed for fast evaluation of biology and pharmacy. The past several years have witnessed remarkable development opportunities in vitro organs and tissues models with multiple functions based on microfluidic devices, termed as “organ-on-a-chip”. Briefly speaking, it is a promising technology in rebuilding physiological functions of tissues and organs, featuring mammalian cell co-culture and artificial microenvironment created by microchannel networks. In this review, we summarized the advances in studies of heart-, vessel-, liver-, neuron-, kidney- and Multi-organs-on-a-chip, and discussed some noteworthy potential on-chip detection schemes.

Application of photonuclear methods of analysis in biology, medicine, ecological studies

International Nuclear Information System (INIS)

Burmistenko, Yu.N.

1986-01-01

Examples of application of photonuclear methods of analysis (PhMA) of the substance composition in biology, medicine, ecology are considered. The methods for determining the element composition of soft and bone tissues, blood, urine are developed. The results of studying the limits of determination of different elements are presented. In ecological investigations PhMA is applied for studying the composition of atmospheric aerosols, industrial sewage, canalization wastes, pollution of soil, plants, animals with toxic elements

Feasibility analysis of marine ecological on-line integrated monitoring system

Science.gov (United States)

Chu, D. Z.; Cao, X.; Zhang, S. W.; Wu, N.; Ma, R.; Zhang, L.; Cao, L.

2017-08-01

The in-situ water quality sensors were susceptible to biological attachment. Moreover, sea water corrosion and wave impact damage, and many sensors scattered distribution would cause maintenance inconvenience. The paper proposed a highly integrated marine ecological on-line integrated monitoring system, which can be used inside monitoring station. All sensors were reasonably classified, the similar in series, the overall in parallel. The system composition and workflow were described. In addition, the paper proposed attention issues of the system design and corresponding solutions. Water quality multi-parameters and 5 nutrient salts as the verification index, in-situ and systematic data comparison experiment were carried out. The results showed that the data consistency of nutrient salt, PH and salinity was better. Temperature and dissolved oxygen data trend was consistent, but the data had deviation. Turbidity fluctuated greatly; the chlorophyll trend was similar with it. Aiming at the above phenomena, three points system optimization direction were proposed.

Computer Simulation and Data Analysis in Molecular Biology and Biophysics An Introduction Using R

CERN Document Server

Bloomfield, Victor

2009-01-01

This book provides an introduction, suitable for advanced undergraduates and beginning graduate students, to two important aspects of molecular biology and biophysics: computer simulation and data analysis. It introduces tools to enable readers to learn and use fundamental methods for constructing quantitative models of biological mechanisms, both deterministic and with some elements of randomness, including complex reaction equilibria and kinetics, population models, and regulation of metabolism and development; to understand how concepts of probability can help in explaining important features of DNA sequences; and to apply a useful set of statistical methods to analysis of experimental data from spectroscopic, genomic, and proteomic sources. These quantitative tools are implemented using the free, open source software program R. R provides an excellent environment for general numerical and statistical computing and graphics, with capabilities similar to Matlab®. Since R is increasingly used in bioinformat...

Visual analysis of transcriptome data in the context of anatomical structures and biological networks

Directory of Open Access Journals (Sweden)

Astrid eJunker

2012-11-01

Full Text Available The complexity and temporal as well as spatial resolution of transcriptome datasets is constantly increasing due to extensive technological developments. Here we present methods for advanced visualization and intuitive exploration of transcriptomics data as necessary prerequisites in order to facilitate the gain of biological knowledge. Color-coding of structural images based on the expression level enables a fast visual data analysis in the background of the examined biological system. The network-based exploration of these visualizations allows for comparative analysis of genes with specific transcript patterns and supports the extraction of functional relationships even from large datasets. In order to illustrate the presented methods, the tool HIVE was applied for visualization and exploration of database-retrieved expression data for master regulators of Arabidopsis thaliana flower and seed development in the context of corresponding tissue-specific regulatory networks.

Headspace solid-phase microextraction procedures for gas chromatographic analysis of biological fluids and materials.

Science.gov (United States)

Mills, G A; Walker, V

2000-12-01

Solid-phase microextraction (SPME) is a new solventless sample preparation technique that is finding wide usage. This review provides updated information on headspace SPME with gas chromatographic separation for the extraction and measurement of volatile and semivolatile analytes in biological fluids and materials. Firstly the background to the technique is given in terms of apparatus, fibres used, extraction conditions and derivatisation procedures. Then the different matrices, urine, blood, faeces, breast milk, hair, breath and saliva are considered separately. For each, methods appropriate for the analysis of drugs and metabolites, solvents and chemicals, anaesthetics, pesticides, organometallics and endogenous compounds are reviewed and the main experimental conditions outlined with specific examples. Then finally, the future potential of SPME for the analysis of biological samples in terms of the development of new devices and fibre chemistries and its coupling with high-performance liquid chromatography is discussed.

Positioning genomics in biology education: content mapping of undergraduate biology textbooks.

Science.gov (United States)

Wernick, Naomi L B; Ndung'u, Eric; Haughton, Dominique; Ledley, Fred D

2014-12-01

Biological thought increasingly recognizes the centrality of the genome in constituting and regulating processes ranging from cellular systems to ecology and evolution. In this paper, we ask whether genomics is similarly positioned as a core concept in the instructional sequence for undergraduate biology. Using quantitative methods, we analyzed the order in which core biological concepts were introduced in textbooks for first-year general and human biology. Statistical analysis was performed using self-organizing map algorithms and conventional methods to identify clusters of terms and their relative position in the books. General biology textbooks for both majors and nonmajors introduced genome-related content after text related to cell biology and biological chemistry, but before content describing higher-order biological processes. However, human biology textbooks most often introduced genomic content near the end of the books. These results suggest that genomics is not yet positioned as a core concept in commonly used textbooks for first-year biology and raises questions about whether such textbooks, or courses based on the outline of these textbooks, provide an appropriate foundation for understanding contemporary biological science.

Prompt gamma cold neutron activation analysis applied to biological materials

International Nuclear Information System (INIS)

Rossbach, M.; Hiep, N.T.

1992-01-01

Cold neutrons at the external neutron guide laboratory (ELLA) of the KFA Juelich are used to demonstrate their profitable application for multielement characterization of biological materials. The set-up and experimental conditions of the Prompt Gamma Cold Neutron Activation Analysis (PGCNAA) device is described in detail. Results for C, H, N, S, K, B, and Cd using synthetic standards and the 'ratio' technique for calculation are reported for several reference materials and prove the method to be reliable and complementary with respect to the elements being determined by INAA. (orig.)

Fostering synergy between cell biology and systems biology.

Science.gov (United States)

Eddy, James A; Funk, Cory C; Price, Nathan D

2015-08-01

In the shared pursuit of elucidating detailed mechanisms of cell function, systems biology presents a natural complement to ongoing efforts in cell biology. Systems biology aims to characterize biological systems through integrated and quantitative modeling of cellular information. The process of model building and analysis provides value through synthesizing and cataloging information about cells and molecules, predicting mechanisms and identifying generalizable themes, generating hypotheses and guiding experimental design, and highlighting knowledge gaps and refining understanding. In turn, incorporating domain expertise and experimental data is crucial for building towards whole cell models. An iterative cycle of interaction between cell and systems biologists advances the goals of both fields and establishes a framework for mechanistic understanding of the genome-to-phenome relationship. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Comparing Effects of Biologic Agents in Treating Patients with Rheumatoid Arthritis: A Multiple Treatment Comparison Regression Analysis.

Directory of Open Access Journals (Sweden)

Ingunn Fride Tvete

Full Text Available Rheumatoid arthritis patients have been treated with disease modifying anti-rheumatic drugs (DMARDs and the newer biologic drugs. We sought to compare and rank the biologics with respect to efficacy. We performed a literature search identifying 54 publications encompassing 9 biologics. We conducted a multiple treatment comparison regression analysis letting the number experiencing a 50% improvement on the ACR score be dependent upon dose level and disease duration for assessing the comparable relative effect between biologics and placebo or DMARD. The analysis embraced all treatment and comparator arms over all publications. Hence, all measured effects of any biologic agent contributed to the comparison of all biologic agents relative to each other either given alone or combined with DMARD. We found the drug effect to be dependent on dose level, but not on disease duration, and the impact of a high versus low dose level was the same for all drugs (higher doses indicated a higher frequency of ACR50 scores. The ranking of the drugs when given without DMARD was certolizumab (ranked highest, etanercept, tocilizumab/ abatacept and adalimumab. The ranking of the drugs when given with DMARD was certolizumab (ranked highest, tocilizumab, anakinra/rituximab, golimumab/ infliximab/ abatacept, adalimumab/ etanercept [corrected]. Still, all drugs were effective. All biologic agents were effective compared to placebo, with certolizumab the most effective and adalimumab (without DMARD treatment and adalimumab/ etanercept (combined with DMARD treatment the least effective. The drugs were in general more effective, except for etanercept, when given together with DMARDs.

Gene expression profiling with principal component analysis depicts the biological continuum from essential thrombocythemia over polycythemia vera to myelofibrosis

DEFF Research Database (Denmark)

Skov, Vibe; Thomassen, Mads; Riley, Caroline H

2012-01-01

The recent discovery of the Janus activating kinase 2 V617F mutation in most patients with polycythemia vera (PV) and half of those with essential thrombocythemia (ET) and primary myelofibrosis (PMF) has favored the hypothesis of a biological continuum from ET over PV to PMF. We performed gene...... with biological relevant overlaps between the different entities. Moreover, the analysis separates Janus activating kinase 2-negative ET patients from Janus activating kinase 2-positive ET patients. Functional annotation analysis demonstrates that clusters of gene ontology terms related to inflammation, immune...... system, apoptosis, RNA metabolism, and secretory system were the most significantly deregulated terms in the three different disease groups. Our results yield further support for the hypothesis of a biological continuum originating from ET over PV to PMF. Functional analysis suggests an important...

Data acquisition and analysis at the Structural Biology Center

International Nuclear Information System (INIS)

Westbrook, M.L.; Coleman, T.A.; Daly, R.T.; Pflugrath, J.W.

1996-01-01

The Structural Biology Center (SBC), a national user facility for macromolecular crystallography located at Argonne National Laboratory's Advanced Photon Source, is currently being built and commissioned. SBC facilities include a bending-magnet beamline, an insertion-device beamline, laboratory and office space adjacent to the beamlines, and associated instrumentation, experimental apparatus, and facilities. SBC technical facilities will support anomalous dispersion phasing experiments, data collection from microcrystals, data collection from crystals with large molecular structures and rapid data collection from multiple related crystal structures for protein engineering and drug design. The SBC Computing Systems and Software Engineering Group is tasked with developing the SBC Control System, which includes computing systems, network, and software. The emphasis of SBC Control System development has been to provide efficient and convenient beamline control, data acquisition, and data analysis for maximal facility and experimenter productivity. This paper describes the SBC Control System development, specifically data acquisition and analysis at the SBC, and the development methods used to meet this goal

SIMS applications in biological research

International Nuclear Information System (INIS)

Prince, K.E.; Burke, P.T.; Kelly, I.J.

2000-01-01

Full text: SIMS has been utilised as a tool for biological research since the early 1970's. SIMS' abilities in isotopic detection with high sensitivity, imaging capabilities at a subcellular level, and the possibility of molecular imaging have been the main areas of interest for biological development. However, whilst hundreds of instruments are available in industrial and university laboratories for semiconductor and materials analysis, only a handful successfully perform biological research. For this reason there is generally a lack of awareness of SIMS by the biological community. Biological SIMS analysis requires a working knowledge of both biology and SIMS. Sample preparation is a critical and time consuming prerequisite for any successful biological SIMS study. In addition, for quantification to be possible a homogeneous, matrix matched standard must be available. Once these difficulties are more widely understood and overcome there will be a greater motivation for the biological community to embrace SIMS as a unique tool in their research. This paper provides an overview of some of the more successful biological SIMS application areas internationally, and summarises the types of biological SIMS requests received by ANSTO

Massively Parallel, Molecular Analysis Platform Developed Using a CMOS Integrated Circuit With Biological Nanopores

Science.gov (United States)

Roever, Stefan

2012-01-01

A massively parallel, low cost molecular analysis platform will dramatically change the nature of protein, molecular and genomics research, DNA sequencing, and ultimately, molecular diagnostics. An integrated circuit (IC) with 264 sensors was fabricated using standard CMOS semiconductor processing technology. Each of these sensors is individually controlled with precision analog circuitry and is capable of single molecule measurements. Under electronic and software control, the IC was used to demonstrate the feasibility of creating and detecting lipid bilayers and biological nanopores using wild type α-hemolysin. The ability to dynamically create bilayers over each of the sensors will greatly accelerate pore development and pore mutation analysis. In addition, the noise performance of the IC was measured to be 30fA(rms). With this noise performance, single base detection of DNA was demonstrated using α-hemolysin. The data shows that a single molecule, electrical detection platform using biological nanopores can be operationalized and can ultimately scale to millions of sensors. Such a massively parallel platform will revolutionize molecular analysis and will completely change the field of molecular diagnostics in the future.

ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis.

Science.gov (United States)

Römer, Michael; Eichner, Johannes; Dräger, Andreas; Wrzodek, Clemens; Wrzodek, Finja; Zell, Andreas

2016-01-01

Bioinformatics analysis has become an integral part of research in biology. However, installation and use of scientific software can be difficult and often requires technical expert knowledge. Reasons are dependencies on certain operating systems or required third-party libraries, missing graphical user interfaces and documentation, or nonstandard input and output formats. In order to make bioinformatics software easily accessible to researchers, we here present a web-based platform. The Center for Bioinformatics Tuebingen (ZBIT) Bioinformatics Toolbox provides web-based access to a collection of bioinformatics tools developed for systems biology, protein sequence annotation, and expression data analysis. Currently, the collection encompasses software for conversion and processing of community standards SBML and BioPAX, transcription factor analysis, and analysis of microarray data from transcriptomics and proteomics studies. All tools are hosted on a customized Galaxy instance and run on a dedicated computation cluster. Users only need a web browser and an active internet connection in order to benefit from this service. The web platform is designed to facilitate the usage of the bioinformatics tools for researchers without advanced technical background. Users can combine tools for complex analyses or use predefined, customizable workflows. All results are stored persistently and reproducible. For each tool, we provide documentation, tutorials, and example data to maximize usability. The ZBIT Bioinformatics Toolbox is freely available at https://webservices.cs.uni-tuebingen.de/.

Analysis and logical modeling of biological signaling transduction networks

Science.gov (United States)

Sun, Zhongyao

The study of network theory and its application span across a multitude of seemingly disparate fields of science and technology: computer science, biology, social science, linguistics, etc. It is the intrinsic similarities embedded in the entities and the way they interact with one another in these systems that link them together. In this dissertation, I present from both the aspect of theoretical analysis and the aspect of application three projects, which primarily focus on signal transduction networks in biology. In these projects, I assembled a network model through extensively perusing literature, performed model-based simulations and validation, analyzed network topology, and proposed a novel network measure. The application of network modeling to the system of stomatal opening in plants revealed a fundamental question about the process that has been left unanswered in decades. The novel measure of the redundancy of signal transduction networks with Boolean dynamics by calculating its maximum node-independent elementary signaling mode set accurately predicts the effect of single node knockout in such signaling processes. The three projects as an organic whole advance the understanding of a real system as well as the behavior of such network models, giving me an opportunity to take a glimpse at the dazzling facets of the immense world of network science.

Immune Monitoring in Cancer Vaccine Clinical Trials: Critical Issues of Functional Flow Cytometry-Based Assays

Directory of Open Access Journals (Sweden)

Iole Macchia

2013-01-01

Full Text Available The development of immune monitoring assays is essential to determine the immune responses against tumor-specific antigens (TSAs and tumor-associated antigens (TAAs and their possible correlation with clinical outcome in cancer patients receiving immunotherapies. Despite the wide range of techniques used, to date these assays have not shown consistent results among clinical trials and failed to define surrogate markers of clinical efficacy to antitumor vaccines. Multiparameter flow cytometry- (FCM- based assays combining different phenotypic and functional markers have been developed in the past decade for informative and longitudinal analysis of polyfunctional T-cells. These technologies were designed to address the complexity and functional heterogeneity of cancer biology and cellular immunity and to define biomarkers predicting clinical response to anticancer treatment. So far, there is still a lack of standardization of some of these immunological tests. The aim of this review is to overview the latest technologies for immune monitoring and to highlight critical steps involved in some of the FCM-based cellular immune assays. In particular, our laboratory is focused on melanoma vaccine research and thus our main goal was the validation of a functional multiparameter test (FMT combining different functional and lineage markers to be applied in clinical trials involving patients with melanoma.

An Integrated Workflow To Assess Technical and Biological Variability of Cell Population Frequencies in Human Peripheral Blood by Flow Cytometry.

Science.gov (United States)

Burel, Julie G; Qian, Yu; Lindestam Arlehamn, Cecilia; Weiskopf, Daniela; Zapardiel-Gonzalo, Jose; Taplitz, Randy; Gilman, Robert H; Saito, Mayuko; de Silva, Aruna D; Vijayanand, Pandurangan; Scheuermann, Richard H; Sette, Alessandro; Peters, Bjoern

2017-02-15

In the context of large-scale human system immunology studies, controlling for technical and biological variability is crucial to ensure that experimental data support research conclusions. In this study, we report on a universal workflow to evaluate both technical and biological variation in multiparameter flow cytometry, applied to the development of a 10-color panel to identify all major cell populations and T cell subsets in cryopreserved PBMC. Replicate runs from a control donation and comparison of different gating strategies assessed the technical variability associated with each cell population and permitted the calculation of a quality control score. Applying our panel to a large collection of PBMC samples, we found that most cell populations showed low intraindividual variability over time. In contrast, certain subpopulations such as CD56 T cells and Temra CD4 T cells were associated with high interindividual variability. Age but not gender had a significant effect on the frequency of several populations, with a drastic decrease in naive T cells observed in older donors. Ethnicity also influenced a significant proportion of immune cell population frequencies, emphasizing the need to account for these covariates in immune profiling studies. We also exemplify the usefulness of our workflow by identifying a novel cell-subset signature of latent tuberculosis infection. Thus, our study provides a universal workflow to establish and evaluate any flow cytometry panel in systems immunology studies. Copyright © 2017 by The American Association of Immunologists, Inc.

A data integration approach for cell cycle analysis oriented to model simulation in systems biology

Directory of Open Access Journals (Sweden)

Mosca Ettore

2007-08-01

Full Text Available Abstract Background The cell cycle is one of the biological processes most frequently investigated in systems biology studies and it involves the knowledge of a large number of genes and networks of protein interactions. A deep knowledge of the molecular aspect of this biological process can contribute to making cancer research more accurate and innovative. In this context the mathematical modelling of the cell cycle has a relevant role to quantify the behaviour of each component of the systems. The mathematical modelling of a biological process such as the cell cycle allows a systemic description that helps to highlight some features such as emergent properties which could be hidden when the analysis is performed only from a reductionism point of view. Moreover, in modelling complex systems, a complete annotation of all the components is equally important to understand the interaction mechanism inside the network: for this reason data integration of the model components has high relevance in systems biology studies. Description In this work, we present a resource, the Cell Cycle Database, intended to support systems biology analysis on the Cell Cycle process, based on two organisms, yeast and mammalian. The database integrates information about genes and proteins involved in the cell cycle process, stores complete models of the interaction networks and allows the mathematical simulation over time of the quantitative behaviour of each component. To accomplish this task, we developed, a web interface for browsing information related to cell cycle genes, proteins and mathematical models. In this framework, we have implemented a pipeline which allows users to deal with the mathematical part of the models, in order to solve, using different variables, the ordinary differential equation systems that describe the biological process. Conclusion This integrated system is freely available in order to support systems biology research on the cell cycle and

Urtica dioica pollen allergy: Clinical, biological, and allergomics analysis.

Science.gov (United States)

Tiotiu, Angelica; Brazdova, Andrea; Longé, Cyril; Gallet, Patrice; Morisset, Martine; Leduc, Virginie; Hilger, Christiane; Broussard, Cédric; Couderc, Rémy; Sutra, Jean-Pierre; Sénéchal, Hélène; Poncet, Pascal

2016-11-01

The most emblematic members of Urticaceae at allergic risk level are wall pellitories (Parietaria), whereas nettle (Urtica) pollen is considered as poorly allergenic. No allergen from nettle pollen has yet been characterized, whereas 4 are listed for Parietaria pollen by the International Union of Immunological Societies. Clinical and biological profiles of 2 adult men who developed symptoms against nettle pollen and/or leaves were studied. To characterize the allergic reaction and identify the potential nettle pollen sensitizing allergens. IgE-mediated reaction to nettle pollen extract was evaluated by skin prick test, immunoassay, nasal provocation, and basophil activation test. To characterize specific nettle pollen allergens, an allergomic (IgE immunoproteomic) analysis was performed combining 1- and 2-dimensional electrophoresis, IgE immunoblots of nettle pollen extract, identification of allergens by mass spectrometry, and database queries. The results of biological and immunochemical analyses revealed that the allergic rhinitis was due to Urtica dioica pollen in both patients. The allergomic analysis of nettle pollen extract allowed the characterization of 4 basic protein allergens: a thaumatin-like protein (osmotin) with a relative molecular mass of 27 to 29 kDa, a pectinesterase (relative molecular mass, 40 kDa), and 2 other basic proteins with relative molecular masses of 14 to 16 kDa and 43 kDa. There is no or only very weak allergen associations between pellitory and nettle pollen. Exposure to nettle pollen can be responsible of allergic symptoms, and several allergens were characterized. Unravelling the allergens of this underestimated allergy might help to improve diagnosis and care for patients, to predict cross-reactivities and design adapted specific immunotherapy. Copyright © 2016 American College of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

Independent component analysis reveals new and biologically significant structures in micro array data

Directory of Open Access Journals (Sweden)

Veerla Srinivas

2006-06-01

Full Text Available Abstract Background An alternative to standard approaches to uncover biologically meaningful structures in micro array data is to treat the data as a blind source separation (BSS problem. BSS attempts to separate a mixture of signals into their different sources and refers to the problem of recovering signals from several observed linear mixtures. In the context of micro array data, "sources" may correspond to specific cellular responses or to co-regulated genes. Results We applied independent component analysis (ICA to three different microarray data sets; two tumor data sets and one time series experiment. To obtain reliable components we used iterated ICA to estimate component centrotypes. We found that many of the low ranking components indeed may show a strong biological coherence and hence be of biological significance. Generally ICA achieved a higher resolution when compared with results based on correlated expression and a larger number of gene clusters with significantly enriched for gene ontology (GO categories. In addition, components characteristic for molecular subtypes and for tumors with specific chromosomal translocations were identified. ICA also identified more than one gene clusters significant for the same GO categories and hence disclosed a higher level of biological heterogeneity, even within coherent groups of genes. Conclusion Although the ICA approach primarily detects hidden variables, these surfaced as highly correlated genes in time series data and in one instance in the tumor data. This further strengthens the biological relevance of latent variables detected by ICA.

Parametric inference for biological sequence analysis.

Science.gov (United States)

Pachter, Lior; Sturmfels, Bernd

2004-11-16

One of the major successes in computational biology has been the unification, by using the graphical model formalism, of a multitude of algorithms for annotating and comparing biological sequences. Graphical models that have been applied to these problems include hidden Markov models for annotation, tree models for phylogenetics, and pair hidden Markov models for alignment. A single algorithm, the sum-product algorithm, solves many of the inference problems that are associated with different statistical models. This article introduces the polytope propagation algorithm for computing the Newton polytope of an observation from a graphical model. This algorithm is a geometric version of the sum-product algorithm and is used to analyze the parametric behavior of maximum a posteriori inference calculations for graphical models.

SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool.

Science.gov (United States)

Zi, Zhike; Zheng, Yanan; Rundell, Ann E; Klipp, Edda

2008-08-15

It has long been recognized that sensitivity analysis plays a key role in modeling and analyzing cellular and biochemical processes. Systems biology markup language (SBML) has become a well-known platform for coding and sharing mathematical models of such processes. However, current SBML compatible software tools are limited in their ability to perform global sensitivity analyses of these models. This work introduces a freely downloadable, software package, SBML-SAT, which implements algorithms for simulation, steady state analysis, robustness analysis and local and global sensitivity analysis for SBML models. This software tool extends current capabilities through its execution of global sensitivity analyses using multi-parametric sensitivity analysis, partial rank correlation coefficient, SOBOL's method, and weighted average of local sensitivity analyses in addition to its ability to handle systems with discontinuous events and intuitive graphical user interface. SBML-SAT provides the community of systems biologists a new tool for the analysis of their SBML models of biochemical and cellular processes.

Sampling and Analysis Instruction for the Demolition of the Masonry Block for the 108-F Biological Laboratory

International Nuclear Information System (INIS)

Byrnes, M. E.

1999-01-01

This sampling and analysis instruction (SAI) has been prepared to clearly define the sampling and analysis activities to be performed in support of the demolition and disposition (or disposal) of the 108-F Biological Laboratory masonry block walls

Geometrical Patterning of Super-Hydrophobic Biosensing Transistors Enables Space and Time Resolved Analysis of Biological Mixtures

KAUST Repository

Gentile, Francesco

2016-01-12

PEDOT:PSS is a conductive polymer that can be integrated into last generation Organic Electrochemical Transistor (OECT) devices for biological inspection, identification and analysis. While a variety of reports in literature demonstrated the chemical and biological sensitivity of these devices, still their ability in resolving complex mixtures remains controversial. Similar OECT devices display good time dynamics behavior but lack spatial resolution. In this work, we integrated PEDOT:PSS with patterns of super-hydrophobic pillars in which a finite number of those pillars is independently controlled for site-selective measurement of a solution. We obtained a multifunctional, hierarchical OECT device that bridges the micro- to the nano-scales for specific, combined time and space resolved analysis of the sample. Due to super-hydrophobic surface properties, the biological species in the drop are driven by convection, diffusion, and the externally applied electric field: the balance/unbalance between these forces will cause the molecules to be transported differently within its volume depending on particle size thus realizing a size-selective separation. Within this framework, the separation and identification of two different molecules, namely Cetyl Trimethyl Ammonium Bromid (CTAB) and adrenaline, in a biological mixture have been demonstrated, showing that geometrical control at the micro-nano scale impart unprecedented selectivity to the devices.

Geometrical Patterning of Super-Hydrophobic Biosensing Transistors Enables Space and Time Resolved Analysis of Biological Mixtures

KAUST Repository

Gentile, Francesco; Ferrara, Lorenzo; Villani, Marco; Bettelli, Manuele; Iannotta, Salvatore; Zappettini, Andrea; Cesarelli, Mario; Di Fabrizio, Enzo M.; Coppedè , Nicola

2016-01-01

PEDOT:PSS is a conductive polymer that can be integrated into last generation Organic Electrochemical Transistor (OECT) devices for biological inspection, identification and analysis. While a variety of reports in literature demonstrated the chemical and biological sensitivity of these devices, still their ability in resolving complex mixtures remains controversial. Similar OECT devices display good time dynamics behavior but lack spatial resolution. In this work, we integrated PEDOT:PSS with patterns of super-hydrophobic pillars in which a finite number of those pillars is independently controlled for site-selective measurement of a solution. We obtained a multifunctional, hierarchical OECT device that bridges the micro- to the nano-scales for specific, combined time and space resolved analysis of the sample. Due to super-hydrophobic surface properties, the biological species in the drop are driven by convection, diffusion, and the externally applied electric field: the balance/unbalance between these forces will cause the molecules to be transported differently within its volume depending on particle size thus realizing a size-selective separation. Within this framework, the separation and identification of two different molecules, namely Cetyl Trimethyl Ammonium Bromid (CTAB) and adrenaline, in a biological mixture have been demonstrated, showing that geometrical control at the micro-nano scale impart unprecedented selectivity to the devices.

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.

Application of LC–MS/MS for quantitative analysis of glucocorticoids and stimulants in biological fluids

Directory of Open Access Journals (Sweden)

Jamshed Haneef

2013-10-01

Full Text Available Liquid chromatography tandem mass chromatography (LC–MS/MS is an important hyphenated technique for quantitative analysis of drugs in biological fluids. Because of high sensitivity and selectivity, LC–MS/MS has been used for pharmacokinetic studies, metabolites identification in the plasma and urine. This manuscript gives comprehensive analytical review, focusing on chromatographic separation approaches (column packing materials, column length and mobile phase as well as different acquisition modes (SIM, MRM for quantitative analysis of glucocorticoids and stimulants. This review is not meant to be exhaustive but rather to provide a general overview for detection and confirmation of target drugs using LC–MS/MS and thus useful in the doping analysis, toxicological studies as well as in pharmaceutical analysis. Keywords: LC–MS/MS, Ionization techniques, Glucocorticoids, Stimulants, Hyphenated techniques, Biological fluid

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

Integrated Network Analysis and Effective Tools in Plant Systems Biology

Directory of Open Access Journals (Sweden)

Atsushi eFukushima

2014-11-01

Full Text Available One of the ultimate goals in plant systems biology is to elucidate the genotype-phenotype relationship in plant cellular systems. Integrated network analysis that combines omics data with mathematical models has received particular attention. Here we focus on the latest cutting-edge computational advances that facilitate their combination. We highlight (1 network visualization tools, (2 pathway analyses, (3 genome-scale metabolic reconstruction, and (4 the integration of high-throughput experimental data and mathematical models. Multi-omics data that contain the genome, transcriptome, proteome, and metabolome and mathematical models are expected to integrate and expand our knowledge of complex plant metabolisms.

Research and Development Strategy in Biological Technologies: A Patent Data Analysis of Japanese Manufacturing Firms

Directory of Open Access Journals (Sweden)

Hidemichi Fujii

2016-04-01

Full Text Available Biological technology allows us to invent new medical approaches, create effective food production methods and reserves and develop new materials for industrial production. There is a diversity of biological technology types, and different technologies have different priorities for invention. This study examines the factors that are important for the invention of biology-related technologies in Japan using patent application data and a decomposition analysis framework. As the results show, patent applications related to biochemistry and biotechnology increased until 1995 because of the expanded scale of R&D activities and the high priority assigned to biological technology. However, the number of patent applications stagnated after 1995, because the importance of biochemistry, especially waste-gas treatment technologies, decreased. Additionally, patent applications for medicines and disease-related technologies increased rapidly from 1971 to 1995. The primary determinant of rapid growth is an increase in research priority, especially among firms in the chemical industry whose technologies are related to supplemental foods and foods with health-promoting benefits. Finally, patent applications involving foodstuff- and agriculture-related technologies increased from 1971 to 1995 due to increased R&D and the increased priority of biological technology.

Data analysis as a source of variability of the HLA-peptide multimer assay

DEFF Research Database (Denmark)

Gouttefangeas, Cécile; Chan, Cliburn; Attig, Sebastian

2015-01-01

by laboratories performing ex vivo T cell immune monitoring. In particular, analysis currently relies on a manual, step-by-step strategy employing serial gating decisions based on visual inspection of one- or two-dimensional plots. It is therefore operator dependent and subjective. In the context of continuing......Multiparameter flow cytometry is an indispensable method for assessing antigen-specific T cells in basic research and cancer immunotherapy. Proficiency panels have shown that cell sample processing, test protocols and data analysis may all contribute to the variability of the results obtained...... efforts to support inter-laboratory T cell assay harmonization, the CIMT Immunoguiding Program organized its third proficiency panel dedicated to the detection of antigen-specific CD8(+) T cells by HLA-peptide multimer staining. We first assessed the contribution of manual data analysis to the variability...

Applications of mass spectrometry in the trace element analysis of biological materials

International Nuclear Information System (INIS)

Moens, L.

1997-01-01

The importance of mass spectrometry for the analysis of biological material is illustrated by reviewing the different mass spectrometric methods applied and describing some typical applications published recently. Though atomic absorption spectrometry is used in the majority of analyses of biological material, most mass spectrometric methods have been used to some extent for trace element determination in biomedical research. The relative importance of the different methods is estimated by reviewing recent research papers. It is striking that especially inductively coupled plasma mass spectrometry is increasingly being applied, partly because the method can be used on-line after chromatographic separation, in speciation studies. Mass spectrometric methods prove to offer unique possibilities in stable isotope tracer studies and for this purpose also experimentally demanding methods such as thermal ionization mass spectrometry and accelerator mass spectrometry are frequently used. (orig.)

A critical analysis of the new biology and the biological revolution: their impact - from medicine to evolution.

Science.gov (United States)

Dev, Sukhendu B

2010-01-01

In this article, I critically analyze the impact of the new biology and the biological revolution. I argue that indiscriminate use of the words such as 'interdisciplinary,' 'integrative,' and 'revolution' has caused only confusion when applied to biology. The recent debate, especially after the exploding field of systems biology, has brought back the controversy whether molecular biology is reductionist or holistic. I look at the issues involved critically. I discuss the problem of defining the word 'gene' and argue that recent attempts to redefine the central dogma of molecular biology about the information flow from DNA to RNA to protein are not justified. I support my view with comments from the scientist who discovered RNA splicing. Several aspects of evo-devo, a new branch of biology, are discussed. I give examples from this evolution-developmental biology to show how some of Darwin's inspired guesses have had resounding victory when it was found that specific genes during embryonic development of the Galapagos finches decided the size and shape of their beaks. I discuss the recent publications which show that the conditions in the island, such as wet to dry to wet season, can bring about evolutionary changes from year to year. Thus it is essential to monitor both short and long-term evolutionary changes to get the full picture of evolution.

A Comparative Analysis of South African Life Sciences and Biology Textbooks for Inclusion of the Nature of Science

Science.gov (United States)

Ramnarain, Umesh; Padayachee, Keshni

2015-01-01

This study reports on the analysis of South African Life Sciences and Biology textbooks for the inclusion of the nature of science using a conceptual framework developed by Chiappetta, Fillman and Sethna (1991). In particular, we investigated the differences between the representation of the nature of science in Biology textbooks that were written…

International Trends in Biology Education Research from 1997 to 2014: A Content Analysis of Papers in Selected Journals

Science.gov (United States)

Gul, Seyda; Sozbilir, Mustafa

2016-01-01

This paper provides a descriptive content analysis of biology education research papers published in eight major academic journals indexed in Social Science Citation Index [SSCI] of Thomson Reuters® from 1997 to 2014. Total of 1376 biology education research [BER] papers were examined. The findings indicated that most of the papers were published…

Potential interferences inherent in neutron-activation analysis of trace elements in biological materials

International Nuclear Information System (INIS)

Cornells, R.; Hoste, J.; Versieck, J.

1982-01-01

A comprehensive review is given of how neutron-activation analysis for trace elements in biological matrices can be jeopardized by radiation damage, by the impurities present in the packing material or by nuclear interferences of major elements. Systematic errors during the counting process and the quantitative interpretation of the γ-ray spectra should not be disregarded. (author)

In search of low cost biological analysis: Wax or acrylic glue bonded paper microfluidic devices

KAUST Repository

Kodzius, Rimantas

2011-01-01

In this body of work we have been developing and characterizing paper based microfluidic fabrication technologies to produce low cost biological analysis. Specifically we investigated the performance of paper microfluidics that had been bonded using wax o

In search of low cost biological analysis: Wax or acrylic glue bonded paper microfluidic devices

KAUST Repository

Kodzius, Rimantas

2011-11-04

In this body of work we have been developing and characterizing paper based microfluidic fabrication technologies to produce low cost biological analysis. Specifically we investigated the performance of paper microfluidics that had been bonded using wax o

Instrumental neutron activation analysis of biological samples

International Nuclear Information System (INIS)

Guinn, V.P.; Gavrilas, M.

1990-01-01

The elemental compositions of 18 biological reference materials have been processed, for 14 stepped combinations of irradiation/decay/counting times, by the INAA Advance Prediction Computer Program. The 18 materials studied include 11 plant materials, 5 animal materials, and 2 other biological materials. Of these 18 materials, 14 are NBS Standard Reference Materials and four are IAEA reference materials. Overall, the results show that a mean of 52% of the input elements can be determined to a relative standard deviation of ±10% or better by reactor flux (thermal plus epithermal) INAA

Adrenocortical carcinoma: the dawn of a new era of genomic and molecular biology analysis.

Science.gov (United States)

Armignacco, R; Cantini, G; Canu, L; Poli, G; Ercolino, T; Mannelli, M; Luconi, M

2018-05-01

Over the last decade, the development of novel and high penetrance genomic approaches to analyze biological samples has provided very new insights in the comprehension of the molecular biology and genetics of tumors. The use of these techniques, consisting of exome sequencing, transcriptome, miRNome, chromosome alteration, genome, and epigenome analysis, has also been successfully applied to adrenocortical carcinoma (ACC). In fact, the analysis of large cohorts of patients allowed the stratification of ACC with different patterns of molecular alterations, associated with different outcomes, thus providing a novel molecular classification of the malignancy to be associated with the classical pathological analysis. Improving our knowledge about ACC molecular features will result not only in a better diagnostic and prognostic accuracy, but also in the identification of more specific therapeutic targets for the development of more effective pharmacological anti-cancer approaches. In particular, the specific molecular alteration profiles identified in ACC may represent targetable events by the use of already developed or newly designed drugs enabling a better and more efficacious management of the ACC patient in the context of new frontiers of personalized precision medicine.

Electron probe analysis of biological fluids: Possibilities and limitations

International Nuclear Information System (INIS)

Roinel, N.

1984-01-01

Physical methods of investigation have become essential to investigations at the cellular or subcellular level. Nuclear magnetic resonance is the most recent and striking example, since it is not only a tool for fundamental physicists and organic chemists, but also an extraordinary powerful imaging tool for physicians. The absorption properties of X rays were used immediately after their discovery to image the bones of skeletons. Later, X rays were also found to be extremely efficient in the measurement of the elemental content of microvolumes irradiated by electron probes. The electron probe analyzer (EPA) was immediately adopted by numerous laboratories of metallurgy, geology, and mineral sciences. In the last fifteen years, since the use of this instrument was suggested for liquid analysis, and a preparative technique was developed, the EPA has been used by an increasing number of biological laboratories for measuring the concentrations of the elements contained in subnanoliter volumes of biological fluids. The so-called microdroplet technique has become a routine laboratory method, the only one able to measure the concentrations of an unlimited number of elements in a single 0.1-nl sample. This explains its use in fields as various as renal, reproductive, digestive, and plant physiology, zoology, etc. Several review papers discuss these applications. The possibilities and limitations of the technique are discussed below

Relative biological efficiency of 592 MeV protons. Analysis of the biological effect of secondary radiation

International Nuclear Information System (INIS)

Legeay, G.; Baarli, J.

1968-01-01

The relative biological efficiency (RBE) of high energy protons is of importance because of their effects in the field of radioprotection around large accelerators and during space-flights. The nature of the interactions between 592 MeV protons and biological tissues makes it necessary to take into consideration the contribution of secondary radiation to the biological effect. Since it is not possible to obtain from a synchrotron a beam having a sufficiently large cross-section to irradiate large animals, one has to resort to certain devices concerning the mode of exposure when small laboratory animals are used. By irradiating rats individually and in groups, and by using the lethal test as a function of time, the authors show that the value of the RBE is different for animals of the same species having the same biological parameters. Thus there appears an increase in the biological effect due to secondary radiation produced in nuclear cascades which develop in a large volume, for example that of a human being. (author) [fr

Optimal fatigue analysis of structures during complex loadings

Directory of Open Access Journals (Sweden)

Karaouni Habib

2016-01-01

Full Text Available A new framework for high cycle fatigue analysis of metallic structures under complex multi-parameter loadings was here developed. This allows to reduce the analysis on a 2-D window with a characterized one-parameter cyclic loading thanks to an equivalence rule relative to damage between any two loadings. The simplified inelastic analysis introduced by J. Zarka [J. Zarka et al. 1990. A new approach in inelastic analysis of structures. CADLM] was used to find the limit state of the structure. A new design rules for fatigue analysis by utilizing automatic learning systems was successfully performed. A database was built by coupling numerical simulations and experimental results on several welded specimens which are considered as a general structure in the proposed approach. This could be possible by the introduction of an intelligent description of a general fatigue case based on the actual theories and models. A software, FATPRO [M.I. Systems, FatPro, available at http://www.mzintsys.com/our_products_fatpro.html], based on this work has been developed at MZ Intelligent Systems.

Improved elucidation of biological processes linked to diabetic nephropathy by single probe-based microarray data analysis.

Directory of Open Access Journals (Sweden)

Clemens D Cohen

Full Text Available BACKGROUND: Diabetic nephropathy (DN is a complex and chronic metabolic disease that evolves into a progressive fibrosing renal disorder. Effective transcriptomic profiling of slowly evolving disease processes such as DN can be problematic. The changes that occur are often subtle and can escape detection by conventional oligonucleotide DNA array analyses. METHODOLOGY/PRINCIPAL FINDINGS: We examined microdissected human renal tissue with or without DN using Affymetrix oligonucleotide microarrays (HG-U133A by standard Robust Multi-array Analysis (RMA. Subsequent gene ontology analysis by Database for Annotation, Visualization and Integrated Discovery (DAVID showed limited detection of biological processes previously identified as central mechanisms in the development of DN (e.g. inflammation and angiogenesis. This apparent lack of sensitivity may be associated with the gene-oriented averaging of oligonucleotide probe signals, as this includes signals from cross-hybridizing probes and gene annotation that is based on out of date genomic data. We then examined the same CEL file data using a different methodology to determine how well it could correlate transcriptomic data with observed biology. ChipInspector (CI is based on single probe analysis and de novo gene annotation that bypasses probe set definitions. Both methods, RMA and CI, used at default settings yielded comparable numbers of differentially regulated genes. However, when verified by RT-PCR, the single probe based analysis demonstrated reduced background noise with enhanced sensitivity and fewer false positives. CONCLUSIONS/SIGNIFICANCE: Using a single probe based analysis approach with de novo gene annotation allowed an improved representation of the biological processes linked to the development and progression of DN. The improved analysis was exemplified by the detection of Wnt signaling pathway activation in DN, a process not previously reported to be involved in this disease.

From Biology to Mathematical Models and Back: Teaching Modeling to Biology Students, and Biology to Math and Engineering Students

Science.gov (United States)

Chiel, Hillel J.; McManus, Jeffrey M.; Shaw, Kendrick M.

2010-01-01

We describe the development of a course to teach modeling and mathematical analysis skills to students of biology and to teach biology to students with strong backgrounds in mathematics, physics, or engineering. The two groups of students have different ways of learning material and often have strong negative feelings toward the area of knowledge…

Normal mode analysis and applications in biological physics.

Science.gov (United States)

Dykeman, Eric C; Sankey, Otto F

2010-10-27

Normal mode analysis has become a popular and often used theoretical tool in the study of functional motions in enzymes, viruses, and large protein assemblies. The use of normal modes in the study of these motions is often extremely fruitful since many of the functional motions of large proteins can be described using just a few normal modes which are intimately related to the overall structure of the protein. In this review, we present a broad overview of several popular methods used in the study of normal modes in biological physics including continuum elastic theory, the elastic network model, and a new all-atom method, recently developed, which is capable of computing a subset of the low frequency vibrational modes exactly. After a review of the various methods, we present several examples of applications of normal modes in the study of functional motions, with an emphasis on viral capsids.

Electrical circuit modeling and analysis of microwave acoustic interaction with biological tissues.

Science.gov (United States)

Gao, Fei; Zheng, Qian; Zheng, Yuanjin

2014-05-01

Numerical study of microwave imaging and microwave-induced thermoacoustic imaging utilizes finite difference time domain (FDTD) analysis for simulation of microwave and acoustic interaction with biological tissues, which is time consuming due to complex grid-segmentation and numerous calculations, not straightforward due to no analytical solution and physical explanation, and incompatible with hardware development requiring circuit simulator such as SPICE. In this paper, instead of conventional FDTD numerical simulation, an equivalent electrical circuit model is proposed to model the microwave acoustic interaction with biological tissues for fast simulation and quantitative analysis in both one and two dimensions (2D). The equivalent circuit of ideal point-like tissue for microwave-acoustic interaction is proposed including transmission line, voltage-controlled current source, envelop detector, and resistor-inductor-capacitor (RLC) network, to model the microwave scattering, thermal expansion, and acoustic generation. Based on which, two-port network of the point-like tissue is built and characterized using pseudo S-parameters and transducer gain. Two dimensional circuit network including acoustic scatterer and acoustic channel is also constructed to model the 2D spatial information and acoustic scattering effect in heterogeneous medium. Both FDTD simulation, circuit simulation, and experimental measurement are performed to compare the results in terms of time domain, frequency domain, and pseudo S-parameters characterization. 2D circuit network simulation is also performed under different scenarios including different sizes of tumors and the effect of acoustic scatterer. The proposed circuit model of microwave acoustic interaction with biological tissue could give good agreement with FDTD simulated and experimental measured results. The pseudo S-parameters and characteristic gain could globally evaluate the performance of tumor detection. The 2D circuit network

The Relationships Between Epistemic Beliefs in Biology and Approaches to Learning Biology Among Biology-Major University Students in Taiwan

Science.gov (United States)

Lin, Yi-Chun; Liang, Jyh-Chong; Tsai, Chin-Chung

2012-12-01

The aim of this study was to investigate the relationships between students' epistemic beliefs in biology and their approaches to learning biology. To this end, two instruments, the epistemic beliefs in biology and the approaches to learning biology surveys, were developed and administered to 520 university biology students, respectively. By and large, it was found that the students reflected "mixed" motives in biology learning, while those who had more sophisticated epistemic beliefs tended to employ deep strategies. In addition, the results of paired t tests revealed that the female students were more likely to possess beliefs about biological knowledge residing in external authorities, to believe in a right answer, and to utilize rote learning as a learning strategy. Moreover, compared to juniors and seniors, freshmen and sophomores tended to hold less mature views on all factors of epistemic beliefs regarding biology. Another comparison indicated that theoretical biology students (e.g. students majoring in the Department of Biology) tended to have more mature beliefs in learning biology and more advanced strategies for biology learning than those students studying applied biology (e.g. in the Department of Biotechnology). Stepwise regression analysis, in general, indicated that students who valued the role of experiments and justify epistemic assumptions and knowledge claims based on evidence were more oriented towards having mixed motives and utilizing deep strategies to learn biology. In contrast, students who believed in the certainty of biological knowledge were more likely to adopt rote learning strategies and to aim to qualify in biology.

Analysis of arsenical metabolites in biological samples.

Science.gov (United States)

Hernandez-Zavala, Araceli; Drobna, Zuzana; Styblo, Miroslav; Thomas, David J

2009-11-01

Quantitation of iAs and its methylated metabolites in biological samples provides dosimetric information needed to understand dose-response relations. Here, methods are described for separation of inorganic and mono-, di-, and trimethylated arsenicals by thin layer chromatography. This method has been extensively used to track the metabolism of the radionuclide [(73)As] in a variety of in vitro assay systems. In addition, a hydride generation-cryotrapping-gas chromatography-atomic absorption spectrometric method is described for the quantitation of arsenicals in biological samples. This method uses pH-selective hydride generation to differentiate among arsenicals containing trivalent or pentavalent arsenic.

Fluorescence-intensity multiplexing: simultaneous seven-marker, two-color immunophenotyping using flow cytometry.

Science.gov (United States)

Bradford, Jolene A; Buller, Gayle; Suter, Michael; Ignatius, Michael; Beechem, Joseph M

2004-10-01

Conventional immuno-based multiparameter flow cytometric analysis has been limited by the requirement of a dedicated detection channel for each antibody-fluorophore set. To address the need to resolve multiple biological targets simultaneously, flow cytometers with as many as 10-15 detection channels have been developed. In this study, a new Zenon immunolabeling technology is developed that allows for multiple antigen detection per detection channel using a single fluorophore, through a unique method of fluorescence-intensity multiplexing. By varying the Zenon labeling reagent-to-antibody molar ratio, the fluorescence intensity of the antibody-labeled cellular targets can be used as a unique identifier. Although demonstrated in the present study with lymphocyte immunophenotyping, this approach is broadly applicable for any immuno-based multiplexed flow cytomety assay. Lymphocyte immunophenotyping of 38 clinical blood specimens using CD3, CD4, CD8, CD16, CD56, CD19, and CD20 antibodies was performed using conventional flow cytometric analysis and fluorescence-intensity multiplexing analysis. Conventional analysis measures a single antibody-fluorophore per photomultiplier tube (PMT). Fluorescence-intensity multiplex analysis simultaneously measures seven markers with two PMTs, using Zenon labeling reagent-antibody complexes in a single tube: CD19, CD4, CD8, and CD16 antibodies labeled with Zenon Alexa Fluor 488 Mouse IgG(1) labeling reagent and CD56, CD3, and CD20 antibodies labeled with Zenon R-Phycoerythrin (R-PE) Mouse IgG(1) or IgG(2b) labeling reagents. The lymphocyte immunophenotyping results from fluorescence-intensity multiplexing using Zenon labeling reagents in a single tube were comparable to results from conventional flow cytometric analysis. Simultaneous evaluation of multiple antigens using a single fluorophore can be performed using antibodies labeled with varying ratios of a Zenon labeling reagent. Labeling two sets of antibodies with different Zenon

Simultaneous Determination of Arsenic, Manganese, and Selenium in Biological Materials by Neutron-Activation Analysis

DEFF Research Database (Denmark)

Heydorn, Kaj; Damsgaard, Else

1973-01-01

A new method was developed for the simultaneous determination of arsenic, manganese, and selenium in biological material by thermal-neutron activation analysis. The use of 81 mSe as indicator for selenium permitted a reduction of activation time to 1 hr for a 1 g sample, and the possibility of loss...

How causal analysis can reveal autonomy in models of biological systems

Science.gov (United States)

Marshall, William; Kim, Hyunju; Walker, Sara I.; Tononi, Giulio; Albantakis, Larissa

2017-11-01

Standard techniques for studying biological systems largely focus on their dynamical or, more recently, their informational properties, usually taking either a reductionist or holistic perspective. Yet, studying only individual system elements or the dynamics of the system as a whole disregards the organizational structure of the system-whether there are subsets of elements with joint causes or effects, and whether the system is strongly integrated or composed of several loosely interacting components. Integrated information theory offers a theoretical framework to (1) investigate the compositional cause-effect structure of a system and to (2) identify causal borders of highly integrated elements comprising local maxima of intrinsic cause-effect power. Here we apply this comprehensive causal analysis to a Boolean network model of the fission yeast (Schizosaccharomyces pombe) cell cycle. We demonstrate that this biological model features a non-trivial causal architecture, whose discovery may provide insights about the real cell cycle that could not be gained from holistic or reductionist approaches. We also show how some specific properties of this underlying causal architecture relate to the biological notion of autonomy. Ultimately, we suggest that analysing the causal organization of a system, including key features like intrinsic control and stable causal borders, should prove relevant for distinguishing life from non-life, and thus could also illuminate the origin of life problem. This article is part of the themed issue 'Reconceptualizing the origins of life'.

[Cybernetics and biology].

Science.gov (United States)

Vasil'ev, G F

2013-01-01

Owing to methodical disadvantages, the theory of control still lacks the potential for the analysis of biological systems. To get the full benefit of the method in addition to the algorithmic model of control (as of today the only used model in the theory of control) a parametric model of control is offered to employ. The reasoning for it is explained. The approach suggested provides the possibility to use all potential of the modern theory of control for the analysis of biological systems. The cybernetic approach is shown taking a system of the rise of glucose concentration in blood as an example.

Multi-parameters sensitivity analysis of natural vibration modal for steel arch bridge

Directory of Open Access Journals (Sweden)

WANG Ying

2014-02-01

Full Text Available Because of the vehicle loads and environmental factors,the behaviors of bridge structure in service is becoming deterioration.The modal parameters are important indexes of structure,so sensitivity analysis of natural vibration is an important way to evaluate the behavior of bridge structure.In this paper,using the finite element software Ansys,calculation model of a steel arch bridge was built,and the natural vibration modals were obtained.In order to compare the different sensitivity of material parameters which may affect the natural vibration modal,5 factors were chosen to perform the calculation.The results indicated that different 5 factors had different sensitivity.The leading factor was elastic modulus of arch rib,and the elastic modulus of suspender had little effect to the sensitivity.Another argument was the opposite sensitivity effect happened between the elastic modulus and density of the material.

What Are They Thinking? Automated Analysis of Student Writing about Acid–Base Chemistry in Introductory Biology

Science.gov (United States)

Haudek, Kevin C.; Prevost, Luanna B.; Moscarella, Rosa A.; Merrill, John; Urban-Lurain, Mark

2012-01-01

Students’ writing can provide better insight into their thinking than can multiple-choice questions. However, resource constraints often prevent faculty from using writing assessments in large undergraduate science courses. We investigated the use of computer software to analyze student writing and to uncover student ideas about chemistry in an introductory biology course. Students were asked to predict acid–base behavior of biological functional groups and to explain their answers. Student explanations were rated by two independent raters. Responses were also analyzed using SPSS Text Analysis for Surveys and a custom library of science-related terms and lexical categories relevant to the assessment item. These analyses revealed conceptual connections made by students, student difficulties explaining these topics, and the heterogeneity of student ideas. We validated the lexical analysis by correlating student interviews with the lexical analysis. We used discriminant analysis to create classification functions that identified seven key lexical categories that predict expert scoring (interrater reliability with experts = 0.899). This study suggests that computerized lexical analysis may be useful for automatically categorizing large numbers of student open-ended responses. Lexical analysis provides instructors unique insights into student thinking and a whole-class perspective that are difficult to obtain from multiple-choice questions or reading individual responses. PMID:22949425

Elemental analysis of biological materials. Current problems and techniques with special reference to trace elements

International Nuclear Information System (INIS)

1980-01-01

Selected techniques were reviewed for the assay of trace and minor elements in biological materials. Other relevant information is also presented on the need for such analyses, sampling, sample preparation and analytical quality control. In order to evaluate and compare the applicability of the various analytical techniques on a meaningful and objective basis, the materials chosen for consideration were intended to be typical of a wide range of biological matrics of different elemental compositions, namely Bowen's kale, representing a plant material, and NBS bovine liver, IAEA animal muscle, and blood serum, representing animal tissues. The subject is reviewed under the following headings: on the need for trace element analyses in the life sciences (4 papers); sampling and sample preparation for trace element analysis (2 papers); analytical techniques for trace and minor elements in biological materials (7 papers); analytical quality control (2 papers)

VANESA - A Software Application for the Visualization and Analysis of Networks in Systems Biology Applications

Directory of Open Access Journals (Sweden)

Brinkrolf Christoph

2014-06-01

Full Text Available VANESA is a modeling software for the automatic reconstruction and analysis of biological networks based on life-science database information. Using VANESA, scientists are able to model any kind of biological processes and systems as biological networks. It is now possible for scientists to automatically reconstruct important molecular systems with information from the databases KEGG, MINT, IntAct, HPRD, and BRENDA. Additionally, experimental results can be expanded with database information to better analyze the investigated elements and processes in an overall context. Users also have the possibility to use graph theoretical approaches in VANESA to identify regulatory structures and significant actors within the modeled systems. These structures can then be further investigated in the Petri net environment of VANESA. It is platform-independent, free-of-charge, and available at http://vanesa.sf.net.

OmicsNet: a web-based tool for creation and visual analysis of biological networks in 3D space.

Science.gov (United States)

Zhou, Guangyan; Xia, Jianguo

2018-06-07

Biological networks play increasingly important roles in omics data integration and systems biology. Over the past decade, many excellent tools have been developed to support creation, analysis and visualization of biological networks. However, important limitations remain: most tools are standalone programs, the majority of them focus on protein-protein interaction (PPI) or metabolic networks, and visualizations often suffer from 'hairball' effects when networks become large. To help address these limitations, we developed OmicsNet - a novel web-based tool that allows users to easily create different types of molecular interaction networks and visually explore them in a three-dimensional (3D) space. Users can upload one or multiple lists of molecules of interest (genes/proteins, microRNAs, transcription factors or metabolites) to create and merge different types of biological networks. The 3D network visualization system was implemented using the powerful Web Graphics Library (WebGL) technology that works natively in most major browsers. OmicsNet supports force-directed layout, multi-layered perspective layout, as well as spherical layout to help visualize and navigate complex networks. A rich set of functions have been implemented to allow users to perform coloring, shading, topology analysis, and enrichment analysis. OmicsNet is freely available at http://www.omicsnet.ca.

A Comparative Analysis of Numbers and Biology Content Domains between Turkey and the USA

Science.gov (United States)

Incikabi, Lutfi; Ozgelen, Sinan; Tjoe, Hartono

2012-01-01

This study aimed to compare Mathematics and Science programs focusing on TIMSS content domains of Numbers and Biology that produced the largest achievement gap among students from Turkey and the USA. Specifically, it utilized the content analysis method within Turkish and New York State (NYS) frameworks. The procedures of study included matching…

Compatibility analysis of 3D printer resin for biological applications

KAUST Repository

Sivashankar, Shilpa

2016-08-30

The salient features of microfluidics such as reduced cost, handling small sample and reagent volumes and less time required to fabricate the devices has inspired the present work. The incompatibility of three-dimensional printer resins in their native form and the method to improve their compatibility to many biological processes via surface modification are reported. The compatibility of the material to build microfluidic devices was evaluated in three different ways: (i) determining if the ultraviolet (UV) cured resin inhibits the polymerase chain reaction (PCR), i.e. testing devices for PCR compatibility; (ii) observing agglutination complex formed on the surface of the UV cured resin when anti-C-reactive protein (CRP) antibodies and CRP proteins were allowed to agglutinate; and (iii) by culturing human embryonic kidney cell line cells and testing for its attachment and viability. It is shown that only a few among four in its native form could be used for fabrication of microchannels and that had the least effect on biological molecules that could be used for PCR and protein interactions and cells, whereas the others were used after treating the surface. Importance in building lab-on-chip/micrototal analysis systems and organ-on-chip devices is found.

Multi-Parameter Analysis of Surface Finish in Electro-Discharge Machining of Tool Steels

Directory of Open Access Journals (Sweden)

Cornelia Victoria Anghel

2006-10-01

Full Text Available The paper presents a multi- parameter analysis of surface finish imparted to tool-steel plates by electro-discharge machining (EDM is presented. The interrelationship between surface texture parameters and process parameters is emphasized. An increased number of parameters is studied including amplitude, spacing, hybrid and fractal parameters,, as well. The correlation of these parameters with the machining conditions is investigated. Observed characteristics become more pronounced, when intensifying machining conditions. Close correlation exists between certain surface finish parameters and EDM input variables and single and multiple statistical regression models are developed.

Applicability and feasibility of systematic review for performing evidence-based risk assessment in food and feed safety

DEFF Research Database (Denmark)

Aiassa, E.; Higgins, J.P.T.; Frampton, G. K.

2015-01-01

for answering questions in health care, and can be implemented to minimise biases in food and feed safety risk assessment. However, no methodological frameworks exist for refining risk assessment multi-parameter models into questions suitable for systematic review, and use of meta-analysis to estimate all......Food and feed safety risk assessment uses multi-parameter models to evaluate the likelihood of adverse events associated with exposure to hazards in human health, plant health, animal health, animal welfare and the environment. Systematic review and meta-analysis are established methods...... parameters in the risk model. This approach to planning and prioritising systematic review seems to have useful implications for producing evidence-based food and feed safety risk assessment....

A Systems Biology Analysis Unfolds the Molecular Pathways and Networks of Two Proteobacteria in Spaceflight and Simulated Microgravity Conditions.

Science.gov (United States)

Roy, Raktim; Shilpa, P Phani; Bagh, Sangram

2016-09-01

Bacteria are important organisms for space missions due to their increased pathogenesis in microgravity that poses risks to the health of astronauts and for projected synthetic biology applications at the space station. We understand little about the effect, at the molecular systems level, of microgravity on bacteria, despite their significant incidence. In this study, we proposed a systems biology pipeline and performed an analysis on published gene expression data sets from multiple seminal studies on Pseudomonas aeruginosa and Salmonella enterica serovar Typhimurium under spaceflight and simulated microgravity conditions. By applying gene set enrichment analysis on the global gene expression data, we directly identified a large number of new, statistically significant cellular and metabolic pathways involved in response to microgravity. Alteration of metabolic pathways in microgravity has rarely been reported before, whereas in this analysis metabolic pathways are prevalent. Several of those pathways were found to be common across studies and species, indicating a common cellular response in microgravity. We clustered genes based on their expression patterns using consensus non-negative matrix factorization. The genes from different mathematically stable clusters showed protein-protein association networks with distinct biological functions, suggesting the plausible functional or regulatory network motifs in response to microgravity. The newly identified pathways and networks showed connection with increased survival of pathogens within macrophages, virulence, and antibiotic resistance in microgravity. Our work establishes a systems biology pipeline and provides an integrated insight into the effect of microgravity at the molecular systems level. Systems biology-Microgravity-Pathways and networks-Bacteria. Astrobiology 16, 677-689.

A tailored 200 parameter VME based data acquisition system for IBA at the Lund Ion Beam Analysis Facility – Hardware and software

International Nuclear Information System (INIS)

Elfman, Mikael; Ros, Linus; Kristiansson, Per; Nilsson, E.J. Charlotta; Pallon, Jan

2016-01-01

With the recent advances towards modern Ion Beam Analysis (IBA), going from one- or few-parameter detector systems to multi-parameter systems, it has been necessary to expand and replace the more than twenty years old CAMAC based system. A new VME multi-parameter (presently up to 200 channels) data acquisition and control system has been developed and implemented at the Lund Ion Beam Analysis Facility (LIBAF). The system is based on the VX-511 Single Board Computer (SBC), acting as master with arbiter functionality and consists of standard VME modules like Analog to Digital Converters (ADC’s), Charge to Digital Converters (QDC’s), Time to Digital Converters (TDC’s), scaler’s, IO-cards, high voltage and waveform units. The modules have been specially selected to support all of the present detector systems in the laboratory, with the option of future expansion. Typically, the detector systems consist of silicon strip detectors, silicon drift detectors and scintillator detectors, for detection of charged particles, X-rays and γ-rays. The data flow of the raw data buffers out from the VME bus to the final storage place on a 16 terabyte network attached storage disc (NAS-disc) is described. The acquisition process, remotely controlled over one of the SBCs ethernet channels, is also discussed. The user interface is written in the Kmax software package, and is used to control the acquisition process as well as for advanced online and offline data analysis through a user-friendly graphical user interface (GUI). In this work the system implementation, layout and performance are presented. The user interface and possibilities for advanced offline analysis are also discussed and illustrated.

A tailored 200 parameter VME based data acquisition system for IBA at the Lund Ion Beam Analysis Facility – Hardware and software

Energy Technology Data Exchange (ETDEWEB)

Elfman, Mikael, E-mail: Mikael.Elfman@nuclear.lu.se; Ros, Linus; Kristiansson, Per; Nilsson, E.J. Charlotta; Pallon, Jan

2016-03-15

With the recent advances towards modern Ion Beam Analysis (IBA), going from one- or few-parameter detector systems to multi-parameter systems, it has been necessary to expand and replace the more than twenty years old CAMAC based system. A new VME multi-parameter (presently up to 200 channels) data acquisition and control system has been developed and implemented at the Lund Ion Beam Analysis Facility (LIBAF). The system is based on the VX-511 Single Board Computer (SBC), acting as master with arbiter functionality and consists of standard VME modules like Analog to Digital Converters (ADC’s), Charge to Digital Converters (QDC’s), Time to Digital Converters (TDC’s), scaler’s, IO-cards, high voltage and waveform units. The modules have been specially selected to support all of the present detector systems in the laboratory, with the option of future expansion. Typically, the detector systems consist of silicon strip detectors, silicon drift detectors and scintillator detectors, for detection of charged particles, X-rays and γ-rays. The data flow of the raw data buffers out from the VME bus to the final storage place on a 16 terabyte network attached storage disc (NAS-disc) is described. The acquisition process, remotely controlled over one of the SBCs ethernet channels, is also discussed. The user interface is written in the Kmax software package, and is used to control the acquisition process as well as for advanced online and offline data analysis through a user-friendly graphical user interface (GUI). In this work the system implementation, layout and performance are presented. The user interface and possibilities for advanced offline analysis are also discussed and illustrated.

Micro-computed tomography imaging and analysis in developmental biology and toxicology.

Science.gov (United States)

Wise, L David; Winkelmann, Christopher T; Dogdas, Belma; Bagchi, Ansuman

2013-06-01

Micro-computed tomography (micro-CT) is a high resolution imaging technique that has expanded and strengthened in use since it was last reviewed in this journal in 2004. The technology has expanded to include more detailed analysis of bone, as well as soft tissues, by use of various contrast agents. It is increasingly applied to questions in developmental biology and developmental toxicology. Relatively high-throughput protocols now provide a powerful and efficient means to evaluate embryos and fetuses subjected to genetic manipulations or chemical exposures. This review provides an overview of the technology, including scanning, reconstruction, visualization, segmentation, and analysis of micro-CT generated images. This is followed by a review of more recent applications of the technology in some common laboratory species that highlight the diverse issues that can be addressed. Copyright © 2013 Wiley Periodicals, Inc.

Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease.

Science.gov (United States)

Torres, Matthew P; Dewhurst, Henry; Sundararaman, Niveda

2016-11-01

Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function - a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) - a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al., 2015). Here, we apply SAPH-ire to the set of eukaryotic protein families containing experimental PTM and 3D structure data - capturing 1,325 protein families with 50,839 unique PTM sites organized into 31,747 modified alignment positions (MAPs), of which 2010 (∼6%) possess known biological function. Here, we show that using an artificial neural network model (SAPH-ire NN) trained to identify MAP hotspots with biological function results in prediction outcomes that far surpass the use of single hotspot features, including nearest neighbor PTM clustering methods. We find the greatest enhancement in prediction for positions with PTM counts of five or less, which represent 98% of all MAPs in the eukaryotic proteome and 90% of all MAPs found to have biological function. Analysis of the top 1092 MAP hotspots revealed 267 of truly unknown function (containing 5443 distinct PTMs). Of these, 165 hotspots could be mapped to human KEGG pathways for normal and/or disease physiology. Many high-ranking hotspots were also found to be disease-associated pathogenic sites of amino acid substitution despite the lack of observable PTM in the human protein family member. Taken together, these experiments demonstrate that the functional relevance of a PTM can be predicted very effectively by neural network models, revealing a large but testable

A critical analysis of the biological impacts of plasticizers on wildlife

Science.gov (United States)

Oehlmann, Jörg; Schulte-Oehlmann, Ulrike; Kloas, Werner; Jagnytsch, Oana; Lutz, Ilka; Kusk, Kresten O.; Wollenberger, Leah; Santos, Eduarda M.; Paull, Gregory C.; Van Look, Katrien J. W.; Tyler, Charles R.

2009-01-01

This review provides a critical analysis of the biological effects of the most widely used plasticizers, including dibutyl phthalate, diethylhexyl phthalate, dimethyl phthalate, butyl benzyl phthalate and bisphenol A (BPA), on wildlife, with a focus on annelids (both aquatic and terrestrial), molluscs, crustaceans, insects, fish and amphibians. Moreover, the paper provides novel data on the biological effects of some of these plasticizers in invertebrates, fish and amphibians. Phthalates and BPA have been shown to affect reproduction in all studied animal groups, to impair development in crustaceans and amphibians and to induce genetic aberrations. Molluscs, crustaceans and amphibians appear to be especially sensitive to these compounds, and biological effects are observed at environmentally relevant exposures in the low ng l−1 to µg l−1 range. In contrast, most effects in fish (except for disturbance in spermatogenesis) occur at higher concentrations. Most plasticizers appear to act by interfering with the functioning of various hormone systems, but some phthalates have wider pathways of disruption. Effect concentrations of plasticizers in laboratory experiments coincide with measured environmental concentrations, and thus there is a very real potential for effects of these chemicals on some wildlife populations. The most striking gaps in our current knowledge on the impacts of plasticizers on wildlife are the lack of data for long-term exposures to environmentally relevant concentrations and their ecotoxicity when part of complex mixtures. Furthermore, the hazard of plasticizers has been investigated in annelids, molluscs and arthropods only, and given the sensitivity of some invertebrates, effects assessments are warranted in other invertebrate phyla. PMID:19528055

Enhancing Interdisciplinary Mathematics and Biology Education: A Microarray Data Analysis Course Bridging These Disciplines

Science.gov (United States)

Tra, Yolande V.; Evans, Irene M.

2010-01-01

"BIO2010" put forth the goal of improving the mathematical educational background of biology students. The analysis and interpretation of microarray high-dimensional data can be very challenging and is best done by a statistician and a biologist working and teaching in a collaborative manner. We set up such a collaboration and designed a course on…

Biological sequence analysis

DEFF Research Database (Denmark)

Durbin, Richard; Eddy, Sean; Krogh, Anders Stærmose

This book provides an up-to-date and tutorial-level overview of sequence analysis methods, with particular emphasis on probabilistic modelling. Discussed methods include pairwise alignment, hidden Markov models, multiple alignment, profile searches, RNA secondary structure analysis, and phylogene...

Analysis of coincidence {gamma}-ray spectra using advanced background elimination, unfolding and fitting algorithms

Energy Technology Data Exchange (ETDEWEB)

Morhac, M. E-mail: fyzimiro@savba.skfyzimiro@flnr.jinr.ru; Matousek, V. E-mail: matousek@savba.sk; Kliman, J.; Krupa, L.L.; Jandel, M

2003-04-21

The efficient algorithms to analyze multiparameter {gamma}-ray spectra are presented. They allow to search for peaks, to separate peaks from background, to improve the resolution and to fit 1-, 2-, 3-parameter {gamma}-ray spectra.

A complex method for the neutron activation analysis of biological materials

International Nuclear Information System (INIS)

Ordogh, M.

1978-05-01

The destructive and nondestructive approach of neutron activation analysis used by the author is reviewed to determine some trace elements in biological materials: Ca, Cl, Co, Cu, Fe, K, Mg, Mn, Na, Rb, Sb, Sc, V and Zn. Bowen's kale was used to determine the accuracy and reliability. The parameters obtained were confirmed by participating in round robins organized by the IAEA: in which potato powder and animal bone have been analyzed for Zn, Co, Fe, Cr, Mn, Rb, Na, K and Cu. Tabulated results are given and compared with recommended values and literature data. Gamma spectra are shown. (T.G.)

Quantitative analysis of biological fluids by electron probe and X ray spectrometry

International Nuclear Information System (INIS)

Girod, Chantal

1986-01-01

In order to know the kidney normal operation and to have an insight on cellular transport mechanisms and hormonal regulations at the nephron level, a technique based on the use of an electron probe has been developed for the elemental analysis of micro-volumes of biological fluids. This academic document reports applications of this technique on animals on which such fluids have been sampled at different levels of the nephron. As these samples are available in too small volumes to be dosed by conventional methods, they have been quantitatively analysed by using an electronic probe based analyser in order to determine concentrations of all elements with an atomic number greater than that of carbon. After a presentation of the implemented method and hardware, the author thus describes how an analysis is performed, and reports and discusses an example (analysis conditions, data acquisition, data processing, minimum detectable concentration, reasons for measurement scattering)

Optoelectronic transport properties in amorphous/crystalline silicon solar cell heterojunctions measured by frequency-domain photocarrier radiometry: Multi-parameter measurement reliability and precision studies

International Nuclear Information System (INIS)

Zhang, Y.; Melnikov, A.; Mandelis, A.; Halliop, B.; Kherani, N. P.; Zhu, R.

2015-01-01

A theoretical one-dimensional two-layer linear photocarrier radiometry (PCR) model including the presence of effective interface carrier traps was used to evaluate the transport parameters of p-type hydrogenated amorphous silicon (a-Si:H) and n-type crystalline silicon (c-Si) passivated by an intrinsic hydrogenated amorphous silicon (i-layer) nanolayer. Several crystalline Si heterojunction structures were examined to investigate the influence of the i-layer thickness and the doping concentration of the a-Si:H layer. The experimental data of a series of heterojunction structures with intrinsic thin layers were fitted to PCR theory to gain insight into the transport properties of these devices. The quantitative multi-parameter results were studied with regard to measurement reliability (uniqueness) and precision using two independent computational best-fit programs. The considerable influence on the transport properties of the entire structure of two key parameters that can limit the performance of amorphous thin film solar cells, namely, the doping concentration of the a-Si:H layer and the i-layer thickness was demonstrated. It was shown that PCR can be applied to the non-destructive characterization of a-Si:H/c-Si heterojunction solar cells yielding reliable measurements of the key parameters

Optoelectronic transport properties in amorphous/crystalline silicon solar cell heterojunctions measured by frequency-domain photocarrier radiometry: multi-parameter measurement reliability and precision studies.

Science.gov (United States)

Zhang, Y; Melnikov, A; Mandelis, A; Halliop, B; Kherani, N P; Zhu, R

2015-03-01

A theoretical one-dimensional two-layer linear photocarrier radiometry (PCR) model including the presence of effective interface carrier traps was used to evaluate the transport parameters of p-type hydrogenated amorphous silicon (a-Si:H) and n-type crystalline silicon (c-Si) passivated by an intrinsic hydrogenated amorphous silicon (i-layer) nanolayer. Several crystalline Si heterojunction structures were examined to investigate the influence of the i-layer thickness and the doping concentration of the a-Si:H layer. The experimental data of a series of heterojunction structures with intrinsic thin layers were fitted to PCR theory to gain insight into the transport properties of these devices. The quantitative multi-parameter results were studied with regard to measurement reliability (uniqueness) and precision using two independent computational best-fit programs. The considerable influence on the transport properties of the entire structure of two key parameters that can limit the performance of amorphous thin film solar cells, namely, the doping concentration of the a-Si:H layer and the i-layer thickness was demonstrated. It was shown that PCR can be applied to the non-destructive characterization of a-Si:H/c-Si heterojunction solar cells yielding reliable measurements of the key parameters.

Lipidomic analysis of biological samples: Comparison of liquid chromatography, supercritical fluid chromatography and direct infusion mass spectrometry methods.

Science.gov (United States)

Lísa, Miroslav; Cífková, Eva; Khalikova, Maria; Ovčačíková, Magdaléna; Holčapek, Michal

2017-11-24

Lipidomic analysis of biological samples in a clinical research represents challenging task for analytical methods given by the large number of samples and their extreme complexity. In this work, we compare direct infusion (DI) and chromatography - mass spectrometry (MS) lipidomic approaches represented by three analytical methods in terms of comprehensiveness, sample throughput, and validation results for the lipidomic analysis of biological samples represented by tumor tissue, surrounding normal tissue, plasma, and erythrocytes of kidney cancer patients. Methods are compared in one laboratory using the identical analytical protocol to ensure comparable conditions. Ultrahigh-performance liquid chromatography/MS (UHPLC/MS) method in hydrophilic interaction liquid chromatography mode and DI-MS method are used for this comparison as the most widely used methods for the lipidomic analysis together with ultrahigh-performance supercritical fluid chromatography/MS (UHPSFC/MS) method showing promising results in metabolomics analyses. The nontargeted analysis of pooled samples is performed using all tested methods and 610 lipid species within 23 lipid classes are identified. DI method provides the most comprehensive results due to identification of some polar lipid classes, which are not identified by UHPLC and UHPSFC methods. On the other hand, UHPSFC method provides an excellent sensitivity for less polar lipid classes and the highest sample throughput within 10min method time. The sample consumption of DI method is 125 times higher than for other methods, while only 40μL of organic solvent is used for one sample analysis compared to 3.5mL and 4.9mL in case of UHPLC and UHPSFC methods, respectively. Methods are validated for the quantitative lipidomic analysis of plasma samples with one internal standard for each lipid class. Results show applicability of all tested methods for the lipidomic analysis of biological samples depending on the analysis requirements

Toward synthesizing executable models in biology.

Science.gov (United States)

Fisher, Jasmin; Piterman, Nir; Bodik, Rastislav

2014-01-01

Over the last decade, executable models of biological behaviors have repeatedly provided new scientific discoveries, uncovered novel insights, and directed new experimental avenues. These models are computer programs whose execution mechanistically simulates aspects of the cell's behaviors. If the observed behavior of the program agrees with the observed biological behavior, then the program explains the phenomena. This approach has proven beneficial for gaining new biological insights and directing new experimental avenues. One advantage of this approach is that techniques for analysis of computer programs can be applied to the analysis of executable models. For example, one can confirm that a model agrees with experiments for all possible executions of the model (corresponding to all environmental conditions), even if there are a huge number of executions. Various formal methods have been adapted for this context, for example, model checking or symbolic analysis of state spaces. To avoid manual construction of executable models, one can apply synthesis, a method to produce programs automatically from high-level specifications. In the context of biological modeling, synthesis would correspond to extracting executable models from experimental data. We survey recent results about the usage of the techniques underlying synthesis of computer programs for the inference of biological models from experimental data. We describe synthesis of biological models from curated mutation experiment data, inferring network connectivity models from phosphoproteomic data, and synthesis of Boolean networks from gene expression data. While much work has been done on automated analysis of similar datasets using machine learning and artificial intelligence, using synthesis techniques provides new opportunities such as efficient computation of disambiguating experiments, as well as the ability to produce different kinds of models automatically from biological data.

Ecology Content in Introductory Biology Courses: A Comparative Analysis

Science.gov (United States)

Pool, Richard F.; Turner, Gregory D.; Böttger, S. Anne

2013-01-01

In recent years the need for ecological literacy and problem solving has increased, but there is no evidence that this need is reflected by increased ecology coverage at institutions of higher education (IHE) across the United States. Because introductory biology courses may serve to direct student interest toward particular biological categories…

Reducing Future International Chemical and Biological Dangers.

Energy Technology Data Exchange (ETDEWEB)

Haddal, Chad [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Bull, Diana L. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Hernandez, Patricia Marie [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Foley, John T. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

2017-12-01

The International Biological and Chemical Threat Reduction Program at Sandia National Laboratories is developing a 15 - year technology road map in support the United States Government efforts to reduce international chemical and biological dangers . In 2017, the program leadership chartered an analysis team to explore dangers in the future international chemical and biological landscape through engagements with national security experts within and beyond Sandia to gain a multidisciplinary perspective on the future . This report offers a hi gh level landscape of future chemical and biological dangers based upon analysis of those engagements and provides support for further technology road map development.

Nanoplasmonic and Microfluidic Devices for Biological Sensing

KAUST Repository

Perozziello, G.; Giugni, Andrea; Allione, Marco; Torre, Bruno; Das, Gobind; Coluccio, M. L.; Marini, Monica; Tirinato, Luca; Moretti, Manola; Limongi, Tania; Candeloro, P.; Di Fabrizio, Enzo M.

2017-01-01

In this chapter we report about recent advances on the development and application of 2D and 3D plasmonic nanostructures used for sensing of biological samples by Raman spectroscopy at unprecedented resolution of analysis. Besides, we explain how the integration of these nanodevices in a microfluidic apparatus can simplify the analysis of biological samples. In the first part we introduce and motivate the convenience of using nanoplasmonic enhancers and Raman spectroscopy for biological sensing, describing the phenomena and the current approaches to fabricate nanoplasmonic structures. In the second part, we explain how specific multi-element devices produce the optimal enhancement of the Raman scattering. We report cases where biological sensing of DNA was performed at few molecules level with nanometer spatial resolutions. Finally, we show an example of microfluidic device integrating plasmonic nanodevices to sort and drive biological samples, like living cells, towards the optical probe in order to obtain optimal conditions of analysis.

Nanoplasmonic and Microfluidic Devices for Biological Sensing

KAUST Repository

Perozziello, G.

2017-02-16

In this chapter we report about recent advances on the development and application of 2D and 3D plasmonic nanostructures used for sensing of biological samples by Raman spectroscopy at unprecedented resolution of analysis. Besides, we explain how the integration of these nanodevices in a microfluidic apparatus can simplify the analysis of biological samples. In the first part we introduce and motivate the convenience of using nanoplasmonic enhancers and Raman spectroscopy for biological sensing, describing the phenomena and the current approaches to fabricate nanoplasmonic structures. In the second part, we explain how specific multi-element devices produce the optimal enhancement of the Raman scattering. We report cases where biological sensing of DNA was performed at few molecules level with nanometer spatial resolutions. Finally, we show an example of microfluidic device integrating plasmonic nanodevices to sort and drive biological samples, like living cells, towards the optical probe in order to obtain optimal conditions of analysis.

Teaching Real Data Interpretation with Models (TRIM): Analysis of Student Dialogue in a Large-Enrollment Cell and Developmental Biology Course

Science.gov (United States)

Zagallo, Patricia; Meddleton, Shanice; Bolger, Molly S.

2016-01-01

We present our design for a cell biology course to integrate content with scientific practices, specifically data interpretation and model-based reasoning. A 2-year research project within this course allowed us to understand how students interpret authentic biological data in this setting. Through analysis of written work, we measured the extent…

Multiple Realizability and Biological Laws

NARCIS (Netherlands)

Raerinne, Jani P.; Eronen, Markus I.

2012-01-01

We critically analyze Alexander Rosenberg's argument based on the multiple realizability of biological properties that there are no biological laws. The argument is intuitive and suggestive. Nevertheless, a closer analysis reveals that the argument rests on dubious assumptions about the nature of

PENGEMBANGAN PENUNTUN PRAKTIKUM BIOLOGI UMUM BERBASIS INKUIRI TERBIMBING MAHASISWA BIOLOGI STKIP PAYAKUMBUH

Directory of Open Access Journals (Sweden)

Sri Nengsi

2016-05-01

Full Text Available One of supporting the implementation of the practicum is the practical guidence. To increase motivation, activities, and learning outcomes it is used inquiry based practical guide for students are invited to experiment with doing practical activities with scientific. The purpose of this study was to reveal the validity, practicalities, and guiding the resulting effectiveness of guidence inquiry based on the general biology lesson for students of biology education STKIP Payakumbuh. This research is the development of Plomp development model which consists of three phases: problem identification and needs analysis, design development and implementation, evaluation. The results of this study indicate that the development of practical guidance guided inquiry based general biology for students of biology education STKIP Payakumbuh valid, practically and effectively.

Correlating Multimodal Physical Sensor Information with Biological Analysis in Ultra Endurance Cycling

Directory of Open Access Journals (Sweden)

Giles D.Warrington

2010-07-01

Full Text Available The sporting domain has traditionally been used as a testing ground for new technologies which subsequently make their way into the public domain. This includes sensors. In this article a range of physical and biological sensors deployed in a 64 hour ultra-endurance non-stop cycling race are described. A novel algorithm to estimate the energy expenditure while cycling and resting during the event are outlined. Initial analysis in this noisy domain of “sensors in the field” are very encouraging and represent a first with respect to cycling.

Towards Synthesizing Executable Models in Biology

Directory of Open Access Journals (Sweden)

Jasmin eFisher

2014-12-01

Full Text Available Over the last decade, executable models of biological behaviors have repeatedly provided new scientific discoveries, uncovered novel insights, and directed new experimental avenues. These models are computer programs whose execution mechanistically simulates aspects of the cell’s behaviors. If the observed behavior of the program agrees with the observed biological behavior, then the program explains the phenomena. This approach has proven beneficial for gaining new biological insights and directing new experimental avenues. One advantage of this approach is that techniques for analysis of computer programs can be applied to the analysis of executable models. For example, one can confirm that a model agrees with experiments for all possible executions of the model (corresponding to all environmental conditions, even if there are a huge number of executions. Various formal methods have been adapted for this context, for example, model checking or symbolic analysis of state spaces. To avoid manual construction of executable models, one can apply synthesis, a method to produce programs automatically from high-level specifications. In the context of biological modelling, synthesis would correspond to extracting executable models from experimental data. We survey recent results about the usage of the techniques underlying synthesis of computer programs for the inference of biological models from experimental data. We describe synthesis of biological models from curated mutation experiment data, inferring network connectivity models from phosphoproteomic data, and synthesis of Boolean networks from gene expression data. While much work has been done on automated analysis of similar datasets using machine learning and artificial intelligence, using synthesis techniques provides new opportunities such as efficient computation of disambiguating experiments, as well as the ability to produce different kinds of models automatically from biological data.

Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

Science.gov (United States)

Chen, Bor-Sen; Wu, Chia-Chou

2013-01-01

Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i) system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii) system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii) system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv) systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering. PMID:24709875

Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

Directory of Open Access Journals (Sweden)

Bor-Sen Chen

2013-10-01

Full Text Available Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering.

Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease*

Science.gov (United States)

Dewhurst, Henry; Sundararaman, Niveda

2016-01-01

Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function - a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) - a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al., 2015). Here, we apply SAPH-ire to the set of eukaryotic protein families containing experimental PTM and 3D structure data - capturing 1,325 protein families with 50,839 unique PTM sites organized into 31,747 modified alignment positions (MAPs), of which 2010 (∼6%) possess known biological function. Here, we show that using an artificial neural network model (SAPH-ire NN) trained to identify MAP hotspots with biological function results in prediction outcomes that far surpass the use of single hotspot features, including nearest neighbor PTM clustering methods. We find the greatest enhancement in prediction for positions with PTM counts of five or less, which represent 98% of all MAPs in the eukaryotic proteome and 90% of all MAPs found to have biological function. Analysis of the top 1092 MAP hotspots revealed 267 of truly unknown function (containing 5443 distinct PTMs). Of these, 165 hotspots could be mapped to human KEGG pathways for normal and/or disease physiology. Many high-ranking hotspots were also found to be disease-associated pathogenic sites of amino acid substitution despite the lack of observable PTM in the human protein family member. Taken together, these experiments demonstrate that the functional relevance of a PTM can be predicted very effectively by neural network models, revealing a large but testable

The common extremalities in biology and physics maximum energy dissipation principle in chemistry, biology, physics and evolution

CERN Document Server

Moroz, Adam

2011-01-01

This book is the first unified systemic description of dissipative phenomena, taking place in biology, and non-dissipative (conservative) phenomena, which is more relevant to physics. Fully updated and revised, this new edition extends our understanding of nonlinear phenomena in biology and physics from the extreme / optimal perspective. The first book to provide understanding of physical phenomena from a biological perspective and biological phenomena from a physical perspective Discusses emerging fields and analysis Provides examples.

Compartmental study of biological systems

International Nuclear Information System (INIS)

Moretti, J.L.

1975-01-01

The compartmental analysis of biological system is dealt with on several chapters devoted successively to: terminology; a mathematical and symbolic account of a system at equilibrium; different compartment systems; analysis of the experimental results. For this it is pointed out that the application of compartmental systems to biological phenomena is not always without danger. Sometimes the compartmental system established in a reference subject fails to conform in the patient. The compartments can divide into two or join together, completely changing the aspect of the system so that parameters calculated with the old model become entirely false. The conclusion is that the setting up of a compartmental system to represent a biological phenomenon is a tricky undertaking and the results must be constantly criticized and questioned [fr

From biology to mathematical models and back: teaching modeling to biology students, and biology to math and engineering students.

Science.gov (United States)

Chiel, Hillel J; McManus, Jeffrey M; Shaw, Kendrick M

2010-01-01

We describe the development of a course to teach modeling and mathematical analysis skills to students of biology and to teach biology to students with strong backgrounds in mathematics, physics, or engineering. The two groups of students have different ways of learning material and often have strong negative feelings toward the area of knowledge that they find difficult. To give students a sense of mastery in each area, several complementary approaches are used in the course: 1) a "live" textbook that allows students to explore models and mathematical processes interactively; 2) benchmark problems providing key skills on which students make continuous progress; 3) assignment of students to teams of two throughout the semester; 4) regular one-on-one interactions with instructors throughout the semester; and 5) a term project in which students reconstruct, analyze, extend, and then write in detail about a recently published biological model. Based on student evaluations and comments, an attitude survey, and the quality of the students' term papers, the course has significantly increased the ability and willingness of biology students to use mathematical concepts and modeling tools to understand biological systems, and it has significantly enhanced engineering students' appreciation of biology.

From Biology to Mathematical Models and Back: Teaching Modeling to Biology Students, and Biology to Math and Engineering Students

Science.gov (United States)

McManus, Jeffrey M.; Shaw, Kendrick M.

2010-01-01

We describe the development of a course to teach modeling and mathematical analysis skills to students of biology and to teach biology to students with strong backgrounds in mathematics, physics, or engineering. The two groups of students have different ways of learning material and often have strong negative feelings toward the area of knowledge that they find difficult. To give students a sense of mastery in each area, several complementary approaches are used in the course: 1) a “live” textbook that allows students to explore models and mathematical processes interactively; 2) benchmark problems providing key skills on which students make continuous progress; 3) assignment of students to teams of two throughout the semester; 4) regular one-on-one interactions with instructors throughout the semester; and 5) a term project in which students reconstruct, analyze, extend, and then write in detail about a recently published biological model. Based on student evaluations and comments, an attitude survey, and the quality of the students' term papers, the course has significantly increased the ability and willingness of biology students to use mathematical concepts and modeling tools to understand biological systems, and it has significantly enhanced engineering students' appreciation of biology. PMID:20810957

The determination of iodine in biological media using radioactivation analysis (1962)

International Nuclear Information System (INIS)

Comar, D.

1962-06-01

The object of this study is to show that the application of radioactivation analysis to the determination of iodine in biological media makes it possible to measure iodine concentrations of the order of 0.0001 μg. After a review of the chemical methods with a mention of the difficulties they present, the optimum conditions for the determination of iodine in biological liquids are given. Three methods are described: - the first consists of a chemical treatment which liberates the protein bound iodine in an inorganic form. After distillation this iodine is irradiated in a flux of thermal neutrons. The induced radioactivity is compared to that of a standard sample irradiated in the same conditions by γ spectrometry. - the second method which is of more general application consists in irradiating the sample and then extracting the iodine; its induced radio-activity is then measured by β-counting. - the third method measures the iodine directly in the thyroid tissue by anti-compton spectrometry. The sensitivity, the reproducibility and the accuracy are discussed. Some applications are described: determination of iodine in its various organic forms in serum, determination of iodine in urines, in food-stuffs, etc., in the thyroid tissue, etc. (author) [fr

Sesquiterpene Lactones from Artemisia Genus: Biological Activities and Methods of Analysis

Directory of Open Access Journals (Sweden)

Bianca Ivanescu

2015-01-01

Full Text Available Sesquiterpene lactones are a large group of natural compounds, found primarily in plants of Asteraceae family, with over 5000 structures reported to date. Within this family, genus Artemisia is very well represented, having approximately 500 species characterized by the presence of eudesmanolides and guaianolides, especially highly oxygenated ones, and rarely of germacranolides. Sesquiterpene lactones exhibit a wide range of biological activities, such as antitumor, anti-inflammatory, analgesic, antiulcer, antibacterial, antifungal, antiviral, antiparasitic, and insect deterrent. Many of the biological activities are attributed to the α-methylene-γ-lactone group in their molecule which reacts through a Michael-addition with free sulfhydryl or amino groups in proteins and alkylates them. Due to the fact that most sesquiterpene lactones are thermolabile, less volatile compounds, they present no specific chromophores in the molecule and are sensitive to acidic and basic mediums, and their identification and quantification represent a difficult task for the analyst. Another problematic aspect is represented by the complexity of vegetal samples, which may contain compounds that can interfere with the analysis. Therefore, this paper proposes an overview of the methods used for the identification and quantification of sesquiterpene lactones found in Artemisia genus, as well as the optimal conditions for their extraction and separation.

Bridging the data gaps in the epidemiology of hepatitis C virus infection in Malaysia using multi-parameter evidence synthesis.

Science.gov (United States)

McDonald, Scott A; Mohamed, Rosmawati; Dahlui, Maznah; Naning, Herlianna; Kamarulzaman, Adeeba

2014-11-07

Collecting adequate information on key epidemiological indicators is a prerequisite to informing a public health response to reduce the impact of hepatitis C virus (HCV) infection in Malaysia. Our goal was to overcome the acute data shortage typical of low/middle income countries using statistical modelling to estimate the national HCV prevalence and the distribution over transmission pathways as of the end of 2009. Multi-parameter evidence synthesis methods were applied to combine all available relevant data sources - both direct and indirect - that inform the epidemiological parameters of interest. An estimated 454,000 (95% credible interval [CrI]: 392,000 to 535,000) HCV antibody-positive individuals were living in Malaysia in 2009; this represents 2.5% (95% CrI: 2.2-3.0%) of the population aged 15-64 years. Among males of Malay ethnicity, for 77% (95% CrI: 69-85%) the route of probable transmission was active or a previous history of injecting drugs. The corresponding proportions were smaller for male Chinese and Indian/other ethnic groups (40% and 71%, respectively). The estimated prevalence in females of all ethnicities was 1% (95% CrI: 0.6 to 1.4%); 92% (95% CrI: 88 to 95%) of infections were attributable to non-drug injecting routes of transmission. The prevalent number of persons living with HCV infection in Malaysia is estimated to be very high. Low/middle income countries often lack a comprehensive evidence base; however, evidence synthesis methods can assist in filling the data gaps required for the development of effective policy to address the future public health and economic burden due to HCV.

Analysis of the traveltime sensitivity kernels for an acoustic transversely isotropic medium with a vertical axis of symmetry

KAUST Repository

Djebbi, Ramzi; Plessix, René -É douard; Alkhalifah, Tariq Ali

2016-01-01

In anisotropic media, several parameters govern the propagation of the compressional waves. To correctly invert surface recorded seismic data in anisotropic media, a multi-parameter inversion is required. However, a tradeoff between parameters

Using image analysis to monitor biological changes in consume fish

DEFF Research Database (Denmark)

Dissing, Bjørn Skovlund; Frosch, Stina; Nielsen, Michael Engelbrecht

2011-01-01

The quality of fish products is largely defined by the visual appearance of the products. Visual appearance includes measurable parameters such as color and texture. Fat content and distribution as well as deposition of carotenoid pigments such as astaxanthin in muscular and fat tissue...... fishes is based on highly laborious chemical analysis. Trichromatic digital imaging and point-wise colorimetric or spectral measurement are also ways of estimating either the redness or the actual astaxanthin concentration of the fillet. These methods all have drawbacks of either cumbersome testing...... are biological parameters with a huge impact on the color and texture of the fish muscle. Consumerdriven quality demands call for rapid methods for quantification of quality parameters such as fat and astaxanthin in the industry. The spectral electromagnetic reflection properties of astaxanthin are well known...

Screening of siRNA nanoparticles for delivery to airway epithelial cells using high-content analysis

LENUS (Irish Health Repository)

Hibbitts, Alan

2011-08-01

Aims: Delivery of siRNA to the lungs via inhalation offers a unique opportunity to develop a new treatment paradigm for a range of respiratory conditions. However, progress has been greatly hindered by safety and delivery issues. This study developed a high-throughput method for screening novel nanotechnologies for pulmonary siRNA delivery. Methodology: Following physicochemical analysis, the ability of PEI–PEG–siRNA nanoparticles to facilitate siRNA delivery was determined using high-content analysis (HCA) in Calu-3 cells. Results obtained from HCA were validated using confocal microscopy. Finally, cytotoxicity of the PEI–PEG–siRNA particles was analyzed by HCA using the Cellomics® multiparameter cytotoxicity assay. Conclusion: PEI–PEG–siRNA nanoparticles facilitated increased siRNA uptake and luciferase knockdown in Calu-3 cells compared with PEI–siRNA.

Continuous multi-parameter heart rate variability analysis heralds onset of sepsis in adults.

Directory of Open Access Journals (Sweden)

Saif Ahmad

Full Text Available BACKGROUND: Early diagnosis of sepsis enables timely resuscitation and antibiotics and prevents subsequent morbidity and mortality. Clinical approaches relying on point-in-time analysis of vital signs or lab values are often insensitive, non-specific and late diagnostic markers of sepsis. Exploring otherwise hidden information within intervals-in-time, heart rate variability (HRV has been documented to be both altered in the presence of sepsis, and correlated with its severity. We hypothesized that by continuously tracking individual patient HRV over time in patients as they develop sepsis, we would demonstrate reduced HRV in association with the onset of sepsis. METHODOLOGY/PRINCIPAL FINDINGS: We monitored heart rate continuously in adult bone marrow transplant (BMT patients (n = 21 beginning a day before their BMT and continuing until recovery or withdrawal (12+/-4 days. We characterized HRV continuously over time with a panel of time, frequency, complexity, and scale-invariant domain techniques. We defined baseline HRV as mean variability for the first 24 h of monitoring and studied individual and population average percentage change (from baseline over time in diverse HRV metrics, in comparison with the time of clinical diagnosis and treatment of sepsis (defined as systemic inflammatory response syndrome along with clinically suspected infection requiring treatment. Of the 21 patients enrolled, 4 patients withdrew, leaving 17 patients who completed the study. Fourteen patients developed sepsis requiring antibiotic therapy, whereas 3 did not. On average, for 12 out of 14 infected patients, a significant (25% reduction prior to the clinical diagnosis and treatment of sepsis was observed in standard deviation, root mean square successive difference, sample and multiscale entropy, fast Fourier transform, detrended fluctuation analysis, and wavelet variability metrics. For infected patients (n = 14, wavelet HRV demonstrated a 25% drop from

Inferring biological tasks using Pareto analysis of high-dimensional data.

Science.gov (United States)

Hart, Yuval; Sheftel, Hila; Hausser, Jean; Szekely, Pablo; Ben-Moshe, Noa Bossel; Korem, Yael; Tendler, Avichai; Mayo, Avraham E; Alon, Uri

2015-03-01

We present the Pareto task inference method (ParTI; http://www.weizmann.ac.il/mcb/UriAlon/download/ParTI) for inferring biological tasks from high-dimensional biological data. Data are described as a polytope, and features maximally enriched closest to the vertices (or archetypes) allow identification of the tasks the vertices represent. We demonstrate that human breast tumors and mouse tissues are well described by tetrahedrons in gene expression space, with specific tumor types and biological functions enriched at each of the vertices, suggesting four key tasks.

Flow Cytometry Section

Data.gov (United States)

Federal Laboratory Consortium — The primary goal of the Flow Cytometry Section is to provide the services of state-of-the-art multi-parameter cellular analysis and cell sorting for researchers and...

Analysis of the multi-component pseudo-pure-mode qP-wave inversion in vertical transverse isotropic (VTI) media

KAUST Repository

Djebbi, Ramzi; Alkhalifah, Tariq Ali

2014-01-01

Multi-parameter inversion in anisotropic media suffers from the inherent trade-off between the anisotropic parameters, even under the acoustic assumption. Multi-component data, often acquired nowadays in ocean bottom acquisition and land data

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.…

Analyzing the Biology on the System Level

OpenAIRE

Tong, Wei

2016-01-01

Although various genome projects have provided us enormous static sequence information, understanding of the sophisticated biology continues to require integrating the computational modeling, system analysis, technology development for experiments, and quantitative experiments all together to analyze the biology architecture on various levels, which is just the origin of systems biology subject. This review discusses the object, its characteristics, and research attentions in systems biology,...

Mini Review - Analysis of Artemether and Dihydroartemisinin by high performance high liquid chromatography in biological fluids-issues and solutions.

Science.gov (United States)

Ali, Shabana; Jafery, Nusrat; Farhat, Kulsoom; Waheed, Akbar

2017-07-01

Artemether-Lumefantrine is the most widely recommended antimalarial combination used to treat millions of patients suffering from malaria. Artemether undergoes rapid metabolism and gets converted to its active metabolite dihydroartemisisn. Drug analysis is a vital aspect to evaluate drugs in research. There are a number of methods available for the determination of artemether in biological fluids. These methods include HPLC based UV detection, GS-MS, HPLC-ECD and HPLC-MS/MS. This article reviews different methods for the determination of artemether in the biological fluids. Among the available methods HPLC-MS/MS proves to be the most accurate and reliable one for analysis. This has the advantage of improved sensitivity and selectivity with smaller sample volume.

The mathematics behind biological invasions

CERN Document Server

Lewis, Mark A; Potts, Jonathan R

2016-01-01

This book investigates the mathematical analysis of biological invasions. Unlike purely qualitative treatments of ecology, it draws on mathematical theory and methods, equipping the reader with sharp tools and rigorous methodology. Subjects include invasion dynamics, species interactions, population spread, long-distance dispersal, stochastic effects, risk analysis, and optimal responses to invaders. While based on the theory of dynamical systems, including partial differential equations and integrodifference equations, the book also draws on information theory, machine learning, Monte Carlo methods, optimal control, statistics, and stochastic processes. Applications to real biological invasions are included throughout. Ultimately, the book imparts a powerful principle: that by bringing ecology and mathematics together, researchers can uncover new understanding of, and effective response strategies to, biological invasions. It is suitable for graduate students and established researchers in mathematical ecolo...

On the interplay between mathematics and biology: hallmarks toward a new systems biology.

Science.gov (United States)

Bellomo, Nicola; Elaiw, Ahmed; Althiabi, Abdullah M; Alghamdi, Mohammed Ali

2015-03-01

This paper proposes a critical analysis of the existing literature on mathematical tools developed toward systems biology approaches and, out of this overview, develops a new approach whose main features can be briefly summarized as follows: derivation of mathematical structures suitable to capture the complexity of biological, hence living, systems, modeling, by appropriate mathematical tools, Darwinian type dynamics, namely mutations followed by selection and evolution. Moreover, multiscale methods to move from genes to cells, and from cells to tissue are analyzed in view of a new systems biology approach. Copyright © 2014 Elsevier B.V. All rights reserved.

RBioplot: an easy-to-use R pipeline for automated statistical analysis and data visualization in molecular biology and biochemistry

Directory of Open Access Journals (Sweden)

Jing Zhang

2016-09-01

Full Text Available Background Statistical analysis and data visualization are two crucial aspects in molecular biology and biology. For analyses that compare one dependent variable between standard (e.g., control and one or multiple independent variables, a comprehensive yet highly streamlined solution is valuable. The computer programming language R is a popular platform for researchers to develop tools that are tailored specifically for their research needs. Here we present an R package RBioplot that takes raw input data for automated statistical analysis and plotting, highly compatible with various molecular biology and biochemistry lab techniques, such as, but not limited to, western blotting, PCR, and enzyme activity assays. Method The package is built based on workflows operating on a simple raw data layout, with minimum user input or data manipulation required. The package is distributed through GitHub, which can be easily installed through one single-line R command. A detailed installation guide is available at http://kenstoreylab.com/?page_id=2448. Users can also download demo datasets from the same website. Results and Discussion By integrating selected functions from existing statistical and data visualization packages with extensive customization, RBioplot features both statistical analysis and data visualization functionalities. Key properties of RBioplot include: -Fully automated and comprehensive statistical analysis, including normality test, equal variance test, Student’s t-test and ANOVA (with post-hoc tests; -Fully automated histogram, heatmap and joint-point curve plotting modules; -Detailed output files for statistical analysis, data manipulation and high quality graphs; -Axis range finding and user customizable tick settings; -High user-customizability.

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.

Cultural variances in composition of biological and supernatural concepts of death: a content analysis of children's literature.

Science.gov (United States)

Lee, Ji Seong; Kim, Eun Young; Choi, Younyoung; Koo, Ja Hyouk

2014-01-01

Children's reasoning about the afterlife emerges naturally as a developmental regularity. Although a biological understanding of death increases in accordance with cognitive development, biological and supernatural explanations of death may coexist in a complementary manner, being deeply imbedded in cultural contexts. This study conducted a content analysis of 40 children's death-themed picture books in Western Europe and East Asia. It can be inferred that causality and non-functionality are highly integrated with the naturalistic and supernatural understanding of death in Western Europe, whereas the literature in East Asia seems to rely on naturalistic aspects of death and focuses on causal explanations.

Aspergilli: Systems biology and industrial applications

DEFF Research Database (Denmark)

Knuf, Christoph; Nielsen, Jens

2012-01-01

possible to implement systems biology tools to advance metabolic engineering. These tools include genome-wide transcription analysis and genome-scale metabolic models. Herein, we review achievements in the field and highlight the impact of Aspergillus systems biology on industrial biotechnology....

Analysis and enumeration algorithms for biological graphs

CERN Document Server

Marino, Andrea

2015-01-01

In this work we plan to revise the main techniques for enumeration algorithms and to show four examples of enumeration algorithms that can be applied to efficiently deal with some biological problems modelled by using biological networks: enumerating central and peripheral nodes of a network, enumerating stories, enumerating paths or cycles, and enumerating bubbles. Notice that the corresponding computational problems we define are of more general interest and our results hold in the case of arbitrary graphs. Enumerating all the most and less central vertices in a network according to their eccentricity is an example of an enumeration problem whose solutions are polynomial and can be listed in polynomial time, very often in linear or almost linear time in practice. Enumerating stories, i.e. all maximal directed acyclic subgraphs of a graph G whose sources and targets belong to a predefined subset of the vertices, is on the other hand an example of an enumeration problem with an exponential number of solutions...

Systematic Review with Network Meta-Analysis: Comparative Efficacy of Biologics in the Treatment of Moderately to Severely Active Ulcerative Colitis.

Directory of Open Access Journals (Sweden)

Adrian D Vickers

Full Text Available Biological therapies are increasingly used to treat ulcerative colitis (UC.To compare the efficacy of biologics in adults with moderately-to-severely active UC, stratified by prior exposure to anti-tumour necrosis factor (anti-TNF therapy.A systematic literature review was undertaken to identify studies of biologics approved for UC. Network meta-analysis was conducted for endpoints at induction and maintenance.Seven studies were included in the meta-analysis of induction treatment for anti-TNF therapy-naïve patients. All biologics were more effective than placebo in inducing clinical response, clinical remission, and mucosal healing. Infliximab demonstrated a statistically significant improvement over adalimumab in clinical response (odds ratio [OR] [95% credible interval (CrI]: 2.19 [1.35-3.55], clinical remission (OR [95% CrI]: 2.81 [1.49-5.49], and mucosal healing (OR [95% CrI]: 2.23 [1.21-4.14]; there were no other significant differences between biologics for induction efficacy. Five studies were included in the meta-analysis of maintenance treatment, two studies rerandomised responder patients at end of induction, and three followed the same patients 'straight through'. To account for design differences, the number of responders at end of induction was assumed to be equivalent to the number rerandomised. Vedolizumab showed significantly different durable clinical response from comparators (OR [95% CrI] infliximab 3.18 [1.14-9.20], golimumab 2.33 [1.04-5.41], and adalimumab 3.96 [1.67-9.84]. In anti-TNF therapy-experienced patients, only vedolizumab and adalimumab could be compared. At induction, no significant differences in efficacy were seen. During maintenance, vedolizumab showed significantly improved rates of mucosal healing versus adalimumab (OR [95% CrI]: 6.72 [1.36-41.0].This study expands the understanding of comparative efficacies of biologic treatments for UC, encompassing outcomes and populations not previously studied. All

Cultural inter-population differences do not reflect biological distances: an example of interdisciplinary analysis of populations from Eastern Adriatic coast.

Science.gov (United States)

Bašić, Željana; Fox, Ayano R; Anterić, Ivana; Jerković, Ivan; Polašek, Ozren; Anđelinović, Šimun; Holland, Mitchell M; Primorac, Dragan

2015-06-01

To compare the population group from the Šopot graveyard with population groups from traditional Croatian medieval graveyards by using anthropological, craniometrics, and mitochondrial (mtDNA) analysis and to examine if the cultural differences between population groups reflect biological differences. We determined sex, age at death, pathological, and traumatic changes of skeletal remains from the Šopot graveyard and compared them with a cumulative medieval sample from the same region. We also performed principal component analysis to compare skeletal remains from Šopot with those from Ostrovica and other Central European samples according to 8 cranial measurements. Finally, we compared 46 skeletons from Šopot with medieval (Ostrovica) and contemporary populations using mDNA haplogroup profiling. The remains from Šopot were similar to the cumulative sample in lifestyle and quality of life markers. Principal component analysis showed that they were closely related to Eastern Adriatic coast sites (including Ostrovica and Šopot) in terms of cranial morphology, indicating similar biological makeup. According to mDNA testing, Šopot population showed no significant differences in the haplogroup prevalence from either medieval or contemporary populations. This study shows that the Šopot population does not significantly differ from other medieval populations from this area. Besides similar quality of life markers, these populations also had similar biological markers. Substantial archeological differences can therefore be attributed to apparent cultural influences, which in this case do not reflect biological differences.

Latin-American Biological Dosimetry Network (LBDNET) Intercomparison Exercise. Evaluation through triage and conventional scoring criteria. Development of a new approach for statistical data analysis

International Nuclear Information System (INIS)

Di Giorgio, M.; Vallerga, M.B.; Radl, A.

2011-01-01

Biological Dosimetry is a necessary support for National Radiation Protection Programs and Emergency Response Schemes. A Latin-American Biological Dosimetry Network (LBDNET) has been constituted by the biological dosimetry laboratories from: Argentina, Brazil, Chile, Cuba, Mexico, Peru, and Uruguay (IAEA Regional Project RLA9/054, 2007). The biological dosimetry laboratory of Argentina organized an international biological dosimetry intercomparison for the analysis of some relevant parameters involved in dose assessment, to reinforce the response capability in accidental situations requiring the activation of mutual assistance mechanisms and thus, constituting the bases of the LBDNET organization. (authors)

Applications of synchrotron radiation in biology and medicine

International Nuclear Information System (INIS)

Khole, V.

1988-01-01

This paper discusses the important role of synchrotron radiation in dealing with problems in various branches of biology and medicine, viz. molecular biology, molecular biophysics, biochemistry, cell biology, X-ray microscopy, molecular surgery, medical diagnostics (angiography, X-ray radiography, forensic medicine, element analysis), environmental biology, pollution control and photobiology. (author). 15 refs., 9 figs

Certification of biological candidates reference materials by neutron activation analysis

Science.gov (United States)

Kabanov, Denis V.; Nesterova, Yulia V.; Merkulov, Viktor G.

2018-03-01

The paper gives the results of interlaboratory certification of new biological candidate reference materials by neutron activation analysis recommended by the Institute of Nuclear Chemistry and Technology (Warsaw, Poland). The correctness and accuracy of the applied method was statistically estimated for the determination of trace elements in candidate reference materials. The procedure of irradiation in the reactor thermal fuel assembly without formation of fast neutrons was carried out. It excluded formation of interfering isotopes leading to false results. The concentration of more than 20 elements (e.g., Ba, Br, Ca, Co, Ce, Cr, Cs, Eu, Fe, Hf, La, Lu, Rb, Sb, Sc, Ta, Th, Tb, Yb, U, Zn) in candidate references of tobacco leaves and bottom sediment compared to certified reference materials were determined. It was shown that the average error of the applied method did not exceed 10%.

Quality in the chemical analysis of biological matrices by fluorescence X-ray by energy dispersive

International Nuclear Information System (INIS)

Sousa, Evely E. de; Paiva, Jose Daniel S. de; Franca, Elvis J. de; Almeida, Macio E.S.; Cantinha, Rebeca S.; Hazin, Clovis A.

2013-01-01

The aim of this study was to obtain multielement analytical curves of high analytical rigor to the analysis of biological matrices by the technique of fluorescence x-ray energy dispersive - EDXRF. Calibration curves were constructed from the reference materials IAEA 140, IAEA 155, IAEA V8, V10 to the International Atomic Energy Agency - IAEA, and SRM1515, SRM 1547, SRM 1570a, SRM 1573a, SEM 1567a, to the National Institute of Standards and Technology - NIST. After energy calibration, all samples were subjected to vacuum to the analyzes by 100 seconds for each group of chemical elements. The voltages used were respectively 15 keV for chemical elements with less than atomic number 22 and 50 keV for the others. After the construction of the curves, the analytical quality was assessed by the analysis of a portion-test of the reference material SRM 2976, also produced by NIST. Based on the number of certified reference materials used for construction of calibration curves in this work, quality analytical protocol was originated with considerable reliability for quantification of chemical elements in biological samples by EDXR

ANALYSIS OF THE APPROACH TO THE ATLANTIC FOREST IN HIGH SCHOOL BIOLOGY TEXTBOOKS

Directory of Open Access Journals (Sweden)

Nicácio Oliveira Freitas

2017-03-01

Full Text Available The textbooks are the main teaching tool for students and teachers. The analysis of these books enables point out several shortcomings in relation to the contents approach. Thus, the objective of this work was to analyze the approach to the Atlantic Forest, considered one of the most degraded environments of the world. A total of seven high school biology textbooks were analyzed, following an evaluation script with general information, biotic and abiotic factors, environmental conservation and anthropic action, which were considered as satisfactory or unsatisfactory in the textbooks evaluation. In general, the Atlantic Forest theme has been addressed by all assessed books, including specific topics, however, some aspects such as the use of images was made improperly, leading to misunderstandings about Atlantic forest. In addition, ecosystem dynamics, its components and the environmental impacts have not been addressed satisfactorily in the majority of the works assessed. In general, the theme Atlantic Forest has been addressed by all assessed books, including specific topics, however, many aspects of this theme presented problems in their approach: update, concepts, definitions and importance, and also presented problems in their illustration of the current situation of Atlantic Forest. Periodic revisions of these textbooks are of great importance to assure student formation that allows them to analyze and know the effects of their actions on the environment and to reflect on ways to alleviates them. Keywords: biology textbooks; ecosystem; contents analysis.

Characterising volcanic cycles at Soufriere Hills Volcano, Montserrat: Time series analysis of multi-parameter satellite data

Science.gov (United States)

Flower, Verity J. B.; Carn, Simon A.

2015-10-01

The identification of cyclic volcanic activity can elucidate underlying eruption dynamics and aid volcanic hazard mitigation. Whilst satellite datasets are often analysed individually, here we exploit the multi-platform NASA A-Train satellite constellation to cross-correlate cyclical signals identified using complementary measurement techniques at Soufriere Hills Volcano (SHV), Montserrat. In this paper we present a Multi-taper (MTM) Fast Fourier Transform (FFT) analysis of coincident SO2 and thermal infrared (TIR) satellite measurements at SHV facilitating the identification of cyclical volcanic behaviour. These measurements were collected by the Ozone Monitoring Instrument (OMI) and Moderate Resolution Imaging Spectroradiometer (MODIS) (respectively) in the A-Train. We identify a correlating cycle in both the OMI and MODIS data (54-58 days), with this multi-week feature attributable to episodes of dome growth. The 50 day cycles were also identified in ground-based SO2 data at SHV, confirming the validity of our analysis and further corroborating the presence of this cycle at the volcano. In addition a 12 day cycle was identified in the OMI data, previously attributed to variable lava effusion rates on shorter timescales. OMI data also display a one week (7-8 days) cycle attributable to cyclical variations in viewing angle resulting from the orbital characteristics of the Aura satellite. Longer period cycles possibly relating to magma intrusion were identified in the OMI record (102-, 121-, and 159 days); in addition to a 238-day cycle identified in the MODIS data corresponding to periodic destabilisation of the lava dome. Through the analysis of reconstructions generated from cycles identified in the OMI and MODIS data, periods of unrest were identified, including the major dome collapse of 20th May 2006 and significant explosive event of 3rd January 2009. Our analysis confirms the potential for identification of cyclical volcanic activity through combined

On avoided words, absent words, and their application to biological sequence analysis.

Science.gov (United States)

Almirantis, Yannis; Charalampopoulos, Panagiotis; Gao, Jia; Iliopoulos, Costas S; Mohamed, Manal; Pissis, Solon P; Polychronopoulos, Dimitris

2017-01-01

The deviation of the observed frequency of a word w from its expected frequency in a given sequence x is used to determine whether or not the word is avoided . This concept is particularly useful in DNA linguistic analysis. The value of the deviation of w , denoted by [Formula: see text], effectively characterises the extent of a word by its edge contrast in the context in which it occurs. A word w of length [Formula: see text] is a [Formula: see text]-avoided word in x if [Formula: see text], for a given threshold [Formula: see text]. Notice that such a word may be completely absent from x . Hence, computing all such words naïvely can be a very time-consuming procedure, in particular for large k . In this article, we propose an [Formula: see text]-time and [Formula: see text]-space algorithm to compute all [Formula: see text]-avoided words of length k in a given sequence of length n over a fixed-sized alphabet. We also present a time-optimal [Formula: see text]-time algorithm to compute all [Formula: see text]-avoided words (of any length) in a sequence of length n over an integer alphabet of size [Formula: see text]. In addition, we provide a tight asymptotic upper bound for the number of [Formula: see text]-avoided words over an integer alphabet and the expected length of the longest one. We make available an implementation of our algorithm. Experimental results, using both real and synthetic data, show the efficiency and applicability of our implementation in biological sequence analysis. The systematic search for avoided words is particularly useful for biological sequence analysis. We present a linear-time and linear-space algorithm for the computation of avoided words of length k in a given sequence x . We suggest a modification to this algorithm so that it computes all avoided words of x , irrespective of their length, within the same time complexity. We also present combinatorial results with regards to avoided words and absent words.

Development of analytical methods for the determination of some radiologically important elements in biological materials using neutron activation analysis

International Nuclear Information System (INIS)

Dang, H.S.; Jaiswal, D.D.; Pullat, V.R.; Krishnamony, S.

1998-01-01

This paper describes the analytical methods developed for the estimation of Cs, I, Sr, Th and U in biological materials such as food and human tissues. The methods employ both, the instrumental neutron activation analysis (INAA) and radiochemical neutron activation analysis (RNAA). The adequacy of these methods to determine the concentrations of the above elements in dietary and tissue materials was also studied. The study showed that the analytical methods described in this paper are adequate for the determination of Cs, Sr, Th and U in all kinds of biological samples. In the case of I however, the method is adequate only for determining its concentration in thyroid, but needs to be modified to improve its sensitivity for the determination of I in diet samples. (author)

Evaluation of machine learning algorithms for classification of primary biological aerosol using a new UV-LIF spectrometer

Science.gov (United States)

Ruske, Simon; Topping, David O.; Foot, Virginia E.; Kaye, Paul H.; Stanley, Warren R.; Crawford, Ian; Morse, Andrew P.; Gallagher, Martin W.

2017-03-01

Characterisation of bioaerosols has important implications within environment and public health sectors. Recent developments in ultraviolet light-induced fluorescence (UV-LIF) detectors such as the Wideband Integrated Bioaerosol Spectrometer (WIBS) and the newly introduced Multiparameter Bioaerosol Spectrometer (MBS) have allowed for the real-time collection of fluorescence, size and morphology measurements for the purpose of discriminating between bacteria, fungal spores and pollen.This new generation of instruments has enabled ever larger data sets to be compiled with the aim of studying more complex environments. In real world data sets, particularly those from an urban environment, the population may be dominated by non-biological fluorescent interferents, bringing into question the accuracy of measurements of quantities such as concentrations. It is therefore imperative that we validate the performance of different algorithms which can be used for the task of classification.For unsupervised learning we tested hierarchical agglomerative clustering with various different linkages. For supervised learning, 11 methods were tested, including decision trees, ensemble methods (random forests, gradient boosting and AdaBoost), two implementations for support vector machines (libsvm and liblinear) and Gaussian methods (Gaussian naïve Bayesian, quadratic and linear discriminant analysis, the k-nearest neighbours algorithm and artificial neural networks).The methods were applied to two different data sets produced using the new MBS, which provides multichannel UV-LIF fluorescence signatures for single airborne biological particles. The first data set contained mixed PSLs and the second contained a variety of laboratory-generated aerosol.Clustering in general performs slightly worse than the supervised learning methods, correctly classifying, at best, only 67. 6 and 91. 1 % for the two data sets respectively. For supervised learning the gradient boosting algorithm was

Graphene liquid cells for multi-technique analysis of biological cells in water environment

Science.gov (United States)

Matruglio, A.; Zucchiatti, P.; Birarda, G.; Marmiroli, B.; D'Amico, F.; Kocabas, C.; Kiskinova, M.; Vaccari, L.

2018-05-01

In-cell exploration of biomolecular constituents is the new frontier of cellular biology that will allow full access to structure-activity correlation of biomolecules, overcoming the limitations imposed by dissecting the cellular milieu. However, the presence of water, which is a very strong IR absorber and incompatible with the vacuum working conditions of all analytical methods using soft x-rays and electrons, poses severe constraint to perform important imaging and spectroscopic analyses under physiological conditions. Recent advances to separate the sample compartment in liquid cell are based on electron and photon transparent but molecular-impermeable graphene membranes. This strategy has opened a unique opportunity to explore technological materials under realistic operation conditions using various types of electron microscopy. However, the widespread of the graphene liquid cell applications is still impeded by the lack of well-established approaches for their massive production. We report on the first preliminary results for the fabrication of reproducible graphene liquid cells appropriate for the analysis of biological specimens in their natural hydrated environment with several crucial analytical techniques, namely FTIR microscopy, Raman spectroscopy, AFM, SEM and TEM.

Application of LC–MS/MS for quantitative analysis of glucocorticoids and stimulants in biological fluids

OpenAIRE

Haneef, Jamshed; Shaharyar, Mohammad; Husain, Asif; Rashid, Mohd; Mishra, Ravinesh; Parveen, Shama; Ahmed, Niyaz; Pal, Manoj; Kumar, Deepak

2013-01-01

Liquid chromatography tandem mass chromatography (LCâMS/MS) is an important hyphenated technique for quantitative analysis of drugs in biological fluids. Because of high sensitivity and selectivity, LCâMS/MS has been used for pharmacokinetic studies, metabolites identification in the plasma and urine. This manuscript gives comprehensive analytical review, focusing on chromatographic separation approaches (column packing materials, column length and mobile phase) as well as different acquisiti...

Application of LC–MS/MS for quantitative analysis of glucocorticoids and stimulants in biological fluids

OpenAIRE

Haneef, Jamshed; Shaharyar, Mohammad; Husain, Asif; Rashid, Mohd; Mishra, Ravinesh; Parveen, Shama; Ahmed, Niyaz; Pal, Manoj; Kumar, Deepak

2013-01-01

Liquid chromatography tandem mass chromatography (LC–MS/MS) is an important hyphenated technique for quantitative analysis of drugs in biological fluids. Because of high sensitivity and selectivity, LC–MS/MS has been used for pharmacokinetic studies, metabolites identification in the plasma and urine. This manuscript gives comprehensive analytical review, focusing on chromatographic separation approaches (column packing materials, column length and mobile phase) as well as different acquisiti...

Selected factors associated with achievement of biology preparatory students and their follow-up to higher level biology courses

Science.gov (United States)

Biermann, Carol A.; Sarinsky, Gary B.

This study was undertaken to determine whether a biology preparatory course given at an urban community college was helping students to develop the proper skills and background necessary for them to successfully complete follow-up courses in biology. A group of students who enrolled in a biology preparatory course, and subsequently, a follow-up anatomy and physiology or general biology course (experimental group) was compared to a group of students who should have registered for the preparatory course, but who enrolled directly into the anatomy and physiology or general biology course (control group). It was shown that there was no significant difference in their anatomy and physiology or general biology grades. Furthermore, only 16% of the initial group of preparatory students enrolled in and passed a follow-up biology course. Examination of the preparatory group using discriminant analysis ascertained that mathematics score was the principle discriminator between pass/fail groups. A stepwise multiple regression analysis of the variables explaining the preparatory grade showed that mathematics score, reading score, and type of high school degree explained 33% of the variance. Of the students who did pass the preparatory course and enrolled in a follow-up biology class, their preparatory grade was a good predictor of their achievement (measured by follow-up course grade), as determined by multiple regression.

SensorDB: a virtual laboratory for the integration, visualization and analysis of varied biological sensor data.

Science.gov (United States)

Salehi, Ali; Jimenez-Berni, Jose; Deery, David M; Palmer, Doug; Holland, Edward; Rozas-Larraondo, Pablo; Chapman, Scott C; Georgakopoulos, Dimitrios; Furbank, Robert T

2015-01-01

To our knowledge, there is no software or database solution that supports large volumes of biological time series sensor data efficiently and enables data visualization and analysis in real time. Existing solutions for managing data typically use unstructured file systems or relational databases. These systems are not designed to provide instantaneous response to user queries. Furthermore, they do not support rapid data analysis and visualization to enable interactive experiments. In large scale experiments, this behaviour slows research discovery, discourages the widespread sharing and reuse of data that could otherwise inform critical decisions in a timely manner and encourage effective collaboration between groups. In this paper we present SensorDB, a web based virtual laboratory that can manage large volumes of biological time series sensor data while supporting rapid data queries and real-time user interaction. SensorDB is sensor agnostic and uses web-based, state-of-the-art cloud and storage technologies to efficiently gather, analyse and visualize data. Collaboration and data sharing between different agencies and groups is thereby facilitated. SensorDB is available online at http://sensordb.csiro.au.

Economic Analysis of Biological Invasions in Forests

Science.gov (United States)

Tomas P. Holmes; Julian Aukema; Jeffrey Englin; Robert G. Haight; Kent Kovacs; Brian Leung

2014-01-01

Biological invasions of native forests by nonnative pests result from complex stochastic processes that are difficult to predict. Although economic optimization models describe efficient controls across the stages of an invasion, the ability to calibrate such models is constrained by lack of information on pest population dynamics and consequent economic damages. Here...

GenFlow: generic flow for integration, management and analysis of molecular biology data

Directory of Open Access Journals (Sweden)

Marcio Katsumi Oikawa

2004-01-01

Full Text Available A large number of DNA sequencing projects all over the world have yielded a fantastic amount of data, whose analysis is, currently, a big challenge for computational biology. The limiting step in this task is the integration of large volumes of data stored in highly heterogeneous repositories of genomic and cDNA sequences, as well as gene expression results. Solving this problem requires automated analytical tools to optimize operations and efficiently generate knowledge. This paper presents an information flow model , called GenFlow, that can tackle this analytical task.

FACE Analysis as a Fast and Reliable Methodology to Monitor the Sulfation and Total Amount of Chondroitin Sulfate in Biological Samples of Clinical Importance

Directory of Open Access Journals (Sweden)

Evgenia Karousou

2014-06-01

Full Text Available Glycosaminoglycans (GAGs due to their hydrophilic character and high anionic charge densities play important roles in various (pathophysiological processes. The identification and quantification of GAGs in biological samples and tissues could be useful prognostic and diagnostic tools in pathological conditions. Despite the noteworthy progress in the development of sensitive and accurate methodologies for the determination of GAGs, there is a significant lack in methodologies regarding sample preparation and reliable fast analysis methods enabling the simultaneous analysis of several biological samples. In this report, developed protocols for the isolation of GAGs in biological samples were applied to analyze various sulfated chondroitin sulfate- and hyaluronan-derived disaccharides using fluorophore-assisted carbohydrate electrophoresis (FACE. Applications to biologic samples of clinical importance include blood serum, lens capsule tissue and urine. The sample preparation protocol followed by FACE analysis allows quantification with an optimal linearity over the concentration range 1.0–220.0 µg/mL, affording a limit of quantitation of 50 ng of disaccharides. Validation of FACE results was performed by capillary electrophoresis and high performance liquid chromatography techniques.

Quantitative multi-parameter mapping of R1, PD*, MT and R2* at 3T: a multi-center validation

Directory of Open Access Journals (Sweden)

Nikolaus eWeiskopf

2013-06-01

Full Text Available Multi-center studies using magnetic resonance imaging facilitate studying small effect sizes, global population variance and rare diseases. The reliability and sensitivity of these multi-center studies crucially depend on the comparability of the data generated at different sites and time points. The level of inter-site comparability is still controversial for conventional anatomical T1-weighted MRI data. Quantitative multi-parameter mapping (MPM was designed to provide MR parameter measures that are comparable across sites and time points, i.e., 1mm high-resolution maps of the longitudinal relaxation rate (R1=1/T1, effective proton density (PD*, magnetization transfer saturation (MT and effective transverse relaxation rate (R2*=1/T2*. MPM was validated at 3T for use in multi-center studies by scanning five volunteers at three different sites. We determined the inter-site bias, inter-site and intra-site coefficient of variation (CoV for typical morphometric measures (i.e., gray matter probability maps used in voxel-based morphometry and the four quantitative parameters. The inter-site bias and CoV were smaller than 3.1% and 8%, respectively, except for the inter-site CoV of R2* (< 20%. The gray matter probability maps based on the MT parameter maps had a 14% higher inter-site reproducibility than maps based on conventional T1-weighted images. The low inter-site bias and variance in the parameters and derived gray matter probability maps confirm the high comparability of the quantitative maps across sites and time points. The reliability, short acquisition time, high resolution and the detailed insights into the brain microstructure provided by MPM makes it an efficient tool for multi-center imaging studies.

Data integration in biological research: an overview.

Science.gov (United States)

Lapatas, Vasileios; Stefanidakis, Michalis; Jimenez, Rafael C; Via, Allegra; Schneider, Maria Victoria

2015-12-01

Data sharing, integration and annotation are essential to ensure the reproducibility of the analysis and interpretation of the experimental findings. Often these activities are perceived as a role that bioinformaticians and computer scientists have to take with no or little input from the experimental biologist. On the contrary, biological researchers, being the producers and often the end users of such data, have a big role in enabling biological data integration. The quality and usefulness of data integration depend on the existence and adoption of standards, shared formats, and mechanisms that are suitable for biological researchers to submit and annotate the data, so it can be easily searchable, conveniently linked and consequently used for further biological analysis and discovery. Here, we provide background on what is data integration from a computational science point of view, how it has been applied to biological research, which key aspects contributed to its success and future directions.

Next-generation biology

DEFF Research Database (Denmark)

Rodrigues da Fonseca, Rute Andreia; Albrechtsen, Anders; Themudo, Goncalo Espregueira Cruz

2016-01-01

we present an overview of the current sequencing technologies and the methods used in typical high-throughput data analysis pipelines. Subsequently, we contextualize high-throughput DNA sequencing technologies within their applications in non-model organism biology. We include tips regarding managing...

Effectiveness of biological surrogates for predicting patterns of marine biodiversity: a global meta-analysis.

Directory of Open Access Journals (Sweden)

Camille Mellin

Full Text Available The use of biological surrogates as proxies for biodiversity patterns is gaining popularity, particularly in marine systems where field surveys can be expensive and species richness high. Yet, uncertainty regarding their applicability remains because of inconsistency of definitions, a lack of standard methods for estimating effectiveness, and variable spatial scales considered. We present a Bayesian meta-analysis of the effectiveness of biological surrogates in marine ecosystems. Surrogate effectiveness was defined both as the proportion of surrogacy tests where predictions based on surrogates were better than random (i.e., low probability of making a Type I error; P and as the predictability of targets using surrogates (R(2. A total of 264 published surrogacy tests combined with prior probabilities elicited from eight international experts demonstrated that the habitat, spatial scale, type of surrogate and statistical method used all influenced surrogate effectiveness, at least according to either P or R(2. The type of surrogate used (higher-taxa, cross-taxa or subset taxa was the best predictor of P, with the higher-taxa surrogates outperforming all others. The marine habitat was the best predictor of R(2, with particularly low predictability in tropical reefs. Surrogate effectiveness was greatest for higher-taxa surrogates at a <10-km spatial scale, in low-complexity marine habitats such as soft bottoms, and using multivariate-based methods. Comparisons with terrestrial studies in terms of the methods used to study surrogates revealed that marine applications still ignore some problems with several widely used statistical approaches to surrogacy. Our study provides a benchmark for the reliable use of biological surrogates in marine ecosystems, and highlights directions for future development of biological surrogates in predicting biodiversity.

Creating biological nanomaterials using synthetic biology

International Nuclear Information System (INIS)

Rice, MaryJoe K; Ruder, Warren C

2014-01-01

Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic biology, discusses how biological systems naturally produce materials, and then presents examples and strategies for incorporating synthetic biology approaches in the development of new materials. In particular, strategies for using synthetic biology to produce both organic and inorganic nanomaterials are discussed. Ultimately, synthetic biology holds the potential to dramatically impact biological materials science with significant potential applications in medical systems. (review)

Creating biological nanomaterials using synthetic biology.

Science.gov (United States)

Rice, MaryJoe K; Ruder, Warren C

2014-02-01

Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic biology, discusses how biological systems naturally produce materials, and then presents examples and strategies for incorporating synthetic biology approaches in the development of new materials. In particular, strategies for using synthetic biology to produce both organic and inorganic nanomaterials are discussed. Ultimately, synthetic biology holds the potential to dramatically impact biological materials science with significant potential applications in medical systems.

Micro-separation toward systems biology.

Science.gov (United States)

Liu, Bi-Feng; Xu, Bo; Zhang, Guisen; Du, Wei; Luo, Qingming

2006-02-17

Current biology is experiencing transformation in logic or philosophy that forces us to reevaluate the concept of cell, tissue or entire organism as a collection of individual components. Systems biology that aims at understanding biological system at the systems level is an emerging research area, which involves interdisciplinary collaborations of life sciences, computational and mathematical sciences, systems engineering, and analytical technology, etc. For analytical chemistry, developing innovative methods to meet the requirement of systems biology represents new challenges as also opportunities and responsibility. In this review, systems biology-oriented micro-separation technologies are introduced for comprehensive profiling of genome, proteome and metabolome, characterization of biomolecules interaction and single cell analysis such as capillary electrophoresis, ultra-thin layer gel electrophoresis, micro-column liquid chromatography, and their multidimensional combinations, parallel integrations, microfabricated formats, and nano technology involvement. Future challenges and directions are also suggested.

Analysis of hazardous biological material by MALDI mass spectrometry

Energy Technology Data Exchange (ETDEWEB)

KL Wahl; KH Jarman; NB Valentine; MT Kingsley; CE Petersen; ST Cebula; AJ Saenz

2000-03-21

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-MS) has become a valuable tool for analyzing microorganisms. The speed with which data can be obtained from MALDI-MS makes this a potentially important tool for biological health hazard monitoring and forensic applications. The excitement in the mass spectrometry community in this potential field of application is evident by the expanding list of research laboratories pursuing development of MALDI-MS for bacterial identification. Numerous research groups have demonstrated the ability to obtain unique MALDI-MS spectra from intact bacterial cells and bacterial cell extracts. The ability to differentiate strains of the same species has been investigated. Reproducibility of MALDI-MS spectra from bacterial species under carefully controlled experimental conditions has also been demonstrated. Wang et al. have reported on interlaboratory reproducibility of the MALDI-MS analysis of several bacterial species. However, there are still issues that need to be addressed, including the careful control of experimental parameters for reproducible spectra and selection of optimal experimental parameters such as solvent and matrix.

Neutron activation analysis on determination of arsenic in biological matrixes

International Nuclear Information System (INIS)

Menezes, Maria Angela de B.C.; Silva, Maria Aparecida

2013-01-01

Aiming at giving support to the Worker's Health Awareness Program of the Municipal Department of Health of Belo Horizonte, an assessment related arsenic was carried out in two galvanising factories by means of hair and toenail samples analysis as biomonitors. The arsenic was determined in all matrixes from the factories where gold electrodeposition process was applied. This is because arsenic salts are usually added to gold bath to improve the metal covering. The high concentration results surprised the health surveillance professionals, and alerted for the need of assessing the influence of a long-term exposure. Studies concerning galvanising process have usually been developed broaching many aspects, but so far few works has pointed out the detection and measurement of other elements like arsenic. The k 0 -Instrumental Neutron Activation method was applied confirming to be a suitable technique on determination of arsenic in biological matrixes. (author)

Neutron activation analysis on determination of arsenic in biological matrixes

Energy Technology Data Exchange (ETDEWEB)

Menezes, Maria Angela de B.C.; Silva, Maria Aparecida, E-mail: menezes@cdtn.br, E-mail: cida@cdtn.br [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN/CNEN-MG), Belo Horizonte, MG (Brazil)

2013-07-01

Aiming at giving support to the Worker's Health Awareness Program of the Municipal Department of Health of Belo Horizonte, an assessment related arsenic was carried out in two galvanising factories by means of hair and toenail samples analysis as biomonitors. The arsenic was determined in all matrixes from the factories where gold electrodeposition process was applied. This is because arsenic salts are usually added to gold bath to improve the metal covering. The high concentration results surprised the health surveillance professionals, and alerted for the need of assessing the influence of a long-term exposure. Studies concerning galvanising process have usually been developed broaching many aspects, but so far few works has pointed out the detection and measurement of other elements like arsenic. The k{sub 0}-Instrumental Neutron Activation method was applied confirming to be a suitable technique on determination of arsenic in biological matrixes. (author)

A molecular informatics view on best practice in multi-parameter compound optimization

NARCIS (Netherlands)

Lusher, S.J.; McGuire, R.; Azevedo, R.; Boiten, J.W.; Schaik, van R.C.; Vlieg, de J.

2011-01-01

The difference between biologically active molecules and drugs is that the latter balance an array of related and unrelated properties required for administration to patients. Inevitability, during optimization, some of these multiple factors will conflict. Although informatics has a crucial role in

Optimization of oncological {sup 18}F-FDG PET/CT imaging based on a multiparameter analysis

Energy Technology Data Exchange (ETDEWEB)

Menezes, Vinicius O., E-mail: vinicius@radtec.com.br [Nuclear Medicine Department, São Rafael Hospital, Salvador 41720-375, Brazil and Nuclear Medicine Department, Hospital das Clínicas da Universidade Federal de Pernambuco/Ebserh, Recife 50670-901 (Brazil); Machado, Marcos A. D. [Nuclear Medicine Department, São Rafael Hospital, Salvador 41720-375, Brazil and Nuclear Medicine Department, Hospital das Clínicas da Universidade Federal de Bahia/Ebserh, Salvador 40110-060 (Brazil); Queiroz, Cleiton C. [Nuclear Medicine Department, São Rafael Hospital, Salvador 41720-375, Brazil and Nuclear Medicine Department, Hospital Universitário Professor Alberto Antunes/Ebserh, Maceió 57072-900 (Brazil); Souza, Susana O. [Department of Physics, Universidade Federal de Sergipe, São Cristóvão 49100-000 (Brazil); D’Errico, Francesco [Department of Diagnostic Radiology, Yale University School of Medicine, New Haven, Connecticut 06520 and School of Engineering, University of Pisa, Pisa 56126 (Italy); Namías, Mauro [Fundación Centro Diagnóstico Nuclear, Buenos Aires C1417CVE (Argentina); Larocca, Ticiana F. [Centro de Biotecnologia e Terapia Celular, São Rafael Hospital, Salvador 41253-190 (Brazil); Soares, Milena B. P. [Centro de Biotecnologia e Terapia Celular, São Rafael Hospital, Salvador 41253-190, Brazil and Fundação Oswaldo Cruz, Centro de Pesq. Gonçalo Moniz, Salvador 40296-710 (Brazil)

2016-02-15

Purpose: This paper describes a method to achieve consistent clinical image quality in {sup 18}F-FDG scans accounting for patient habitus, dose regimen, image acquisition, and processing techniques. Methods: Oncological PET/CT scan data for 58 subjects were evaluated retrospectively to derive analytical curves that predict image quality. Patient noise equivalent count rate and coefficient of variation (CV) were used as metrics in their analysis. Optimized acquisition protocols were identified and prospectively applied to 179 subjects. Results: The adoption of different schemes for three body mass ranges (<60 kg, 60–90 kg, >90 kg) allows improved image quality with both point spread function and ordered-subsets expectation maximization-3D reconstruction methods. The application of this methodology showed that CV improved significantly (p < 0.0001) in clinical practice. Conclusions: Consistent oncological PET/CT image quality on a high-performance scanner was achieved from an analysis of the relations existing between dose regimen, patient habitus, acquisition, and processing techniques. The proposed methodology may be used by PET/CT centers to develop protocols to standardize PET/CT imaging procedures and achieve better patient management and cost-effective operations.

Stability Analysis of Nonlinear Time–Delayed Systems with Application to Biological Models

Directory of Open Access Journals (Sweden)

Kruthika H.A.

2017-03-01

Full Text Available In this paper, we analyse the local stability of a gene-regulatory network and immunotherapy for cancer modelled as nonlinear time-delay systems. A numerically generated kernel, using the sum-of-squares decomposition of multivariate polynomials, is used in the construction of an appropriate Lyapunov–Krasovskii functional for stability analysis of the networks around an equilibrium point. This analysis translates to verifying equivalent LMI conditions. A delay-independent asymptotic stability of a second-order model of a gene regulatory network, taking into consideration multiple commensurate delays, is established. In the case of cancer immunotherapy, a predator–prey type model is adopted to describe the dynamics with cancer cells and immune cells contributing to the predator–prey population, respectively. A delay-dependent asymptotic stability of the cancer-free equilibrium point is proved. Apart from the system and control point of view, in the case of gene-regulatory networks such stability analysis of dynamics aids mimicking gene networks synthetically using integrated circuits like neurochips learnt from biological neural networks, and in the case of cancer immunotherapy it helps determine the long-term outcome of therapy and thus aids oncologists in deciding upon the right approach.

Biological sciences teaching undergraduates’ environmental knowledge: a critical analysis

Directory of Open Access Journals (Sweden)

Silvana do Nascimento Silva

2013-12-01

Full Text Available Nowadays, environmental issues have been addressed in a way that goes beyond the natural impacts, embracing socio-economic, political and cultural aspects. This paper makes a description of the types of environmental conceptions, giving special emphasis to the interactions that permeate it, and develops an empirical work by analyzing the conceptions about the environmental knowledge of students majoring in a teacher preparation course on biological sciences of a university in the State of Bahia, Brazil. In a qualitative research, data were collected by application of a questionnaire with open questions with answers in text and drawings. The results revealed a predominance of naturalistic conceptions, while socio-environmental conceptions of systemic or socio-metabolic characteristics were not found. These findings lead to the need for the integration of these critical approaches about the environmental issue in Sciences and Biology teachers’ training, emphasizing the interactions between work, nature and society. Finally, some suggestions also emerge for future research, among which to analyze the biological sciences university teachers’ environmental conceptions and an action-research with these investigated undergraduates concerning environmental critical approaches.

Pectin: cell biology and prospects for functional analysis.

Science.gov (United States)

Willats, W G; McCartney, L; Mackie, W; Knox, J P

2001-09-01

Pectin is a major component of primary cell walls of all land plants and encompasses a range of galacturonic acid-rich polysaccharides. Three major pectic polysaccharides (homogalacturonan, rhamnogalacturonan-I and rhamnogalacturonan-II) are thought to occur in all primary cell walls. This review surveys what is known about the structure and function of these pectin domains. The high degree of structural complexity and heterogeneity of the pectic matrix is produced both during biosynthesis in the endomembrane system and as a result of the action of an array of wall-based pectin-modifying enzymes. Recent developments in analytical techniques and in the generation of anti-pectin probes have begun to place the structural complexity of pectin in cell biological and developmental contexts. The in muro de-methyl-esterification of homogalacturonan by pectin methyl esterases is emerging as a key process for the local modulation of matrix properties. Rhamnogalacturonan-I comprises a highly diverse population of spatially and developmentally regulated polymers, whereas rhamnogalacturonan-II appears to be a highly conserved and stable pectic domain. Current knowledge of biosynthetic enzymes, plant and microbial pectinases and the interactions of pectin with other cell wall components and the impact of molecular genetic approaches are reviewed in terms of the functional analysis of pectic polysaccharides in plant growth and development.

Parasites as biological tags of fish stocks: a meta-analysis of their discriminatory power.

Science.gov (United States)

Poulin, Robert; Kamiya, Tsukushi

2015-01-01

The use of parasites as biological tags to discriminate among marine fish stocks has become a widely accepted method in fisheries management. Here, we first link this approach to its unstated ecological foundation, the decay in the similarity of the species composition of assemblages as a function of increasing distance between them, a phenomenon almost universal in nature. We explain how distance decay of similarity can influence the use of parasites as biological tags. Then, we perform a meta-analysis of 61 uses of parasites as tags of marine fish populations in multivariate discriminant analyses, obtained from 29 articles. Our main finding is that across all studies, the observed overall probability of correct classification of fish based on parasite data was about 71%. This corresponds to a two-fold improvement over the rate of correct classification expected by chance alone, and the average effect size (Zr = 0·463) computed from the original values was also indicative of a medium-to-large effect. However, none of the moderator variables included in the meta-analysis had a significant effect on the proportion of correct classification; these moderators included the total number of fish sampled, the number of parasite species used in the discriminant analysis, the number of localities from which fish were sampled, the minimum and maximum distance between any pair of sampling localities, etc. Therefore, there are no clear-cut situations in which the use of parasites as tags is more useful than others. Finally, we provide recommendations for the future usage of parasites as tags for stock discrimination, to ensure that future applications of the method achieve statistical rigour and a high discriminatory power.

Computing Platforms for Big Biological Data Analytics: Perspectives and Challenges.

Science.gov (United States)

Yin, Zekun; Lan, Haidong; Tan, Guangming; Lu, Mian; Vasilakos, Athanasios V; Liu, Weiguo

2017-01-01

The last decade has witnessed an explosion in the amount of available biological sequence data, due to the rapid progress of high-throughput sequencing projects. However, the biological data amount is becoming so great that traditional data analysis platforms and methods can no longer meet the need to rapidly perform data analysis tasks in life sciences. As a result, both biologists and computer scientists are facing the challenge of gaining a profound insight into the deepest biological functions from big biological data. This in turn requires massive computational resources. Therefore, high performance computing (HPC) platforms are highly needed as well as efficient and scalable algorithms that can take advantage of these platforms. In this paper, we survey the state-of-the-art HPC platforms for big biological data analytics. We first list the characteristics of big biological data and popular computing platforms. Then we provide a taxonomy of different biological data analysis applications and a survey of the way they have been mapped onto various computing platforms. After that, we present a case study to compare the efficiency of different computing platforms for handling the classical biological sequence alignment problem. At last we discuss the open issues in big biological data analytics.

Correlative analysis of metabolite profiling of Danggui Buxue Tang in rat biological fluids by rapid resolution LC-TOF/MS.

Science.gov (United States)

Li, Chang-Yin; Qi, Lian-Wen; Li, Ping

2011-04-28

In this work, the metabolite profiles of Danggui Buxue Tang (DBT) in rat bile and plasma were qualitatively described, and the possible metabolic pathways of DBT were subsequently proposed. Emphasis was put on correlative analysis of metabolite profiling in different biological fluids. After oral administration of DBT, bile and plasma samples were collected and pretreated by solid phase extraction. Rapid resolution liquid chromatography coupled to time-of-flight mass spectrometry (RRLC-TOFMS) was used for characterization of DBT-related compounds (parent compounds and metabolites) in biological matrices. A total of 142 metabolites were detected and tentatively identified from the drug-containing bile and plasma samples. Metabolite profiling shows that rat bile contained relatively more glutathione-derived conjugates, more saponins compounds and more diverse forms of metabolites than urine. The metabolite profile in plasma revealed that glucuronide conjugates of isoflavonoids, dimmers, acetylcysteine conjugates and parent form of phthalides, as well as saponin aglycones were the major circulating forms of DBT. Collectively, the metabolite profile analysis of DBT in different biological matrices provided a comprehensive understanding of the in vivo metabolic fates of constituents in DBT. Copyright © 2011 Elsevier B.V. All rights reserved.

Biclustering methods: biological relevance and application in gene expression analysis.

Directory of Open Access Journals (Sweden)

Ali Oghabian

Full Text Available DNA microarray technologies are used extensively to profile the expression levels of thousands of genes under various conditions, yielding extremely large data-matrices. Thus, analyzing this information and extracting biologically relevant knowledge becomes a considerable challenge. A classical approach for tackling this challenge is to use clustering (also known as one-way clustering methods where genes (or respectively samples are grouped together based on the similarity of their expression profiles across the set of all samples (or respectively genes. An alternative approach is to develop biclustering methods to identify local patterns in the data. These methods extract subgroups of genes that are co-expressed across only a subset of samples and may feature important biological or medical implications. In this study we evaluate 13 biclustering and 2 clustering (k-means and hierarchical methods. We use several approaches to compare their performance on two real gene expression data sets. For this purpose we apply four evaluation measures in our analysis: (1 we examine how well the considered (biclustering methods differentiate various sample types; (2 we evaluate how well the groups of genes discovered by the (biclustering methods are annotated with similar Gene Ontology categories; (3 we evaluate the capability of the methods to differentiate genes that are known to be specific to the particular sample types we study and (4 we compare the running time of the algorithms. In the end, we conclude that as long as the samples are well defined and annotated, the contamination of the samples is limited, and the samples are well replicated, biclustering methods such as Plaid and SAMBA are useful for discovering relevant subsets of genes and samples.

Network analysis reveals stage-specific changes in zebrafish embryo development using time course whole transcriptome profiling and prior biological knowledge.

Science.gov (United States)

Zhang, Yuji

2015-01-01

Molecular networks act as the backbone of molecular activities within cells, offering a unique opportunity to better understand the mechanism of diseases. While network data usually constitute only static network maps, integrating them with time course gene expression information can provide clues to the dynamic features of these networks and unravel the mechanistic driver genes characterizing cellular responses. Time course gene expression data allow us to broadly "watch" the dynamics of the system. However, one challenge in the analysis of such data is to establish and characterize the interplay among genes that are altered at different time points in the context of a biological process or functional category. Integrative analysis of these data sources will lead us a more complete understanding of how biological entities (e.g., genes and proteins) coordinately perform their biological functions in biological systems. In this paper, we introduced a novel network-based approach to extract functional knowledge from time-dependent biological processes at a system level using time course mRNA sequencing data in zebrafish embryo development. The proposed method was applied to investigate 1α, 25(OH)2D3-altered mechanisms in zebrafish embryo development. We applied the proposed method to a public zebrafish time course mRNA-Seq dataset, containing two different treatments along four time points. We constructed networks between gene ontology biological process categories, which were enriched in differential expressed genes between consecutive time points and different conditions. The temporal propagation of 1α, 25-Dihydroxyvitamin D3-altered transcriptional changes started from a few genes that were altered initially at earlier stage, to large groups of biological coherent genes at later stages. The most notable biological processes included neuronal and retinal development and generalized stress response. In addition, we also investigated the relationship among

ERLN Biological Focus Area

Science.gov (United States)

The Environmental Response Laboratory Network supports the goal to increase national capacity for biological analysis of environmental samples. This includes methods development and verification, technology transfer, and collaboration with USDA, FERN, CDC.

Data publication with the structural biology data grid supports live analysis

NARCIS (Netherlands)

Meyer, Peter A.; Socias, Stephanie; Key, Jason; Ransey, Elizabeth; Tjon, Emily C.; Buschiazzo, Alejandro; Lei, Ming; Botka, Chris; Withrow, James; Neau, David; Rajashankar, Kanagalaghatta; Anderson, Karen S.; Baxter, Richard H.; Blacklow, Stephen C.; Boggon, Titus J.; Bonvin, Alexandre M J J|info:eu-repo/dai/nl/113691238; Borek, Dominika; Brett, Tom J.; Caflisch, Amedeo; Chang, Chung I.; Chazin, Walter J.; Corbett, Kevin D.; Cosgrove, Michael S.; Crosson, Sean; Dhe-Paganon, Sirano; Di Cera, Enrico; Drennan, Catherine L.; Eck, Michael J.; Eichman, Brandt F.; Fan, Qing R.; Ferré-D'Amaré, Adrian R.; Fromme, J. Christopher; Garcia, K. Christopher; Gaudet, Rachelle; Gong, Peng; Harrison, Stephen C.; Heldwein, Ekaterina E.; Jia, Zongchao; Keenan, Robert J.; Kruse, Andrew C.; Kvansakul, Marc; McLellan, Jason S.; Modis, Yorgo; Nam, Yunsun; Otwinowski, Zbyszek; Pai, Emil F.; Pereira, Pedro José Barbosa; Petosa, Carlo; Raman, C. S.; Rapoport, Tom A.; Roll-Mecak, Antonina; Rosen, Michael K.; Rudenko, Gabby; Schlessinger, Joseph; Schwartz, Thomas U.; Shamoo, Yousif; Sondermann, Holger; Tao, Yizhi J.; Tolia, Niraj H.; Tsodikov, Oleg V.; Westover, Kenneth D.; Wu, Hao; Foster, Ian; Fraser, James S.; Maia, Filipe R N C; Gonen, Tamir; Kirchhausen, Tom; Diederichs, Kay; Crosas, Mercé; Sliz, Piotr

2016-01-01

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology

Some applications of neutron activation analysis in plant biology and agronomy

International Nuclear Information System (INIS)

Fourcy, A.

1966-06-01

Plants materials are not so commonly analysed by radioactivation than biological extracts of medical importance. With help of concrete examples, applications of neutrons activation analysis to the determination of some metals (Mn, Cu, Co, Fe, Zn, and K) in plant materials, are proposed. Samples are activated in a swimming-pool reactor at the thermal flux of 5.10 12 n.cm -2 s -1 for a time varying between few minutes and several days according to the element being analysed. The induced radioactivity is measured by spectrometry, with radiochemical separation ( Cu, Co, Fe, Zn and K) or without separation in best cases (Mn,Cu, K). Described dosages are related to: manganese in a graminaceous plant, copper in vine treatments, cobalt, iron and zinc in animal feeding, potassium in a radiological experiment. (author) [fr

Multifactorial and microdosimetrical analysis of the biological influence of galactic cosmic rays on Bacillus subtilis spores in the biostack experiment

International Nuclear Information System (INIS)

Facius, R.

1981-01-01

In this paper a partial experiment is presented which has been performed during several years and several space flight missions. This experiment is part of a research program to study the radiation biological - and in particular the medical relevance of the 'hard' cosmic ray component. The identification of particles (Z, LET, E) was not hindered by the combination with biological objects and could be performed with sufficient accuracy. Refering to semi-empirical findings the distribution of LET values in the bacillus subtilis could be determined in agreement with other experimental results. The localisation and correlation of particle tracks with the individual cells of the target regions is significant. As a result the LET does not seem to be an important parameter for the biological activity within the parameter range studied here. The energy deposition in the spores by delta-electrons could be calculated on the basis of a microdosimetrical analysis. A more detailed analysis was essentially hampered by an insufficient accuracy for the measurement of the distance between particle tracks and the spores. Thus a dose-survival-curve could not be established. In spite of that the relative biological activity (RBW) has been estimated on the basis of density distributions. The failure of these experiments, a review of the relevant literature, and a detailed discussion contribute essentially to the problem of the existence of specific mechanisms for heavy ions and their radiation biological activity. According to the actual knowledge the existence of such a mechanism in addition to delta-electrons has to be considered as most probable. (orig./MG) [de

BSPS Program (ESI-Mass Spectrometry) Biological Sample Data Analysis; Disruption of Bacteria Spores

National Research Council Canada - National Science Library

Lall, Ravi P

2005-01-01

The various biological processing technologies and biological identification approaches are essential for support of the mission to develop and demonstrate an advanced Biological Sample Preparation System...

Adverse effects of biologics: a network meta-analysis and Cochrane overview

DEFF Research Database (Denmark)

Singh, J. A.; Wells, G. A.; Christensen, Robin Daniel Kjersgaard

2011-01-01

Background Biologics are used for the treatment of rheumatoid arthritis and many other conditions. While the efficacy of biologics has been established, there is uncertainty regarding the adverse effects of this treatment. Since serious risks such as tuberculosis (TB) reactivation, serious...

Extended automated separation techniques in destructive neutron activation analysis; application to various biological materials, including human tissues and blood

International Nuclear Information System (INIS)

Tjioe, P.S.; Goeij, J.J.M. de; Houtman, J.P.W.

1976-09-01

Neutron activation analysis may be performed as a multi-element and low-level technique for many important trace elements in biological materials, provided that post-irradiation chemical separations are applied. This paper describes a chemical separation consisting of automated procedures for destruction, distillation, and anion-chromatography. The system developed enables the determination of 14 trace elements in biological materials, viz. antimony, arsenic, bromine, cadmium, chromium, cobalt, copper, gold, iron, mercury, molybdenum, nickel, selenium, and zinc. The aspects of sample preparation, neutron irradiation, gamma-spectrum evaluation, and blank-value contribution are also discussed