Method of measurement in biological systems

DOEpatents

Turteltaub, Kenneth W.; Vogel, John S.; Felton, James S.; Gledhill, Barton L.; Davis, Jay C.; Stanker, Larry H.

1993-05-11

Disclosed is a method of quantifying molecules in biological substances, comprising: a. selecting a biological host in which radioisotopes are present in concentrations equal to or less than those in the ambient biosphere, b. preparing a long-lived radioisotope labeled reactive chemical specie, c. administering said chemical specie to said biological host in doses sufficiently low to avoid significant overt damage to the biological system thereof, d. allowing a period of time to elapse sufficient for dissemination and interaction of said chemical specie with said host throughout said biological system of said host, e. isolating a reacted fraction of the biological substance from said host in a manner sufficient to avoid contamination of said substance from extraneous sources, f. converting said fraction of biological substance by suitable means to a material which efficiently produces charged ions in at least one of several possible ion sources without introduction of significant isotopic fractionation, and, g. measuring the radioisotope concentration in said material by means of direct isotopic counting.

Method of measurement in biological systems

DOEpatents

Turteltaub, Kenneth W.; Vogel, John S.; Felton, James S.; Gledhill, Barton L.; Davis, Jay C.

1994-01-01

Disclosed is a method of quantifying molecules in biological substances comprising: a. selecting a biological host in which radioisotopes are present in concentrations equal to or less than those in the ambient biosphere, b. preparing a long-lived radioisotope labeled reactive chemical specie, c. administering said chemical specie to said biological host in doses sufficiently low to avoid significant overt damage to the biological system thereof, d. allowing a period of time to elapse sufficient for dissemination and interaction of said chemical specie with said host throughout said biological system of said host, e. isolating a reacted fraction of the biological substance from said host in a manner sufficient to avoid contamination of said substance from extraneous sources, f. converting said fraction of biological substance by suitable means to a material which efficiently produces charged ions in at least one of several possible ion sources without introduction of significant isotopic fractionation, and, g. measuring the radioisotope concentration in said material by means of direct isotopic counting.

Cosmo Cassette: A Microfluidic Microgravity Microbial System For Synthetic Biology Unit Tests and Satellite Missions

NASA Technical Reports Server (NTRS)

Berliner, Aaron J.

2013-01-01

Although methods in the design-build-test life cycle of the synthetic biology field have grown rapidly, the expansion has been non-uniform. The design and build stages in development have seen innovations in the form of biological CAD and more efficient means for building DNA, RNA, and other biological constructs. The testing phase of the cycle remains in need of innovation. Presented will be both a theoretical abstraction of biological measurement and a practical demonstration of a microfluidics-based platform for characterizing synthetic biological phenomena. Such a platform demonstrates a design of additive manufacturing (3D printing) for construction of a microbial fuel cell (MFC) to be used in experiments carried out in space. First, the biocompatibility of the polypropylene chassis will be demonstrated. The novel MFCs will be cheaper, and faster to make and iterate through designs. The novel design will contain a manifold switchingdistribution system and an integrated in-chip set of reagent reservoirs fabricated via 3D printing. The automated nature of the 3D printing yields itself to higher resolution switching valves and leads to smaller sized payloads, lower cost, reduced power and a standardized platform for synthetic biology unit tests on Earth and in space. It will be demonstrated that the application of unit testing in synthetic biology will lead to the automatic construction and validation of desired constructs. Unit testing methodologies offer benefits of preemptive problem identification, change of facility, simplicity of integration, ease of documentation, and separation of interface from implementation, and automated design.

Methods of biological dosimetry employing chromosome-specific staining

DOEpatents

Gray, Joe W.; Pinkel, Daniel

2000-01-01

Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods are provided to disable the hybridization capacity of shared, high copy repetitive sequences and/or remove such sequences to provide for useful contrast. Still further methods are provided to produce chromosome-specific staining reagents which are made specific to the targeted chromosomal material, which can be one or more whole chromosomes, one or more regions on one or more chromosomes, subsets of chromosomes and/or the entire genome. Probes and test kits are provided for use in tumor cytogenetics, in the detection of disease related loci, in analysis of structural abnormalities, such as translocations, and for biological dosimetry. Further, methods and prenatal test kits are provided to stain targeted chromosomal material of fetal cells, including fetal cells obtained from maternal blood. Still further, the invention provides for automated means to detect and analyse chromosomal abnormalities.

40 CFR 230.61 - Chemical, biological, and physical evaluation and testing.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 26 2012-07-01 2011-07-01 true Chemical, biological, and physical... FILL MATERIAL Evaluation and Testing § 230.61 Chemical, biological, and physical evaluation and testing... approaches or procedures will be furnished by the permitting authority. (b) Chemical-biological interactive...

Mathematical methods in systems biology.

PubMed

Kashdan, Eugene; Duncan, Dominique; Parnell, Andrew; Schattler, Heinz

2016-12-01

The editors of this Special Issue of Mathematical Biosciences and Engineering were the organizers for the Third International Workshop "Mathematical Methods in System Biology" that took place on June 15-18, 2015 at the University College Dublin in Ireland. As stated in the workshop goals, we managed to attract a good mix of mathematicians and statisticians working on biological and medical applications with biologists and clinicians interested in presenting their challenging problems and looking to find mathematical and statistical tools for their solutions.

Using synthetic biology to make cells tomorrow's test tubes.

PubMed

Garcia, Hernan G; Brewster, Robert C; Phillips, Rob

2016-04-18

The main tenet of physical biology is that biological phenomena can be subject to the same quantitative and predictive understanding that physics has afforded in the context of inanimate matter. However, the inherent complexity of many of these biological processes often leads to the derivation of complex theoretical descriptions containing a plethora of unknown parameters. Such complex descriptions pose a conceptual challenge to the establishment of a solid basis for predictive biology. In this article, we present various exciting examples of how synthetic biology can be used to simplify biological systems and distill these phenomena down to their essential features as a means to enable their theoretical description. Here, synthetic biology goes beyond previous efforts to engineer nature and becomes a tool to bend nature to understand it. We discuss various recent and classic experiments featuring applications of this synthetic approach to the elucidation of problems ranging from bacteriophage infection, to transcriptional regulation in bacteria and in developing embryos, to evolution. In all of these examples, synthetic biology provides the opportunity to turn cells into the equivalent of a test tube, where biological phenomena can be reconstituted and our theoretical understanding put to test with the same ease that these same phenomena can be studied in the in vitro setting.

Testing and Validation of Computational Methods for Mass Spectrometry.

PubMed

Gatto, Laurent; Hansen, Kasper D; Hoopmann, Michael R; Hermjakob, Henning; Kohlbacher, Oliver; Beyer, Andreas

2016-03-04

High-throughput methods based on mass spectrometry (proteomics, metabolomics, lipidomics, etc.) produce a wealth of data that cannot be analyzed without computational methods. The impact of the choice of method on the overall result of a biological study is often underappreciated, but different methods can result in very different biological findings. It is thus essential to evaluate and compare the correctness and relative performance of computational methods. The volume of the data as well as the complexity of the algorithms render unbiased comparisons challenging. This paper discusses some problems and challenges in testing and validation of computational methods. We discuss the different types of data (simulated and experimental validation data) as well as different metrics to compare methods. We also introduce a new public repository for mass spectrometric reference data sets ( http://compms.org/RefData ) that contains a collection of publicly available data sets for performance evaluation for a wide range of different methods.

Biological Methods and Manual Development

EPA Pesticide Factsheets

EPA scientists conduct research to develop and evaluate analytical methods for the identification, enumeration, evaluation of aquatic organisms exposed to environmental stressors and to correlate exposures with effects on chemical and biological indicators

Using biological and physico-chemical test methods to assess the role of concrete mixture design in resistance to microbially induced corrosion

NASA Astrophysics Data System (ADS)

House, Mitchell Wayne

Concrete is the most widely used material for construction of wastewater collection, storage, and treatment infrastructure. The chemical and physical characteristics of hydrated portland cement make it susceptible to degradation under highly acidic conditions. As a result, some concrete wastewater infrastructure may be susceptible to a multi-stage degradation process known as microbially induced corrosion, or MIC. MIC begins with the production of aqueous hydrogen sulfide (H2S(aq)) by anaerobic sulfate reducing bacteria present below the waterline. H2S(aq) partitions to the gas phase where it is oxidized to sulfuric acid by the aerobic sulfur oxidizing bacteria Thiobacillus that resides on concrete surfaces above the waterline. Sulfuric acid then attacks the cement paste portion of the concrete matrix through decalcification of calcium hydroxide and calcium silica hydrate coupled with the formation of expansive corrosion products. The attack proceeds inward resulting in reduced service life and potential failure of the concrete structure. There are several challenges associated with assessing a concrete's susceptibility to MIC. First, no standard laboratory tests exist to assess concrete resistance to MIC. Straightforward reproduction of MIC in the laboratory is complicated by the use of microorganisms and hydrogen sulfide gas. Physico-chemical tests simulating MIC by immersing concrete specimens in sulfuric acid offer a convenient alternative, but do not accurately capture the damage mechanisms associated with biological corrosion. Comparison of results between research studies is difficult due to discrepancies that can arise in experimental methods even if current ASTM standards are followed. This thesis presents two experimental methods to evaluate concrete resistance to MIC: one biological and one physico-chemical. Efforts are made to address the critical aspects of each testing method currently absent in the literature. The first method presented is a new test

TEST BOOKLET FOR HIGH SCHOOL BIOLOGY, EXPERIMENTAL MATERIALS FOR USE 1966-1968.

ERIC Educational Resources Information Center

Biological Sciences Curriculum Study, Boulder, CO.

SUPPLEMENTARY TEST QUESTIONS FOR USE BY SECONDARY BIOLOGICAL SCIENCES CURRICULUM STUDY GREEN VERSION BIOLOGY TEACHERS IN THE CONSTRUCTION OF EXAMINATIONS ARE CONTAINED IN THIS EXPERIMENTAL MANUAL. THE ITEMS WERE PREPARED BY THE BIOLOGICAL SCIENCES CURRICULUM STUDY TEST CONSTRUCTION COMMITTEE IN RESPONSE TO TEACHER REQUESTS FOR SHORT-RANGE TESTS.…

Multidimensional Computerized Adaptive Testing for Indonesia Junior High School Biology

ERIC Educational Resources Information Center

Kuo, Bor-Chen; Daud, Muslem; Yang, Chih-Wei

2015-01-01

This paper describes a curriculum-based multidimensional computerized adaptive test that was developed for Indonesia junior high school Biology. In adherence to the Indonesian curriculum of different Biology dimensions, 300 items was constructed, and then tested to 2238 students. A multidimensional random coefficients multinomial logit model was…

40 CFR 230.61 - Chemical, biological, and physical evaluation and testing.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 25 2014-07-01 2014-07-01 false Chemical, biological, and physical... FILL MATERIAL Evaluation and Testing § 230.61 Chemical, biological, and physical evaluation and testing... appropriate physical and chemical environmental characteristics. (d) Physical tests and evaluation. The effect...

Improved image alignment method in application to X-ray images and biological images.

PubMed

Wang, Ching-Wei; Chen, Hsiang-Chou

2013-08-01

Alignment of medical images is a vital component of a large number of applications throughout the clinical track of events; not only within clinical diagnostic settings, but prominently so in the area of planning, consummation and evaluation of surgical and radiotherapeutical procedures. However, image registration of medical images is challenging because of variations on data appearance, imaging artifacts and complex data deformation problems. Hence, the aim of this study is to develop a robust image alignment method for medical images. An improved image registration method is proposed, and the method is evaluated with two types of medical data, including biological microscopic tissue images and dental X-ray images and compared with five state-of-the-art image registration techniques. The experimental results show that the presented method consistently performs well on both types of medical images, achieving 88.44 and 88.93% averaged registration accuracies for biological tissue images and X-ray images, respectively, and outperforms the benchmark methods. Based on the Tukey's honestly significant difference test and Fisher's least square difference test tests, the presented method performs significantly better than all existing methods (P ≤ 0.001) for tissue image alignment, and for the X-ray image registration, the proposed method performs significantly better than the two benchmark b-spline approaches (P < 0.001). The software implementation of the presented method and the data used in this study are made publicly available for scientific communities to use (http://www-o.ntust.edu.tw/∼cweiwang/ImprovedImageRegistration/). cweiwang@mail.ntust.edu.tw.

General method to find the attractors of discrete dynamic models of biological systems.

PubMed

Gan, Xiao; Albert, Réka

2018-04-01

Analyzing the long-term behaviors (attractors) of dynamic models of biological networks can provide valuable insight. We propose a general method that can find the attractors of multilevel discrete dynamical systems by extending a method that finds the attractors of a Boolean network model. The previous method is based on finding stable motifs, subgraphs whose nodes' states can stabilize on their own. We extend the framework from binary states to any finite discrete levels by creating a virtual node for each level of a multilevel node, and describing each virtual node with a quasi-Boolean function. We then create an expanded representation of the multilevel network, find multilevel stable motifs and oscillating motifs, and identify attractors by successive network reduction. In this way, we find both fixed point attractors and complex attractors. We implemented an algorithm, which we test and validate on representative synthetic networks and on published multilevel models of biological networks. Despite its primary motivation to analyze biological networks, our motif-based method is general and can be applied to any finite discrete dynamical system.

General method to find the attractors of discrete dynamic models of biological systems

NASA Astrophysics Data System (ADS)

Gan, Xiao; Albert, Réka

2018-04-01

Analyzing the long-term behaviors (attractors) of dynamic models of biological networks can provide valuable insight. We propose a general method that can find the attractors of multilevel discrete dynamical systems by extending a method that finds the attractors of a Boolean network model. The previous method is based on finding stable motifs, subgraphs whose nodes' states can stabilize on their own. We extend the framework from binary states to any finite discrete levels by creating a virtual node for each level of a multilevel node, and describing each virtual node with a quasi-Boolean function. We then create an expanded representation of the multilevel network, find multilevel stable motifs and oscillating motifs, and identify attractors by successive network reduction. In this way, we find both fixed point attractors and complex attractors. We implemented an algorithm, which we test and validate on representative synthetic networks and on published multilevel models of biological networks. Despite its primary motivation to analyze biological networks, our motif-based method is general and can be applied to any finite discrete dynamical system.

The Effect of Gender on the Achievement of Students in Biology Using the Jigsaw Method

ERIC Educational Resources Information Center

Amedu, Odagboyi Isaiah

2015-01-01

This paper examined the effect of gender on the achievement of students in biology using the jigsaw method. The sample was made up of 87 students in SS1 in a secondary school. The study utilized an intact class because the study took place in a normal school term. There were 39 males and 49 females. The Biology Achievement Test (BAT) was…

Alternative Test Methods for Developmental Neurotoxicity: A ...

EPA Pesticide Factsheets

Exposure to environmental contaminants is well documented to adversely impact the development of the nervous system. However, the time, animal and resource intensive EPA and OECD testing guideline methods for developmental neurotoxicity (DNT) are not a viable solution to characterizing potential chemical hazards for the thousands of untested chemicals currently in commerce. Thus, research efforts over the past decade have endeavored to develop cost-effective alternative DNT testing methods. These efforts have begun to generate data that can inform regulatory decisions. Yet there are major challenges to both the acceptance and use of this data. Major scientific challenges for DNT include development of new methods and models that are “fit for purpose”, development of a decision-use framework, and regulatory acceptance of the methods. It is critical to understand that use of data from these methods will be driven mainly by the regulatory problems being addressed. Some problems may be addressed with limited datasets, while others may require data for large numbers of chemicals, or require the development and use of new biological and computational models. For example mechanistic information derived from in vitro DNT assays can be used to inform weight of evidence (WoE) or integrated approaches to testing and assessment (IATA) approaches for chemical-specific assessments. Alternatively, in vitro data can be used to prioritize (for further testing) the thousands

Creative design inspired by biological knowledge: Technologies and methods

NASA Astrophysics Data System (ADS)

Tan, Runhua; Liu, Wei; Cao, Guozhong; Shi, Yuan

2018-05-01

Biological knowledge is becoming an important source of inspiration for developing creative solutions to engineering design problems and even has a huge potential in formulating ideas that can help firms compete successfully in a dynamic market. To identify the technologies and methods that can facilitate the development of biologically inspired creative designs, this research briefly reviews the existing biological-knowledge-based theories and methods and examines the application of biological-knowledge-inspired designs in various fields. Afterward, this research thoroughly examines the four dimensions of key technologies that underlie the biologically inspired design (BID) process. This research then discusses the future development trends of the BID process before presenting the conclusions.

Report of the Interagency biological methods workshop

USGS Publications Warehouse

Gurtz, Martin E.; Muir, Thomas A.

1994-01-01

The U.S. Geological Survey hosted the Interagency Biological Methods Workshop in Reston, Virginia, during June 22-23, 1993. The purposes of the workshop were to (1) promote better communication among Federal agencies that are using or developing biological methods in water-quality assessment programs for streams and rivers, and (2) facilitate the sharing of data and interagency collaboration. The workshop was attended by 45 biologists representing numerous Federal agencies and programs, and a few regional and State programs that were selected to provide additional perspectives. The focus of the workshop was community assessment methods for fish, invertebrates, and algae; physical habitat characterization; and chemical analyses of biological tissues. Charts comparing program objectives, design features, and sampling methods were compiled from materials that were provided by participating agencies prior to the workshop and formed the basis for small workgroup discussions. Participants noted that differences in methods among programs were often necessitated by differences in program objectives. However, participants agreed that where programs have identified similar data needs, the use of common methods is beneficial. Opportunities discussed for improving data compatibility and information sharing included (1) modifying existing methods, (2) adding parameters, (3) improving access to data through shared databases (potentially with common database structures), and (4) future collaborative efforts that range from research on selected protocol questions to followup meetings and continued discussions.

Adaptive Set-Based Methods for Association Testing

PubMed Central

Su, Yu-Chen; Gauderman, W. James; Kiros, Berhane; Lewinger, Juan Pablo

2017-01-01

With a typical sample size of a few thousand subjects, a single genomewide association study (GWAS) using traditional one-SNP-at-a-time methods can only detect genetic variants conferring a sizable effect on disease risk. Set-based methods, which analyze sets of SNPs jointly, can detect variants with smaller effects acting within a gene, a pathway, or other biologically relevant sets. While self-contained set-based methods (those that test sets of variants without regard to variants not in the set) are generally more powerful than competitive set-based approaches (those that rely on comparison of variants in the set of interest with variants not in the set), there is no consensus as to which self-contained methods are best. In particular, several self-contained set tests have been proposed to directly or indirectly ‘adapt’ to the a priori unknown proportion and distribution of effects of the truly associated SNPs in the set, which is a major determinant of their power. A popular adaptive set-based test is the adaptive rank truncated product (ARTP), which seeks the set of SNPs that yields the best-combined evidence of association. We compared the standard ARTP, several ARTP variations we introduced, and other adaptive methods in a comprehensive simulation study to evaluate their performance. We used permutations to assess significance for all the methods and thus provide a level playing field for comparison. We found the standard ARTP test to have the highest power across our simulations followed closely by the global model of random effects (GMRE) and a LASSO based test. PMID:26707371

Biology, Philosophy, and Scientific Method.

ERIC Educational Resources Information Center

Hill, L.

1985-01-01

The limits of falsification are discussed and the historically based models of science described by Lakatos and Kuhn are shown to offer greater insights into the practice of science. The theory of natural selection is used to relate biology to philosophy and scientific method. (Author/JN)

Methods for evaluating the biological impact of potentially toxic waste applied to soils

DOE Office of Scientific and Technical Information (OSTI.GOV)

Neuhauser, E.F.; Loehr, R.C.; Malecki, M.R.

1985-12-01

The study was designed to evaluate two methods that can be used to estimate the biological impact of organics and inorganics that may be in wastes applied to land for treatment and disposal. The two methods were the contact test and the artificial soil test. The contact test is a 48 hr test using an adult worm, a small glass vial, and filter paper to which the test chemical or waste is applied. The test is designed to provide close contact between the worm and a chemical similar to the situation in soils. The method provides a rapid estimate ofmore » the relative toxicity of chemicals and industrial wastes. The artificial soil test uses a mixture of sand, kaolin, peat, and calcium carbonate as a representative soil. Different concentrations of the test material are added to the artificial soil, adult worms are added and worm survival is evaluated after two weeks. These studies have shown that: earthworms can distinguish between a wide variety of chemicals with a high degree of accuracy.« less

[Bio-objects and biological methods of space radiation effects evaluation].

PubMed

Kaminskaia, E V; Nevzgodina, L V; Platova, N G

2009-01-01

The unique conditions of space experiments place austere requirements to bio-objects and biological methods of radiation effects evaluation. The paper discusses suitability of a number of bio-objects varying in stage of evolution and metabolism for space researches aimed to state common patterns of the radiation damage caused by heavy ions (HI), and character of HI-cell interaction. Physical detectors in space experiments of the BIOBLOCK series make it possible to identify bio-objects hit by space HI and to set correlation between HI track topography and biological effect. The paper provides an all-round description of the bio-objects chosen for two BIOBLOCK experiments (population of hydrophyte Wolffia arrhiza (fam. duckweed) and Lactuca sativa seeds) and the method of evaluating effects from single space radiation HI. Direct effects of heavy ions on cells can be determined by the criteria of chromosomal aberrations and delayed morphologic abnormalities. The evaluation results are compared with the data about human blood lymphocytes. Consideration is being given to the procedures of test-objects' treatment and investigation.

Cosmic heavy ion tracks in mesoscopic biological test objects

NASA Technical Reports Server (NTRS)

Facius, R.

1994-01-01

Since more than 20 years ago, when the National Academy of Sciences and the National Research Council of the U.S.A. released their report on 'HZE particle effects in manned spaced flight', it has been emphasized how difficult - if not even impossible - it is to assess their radiobiological impact on man from conventional studies where biological test organisms are stochastically exposed to 'large' fluences of heavy ions. An alternative, competing approach had been realized in the BIOSTACK experiments, where the effects of single cosmic as well as accelerator - heavy ions on individual biological test organisms could be investigated. Although presented from the beginning as the preferable approach for terrestrial investigations with accelerator heavy ions too ('The BIOSTACK as an approach to high LET radiation research'), only recently this insight is gaining more widespread recognition. In space flight experiments, additional constraints imposed by the infrastructure of the vehicle or satellite further impede such investigations. Restrictions concern the physical detector systems needed for the registration of the cosmic heavy ions' trajectories as well as the biological systems eligible as test organisms. Such optimized procedures and techniques were developed for the investigations on chromosome aberrations induced by cosmic heavy ions in cells of the stem meristem of lettuce seeds (Lactuca sativa) and for the investigation of the radiobiological response of Wolffia arriza, which is the smallest flowering (water) plant. The biological effects were studied by the coworkers of the Russian Institute of Biomedical Problems (IBMP) which in cooperation with the European Space Agency ESA organized the exposure in the Biosatellites of the Cosmos series. Since biological investigations and physical measurements of particle tracks had to be performed in laboratories widely separated, the preferred fixed contact between biological test objects and the particle detectors

Apparatus and Methods for Manipulation and Optimization of Biological Systems

NASA Technical Reports Server (NTRS)

Sun, Ren (Inventor); Ho, Chih-Ming (Inventor); Wong, Pak Kin (Inventor); Yu, Fuqu (Inventor)

2014-01-01

The invention provides systems and methods for manipulating biological systems, for example to elicit a more desired biological response from a biological sample, such as a tissue, organ, and/or a cell. In one aspect, the invention operates by efficiently searching through a large parametric space of stimuli and system parameters to manipulate, control, and optimize the response of biological samples sustained in the system. In one aspect, the systems and methods of the invention use at least one optimization algorithm to modify the actuator's control inputs for stimulation, responsive to the sensor's output of response signals. The invention can be used, e.g., to optimize any biological system, e.g., bioreactors for proteins, and the like, small molecules, polysaccharides, lipids, and the like. Another use of the apparatus and methods includes is for the discovery of key parameters in complex biological systems.

Adaptive Set-Based Methods for Association Testing.

PubMed

Su, Yu-Chen; Gauderman, William James; Berhane, Kiros; Lewinger, Juan Pablo

2016-02-01

With a typical sample size of a few thousand subjects, a single genome-wide association study (GWAS) using traditional one single nucleotide polymorphism (SNP)-at-a-time methods can only detect genetic variants conferring a sizable effect on disease risk. Set-based methods, which analyze sets of SNPs jointly, can detect variants with smaller effects acting within a gene, a pathway, or other biologically relevant sets. Although self-contained set-based methods (those that test sets of variants without regard to variants not in the set) are generally more powerful than competitive set-based approaches (those that rely on comparison of variants in the set of interest with variants not in the set), there is no consensus as to which self-contained methods are best. In particular, several self-contained set tests have been proposed to directly or indirectly "adapt" to the a priori unknown proportion and distribution of effects of the truly associated SNPs in the set, which is a major determinant of their power. A popular adaptive set-based test is the adaptive rank truncated product (ARTP), which seeks the set of SNPs that yields the best-combined evidence of association. We compared the standard ARTP, several ARTP variations we introduced, and other adaptive methods in a comprehensive simulation study to evaluate their performance. We used permutations to assess significance for all the methods and thus provide a level playing field for comparison. We found the standard ARTP test to have the highest power across our simulations followed closely by the global model of random effects (GMRE) and a least absolute shrinkage and selection operator (LASSO)-based test. © 2015 WILEY PERIODICALS, INC.

Chaste: A test-driven approach to software development for biological modelling

NASA Astrophysics Data System (ADS)

Pitt-Francis, Joe; Pathmanathan, Pras; Bernabeu, Miguel O.; Bordas, Rafel; Cooper, Jonathan; Fletcher, Alexander G.; Mirams, Gary R.; Murray, Philip; Osborne, James M.; Walter, Alex; Chapman, S. Jon; Garny, Alan; van Leeuwen, Ingeborg M. M.; Maini, Philip K.; Rodríguez, Blanca; Waters, Sarah L.; Whiteley, Jonathan P.; Byrne, Helen M.; Gavaghan, David J.

2009-12-01

Chaste ('Cancer, heart and soft-tissue environment') is a software library and a set of test suites for computational simulations in the domain of biology. Current functionality has arisen from modelling in the fields of cancer, cardiac physiology and soft-tissue mechanics. It is released under the LGPL 2.1 licence. Chaste has been developed using agile programming methods. The project began in 2005 when it was reasoned that the modelling of a variety of physiological phenomena required both a generic mathematical modelling framework, and a generic computational/simulation framework. The Chaste project evolved from the Integrative Biology (IB) e-Science Project, an inter-institutional project aimed at developing a suitable IT infrastructure to support physiome-level computational modelling, with a primary focus on cardiac and cancer modelling. Program summaryProgram title: Chaste Catalogue identifier: AEFD_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFD_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: LGPL 2.1 No. of lines in distributed program, including test data, etc.: 5 407 321 No. of bytes in distributed program, including test data, etc.: 42 004 554 Distribution format: tar.gz Programming language: C++ Operating system: Unix Has the code been vectorised or parallelized?: Yes. Parallelized using MPI. RAM:<90 Megabytes for two of the scenarios described in Section 6 of the manuscript (Monodomain re-entry on a slab or Cylindrical crypt simulation). Up to 16 Gigabytes (distributed across processors) for full resolution bidomain cardiac simulation. Classification: 3. External routines: Boost, CodeSynthesis XSD, CxxTest, HDF5, METIS, MPI, PETSc, Triangle, Xerces Nature of problem: Chaste may be used for solving coupled ODE and PDE systems arising from modelling biological systems. Use of Chaste in two application areas are described in this paper: cardiac electrophysiology and

Personalized genetic testing as a tool for integrating ethics instruction into biology courses.

PubMed

Zhang, Tenny R; Anderson, Misti Ault

2014-12-01

Personalized genetic testing (PGT) has been used by some educational institutions as a pedagogical tool for teaching human genetics. While work has been done that examines the potential for PGT to improve students' interest and understanding of the science involved in genetic testing, there has been less dialogue about how this method might be useful for integrating ethical and societal issues surrounding genetic testing into classroom discussions. Citing the importance of integrating ethics into the biology classroom, we argue that PGT can be an effective educational tool for integrating ethics and science education, and discuss relevant ethical considerations for instructors using this approach.

Near-infrared fluorescence image quality test methods for standardized performance evaluation

NASA Astrophysics Data System (ADS)

Kanniyappan, Udayakumar; Wang, Bohan; Yang, Charles; Ghassemi, Pejhman; Wang, Quanzeng; Chen, Yu; Pfefer, Joshua

2017-03-01

Near-infrared fluorescence (NIRF) imaging has gained much attention as a clinical method for enhancing visualization of cancers, perfusion and biological structures in surgical applications where a fluorescent dye is monitored by an imaging system. In order to address the emerging need for standardization of this innovative technology, it is necessary to develop and validate test methods suitable for objective, quantitative assessment of device performance. Towards this goal, we develop target-based test methods and investigate best practices for key NIRF imaging system performance characteristics including spatial resolution, depth of field and sensitivity. Characterization of fluorescence properties was performed by generating excitation-emission matrix properties of indocyanine green and quantum dots in biological solutions and matrix materials. A turbid, fluorophore-doped target was used, along with a resolution target for assessing image sharpness. Multi-well plates filled with either liquid or solid targets were generated to explore best practices for evaluating detection sensitivity. Overall, our results demonstrate the utility of objective, quantitative, target-based testing approaches as well as the need to consider a wide range of factors in establishing standardized approaches for NIRF imaging system performance.

IERL-RTP PROCEDURES MANUAL: LEVEL 1 ENVIRONMENTAL ASSESSMENT BIOLOGICAL TESTS

EPA Science Inventory

The manual gives revised procedures for Level 1 environmental assessment biological tests, and supersedes the first edition, EPA-600/7-77-043 (NTIS No. PB 268484), published in April 1977. The revised biological procedures complement the Level 1 chemical and physical procedures p...

Personalized Genetic Testing as a Tool for Integrating Ethics Instruction into Biology Courses

PubMed Central

Zhang, Tenny R.; Anderson, Misti Ault

2014-01-01

Personalized genetic testing (PGT) has been used by some educational institutions as a pedagogical tool for teaching human genetics. While work has been done that examines the potential for PGT to improve students’ interest and understanding of the science involved in genetic testing, there has been less dialogue about how this method might be useful for integrating ethical and societal issues surrounding genetic testing into classroom discussions. Citing the importance of integrating ethics into the biology classroom, we argue that PGT can be an effective educational tool for integrating ethics and science education, and discuss relevant ethical considerations for instructors using this approach. PMID:25574278

Apparatus and methods for manipulation and optimization of biological systems

NASA Technical Reports Server (NTRS)

Sun, Ren (Inventor); Ho, Chih-Ming (Inventor); Wong, Pak Kin (Inventor); Yu, Fuqu (Inventor)

2012-01-01

The invention provides systems and methods for manipulating, e.g., optimizing and controlling, biological systems, e.g., for eliciting a more desired biological response of biological sample, such as a tissue, organ, and/or a cell. In one aspect, systems and methods of the invention operate by efficiently searching through a large parametric space of stimuli and system parameters to manipulate, control, and optimize the response of biological samples sustained in the system, e.g., a bioreactor. In alternative aspects, systems include a device for sustaining cells or tissue samples, one or more actuators for stimulating the samples via biochemical, electromagnetic, thermal, mechanical, and/or optical stimulation, one or more sensors for measuring a biological response signal of the samples resulting from the stimulation of the sample. In one aspect, the systems and methods of the invention use at least one optimization algorithm to modify the actuator's control inputs for stimulation, responsive to the sensor's output of response signals. The compositions and methods of the invention can be used, e.g., to for systems optimization of any biological manufacturing or experimental system, e.g., bioreactors for proteins, e.g., therapeutic proteins, polypeptides or peptides for vaccines, and the like, small molecules (e.g., antibiotics), polysaccharides, lipids, and the like. Another use of the apparatus and methods includes combination drug therapy, e.g. optimal drug cocktail, directed cell proliferations and differentiations, e.g. in tissue engineering, e.g. neural progenitor cells differentiation, and discovery of key parameters in complex biological systems.

Biologic variability and correlation of platelet function testing in healthy dogs.

PubMed

Blois, Shauna L; Lang, Sean T; Wood, R Darren; Monteith, Gabrielle

2015-12-01

Platelet function tests are influenced by biologic variability, including inter-individual (CVG ) and intra-individual (CVI ), as well as analytic (CVA ) variability. Variability in canine platelet function testing is unknown, but if excessive, would make it difficult to interpret serial results. Additionally, the correlation between platelet function tests is poor in people, but not well described in dogs. The aims were to: (1) identify the effect of variation in preanalytic factors (venipuncture, elapsed time until analysis) on platelet function tests; (2) calculate analytic and biologic variability of adenosine diphosphate (ADP) and arachidonic acid (AA)-induced thromboelastograph platelet mapping (TEG-PM), ADP-, AA-, and collagen-induced whole blood platelet aggregometry (WBA), and collagen/ADP and collagen/epinephrine platelet function analysis (PFA-CADP, PFA-CEPI); and (3) determine the correlation between these variables. In this prospective observational trial, platelet function was measured once every 7 days, for 4 consecutive weeks, in 9 healthy dogs. In addition, CBC, TEG-PM, WBA, and PFA were performed. Overall coefficients of variability ranged from 13.3% to 87.8% for the platelet function tests. Biologic variability was highest for AA-induced maximum amplitude generated during TEG-PM (MAAA; CVG = 95.3%, CVI = 60.8%). Use of population-based reference intervals (RI) was determined appropriate only for PFA-CADP (index of individuality = 10.7). There was poor correlation between most platelet function tests. Use of population-based RI appears inappropriate for most platelet function tests, and tests poorly correlate with one another. Future studies on biologic variability and correlation of platelet function tests should be performed in dogs with platelet dysfunction and those treated with antiplatelet therapy. © 2015 American Society for Veterinary Clinical Pathology.

Materials and methods for delivery of biological drugs

NASA Astrophysics Data System (ADS)

Zelikin, Alexander N.; Ehrhardt, Carsten; Healy, Anne Marie

2016-11-01

Biological drugs generated via recombinant techniques are uniquely positioned due to their high potency and high selectivity of action. The major drawback of this class of therapeutics, however, is their poor stability upon oral administration and during subsequent circulation. As a result, biological drugs have very low bioavailability and short therapeutic half-lives. Fortunately, tools of chemistry and biotechnology have been developed into an elaborate arsenal, which can be applied to improve the pharmacokinetics of biological drugs. Depot-type release systems are available to achieve sustained release of drugs over time. Conjugation to synthetic or biological polymers affords long circulating formulations. Administration of biological drugs through non-parenteral routes shows excellent performance and the first products have reached the market. This Review presents the main accomplishments in this field and illustrates the materials and methods behind existing and upcoming successful formulations and delivery strategies for biological drugs.

Mixed-Methods Design in Biology Education Research: Approach and Uses.

PubMed

Warfa, Abdi-Rizak M

Educational research often requires mixing different research methodologies to strengthen findings, better contextualize or explain results, or minimize the weaknesses of a single method. This article provides practical guidelines on how to conduct such research in biology education, with a focus on mixed-methods research (MMR) that uses both quantitative and qualitative inquiries. Specifically, the paper provides an overview of mixed-methods design typologies most relevant in biology education research. It also discusses common methodological issues that may arise in mixed-methods studies and ways to address them. The paper concludes with recommendations on how to report and write about MMR. © 2016 L. A.-R. M. Warfa. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Biological testing of a digested sewage sludge and derived composts.

PubMed

Moreira, R; Sousa, J P; Canhoto, C

2008-11-01

Aiming to evaluate a possible loss of soil habitat function after amendment with organic wastes, a digested sewage sludge and derived composts produced with green residues, where biologically tested in the laboratory using soil animals (Eisenia andrei and Folsomia candida) and plants (Brassica rapa and Avena sativa). Each waste was tested mimicking a field application of 6ton/ha or 12ton/ha. Avoidance tests did not reveal any impact of sludge and composts to soil biota. Germination and growth tests showed that application of composts were beneficial for both plants. Composts did not affect earthworm's mass increase or reproduction, but the highest sludge amendment revealed negative effects on both parameters. Only the amendment of composts at the highest dose originated an impairment of springtails reproductive output. We suggest that bioassays using different test species may be an additional tool to evaluate effects of amendment of organic wastes in soil. Biological tests are sensitive to pollutants at low concentrations and to interactions undetected by routine chemical analysis.

Evaluation of three force-position hybrid control methods for a robot-based biological joint-testing system.

PubMed

Hsieh, Hong-Jung; Hu, Chih-Chung; Lu, Tung-Wu; Lu, Hsuan-Lun; Kuo, Mei-Ying; Kuo, Chien-Chung; Hsu, Horng-Chaung

2016-06-07

Robot-based joint-testing systems (RJTS) can be used to perform unconstrained laxity tests, measuring the stiffness of a degree of freedom (DOF) of the joint at a fixed flexion angle while allowing the other DOFs unconstrained movement. Previous studies using the force-position hybrid (FPH) control method proposed by Fujie et al. (J Biomech Eng 115(3):211-7, 1993) focused on anterior/posterior tests. Its convergence and applicability on other clinically relevant DOFs such as valgus/varus have not been demonstrated. The current s1tudy aimed to develop a 6-DOF RJTS using an industrial robot, to propose two new force-position hybrid control methods, and to evaluate the performance of the methods and FPH in controlling the RJTS for anterior/posterior and valgus/varus laxity tests of the knee joint. An RJTS was developed using an industrial 6-DOF robot with a 6-component load-cell attached at the effector. The performances of FPH and two new control methods, namely force-position alternate control (FPA) and force-position hybrid control with force-moment control (FPHFM), for unconstrained anterior/posterior and valgus/varus laxity tests were evaluated and compared with traditional constrained tests (CT) in terms of the number of control iterations, total time and the constraining forces and moments. As opposed to CT, the other three control methods successfully reduced the constraining forces and moments for both anterior/posterior and valgus/varus tests, FPHFM being the best followed in order by FPA and FPH. FPHFM had root-mean-squared constraining forces and moments of less than 2.2 N and 0.09 Nm, respectively at 0° flexion, and 2.3 N and 0.14 Nm at 30° flexion. The corresponding values for FPH were 8.5 N and 0.33 Nm, and 11.5 N and 0.45 Nm, respectively. Given the same control parameters including the compliance matrix, FPHFM and FPA reduced the constraining loads of FPH at the expense of additional control iterations, and thus increased total time, FPA

Similitude assessment method for comparing PMHS response data from impact loading across multiple test devices.

PubMed

Dooley, Christopher J; Tenore, Francesco V; Gayzik, F Scott; Merkle, Andrew C

2018-04-27

Biological tissue testing is inherently susceptible to the wide range of variability specimen to specimen. A primary resource for encapsulating this range of variability is the biofidelity response corridor or BRC. In the field of injury biomechanics, BRCs are often used for development and validation of both physical, such as anthropomorphic test devices, and computational models. For the purpose of generating corridors, post-mortem human surrogates were tested across a range of loading conditions relevant to under-body blast events. To sufficiently cover the wide range of input conditions, a relatively small number of tests were performed across a large spread of conditions. The high volume of required testing called for leveraging the capabilities of multiple impact test facilities, all with slight variations in test devices. A method for assessing similitude of responses between test devices was created as a metric for inclusion of a response in the resulting BRC. The goal of this method was to supply a statistically sound, objective method to assess the similitude of an individual response against a set of responses to ensure that the BRC created from the set was affected primarily by biological variability, not anomalies or differences stemming from test devices. Copyright © 2018 Elsevier Ltd. All rights reserved.

A novel method for single sample multi-axial nanoindentation of hydrated heterogeneous tissues based on testing great white shark jaws.

PubMed

Ferrara, Toni L; Boughton, Philip; Slavich, Eve; Wroe, Stephen

2013-01-01

Nanomechanical testing methods that are suitable for a range of hydrated tissues are crucial for understanding biological systems. Nanoindentation of tissues can provide valuable insights into biology, tissue engineering and biomimetic design. However, testing hydrated biological samples still remains a significant challenge. Shark jaw cartilage is an ideal substrate for developing a method to test hydrated tissues because it is a unique heterogeneous composite of both mineralized (hard) and non-mineralized (soft) layers and possesses a jaw geometry that is challenging to test mechanically. The aim of this study is to develop a novel method for obtaining multidirectional nanomechanical properties for both layers of jaw cartilage from a single sample, taken from the great white shark (Carcharodon carcharias). A method for obtaining multidirectional data from a single sample is necessary for examining tissue mechanics in this shark because it is a protected species and hence samples may be difficult to obtain. Results show that this method maintains hydration of samples that would otherwise rapidly dehydrate. Our study is the first analysis of nanomechanical properties of great white shark jaw cartilage. Variation in nanomechanical properties were detected in different orthogonal directions for both layers of jaw cartilage in this species. The data further suggest that the mineralized layer of shark jaw cartilage is less stiff than previously posited. Our method allows multidirectional nanomechanical properties to be obtained from a single, small, hydrated heterogeneous sample. Our technique is therefore suitable for use when specimens are rare, valuable or limited in quantity, such as samples obtained from endangered species or pathological tissues. We also outline a method for tip-to-optic calibration that facilitates nanoindentation of soft biological tissues. Our technique may help address the critical need for a nanomechanical testing method that is applicable

A method for validating Rent's rule for technological and biological networks.

PubMed

Alcalde Cuesta, Fernando; González Sequeiros, Pablo; Lozano Rojo, Álvaro

2017-07-14

Rent's rule is empirical power law introduced in an effort to describe and optimize the wiring complexity of computer logic graphs. It is known that brain and neuronal networks also obey Rent's rule, which is consistent with the idea that wiring costs play a fundamental role in brain evolution and development. Here we propose a method to validate this power law for a certain range of network partitions. This method is based on the bifurcation phenomenon that appears when the network is subjected to random alterations preserving its degree distribution. It has been tested on a set of VLSI circuits and real networks, including biological and technological ones. We also analyzed the effect of different types of random alterations on the Rentian scaling in order to test the influence of the degree distribution. There are network architectures quite sensitive to these randomization procedures with significant increases in the values of the Rent exponents.

Cosmic heavy ion tracks in mesoscopic biological test objects

DOE Office of Scientific and Technical Information (OSTI.GOV)

Facius, R.

1994-12-31

Since more than 20 years ago, when the National Academy of Sciences and the National Research Council of the U.S.A. released their report on `HZE particle effects in manned spaced flight`, it has been emphasized how difficult - if not even impossible - it is to assess their radiobiological impact on man from conventional studies where biological test organisms are stochastically exposed to `large` fluences of heavy ions. An alternative, competing approach had been realized in the BIOSTACK experiments, where the effects of single cosmic as well as accelerator - heavy ions on individual biological test organisms could be investigated.more » Although presented from the beginning as the preferable approach for terrestrial investigations with accelerator heavy ions too (`The BIOSTACK as an approach to high LET radiation research`), only recently this insight is gaining more widespread recognition. In space flight experiments, additional constraints imposed by the infrastructure of the vehicle or satellite further impede such investigations. Restrictions concern the physical detector systems needed for the registration of the cosmic heavy ions` trajectories as well as the biological systems eligible as test organisms. Such optimized procedures and techniques were developed for the investigations on chromosome aberrations induced by cosmic heavy ions in cells of the stem meristem of lettuce seeds (Lactuca sativa) and for the investigation of the radiobiological response of Wolffia arriza, which is the smallest flowering (water) plant. The biological effects were studied by the coworkers of the Russian Institute of Biomedical Problems (IBMP) which in cooperation with the European Space Agency ESA organized the exposure in the Biosatellites of the Cosmos series.« less

Biological Dialogues: How to Teach Your Students to Learn Fluency in Biology

ERIC Educational Resources Information Center

May, S. Randolph; Cook, David L.; May, Marilyn K.

2013-01-01

Biology courses have thousands of words to learn in order to intelligently discuss the subject and take tests over the material. Biological fluency is an important goal for students, and practical methods based on constructivist pedagogies can be employed to promote it. We present a method in which pairs of students write dialogues from…

Advantages and limitations of common testing methods for antioxidants.

PubMed

Amorati, R; Valgimigli, L

2015-05-01

Owing to the importance of antioxidants in the protection of both natural and man-made materials, a large variety of testing methods have been proposed and applied. These include methods based on inhibited autoxidation studies, which are better followed by monitoring the kinetics of oxygen consumption or of the formation of hydroperoxides, the primary oxidation products. Analytical determination of secondary oxidation products (e.g. carbonyl compounds) has also been used. The majority of testing methods, however, do not involve substrate autoxidation. They are based on the competitive bleaching of a probe (e.g. ORAC assay, β-carotene, crocin bleaching assays, and luminol assay), on reaction with a different probe (e.g. spin-trapping and TOSC assay), or they are indirect methods based on the reduction of persistent radicals (e.g. galvinoxyl, DPPH and TEAC assays), or of inorganic oxidizing species (e.g. FRAP, CUPRAC and Folin-Ciocalteu assays). Yet other methods are specific for preventive antioxidants. The relevance, advantages, and limitations of these methods are critically discussed, with respect to their chemistry and the mechanisms of antioxidant activity. A variety of cell-based assays have also been proposed, to investigate the biological activity of antioxidants. Their importance and critical aspects are discussed, along with arguments for the selection of the appropriate testing methods according to the different needs.

Laboratory based instruction in Pakistan: Comparative evaluation of three laboratory instruction methods in biological science at higher secondary school level

NASA Astrophysics Data System (ADS)

Cheema, Tabinda Shahid

This study of laboratory based instruction at higher secondary school level was an attempt to gain some insight into the effectiveness of three laboratory instruction methods: cooperative group instruction method, individualised instruction method and lecture demonstration method on biology achievement and retention. A Randomised subjects, Pre-test Post-test Comparative Methods Design was applied. Three groups of students from a year 11 class in Pakistan conducted experiments using the different laboratory instruction methods. Pre-tests, achievement tests after the experiments and retention tests one month later were administered. Results showed no significant difference between the groups on total achievement and retention, nor was there any significant difference on knowledge and comprehension test scores or skills performance. Future research investigating a similar problem is suggested.

Biological shielding test of hot cells with high active source 60Co (300 TBq)

NASA Astrophysics Data System (ADS)

Švrčula, P.; Zoul, D.; Zimina, M.; Petříčková, A.; Adamíková, T.; Schulc, M.; Srba, O.

2017-11-01

This article describes a method for testing of the efficiency of the biological shielding of the hot cell facility, which were constructed as a part of the project SUSEN. Ten hot cells and one semi-hot cell are present in the facility Radiochemistry II. The shielding is made from steel plates. In order to demonstrate sufficient efficiency of the biological shielding of the hot cells and a correspondence between measured and contractual values at selected points. The test was done using sealed high activity 60Co sources. The results are also used as a proof of the optimization of radiation protection for the workplace of this type. The results confirm significant optimization of radiation protection at the workplace. The dose received by a staff do not exceed one tens of annual limit during active service. Obtained results fulfill general requirements of radiation protection and will be used for further active service of hot cells facility.

Guidelines for human epidermal growth factor receptor 2 testing: biologic and methodologic considerations.

PubMed

Sauter, Guido; Lee, James; Bartlett, John M S; Slamon, Dennis J; Press, Michael F

2009-03-10

The goal of this review is to systematically address a number of issues raised in the American Society of Clinical Oncology-College of American Pathologists (ASCO-CAP) guidelines on testing for the human epidermal growth factor receptor 2 (HER-2) alteration. A group of investigators who are experienced in the conduct and interpretation of HER-2 assay methods reviewed the ASCO-CAP guidelines and address several areas of the HER-2 testing guidelines with a particular emphasis on biologic and methodologic considerations. Although HER-2 status determined by immunohistochemistry (IHC) and the status determined by fluorescent in situ hybridization (FISH) are significantly correlated, we feel that standard considerations of laboratory testing, including test accuracy, reproducibility, and precision, as well as the current data favor FISH over IHC assay methods for determining HER-2 status. These considerations are clearly important in clinical practice because HER2 amplification is directly linked to protein expression levels in breast cancer. However, this protein is not consistently analyzed in formalin-fixed tissues as a result of variability in fixation methods and times and the impact of fixation on HER-2 protein antigenicity. Conversely, gene amplification and FISH are significantly less dependent on tissue fixation methods, making this assay more reproducible between central and peripheral laboratories than IHC. Moreover, review of the existing data demonstrate that FISH is more strongly correlated with responsiveness to either trastuzumab or lapatinib treatment. Until other methods achieve similar test accuracy, reproducibility, and predictive value, we suggest FISH as the primary HER-2 testing modality for women with breast cancer who are candidates for HER-2-targeted therapies.

Generation and characterization of biological aerosols for laser measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, Yung-Sung; Barr, E.B.

1995-12-01

Concerns for proliferation of biological weapons including bacteria, fungi, and viruses have prompted research and development on methods for the rapid detection of biological aerosols in the field. Real-time instruments that can distinguish biological aerosols from background dust would be especially useful. Sandia National Laboratories (SNL) is developing a laser-based, real-time instrument for rapid detection of biological aerosols, and ITRI is working with SNL scientists and engineers to evaluate this technology for a wide range of biological aerosols. This paper describes methods being used to generate the characterize the biological aerosols for these tests. In summary, a biosafe system hasmore » been developed for generating and characterizing biological aerosols and using those aerosols to test the SNL laser-based real-time instrument. Such tests are essential in studying methods for rapid detection of airborne biological materials.« less

Advanced systems biology methods in drug discovery and translational biomedicine.

PubMed

Zou, Jun; Zheng, Ming-Wu; Li, Gen; Su, Zhi-Guang

2013-01-01

Systems biology is in an exponential development stage in recent years and has been widely utilized in biomedicine to better understand the molecular basis of human disease and the mechanism of drug action. Here, we discuss the fundamental concept of systems biology and its two computational methods that have been commonly used, that is, network analysis and dynamical modeling. The applications of systems biology in elucidating human disease are highlighted, consisting of human disease networks, treatment response prediction, investigation of disease mechanisms, and disease-associated gene prediction. In addition, important advances in drug discovery, to which systems biology makes significant contributions, are discussed, including drug-target networks, prediction of drug-target interactions, investigation of drug adverse effects, drug repositioning, and drug combination prediction. The systems biology methods and applications covered in this review provide a framework for addressing disease mechanism and approaching drug discovery, which will facilitate the translation of research findings into clinical benefits such as novel biomarkers and promising therapies.

Method And System For Examining Biological Materials Using Low Power Cw Excitation Raman Spectroscopy.

DOEpatents

Alfano, Robert R.; Wang, Wubao

2003-05-06

A method and system for examining biological materials using low-power cw excitation Raman spectroscopy. A low-power continuous wave (cw) pump laser beam and a low-power cw Stokes (or anti-Stokes) probe laser beam simultaneously illuminate a biological material and traverse the biological material in collinearity. The pump beam, whose frequency is varied, is used to induce Raman emission from the biological material. The intensity of the probe beam, whose frequency is kept constant, is monitored as it leaves the biological material. When the difference between the pump and probe excitation frequencies is equal to a Raman vibrational mode frequency of the biological material, the weak probe signal becomes amplified by one or more orders of magnitude (typically up to about 10.sup.4 -10.sup.6) due to the Raman emission from the pump beam. In this manner, by monitoring the intensity of the probe beam emitted from the biological material as the pump beam is varied in frequency, one can obtain an excitation Raman spectrum for the biological material tested. The present invention may be applied to in the in vivo and/or in vitro diagnosis of diabetes, heart disease, hepatitis, cancers and other diseases by measuring the characteristic excitation Raman lines of blood glucose, cholesterol, serum glutamic oxalacetic transaminase (SGOT)/serum glutamic pyruvic transaminase (SGPT), tissues and other corresponding Raman-active body constituents, respectively.

Expertise for Teaching Biology Situated in the Context of Genetic Testing

ERIC Educational Resources Information Center

van der Zande, Paul; Akkerman, Sanne F.; Brekelmans, Mieke; Waarlo, Arend Jan; Vermunt, Jan D.

2012-01-01

Contemporary genomics research will impact the daily practice of biology teachers who want to teach up-to-date genetics in secondary education. This article reports on a research project aimed at enhancing biology teachers' expertise for teaching genetics situated in the context of genetic testing. The increasing body of scientific knowledge…

Lipidomic analysis of biological samples: Comparison of liquid chromatography, supercritical fluid chromatography and direct infusion mass spectrometry methods.

PubMed

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

Mixed-Methods Design in Biology Education Research: Approach and Uses

PubMed Central

Warfa, Abdi-Rizak M.

2016-01-01

Educational research often requires mixing different research methodologies to strengthen findings, better contextualize or explain results, or minimize the weaknesses of a single method. This article provides practical guidelines on how to conduct such research in biology education, with a focus on mixed-methods research (MMR) that uses both quantitative and qualitative inquiries. Specifically, the paper provides an overview of mixed-methods design typologies most relevant in biology education research. It also discusses common methodological issues that may arise in mixed-methods studies and ways to address them. The paper concludes with recommendations on how to report and write about MMR. PMID:27856556

Overview of chemical imaging methods to address biological questions.

PubMed

da Cunha, Marcel Menezes Lyra; Trepout, Sylvain; Messaoudi, Cédric; Wu, Ting-Di; Ortega, Richard; Guerquin-Kern, Jean-Luc; Marco, Sergio

2016-05-01

Chemical imaging offers extensive possibilities for better understanding of biological systems by allowing the identification of chemical components at the tissue, cellular, and subcellular levels. In this review, we introduce modern methods for chemical imaging that can be applied to biological samples. This work is mainly addressed to the biological sciences community and includes the bases of different technologies, some examples of its application, as well as an introduction to approaches on combining multimodal data. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

[VIDAS Stallertest: clinico-biological evaluation of a new global test for respiratory allergy].

PubMed

Felden, F; Croizier, A

1998-12-01

"VIDAS Stallertest" is a new screening test for breathing allergy. It allows the detection of 10 different lung specific allergens including domestic acarids (D1), pollents (G3, W6, W21, T3 and T9), pets dander (E1 and E2), moulds (M6), cockroach (16). The method is an immunoenzymatic reaction that contains a cartridge and a cone that is cover with the allergen's mixture and is automated on the VIDAS system. The results are compared to various skin tests analyzed by instantaneous reading for 102 patients. "VIDAS Stallertest" shows an excellent agreement (93%) with the allergic patients as well as with those that are not. The specificity of the new screening test is very high (91%). A comparative study between "VIDAS Stallertest" and "Phadiatop" performed on 155 consultants in allergist office shows a correlation of 93%, a sensitivity and a specificity of 91 and 95%, respectively. "VIDAS Stallertest" is a reliable method in first intention for the general practitioner who faces a putative breathing allergy. Moreover, this is an excellent biological check-up for a questionable or negative skin test.

Physical methods for investigating structural colours in biological systems

PubMed Central

Vukusic, P.; Stavenga, D.G.

2009-01-01

Many biological systems are known to use structural colour effects to generate aspects of their appearance and visibility. The study of these phenomena has informed an eclectic group of fields ranging, for example, from evolutionary processes in behavioural biology to micro-optical devices in technologically engineered systems. However, biological photonic systems are invariably structurally and often compositionally more elaborate than most synthetically fabricated photonic systems. For this reason, an appropriate gamut of physical methods and investigative techniques must be applied correctly so that the systems' photonic behaviour may be appropriately understood. Here, we survey a broad range of the most commonly implemented, successfully used and recently innovated physical methods. We discuss the costs and benefits of various spectrometric methods and instruments, namely scatterometers, microspectrophotometers, fibre-optic-connected photodiode array spectrometers and integrating spheres. We then discuss the role of the materials' refractive index and several of the more commonly used theoretical approaches. Finally, we describe the recent developments in the research field of photonic crystals and the implications for the further study of structural coloration in animals. PMID:19158009

Biological detector and method

DOEpatents

Sillerud, Laurel; Alam, Todd M; McDowell, Andrew F

2013-02-26

A biological detector includes a conduit for receiving a fluid containing one or more magnetic nanoparticle-labeled, biological objects to be detected and one or more permanent magnets or electromagnet for establishing a low magnetic field in which the conduit is disposed. A microcoil is disposed proximate the conduit for energization at a frequency that permits detection by NMR spectroscopy of whether the one or more magnetically-labeled biological objects is/are present in the fluid.

Biological detector and method

DOEpatents

Sillerud, Laurel; Alam, Todd M; McDowell, Andrew F

2014-04-15

A biological detector includes a conduit for receiving a fluid containing one or more magnetic nanoparticle-labeled, biological objects to be detected and one or more permanent magnets or electromagnet for establishing a low magnetic field in which the conduit is disposed. A microcoil is disposed proximate the conduit for energization at a frequency that permits detection by NMR spectroscopy of whether the one or more magnetically-labeled biological objects is/are present in the fluid.

Biological detector and method

DOEpatents

Sillerud, Laurel; Alam, Todd M.; McDowell, Andrew F.

2015-11-24

A biological detector includes a conduit for receiving a fluid containing one or more magnetic nanoparticle-labeled, biological objects to be detected and one or more permanent magnets or electromagnet for establishing a low magnetic field in which the conduit is disposed. A microcoil is disposed proximate the conduit for energization at a frequency that permits detection by NMR spectroscopy of whether the one or more magnetically-labeled biological objects is/are present in the fluid.

Biological detector and method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sillerud, Laurel; Alam, Todd M.; McDowell, Andrew F.

A biological detector includes a conduit for receiving a fluid containing one or more magnetic nanoparticle-labeled, biological objects to be detected and one or more permanent magnets or electromagnet for establishing a low magnetic field in which the conduit is disposed. A microcoil is disposed proximate the conduit for energization at a frequency that permits detection by NMR spectroscopy of whether the one or more magnetically-labeled biological objects is/are present in the fluid.

Determining Biology Student Teachers' Cognitive Structure on the Concept of "Diffusion" through the Free Word-Association Test and the Drawing-Writing Technique

ERIC Educational Resources Information Center

Kurt, Hakan; Ekici, Gülay; Aktas, Murat; Aksu, Özlem

2013-01-01

The aim of the current study is to investigate student biology teachers' cognitive structures related to "diffusion" through the free word-association test and the drawing-writing technique. As the research design of the study, the qualitative research method was applied. The data were collected from 44 student biology teachers. The free…

UNDERSTANDINGS OF BSCS BIOLOGY STUDENTS AS DETERMINED BY INSTRUCTIONAL TESTS.

ERIC Educational Resources Information Center

ROBINSON, JAMES T.

EIGHT INSTRUCTIONAL TESTS SPANNED THE CURRICULUM OF ONE YEAR OF BIOLOGY STUDY. THE FIRST CONCERNED THE NATURE OF SCIENCE INCLUDED 4 AREAS OF EMPHASIS--THE NATURE AND FUNCTION OF HYPOTHESIS, THE IDEA OF CONTROLS IN EXPERIMENTS, INTERPRETATION OF GRAPHED DATA, AND THE NATURE OF DATA. THE SECOND TEST WAS DESIGNED TO SHOW AN UNDERSTANDING OF…

Progeny Clustering: A Method to Identify Biological Phenotypes

PubMed Central

Hu, Chenyue W.; Kornblau, Steven M.; Slater, John H.; Qutub, Amina A.

2015-01-01

Estimating the optimal number of clusters is a major challenge in applying cluster analysis to any type of dataset, especially to biomedical datasets, which are high-dimensional and complex. Here, we introduce an improved method, Progeny Clustering, which is stability-based and exceptionally efficient in computing, to find the ideal number of clusters. The algorithm employs a novel Progeny Sampling method to reconstruct cluster identity, a co-occurrence probability matrix to assess the clustering stability, and a set of reference datasets to overcome inherent biases in the algorithm and data space. Our method was shown successful and robust when applied to two synthetic datasets (datasets of two-dimensions and ten-dimensions containing eight dimensions of pure noise), two standard biological datasets (the Iris dataset and Rat CNS dataset) and two biological datasets (a cell phenotype dataset and an acute myeloid leukemia (AML) reverse phase protein array (RPPA) dataset). Progeny Clustering outperformed some popular clustering evaluation methods in the ten-dimensional synthetic dataset as well as in the cell phenotype dataset, and it was the only method that successfully discovered clinically meaningful patient groupings in the AML RPPA dataset. PMID:26267476

Expertise for Teaching Biology Situated in the Context of Genetic Testing

NASA Astrophysics Data System (ADS)

Van der Zande, Paul; Akkerman, Sanne F.; Brekelmans, Mieke; Waarlo, Arend Jan; Vermunt, Jan D.

2012-07-01

Contemporary genomics research will impact the daily practice of biology teachers who want to teach up-to-date genetics in secondary education. This article reports on a research project aimed at enhancing biology teachers' expertise for teaching genetics situated in the context of genetic testing. The increasing body of scientific knowledge concerning genetic testing and the related consequences for decision-making indicate the societal relevance of an educational approach based on situated learning. What expertise do biology teachers need for teaching genetics in the personal health context of genetic testing? This article describes the required expertise by exploring the educational practice. Nine experienced teachers were interviewed about the pedagogical content, moral and interpersonal expertise areas concerning how to teach genetics in the personal health context of genetic testing, and the lessons of five of them were observed. The findings showed that the required teacher expertise encompasses specific pedagogical content expertise, interpersonal expertise and a preference for teacher roles and teaching approaches for the moral aspects of teaching in this context. A need for further development of teaching and learning activities for (reflection on) moral reasoning came to the fore. Suggestions regarding how to apply this expertise into context-based genetics education are discussed.

Using the Scientific Method to Motivate Biology Students to Study Precalculus

ERIC Educational Resources Information Center

Fulton, James P.; Sabatino, Linda

2008-01-01

During the last two years we have developed a precalculus course customized around biology by using the scientific method as a framework to engage and motivate biology students. Historically, the precalculus and calculus courses required for the Suffolk County Community College biology curriculum were designed using examples from the physical…

In silico model-based inference: a contemporary approach for hypothesis testing in network biology

PubMed Central

Klinke, David J.

2014-01-01

Inductive inference plays a central role in the study of biological systems where one aims to increase their understanding of the system by reasoning backwards from uncertain observations to identify causal relationships among components of the system. These causal relationships are postulated from prior knowledge as a hypothesis or simply a model. Experiments are designed to test the model. Inferential statistics are used to establish a level of confidence in how well our postulated model explains the acquired data. This iterative process, commonly referred to as the scientific method, either improves our confidence in a model or suggests that we revisit our prior knowledge to develop a new model. Advances in technology impact how we use prior knowledge and data to formulate models of biological networks and how we observe cellular behavior. However, the approach for model-based inference has remained largely unchanged since Fisher, Neyman and Pearson developed the ideas in the early 1900’s that gave rise to what is now known as classical statistical hypothesis (model) testing. Here, I will summarize conventional methods for model-based inference and suggest a contemporary approach to aid in our quest to discover how cells dynamically interpret and transmit information for therapeutic aims that integrates ideas drawn from high performance computing, Bayesian statistics, and chemical kinetics. PMID:25139179

In silico model-based inference: a contemporary approach for hypothesis testing in network biology.

PubMed

Klinke, David J

2014-01-01

Inductive inference plays a central role in the study of biological systems where one aims to increase their understanding of the system by reasoning backwards from uncertain observations to identify causal relationships among components of the system. These causal relationships are postulated from prior knowledge as a hypothesis or simply a model. Experiments are designed to test the model. Inferential statistics are used to establish a level of confidence in how well our postulated model explains the acquired data. This iterative process, commonly referred to as the scientific method, either improves our confidence in a model or suggests that we revisit our prior knowledge to develop a new model. Advances in technology impact how we use prior knowledge and data to formulate models of biological networks and how we observe cellular behavior. However, the approach for model-based inference has remained largely unchanged since Fisher, Neyman and Pearson developed the ideas in the early 1900s that gave rise to what is now known as classical statistical hypothesis (model) testing. Here, I will summarize conventional methods for model-based inference and suggest a contemporary approach to aid in our quest to discover how cells dynamically interpret and transmit information for therapeutic aims that integrates ideas drawn from high performance computing, Bayesian statistics, and chemical kinetics. © 2014 American Institute of Chemical Engineers.

The Influence of Alternative Pedagogical Methods in Postsecondary Biology Education: How Do Students Experience a Multimedia Case-Study Environment?

ERIC Educational Resources Information Center

Wolter, Bjorn Hugo Karl

2010-01-01

The purpose of this study was to better understand how an online, multimedia case study method influenced students' motivation, performance, and perceptions of science in collegiate level biology classes. It utilized a mix-methods design including data from pre- and post-test, student surveys, and focus group interviews to answer one primary…

Synthesis of silver nanoparticles: chemical, physical and biological methods

PubMed Central

Iravani, S.; Korbekandi, H.; Mirmohammadi, S.V.; Zolfaghari, B.

2014-01-01

Silver nanoparticles (NPs) have been the subjects of researchers because of their unique properties (e.g., size and shape depending optical, antimicrobial, and electrical properties). A variety of preparation techniques have been reported for the synthesis of silver NPs; notable examples include, laser ablation, gamma irradiation, electron irradiation, chemical reduction, photochemical methods, microwave processing, and biological synthetic methods. This review presents an overview of silver nanoparticle preparation by physical, chemical, and biological synthesis. The aim of this review article is, therefore, to reflect on the current state and future prospects, especially the potentials and limitations of the above mentioned techniques for industries. PMID:26339255

Performance of Traditional and Molecular Methods for Detecting Biological Agents in Drinking Water

USGS Publications Warehouse

Francy, Donna S.; Bushon, Rebecca N.; Brady, Amie M.G.; Bertke, Erin E.; Kephart, Christopher M.; Likirdopulos, Christina A.; Mailot, Brian E.; Schaefer, Frank W.; Lindquist, H.D. Alan

2009-01-01

To reduce the impact from a possible bioterrorist attack on drinking-water supplies, analytical methods are needed to rapidly detect the presence of biological agents in water. To this end, 13 drinking-water samples were collected at 9 water-treatment plants in Ohio to assess the performance of a molecular method in comparison to traditional analytical methods that take longer to perform. Two 100-liter samples were collected at each site during each sampling event; one was seeded in the laboratory with six biological agents - Bacillus anthracis (B. anthracis), Burkholderia cepacia (as a surrogate for Bu. pseudomallei), Francisella tularensis (F. tularensis), Salmonella Typhi (S. Typhi), Vibrio cholerae (V. cholerae), and Cryptospordium parvum (C. parvum). The seeded and unseeded samples were processed by ultrafiltration and analyzed by use of quantiative polymerase chain reaction (qPCR), a molecular method, and culture methods for bacterial agents or the immunomagnetic separation/fluorescent antibody (IMS/FA) method for C. parvum as traditional methods. Six replicate seeded samples were also processed and analyzed. For traditional methods, recoveries were highly variable between samples and even between some replicate samples, ranging from below detection to greater than 100 percent. Recoveries were significantly related to water pH, specific conductance, and dissolved organic carbon (DOC) for all bacteria combined by culture methods, but none of the water-quality characteristics tested were related to recoveries of C. parvum by IMS/FA. Recoveries were not determined by qPCR because of problems in quantifying organisms by qPCR in the composite seed. Instead, qPCR results were reported as detected, not detected (no qPCR signal), or +/- detected (Cycle Threshold or 'Ct' values were greater than 40). Several sample results by qPCR were omitted from the dataset because of possible problems with qPCR reagents, primers, and probes. For the remaining 14 qPCR results

Measuring and monitoring biological diversity: Standard methods for mammals

USGS Publications Warehouse

Wilson, Don E.; Cole, F. Russell; Nichols, James D.; Rudran, Rasanayagam; Foster, Mercedes S.

1996-01-01

Measuring and Monitoring Biological Diversity: Standard Methods for Mammals provides a comprehensive manual for designing and implementing inventories of mammalian biodiversity anywhere in the world and for any group, from rodents to open-country grazers. The book emphasizes formal estimation approaches, which supply data that can be compared across habitats and over time. Beginning with brief natural histories of the twenty-six orders of living mammals, the book details the field techniques—observation, capture, and sign interpretation—appropriate to different species. The contributors provide guidelines for study design, discuss survey planning, describe statistical techniques, and outline methods of translating field data into electronic formats. Extensive appendixes address such issues as the ethical treatment of animals in research, human health concerns, preserving voucher specimens, and assessing age, sex, and reproductive condition in mammals.Useful in both developed and developing countries, this volume and the Biological Diversity Handbook Series as a whole establish essential standards for a key aspect of conservation biology and resource management.

Towards sound epistemological foundations of statistical methods for high-dimensional biology.

PubMed

Mehta, Tapan; Tanik, Murat; Allison, David B

2004-09-01

A sound epistemological foundation for biological inquiry comes, in part, from application of valid statistical procedures. This tenet is widely appreciated by scientists studying the new realm of high-dimensional biology, or 'omic' research, which involves multiplicity at unprecedented scales. Many papers aimed at the high-dimensional biology community describe the development or application of statistical techniques. The validity of many of these is questionable, and a shared understanding about the epistemological foundations of the statistical methods themselves seems to be lacking. Here we offer a framework in which the epistemological foundation of proposed statistical methods can be evaluated.

The impact of a scheduling change on ninth grade high school performance on biology benchmark exams and the California Standards Test

NASA Astrophysics Data System (ADS)

Leonardi, Marcelo

The primary purpose of this study was to examine the impact of a scheduling change from a trimester 4x4 block schedule to a modified hybrid schedule on student achievement in ninth grade biology courses. This study examined the impact of the scheduling change on student achievement through teacher created benchmark assessments in Genetics, DNA, and Evolution and on the California Standardized Test in Biology. The secondary purpose of this study examined the ninth grade biology teacher perceptions of ninth grade biology student achievement. Using a mixed methods research approach, data was collected both quantitatively and qualitatively as aligned to research questions. Quantitative methods included gathering data from departmental benchmark exams and California Standardized Test in Biology and conducting multiple analysis of covariance and analysis of covariance to determine significance differences. Qualitative methods include journal entries questions and focus group interviews. The results revealed a statistically significant increase in scores on both the DNA and Evolution benchmark exams. DNA and Evolution benchmark exams showed significant improvements from a change in scheduling format. The scheduling change was responsible for 1.5% of the increase in DNA benchmark scores and 2% of the increase in Evolution benchmark scores. The results revealed a statistically significant decrease in scores on the Genetics Benchmark exam as a result of the scheduling change. The scheduling change was responsible for 1% of the decrease in Genetics benchmark scores. The results also revealed a statistically significant increase in scores on the CST Biology exam. The scheduling change was responsible for .7% of the increase in CST Biology scores. Results of the focus group discussions indicated that all teachers preferred the modified hybrid schedule over the trimester schedule and that it improved student achievement.

Using aquatic macroinvertebrate species traits to build test batteries for sediment toxicity assessment: accounting for the diversity of potential biological responses to toxicants.

PubMed

Ducrot, Virginie; Usseglio-Polatera, Philippe; Péry, T Alexandre R R; Mouthon, Jacques; Lafont, Michel; Roger, Marie-Claude; Garric, Jeanne; Férard, Jean-François

2005-09-01

An original species-selection method for the building of test batteries is presented. This method is based on the statistical analysis of the biological and ecological trait patterns of species. It has been applied to build a macroinvertebrate test battery for the assessment of sediment toxicity, which efficiently describes the diversity of benthic macroinvertebrate biological responses to toxicants in a large European lowland river. First, 109 potential representatives of benthic communities of European lowland rivers were selected from a list of 479 taxa, considering 11 biological traits accounting for the main routes of exposure to a sediment-bound toxicant and eight ecological traits providing an adequate description of habitat characteristics used by the taxa. Second, their biological and ecological trait patterns were compared using coinertia analysis. This comparison allowed the clustering of taxa into groups of organisms that exhibited similar life-history characteristics, physiological and behavioral features, and similar habitat use. Groups exhibited various sizes (7-35 taxa), taxonomic compositions, and biological and ecological features. Main differences among group characteristics concerned morphology, substrate preferendum and habitat utilization, nutritional features, maximal size, and life-history strategy. Third, the best representatives of the mean biological and ecological characteristics of each group were included in the test battery. The final selection was composed of Chironomus riparius (Insecta: Diptera), Branchiura sowerbyi (Oligochaeta: Tubificidae), Lumbriculus variegatus (Oligochaeta: Lumbriculidae), Valvata piscinalis (Gastropoda: Valvatidae), and Sericostoma personatum (Trichoptera: Sericostomatidae). This approach permitted the biological and ecological variety of the battery to be maximized. Because biological and ecological traits of taxa determine species sensitivity, such maximization should permit the battery to better account

Covariance Association Test (CVAT) Identifies Genetic Markers Associated with Schizophrenia in Functionally Associated Biological Processes.

PubMed

Rohde, Palle Duun; Demontis, Ditte; Cuyabano, Beatriz Castro Dias; Børglum, Anders D; Sørensen, Peter

2016-08-01

Schizophrenia is a psychiatric disorder with large personal and social costs, and understanding the genetic etiology is important. Such knowledge can be obtained by testing the association between a disease phenotype and individual genetic markers; however, such single-marker methods have limited power to detect genetic markers with small effects. Instead, aggregating genetic markers based on biological information might increase the power to identify sets of genetic markers of etiological significance. Several set test methods have been proposed: Here we propose a new set test derived from genomic best linear unbiased prediction (GBLUP), the covariance association test (CVAT). We compared the performance of CVAT to other commonly used set tests. The comparison was conducted using a simulated study population having the same genetic parameters as for schizophrenia. We found that CVAT was among the top performers. When extending CVAT to utilize a mixture of SNP effects, we found an increase in power to detect the causal sets. Applying the methods to a Danish schizophrenia case-control data set, we found genomic evidence for association of schizophrenia with vitamin A metabolism and immunological responses, which previously have been implicated with schizophrenia based on experimental and observational studies. Copyright © 2016 by the Genetics Society of America.

Clinical history and biologic age predicted falls better than objective functional tests.

PubMed

Gerdhem, Paul; Ringsberg, Karin A M; Akesson, Kristina; Obrant, Karl J

2005-03-01

Fall risk assessment is important because the consequences, such as a fracture, may be devastating. The objective of this study was to find the test or tests that best predicted falls in a population-based sample of elderly women. The fall-predictive ability of a questionnaire, a subjective estimate of biologic age and objective functional tests (gait, balance [Romberg and sway test], thigh muscle strength, and visual acuity) were compared in 984 randomly selected women, all 75 years of age. A recalled fall was the most important predictor for future falls. Only recalled falls and intake of psycho-active drugs independently predicted future falls. Women with at least five of the most important fall predictors (previous falls, conditions affecting the balance, tendency to fall, intake of psychoactive medication, inability to stand on one leg, high biologic age) had an odds ratio of 11.27 (95% confidence interval 4.61-27.60) for a fall (sensitivity 70%, specificity 79%). The more time-consuming objective functional tests were of limited importance for fall prediction. A simple clinical history, the inability to stand on one leg, and a subjective estimate of biologic age were more important as part of the fall risk assessment.

Ignitability test method

NASA Technical Reports Server (NTRS)

Bement, Laurence J.; Schimmel, Morry L.

1989-01-01

To overcome serious weaknesses in determining the performance of initiating devices, a novel 'ignitability test method', representing actual design interfaces and ignition materials, has been developed. Ignition device output consists of heat, light, gas an burning particles. Past research methods have evaluated these parameters individually. This paper describes the development and demonstration of an ignitability test method combining all these parameters, and the quantitative assessment of the ignition performance of two widely used percussion primers, the M42C1-PA101 and the M42C2-793. The ignition materials used for this evaluation were several powder, granule and pellet sizes of black powder and boron-potassium nitrate. This test method should be useful for performance evaluation of all initiator types, quality assurance, evaluation of ignition interfaces, and service life studies of initiators and ignition materials.

Methods for collection and analysis of aquatic biological and microbiological samples

USGS Publications Warehouse

Britton, L.J.; Greeson, P.E.

1988-01-01

Chapter A4, methods for collection and analyses of aquatic biological and microbiological samples, contains methods used by the U.S. Geological Survey to collect, preserve, and analyze waters to determine their biological and microbiological properties. Part 1 consists of detailed descriptions of more than 45 individual methods, including those for bacteria, phytoplankton, zooplankton, seston, periphyton, macrophytes, benthic invertebrates, fish and other vertebrates, cellular contents, productivity and bioassay. Each method is summarized, and the applications, interferences, apparatus, reagents, analyses, calculations, reporting of results, precisions, and references are given. Part 2 consists of a glossary. Part 3 is a list of taxonomic references. (USGS)

Ground truth methods for optical cross-section modeling of biological aerosols

NASA Astrophysics Data System (ADS)

Kalter, J.; Thrush, E.; Santarpia, J.; Chaudhry, Z.; Gilberry, J.; Brown, D. M.; Brown, A.; Carter, C. C.

2011-05-01

Light detection and ranging (LIDAR) systems have demonstrated some capability to meet the needs of a fastresponse standoff biological detection method for simulants in open air conditions. These systems are designed to exploit various cloud signatures, such as differential elastic backscatter, fluorescence, and depolarization in order to detect biological warfare agents (BWAs). However, because the release of BWAs in open air is forbidden, methods must be developed to predict candidate system performance against real agents. In support of such efforts, the Johns Hopkins University Applied Physics Lab (JHU/APL) has developed a modeling approach to predict the optical properties of agent materials from relatively simple, Biosafety Level 3-compatible bench top measurements. JHU/APL has fielded new ground truth instruments (in addition to standard particle sizers, such as the Aerodynamic particle sizer (APS) or GRIMM aerosol monitor (GRIMM)) to more thoroughly characterize the simulant aerosols released in recent field tests at Dugway Proving Ground (DPG). These instruments include the Scanning Mobility Particle Sizer (SMPS), the Ultraviolet Aerodynamic Particle Sizer (UVAPS), and the Aspect Aerosol Size and Shape Analyser (Aspect). The SMPS was employed as a means of measuring smallparticle concentrations for more accurate Mie scattering simulations; the UVAPS, which measures size-resolved fluorescence intensity, was employed as a path toward fluorescence cross section modeling; and the Aspect, which measures particle shape, was employed as a path towards depolarization modeling.

A Knowledge Base for Teaching Biology Situated in the Context of Genetic Testing

NASA Astrophysics Data System (ADS)

van der Zande, Paul; Waarlo, Arend Jan; Brekelmans, Mieke; Akkerman, Sanne F.; Vermunt, Jan D.

2011-10-01

Recent developments in the field of genomics will impact the daily practice of biology teachers who teach genetics in secondary education. This study reports on the first results of a research project aimed at enhancing biology teacher knowledge for teaching genetics in the context of genetic testing. The increasing body of scientific knowledge concerning genetic testing and the related consequences for decision-making indicate the societal relevance of such a situated learning approach. What content knowledge do biology teachers need for teaching genetics in the personal health context of genetic testing? This study describes the required content knowledge by exploring the educational practice and clinical genetic practices. Nine experienced teachers and 12 respondents representing the clinical genetic practices (clients, medical professionals, and medical ethicists) were interviewed about the biological concepts and ethical, legal, and social aspects (ELSA) of testing they considered relevant to empowering students as future health care clients. The ELSA suggested by the respondents were complemented by suggestions found in the literature on genetic counselling. The findings revealed that the required teacher knowledge consists of multiple layers that are embedded in specific genetic test situations: on the one hand, the knowledge of concepts represented by the curricular framework and some additional concepts (e.g. multifactorial and polygenic disorder) and, on the other hand, more knowledge of ELSA and generic characteristics of genetic test practice (uncertainty, complexity, probability, and morality). Suggestions regarding how to translate these characteristics, concepts, and ELSA into context-based genetics education are discussed.

Methods of increasing secretion of polypeptides having biological activity

DOEpatents

Merino, Sandra

2014-05-27

The present invention relates to methods for producing a secreted polypeptide having biological activity, comprising: (a) transforming a fungal host cell with a fusion protein construct encoding a fusion protein, which comprises: (i) a first polynucleotide encoding a signal peptide; (ii) a second polynucleotide encoding at least a catalytic domain of an endoglucanase or a portion thereof; and (iii) a third polynucleotide encoding at least a catalytic domain of a polypeptide having biological activity; wherein the signal peptide and at least the catalytic domain of the endoglucanase increases secretion of the polypeptide having biological activity compared to the absence of at least the catalytic domain of the endoglucanase; (b) cultivating the transformed fungal host cell under conditions suitable for production of the fusion protein; and (c) recovering the fusion protein, a component thereof, or a combination thereof, having biological activity, from the cultivation medium.

Methods of increasing secretion of polypeptides having biological activity

DOEpatents

Merino, Sandra

2014-10-28

The present invention relates to methods for producing a secreted polypeptide having biological activity, comprising: (a) transforming a fungal host cell with a fusion protein construct encoding a fusion protein, which comprises: (i) a first polynucleotide encoding a signal peptide; (ii) a second polynucleotide encoding at least a catalytic domain of an endoglucanase or a portion thereof; and (iii) a third polynucleotide encoding at least a catalytic domain of a polypeptide having biological activity; wherein the signal peptide and at least the catalytic domain of the endoglucanase increases secretion of the polypeptide having biological activity compared to the absence of at least the catalytic domain of the endoglucanase; (b) cultivating the transformed fungal host cell under conditions suitable for production of the fusion protein; and (c) recovering the fusion protein, a component thereof, or a combination thereof, having biological activity, from the cultivation medium.

Methods of increasing secretion of polypeptides having biological activity

DOEpatents

Merino, Sandra

2015-04-14

The present invention relates to methods for producing a secreted polypeptide having biological activity, comprising: (a) transforming a fungal host cell with a fusion protein construct encoding a fusion protein, which comprises: (i) a first polynucleotide encoding a signal peptide; (ii) a second polynucleotide encoding at least a catalytic domain of an endoglucanase or a portion thereof; and (iii) a third polynucleotide encoding at least a catalytic domain of a polypeptide having biological activity; wherein the signal peptide and at least the catalytic domain of the endoglucanase increases secretion of the polypeptide having biological activity compared to the absence of at least the catalytic domain of the endoglucanase; (b) cultivating the transformed fungal host cell under conditions suitable for production of the fusion protein; and (c) recovering the fusion protein, a component thereof, or a combination thereof, having biological activity, from the cultivation medium.

Methods of increasing secretion of polypeptides having biological activity

DOEpatents

Merino, Sandra

2013-10-01

The present invention relates to methods for producing a secreted polypeptide having biological activity, comprising: (a) transforming a fungal host cell with a fusion protein construct encoding a fusion protein, which comprises: (i) a first polynucleotide encoding a signal peptide; (ii) a second polynucleotide encoding at least a catalytic domain of an endoglucanase or a portion thereof; and (iii) a third polynucleotide encoding at least a catalytic domain of a polypeptide having biological activity; wherein the signal peptide and at least the catalytic domain of the endoglucanase increases secretion of the polypeptide having biological activity compared to the absence of at least the catalytic domain of the endoglucanase; (b) cultivating the transformed fungal host cell under conditions suitable for production of the fusion protein; and (c) recovering the fusion protein, a component thereof, or a combination thereof, having biological activity, from the cultivation medium.

A generic standard additions based method to determine endogenous analyte concentrations by immunoassays to overcome complex biological matrix interference.

PubMed

Pang, Susan; Cowen, Simon

2017-12-13

We describe a novel generic method to derive the unknown endogenous concentrations of analyte within complex biological matrices (e.g. serum or plasma) based upon the relationship between the immunoassay signal response of a biological test sample spiked with known analyte concentrations and the log transformed estimated total concentration. If the estimated total analyte concentration is correct, a portion of the sigmoid on a log-log plot is very close to linear, allowing the unknown endogenous concentration to be estimated using a numerical method. This approach obviates conventional relative quantification using an internal standard curve and need for calibrant diluent, and takes into account the individual matrix interference on the immunoassay by spiking the test sample itself. This technique is based on standard additions for chemical analytes. Unknown endogenous analyte concentrations within even 2-fold diluted human plasma may be determined reliably using as few as four reaction wells.

Biological intuition in alignment-free methods: response to Posada.

PubMed

Ragan, Mark A; Chan, Cheong Xin

2013-08-01

A recent editorial in Journal of Molecular Evolution highlights opportunities and challenges facing molecular evolution in the era of next-generation sequencing. Abundant sequence data should allow more-complex models to be fit at higher confidence, making phylogenetic inference more reliable and improving our understanding of evolution at the molecular level. However, concern that approaches based on multiple sequence alignment may be computationally infeasible for large datasets is driving the development of so-called alignment-free methods for sequence comparison and phylogenetic inference. The recent editorial characterized these approaches as model-free, not based on the concept of homology, and lacking in biological intuition. We argue here that alignment-free methods have not abandoned models or homology, and can be biologically intuitive.

2010 Diffraction Methods in Structural Biology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dr. Ana Gonzalez

2011-03-10

Advances in basic methodologies have played a major role in the dramatic progress in macromolecular crystallography over the past decade, both in terms of overall productivity and in the increasing complexity of the systems being successfully tackled. The 2010 Gordon Research Conference on Diffraction Methods in Structural Biology will, as in the past, focus on the most recent developments in methodology, covering all aspects of the process from crystallization to model building and refinement, complemented by examples of structural highlights and complementary methods. Extensive discussion will be encouraged and it is hoped that all attendees will participate by giving oralmore » or poster presentations, the latter using the excellent poster display area available at Bates College. The relatively small size and informal atmosphere of the meeting provides an excellent opportunity for all participants, especially younger scientists, to meet and exchange ideas with leading methods developers.« less

Methods for collection and analysis of aquatic biological and microbiological samples

USGS Publications Warehouse

Britton, L.J.; Greeson, P.E.

1989-01-01

The series of chapters on techniques describes methods used by the U.S. Geological Survey for planning and conducting water-resources investigations. The material is arranged under major subject headings called books and is further subdivided into sections and chapters. Book 5 is on laboratory analysis. Section A is on water. The unit of publication, the chapter, is limited to a narrow field of subject matter. "Methods for Collection and Analysis of Aquatic Biological and Microbiological Samples" is the fourth chapter to be published under Section A of Book 5. The chapter number includes the letter of the section.This chapter was prepared by several aquatic biologists and microbiologists of the U.S. Geological Survey to provide accurate and precise methods for the collection and analysis of aquatic biological and microbiological samples.Use of brand, firm, and trade names in this chapter is for identification purposes only and does not constitute endorsement by the U.S. Geological Survey.This chapter supersedes "Methods for Collection and Analysis of Aquatic Biological and Microbiological Samples" edited by P.E. Greeson, T.A. Ehlke, G.A. Irwin, B.W. Lium, and K.V. Slack (U.S. Geological Survey Techniques of Water-Resources Investigations, Book 5, Chapter A4, 1977) and also supersedes "A Supplement to-Methods for Collection and Analysis of Aquatic Biological and Microbiological Samples" by P.E. Greeson (U.S. Geological Survey Techniques of Water-Resources Investigations, Book 5, Chapter A4), Open-File Report 79-1279, 1979.

Biological and psychological markers of stress in humans: focus on the Trier Social Stress Test.

PubMed

Allen, Andrew P; Kennedy, Paul J; Cryan, John F; Dinan, Timothy G; Clarke, Gerard

2014-01-01

Validated biological and psychological markers of acute stress in humans are an important tool in translational research. The Trier Social Stress Test (TSST), involving public interview and mental arithmetic performance, is among the most popular methods of inducing acute stress in experimental settings, and reliably increases hypothalamic-pituitary-adrenal axis activation. However, although much research has focused on HPA axis activity, the TSST also affects the sympathetic-adrenal-medullary system, the immune system, cardiovascular outputs, gastric function and cognition. We critically assess the utility of different biological and psychological markers, with guidance for future research, and discuss factors which can moderate TSST effects. We outline the effects of the TSST in stress-related disorders, and if these responses can be abrogated by pharmacological and psychological treatments. Modified TSST protocols are discussed, and the TSST is compared to alternative methods of inducing acute stress. Our analysis suggests that multiple readouts are necessary to derive maximum information; this strategy will enhance our understanding of the psychobiology of stress and provide the means to assess novel therapeutic agents. Copyright © 2013 Elsevier Ltd. All rights reserved.

LEAKAGE TESTING METHOD

DOEpatents

McAdams, Wm.A.; Foss, M.H.

1958-08-12

A method of testing containers for leaks is described, particularly the testing of containers or cans in which the uranium slugs for nuelear reactors are jacketed. This method involves the immersion of the can in water under l50 pounds of pressure, then removing, drying, and coating the can with anhydrous copper sulfate. Amy water absorbed by the can under pressure will exude and discolor the copper sulfate in the area about the leak.

BinQuasi: a peak detection method for ChIP-sequencing data with biological replicates.

PubMed

Goren, Emily; Liu, Peng; Wang, Chao; Wang, Chong

2018-04-19

ChIP-seq experiments that are aimed at detecting DNA-protein interactions require biological replication to draw inferential conclusions, however there is no current consensus on how to analyze ChIP-seq data with biological replicates. Very few methodologies exist for the joint analysis of replicated ChIP-seq data, with approaches ranging from combining the results of analyzing replicates individually to joint modeling of all replicates. Combining the results of individual replicates analyzed separately can lead to reduced peak classification performance compared to joint modeling. Currently available methods for joint analysis may fail to control the false discovery rate at the nominal level. We propose BinQuasi, a peak caller for replicated ChIP-seq data, that jointly models biological replicates using a generalized linear model framework and employs a one-sided quasi-likelihood ratio test to detect peaks. When applied to simulated data and real datasets, BinQuasi performs favorably compared to existing methods, including better control of false discovery rate than existing joint modeling approaches. BinQuasi offers a flexible approach to joint modeling of replicated ChIP-seq data which is preferable to combining the results of replicates analyzed individually. Source code is freely available for download at https://cran.r-project.org/package=BinQuasi, implemented in R. pliu@iastate.edu or egoren@iastate.edu. Supplementary material is available at Bioinformatics online.

Metacognitive Ability Relationship with Test Result of Senior High School of Biology Teacher Competence in Sijunjung District

NASA Astrophysics Data System (ADS)

Ardi, A.; Fadilah, M.; Ichsani, W.

2018-04-01

This research aimed to reveal how the relationship between metacognitive ability and the test result of biology teacher competence in Sijunjung District. The population of this descriptive research were all high school biology teachers in Sijunjung District, and sample is all teachers who are members of the population, which is 23 biology teachers. The instrument used in this research are a questionnaire of research on teacher's metacognitive ability and document about teacher competence test result. The questionnaire was validated first by two lecturers of biology and one lecturer of English. Data analysis using Pearson Product Moment's. Based on the results of research and discussion that have been described, it can generally be concluded that there is a low relationship between metacognitive ability with competence test results of high school biology teachers in Sijunjung District. Partially, the relationship of metacognitive ability with the test result of professional competence of biology teacher showed significant result, with correlation coefficient 0,46 and t table 1,72 while titung 2,37. The contribution of metacognitive ability to the competence test result of the teacher is 21.6%, while the other 78.4% have not been revealed in this research.

Can mixed assessment methods make biology classes more equitable?

PubMed

Cotner, Sehoya; Ballen, Cissy J

2017-01-01

Many factors have been proposed to explain the attrition of women in science, technology, engineering and math fields, among them the lower performance of women in introductory courses resulting from deficits in incoming preparation. We focus on the impact of mixed methods of assessment, which minimizes the impact of high-stakes exams and rewards other methods of assessment such as group participation, low-stakes quizzes and assignments, and in-class activities. We hypothesized that these mixed methods would benefit individuals who otherwise underperform on high-stakes tests. Here, we analyze gender-based performance trends in nine large (N > 1000 students) introductory biology courses in fall 2016. Females underperformed on exams compared to their male counterparts, a difference that does not exist with other methods of assessment that compose course grade. Further, we analyzed three case studies of courses that transitioned their grading schemes to either de-emphasize or emphasize exams as a proportion of total course grade. We demonstrate that the shift away from an exam emphasis consequently benefits female students, thereby closing gaps in overall performance. Further, the exam performance gap itself is reduced when the exams contribute less to overall course grade. We discuss testable predictions that follow from our hypothesis, and advocate for the use of mixed methods of assessments (possibly as part of an overall shift to active learning techniques). We conclude by challenging the student deficit model, and suggest a course deficit model as explanatory of these performance gaps, whereby the microclimate of the classroom can either raise or lower barriers to success for underrepresented groups in STEM.

Treatment of laundry wastewater by biological and electrocoagulation methods.

PubMed

Ramcharan, Terelle; Bissessur, Ajay

2017-01-01

The present study describes an improvement in the current electrocoagulation treatment process and focuses on a comparative study for the clean-up of laundry wastewater (LWW) after each wash and rinse cycle by biological and electrocoagulation treatment methods. For biological treatment, the wastewater was treated with a Bacillus strain of aerobic bacteria especially suited for the degradation of fats, lipids, protein, detergents and hydrocarbons. Treatment of the LWW by electrocoagulation involved the oxidation of aluminium metal upon the application of a controlled voltage which produces various aluminium hydroxy species capable of adsorbing pollutants from the wastewater. The efficiency of the clean-up of LWW using each method was assessed by determination of surfactant concentration, chemical oxygen demand and total dissolved solids. A rapid decrease in surfactant concentration was noted within 0.5 hour of electrocoagulation, whereas a notable decrease in the surfactant concentration was observed only after 12 hour of biological treatment. The rapid generation of aluminium hydroxy species in the electrocoagulation cell allowed adsorption of pollutants at a faster rate when compared to the aerobic degradation of the surfactant; hence a reduced period of time is required for treatment of LWW by electrocoagulation.

Testing of Synthetic Biological Membranes for Forward Osmosis Applications

NASA Technical Reports Server (NTRS)

Parodi, Jurek; Mangado, Jaione Romero; Stefanson, Ofir; Flynn, Michael; Mancinelli, Rocco; Kawashima, Brian; Trieu, Serena; Brozell, Adrian; Rosenberg, Kevan

2016-01-01

Commercially available forward osmosis membranes have been extensively tested for human space flight wastewater treatment. Despite the improvements achieved in the last decades, there is still a challenge to produce reliable membranes with anti-fouling properties, chemical resistance, and high flux and selectivity. Synthetic biological membranes that mimic the ones present in nature, which underwent millions of years of evolution, represent a potential solution for further development and progress in membrane technology. Biomimetic forward osmosis membranes based on a polymeric support filter and coated with surfactant multilayers have been engineered to investigate how different manufacturing processes impact the performance and structure of the membrane. However, initial results of the first generation prototype membranes tests reveal a high scatter in the data, due to the current testing apparatus set up. The testing apparatus has been upgraded to improve data collection, reduce errors, and to allow higher control of the testing process.

Australian Biology Test Item Bank, Years 11 and 12. Volume II: Year 12.

ERIC Educational Resources Information Center

Brown, David W., Ed.; Sewell, Jeffrey J., Ed.

This document consists of test items which are applicable to biology courses throughout Australia (irrespective of course materials used); assess key concepts within course statement (for both core and optional studies); assess a wide range of cognitive processes; and are relevant to current biological concepts. These items are arranged under…

Australian Biology Test Item Bank, Years 11 and 12. Volume I: Year 11.

ERIC Educational Resources Information Center

Brown, David W., Ed.; Sewell, Jeffrey J., Ed.

This document consists of test items which are applicable to biology courses throughout Australia (irrespective of course materials used); assess key concepts within course statement (for both core and optional studies); assess a wide range of cognitive processes; and are relevant to current biological concepts. These items are arranged under…

Method for photo-altering a biological system to improve biological effect

DOEpatents

Hill, Richard A.; Doiron, Daniel R.; Crean, David H.

2000-08-01

Photodynamic therapy is a new adjunctive therapy for filtration surgery that does not use chemotherapy agents or radiation, but uses pharmacologically-active sensitizing compounds to produce a titratable, localized, transient, post operative avascular conjunctiva. A photosensitizing agent in a biological system is selectively activated by delivering the photosensitive agent to the biological system and laser activating only a spatially selected portion of the delivered photosensitive agent. The activated portion of the photosensitive agent reacts with the biological system to obtain a predetermined biological effect. As a result, an improved spatial disposition and effectuation of the biological effect by the photosensitive agent in the biological system is achieved.

Method And System For Examining Biological Materials Using Low Power Cw Excitation Raman Spectroscopy.

DOEpatents

Alfano, Robert R.; Wang, Wubao

2000-11-21

A method and system for examining biological materials using low-power cw excitation Raman spectroscopy. In accordance with the teachings of the invention, a low-power continuous wave (cw) pump laser beam and a low-power cw Stokes (or anti-Stokes) probe laser beam simultaneously illuminate a biological material and traverse the biological material in collinearity. The pump beam, whose frequency is varied, is used to induce Raman emission from the biological material. The intensity of the probe beam, whose frequency is kept constant, is monitored as it leaves the biological material. When the difference between the pump and probe excitation frequencies is equal to a Raman vibrational mode frequency of the biological material, the weak probe signal becomes amplified by one or more orders of magnitude (typically up to about 10.sup.4 -10.sup.6) due to the Raman emission from the pump beam. In this manner, by monitoring the intensity of the probe beam emitted from the biological material as the pump beam is varied in frequency, one can obtain an excitation Raman spectrum for the biological material tested. The present invention may be applied to in the in vivo and/or in vitro diagnosis of diabetes, heart disease, hepatitis, cancers and other diseases by measuring the characteristic excitation Raman lines of blood glucose, cholesterol, serum glutamic oxalacetic transaminase (SGOT)/serum glutamic pyruvic tansaminase (SGPT), tissues and other corresponding Raman-active body constituents, respectively. For example, it may also be used to diagnose diseases associated with the concentration of Raman-active constituents in urine, lymph and saliva It may be used to identify cancer in the breast, cervix, uterus, ovaries and the like by measuring the fingerprint excitation Raman spectra of these tissues. It may also be used to reveal the growing of tumors or cancers by measuring the levels of nitric oxide in tissue.

Methods for collection and analysis of aquatic biological and microbiological samples

USGS Publications Warehouse

Greeson, Phillip E.; Ehlke, T.A.; Irwin, G.A.; Lium, B.W.; Slack, K.V.

1977-01-01

Chapter A4 contains methods used by the U.S. Geological Survey to collect, preserve, and analyze waters to determine their biological and microbiological properties. Part 1 discusses biological sampling and sampling statistics. The statistical procedures are accompanied by examples. Part 2 consists of detailed descriptions of more than 45 individual methods, including those for bacteria, phytoplankton, zooplankton, seston, periphyton, macrophytes, benthic invertebrates, fish and other vertebrates, cellular contents, productivity, and bioassays. Each method is summarized, and the application, interferences, apparatus, reagents, collection, analysis, calculations, reporting of results, precision and references are given. Part 3 consists of a glossary. Part 4 is a list of taxonomic references.

Microbiological methods for the water recovery systems test, revision 1.1

NASA Technical Reports Server (NTRS)

Rhoads, Tim; Kilgore, M. V., Jr.; Mikell, A. T., Jr.

1990-01-01

Current microbiological parameters specified to verify microbiological quality of Space Station Freedom water quality include the enumeration of total bacteria, anaerobes, aerobes, yeasts and molds, enteric bacteria, gram positives, gram negatives, and E. coli. In addition, other parameters have been identified as necessary to support the Water Recovery Test activities to be conducted at the NASA/MSFC later this year. These other parameters include aerotolerant eutrophic mesophiles, legionellae, and an additional method for heterotrophic bacteria. If inter-laboratory data are to be compared to evaluate quality, analytical methods must be eliminated as a variable. Therefore, each participating laboratory must utilize the same analytical methods and procedures. Without this standardization, data can be neither compared nor validated between laboratories. Multiple laboratory participation represents a conservative approach to insure quality and completeness of data. Invariably, sample loss will occur in transport and analyses. Natural variance is a reality on any test of this magnitude and is further enhanced because biological entities, capable of growth and death, are specific parameters of interest. The large variation due to the participation of human test subjects has been noted with previous testing. The resultant data might be dismissed as 'out of control' unless intra-laboratory control is included as part of the method or if participating laboratories are not available for verification. The purpose of this document is to provide standardized laboratory procedures for the enumeration of certain microorganisms in water and wastewater specific to the water recovery systems test. The document consists of ten separate cultural methods and one direct count procedure. It is not intended nor is it implied to be a complete microbiological methods manual.

A Knowledge Base for Teaching Biology Situated in the Context of Genetic Testing

ERIC Educational Resources Information Center

van der Zande, Paul; Waarlo, Arend Jan; Brekelmans, Mieke; Akkerman, Sanne F.; Vermunt, Jan D.

2011-01-01

Recent developments in the field of genomics will impact the daily practice of biology teachers who teach genetics in secondary education. This study reports on the first results of a research project aimed at enhancing biology teacher knowledge for teaching genetics in the context of genetic testing. The increasing body of scientific knowledge…

Optimization and validation of spectrophotometric methods for determination of finasteride in dosage and biological forms

PubMed Central

Amin, Alaa S.; Kassem, Mohammed A.

2012-01-01

Aim and Background: Three simple, accurate and sensitive spectrophotometric methods for the determination of finasteride in pure, dosage and biological forms, and in the presence of its oxidative degradates were developed. Materials and Methods: These methods are indirect, involve the addition of excess oxidant potassium permanganate for method A; cerric sulfate [Ce(SO4)2] for methods B; and N-bromosuccinimide (NBS) for method C of known concentration in acid medium to finasteride, and the determination of the unreacted oxidant by measurement of the decrease in absorbance of methylene blue for method A, chromotrope 2R for method B, and amaranth for method C at a suitable maximum wavelength, λmax: 663, 528, and 520 nm, for the three methods, respectively. The reaction conditions for each method were optimized. Results: Regression analysis of the Beer plots showed good correlation in the concentration ranges of 0.12–3.84 μg mL–1 for method A, and 0.12–3.28 μg mL–1 for method B and 0.14 – 3.56 μg mL–1 for method C. The apparent molar absorptivity, Sandell sensitivity, detection and quantification limits were evaluated. The stoichiometric ratio between the finasteride and the oxidant was estimated. The validity of the proposed methods was tested by analyzing dosage forms and biological samples containing finasteride with relative standard deviation ≤ 0.95. Conclusion: The proposed methods could successfully determine the studied drug with varying excess of its oxidative degradation products, with recovery between 99.0 and 101.4, 99.2 and 101.6, and 99.6 and 101.0% for methods A, B, and C, respectively. PMID:23781478

An overview of bioinformatics methods for modeling biological pathways in yeast

PubMed Central

Hou, Jie; Acharya, Lipi; Zhu, Dongxiao

2016-01-01

The advent of high-throughput genomics techniques, along with the completion of genome sequencing projects, identification of protein–protein interactions and reconstruction of genome-scale pathways, has accelerated the development of systems biology research in the yeast organism Saccharomyces cerevisiae. In particular, discovery of biological pathways in yeast has become an important forefront in systems biology, which aims to understand the interactions among molecules within a cell leading to certain cellular processes in response to a specific environment. While the existing theoretical and experimental approaches enable the investigation of well-known pathways involved in metabolism, gene regulation and signal transduction, bioinformatics methods offer new insights into computational modeling of biological pathways. A wide range of computational approaches has been proposed in the past for reconstructing biological pathways from high-throughput datasets. Here we review selected bioinformatics approaches for modeling biological pathways in S. cerevisiae, including metabolic pathways, gene-regulatory pathways and signaling pathways. We start with reviewing the research on biological pathways followed by discussing key biological databases. In addition, several representative computational approaches for modeling biological pathways in yeast are discussed. PMID:26476430

Unidirectional Fabric Drape Testing Method

PubMed Central

Mei, Zaihuan; Yang, Jingzhi; Zhou, Ting; Zhou, Hua

2015-01-01

In most cases, fabrics such as curtains, skirts, suit pants and so on are draped under their own gravity parallel to fabric plane while the gravity is perpendicular to fabric plane in traditional drape testing method. As a result, it does not conform to actual situation and the test data is not convincing enough. To overcome this problem, this paper presents a novel method which simulates the real mechanical conditions and ensures the gravity is parallel to the fabric plane. This method applied a low-cost Kinect Sensor device to capture the 3-dimensional (3D) drape profile, thus we obtained the drape degree parameters and aesthetic parameters by 3D reconstruction and image processing and analysis techniques. The experiment was conducted on our self-devised drape-testing instrument by choosing different kinds of weave structure fabrics as our testing samples and the results were compared with those of traditional method and subjective evaluation. Through regression and correlation analysis we found that this novel testing method was significantly correlated with the traditional and subjective evaluation method. We achieved a new, non-contact 3D measurement method for drape testing, namely unidirectional fabric drape testing method. This method is more suitable for evaluating drape behavior because it is more in line with actual mechanical conditions of draped fabrics and has a well consistency with the requirements of visual and aesthetic style of fabrics. PMID:26600387

Complete Host Range Testing on Common Reed with Potential Biological Control Agents and Investigation into Biological Control for Flowering Rush

DTIC Science & Technology

2016-07-01

ER D C/ EL C R- 16 -5 Aquatic Plant Control Research Program Complete Host Range Testing on Common Reed with Potential Biological...client/default. Aquatic Plant Control Research Program ERDC/EL CR-16-5 July 2016 Complete Host Range Testing on Common Reed with Potential...and started with sequential no-choice oviposition tests. So far, no eggs were found on any of the 22 test plants offered. The authors also found the

Mixed-Methods Design in Biology Education Research: Approach and Uses

ERIC Educational Resources Information Center

Warfa, Abdi-Rizak M.

2016-01-01

Educational research often requires mixing different research methodologies to strengthen findings, better contextualize or explain results, or minimize the weaknesses of a single method. This article provides practical guidelines on how to conduct such research in biology education, with a focus on mixed-methods research (MMR) that uses both…

Student perception of relevance of biology content to everyday life: A study in higher education biology courses

NASA Astrophysics Data System (ADS)

Himschoot, Agnes Rose

The purpose of this mixed method case study was to examine the effects of methods of instruction on students' perception of relevance in higher education non-biology majors' courses. Nearly ninety percent of all students in a liberal arts college are required to take a general biology course. It is proposed that for many of those students, this is the last science course they will take for life. General biology courses are suspected of discouraging student interest in biology with large enrollment, didactic instruction, covering a huge amount of content in one semester, and are charged with promoting student disengagement with biology by the end of the course. Previous research has been aimed at increasing student motivation and interest in biology as measured by surveys and test results. Various methods of instruction have been tested and show evidence of improved learning gains. This study focused on students' perception of relevance of biology content to everyday life and the methods of instruction that increase it. A quantitative survey was administered to assess perception of relevance pre and post instruction over three topics typically taught in a general biology course. A second quantitative survey of student experiences during instruction was administered to identify methods of instruction used in the course lecture and lab. While perception of relevance dropped in the study, qualitative focus groups provided insight into the surprising results by identifying topics that are more relevant than the ones chosen for the study, conveying the affects of the instructor's personal and instructional skills on student engagement, explanation of how active engagement during instruction promotes understanding of relevance, the roll of laboratory in promoting students' understanding of relevance as well as identifying external factors that affect student engagement. The study also investigated the extent to which gender affected changes in students' perception of

Methods of Model Reduction for Large-Scale Biological Systems: A Survey of Current Methods and Trends.

PubMed

Snowden, Thomas J; van der Graaf, Piet H; Tindall, Marcus J

2017-07-01

Complex models of biochemical reaction systems have become increasingly common in the systems biology literature. The complexity of such models can present a number of obstacles for their practical use, often making problems difficult to intuit or computationally intractable. Methods of model reduction can be employed to alleviate the issue of complexity by seeking to eliminate those portions of a reaction network that have little or no effect upon the outcomes of interest, hence yielding simplified systems that retain an accurate predictive capacity. This review paper seeks to provide a brief overview of a range of such methods and their application in the context of biochemical reaction network models. To achieve this, we provide a brief mathematical account of the main methods including timescale exploitation approaches, reduction via sensitivity analysis, optimisation methods, lumping, and singular value decomposition-based approaches. Methods are reviewed in the context of large-scale systems biology type models, and future areas of research are briefly discussed.

Can mixed assessment methods make biology classes more equitable?

PubMed Central

Ballen, Cissy J.

2017-01-01

Many factors have been proposed to explain the attrition of women in science, technology, engineering and math fields, among them the lower performance of women in introductory courses resulting from deficits in incoming preparation. We focus on the impact of mixed methods of assessment, which minimizes the impact of high-stakes exams and rewards other methods of assessment such as group participation, low-stakes quizzes and assignments, and in-class activities. We hypothesized that these mixed methods would benefit individuals who otherwise underperform on high-stakes tests. Here, we analyze gender-based performance trends in nine large (N > 1000 students) introductory biology courses in fall 2016. Females underperformed on exams compared to their male counterparts, a difference that does not exist with other methods of assessment that compose course grade. Further, we analyzed three case studies of courses that transitioned their grading schemes to either de-emphasize or emphasize exams as a proportion of total course grade. We demonstrate that the shift away from an exam emphasis consequently benefits female students, thereby closing gaps in overall performance. Further, the exam performance gap itself is reduced when the exams contribute less to overall course grade. We discuss testable predictions that follow from our hypothesis, and advocate for the use of mixed methods of assessments (possibly as part of an overall shift to active learning techniques). We conclude by challenging the student deficit model, and suggest a course deficit model as explanatory of these performance gaps, whereby the microclimate of the classroom can either raise or lower barriers to success for underrepresented groups in STEM. PMID:29281676

Quantitative biology: where modern biology meets physical sciences.

PubMed

Shekhar, Shashank; Zhu, Lian; Mazutis, Linas; Sgro, Allyson E; Fai, Thomas G; Podolski, Marija

2014-11-05

Quantitative methods and approaches have been playing an increasingly important role in cell biology in recent years. They involve making accurate measurements to test a predefined hypothesis in order to compare experimental data with predictions generated by theoretical models, an approach that has benefited physicists for decades. Building quantitative models in experimental biology not only has led to discoveries of counterintuitive phenomena but has also opened up novel research directions. To make the biological sciences more quantitative, we believe a two-pronged approach needs to be taken. First, graduate training needs to be revamped to ensure biology students are adequately trained in physical and mathematical sciences and vice versa. Second, students of both the biological and the physical sciences need to be provided adequate opportunities for hands-on engagement with the methods and approaches necessary to be able to work at the intersection of the biological and physical sciences. We present the annual Physiology Course organized at the Marine Biological Laboratory (Woods Hole, MA) as a case study for a hands-on training program that gives young scientists the opportunity not only to acquire the tools of quantitative biology but also to develop the necessary thought processes that will enable them to bridge the gap between these disciplines. © 2014 Shekhar, Zhu, Mazutis, Sgro, Fai, and Podolski. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

An overview of bioinformatics methods for modeling biological pathways in yeast.

PubMed

Hou, Jie; Acharya, Lipi; Zhu, Dongxiao; Cheng, Jianlin

2016-03-01

The advent of high-throughput genomics techniques, along with the completion of genome sequencing projects, identification of protein-protein interactions and reconstruction of genome-scale pathways, has accelerated the development of systems biology research in the yeast organism Saccharomyces cerevisiae In particular, discovery of biological pathways in yeast has become an important forefront in systems biology, which aims to understand the interactions among molecules within a cell leading to certain cellular processes in response to a specific environment. While the existing theoretical and experimental approaches enable the investigation of well-known pathways involved in metabolism, gene regulation and signal transduction, bioinformatics methods offer new insights into computational modeling of biological pathways. A wide range of computational approaches has been proposed in the past for reconstructing biological pathways from high-throughput datasets. Here we review selected bioinformatics approaches for modeling biological pathways inS. cerevisiae, including metabolic pathways, gene-regulatory pathways and signaling pathways. We start with reviewing the research on biological pathways followed by discussing key biological databases. In addition, several representative computational approaches for modeling biological pathways in yeast are discussed. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Biosocial Conservation: Integrating Biological and Ethnographic Methods to Study Human-Primate Interactions.

PubMed

Setchell, Joanna M; Fairet, Emilie; Shutt, Kathryn; Waters, Siân; Bell, Sandra

2017-01-01

Biodiversity conservation is one of the grand challenges facing society. Many people interested in biodiversity conservation have a background in wildlife biology. However, the diverse social, cultural, political, and historical factors that influence the lives of people and wildlife can be investigated fully only by incorporating social science methods, ideally within an interdisciplinary framework. Cultural hierarchies of knowledge and the hegemony of the natural sciences create a barrier to interdisciplinary understandings. Here, we review three different projects that confront this difficulty, integrating biological and ethnographic methods to study conservation problems. The first project involved wildlife foraging on crops around a newly established national park in Gabon. Biological methods revealed the extent of crop loss, the species responsible, and an effect of field isolation, while ethnography revealed institutional and social vulnerability to foraging wildlife. The second project concerned great ape tourism in the Central African Republic. Biological methods revealed that gorilla tourism poses risks to gorillas, while ethnography revealed why people seek close proximity to gorillas. The third project focused on humans and other primates living alongside one another in Morocco. Incorporating shepherds in the coproduction of ecological knowledge about primates built trust and altered attitudes to the primates. These three case studies demonstrate how the integration of biological and social methods can help us to understand the sustainability of human-wildlife interactions, and thus promote coexistence. In each case, an integrated biosocial approach incorporating ethnographic data produced results that would not otherwise have come to light. Research that transcends conventional academic boundaries requires the openness and flexibility to move beyond one's comfort zone to understand and acknowledge the legitimacy of "other" kinds of knowledge. It is

Methods for Scaling Icing Test Conditions

NASA Technical Reports Server (NTRS)

Anderson, David N.

1995-01-01

This report presents the results of tests at NASA Lewis to evaluate several methods to establish suitable alternative test conditions when the test facility limits the model size or operating conditions. The first method was proposed by Olsen. It can be applied when full-size models are tested and all the desired test conditions except liquid-water content can be obtained in the facility. The other two methods discussed are: a modification of the French scaling law and the AEDC scaling method. Icing tests were made with cylinders at both reference and scaled conditions representing mixed and glaze ice in the NASA Lewis Icing Research Tunnel. Reference and scale ice shapes were compared to evaluate each method. The Olsen method was tested with liquid-water content varying from 1.3 to .8 g/m(exp3). Over this range, ice shapes produced using the Olsen method were unchanged. The modified French and AEDC methods produced scaled ice shapes which approximated the reference shapes when model size was reduced to half the reference size for the glaze-ice cases tested.

In Situ Biological Treatment Test at Kelly Air Force Base. Volume 2. Field Test Results and Cost Model

DTIC Science & Technology

1987-07-01

Groundwater." Developments in Industrial Microbiology, Volume 24, pp. 225-234. Society of Industrial Microbiology, Arlington, Virginia. 18. Product ...ESL-TR-85-52 cv) VOLUME II CN IN SITU BIOLOGICAL TREATMENT TEST AT KELLY AIR FORCE BASE, VOLUME !1: FIELD TEST RESULTS AND COST MODEL R.S. WETZEL...Kelly Air Force Base, Volume II: Field Test Results and Cost Model (UNCLASSIFIED) 12 PERSONAL AUTHOR(S) Roger S. Wetzel, Connie M. Durst, Donald H

A method for three-dimensional quantitative observation of the microstructure of biological samples

NASA Astrophysics Data System (ADS)

Wang, Pengfei; Chen, Dieyan; Ma, Wanyun; Wu, Hongxin; Ji, Liang; Sun, Jialin; Lv, Danyu; Zhang, Lu; Li, Ying; Tian, Ning; Zheng, Jinggao; Zhao, Fengying

2009-07-01

Contemporary biology has developed into the era of cell biology and molecular biology, and people try to study the mechanism of all kinds of biological phenomena at the microcosmic level now. Accurate description of the microstructure of biological samples is exigent need from many biomedical experiments. This paper introduces a method for 3-dimensional quantitative observation on the microstructure of vital biological samples based on two photon laser scanning microscopy (TPLSM). TPLSM is a novel kind of fluorescence microscopy, which has excellence in its low optical damage, high resolution, deep penetration depth and suitability for 3-dimensional (3D) imaging. Fluorescent stained samples were observed by TPLSM, and afterward the original shapes of them were obtained through 3D image reconstruction. The spatial distribution of all objects in samples as well as their volumes could be derived by image segmentation and mathematic calculation. Thus the 3-dimensionally and quantitatively depicted microstructure of the samples was finally derived. We applied this method to quantitative analysis of the spatial distribution of chromosomes in meiotic mouse oocytes at metaphase, and wonderful results came out last.

Surface-Tension Replica-Exchange Molecular Dynamics Method for Enhanced Sampling of Biological Membrane Systems.

PubMed

Mori, Takaharu; Jung, Jaewoon; Sugita, Yuji

2013-12-10

Conformational sampling is fundamentally important for simulating complex biomolecular systems. The generalized-ensemble algorithm, especially the temperature replica-exchange molecular dynamics method (T-REMD), is one of the most powerful methods to explore structures of biomolecules such as proteins, nucleic acids, carbohydrates, and also of lipid membranes. T-REMD simulations have focused on soluble proteins rather than membrane proteins or lipid bilayers, because explicit membranes do not keep their structural integrity at high temperature. Here, we propose a new generalized-ensemble algorithm for membrane systems, which we call the surface-tension REMD method. Each replica is simulated in the NPγT ensemble, and surface tensions in a pair of replicas are exchanged at certain intervals to enhance conformational sampling of the target membrane system. We test the method on two biological membrane systems: a fully hydrated DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine) lipid bilayer and a WALP23-POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) membrane system. During these simulations, a random walk in surface tension space is realized. Large-scale lateral deformation (shrinking and stretching) of the membranes takes place in all of the replicas without collapse of the lipid bilayer structure. There is accelerated lateral diffusion of DPPC lipid molecules compared with conventional MD simulation, and a much wider range of tilt angle of the WALP23 peptide is sampled due to large deformation of the POPC lipid bilayer and through peptide-lipid interactions. Our method could be applicable to a wide variety of biological membrane systems.

Biological variability of the sweat chloride in diagnostic sweat tests: A retrospective analysis.

PubMed

Vermeulen, F; Lebecque, P; De Boeck, K; Leal, T

2017-01-01

The sweat test is the current gold standard for the diagnosis of cystic fibrosis (CF). CF is unlikely when sweat chloride (Cl sw ) is lower than 30mmol/L, Cl sw >60 is suggestive of CF, with intermediate values between 30 and 60mmol/L. To correctly interpret a sweat chloride value, the biological variability of the sweat chloride has to be known. Sweat tests performed in two centers using the classic Gibson and Cooke method were retrospectively reviewed (n=5904). Within test variability of Cl sw was measured by comparing results from right and left arm collected on the same day. Between test variability was calculated from subjects with sweat tests performed on more than one occasion. Within test variability of Cl sw calculated in 1022 subjects was low with differences between -3.2 (p5) and +3.6mmol/L (p95). Results from left and right arm were classified differently in only 3 subjects. Between test variability of Cl sw in 197 subjects was larger, with differences between -18.2mmol/L (p5) and +14.1mmol/L (p95) between repeat tests. Changes in diagnostic conclusion were seen in 55/197 subjects, the most frequent being changing from indeterminate to 'CF unlikely' range (48/102). Variability of sweat chloride is substantial, with frequent changes in diagnostic conclusion, especially in the intermediate range. Copyright © 2016 European Cystic Fibrosis Society. Published by Elsevier B.V. All rights reserved.

Collaborative Testing in Practical Laboratories: An Effective Teaching-Learning Method in Histology.

PubMed

Guo, Yuping; Li, Enzhong

2016-01-01

This article presents an experimental teaching and learning program used in histology with first-year students in the second term in the Faculty of Biology at Huanghuai University, China. Eighty-six students were divided randomly into two groups (n=43 per group). Tests were conducted at the end of each practical laboratory (10 laboratories in total) in which collaborative testing was used in the experimental group and traditional testing in the control group. To assess achievement, a final examination in histology was carried out at the end of the course. To determine students' attitude to the teaching styles, a questionnaire survey was conducted at the end of the term. Results showed that students preferred the collaborative testing format. In the experimental group, students' scores were significantly higher than those of students in the control group in final examinations. These findings indicate that collaborative testing enhances student learning and understanding of the material taught, and suggest that collaborative testing is an effective teaching-learning method in histology.

49 CFR 383.133 - Test methods.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 5 2014-10-01 2014-10-01 false Test methods. 383.133 Section 383.133... STANDARDS; REQUIREMENTS AND PENALTIES Tests § 383.133 Test methods. (a) All tests must be constructed in... and provides to all State Driver Licensing Agencies. (2) The State method of generating knowledge...

49 CFR 383.133 - Test methods.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 5 2012-10-01 2012-10-01 false Test methods. 383.133 Section 383.133... STANDARDS; REQUIREMENTS AND PENALTIES Tests § 383.133 Test methods. (a) All tests must be constructed in... and provides to all State Driver Licensing Agencies. (2) The State method of generating knowledge...

49 CFR 383.133 - Test methods.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 5 2011-10-01 2011-10-01 false Test methods. 383.133 Section 383.133... STANDARDS; REQUIREMENTS AND PENALTIES Tests § 383.133 Test methods. (a) All tests must be constructed in... and provides to all State Driver Licensing Agencies. (2) The State method of generating knowledge...

49 CFR 383.133 - Test methods.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 5 2013-10-01 2013-10-01 false Test methods. 383.133 Section 383.133... STANDARDS; REQUIREMENTS AND PENALTIES Tests § 383.133 Test methods. (a) All tests must be constructed in... and provides to all State Driver Licensing Agencies. (2) The State method of generating knowledge...

The Method Effect in Communicative Testing.

ERIC Educational Resources Information Center

Canale, Michael

1981-01-01

A focus on test validity includes a consideration of the way a test measures that which it proposes to test; in other words, the validity of a test depends on method as well as content. This paper examines three areas of concern: (1) some features of communication that test method should reflect, (2) the main components of method, and (3) some…

49 CFR 383.133 - Testing methods.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 5 2010-10-01 2010-10-01 false Testing methods. 383.133 Section 383.133... STANDARDS; REQUIREMENTS AND PENALTIES Tests § 383.133 Testing methods. (a) All tests shall be constructed in... must be at least as stringent as the Federal standards. (c) States shall determine specific methods for...

A method to identify and analyze biological programs through automated reasoning

PubMed Central

Yordanov, Boyan; Dunn, Sara-Jane; Kugler, Hillel; Smith, Austin; Martello, Graziano; Emmott, Stephen

2016-01-01

Predictive biology is elusive because rigorous, data-constrained, mechanistic models of complex biological systems are difficult to derive and validate. Current approaches tend to construct and examine static interaction network models, which are descriptively rich, but often lack explanatory and predictive power, or dynamic models that can be simulated to reproduce known behavior. However, in such approaches implicit assumptions are introduced as typically only one mechanism is considered, and exhaustively investigating all scenarios is impractical using simulation. To address these limitations, we present a methodology based on automated formal reasoning, which permits the synthesis and analysis of the complete set of logical models consistent with experimental observations. We test hypotheses against all candidate models, and remove the need for simulation by characterizing and simultaneously analyzing all mechanistic explanations of observed behavior. Our methodology transforms knowledge of complex biological processes from sets of possible interactions and experimental observations to precise, predictive biological programs governing cell function. PMID:27668090

A Residual Mass Ballistic Testing Method to Compare Armor Materials or Components (Residual Mass Ballistic Testing Method)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Benjamin Langhorst; Thomas M Lillo; Henry S Chu

2014-05-01

A statistics based ballistic test method is presented for use when comparing multiple groups of test articles of unknown relative ballistic perforation resistance. The method is intended to be more efficient than many traditional methods for research and development testing. To establish the validity of the method, it is employed in this study to compare test groups of known relative ballistic performance. Multiple groups of test articles were perforated using consistent projectiles and impact conditions. Test groups were made of rolled homogeneous armor (RHA) plates and differed in thickness. After perforation, each residual projectile was captured behind the target andmore » its mass was measured. The residual masses measured for each test group were analyzed to provide ballistic performance rankings with associated confidence levels. When compared to traditional V50 methods, the residual mass (RM) method was found to require fewer test events and be more tolerant of variations in impact conditions.« less

DAISY: a new software tool to test global identifiability of biological and physiological systems.

PubMed

Bellu, Giuseppina; Saccomani, Maria Pia; Audoly, Stefania; D'Angiò, Leontina

2007-10-01

A priori global identifiability is a structural property of biological and physiological models. It is considered a prerequisite for well-posed estimation, since it concerns the possibility of recovering uniquely the unknown model parameters from measured input-output data, under ideal conditions (noise-free observations and error-free model structure). Of course, determining if the parameters can be uniquely recovered from observed data is essential before investing resources, time and effort in performing actual biomedical experiments. Many interesting biological models are nonlinear but identifiability analysis for nonlinear system turns out to be a difficult mathematical problem. Different methods have been proposed in the literature to test identifiability of nonlinear models but, to the best of our knowledge, so far no software tools have been proposed for automatically checking identifiability of nonlinear models. In this paper, we describe a software tool implementing a differential algebra algorithm to perform parameter identifiability analysis for (linear and) nonlinear dynamic models described by polynomial or rational equations. Our goal is to provide the biological investigator a completely automatized software, requiring minimum prior knowledge of mathematical modelling and no in-depth understanding of the mathematical tools. The DAISY (Differential Algebra for Identifiability of SYstems) software will potentially be useful in biological modelling studies, especially in physiology and clinical medicine, where research experiments are particularly expensive and/or difficult to perform. Practical examples of use of the software tool DAISY are presented. DAISY is available at the web site http://www.dei.unipd.it/~pia/.

DAISY: a new software tool to test global identifiability of biological and physiological systems

PubMed Central

Bellu, Giuseppina; Saccomani, Maria Pia; Audoly, Stefania; D’Angiò, Leontina

2009-01-01

A priori global identifiability is a structural property of biological and physiological models. It is considered a prerequisite for well-posed estimation, since it concerns the possibility of recovering uniquely the unknown model parameters from measured input-output data, under ideal conditions (noise-free observations and error-free model structure). Of course, determining if the parameters can be uniquely recovered from observed data is essential before investing resources, time and effort in performing actual biomedical experiments. Many interesting biological models are nonlinear but identifiability analysis for nonlinear system turns out to be a difficult mathematical problem. Different methods have been proposed in the literature to test identifiability of nonlinear models but, to the best of our knowledge, so far no software tools have been proposed for automatically checking identifiability of nonlinear models. In this paper, we describe a software tool implementing a differential algebra algorithm to perform parameter identifiability analysis for (linear and) nonlinear dynamic models described by polynomial or rational equations. Our goal is to provide the biological investigator a completely automatized software, requiring minimum prior knowledge of mathematical modelling and no in-depth understanding of the mathematical tools. The DAISY (Differential Algebra for Identifiability of SYstems) software will potentially be useful in biological modelling studies, especially in physiology and clinical medicine, where research experiments are particularly expensive and/or difficult to perform. Practical examples of use of the software tool DAISY are presented. DAISY is available at the web site http://www.dei.unipd.it/~pia/. PMID:17707944

Biological Aerosol Test Method and Personal Protective Equipment (PPE) Decon

DTIC Science & Technology

2011-05-01

supply to the porous tube diluter. This stops all air into the LSAT. 6. Power off the vacuum pump and the compressed air supply. 22 Distribution...Experiment from Template from the menu. 10. Scroll down the template list until you find APHL Flu Assay 04272009. 11. Highlight the test, then click

COMPUTATIONAL METHODS FOR STUDYING THE INTERACTION BETWEEN POLYCYCLIC AROMATIC HYDROCARBONS AND BIOLOGICAL MACROMOLECULES

EPA Science Inventory

Computational Methods for Studying the Interaction between Polycyclic Aromatic Hydrocarbons and Biological Macromolecules .

The mechanisms for the processes that result in significant biological activity of PAHs depend on the interaction of these molecules or their metabol...

40 CFR 63.547 - Test methods.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 9 2010-07-01 2010-07-01 false Test methods. 63.547 Section 63.547... Hazardous Air Pollutants from Secondary Lead Smelting § 63.547 Test methods. (a) The following test methods...), and 63.545(e): (1) Method 1 shall be used to select the sampling port location and the number of...

40 CFR 63.547 - Test methods.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 9 2011-07-01 2011-07-01 false Test methods. 63.547 Section 63.547... Hazardous Air Pollutants from Secondary Lead Smelting § 63.547 Test methods. (a) The following test methods...), and 63.545(e): (1) Method 1 shall be used to select the sampling port location and the number of...

Method and apparatus to image biological interactions in plants

DOEpatents

Weisenberger, Andrew; Bonito, Gregory M.; Reid, Chantal D.; Smith, Mark Frederick

2015-12-22

A method to dynamically image the actual translocation of molecular compounds of interest in a plant root, root system, and rhizosphere without disturbing the root or the soil. The technique makes use of radioactive isotopes as tracers to label molecules of interest and to image their distribution in the plant and/or soil. The method allows for the study and imaging of various biological and biochemical interactions in the rhizosphere of a plant, including, but not limited to, mycorrhizal associations in such regions.

Fractal propagation method enables realistic optical microscopy simulations in biological tissues

PubMed Central

Glaser, Adam K.; Chen, Ye; Liu, Jonathan T.C.

2017-01-01

Current simulation methods for light transport in biological media have limited efficiency and realism when applied to three-dimensional microscopic light transport in biological tissues with refractive heterogeneities. We describe here a technique which combines a beam propagation method valid for modeling light transport in media with weak variations in refractive index, with a fractal model of refractive index turbulence. In contrast to standard simulation methods, this fractal propagation method (FPM) is able to accurately and efficiently simulate the diffraction effects of focused beams, as well as the microscopic heterogeneities present in tissue that result in scattering, refractive beam steering, and the aberration of beam foci. We validate the technique and the relationship between the FPM model parameters and conventional optical parameters used to describe tissues, and also demonstrate the method’s flexibility and robustness by examining the steering and distortion of Gaussian and Bessel beams in tissue with comparison to experimental data. We show that the FPM has utility for the accurate investigation and optimization of optical microscopy methods such as light-sheet, confocal, and nonlinear microscopy. PMID:28983499

An Evaluation of Two Different Methods of Assessing Independent Investigations in an Operational Pre-University Level Examination in Biology in England.

ERIC Educational Resources Information Center

Brown, Chris

1998-01-01

Explored aspects of assessment of extended investigation ("project") practiced in the operational examinations of The University of Cambridge Local Examinations Syndicate (UCLES) for the perspective of construct validity. Samples of the 1993 (n=333) and 1996 (n=259) biology test results reveal two methods of assessing the project. (MAK)

Testing with Feedback Yields Potent, but Piecewise, Learning of History and Biology Facts

ERIC Educational Resources Information Center

Pan, Steven C.; Gopal, Arpita; Rickard, Timothy C.

2016-01-01

Does correctly answering a test question about a multiterm fact enhance memory for the entire fact? We explored that issue in 4 experiments. Subjects first studied Advanced Placement History or Biology facts. Half of those facts were then restudied, whereas the remainder were tested using "5 W" (i.e., "who, what, when, where",…

Method of Testing Oxygen Regulators

NASA Technical Reports Server (NTRS)

Sontag, Harcourt; Borlik, E L

1935-01-01

Oxygen regulators are used in aircraft to regulate automatically the flow of oxygen to the pilot from a cylinder at pressures ranging up to 150 atmospheres. The instruments are adjusted to open at an altitude of about 15,000 ft. and thereafter to deliver oxygen at a rate which increases with the altitude. The instruments are tested to determine the rate of flow of oxygen delivered at various altitudes and to detect any mechanical defects which may exist. A method of testing oxygen regulators was desired in which the rate of flow could be determined more accurately than by the test method previously used (reference 1) and by which instruments defective mechanically could be detected. The new method of test fulfills these requirements.

Concentrated formulations and methods for neutralizing chemical and biological toxants

DOEpatents

Tucker, Mark D.; Betty, Rita G.; Tadros, Maher E.

2004-04-20

A formulation and method of making and using that neutralizes the adverse health effects of both chemical and biological toxants, especially chemical warfare (CW) and biological warfare (BW) agents. The aqueous formulation is non-toxic and non-corrosive and can be delivered as a long-lasting foam, spray, or fog. The formulation includes solubilizing compounds that serve to effectively render the CW or BW toxant susceptible to attack, so that a nucleophillic agent can attack the compound via a hydrolysis or oxidation reaction. The formulation can kill up to 99.99999% of bacterial spores within one hour of exposure.

Method and apparatus for sustaining viability of biological cells on a substrate

DOEpatents

McKnight, Timothy E.; Melechko, Anatoli V.; Simpson, Michael L.

2013-01-01

A method for the transient transformation of a living biological cell having an intact cell membrane defining an intracellular domain, and an apparatus for the transient transformation of biological cells. The method and apparatus include introducing a compartmentalized extracellular component fixedly attached to a cellular penetrant structure to the intracellular domain of the cell, wherein the cell is fixed in a predetermined location and wherein the component is expressed within in the cell while being retained within the compartment and wherein the compartment restricts the mobility and interactions of the component within the cell and prevents transference of the component to the cell.

Method and apparatus for sustaining viability of biological cells on a substrate

DOEpatents

McKnight, Timothy E [Greenback, TN; Melechko, Anatoli V [Oak Ridge, TN; Simpson, Michael L [Knoxville, TN

2011-12-13

A method for the transient transformation of a living biological cell having an intact cell membrane defining an intracellular domain, and an apparatus for the transient transformation of biological cells. The method and apparatus include introducing a compartmentalized extracellular component fixedly attached to a cellular penetrant structure to the intracellular domain of the cell, wherein the cell is fixed in a predetermined location and wherein the component is expressed within in the cell while being retained within the compartment and wherein the compartment restricts the mobility and interactions of the component within the cell and prevents transference of the component to the cell.

40 CFR 80.3 - Test methods.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 17 2012-07-01 2012-07-01 false Test methods. 80.3 Section 80.3... FUELS AND FUEL ADDITIVES General Provisions § 80.3 Test methods. The lead and phosphorus content of gasoline shall be determined in accordance with test methods set forth in the appendices to this part. [47...

40 CFR 63.1546 - Test methods.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 12 2010-07-01 2010-07-01 true Test methods. 63.1546 Section 63.1546... Hazardous Air Pollutants for Primary Lead Smelting § 63.1546 Test methods. (a) The following procedure shall....1543(a)(1) through § 63.1543(a)(9) shall be determined according to the following test methods in...

40 CFR 80.3 - Test methods.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 17 2014-07-01 2014-07-01 false Test methods. 80.3 Section 80.3... FUELS AND FUEL ADDITIVES General Provisions § 80.3 Test methods. The lead and phosphorus content of gasoline shall be determined in accordance with test methods set forth in the appendices to this part. [47...

40 CFR 63.1546 - Test methods.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 12 2011-07-01 2009-07-01 true Test methods. 63.1546 Section 63.1546... Hazardous Air Pollutants for Primary Lead Smelting § 63.1546 Test methods. (a) The following procedure shall....1543(a)(1) through § 63.1543(a)(9) shall be determined according to the following test methods in...

40 CFR 80.3 - Test methods.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 16 2010-07-01 2010-07-01 false Test methods. 80.3 Section 80.3... FUELS AND FUEL ADDITIVES General Provisions § 80.3 Test methods. The lead and phosphorus content of gasoline shall be determined in accordance with test methods set forth in the appendices to this part. [47...

40 CFR 80.3 - Test methods.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 16 2011-07-01 2011-07-01 false Test methods. 80.3 Section 80.3... FUELS AND FUEL ADDITIVES General Provisions § 80.3 Test methods. The lead and phosphorus content of gasoline shall be determined in accordance with test methods set forth in the appendices to this part. [47...

40 CFR 80.3 - Test methods.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 17 2013-07-01 2013-07-01 false Test methods. 80.3 Section 80.3... FUELS AND FUEL ADDITIVES General Provisions § 80.3 Test methods. The lead and phosphorus content of gasoline shall be determined in accordance with test methods set forth in the appendices to this part. [47...

30 CFR 27.31 - Testing methods.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 30 Mineral Resources 1 2014-07-01 2014-07-01 false Testing methods. 27.31 Section 27.31 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR TESTING, EVALUATION, AND APPROVAL OF MINING PRODUCTS METHANE-MONITORING SYSTEMS Test Requirements § 27.31 Testing methods. A methane...

30 CFR 27.31 - Testing methods.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 30 Mineral Resources 1 2012-07-01 2012-07-01 false Testing methods. 27.31 Section 27.31 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR TESTING, EVALUATION, AND APPROVAL OF MINING PRODUCTS METHANE-MONITORING SYSTEMS Test Requirements § 27.31 Testing methods. A methane...

30 CFR 27.31 - Testing methods.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Testing methods. 27.31 Section 27.31 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR TESTING, EVALUATION, AND APPROVAL OF MINING PRODUCTS METHANE-MONITORING SYSTEMS Test Requirements § 27.31 Testing methods. A methane...

30 CFR 27.31 - Testing methods.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Testing methods. 27.31 Section 27.31 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR TESTING, EVALUATION, AND APPROVAL OF MINING PRODUCTS METHANE-MONITORING SYSTEMS Test Requirements § 27.31 Testing methods. A methane...

30 CFR 27.31 - Testing methods.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 30 Mineral Resources 1 2013-07-01 2013-07-01 false Testing methods. 27.31 Section 27.31 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR TESTING, EVALUATION, AND APPROVAL OF MINING PRODUCTS METHANE-MONITORING SYSTEMS Test Requirements § 27.31 Testing methods. A methane...

Test methods for textile composites

NASA Technical Reports Server (NTRS)

Minguet, Pierre J.; Fedro, Mark J.; Gunther, Christian K.

1994-01-01

Various test methods commonly used for measuring properties of tape laminate composites were evaluated to determine their suitability for the testing of textile composites. Three different types of textile composites were utilized in this investigation: two-dimensional (2-D) triaxial braids, stitched uniweave fabric, and three-dimensional (3-D) interlock woven fabric. Four 2-D braid architectures, five stitched laminates, and six 3-D woven architectures were tested. All preforms used AS4 fibers and were resin-transfer-molded with Shell RSL-1895 epoxy resin. Ten categories of material properties were investigated: tension, open-hole tension, compression, open-hole compression, in-plane shear, filled-hole tension, bolt bearing, interlaminar tension, interlaminar shear, and interlaminar fracture toughness. Different test methods and specimen sizes were considered for each category of test. Strength and stiffness properties obtained with each of these methods are documented in this report for all the material systems mentioned above.

40 CFR 63.547 - Test methods.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 10 2012-07-01 2012-07-01 false Test methods. 63.547 Section 63.547... Hazardous Air Pollutants From Secondary Lead Smelting § 63.547 Test methods. (a) You must use the test methods from appendix A of part 60 as listed in paragraphs (a)(1) through (5) of this section to determine...

40 CFR 63.547 - Test methods.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 10 2014-07-01 2014-07-01 false Test methods. 63.547 Section 63.547... Hazardous Air Pollutants From Secondary Lead Smelting § 63.547 Test methods. (a) You must use the test methods from appendix A of part 60 as listed in paragraphs (a)(1) through (5) of this section to determine...

40 CFR 63.547 - Test methods.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 10 2013-07-01 2013-07-01 false Test methods. 63.547 Section 63.547... Hazardous Air Pollutants From Secondary Lead Smelting § 63.547 Test methods. (a) You must use the test methods from appendix A of part 60 as listed in paragraphs (a)(1) through (5) of this section to determine...

Interpretation of biological and mechanical variations between the Lowry versus Bradford method for protein quantification.

PubMed

Lu, Tzong-Shi; Yiao, Szu-Yu; Lim, Kenneth; Jensen, Roderick V; Hsiao, Li-Li

2010-07-01

The identification of differences in protein expression resulting from methodical variations is an essential component to the interpretation of true, biologically significant results. We used the Lowry and Bradford methods- two most commonly used methods for protein quantification, to assess whether differential protein expressions are a result of true biological or methodical variations. MATERIAL #ENTITYSTARTX00026; Differential protein expression patterns was assessed by western blot following protein quantification by the Lowry and Bradford methods. We have observed significant variations in protein concentrations following assessment with the Lowry versus Bradford methods, using identical samples. Greater variations in protein concentration readings were observed over time and in samples with higher concentrations, with the Bradford method. Identical samples quantified using both methods yielded significantly different expression patterns on Western blot. We show for the first time that methodical variations observed in these protein assay techniques, can potentially translate into differential protein expression patterns, that can be falsely taken to be biologically significant. Our study therefore highlights the pivotal need to carefully consider methodical approaches to protein quantification in techniques that report quantitative differences.

Evaluation of Immunoassays and General Biological Indicator Tests for Field Screening of Bacillus anthracis and Ricin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bartholomew, Rachel A.; Ozanich, Richard M.; Arce, Jennifer S.

2017-02-01

The goal of this testing was to evaluate the ability of currently available commercial off-the-shelf (COTS) biological indicator tests and immunoassays to detect Bacillus anthracis (Ba) spores and ricin. In general, immunoassays provide more specific identification of biological threats as compared to indicator tests [3]. Many of these detection products are widely used by first responders and other end users. In most cases, performance data for these instruments are supplied directly from the manufacturer, but have not been verified by an external, independent assessment [1]. Our test plan modules included assessments of inclusivity (ability to generate true positive results), commonlymore » encountered hoax powders (which can cause potential interferences or false positives), and estimation of limit of detection (LOD) (sensitivity) testing.« less

Method and apparatus for determining nutrient stimulation of biological processes

DOEpatents

Colwell, F.S.; Geesey, G.G.; Gillis, R.J.; Lehman, R.M.

1997-11-11

A method and apparatus is described for determining the nutrients to stimulate microorganisms in a particular environment. A representative sample of microorganisms from a particular environment are contacted with multiple support means wherein each support means has intimately associated with the surface of the support means a different nutrient composition for said microorganisms in said sample. The multiple support means is allowed to remain in contact with the microorganisms in the sample for a time period sufficient to measure differences in microorganism effects for the multiple support means. Microorganism effects for the multiple support means are then measured and compared. The invention is particularly adaptable to being conducted in situ. The additional steps of regulating nutrients added to the particular environment of microorganisms can enhance the desired results. Biological systems particularly suitable for this invention are bioremediation, biologically enhanced oil recovery, biological leaching of metals, and agricultural bioprocesses. 5 figs.

Method and apparatus for determining nutrient stimulation of biological processes

DOEpatents

Colwell, Frederick S.; Geesey, Gill G.; Gillis, Richard J.; Lehman, R. Michael

1999-01-01

A method and apparatus for determining the nutrients to stimulate microorganisms in a particular environment. A representative sample of microorganisms from a particular environment are contacted with multiple support means wherein each support means has intimately associated with the surface of the support means a different nutrient composition for said microorganisms in said sample. The multiple support means is allowed to remain in contact with the microorganisms in the sample for a time period sufficient to measure difference in microorganism effects for the multiple support means. Microorganism effects for the multiple support means are then measured and compared. The invention is particularly adaptable to being conducted in situ. The additional steps of regulating nutrients added to the particular environment of microorganisms can enhance the desired results. Biological systems particularly suitable for this invention are bioremediation, biologically enhanced oil recovery, biological leaching of metals, and agricultural bioprocesses.

Method and apparatus for determining nutrient stimulation of biological processes

DOEpatents

Colwell, F.S.; Geesey, G.G.; Gillis, R.J.; Lehman, R.M.

1999-07-13

A method and apparatus are disclosed for determining the nutrients to stimulate microorganisms in a particular environment. A representative sample of microorganisms from a particular environment are contacted with multiple support means wherein each support means has intimately associated with the surface of the support means a different nutrient composition for microorganisms in the sample. The multiple support means is allowed to remain in contact with the microorganisms in the sample for a time period sufficient to measure difference in microorganism effects for the multiple support means. Microorganism effects for the multiple support means are then measured and compared. The invention is particularly adaptable to being conducted in situ. The additional steps of regulating nutrients added to the particular environment of microorganisms can enhance the desired results. Biological systems particularly suitable for this invention are bioremediation, biologically enhanced oil recovery, biological leaching of metals, and agricultural bioprocesses. 5 figs.

Method and apparatus for determining nutrient stimulation of biological processes

DOEpatents

Colwell, Frederick S.; Geesey, Gill G.; Gillis, Richard J.; Lehman, R. Michael

1997-01-01

A method and apparatus for determining the nutrients to stimulate microorganisms in a particular environment. A representative sample of microorganisms from a particular environment are contacted with multiple support means wherein each support means has intimately associated with the surface of the support means a different nutrient composition for said microorganisms in said sample. The multiple support means is allowed to remain in contact with the microorganisms in the sample for a time period sufficient to measure differences in microorganism effects for the multiple support means. Microorganism effects for the multiple support means are then measured and compared. The invention is particularly adaptable to being conducted in situ. The additional steps of regulating nutrients added to the particular environment of microorganisms can enhance the desired results. Biological systems particularly suitable for this invention are bioremediation, biologically enhanced oil recovery, biological leaching of metals, and agricultural bioprocesses.

7 CFR 58.644 - Test methods.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 3 2012-01-01 2012-01-01 false Test methods. 58.644 Section 58.644 Agriculture... Procedures § 58.644 Test methods. (a) Microbiological. Microbiological determinations shall be made in accordance with the methods described in the latest edition of Standard Methods for the Examination of Dairy...

7 CFR 58.644 - Test methods.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 3 2011-01-01 2011-01-01 false Test methods. 58.644 Section 58.644 Agriculture... Procedures § 58.644 Test methods. (a) Microbiological. Microbiological determinations shall be made in accordance with the methods described in the latest edition of Standard Methods for the Examination of Dairy...

7 CFR 58.644 - Test methods.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 3 2013-01-01 2013-01-01 false Test methods. 58.644 Section 58.644 Agriculture... Procedures § 58.644 Test methods. (a) Microbiological. Microbiological determinations shall be made in accordance with the methods described in the latest edition of Standard Methods for the Examination of Dairy...

7 CFR 58.644 - Test methods.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 3 2010-01-01 2010-01-01 false Test methods. 58.644 Section 58.644 Agriculture... Procedures § 58.644 Test methods. (a) Microbiological. Microbiological determinations shall be made in accordance with the methods described in the latest edition of Standard Methods for the Examination of Dairy...

7 CFR 58.644 - Test methods.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 3 2014-01-01 2014-01-01 false Test methods. 58.644 Section 58.644 Agriculture... Procedures § 58.644 Test methods. (a) Microbiological. Microbiological determinations shall be made in accordance with the methods described in the latest edition of Standard Methods for the Examination of Dairy...

Biological and analytical variations of 16 parameters related to coagulation screening tests and the activity of coagulation factors.

PubMed

Chen, Qian; Shou, Weiling; Wu, Wei; Guo, Ye; Zhang, Yujuan; Huang, Chunmei; Cui, Wei

2015-04-01

To accurately estimate longitudinal changes in individuals, it is important to take into consideration the biological variability of the measurement. The few studies available on the biological variations of coagulation parameters are mostly outdated. We confirmed the published results using modern, fully automated methods. Furthermore, we added data for additional coagulation parameters. At 8:00 am, 12:00 pm, and 4:00 pm on days 1, 3, and 5, venous blood was collected from 31 healthy volunteers. A total of 16 parameters related to coagulation screening tests as well as the activity of coagulation factors were analyzed; these included prothrombin time, fibrinogen (Fbg), activated partial thromboplastin time, thrombin time, international normalized ratio, prothrombin time activity, activated partial thromboplastin time ratio, fibrin(-ogen) degradation products, as well as the activity of factor II, factor V, factor VII, factor VIII, factor IX, and factor X. All intraindividual coefficients of variation (CVI) values for the parameters of the screening tests (except Fbg) were less than 5%. Conversely, the CVI values for the activity of coagulation factors were all greater than 5%. In addition, we calculated the reference change value to determine whether a significant difference exists between two test results from the same individual. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

Effect of olive mill wastewaters on the oxygen consumption by activated sludge microorganisms: an acute toxicity test method.

PubMed

Paixão, S M; Anselmo, A M

2002-01-01

The test for inhibition of oxygen consumption by activated sludge (ISO 8192-1986 (E)) was evaluated as a tool for assessing, the acute toxicity of olive mill wastewaters (OMW). According to the ISO test, information generated by this method may be helpful in estimating the effect of a test material on bacterial communities in the aquatic environment, especially in aerobic biological treatment systems. However, the lack of standardized bioassay methodology for effluents imposed that the test conditions were modified and adapted. The experiments were conducted in the presence or absence of an easily biodegradable carbon source (glucose) with different contact times (20 min and 24 h). The results obtained showed a remarkable stimulatory effect of this effluent to the activated sludge microorganisms. In fact, the oxygen uptake rate values increase with increasing effluent concentrations and contact times up to 0.98 microl O(2) h(-1) mg(-1) dry weight for a 100% OMW sample, 24 h contact time, with blanks exhibiting an oxygen uptake rate of ca. 1/10 of this value (0.07-0.10). It seems that the application of the ISO test as an acute toxicity test for effluents should be reconsidered, with convenient adaptation for its utilization as a method of estimating the effect on bacterial communities present in aerobic biological treatment systems. Copyright 2002 John Wiley & Sons, Ltd.

River Pollution: Part II. Biological Methods for Assessing Water Quality.

ERIC Educational Resources Information Center

Openshaw, Peter

1984-01-01

Discusses methods used in the biological assessment of river quality and such indicators of clean and polluted waters as the Trent Biotic Index, Chandler Score System, and species diversity indexes. Includes a summary of a river classification scheme based on quality criteria related to water use. (JN)

Estimation of biological variation and reference change value of glycated hemoglobin (HbA(1c)) when two analytical methods are used.

PubMed

Ucar, Fatma; Erden, Gonul; Ginis, Zeynep; Ozturk, Gulfer; Sezer, Sevilay; Gurler, Mukaddes; Guneyk, Ahmet

2013-10-01

Available data on biological variation of HbA1c revealed marked heterogeneity. We therefore investigated and estimated the components of biological variation for HbA1c in a group of healthy individuals by applying a recommended and strictly designed study protocol using two different assay methods. Each month, samples were derived on the same day, for three months. Four EDTA whole blood samples were collected from each individual (20 women, 9 men; 20-45 years of age) and stored at -80°C until analysis. HbA1c values were measured by both high performance liquid chromatography (HPLC) (Shimadzu, Prominence, Japan) and boronate affinity chromatography methods (Trinity Biotech, Premier Hb9210, Ireland). All samples were assayed in duplicate in a single batch for each assay method. Estimations were calculated according to the formulas described by Fraser and Harris. The within subject (CV(I))-between subject (CV(G)) biological variations were 1.17% and 5.58%, respectively for HPLC. The calculated CV(I) and CV(G) were 2.15% and 4.03%, respectively for boronate affinity chromatography. Reference change value (RCV) for HPLC and boronate affinity chromatography was 5.4% and 10.4% respectively and individuality index of HbA(1c) was 0.35 and 0.93 respectively. This study for the first time described the components of biological variation for HbA1c in healthy individuals by two different assay methods. Obtained findings showed that the difference between CV(A) values of the methods might considerably affect RCV. These data regarding biological variation of HbA(1c) could be useful for a better evaluation of HbA(1c) test results in clinical interpretation. Copyright © 2013 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Green Jobs: Definition and Method of Appraisal of Chemical and Biological Risks

PubMed Central

Cheneval, Erwan; Busque, Marc-Antoine; Ostiguy, Claude; Lavoie, Jacques; Bourbonnais, Robert; Labrèche, France; Bakhiyi, Bouchra; Zayed, Joseph

2016-01-01

In the wake of sustainable development, green jobs are developing rapidly, changing the work environment. However a green job is not automatically a safe job. The aim of the study was to define green jobs, and to establish a preliminary risk assessment of chemical substances and biological agents for workers in Quebec. An operational definition was developed, along with criteria and sustainable development principles to discriminate green jobs from regular jobs. The potential toxicity or hazard associated with their chemical and biological exposures was assessed, and the workers’ exposure appraised using an expert assessment method. A control banding approach was then used to assess risks for workers in selected green jobs. A double entry model allowed us to set priorities in terms of chemical or biological risk. Among jobs that present the highest risk potential, several are related to waste management. The developed method is flexible and could be adapted to better appraise the risks that workers are facing or to propose control measures. PMID:26718400

40 CFR 63.1161 - Performance testing and test methods.

Code of Federal Regulations, 2012 CFR

2012-07-01

... Facilities and Hydrochloric Acid Regeneration Plants § 63.1161 Performance testing and test methods. (a...) or measure the concentration of HCl (and Cl2 for hydrochloric acid regeneration plants) in gases... to the initial test or tests. (c) Establishment of hydrochloric acid regeneration plant operating...

40 CFR 63.1161 - Performance testing and test methods.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Facilities and Hydrochloric Acid Regeneration Plants § 63.1161 Performance testing and test methods. (a...) or measure the concentration of HCl (and Cl2 for hydrochloric acid regeneration plants) in gases... to the initial test or tests. (c) Establishment of hydrochloric acid regeneration plant operating...

40 CFR 63.1161 - Performance testing and test methods.

Code of Federal Regulations, 2011 CFR

2011-07-01

... Facilities and Hydrochloric Acid Regeneration Plants § 63.1161 Performance testing and test methods. (a...) or measure the concentration of HCl (and Cl2 for hydrochloric acid regeneration plants) in gases... to the initial test or tests. (c) Establishment of hydrochloric acid regeneration plant operating...

Generalized empirical Bayesian methods for discovery of differential data in high-throughput biology.

PubMed

Hardcastle, Thomas J

2016-01-15

High-throughput data are now commonplace in biological research. Rapidly changing technologies and application mean that novel methods for detecting differential behaviour that account for a 'large P, small n' setting are required at an increasing rate. The development of such methods is, in general, being done on an ad hoc basis, requiring further development cycles and a lack of standardization between analyses. We present here a generalized method for identifying differential behaviour within high-throughput biological data through empirical Bayesian methods. This approach is based on our baySeq algorithm for identification of differential expression in RNA-seq data based on a negative binomial distribution, and in paired data based on a beta-binomial distribution. Here we show how the same empirical Bayesian approach can be applied to any parametric distribution, removing the need for lengthy development of novel methods for differently distributed data. Comparisons with existing methods developed to address specific problems in high-throughput biological data show that these generic methods can achieve equivalent or better performance. A number of enhancements to the basic algorithm are also presented to increase flexibility and reduce computational costs. The methods are implemented in the R baySeq (v2) package, available on Bioconductor http://www.bioconductor.org/packages/release/bioc/html/baySeq.html. tjh48@cam.ac.uk Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Applying systems biology methods to the study of human physiology in extreme environments

PubMed Central

2013-01-01

Systems biology is defined in this review as ‘an iterative process of computational model building and experimental model revision with the aim of understanding or simulating complex biological systems’. We propose that, in practice, systems biology rests on three pillars: computation, the omics disciplines and repeated experimental perturbation of the system of interest. The number of ethical and physiologically relevant perturbations that can be used in experiments on healthy humans is extremely limited and principally comprises exercise, nutrition, infusions (e.g. Intralipid), some drugs and altered environment. Thus, we argue that systems biology and environmental physiology are natural symbionts for those interested in a system-level understanding of human biology. However, despite excellent progress in high-altitude genetics and several proteomics studies, systems biology research into human adaptation to extreme environments is in its infancy. A brief description and overview of systems biology in its current guise is given, followed by a mini review of computational methods used for modelling biological systems. Special attention is given to high-altitude research, metabolic network reconstruction and constraint-based modelling. PMID:23849719

Standard Test Methods for Textile Composites

NASA Technical Reports Server (NTRS)

Masters, John E.; Portanova, Marc A.

1996-01-01

Standard testing methods for composite laminates reinforced with continuous networks of braided, woven, or stitched fibers have been evaluated. The microstructure of these textile' composite materials differs significantly from that of tape laminates. Consequently, specimen dimensions and loading methods developed for tape type composites may not be applicable to textile composites. To this end, a series of evaluations were made comparing testing practices currently used in the composite industry. Information was gathered from a variety of sources and analyzed to establish a series of recommended test methods for textile composites. The current practices established for laminated composite materials by ASTM and the MIL-HDBK-17 Committee were considered. This document provides recommended test methods for determining both in-plane and out-of-plane properties. Specifically, test methods are suggested for: unnotched tension and compression; open and filled hole tension; open hole compression; bolt bearing; and interlaminar tension. A detailed description of the material architectures evaluated is also provided, as is a recommended instrumentation practice.

Effect of chemical and biological surfactants on activated sludge of MBR system: microscopic analysis and foam test.

PubMed

Capodici, Marco; Di Bella, Gaetano; Nicosia, Salvatore; Torregrossa, Michele

2015-02-01

A bench-scale MBR unit was operated, under stressing condition, with the aim of stimulating the onset of foaming in the activated sludge. Possible synergies between synthetic surfactants in the wastewater and biological surfactants (Extra-Cellular Polymeric Substances, EPSs) were investigated by changing C/N ratio. The growth of filamentous bacteria was also discussed. The MBR unit provided satisfactory overall carbon removal overall efficiencies: in particular, synthetic surfactants were removed with efficiency higher than 90% and 95% for non-ionic and ionic surfactants, respectively. Lab investigation suggested also the importance to reduce synthetic surfactants presence entering into mixed liquor: otherwise, their presence can significantly worsen the natural foaming caused by biological surfactants (EPSs) produced by bacteria. Finally, a new analytic method based on "ink test" has been proposed as a useful tool to achieve a valuation of EPSs bound fraction. Copyright © 2014 Elsevier Ltd. All rights reserved.

All biology is computational biology.

PubMed

Markowetz, Florian

2017-03-01

Here, I argue that computational thinking and techniques are so central to the quest of understanding life that today all biology is computational biology. Computational biology brings order into our understanding of life, it makes biological concepts rigorous and testable, and it provides a reference map that holds together individual insights. The next modern synthesis in biology will be driven by mathematical, statistical, and computational methods being absorbed into mainstream biological training, turning biology into a quantitative science.

[Inappropriate test methods in allergy].

PubMed

Kleine-Tebbe, J; Herold, D A

2010-11-01

Inappropriate test methods are increasingly utilized to diagnose allergy. They fall into two categories: I. Tests with obscure theoretical basis, missing validity and lacking reproducibility, such as bioresonance, electroacupuncture, applied kinesiology and the ALCAT-test. These methods lack both the technical and clinical validation needed to justify their use. II. Tests with real data, but misleading interpretation: Detection of IgG or IgG4-antibodies or lymphocyte proliferation tests to foods do not allow to separate healthy from diseased subjects, neither in case of food intolerance, allergy or other diagnoses. The absence of diagnostic specificity induces many false positive findings in healthy subjects. As a result unjustified diets might limit quality of life and lead to malnutrition. Proliferation of lymphocytes in response to foods can show elevated rates in patients with allergies. These values do not allow individual diagnosis of hypersensitivity due to their broad variation. Successful internet marketing, infiltration of academic programs and superficial reporting by the media promote the popularity of unqualified diagnostic tests; also in allergy. Therefore, critical observation and quick analysis of and clear comments to unqualified methods by the scientific medical societies are more important than ever.

30 CFR 36.41 - Testing methods.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 30 Mineral Resources 1 2014-07-01 2014-07-01 false Testing methods. 36.41 Section 36.41 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR TESTING, EVALUATION, AND APPROVAL OF... Requirements § 36.41 Testing methods. Mobile diesel-powered transportation equipment submitted for...

30 CFR 36.41 - Testing methods.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Testing methods. 36.41 Section 36.41 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR TESTING, EVALUATION, AND APPROVAL OF... Requirements § 36.41 Testing methods. Mobile diesel-powered transportation equipment submitted for...

30 CFR 36.41 - Testing methods.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 30 Mineral Resources 1 2013-07-01 2013-07-01 false Testing methods. 36.41 Section 36.41 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR TESTING, EVALUATION, AND APPROVAL OF... Requirements § 36.41 Testing methods. Mobile diesel-powered transportation equipment submitted for...

30 CFR 36.41 - Testing methods.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 30 Mineral Resources 1 2012-07-01 2012-07-01 false Testing methods. 36.41 Section 36.41 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR TESTING, EVALUATION, AND APPROVAL OF... Requirements § 36.41 Testing methods. Mobile diesel-powered transportation equipment submitted for...

30 CFR 36.41 - Testing methods.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Testing methods. 36.41 Section 36.41 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR TESTING, EVALUATION, AND APPROVAL OF... Requirements § 36.41 Testing methods. Mobile diesel-powered transportation equipment submitted for...

SAS molecular tests Salmonella detection kit. Performance tested method 021202.

PubMed

Bapanpally, Chandra; Montier, Laura; Khan, Shah; Kasra, Akif; Brunelle, Sharon L

2014-01-01

The SAS Molecular tests Salmonella Detection method, a Loop-mediated Isothermal Amplification method, performed as well as or better than the U.S. Department of Agriculture-Food Safety Inspection Service Microbiology Laboratory Guidebook and the U.S. Food and Drug Administration Bacteriological Analytical Manual reference methods for ground beef, beef trim, ground turkey, chicken carcass rinses, bagged mixed lettuce, and fresh spinach. The ground beef (30% fat, 25 g test portion), poultry matrixes and leafy greens were validated in a 6-7 h enrichment, and ground beef (30% fat, 375 g composite test portion) and beef trim (375 g composite test portion) were validated in a 16-20 h enrichment. The method performance for meat and leafy green matrixes was shown to be acceptable under conditions of co-enrichment with Escherichia coli 0157. Thus, after a short 6-7 h co-enrichment step, ground beef, beef trim, lettuce, and spinach can be tested for both Salmonella and E. coli O157. Inclusivity and exclusivity testing revealed no false negatives and no false positives among the 100 Salmonella serovars and 30 non-Salmonella species examined. The method was shown to be robust when enrichment time, DNA extract hold time, and DNA volume were varied.

Membrane materials for storing biological samples intended for comparative nanotoxicological testing

NASA Astrophysics Data System (ADS)

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

2015-11-01

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

[Methods of testing inactivated antirabies vaccines].

PubMed

Nedosekov, V V; Vishniakov, I F; Gruzdev, K N

2001-01-01

Methods for evaluating the potency of inactivated rabies vaccines are reviewed. Shortcomings of the traditional NIH method and advantages of modern rapid immunological in vitro methods (antibody binding test, radial immunodiffusion test, enzyme linked immunoadsorbent assay) for estimation of antigenic activity of vaccines are discussed.

Nitrate removal from drinking water with a focus on biological methods: a review.

PubMed

Rezvani, Fariba; Sarrafzadeh, Mohammad-Hossein; Ebrahimi, Sirous; Oh, Hee-Mock

2017-05-31

This article summarizes several developed and industrial technologies for nitrate removal from drinking water, including physicochemical and biological techniques, with a focus on autotrophic nitrate removal. Approaches are primarily classified into separation-based and elimination-based methods according to the fate of the nitrate in water treatment. Biological denitrification as a cost-effective and promising method of biological nitrate elimination is reviewed in terms of its removal process, applicability, efficiency, and associated disadvantages. The various pathways during biological nitrate removal, including assimilatory and dissimilatory nitrate reduction, are also explained. A comparative study was carried out to provide a better understanding of the advantages and disadvantages of autotrophic and heterotrophic denitrification. Sulfur-based and hydrogen-based denitrifications, which are the most common autotrophic processes of nitrate removal, are reviewed with the aim of presenting the salient features of hydrogenotrophic denitrification along with some drawbacks of the technology and research areas in which it could be used but currently is not. The application of algae-based water treatment is also introduced as a nature-inspired approach that may broaden future horizons of nitrate removal technology.

Test methods for environment-assisted cracking

NASA Astrophysics Data System (ADS)

Turnbull, A.

1992-03-01

The test methods for assessing environment assisted cracking of metals in aqueous solution are described. The advantages and disadvantages are examined and the interrelationship between results from different test methods is discussed. The source of differences in susceptibility to cracking occasionally observed from the varied mechanical test methods arises often from the variation between environmental parameters in the different test conditions and the lack of adequate specification, monitoring, and control of environmental variables. Time is also a significant factor when comparing results from short term tests with long exposure tests. In addition to these factors, the intrinsic difference in the important mechanical variables, such as strain rate, associated with the various mechanical tests methods can change the apparent sensitivity of the material to stress corrosion cracking. The increasing economic pressure for more accelerated testing is in conflict with the characteristic time dependence of corrosion processes. Unreliable results may be inevitable in some cases but improved understanding of mechanisms and the development of mechanistically based models of environment assisted cracking which incorporate the key mechanical, material, and environmental variables can provide the framework for a more realistic interpretation of short term data.

Comparison of three commercially available fit-test methods.

PubMed

Janssen, Larry L; Luinenburg, D Michael; Mullins, Haskell E; Nelson, Thomas J

2002-01-01

American National Standards Institute (ANSI) standard Z88.10, Respirator Fit Testing Methods, includes criteria to evaluate new fit-tests. The standard allows generated aerosol, particle counting, or controlled negative pressure quantitative fit-tests to be used as the reference method to determine acceptability of a new test. This study examined (1) comparability of three Occupational Safety and Health Administration-accepted fit-test methods, all of which were validated using generated aerosol as the reference method; and (2) the effect of the reference method on the apparent performance of a fit-test method under evaluation. Sequential fit-tests were performed using the controlled negative pressure and particle counting quantitative fit-tests and the bitter aerosol qualitative fit-test. Of 75 fit-tests conducted with each method, the controlled negative pressure method identified 24 failures; bitter aerosol identified 22 failures; and the particle counting method identified 15 failures. The sensitivity of each method, that is, agreement with the reference method in identifying unacceptable fits, was calculated using each of the other two methods as the reference. None of the test methods met the ANSI sensitivity criterion of 0.95 or greater when compared with either of the other two methods. These results demonstrate that (1) the apparent performance of any fit-test depends on the reference method used, and (2) the fit-tests evaluated use different criteria to identify inadequately fitting respirators. Although "acceptable fit" cannot be defined in absolute terms at this time, the ability of existing fit-test methods to reject poor fits can be inferred from workplace protection factor studies.

77 FR 22282 - Draft Guidelines on Biologics Quality Monitoring: Testing for the Detection of Mycoplasma...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-13

...] Draft Guidelines on Biologics Quality Monitoring: Testing for the Detection of Mycoplasma Contamination... Detection of Mycoplasma Contamination.'' This draft guideline identifies stages of manufacture where... contamination. Because the guidelines apply to final product and master seed/cell testing in veterinary vaccines...

Biological characteristics of crucian by quantitative inspection method

NASA Astrophysics Data System (ADS)

Chu, Mengqi

2015-04-01

Biological characteristics of crucian by quantitative inspection method Through quantitative inspection method , the biological characteristics of crucian was preliminary researched. Crucian , Belongs to Cypriniformes, Cyprinidae, Carassius auratus, is a kind of main plant-eating omnivorous fish,like Gregarious, selection and ranking. Crucian are widely distributed, perennial water all over the country all have production. Determine the indicators of crucian in the experiment, to understand the growth, reproduction situation of crucian in this area . Using the measured data (such as the scale length ,scale size and wheel diameter and so on) and related functional to calculate growth of crucian in any one year.According to the egg shape, color, weight ,etc to determine its maturity, with the mean egg diameter per 20 eggs and the number of eggs per 0.5 grams, to calculate the relative and absolute fecundity of the fish .Measured crucian were female puberty. Based on the relation between the scale diameter and length and the information, linear relationship between crucian scale diameter and length: y=1.530+3.0649. From the data, the fertility and is closely relative to the increase of age. The older, the more mature gonad development. The more amount of eggs. In addition, absolute fecundity increases with the pituitary gland.Through quantitative check crucian bait food intake by the object, reveals the main food, secondary foods, and chance food of crucian ,and understand that crucian degree of be fond of of all kinds of bait organisms.Fish fertility with weight gain, it has the characteristics of species and populations, and at the same tmes influenced by the age of the individual, body length, body weight, environmental conditions (especially the nutrition conditions), and breeding habits, spawning times factors and the size of the egg. After a series of studies of crucian biological character, provide the ecological basis for local crucian's feeding, breeding

New methods of pregnancy testing in adolescent girls.

PubMed

Saxena, B B

1981-05-01

The knowledge and use of newer, more sensitive, and reliable pregnancy tests which are easily accessible and of moderate cost are the 1st steps in the early diagnosis and management of pregnancy, especially in adolescent girls. Accurate diagnosis of pregnancy soon after conception offers the option of abortion by simple, effective, and inexpensive procedures or early initiation of prenatal maternity care. Discussion focuses on the symptoms of pregnancy and the historical development and basis of pregnancy tests as well as the specific types of pregnancy tests. The most familiar sign of pregnancy is the missed period. Other symptoms that provide presumptive evidence of pregnancy include fatigue and lassitude, increased body temperature, and breast fullness or pain. Feelings of nausea, vomiting, and weight gain may appear after 2 weeks. The diagnosis of pregnancy by the detection of the human chorionic gonadotropin was initially described 53 years ago by Selmar Aschheim and Bernhardt Zondek. Improvements in the techniques for the measurement of human chorionic gonadotropin (hCG) have been directly related to the progress in the purification and isolation of hCG and elucidation of the amino acid sequence of the hormone-nonspecific alpha subunit and hormone-specific beta subunit of hCG. The history, physical examination, and pregnancy tests will generally provide sufficient information for a definite diagnosis of pregnancy. The presence of hCG in the urine or blood is the most accurate of all the indications of pregnancy. During the last century, 4 different techniques for the determination of hCG in blood and/or urine have been developed. These include the following and are reviewed in detail: 1) bioassays in intact laboratory animals; 2) immunologic tube or slide methods with heme- or latex-agglutination inhibition, as well as the more recently developed competitive protein binding method such as 3) radioimmunoassay (RIA) for the use of radioisotope labeled hormone

Assessment of test method variables for in vitro skin irritation testing of medical device extracts.

PubMed

Olsen, Daniel S; Lee, Michelle; Turley, Audrey P

2018-08-01

Skin irritation is an important component of the biological safety evaluation of medical devices. This testing has typically been performed using in vivo models. However, in an effort to reduce the need for in vivo testing, alternative methods for assessing skin irritation potential in vitro have been developed using a Reconstructed Human Epidermis (RhE) model. During the development of the protocol for the round robin validation of in vitro irritation testing for medical device extracts, it became clear that there were three points in the procedure where different options may be validated within each laboratory for routine testing: sample exposure time (18 vs 24h), SDS positive control concentration, and cytokine (IL-1α) release testing. The goal of our study was to evaluate the effect of these variables. EpiDerm™ tissues were exposed to extracts of three plain polymer samples, and four polymers embedded with known irritant chemicals. Exposures were performed for 18 and 24h. Resulting tissue viability was assessed by MTT reduction and IL-1α release was assessed by ELISA. Testing was also performed using various concentrations of SDS ranging from 0.5 to 1% (w/v). Overall, results were similar for samples tested and 18 and 24h, but the 18h exposure time has the potential to have an impact on the results of some sample types. IL-1α testing was shown to be useful to clarify conflicting tissue viability results. Use of a lower concentration of SDS as a positive control can help prevent issues that arise from excessive tissue damage often caused by 1% SDS. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Systems Biology-Driven Hypotheses Tested In Vivo: The Need to Advancing Molecular Imaging Tools.

PubMed

Verma, Garima; Palombo, Alessandro; Grigioni, Mauro; La Monaca, Morena; D'Avenio, Giuseppe

2018-01-01

Processing and interpretation of biological images may provide invaluable insights on complex, living systems because images capture the overall dynamics as a "whole." Therefore, "extraction" of key, quantitative morphological parameters could be, at least in principle, helpful in building a reliable systems biology approach in understanding living objects. Molecular imaging tools for system biology models have attained widespread usage in modern experimental laboratories. Here, we provide an overview on advances in the computational technology and different instrumentations focused on molecular image processing and analysis. Quantitative data analysis through various open source software and algorithmic protocols will provide a novel approach for modeling the experimental research program. Besides this, we also highlight the predictable future trends regarding methods for automatically analyzing biological data. Such tools will be very useful to understand the detailed biological and mathematical expressions under in-silico system biology processes with modeling properties.

Electrophoresis tests on STS-3 and ground control experiments - A basis for future biological sample selections

NASA Technical Reports Server (NTRS)

Morrison, D. R.; Lewis, M. L.

1982-01-01

Static zone electrophoresis is an electrokinetic method of separating macromolecules and small particles. However, its application for the isolation of biological cells and concentrated protein solutions is limited by sedimentation and convection. Microgravity eliminates or reduces sedimentation, floatation, and density-driven convection arising from either Joule heating or concentration differences. The advantages of such an environment were first demonstrated in space during the Apollo 14 and 16 missions. In 1975 the Electrophoresis Technology Experiment (MA-011) was conducted during the Apollo-Soyuz Test Project flight. In 1979 a project was initiated to repeat the separations of human kidney cells. One of the major objectives of the Electrophoresis Equipment Verification Tests (EEVT) on STS-3 was to repeat and thereby validate the first successful electrophoretic separation of human kidney cells. Attention is given to the EEVT apparatus, the preflight electrophoresis, and inflight operational results.

A NEW METHOD OF SWEAT TESTING: THE CF QUANTUM® SWEAT TEST

PubMed Central

Rock, Michael J.; Makholm, Linda; Eickhoff, Jens

2015-01-01

Background Conventional methods of sweat testing are time consuming and have many steps that can and do lead to errors. This study compares conventional sweat testing to a new quantitative method, the CF Quantum® (CFQT) sweat test. This study tests the diagnostic accuracy and analytic validity of the CFQT. Methods Previously diagnosed CF patients and patients who required a sweat test for clinical indications were invited to have the CFQT test performed. Both conventional sweat testing and the CFQT were performed bilaterally on the same day. Pairs of data from each test are plotted as a correlation graph and Bland Altman plot. Sensitivity and specificity were calculated as well as the means and coefficient of variation by test and by extremity. After completing the study, subjects or their parents were asked for their preference of the CFQT and conventional sweat testing. Results The correlation coefficient between the CFQT and conventional sweat testing was 0.98 (95% confidence interval: 0.97–0.99). The sensitivity and specificity of the CFQT in diagnosing CF was 100% (95% confidence interval: 94–100%) and 96% (95% confidence interval: 89–99%), respectively. In one center in this three center multicenter study, there were higher sweat chloride values in patients with CF and also more tests that were invalid due to discrepant values between the two extremities. The percentage of invalid tests was higher in the CFQT method (16.5%) compared to conventional sweat testing (3.8%)(p < 0.001). In the post-test questionnaire, 88% of subjects/parents preferred the CFQT test. Conclusions The CFQT is a fast and simple method of quantitative sweat chloride determination. This technology requires further refinement to improve the analytic accuracy at higher sweat chloride values and to decrease the number of invalid tests. PMID:24862724

Evaluation of methods of determining humic acids in nucleic acid samples for molecular biological analysis.

PubMed

Wang, Yong; Fujii, Takeshi

2011-01-01

It is important in molecular biological analyses to evaluate contamination of co-extracted humic acids in DNA/RNA extracted from soil. We compared the sensitivity of various methods for measurement of humic acids, and influences of DNA/RNA and proteins on the measurement. Considering the results, we give suggestions as to choice of methods for measurement of humic acids in molecular biological analyses.

40 CFR 63.1161 - Performance testing and test methods.

Code of Federal Regulations, 2013 CFR

2013-07-01

... Facilities and Hydrochloric Acid Regeneration Plants § 63.1161 Performance testing and test methods. (a...) Establishment of hydrochloric acid regeneration plant operating parameters. (1) During the performance test for hydrochloric acid regeneration plants, the owner or operator shall establish site-specific operating parameter...

40 CFR 63.1161 - Performance testing and test methods.

Code of Federal Regulations, 2014 CFR

2014-07-01

... Facilities and Hydrochloric Acid Regeneration Plants § 63.1161 Performance testing and test methods. (a...) Establishment of hydrochloric acid regeneration plant operating parameters. (1) During the performance test for hydrochloric acid regeneration plants, the owner or operator shall establish site-specific operating parameter...

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

PubMed

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/.

Myasthenia Gravis: Tests and Diagnostic Methods

MedlinePlus

... Focus on MG Newsletter MG Quarterly Test & Diagnostic methods In addition to a complete medical and neurological ... How can I help? About MGFA Test & Diagnostic methods Treatment for MG FAQ's Upcoming Events 2018 MG ...

Biological induced corrosion of materials II: New test methods and experiences from mir station

NASA Astrophysics Data System (ADS)

Klintworth, R.; Reher, H. J.; Viktorov, A. N.; Bohle, D.

1999-09-01

During previous long-term manned missions, more than 100 species of microorganisms have been identified on surfaces of materials (bacteria and fungi). Among them were potentially pathogenic ones (saprophytes) which are capable of active growth on artificial substrates, as well as technophilic bacteria and fungi causing damages (destruction and degradation) to various materials (metals and polymers), resulting in failures and disruptions in the functioning of equipment and hardware. Aboard a space vehicle some microclimatic parameters are optimal for microorganism growth: the atmospheric fluid condensate with its specific composition, chemical and/or antropogenic contaminants (human metobolic products, etc.) all are stimulating factors for the development of bacteria and mould fungi on materials of the interior and equipment of an orbital station during its operational phase(s). Especially Russian long-term missions (SALJUT, MIR) have demonstrated that uncontrolled interactions of microorganisms with materials will ultimately lead to the appearence of technological and medical risks, significantly influencing safety and reliability characteristics of individual as well as whole systems and/ or subsystems. For a first conclusion, it could be summarized, that countermeasures and anti-strategies focussing on Microbial Contamination Management (MCM) for the International Space Station (ISS, next long-term manned mission) at least require a new materials test approach. Our respective concept includes a combined age-ing/biocorrosion test sequence. It is represented here, as well as current status of MCM program, e.g. continuous monitoring (microbiological analyses), long-term disinfection, frequent cleaning methods, mathematical modeling of ISS, etc.

Combined ultraviolet and water exposure as a preconditioning method in laboratory fungal durability testing

Treesearch

Rebecca E. Ibach; Craig M. Clemons; Nicole M. Stark

2003-01-01

During outdoor exposure, woodfiber-plastic composites (WPC) are subject to biological, moisture, and ultraviolet (UV) degradation. The purpose of laboratory evaluations is to simulate outdoor conditions and accelerate the testing for quicker results. Traditionally, biological, moisture, and W laboratory tests are done separately, and only combined in outdoor field...

Future Food Production System Development Pulling From Space Biology Crop Growth Testing in Veggie

NASA Technical Reports Server (NTRS)

Massa, Gioia; Romeyn, Matt; Fritsche, Ralph

2017-01-01

Preliminary crop testing using Veggie indicates the environmental conditions provided by the ISS are generally suitable for food crop production. When plant samples were returned to Earth for analysis, their levels of nutrients were comparable to Earth-grown ground controls. Veggie-grown produce food safety microbiology analysis indicated that space-grown crops are safe to consume. Produce sanitizing wipes were used on-orbit to further reduce risk of foodborne illness. Validation growth tests indicated abiotic challenges of insufficient or excess fluid delivery, potentially reduced air flow leading to excess water, elevated CO2 leading to physiological responses, and microorganisms that became opportunistic pathogens. As NASA works to develop future space food production, several areas of research to define these systems pull from the Veggie technology validation tests. Research into effective, reusable water delivery and water recovery methods for future food production systems arises from abiotic challenges observed. Additionally, impacts of elevated CO2 and refinement of fertilizer and light recipes for crops needs to be assessed. Biotic pulls include methods or technologies to effectively sanitize produce with few consumables and low inputs; work to understand the phytomicrobiome and potentially use it to protect crops or enhance growth; selection of crops with high harvest index and desirable flavors for supplemental nutrition; crops that provide psychosocial benefits, and custom space crop development. Planning for future food production in a deep space gateway or a deep space transit vehicle requires methods of handling and storing seeds, and ensuring space seeds are free of contaminants and long-lived. Space food production systems may require mechanization and autonomous operation, with preliminary testing initiated to identify operations and capabilities that are candidates for automation. Food production design is also pulling from Veggie logistics

Future Food Production System Development Pulling from Space Biology Crop Growth Testing in Veggie

NASA Technical Reports Server (NTRS)

Massa, G. D.; Romeyn, M. W.; Fritsche, R. F.

2017-01-01

Preliminary crop testing using Veggie indicates the environmental conditions provided by the ISS are generally suitable for food crop production. When plant samples were returned to Earth for analysis, their levels of nutrients were comparable to Earth-grown ground controls. Veggie-grown produce food safety microbiology analysis indicated that space-grown crops are safe to consume. Produce sanitizing wipes were used on-orbit to further reduce risk of foodborne illness. Validation growth tests indicated abiotic challenges of insufficient or excess fluid delivery, potentially reduced air flow leading to excess water, elevated CO2 leading to physiological responses, and microorganisms that became opportunistic pathogens. As NASA works to develop future space food production, several areas of research to define these systems pull from the Veggie technology validation tests. Research into effective, reusable water delivery and water recovery methods for future food production systems arises from abiotic challenges observed. Additionally, impacts of elevated CO2 and refinement of fertilizer and light recipes for crops needs to be assessed. Biotic pulls include methods or technologies to effectively sanitize produce with few consumables and low inputs; work to understand the phytomicrobiome and potentially use it to protect crops or enhance growth; selection of crops with high harvest index and desirable flavors for supplemental nutrition; crops that provide psychosocial benefits, and custom space crop development. Planning for future food production in a deep space gateway or a deep space transit vehicle requires methods of handling and storing seeds, and ensuring space seeds are free of contaminants and long-lived. Space food production systems may require mechanization and autonomous operation, with preliminary testing initiated to identify operations and capabilities that are candidates for automation. Food production design is also pulling from Veggie logistics

A COMPARISON OF TWO RAPID BIOLOGICAL ASSESSMENT SAMPLING METHODS FOR MACROINVERTEBRATES

EPA Science Inventory

In 2003, the Office of Research and Developments (ORD's) National Exposure Research Laboratory initiated a collaborative research effort with U.S. EPA Region 3 to conduct a study comparing two rapid biological assessment methods for collecting stream macroinvertebrates. One metho...

Method For Testing Properties Of Corrosive Lubricants

DOEpatents

Ohi, James; De La Cruz, Jose L.; Lacey, Paul I.

2006-01-03

A method of testing corrosive lubricating media using a wear testing apparatus without a mechanical seal. The wear testing apparatus and methods are effective for testing volatile corrosive lubricating media under pressure and at high temperatures.

Green Jobs: Definition and Method of Appraisal of Chemical and Biological Risks.

PubMed

Cheneval, Erwan; Busque, Marc-Antoine; Ostiguy, Claude; Lavoie, Jacques; Bourbonnais, Robert; Labrèche, France; Bakhiyi, Bouchra; Zayed, Joseph

2016-04-01

In the wake of sustainable development, green jobs are developing rapidly, changing the work environment. However a green job is not automatically a safe job. The aim of the study was to define green jobs, and to establish a preliminary risk assessment of chemical substances and biological agents for workers in Quebec. An operational definition was developed, along with criteria and sustainable development principles to discriminate green jobs from regular jobs. The potential toxicity or hazard associated with their chemical and biological exposures was assessed, and the workers' exposure appraised using an expert assessment method. A control banding approach was then used to assess risks for workers in selected green jobs. A double entry model allowed us to set priorities in terms of chemical or biological risk. Among jobs that present the highest risk potential, several are related to waste management. The developed method is flexible and could be adapted to better appraise the risks that workers are facing or to propose control measures. © The Author 2015. Published by Oxford University Press on behalf of the British Occupational Hygiene Society.

40 CFR 63.465 - Test methods.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 9 2011-07-01 2011-07-01 false Test methods. 63.465 Section 63.465... Halogenated Solvent Cleaning § 63.465 Test methods. (a) Except as provided in paragraphs (f) and (g) of this... Reference Method 307 in appendix A of this part. (b) Except as provided in paragraph (g) of this section for...

40 CFR 63.465 - Test methods.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 10 2012-07-01 2012-07-01 false Test methods. 63.465 Section 63.465... Halogenated Solvent Cleaning § 63.465 Test methods. (a) Except as provided in paragraphs (f) and (g) of this... Reference Method 307 in appendix A of this part. (b) Except as provided in paragraph (g) of this section for...

40 CFR 63.465 - Test methods.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 9 2010-07-01 2010-07-01 false Test methods. 63.465 Section 63.465... Halogenated Solvent Cleaning § 63.465 Test methods. (a) Except as provided in paragraphs (f) and (g) of this... Reference Method 307 in appendix A of this part. (b) Except as provided in paragraph (g) of this section for...

40 CFR 63.465 - Test methods.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 10 2014-07-01 2014-07-01 false Test methods. 63.465 Section 63.465... Halogenated Solvent Cleaning § 63.465 Test methods. (a) Except as provided in paragraphs (f) and (g) of this... Reference Method 307 in appendix A of this part. (b) Except as provided in paragraph (g) of this section for...

40 CFR 63.465 - Test methods.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 10 2013-07-01 2013-07-01 false Test methods. 63.465 Section 63.465... Halogenated Solvent Cleaning § 63.465 Test methods. (a) Except as provided in paragraphs (f) and (g) of this... Reference Method 307 in appendix A of this part. (b) Except as provided in paragraph (g) of this section for...

Biology Student Teachers' Cognitive Structure about "Living Thing"

ERIC Educational Resources Information Center

Kurt, Hakan

2013-01-01

The current study aims to determine biology student teachers' cognitive structure on the concept of "living thing" through revealing their conceptual framework. Qualitative research method was applied in this study. The data were collected from 44 biology student teachers. A free word association test was used as a data collection…

Measuring the Outcome of At-Risk Students on Biology Standardized Tests When Using Different Instructional Strategies

NASA Astrophysics Data System (ADS)

Burns, Dana

Over the last two decades, online education has become a popular concept in universities as well as K-12 education. This generation of students has grown up using technology and has shown interest in incorporating technology into their learning. The idea of using technology in the classroom to enhance student learning and create higher achievement has become necessary for administrators, teachers, and policymakers. Although online education is a popular topic, there has been minimal research on the effectiveness of online and blended learning strategies compared to the student learning in a traditional K-12 classroom setting. The purpose of this study was to investigate differences in standardized test scores from the Biology End of Course exam when at-risk students completed the course using three different educational models: online format, blended learning, and traditional face-to-face learning. Data was collected from over 1,000 students over a five year time period. Correlation analyzed data from standardized tests scores of eighth grade students was used to define students as "at-risk" for failing high school courses. The results indicated a high correlation between eighth grade standardized test scores and Biology End of Course exam scores. These students were deemed "at-risk" for failing high school courses. Standardized test scores were measured for the at-risk students when those students completed Biology in the different models of learning. Results indicated significant differences existed among the learning models. Students had the highest test scores when completing Biology in the traditional face-to-face model. Further evaluation of subgroup populations indicated statistical differences in learning models for African-American populations, female students, and for male students.

Gene expression-based biological test for major depressive disorder: an advanced study.

PubMed

Watanabe, Shin-Ya; Numata, Shusuke; Iga, Jun-Ichi; Kinoshita, Makoto; Umehara, Hidehiro; Ishii, Kazuo; Ohmori, Tetsuro

2017-01-01

Recently, we could distinguished patients with major depressive disorder (MDD) from nonpsychiatric controls with high accuracy using a panel of five gene expression markers ( ARHGAP24, HDAC5, PDGFC, PRNP , and SLC6A4 ) in leukocyte. In the present study, we examined whether this biological test is able to discriminate patients with MDD from those without MDD, including those with schizophrenia and bipolar disorder. We measured messenger ribonucleic acid expression levels of the aforementioned five genes in peripheral leukocytes in 17 patients with schizophrenia and 36 patients with bipolar disorder using quantitative real-time polymerase chain reaction (PCR), and we combined these expression data with our previous expression data of 25 patients with MDD and 25 controls. Subsequently, a linear discriminant function was developed for use in discriminating between patients with MDD and without MDD. This expression panel was able to segregate patients with MDD from those without MDD with a sensitivity and specificity of 64% and 67.9%, respectively. Further research to identify MDD-specific markers is needed to improve the performance of this biological test.

Validation of alternative methods for toxicity testing.

PubMed Central

Bruner, L H; Carr, G J; Curren, R D; Chamberlain, M

1998-01-01

Before nonanimal toxicity tests may be officially accepted by regulatory agencies, it is generally agreed that the validity of the new methods must be demonstrated in an independent, scientifically sound validation program. Validation has been defined as the demonstration of the reliability and relevance of a test method for a particular purpose. This paper provides a brief review of the development of the theoretical aspects of the validation process and updates current thinking about objectively testing the performance of an alternative method in a validation study. Validation of alternative methods for eye irritation testing is a specific example illustrating important concepts. Although discussion focuses on the validation of alternative methods intended to replace current in vivo toxicity tests, the procedures can be used to assess the performance of alternative methods intended for other uses. Images Figure 1 PMID:9599695

Methods of analysis by the U.S. Geological Survey National Water Quality Laboratory; preparation procedure for aquatic biological material determined for trace metals

USGS Publications Warehouse

Hoffman, Gerald L.

1996-01-01

A method for the chemical preparation of tissue samples that are subsequently analyzed for 22 trace metals is described. The tissue-preparation procedure was tested with three National Institute of Standards and Technology biological standard reference materials and two National Water Quality Laboratory homogenized biological materials. A low-temperature (85 degrees Celsius) nitric acid digestion followed by the careful addition of hydrogen peroxide (30-percent solution) is used to decompose the biological material. The solutions are evaporated to incipient dryness, reconstituted with 5 percent nitric acid, and filtered. After filtration the solutions were diluted to a known volume and analyzed by inductively coupled plasma-mass spectrometry (ICP-MS), inductively coupled plasma-atomic emission spectrometry (ICP-AES), and cold vapor-atomic absorption spectrophotometry (CV-AAS). Many of the metals were determined by both ICP-MS and ICP-AES. This report does not provide a detailed description of the instrumental procedures and conditions used with the three types of instrumentation for the quantitation of trace metals determined in this study. Statistical data regarding recovery, accuracy, and precision for individual trace metals determined in the biological material tested are summarized.

40 CFR 63.827 - Performance test methods.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 11 2014-07-01 2014-07-01 false Performance test methods. 63.827...) National Emission Standards for the Printing and Publishing Industry § 63.827 Performance test methods... test method for determining their values for approval by the Administrator in accordance with § 63.7(f...

40 CFR 63.1352 - Additional test methods.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 12 2014-07-01 2014-07-01 false Additional test methods. 63.1352... Monitoring and Compliance Provisions § 63.1352 Additional test methods. (a) If you are conducting tests to... manufacturing facilities, for use in applicability determinations under § 63.1340, you may use Method 320 or...

Biology, host specificity tests, and risk assessment of the sawfly Heteroperreyia hubrichi, a potential biological control agent of Schinus terebinthifolius in Hawaii

USDA-ARS?s Scientific Manuscript database

Abstract. Heteroperreyia hubrichi Malaise (Hymenoptera: Pergidae), a foliage feeding sawfly of Schinus terebinthifolius Raddi (Sapindales: Anacardiaceae), was studied to assess its suitability as a classical biological control agent of this invasive weed in Hawaii. Nochoice host-specificity tests we...

Science Teacher Efficacy and Outcome Expectancy as Predictors of Students' End-of-Instruction (EOI) Biology I Test Scores

ERIC Educational Resources Information Center

Angle, Julie; Moseley, Christine

2009-01-01

The purpose of this study was to compare teacher efficacy beliefs of secondary Biology I teachers whose students' mean scores on the statewide End-of-Instruction (EOI) Biology I test met or exceeded the state academic proficiency level (Proficient Group) to teacher efficacy beliefs of secondary Biology I teachers whose students' mean scores on the…

Flight-Test Evaluation of Flutter-Prediction Methods

NASA Technical Reports Server (NTRS)

Lind, RIck; Brenner, Marty

2003-01-01

The flight-test community routinely spends considerable time and money to determine a range of flight conditions, called a flight envelope, within which an aircraft is safe to fly. The cost of determining a flight envelope could be greatly reduced if there were a method of safely and accurately predicting the speed associated with the onset of an instability called flutter. Several methods have been developed with the goal of predicting flutter speeds to improve the efficiency of flight testing. These methods include (1) data-based methods, in which one relies entirely on information obtained from the flight tests and (2) model-based approaches, in which one relies on a combination of flight data and theoretical models. The data-driven methods include one based on extrapolation of damping trends, one that involves an envelope function, one that involves the Zimmerman-Weissenburger flutter margin, and one that involves a discrete-time auto-regressive model. An example of a model-based approach is that of the flutterometer. These methods have all been shown to be theoretically valid and have been demonstrated on simple test cases; however, until now, they have not been thoroughly evaluated in flight tests. An experimental apparatus called the Aerostructures Test Wing (ATW) was developed to test these prediction methods.

Quantum chemical methods for the investigation of photoinitiated processes in biological systems: theory and applications.

PubMed

Dreuw, Andreas

2006-11-13

With the advent of modern computers and advances in the development of efficient quantum chemical computer codes, the meaningful computation of large molecular systems at a quantum mechanical level became feasible. Recent experimental effort to understand photoinitiated processes in biological systems, for instance photosynthesis or vision, at a molecular level also triggered theoretical investigations in this field. In this Minireview, standard quantum chemical methods are presented that are applicable and recently used for the calculation of excited states of photoinitiated processes in biological molecular systems. These methods comprise configuration interaction singles, the complete active space self-consistent field method, and time-dependent density functional theory and its variants. Semiempirical approaches are also covered. Their basic theoretical concepts and mathematical equations are briefly outlined, and their properties and limitations are discussed. Recent successful applications of the methods to photoinitiated processes in biological systems are described and theoretical tools for the analysis of excited states are presented.

40 CFR 63.694 - Testing methods and procedures.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 11 2014-07-01 2014-07-01 false Testing methods and procedures. 63.694....694 Testing methods and procedures. (a) This section specifies the testing methods and procedures... this subpart, the testing methods and procedures are specified in paragraph (b) of this section. (2) To...

40 CFR 59.207 - Test methods.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 6 2012-07-01 2012-07-01 false Test methods. 59.207 Section 59.207 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) NATIONAL... Compound Emission Standards for Consumer Products § 59.207 Test methods. Each manufacturer or importer...

40 CFR 59.207 - Test methods.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 5 2010-07-01 2010-07-01 false Test methods. 59.207 Section 59.207 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) NATIONAL... Compound Emission Standards for Consumer Products § 59.207 Test methods. Each manufacturer or importer...

40 CFR 59.207 - Test methods.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 6 2014-07-01 2014-07-01 false Test methods. 59.207 Section 59.207 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) NATIONAL... Compound Emission Standards for Consumer Products § 59.207 Test methods. Each manufacturer or importer...

40 CFR 59.207 - Test methods.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 5 2011-07-01 2011-07-01 false Test methods. 59.207 Section 59.207 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) NATIONAL... Compound Emission Standards for Consumer Products § 59.207 Test methods. Each manufacturer or importer...

40 CFR 59.207 - Test methods.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 6 2013-07-01 2013-07-01 false Test methods. 59.207 Section 59.207 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) NATIONAL... Compound Emission Standards for Consumer Products § 59.207 Test methods. Each manufacturer or importer...

[Seed quality test methods of Paeonia suffruticosa].

PubMed

Cao, Ya-Yue; Zhu, Zai-Biao; Guo, Qiao-Sheng; Liu, Li; Wang, Chang-Lin

2014-11-01

In order to optimize the testing methods for Paeonia suffruticosa seed quality, and provide basis for establishing seed testing rules and seed quality standard of P. suffruticosa. The seed quality of P. suffruticosa from different producing areas was measured based on the related seed testing regulations. The seed testing methods for quality items of P. suffruticosa was established preliminarily. The samples weight of P. suffruticosa was at least 7 000 g for purity analysis and was at least 700 g for test. The phenotypic observation and size measurement were used for authenticity testing. The 1 000-seed weight was determined by 100-seed method, and the water content was carried out by low temperature drying method (10 hours). After soaking in distilled water for 24 h, the seeds was treated with different temperature stratifications of day and night (25 degrees C/20 degrees C, day/night) in the dark for 60 d. After soaking in the liquor of GA3 300 mg x L(-1) for 24 h, the P. suffruticos seeds were cultured in wet sand at 15 degrees C for 12-60 days for germination testing. Seed viability was tested by TlC method.

Test Methods for Robot Agility in Manufacturing.

PubMed

Downs, Anthony; Harrison, William; Schlenoff, Craig

2016-01-01

The paper aims to define and describe test methods and metrics to assess industrial robot system agility in both simulation and in reality. The paper describes test methods and associated quantitative and qualitative metrics for assessing robot system efficiency and effectiveness which can then be used for the assessment of system agility. The paper describes how the test methods were implemented in a simulation environment and real world environment. It also shows how the metrics are measured and assessed as they would be in a future competition. The test methods described in this paper will push forward the state of the art in software agility for manufacturing robots, allowing small and medium manufacturers to better utilize robotic systems. The paper fulfills the identified need for standard test methods to measure and allow for improvement in software agility for manufacturing robots.

Method for separating biological cells. [suspended in aqueous polymer systems

NASA Technical Reports Server (NTRS)

Brooks, D. E. (Inventor)

1980-01-01

A method for separating biological cells by suspending a mixed cell population in a two-phase polymer system is described. The polymer system consists of droplet phases with different surface potentials for which the cell populations exhibit different affinities. The system is subjected to an electrostatic field of sufficient intensity to cause migration of the droplets with an attendant separation of cells.

Evaluation of Immunoassays and General Biological Indicator Tests for Field Screening of Bacillus anthracis and Ricin

PubMed Central

Bartholomew, Rachel A.; Ozanich, Richard M.; Arce, Jennifer S.; Engelmann, Heather E.; Heredia-Langner, Alejandro; Hofstad, Beth A.; Hutchison, Janine R.; Jarman, Kristin; Melville, Angela M.; Victry, Kristin D.

2017-01-01

There is little published data on the performance of biological indicator tests and immunoassays that could be used by first responders to determine if a suspicious powder contains a potential biothreat agent. We evaluated a range of biological indicator tests, including 3 protein tests, 2 ATP tests, 1 DNA test, and 1 FTIR spectroscopy instrument for their ability to screen suspicious powders for Bacillus anthracis (B. anthracis) spores and ricin. We also evaluated 12 immunoassays (mostly lateral flow immunoassays) for their ability to screen for B. anthracis and ricin. We used a cost-effective, statistically based test plan that allows instruments to be evaluated at performance levels ranging from 0.85 to 0.95 lower confidence bound of the probability of detection at confidence levels of 80% to 95%. We also assessed interference with 22 common suspicious powders encountered in the field. The detection reproducibility for the biological indicators was evaluated at 108 B. anthracis spores and 62.5 μg ricin, and the immunoassay detection reproducibility was evaluated at 107 spores/mL (B. anthracis) and 0.1 μg/mL (ricin). Seven out of 12 immunoassays met our most stringent criteria for B. anthracis detection, while 9 out of 12 met our most stringent test criteria for ricin detection. Most of the immunoassays also detected ricin in 3 different crude castor seed preparations. Our testing results varied across products and sample preparations, indicating the importance of reviewing performance data for specific instruments and sample types of interest for the application in order to make informed decisions regarding the selection of biodetection equipment for field use. PMID:28192054

Evaluation of Immunoassays and General Biological Indicator Tests for Field Screening of Bacillus anthracis and Ricin.

PubMed

Bartholomew, Rachel A; Ozanich, Richard M; Arce, Jennifer S; Engelmann, Heather E; Heredia-Langner, Alejandro; Hofstad, Beth A; Hutchison, Janine R; Jarman, Kristin; Melville, Angela M; Victry, Kristin D; Bruckner-Lea, Cynthia J

There is little published data on the performance of biological indicator tests and immunoassays that could be used by first responders to determine if a suspicious powder contains a potential biothreat agent. We evaluated a range of biological indicator tests, including 3 protein tests, 2 ATP tests, 1 DNA test, and 1 FTIR spectroscopy instrument for their ability to screen suspicious powders for Bacillus anthracis (B. anthracis) spores and ricin. We also evaluated 12 immunoassays (mostly lateral flow immunoassays) for their ability to screen for B. anthracis and ricin. We used a cost-effective, statistically based test plan that allows instruments to be evaluated at performance levels ranging from 0.85 to 0.95 lower confidence bound of the probability of detection at confidence levels of 80% to 95%. We also assessed interference with 22 common suspicious powders encountered in the field. The detection reproducibility for the biological indicators was evaluated at 10 8 B. anthracis spores and 62.5 μg ricin, and the immunoassay detection reproducibility was evaluated at 10 7 spores/mL (B. anthracis) and 0.1 μg/mL (ricin). Seven out of 12 immunoassays met our most stringent criteria for B. anthracis detection, while 9 out of 12 met our most stringent test criteria for ricin detection. Most of the immunoassays also detected ricin in 3 different crude castor seed preparations. Our testing results varied across products and sample preparations, indicating the importance of reviewing performance data for specific instruments and sample types of interest for the application in order to make informed decisions regarding the selection of biodetection equipment for field use.

[The assessment of biological maturation for talent selection - which method can be used?].

PubMed

Müller, L; Müller, E; Hildebrandt, C; Kapelari, K; Raschner, C

2015-03-01

. Approximately 95 % of the points in the plot should lie within the limits; then the concordance between the two methods of measurement is given 28. Additionally, intraclass correlation coefficients (ICC(3,1); two-way-mixed, total agreement) were calculated between difference in APHV and difference SA-CA. Chi²-tests were used to assess the difference in the percentage of pupils classified as on time, early or late maturing between the classifications based on the SA and on APHV, respectively. The level of significance was set at p < 0.05 and for highly significant at p < 0.01. All of the calculations were performed using PASW Statistics V.21.0. Chi²-tests did not show any significant differences (p = 0.404) in the percentage of participants classified as on time, early or late maturing between the two classifications based on SA and on APHV, respectively, neither for the total sample, nor for the two groups ski racers and non-athletes. The Bland-Altman analysis showed that more than 95 % of the points in the plot lie within the limits; consequently, there is concordance between the two methods with regard to estimating biological maturation. The ICC(3,1) statistics showed a highly significant correlation: p = 0.002, ICC (95 % CI) = 0.48 (0.13 - 0.69). The prediction equations to determine APHV seem to be a valid method of assessing the biological maturity status of youths aged 10 - 13 years. The percentage of pupils classified as on time, early or late maturing did not differ significantly between the classifications based on the two methods. Also the Bland-Altman analysis proved the concordance between the two methods. The RAE could be influenced and strengthened by the biological age in sports in which advantages in maturity parameters are important. Athletes born early in the selection year, who are also at the same time advanced in maturity, might be advantaged in the selection process. However, since the prediction equations seem to be valid

Bayes in biological anthropology.

PubMed

Konigsberg, Lyle W; Frankenberg, Susan R

2013-12-01

In this article, we both contend and illustrate that biological anthropologists, particularly in the Americas, often think like Bayesians but act like frequentists when it comes to analyzing a wide variety of data. In other words, while our research goals and perspectives are rooted in probabilistic thinking and rest on prior knowledge, we often proceed to use statistical hypothesis tests and confidence interval methods unrelated (or tenuously related) to the research questions of interest. We advocate for applying Bayesian analyses to a number of different bioanthropological questions, especially since many of the programming and computational challenges to doing so have been overcome in the past two decades. To facilitate such applications, this article explains Bayesian principles and concepts, and provides concrete examples of Bayesian computer simulations and statistics that address questions relevant to biological anthropology, focusing particularly on bioarchaeology and forensic anthropology. It also simultaneously reviews the use of Bayesian methods and inference within the discipline to date. This article is intended to act as primer to Bayesian methods and inference in biological anthropology, explaining the relationships of various methods to likelihoods or probabilities and to classical statistical models. Our contention is not that traditional frequentist statistics should be rejected outright, but that there are many situations where biological anthropology is better served by taking a Bayesian approach. To this end it is hoped that the examples provided in this article will assist researchers in choosing from among the broad array of statistical methods currently available. Copyright © 2013 Wiley Periodicals, Inc.

40 CFR 60.675 - Test methods and procedures.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 6 2011-07-01 2011-07-01 false Test methods and procedures. 60.675... Mineral Processing Plants § 60.675 Test methods and procedures. (a) In conducting the performance tests required in § 60.8, the owner or operator shall use as reference methods and procedures the test methods in...

40 CFR 60.503 - Test methods and procedures.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 7 2014-07-01 2014-07-01 false Test methods and procedures. 60.503... Terminals § 60.503 Test methods and procedures. (a) In conducting the performance tests required in § 60.8, the owner or operator shall use as reference methods and procedures the test methods in appendix A of...

40 CFR 60.503 - Test methods and procedures.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 6 2011-07-01 2011-07-01 false Test methods and procedures. 60.503... Terminals § 60.503 Test methods and procedures. (a) In conducting the performance tests required in § 60.8, the owner or operator shall use as reference methods and procedures the test methods in appendix A of...

40 CFR 60.503 - Test methods and procedures.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 7 2013-07-01 2013-07-01 false Test methods and procedures. 60.503... Terminals § 60.503 Test methods and procedures. (a) In conducting the performance tests required in § 60.8, the owner or operator shall use as reference methods and procedures the test methods in appendix A of...

40 CFR 60.503 - Test methods and procedures.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 7 2012-07-01 2012-07-01 false Test methods and procedures. 60.503... Terminals § 60.503 Test methods and procedures. (a) In conducting the performance tests required in § 60.8, the owner or operator shall use as reference methods and procedures the test methods in appendix A of...

40 CFR 60.503 - Test methods and procedures.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 6 2010-07-01 2010-07-01 false Test methods and procedures. 60.503... Terminals § 60.503 Test methods and procedures. (a) In conducting the performance tests required in § 60.8, the owner or operator shall use as reference methods and procedures the test methods in appendix A of...

[Comparative cost analysis of molecular biology methods in the diagnosis of sarcomas].

PubMed

Baffert, Sandrine; Italiano, Antoine; Pierron, Gaëlle; Traoré, Marie-Angèle; Rapp, Jocelyn; Escande, Fabienne; Ghnassia, Jean-Pierre; Terrier, Philippe; Voegeli, Anne-Claire; Ranchere-Vince, Dominique; Coindre, Jean-Michel; Pedeutour, Florence

2013-10-01

Sarcomas represent a complex and heterogeneous group of rare malignant tumors and their correct diagnosis is often difficult. Recent molecular biological techniques have been of great diagnostic use and there is a need to assess the cost of these procedures in routine clinical practice. Using prospective and observational data from eight molecular biology laboratories in France, we used "microcosting" method to assess the cost of molecular biological techniques in the diagnosis of five types of sarcoma. The mean cost of fluorescence in situ hybridization (FISH) was 318 € (273-393) per sample; mean reverse transcription polymerase chain reaction (RT-PCR) cost ranged from 300 € (229-481) per formalin-fixed, paraffin-embedded specimen to 258 € (213-339) per frozen specimen; mean quantitative polymerase chain reaction (Q-PCR) cost was 184 € (112-229) and mean CGH-array cost was 332 € (329-335). The cost of these recently implemented techniques varied according to the type of sarcoma; the method of tissue collection and local organizational factors including the level of local expertise and investment. The cost of molecular diagnostic techniques needs to be balanced against their respective performance.

SLEPR: A Sample-Level Enrichment-Based Pathway Ranking Method — Seeking Biological Themes through Pathway-Level Consistency

PubMed Central

Yi, Ming; Stephens, Robert M.

2008-01-01

Analysis of microarray and other high throughput data often involves identification of genes consistently up or down-regulated across samples as the first step in extraction of biological meaning. This gene-level paradigm can be limited as a result of valid sample fluctuations and biological complexities. In this report, we describe a novel method, SLEPR, which eliminates this limitation by relying on pathway-level consistencies. Our method first selects the sample-level differentiated genes from each individual sample, capturing genes missed by other analysis methods, ascertains the enrichment levels of associated pathways from each of those lists, and then ranks annotated pathways based on the consistency of enrichment levels of individual samples from both sample classes. As a proof of concept, we have used this method to analyze three public microarray datasets with a direct comparison with the GSEA method, one of the most popular pathway-level analysis methods in the field. We found that our method was able to reproduce the earlier observations with significant improvements in depth of coverage for validated or expected biological themes, but also produced additional insights that make biological sense. This new method extends existing analyses approaches and facilitates integration of different types of HTP data. PMID:18818771

Topic modeling for cluster analysis of large biological and medical datasets

PubMed Central

2014-01-01

Background 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. Results 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. Conclusion 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

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

PubMed

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

Analysis of Nonstationary Time Series for Biological Rhythms Research.

PubMed

Leise, Tanya L

2017-06-01

This article is part of a Journal of Biological Rhythms series exploring analysis and statistics topics relevant to researchers in biological rhythms and sleep research. The goal is to provide an overview of the most common issues that arise in the analysis and interpretation of data in these fields. In this article on time series analysis for biological rhythms, we describe some methods for assessing the rhythmic properties of time series, including tests of whether a time series is indeed rhythmic. Because biological rhythms can exhibit significant fluctuations in their period, phase, and amplitude, their analysis may require methods appropriate for nonstationary time series, such as wavelet transforms, which can measure how these rhythmic parameters change over time. We illustrate these methods using simulated and real time series.

Test Methods for Robot Agility in Manufacturing

PubMed Central

Downs, Anthony; Harrison, William; Schlenoff, Craig

2017-01-01

Purpose The paper aims to define and describe test methods and metrics to assess industrial robot system agility in both simulation and in reality. Design/methodology/approach The paper describes test methods and associated quantitative and qualitative metrics for assessing robot system efficiency and effectiveness which can then be used for the assessment of system agility. Findings The paper describes how the test methods were implemented in a simulation environment and real world environment. It also shows how the metrics are measured and assessed as they would be in a future competition. Practical Implications The test methods described in this paper will push forward the state of the art in software agility for manufacturing robots, allowing small and medium manufacturers to better utilize robotic systems. Originality / value The paper fulfills the identified need for standard test methods to measure and allow for improvement in software agility for manufacturing robots. PMID:28203034

Method and apparatus for testing microfilaments

DOEpatents

Schleitweiler, P.M.; Merten, C.W. Jr.

1995-08-01

A method and apparatus are disclosed for testing tensile strength of microfilaments. Fibers as small as 0.001 inch in diameter and 0.04 inches in length have been tested, although the method and apparatus of the invention are capable of testing fibers of smaller diameter and length. The invention utilizes a method wherein one or both ends of a microfilament is gripped using resin which is softened sufficiently to accept an end of the microfilament and then allowed to harden. The invention also employs the use of a translation stage capable of controlled three-dimensional movement suited to facilitating gripping of the microfilament. 2 figs.

Method and apparatus for testing microfilaments

DOEpatents

Schleitweiler, Patrick M.; Merten, Jr., Charles W.

1995-08-01

A method and apparatus are disclosed for testing tensile strength of microfilaments. Fibers as small as 0.001 inch in diameter and 0.04 inches in length have been tested, although the method and apparatus of the invention are capable of testing fibers of smaller diameter and length. The invention utilizes a method wherein one or both ends of a microfilament is gripped using resin which is softened sufficiently to accept an end of the microfilament and then allowed to harden. The invention also employs the use of a translation stage capable of controlled three-dimensional movement suited to facilitating gripping of the microfilament.

Fluorescence background removal method for biological Raman spectroscopy based on empirical mode decomposition.

PubMed

Leon-Bejarano, Maritza; Dorantes-Mendez, Guadalupe; Ramirez-Elias, Miguel; Mendez, Martin O; Alba, Alfonso; Rodriguez-Leyva, Ildefonso; Jimenez, M

2016-08-01

Raman spectroscopy of biological tissue presents fluorescence background, an undesirable effect that generates false Raman intensities. This paper proposes the application of the Empirical Mode Decomposition (EMD) method to baseline correction. EMD is a suitable approach since it is an adaptive signal processing method for nonlinear and non-stationary signal analysis that does not require parameters selection such as polynomial methods. EMD performance was assessed through synthetic Raman spectra with different signal to noise ratio (SNR). The correlation coefficient between synthetic Raman spectra and the recovered one after EMD denoising was higher than 0.92. Additionally, twenty Raman spectra from skin were used to evaluate EMD performance and the results were compared with Vancouver Raman algorithm (VRA). The comparison resulted in a mean square error (MSE) of 0.001554. High correlation coefficient using synthetic spectra and low MSE in the comparison between EMD and VRA suggest that EMD could be an effective method to remove fluorescence background in biological Raman spectra.

16 CFR 1513.4 - Test methods.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 16 Commercial Practices 2 2010-01-01 2010-01-01 false Test methods. 1513.4 Section 1513.4 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION FEDERAL HAZARDOUS SUBSTANCES ACT REGULATIONS REQUIREMENTS FOR BUNK BEDS § 1513.4 Test methods. (a) Guardrails (see § 1513.3(a)(6)). With no mattress on the...

16 CFR 1513.4 - Test methods.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 16 Commercial Practices 2 2014-01-01 2014-01-01 false Test methods. 1513.4 Section 1513.4 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION FEDERAL HAZARDOUS SUBSTANCES ACT REGULATIONS REQUIREMENTS FOR BUNK BEDS § 1513.4 Test methods. (a) Guardrails (see § 1513.3(a)(6)). With no mattress on the...

16 CFR 1513.4 - Test methods.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 16 Commercial Practices 2 2011-01-01 2011-01-01 false Test methods. 1513.4 Section 1513.4 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION FEDERAL HAZARDOUS SUBSTANCES ACT REGULATIONS REQUIREMENTS FOR BUNK BEDS § 1513.4 Test methods. (a) Guardrails (see § 1513.3(a)(6)). With no mattress on the...

16 CFR 1213.4 - Test methods.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 16 Commercial Practices 2 2012-01-01 2012-01-01 false Test methods. 1213.4 Section 1213.4 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION CONSUMER PRODUCT SAFETY ACT REGULATIONS SAFETY STANDARD FOR ENTRAPMENT HAZARDS IN BUNK BEDS § 1213.4 Test methods. (a) Guardrails (see § 1213.3(a)(6...

16 CFR 1213.4 - Test methods.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 16 Commercial Practices 2 2011-01-01 2011-01-01 false Test methods. 1213.4 Section 1213.4 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION CONSUMER PRODUCT SAFETY ACT REGULATIONS SAFETY STANDARD FOR ENTRAPMENT HAZARDS IN BUNK BEDS § 1213.4 Test methods. (a) Guardrails (see § 1213.3(a)(6...

16 CFR 1513.4 - Test methods.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 16 Commercial Practices 2 2012-01-01 2012-01-01 false Test methods. 1513.4 Section 1513.4 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION FEDERAL HAZARDOUS SUBSTANCES ACT REGULATIONS REQUIREMENTS FOR BUNK BEDS § 1513.4 Test methods. (a) Guardrails (see § 1513.3(a)(6)). With no mattress on the...

16 CFR 1213.4 - Test methods.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 16 Commercial Practices 2 2010-01-01 2010-01-01 false Test methods. 1213.4 Section 1213.4 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION CONSUMER PRODUCT SAFETY ACT REGULATIONS SAFETY STANDARD FOR ENTRAPMENT HAZARDS IN BUNK BEDS § 1213.4 Test methods. (a) Guardrails (see § 1213.3(a)(6...

16 CFR 1213.4 - Test methods.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 16 Commercial Practices 2 2014-01-01 2014-01-01 false Test methods. 1213.4 Section 1213.4 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION CONSUMER PRODUCT SAFETY ACT REGULATIONS SAFETY STANDARD FOR ENTRAPMENT HAZARDS IN BUNK BEDS § 1213.4 Test methods. (a) Guardrails (see § 1213.3(a)(6...

The effects of co-teaching on student test performance and attitudes towards science in high school biology

NASA Astrophysics Data System (ADS)

Cole, Virginia Scott

Reform efforts in response to the inclusion of students with disabilities into general education classrooms have become necessary to shift students' placements into the science classroom. An investigation into the effects of co-teaching in high school biology classrooms was conducted to explore the impact of two models of co-teaching on biology students' achievement and their attitudes towards science. Quantitative data were collected using a diagnostic exam, student chapter test scores, and the Scientific Attitude Inventory II (SAI II) (Moore & Foy, 1997). Additionally, qualitative data were collected from student and teacher interviews, as well as reflections recorded by the general education participating teacher. The study occurred at a predominantly African-American high school in an Alabama city school with approximately 700 students. The population for the study was composed of 62 high school biology students, with 18 of those students placed inclusively in the biology classroom as a result of No Child Left Behind legislation. The participating teachers consisted of one general education biology teacher and one highly qualified, science special education teacher. Twelve students, along with the special education participating teacher, were interviewed and provided qualitative data after completion of the study. The general education teacher provided teacher reflection responses to contribute qualitatively on the impact of co-teaching in high school biology. Quantitative data analysis was performed using descriptive statistics, ANOVA, and paired samples t tests analyses. ANOVA results revealed that there were no changes in student test scores of achievement due to the models of instruction implemented. The implementation of no co-teaching, station teaching, and the one-teaching, one-drifting co-teaching models of instruction did not result in significant changes in students' achievement. Furthermore, paired samples t tests revealed no change in students

Computational systems biology and dose-response modeling in relation to new directions in toxicity testing.

PubMed

Zhang, Qiang; Bhattacharya, Sudin; Andersen, Melvin E; Conolly, Rory B

2010-02-01

The new paradigm envisioned for toxicity testing in the 21st century advocates shifting from the current animal-based testing process to a combination of in vitro cell-based studies, high-throughput techniques, and in silico modeling. A strategic component of the vision is the adoption of the systems biology approach to acquire, analyze, and interpret toxicity pathway data. As key toxicity pathways are identified and their wiring details elucidated using traditional and high-throughput techniques, there is a pressing need to understand their qualitative and quantitative behaviors in response to perturbation by both physiological signals and exogenous stressors. The complexity of these molecular networks makes the task of understanding cellular responses merely by human intuition challenging, if not impossible. This process can be aided by mathematical modeling and computer simulation of the networks and their dynamic behaviors. A number of theoretical frameworks were developed in the last century for understanding dynamical systems in science and engineering disciplines. These frameworks, which include metabolic control analysis, biochemical systems theory, nonlinear dynamics, and control theory, can greatly facilitate the process of organizing, analyzing, and understanding toxicity pathways. Such analysis will require a comprehensive examination of the dynamic properties of "network motifs"--the basic building blocks of molecular circuits. Network motifs like feedback and feedforward loops appear repeatedly in various molecular circuits across cell types and enable vital cellular functions like homeostasis, all-or-none response, memory, and biological rhythm. These functional motifs and associated qualitative and quantitative properties are the predominant source of nonlinearities observed in cellular dose response data. Complex response behaviors can arise from toxicity pathways built upon combinations of network motifs. While the field of computational cell

Critical tests for determination of microbiological quality and biological activity in commercial vermicompost samples of different origins.

PubMed

Grantina-Ievina, Lelde; Andersone, Una; Berkolde-Pīre, Dace; Nikolajeva, Vizma; Ievinsh, Gederts

2013-12-01

The aim of the present paper was to show that differences in biological activity among commercially produced vermicompost samples can be found by using a relatively simple test system consisting of microorganism tests on six microbiological media and soilless seedling growth tests with four vegetable crop species. Significant differences in biological properties among analyzed samples were evident both at the level of microbial load as well as plant growth-affecting activity. These differences were mostly manufacturer- and feedstock-associated, but also resulted from storage conditions of vermicompost samples. A mature vermicompost sample that was produced from sewage sludge still contained considerable number of Escherichia coli. Samples from all producers contained several potentially pathogenic fungal species such as Aspergillus fumigatus, Pseudallescheria boidii, Pseudallescheria fimeti, Pseudallescheria minutispora, Scedosporium apiospermum, Scedosporium prolificans, Scopulariopsis brevicaulis, Stachybotrys chartarum, Geotrichum spp., Aphanoascus terreus, and Doratomyces columnaris. In addition, samples from all producers contained plant growth-promoting fungi from the genera Trichoderma and Mortierella. The described system can be useful both for functional studies aiming at understanding of factors affecting quality characteristics of vermicompost preparations and for routine testing of microbiological quality and biological activity of organic waste-derived composts and vermicomposts.

In silico experiment system for testing hypothesis on gene functions using three condition specific biological networks.

PubMed

Lee, Chai-Jin; Kang, Dongwon; Lee, Sangseon; Lee, Sunwon; Kang, Jaewoo; Kim, Sun

2018-05-25

Determining functions of a gene requires time consuming, expensive biological experiments. Scientists can speed up this experimental process if the literature information and biological networks can be adequately provided. In this paper, we present a web-based information system that can perform in silico experiments of computationally testing hypothesis on the function of a gene. A hypothesis that is specified in English by the user is converted to genes using a literature and knowledge mining system called BEST. Condition-specific TF, miRNA and PPI (protein-protein interaction) networks are automatically generated by projecting gene and miRNA expression data to template networks. Then, an in silico experiment is to test how well the target genes are connected from the knockout gene through the condition-specific networks. The test result visualizes path from the knockout gene to the target genes in the three networks. Statistical and information-theoretic scores are provided on the resulting web page to help scientists either accept or reject the hypothesis being tested. Our web-based system was extensively tested using three data sets, such as E2f1, Lrrk2, and Dicer1 knockout data sets. We were able to re-produce gene functions reported in the original research papers. In addition, we comprehensively tested with all disease names in MalaCards as hypothesis to show the effectiveness of our system. Our in silico experiment system can be very useful in suggesting biological mechanisms which can be further tested in vivo or in vitro. http://biohealth.snu.ac.kr/software/insilico/. Copyright © 2018 Elsevier Inc. All rights reserved.

40 CFR 63.344 - Performance test requirements and test methods.

Code of Federal Regulations, 2014 CFR

2014-07-01

... blanket type fume suppressants are used to control chromium emissions from a hard chromium electroplating... National Emission Standards for Chromium Emissions From Hard and Decorative Chromium Electroplating and Chromium Anodizing Tanks § 63.344 Performance test requirements and test methods. (a) Performance test...

40 CFR 63.344 - Performance test requirements and test methods.

Code of Federal Regulations, 2012 CFR

2012-07-01

... blanket type fume suppressants are used to control chromium emissions from a hard chromium electroplating... National Emission Standards for Chromium Emissions From Hard and Decorative Chromium Electroplating and Chromium Anodizing Tanks § 63.344 Performance test requirements and test methods. (a) Performance test...

40 CFR 63.344 - Performance test requirements and test methods.

Code of Federal Regulations, 2013 CFR

2013-07-01

... blanket type fume suppressants are used to control chromium emissions from a hard chromium electroplating... National Emission Standards for Chromium Emissions From Hard and Decorative Chromium Electroplating and Chromium Anodizing Tanks § 63.344 Performance test requirements and test methods. (a) Performance test...

Methods to Detect Nitric Oxide and its Metabolites in Biological Samples

PubMed Central

Bryan, Nathan S.; Grisham, Matthew B.

2007-01-01

Nitric oxide (NO) methodology is a complex and often confusing science and the focus of many debates and discussion concerning NO biochemistry. NO is involved in many physiological processes including regulation of blood pressure, immune response and neural communication. Therefore its accurate detection and quantification is critical to understanding health and disease. Due to the extremely short physiological half life of this gaseous free radical, alternative strategies for the detection of reaction products of NO biochemistry have been developed. The quantification of NO metabolites in biological samples provides valuable information with regards to in vivo NO production, bioavailability and metabolism. Simply sampling a single compartment such as blood or plasma may not always provide an accurate assessment of whole body NO status, particularly in tissues. Therefore, extrapolation of plasma or blood NO status to specific tissues of interest is no longer a valid approach. As a result, methods continue to be developed and validated which allow the detection and quantification of NO and NO-related products/metabolites in multiple compartments of experimental animals in vivo. The methods described in this review is not an exhaustive or comprehensive discussion of all methods available for the detection of NO but rather a description of the most commonly used and practical methods which allow accurate and sensitive quantification of NO products/metabolites in multiple biological matrices under normal physiological conditions. PMID:17664129

49 CFR 230.45 - Method of testing.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 4 2010-10-01 2010-10-01 false Method of testing. 230.45 Section 230.45 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL RAILROAD ADMINISTRATION... Steam Gauges § 230.45 Method of testing. Steam gauges shall be compared with an accurate test gauge or...

A Comparison of Two Low-Stakes Methods for Administering a Program-Level Biology Concept Assessment.

PubMed

Couch, Brian A; Knight, Jennifer K

2015-12-01

Concept assessments are used commonly in undergraduate science courses to assess student learning and diagnose areas of student difficulty. While most concept assessments align with the content of individual courses or course topics, some concept assessments have been developed for use at the programmatic level to gauge student progress and achievement over a series of courses or an entire major. The broad scope of a program-level assessment, which exceeds the content of any single course, creates several test administration issues, including finding a suitable time for students to take the assessment and adequately incentivizing student participation. These logistical considerations must also be weighed against test security and the ability of students to use unauthorized resources that could compromise test validity. To understand how potential administration methods affect student outcomes, we administered the Molecular Biology Capstone Assessment (MBCA) to three pairs of matched upper-division courses in two ways: an online assessment taken by students outside of class and a paper-based assessment taken during class. We found that overall test scores were not significantly different and that individual item difficulties were highly correlated between these two administration methods. However, in-class administration resulted in reduced completion rates of items at the end of the assessment. Taken together, these results suggest that an online, outside-of-class administration produces scores that are comparable to a paper-based, in-class format and has the added advantages that instructors do not have to dedicate class time and students are more likely to complete the entire assessment.

Valid methods: the quality assurance of test method development, validation, approval, and transfer for veterinary testing laboratories.

PubMed

Wiegers, Ann L

2003-07-01

Third-party accreditation is a valuable tool to demonstrate a laboratory's competence to conduct testing. Accreditation, internationally and in the United States, has been discussed previously. However, accreditation is only I part of establishing data credibility. A validated test method is the first component of a valid measurement system. Validation is defined as confirmation by examination and the provision of objective evidence that the particular requirements for a specific intended use are fulfilled. The international and national standard ISO/IEC 17025 recognizes the importance of validated methods and requires that laboratory-developed methods or methods adopted by the laboratory be appropriate for the intended use. Validated methods are therefore required and their use agreed to by the client (i.e., end users of the test results such as veterinarians, animal health programs, and owners). ISO/IEC 17025 also requires that the introduction of methods developed by the laboratory for its own use be a planned activity conducted by qualified personnel with adequate resources. This article discusses considerations and recommendations for the conduct of veterinary diagnostic test method development, validation, evaluation, approval, and transfer to the user laboratory in the ISO/IEC 17025 environment. These recommendations are based on those of nationally and internationally accepted standards and guidelines, as well as those of reputable and experienced technical bodies. They are also based on the author's experience in the evaluation of method development and transfer projects, validation data, and the implementation of quality management systems in the area of method development.

40 CFR 61.304 - Test methods and procedures.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 9 2013-07-01 2013-07-01 false Test methods and procedures. 61.304... Emissions From Benzene Transfer Operations § 61.304 Test methods and procedures. (a) The procedures for... testing equipment shall be prepared and installed as specified in the appropriate test methods. (2) The...

40 CFR 61.304 - Test methods and procedures.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 8 2011-07-01 2011-07-01 false Test methods and procedures. 61.304... Emissions From Benzene Transfer Operations § 61.304 Test methods and procedures. (a) The procedures for... testing equipment shall be prepared and installed as specified in the appropriate test methods. (2) The...

40 CFR 61.304 - Test methods and procedures.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 9 2014-07-01 2014-07-01 false Test methods and procedures. 61.304... Emissions From Benzene Transfer Operations § 61.304 Test methods and procedures. (a) The procedures for... testing equipment shall be prepared and installed as specified in the appropriate test methods. (2) The...

40 CFR 61.304 - Test methods and procedures.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 8 2010-07-01 2010-07-01 false Test methods and procedures. 61.304... Emissions From Benzene Transfer Operations § 61.304 Test methods and procedures. (a) The procedures for... testing equipment shall be prepared and installed as specified in the appropriate test methods. (2) The...

40 CFR 61.304 - Test methods and procedures.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 9 2012-07-01 2012-07-01 false Test methods and procedures. 61.304... Emissions From Benzene Transfer Operations § 61.304 Test methods and procedures. (a) The procedures for... testing equipment shall be prepared and installed as specified in the appropriate test methods. (2) The...

The stability of the reactive oxygen metabolites (d-ROMs) and biological antioxidant potential (BAP) tests on stored horse blood.

PubMed

Celi, P; Sullivan, M; Evans, D

2010-02-01

Increasing interest in the role of oxidative stress (OS) in equine medicine has highlighted the need to develop reliable methods to quantify it. In this study we describe the effect of refrigeration (at 4 degrees C) on the stability of the reactive oxygen metabolites (d-ROMs) and biological antioxidant potential (BAP) tests carried out on 15 healthy horses. Blood samples, collected from the jugular vein, were immediately placed on ice and analysed using both the d-ROMs and BAP tests. Samples were also refrigerated at 4 degrees C and tested after 3, 7 and 24 h. The average results were similar for up to 24 h and minimal variations were found for each horse. The findings suggest that refrigeration is suitable for preserving equine blood samples for these assays and this approach will provide veterinarians with a technically simple, reliable test to measure OS under field conditions. Copyright (c) 2008 Elsevier Ltd. All rights reserved.

Method of well testing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ringgenberg, P.D.; Burris, W.J.

1988-06-28

A method is described of flow testing a formation in a wellbore, comprising: providing a testing string including at least one annulus pressure responsive tool bore closure valve; providing a packer and setting the packer in the wellbore to seal thereacross; running the testing string into the wellbore with the tool bore closure valve in an open position; stinging into the set packer with the bottom of the testing string; increasing pressure a first time in the wellbore annulus around the testing string and above the set packer without cycling the tool bore closure valve; reducing pressure in the wellboremore » annulus; closing the tool bore closure valve responsive to the pressure reduction; increasing pressure a second time in the wellbore annulus; reopening the tool bore closure valve responsive to the second increase; and flowing fluids from the formation through the reopened tool bore closure valve.« less

Cellular phone-based image acquisition and quantitative ratiometric method for detecting cocaine and benzoylecgonine for biological and forensic applications.

PubMed

Cadle, Brian A; Rasmus, Kristin C; Varela, Juan A; Leverich, Leah S; O'Neill, Casey E; Bachtell, Ryan K; Cooper, Donald C

2010-01-01

Here we describe the first report of using low-cost cellular or web-based digital cameras to image and quantify standardized rapid immunoassay strips as a new point-of-care diagnostic and forensics tool with health applications. Quantitative ratiometric pixel density analysis (QRPDA) is an automated method requiring end-users to utilize inexpensive (∼ $1 USD/each) immunotest strips, a commonly available web or mobile phone camera or scanner, and internet or cellular service. A model is described whereby a central computer server and freely available IMAGEJ image analysis software records and analyzes the incoming image data with time-stamp and geo-tag information and performs the QRPDA using custom JAVA based macros (http://www.neurocloud.org). To demonstrate QRPDA we developed a standardized method using rapid immunotest strips directed against cocaine and its major metabolite, benzoylecgonine. Images from standardized samples were acquired using several devices, including a mobile phone camera, web cam, and scanner. We performed image analysis of three brands of commercially available dye-conjugated anti-cocaine/benzoylecgonine (COC/BE) antibody test strips in response to three different series of cocaine concentrations ranging from 0.1 to 300 ng/ml and BE concentrations ranging from 0.003 to 0.1 ng/ml. This data was then used to create standard curves to allow quantification of COC/BE in biological samples. Across all devices, QRPDA quantification of COC and BE proved to be a sensitive, economical, and faster alternative to more costly methods, such as gas chromatography-mass spectrometry, tandem mass spectrometry, or high pressure liquid chromatography. The limit of detection was determined to be between 0.1 and 5 ng/ml. To simulate conditions in the field, QRPDA was found to be robust under a variety of image acquisition and testing conditions that varied temperature, lighting, resolution, magnification and concentrations of biological fluid in a sample. To

Alternative Test Methods for Electronic Parts

NASA Technical Reports Server (NTRS)

Plante, Jeannette

2004-01-01

It is common practice within NASA to test electronic parts at the manufacturing lot level to demonstrate, statistically, that parts from the lot tested will not fail in service using generic application conditions. The test methods and the generic application conditions used have been developed over the years through cooperation between NASA, DoD, and industry in order to establish a common set of standard practices. These common practices, found in MIL-STD-883, MIL-STD-750, military part specifications, EEE-INST-002, and other guidelines are preferred because they are considered to be effective and repeatable and their results are usually straightforward to interpret. These practices can sometimes be unavailable to some NASA projects due to special application conditions that must be addressed, such as schedule constraints, cost constraints, logistical constraints, or advances in the technology that make the historical standards an inappropriate choice for establishing part performance and reliability. Alternate methods have begun to emerge and to be used by NASA programs to test parts individually or as part of a system, especially when standard lot tests cannot be applied. Four alternate screening methods will be discussed in this paper: Highly accelerated life test (HALT), forward voltage drop tests for evaluating wire-bond integrity, burn-in options during or after highly accelerated stress test (HAST), and board-level qualification.

COMPARISON OF ANALYTICAL METHODS FOR THE MEASUREMENT OF NON-VIABLE BIOLOGICAL PM

EPA Science Inventory

The paper describes a preliminary research effort to develop a methodology for the measurement of non-viable biologically based particulate matter (PM), analyzing for mold, dust mite, and ragweed antigens and endotoxins. Using a comparison of analytical methods, the research obj...

40 CFR 60.644 - Test methods and procedures.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 6 2011-07-01 2011-07-01 false Test methods and procedures. 60.644... Gas Processing: SO2 Emissions § 60.644 Test methods and procedures. (a) In conducting the performance tests required in § 60.8, the owner or operator shall use as reference methods and procedures the test...

Two Proposed Test Methods and Guidance for Antimicrobial Efficacy Testing

EPA Pesticide Factsheets

EPA is announcing the availability for public comment of two proposed test methods and associated testing guidance for evaluating antimicrobial pesticides against two biofilm bacteria, Pseudomonas aeruginosa and Staphylococcus aureus.

A direct solid sampling analysis method for the detection of silver nanoparticles in biological matrices.

PubMed

Feichtmeier, Nadine S; Ruchter, Nadine; Zimmermann, Sonja; Sures, Bernd; Leopold, Kerstin

2016-01-01

Engineered silver nanoparticles (AgNPs) are implemented in food contact materials due to their powerful antimicrobial properties and so may enter the human food chain. Hence, it is desirable to develop easy, sensitive and fast analytical screening methods for the determination of AgNPs in complex biological matrices. This study describes such a method using solid sampling high-resolution continuum source graphite furnace atomic absorption spectrometry (GFAAS). A recently reported novel evaluation strategy uses the atomization delay of the respective GFAAS signal as significant indicator for AgNPs and thereby allows discrimination of AgNPs from ionic silver (Ag(+)) in the samples without elaborate sample pre-treatment. This approach was further developed and applied to a variety of biological samples. Its suitability was approved by investigation of eight different food samples (parsley, apple, pepper, cheese, onion, pasta, maize meal and wheat flour) spiked with ionic silver or AgNPs. Furthermore, the migration of AgNPs from silver-impregnated polypropylene food storage boxes to fresh pepper was observed and a mussel sample obtained from a laboratory exposure study with silver was investigated. The differences in the atomization delays (Δt(ad)) between silver ions and 20-nm AgNPs vary in a range from -2.01 ± 1.38 s for maize meal to +2.06 ± 1.08 s for mussel tissue. However, the differences were significant in all investigated matrices and so indicative of the presence/absence of AgNPs. Moreover, investigation of model matrices (cellulose, gelatine and water) gives the first indication of matrix-dependent trends. Reproducibility and homogeneity tests confirm the applicability of the method.

Methods of Testing Thermal Insulation and Associated Test Apparatus

NASA Technical Reports Server (NTRS)

Fesmire, James E. (Inventor); Augustynowicz, Stanislaw D. (Inventor)

2004-01-01

The system and method for testing thermal insulation uses a cryostatic insulation tester having a vacuum chamber and a cold mass including a test chamber and upper and lower guard chambers adjacent thereto. The thermal insulation is positioned within the vacuum chamber and adjacent the cold mass. Cryogenic liquid is supplied to the test chamber, upper guard and lower guard to create a first gas layer in an upper portion of the lower guard chamber and a second gas layer in an upper portion of the test chamber. Temperature are sensed within the vacuum chamber to test the thermal insulation.

Hazardous Waste Test Methods / SW-846

EPA Pesticide Factsheets

The Resource Conservation and Recovery Act Test Methods for Evaluating Solid Waste: Physical/Chemical Methods (SW-846) provide guidance to analytical scientists, enforcement officers and method developers across a variety of sectors.

Methods for Equating Mental Tests.

DTIC Science & Technology

1984-11-01

1983) compared conventional and IRT methods for equating the Test of English as a Foreign Language ( TOEFL ) after chaining. Three conventional and...three IRT equating methods were examined in this study; two sections of TOEFL were each (separately) equated. The IRT methods included the following: (a...group. A separate base form was established for each of the six equating methods. Instead of equating the base-form TOEFL to itself, the last (eighth

Thermal well-test method

DOEpatents

Tsang, C.F.; Doughty, C.A.

1984-02-24

A well-test method involving injection of hot (or cold) water into a groundwater aquifer, or injecting cold water into a geothermal reservoir is disclosed. By making temperature measurements at various depths in one or more observation wells, certain properties of the aquifer are determined. These properties, not obtainable from conventional well test procedures, include the permeability anisotropy, and layering in the aquifer, and in-situ thermal properties. The temperature measurements at various depths are obtained from thermistors mounted in the observation wells.

Thermal well-test method

DOEpatents

Tsang, Chin-Fu; Doughty, Christine A.

1985-01-01

A well-test method involving injection of hot (or cold) water into a groundwater aquifer, or injecting cold water into a geothermal reservoir. By making temperature measurements at various depths in one or more observation wells, certain properties of the aquifer are determined. These properties, not obtainable from conventional well test procedures, include the permeability anisotropy, and layering in the aquifer, and in-situ thermal properties. The temperature measurements at various depths are obtained from thermistors mounted in the observation wells.

Physical and Biological Carbon Isotope Fractionation in Methane During Gas-Push-Pull-Tests

NASA Astrophysics Data System (ADS)

Gonzalez-Gil, G.; Schroth, M. H.; Gomez, K.; Zeyer, J.

2005-12-01

Stable isotope analyses have become a common tool to assess microbially-mediated processes in subsurface environments. We investigated if stable carbon isotope analysis can be used as a tool to complement gas push-pull tests (GPPTs), a novel technique that was recently developed and tested for the in-situ quantification of CH4 oxidation in soils. During a GPPT a gas mixture containing CH4, O2 and nonreactive tracer gases is injected into the soil, where CH4 is oxidized by indigenous microorganisms. Thereafter, a blend of injected gas mixture and soil air is extracted from the same location, and CH4 oxidation is quantified from an analysis of extracted CH4 and tracer gases. To assess the magnitude of physical isotope fractionation due to molecular diffusion during GPPTs, we conducted laboratory experiments in the absence of microbial activity in a 1m-high, 1m-diameter tank filled with dry sand. During the GPPTs' extraction phase, the isotopic composition of methane was analyzed. Results indicated strong carbon isotope fractionation (>20 per mil) during GPPTs. To assess the combined effect of physical and biological isotope fractionation, numerical simulations of GPPTs were conducted in which microbial CH4 isotope fractionation was simulated using first-order rate constants and microbial kinetic isotope fractionation factors previously reported for methane oxidation in landfill environments. Results of these simulations indicated that for small CH4 oxidation rates, overall isotope fractionation in CH4 is dominated by physical fractionation. Conversely, for high CH4 oxidation rates, overall fractionation is dominated by biological fractionation. Thus, CH4 isotope fractionation data alone from a single GPPT cannot be used to assess microbial CH4 oxidation. However, biological fractionation may be quantified if physical fractionation due to diffusion is known. This can be achieved by conducting two sequential GPPTs, with microbial activity being inhibited in the second

40 CFR 63.1208 - What are the test methods?

Code of Federal Regulations, 2010 CFR

2010-07-01

... test must be repeated. (5) The post-test analyte spike procedure of section 11.2.7 of ASTM Method D6735... 40 Protection of Environment 11 2010-07-01 2010-07-01 true What are the test methods? 63.1208... § 63.1208 What are the test methods? (a) [Reserved] (b) Test methods. You must use the following test...

40 CFR 63.1208 - What are the test methods?

Code of Federal Regulations, 2011 CFR

2011-07-01

... test must be repeated. (5) The post-test analyte spike procedure of section 11.2.7 of ASTM Method D6735... 40 Protection of Environment 11 2011-07-01 2011-07-01 false What are the test methods? 63.1208... § 63.1208 What are the test methods? (a) [Reserved] (b) Test methods. You must use the following test...

40 CFR 63.1208 - What are the test methods?

Code of Federal Regulations, 2012 CFR

2012-07-01

... test must be repeated. (5) The post-test analyte spike procedure of section 11.2.7 of ASTM Method D6735... 40 Protection of Environment 12 2012-07-01 2011-07-01 true What are the test methods? 63.1208... § 63.1208 What are the test methods? (a) [Reserved] (b) Test methods. You must use the following test...

40 CFR 63.805 - Performance test methods.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 11 2014-07-01 2014-07-01 false Performance test methods. 63.805...) National Emission Standards for Wood Furniture Manufacturing Operations § 63.805 Performance test methods. (a)(1) The EPA Method 311 of appendix A of part 63 shall be used in conjunction with formulation data...

40 CFR 75.22 - Reference test methods.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 17 2012-07-01 2012-07-01 false Reference test methods. 75.22 Section...) CONTINUOUS EMISSION MONITORING Operation and Maintenance Requirements § 75.22 Reference test methods. (a) The owner or operator shall use the following methods, which are found in appendices A-1 through A-4 to part...

Hearing Tests Based on Biologically Calibrated Mobile Devices: Comparison With Pure-Tone Audiometry

PubMed Central

Grysiński, Tomasz; Kręcicki, Tomasz

2018-01-01

Background Hearing screening tests based on pure-tone audiometry may be conducted on mobile devices, provided that the devices are specially calibrated for the purpose. Calibration consists of determining the reference sound level and can be performed in relation to the hearing threshold of normal-hearing persons. In the case of devices provided by the manufacturer, together with bundled headphones, the reference sound level can be calculated once for all devices of the same model. Objective This study aimed to compare the hearing threshold measured by a mobile device that was calibrated using a model-specific, biologically determined reference sound level with the hearing threshold obtained in pure-tone audiometry. Methods Trial participants were recruited offline using face-to-face prompting from among Otolaryngology Clinic patients, who own Android-based mobile devices with bundled headphones. The hearing threshold was obtained on a mobile device by means of an open access app, Hearing Test, with incorporated model-specific reference sound levels. These reference sound levels were previously determined in uncontrolled conditions in relation to the hearing threshold of normal-hearing persons. An audiologist-assisted self-measurement was conducted by the participants in a sound booth, and it involved determining the lowest audible sound generated by the device within the frequency range of 250 Hz to 8 kHz. The results were compared with pure-tone audiometry. Results A total of 70 subjects, 34 men and 36 women, aged 18-71 years (mean 36, standard deviation [SD] 11) participated in the trial. The hearing threshold obtained on mobile devices was significantly different from the one determined by pure-tone audiometry with a mean difference of 2.6 dB (95% CI 2.0-3.1) and SD of 8.3 dB (95% CI 7.9-8.7). The number of differences not greater than 10 dB reached 89% (95% CI 88-91), whereas the mean absolute difference was obtained at 6.5 dB (95% CI 6.2-6.9). Sensitivity and

Integrating Formal Methods and Testing 2002

NASA Technical Reports Server (NTRS)

Cukic, Bojan

2002-01-01

Traditionally, qualitative program verification methodologies and program testing are studied in separate research communities. None of them alone is powerful and practical enough to provide sufficient confidence in ultra-high reliability assessment when used exclusively. Significant advances can be made by accounting not only tho formal verification and program testing. but also the impact of many other standard V&V techniques, in a unified software reliability assessment framework. The first year of this research resulted in the statistical framework that, given the assumptions on the success of the qualitative V&V and QA procedures, significantly reduces the amount of testing needed to confidently assess reliability at so-called high and ultra-high levels (10-4 or higher). The coming years shall address the methodologies to realistically estimate the impacts of various V&V techniques to system reliability and include the impact of operational risk to reliability assessment. Combine formal correctness verification, process and product metrics, and other standard qualitative software assurance methods with statistical testing with the aim of gaining higher confidence in software reliability assessment for high-assurance applications. B) Quantify the impact of these methods on software reliability. C) Demonstrate that accounting for the effectiveness of these methods reduces the number of tests needed to attain certain confidence level. D) Quantify and justify the reliability estimate for systems developed using various methods.

A method for operative quantitative interpretation of multispectral images of biological tissues

NASA Astrophysics Data System (ADS)

Lisenko, S. A.; Kugeiko, M. M.

2013-10-01

A method for operative retrieval of spatial distributions of biophysical parameters of a biological tissue by using a multispectral image of it has been developed. The method is based on multiple regressions between linearly independent components of the diffuse reflection spectrum of the tissue and unknown parameters. Possibilities of the method are illustrated by an example of determining biophysical parameters of the skin (concentrations of melanin, hemoglobin and bilirubin, blood oxygenation, and scattering coefficient of the tissue). Examples of quantitative interpretation of the experimental data are presented.

Mining textural knowledge in biological images: Applications, methods and trends.

PubMed

Di Cataldo, Santa; Ficarra, Elisa

2017-01-01

Texture analysis is a major task in many areas of computer vision and pattern recognition, including biological imaging. Indeed, visual textures can be exploited to distinguish specific tissues or cells in a biological sample, to highlight chemical reactions between molecules, as well as to detect subcellular patterns that can be evidence of certain pathologies. This makes automated texture analysis fundamental in many applications of biomedicine, such as the accurate detection and grading of multiple types of cancer, the differential diagnosis of autoimmune diseases, or the study of physiological processes. Due to their specific characteristics and challenges, the design of texture analysis systems for biological images has attracted ever-growing attention in the last few years. In this paper, we perform a critical review of this important topic. First, we provide a general definition of texture analysis and discuss its role in the context of bioimaging, with examples of applications from the recent literature. Then, we review the main approaches to automated texture analysis, with special attention to the methods of feature extraction and encoding that can be successfully applied to microscopy images of cells or tissues. Our aim is to provide an overview of the state of the art, as well as a glimpse into the latest and future trends of research in this area.

Alternative Test Method for Olefins in Gasoline

EPA Pesticide Factsheets

This action proposes to allow for an additional alternative test method for olefins in gasoline, ASTM D6550-05. The allowance of this additional alternative test method will provide more flexibility to the regulated industry.

A new method of sweat testing: the CF Quantum®sweat test.

PubMed

Rock, Michael J; Makholm, Linda; Eickhoff, Jens

2014-09-01

Conventional methods of sweat testing are time consuming and have many steps that can and do lead to errors. This study compares conventional sweat testing to a new quantitative method, the CF Quantum® (CFQT) sweat test. This study tests the diagnostic accuracy and analytic validity of the CFQT. Previously diagnosed CF patients and patients who required a sweat test for clinical indications were invited to have the CFQT test performed. Both conventional sweat testing and the CFQT were performed bilaterally on the same day. Pairs of data from each test are plotted as a correlation graph and Bland-Altman plot. Sensitivity and specificity were calculated as well as the means and coefficient of variation by test and by extremity. After completing the study, subjects or their parents were asked for their preference of the CFQT and conventional sweat testing. The correlation coefficient between the CFQT and conventional sweat testing was 0.98 (95% confidence interval: 0.97-0.99). The sensitivity and specificity of the CFQT in diagnosing CF was 100% (95% confidence interval: 94-100%) and 96% (95% confidence interval: 89-99%), respectively. In one center in this three center multicenter study, there were higher sweat chloride values in patients with CF and also more tests that were invalid due to discrepant values between the two extremities. The percentage of invalid tests was higher in the CFQT method (16.5%) compared to conventional sweat testing (3.8%) (p < 0.001). In the post-test questionnaire, 88% of subjects/parents preferred the CFQT test. The CFQT is a fast and simple method of quantitative sweat chloride determination. This technology requires further refinement to improve the analytic accuracy at higher sweat chloride values and to decrease the number of invalid tests. Copyright © 2014 European Cystic Fibrosis Society. Published by Elsevier B.V. All rights reserved.

An novel frequent probability pattern mining algorithm based on circuit simulation method in uncertain biological networks

PubMed Central

2014-01-01

Background Motif mining has always been a hot research topic in bioinformatics. Most of current research on biological networks focuses on exact motif mining. However, due to the inevitable experimental error and noisy data, biological network data represented as the probability model could better reflect the authenticity and biological significance, therefore, it is more biological meaningful to discover probability motif in uncertain biological networks. One of the key steps in probability motif mining is frequent pattern discovery which is usually based on the possible world model having a relatively high computational complexity. Methods In this paper, we present a novel method for detecting frequent probability patterns based on circuit simulation in the uncertain biological networks. First, the partition based efficient search is applied to the non-tree like subgraph mining where the probability of occurrence in random networks is small. Then, an algorithm of probability isomorphic based on circuit simulation is proposed. The probability isomorphic combines the analysis of circuit topology structure with related physical properties of voltage in order to evaluate the probability isomorphism between probability subgraphs. The circuit simulation based probability isomorphic can avoid using traditional possible world model. Finally, based on the algorithm of probability subgraph isomorphism, two-step hierarchical clustering method is used to cluster subgraphs, and discover frequent probability patterns from the clusters. Results The experiment results on data sets of the Protein-Protein Interaction (PPI) networks and the transcriptional regulatory networks of E. coli and S. cerevisiae show that the proposed method can efficiently discover the frequent probability subgraphs. The discovered subgraphs in our study contain all probability motifs reported in the experiments published in other related papers. Conclusions The algorithm of probability graph isomorphism

40 CFR 63.1208 - What are the test methods?

Code of Federal Regulations, 2013 CFR

2013-07-01

... test must be repeated. (5) The post-test analyte spike procedure of section 11.2.7 of ASTM Method D6735... 40 Protection of Environment 12 2013-07-01 2013-07-01 false What are the test methods? 63.1208... Compliance Provisions § 63.1208 What are the test methods? (a) [Reserved] (b) Test methods. You must use the...

40 CFR 63.1208 - What are the test methods?

Code of Federal Regulations, 2014 CFR

2014-07-01

... test must be repeated. (5) The post-test analyte spike procedure of section 11.2.7 of ASTM Method D6735... 40 Protection of Environment 12 2014-07-01 2014-07-01 false What are the test methods? 63.1208... Compliance Provisions § 63.1208 What are the test methods? (a) [Reserved] (b) Test methods. You must use the...

Non-contact, Ultrasound-based Indentation Method for Measuring Elastic Properties of Biological Tissues Using Harmonic Motion Imaging (HMI)

PubMed Central

Vappou, Jonathan; Hou, Gary Y.; Marquet, Fabrice; Shahmirzadi, Danial; Grondin, Julien; Konofagou, Elisa E.

2015-01-01

Noninvasive measurement of mechanical properties of biological tissues in vivo could play a significant role in improving the current understanding of tissue biomechanics. In this study, we propose a method for measuring elastic properties non-invasively by using internal indentation as generated by Harmonic Motion Imaging (HMI). In HMI, an oscillating acoustic radiation force is produced by a focused ultrasound transducer at the focal region, and the resulting displacements are estimated by tracking RF signals acquired by an imaging transducer. In this study, the focal spot region was modeled as a rigid cylindrical piston that exerts an oscillatory, uniform internal force to the underlying tissue. The HMI elastic modulus EHMI was defined as the ratio of the applied force to the axial strain measured by 1D ultrasound imaging. The accuracy and the precision of the EHMI estimate were assessed both numerically and experimentally in polyacrylamide tissue-mimicking phantoms. Initial feasibility of this method in soft tissues was also shown in canine liver specimens in vitro. Very good correlation and agreement was found between the actual Young’s modulus and the HMI modulus in the numerical study (r2>0.99, relative error <10%) and on polyacrylamide gels (r2=0.95, relative error <24%). The average HMI modulus on five liver samples was found to EHMI=2.62±0.41 kPa, compared to EMechTesting=4.2±2.58 kPa measured by rheometry. This study has demonstrated for the first time the initial feasibility of a non-invasive, model-independent method to estimate local elastic properties of biological tissues at a submillimeter scale using an internal indentation-like approach. Ongoing studies include in vitro experiments in a larger number of samples and feasibility testing in in vivo models as well as pathological human specimens. PMID:25776065

An evolutionary firefly algorithm for the estimation of nonlinear biological model parameters.

PubMed

Abdullah, Afnizanfaizal; Deris, Safaai; Anwar, Sohail; Arjunan, Satya N V

2013-01-01

The development of accurate computational models of biological processes is fundamental to computational systems biology. These models are usually represented by mathematical expressions that rely heavily on the system parameters. The measurement of these parameters is often difficult. Therefore, they are commonly estimated by fitting the predicted model to the experimental data using optimization methods. The complexity and nonlinearity of the biological processes pose a significant challenge, however, to the development of accurate and fast optimization methods. We introduce a new hybrid optimization method incorporating the Firefly Algorithm and the evolutionary operation of the Differential Evolution method. The proposed method improves solutions by neighbourhood search using evolutionary procedures. Testing our method on models for the arginine catabolism and the negative feedback loop of the p53 signalling pathway, we found that it estimated the parameters with high accuracy and within a reasonable computation time compared to well-known approaches, including Particle Swarm Optimization, Nelder-Mead, and Firefly Algorithm. We have also verified the reliability of the parameters estimated by the method using an a posteriori practical identifiability test.

An Evolutionary Firefly Algorithm for the Estimation of Nonlinear Biological Model Parameters

PubMed Central

Abdullah, Afnizanfaizal; Deris, Safaai; Anwar, Sohail; Arjunan, Satya N. V.

2013-01-01

The development of accurate computational models of biological processes is fundamental to computational systems biology. These models are usually represented by mathematical expressions that rely heavily on the system parameters. The measurement of these parameters is often difficult. Therefore, they are commonly estimated by fitting the predicted model to the experimental data using optimization methods. The complexity and nonlinearity of the biological processes pose a significant challenge, however, to the development of accurate and fast optimization methods. We introduce a new hybrid optimization method incorporating the Firefly Algorithm and the evolutionary operation of the Differential Evolution method. The proposed method improves solutions by neighbourhood search using evolutionary procedures. Testing our method on models for the arginine catabolism and the negative feedback loop of the p53 signalling pathway, we found that it estimated the parameters with high accuracy and within a reasonable computation time compared to well-known approaches, including Particle Swarm Optimization, Nelder-Mead, and Firefly Algorithm. We have also verified the reliability of the parameters estimated by the method using an a posteriori practical identifiability test. PMID:23469172

40 CFR 264.1034 - Test methods and procedures.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 27 2013-07-01 2013-07-01 false Test methods and procedures. 264.1034... Air Emission Standards for Process Vents § 264.1034 Test methods and procedures. (a) Each owner or operator subject to the provisions of this subpart shall comply with the test methods and procedures...

40 CFR 264.1063 - Test methods and procedures.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 27 2013-07-01 2013-07-01 false Test methods and procedures. 264.1063... Air Emission Standards for Equipment Leaks § 264.1063 Test methods and procedures. (a) Each owner or operator subject to the provisions of this subpart shall comply with the test methods and procedures...

40 CFR 60.614 - Test methods and procedures.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 6 2011-07-01 2011-07-01 false Test methods and procedures. 60.614... Unit Processes § 60.614 Test methods and procedures. (a) For the purpose of demonstrating compliance... any performance test. (b) The following methods in appendix A to this part, except as provided under...

40 CFR 60.614 - Test methods and procedures.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 7 2013-07-01 2013-07-01 false Test methods and procedures. 60.614... Unit Processes § 60.614 Test methods and procedures. (a) For the purpose of demonstrating compliance... any performance test. (b) The following methods in appendix A to this part, except as provided under...

40 CFR 60.614 - Test methods and procedures.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 7 2014-07-01 2014-07-01 false Test methods and procedures. 60.614... Unit Processes § 60.614 Test methods and procedures. (a) For the purpose of demonstrating compliance... any performance test. (b) The following methods in appendix A to this part, except as provided under...

Methods of integrating Islamic values in teaching biology for shaping attitude and character

NASA Astrophysics Data System (ADS)

Listyono; Supardi, K. I.; Hindarto, N.; Ridlo, S.

2018-03-01

Learning is expected to develop the potential of learners to have the spiritual attitude: moral strength, self-control, personality, intelligence, noble character, as well as the skills needed by themselves, society, and nation. Implementation of role and morale in learning is an alternative way which is expected to answer the challenge. The solution offered is to inject student with religious material Islamic in learning biology. The content value of materials teaching biology includes terms of practical value, religious values, daily life value, socio-political value, and the value of art. In Islamic religious values (Qur'an and Hadith) various methods can touch human feelings, souls, and generate motivation. Integrating learning with Islamic value can be done by the deductive or inductive approach. The appropriate method of integration is the amtsal (analog) method, hiwar (dialog) method, targhib & tarhib (encouragement & warning) method, and example method (giving a noble role model / good example). The right strategy in integrating Islamic values is outlined in the design of lesson plan. The integration of Islamic values in lesson plan will facilitate teachers to build students' character because Islamic values can be implemented in every learning steps so students will be accustomed to receiving the character value in this integrated learning.

Biological optimization systems for enhancing photosynthetic efficiency and methods of use

DOEpatents

Hunt, Ryan W.; Chinnasamy, Senthil; Das, Keshav C.; de Mattos, Erico Rolim

2012-11-06

Biological optimization systems for enhancing photosynthetic efficiency and methods of use. Specifically, methods for enhancing photosynthetic efficiency including applying pulsed light to a photosynthetic organism, using a chlorophyll fluorescence feedback control system to determine one or more photosynthetic efficiency parameters, and adjusting one or more of the photosynthetic efficiency parameters to drive the photosynthesis by the delivery of an amount of light to optimize light absorption of the photosynthetic organism while providing enough dark time between light pulses to prevent oversaturation of the chlorophyll reaction centers are disclosed.

Current status of antifungal susceptibility testing methods.

PubMed

Arikan, Sevtap

2007-11-01

Antifungal susceptibility testing is a very dynamic field of medical mycology. Standardization of in vitro susceptibility tests by the Clinical and Laboratory Standards Institute (CLSI) and the European Committee for Antimicrobial Susceptibility Testing (EUCAST), and current availability of reference methods constituted the major remarkable steps in the field. Based on the established minimum inhibitory concentration (MIC) breakpoints, it is now possible to determine the susceptibilities of Candida strains to fluconazole, itraconazole, voriconazole, and flucytosine. Moreover, utility of fluconazole antifungal susceptibility tests as an adjunct in optimizing treatment of candidiasis has now been validated. While the MIC breakpoints and clinical significance of susceptibility testing for the remaining fungi and antifungal drugs remain yet unclear, modifications of the available methods as well as other methodologies are being intensively studied to overcome the present drawbacks and limitations. Among the other methods under investigation are Etest, colorimetric microdilution, agar dilution, determination of fungicidal activity, flow cytometry, and ergosterol quantitation. Etest offers the advantage of practical application and favorable agreement rates with the reference methods that are frequently above acceptable limits. However, MIC breakpoints for Etest remain to be evaluated and established. Development of commercially available, standardized colorimetric panels that are based on CLSI method parameters has added more to the antifungal susceptibility testing armamentarium. Flow cytometry, on the other hand, appears to offer rapid susceptibility testing but requires specified equipment and further evaluation for reproducibility and standardization. Ergosterol quantitation is another novel approach, which appears potentially beneficial particularly in discrimination of azole-resistant isolates from heavy trailers. The method is yet investigational and requires to

Introducing Statistical Inference to Biology Students through Bootstrapping and Randomization

ERIC Educational Resources Information Center

Lock, Robin H.; Lock, Patti Frazer

2008-01-01

Bootstrap methods and randomization tests are increasingly being used as alternatives to standard statistical procedures in biology. They also serve as an effective introduction to the key ideas of statistical inference in introductory courses for biology students. We discuss the use of such simulation based procedures in an integrated curriculum…

40 CFR 63.945 - Test methods and procedures.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 11 2014-07-01 2014-07-01 false Test methods and procedures. 63.945...) National Emission Standards for Surface Impoundments § 63.945 Test methods and procedures. (a) Procedure...) The test shall be conducted in accordance with the procedures specified in Method 21 of 40 CFR part 60...

Error response test system and method using test mask variable

NASA Technical Reports Server (NTRS)

Gender, Thomas K. (Inventor)

2006-01-01

An error response test system and method with increased functionality and improved performance is provided. The error response test system provides the ability to inject errors into the application under test to test the error response of the application under test in an automated and efficient manner. The error response system injects errors into the application through a test mask variable. The test mask variable is added to the application under test. During normal operation, the test mask variable is set to allow the application under test to operate normally. During testing, the error response test system can change the test mask variable to introduce an error into the application under test. The error response system can then monitor the application under test to determine whether the application has the correct response to the error.

Biological materials by design.

PubMed

Qin, Zhao; Dimas, Leon; Adler, David; Bratzel, Graham; Buehler, Markus J

2014-02-19

In this topical review we discuss recent advances in the use of physical insight into the way biological materials function, to design novel engineered materials 'from scratch', or from the level of fundamental building blocks upwards and by using computational multiscale methods that link chemistry to material function. We present studies that connect advances in multiscale hierarchical material structuring with material synthesis and testing, review case studies of wood and other biological materials, and illustrate how engineered fiber composites and bulk materials are designed, modeled, and then synthesized and tested experimentally. The integration of experiment and simulation in multiscale design opens new avenues to explore the physics of materials from a fundamental perspective, and using complementary strengths from models and empirical techniques. Recent developments in this field illustrate a new paradigm by which complex material functionality is achieved through hierarchical structuring in spite of simple material constituents.

Test Methods for Composites: A Status Report. Volume 2. Compression Test Methods

DTIC Science & Technology

1993-06-01

glass and Kevlar fibers in a phenolic matrix) were relatively thick (24 plies), and more importantly, failed at very low compressive strength levels...ICH LAMINATE SPECIMEN TEST METHOD ........................................ 29 2.4 RECOMMENDATIONS...Thickness in the Middle of the Gage Section, for Four Laminate Thicknesses [711 ................... 143 52. Axial Stress Distributions in an AS4/3502 Carbon

40 CFR 60.335 - Test methods and procedures.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 7 2012-07-01 2012-07-01 false Test methods and procedures. 60.335... Turbines § 60.335 Test methods and procedures. (a) The owner or operator shall conduct the performance tests required in § 60.8, using either (1) EPA Method 20, (2) ASTM D6522-00 (incorporated by reference...

40 CFR 60.335 - Test methods and procedures.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 6 2010-07-01 2010-07-01 false Test methods and procedures. 60.335... Turbines § 60.335 Test methods and procedures. (a) The owner or operator shall conduct the performance tests required in § 60.8, using either (1) EPA Method 20, (2) ASTM D6522-00 (incorporated by reference...

40 CFR 60.335 - Test methods and procedures.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 7 2013-07-01 2013-07-01 false Test methods and procedures. 60.335... Turbines § 60.335 Test methods and procedures. (a) The owner or operator shall conduct the performance tests required in § 60.8, using either (1) EPA Method 20, (2) ASTM D6522-00 (incorporated by reference...

40 CFR 60.335 - Test methods and procedures.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 7 2014-07-01 2014-07-01 false Test methods and procedures. 60.335... Turbines § 60.335 Test methods and procedures. (a) The owner or operator shall conduct the performance tests required in § 60.8, using either (1) EPA Method 20, (2) ASTM D6522-00 (incorporated by reference...

Antimicrobial Testing Methods & Procedures: MB-31

EPA Pesticide Factsheets

Information about ATMP - SOP Quantitative Disk Carrier Test Method (QCT-2) Modified for Testing Antimicrobial Products Against Spores of Clostridium difficile (ATCC 43598) on Inanimate, Hard, Non-porous Surfaces - MB-31-Final

Putting the Biological Species Concept to the Test: Using Mating Networks to Delimit Species

PubMed Central

Lagache, Lélia; Leger, Jean-Benoist; Daudin, Jean-Jacques; Petit, Rémy J.; Vacher, Corinne

2013-01-01

Although interfertility is the key criterion upon which Mayr’s biological species concept is based, it has never been applied directly to delimit species under natural conditions. Our study fills this gap. We used the interfertility criterion to delimit two closely related oak species in a forest stand by analyzing the network of natural mating events between individuals. The results reveal two groups of interfertile individuals connected by only few mating events. These two groups were largely congruent with those determined using other criteria (morphological similarity, genotypic similarity and individual relatedness). Our study, therefore, shows that the analysis of mating networks is an effective method to delimit species based on the interfertility criterion, provided that adequate network data can be assembled. Our study also shows that although species boundaries are highly congruent across methods of species delimitation, they are not exactly the same. Most of the differences stem from assignment of individuals to an intermediate category. The discrepancies between methods may reflect a biological reality. Indeed, the interfertility criterion is an environment-dependant criterion as species abundances typically affect rates of hybridization under natural conditions. Thus, the methods of species delimitation based on the interfertility criterion are expected to give results slightly different from those based on environment-independent criteria (such as the genotypic similarity criteria). However, whatever the criterion chosen, the challenge we face when delimiting species is to summarize continuous but non-uniform variations in biological diversity. The grade of membership model that we use in this study appears as an appropriate tool. PMID:23818990

Simple Test Functions in Meshless Local Petrov-Galerkin Methods

NASA Technical Reports Server (NTRS)

Raju, Ivatury S.

2016-01-01

Two meshless local Petrov-Galerkin (MLPG) methods based on two different trial functions but that use a simple linear test function were developed for beam and column problems. These methods used generalized moving least squares (GMLS) and radial basis (RB) interpolation functions as trial functions. These two methods were tested on various patch test problems. Both methods passed the patch tests successfully. Then the methods were applied to various beam vibration problems and problems involving Euler and Beck's columns. Both methods yielded accurate solutions for all problems studied. The simple linear test function offers considerable savings in computing efforts as the domain integrals involved in the weak form are avoided. The two methods based on this simple linear test function method produced accurate results for frequencies and buckling loads. Of the two methods studied, the method with radial basis trial functions is very attractive as the method is simple, accurate, and robust.

Rapid classification of biological components

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thompson, Vicki S.; Barrett, Karen B.; Key, Diane E.

A method is disclosed for analyzing a biological sample by antibody profiling for identifying forensic samples or for detecting the presence of an analyte. In an illustrative embodiment of the invention, the analyte is a drug, such as marijuana, Cocaine (crystalline tropane alkaloid), methamphetamine, methyltestosterone, or mesterolone. The method involves attaching antigens of the surface of a solid support in a preselected pattern to form an array wherein the locations of the antigens are known; contacting the array with the biological sample such that a portion of antibodies in the sample reacts with and binds to antigens in the array,more » thereby forming immune complexes; washing away antibodies that do not form immune complexes; and detecting the immune complexes, thereby forming an antibody profile. Forensic samples are identified by comparing a sample from an unknown source with a sample from a known source. Further, an assay, such as a test for illegal drug use, can be coupled to a test for identity such that the results of the assay can be positively correlated to a subject's identity.« less

Rapid classification of biological components

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thompson, Vicki S.; Barrett, Karen B.; Key, Diane E.

A method is disclosed for analyzing a biological sample by antibody profiling for identifying forensic samples or for detecting the presence of an analyte. In an illustrative embodiment of the invention, the analyte is a drug, such as marijuana, cocaine (crystalline tropane alkaloid), methamphetamine, methyltestosterone, or mesterolone. The method involves attaching antigens to a surface of a solid support in a preselected pattern to form an array wherein the locations of the antigens are known; contacting the array with the biological sample such that a portion of antibodies in the sample reacts with and binds to antigens in the array,more » thereby forming immune complexes; washing away antibodies that do not form immune complexes; and detecting the immune complexes, thereby forming an antibody profile. Forensic samples are identified by comparing a sample from an unknown source with a sample from a known source. Further, an assay, such as a test for illegal drug use, can be coupled to a test for identity such that the results of the assay can be positively correlated to a subject's identity.« less

Rapid classification of biological components

DOEpatents

Thompson, Vicki S.; Barrett, Karen B.; Key, Diane E.

2013-10-15

A method is disclosed for analyzing a biological sample by antibody profiling for identifying forensic samples or for detecting the presence of an analyte. In an illustrative embodiment of the invention, the analyte is a drug, such as marijuana, cocaine (crystalline tropane alkaloid), methamphetamine, methyltestosterone, or mesterolone. The method involves attaching antigens to a surface of a solid support in a preselected pattern to form an array wherein the locations of the antigens are known; contacting the array with the biological sample such that a portion of antibodies in the sample reacts with and binds to antigens in the array, thereby forming immune complexes; washing away antibodies that do not form immune complexes; and detecting the immune complexes, thereby forming an antibody profile. Forensic samples are identified by comparing a sample from an unknown source with a sample from a known source. Further, an assay, such as a test for illegal drug use, can be coupled to a test for identity such that the results of the assay can be positively correlated to a subject's identity.

Rapid classification of biological components

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thompson, Vicki S.; Barrett, Karen B.; Key, Diane E.

A method is disclosed for analyzing a biological sample by antibody profiling for identifying forensic samples or for detecting the presence of an analyte. In an illustrative embodiment of the invention, the analyte is a drug, such as marijuana, cocaine, methamphetamine, methyltestosterone, or mesterolone. The method involves attaching antigens to the surface of a solid support in a preselected pattern to form an array wherein the locations of the antigens are known; contacting the array with the biological sample such that a portion of antibodies in the sample reacts with and binds to antigens in the array, thereby forming immunemore » complexes; washing away antibodies that do form immune complexes; and detecting the immune complexes, thereby forming an antibody profile. Forensic samples are identified by comparing a sample from an unknown source with a sample from a known source. Further, an assay, such as a test for illegal drug use, can be coupled to a test for identity such that the results of the assay can be positively correlated to the subject's identity.« less

Effects of Scoring by Section and Independent Scorers' Patterns on Scorer Reliability in Biology Essay Tests

ERIC Educational Resources Information Center

Ebuoh, Casmir N.; Ezeudu, S. A.

2015-01-01

The study investigated the effects of scoring by section, use of independent scorers and conventional patterns on scorer reliability in Biology essay tests. It was revealed from literature review that conventional pattern of scoring all items at a time in essay tests had been criticized for not being reliable. The study was true experimental study…

Advanced Testing Method for Ground Thermal Conductivity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Xiaobing; Clemenzi, Rick; Liu, Su

A new method is developed that can quickly and more accurately determine the effective ground thermal conductivity (GTC) based on thermal response test (TRT) results. Ground thermal conductivity is an important parameter for sizing ground heat exchangers (GHEXs) used by geothermal heat pump systems. The conventional GTC test method usually requires a TRT for 48 hours with a very stable electric power supply throughout the entire test. In contrast, the new method reduces the required test time by 40%–60% or more, and it can determine GTC even with an unstable or intermittent power supply. Consequently, it can significantly reduce themore » cost of GTC testing and increase its use, which will enable optimal design of geothermal heat pump systems. Further, this new method provides more information about the thermal properties of the GHEX and the ground than previous techniques. It can verify the installation quality of GHEXs and has the potential, if developed, to characterize the heterogeneous thermal properties of the ground formation surrounding the GHEXs.« less

Cell biology perspectives in phage biology.

PubMed

Ansaldi, Mireille

2012-01-01

Cellular biology has long been restricted to large cellular organisms. However, as the resolution of microscopic methods increased, it became possible to study smaller cells, in particular bacterial cells. Bacteriophage biology is one aspect of bacterial cell biology that has recently gained insight from cell biology. Despite their small size, bacteriophages could be successfully labeled and their cycle studied in the host cells. This review aims to put together, although non-extensively, several cell biology studies that recently pushed the elucidation of key mechanisms in phage biology, such as the lysis-lysogeny decision in temperate phages or genome replication and transcription, one step further.

40 CFR 60.664 - Test methods and procedures.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 6 2011-07-01 2011-07-01 false Test methods and procedures. 60.664... Operations § 60.664 Test methods and procedures. (a) For the purpose of demonstrating compliance with § 60... performance test. (b) The following methods in appendix A to this part, except as provided under § 60.8(b...

40 CFR 60.664 - Test methods and procedures.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 7 2014-07-01 2014-07-01 false Test methods and procedures. 60.664... Operations § 60.664 Test methods and procedures. (a) For the purpose of demonstrating compliance with § 60... performance test. (b) The following methods in appendix A to this part, except as provided under § 60.8(b...

40 CFR 60.664 - Test methods and procedures.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 7 2013-07-01 2013-07-01 false Test methods and procedures. 60.664... Operations § 60.664 Test methods and procedures. (a) For the purpose of demonstrating compliance with § 60... performance test. (b) The following methods in appendix A to this part, except as provided under § 60.8(b...

Absorbing Software Testing into the Scrum Method

NASA Astrophysics Data System (ADS)

Tuomikoski, Janne; Tervonen, Ilkka

In this paper we study, how to absorb software testing into the Scrum method. We conducted the research as an action research during the years 2007-2008 with three iterations. The result showed that testing can and even should be absorbed to the Scrum method. The testing team was merged into the Scrum teams. The teams can now deliver better working software in a shorter time, because testing keeps track of the progress of the development. Also the team spirit is higher, because the Scrum team members are committed to the same goal. The biggest change from test manager’s point of view was the organized Product Owner Team. Test manager don’t have testing team anymore, and in the future all the testing tasks have to be assigned through the Product Backlog.

Biological relevance of CNV calling methods using familial relatedness including monozygotic twins.

PubMed

Castellani, Christina A; Melka, Melkaye G; Wishart, Andrea E; Locke, M Elizabeth O; Awamleh, Zain; O'Reilly, Richard L; Singh, Shiva M

2014-04-21

Studies involving the analysis of structural variation including Copy Number Variation (CNV) have recently exploded in the literature. Furthermore, CNVs have been associated with a number of complex diseases and neurodevelopmental disorders. Common methods for CNV detection use SNP, CNV, or CGH arrays, where the signal intensities of consecutive probes are used to define the number of copies associated with a given genomic region. These practices pose a number of challenges that interfere with the ability of available methods to accurately call CNVs. It has, therefore, become necessary to develop experimental protocols to test the reliability of CNV calling methods from microarray data so that researchers can properly discriminate biologically relevant data from noise. We have developed a workflow for the integration of data from multiple CNV calling algorithms using the same array results. It uses four CNV calling programs: PennCNV (PC), Affymetrix® Genotyping Console™ (AGC), Partek® Genomics Suite™ (PGS) and Golden Helix SVS™ (GH) to analyze CEL files from the Affymetrix® Human SNP 6.0 Array™. To assess the relative suitability of each program, we used individuals of known genetic relationships. We found significant differences in CNV calls obtained by different CNV calling programs. Although the programs showed variable patterns of CNVs in the same individuals, their distribution in individuals of different degrees of genetic relatedness has allowed us to offer two suggestions. The first involves the use of multiple algorithms for the detection of the largest possible number of CNVs, and the second suggests the use of PennCNV over all other methods when the use of only one software program is desirable.

SAS molecular tests Escherichia coli O157 detection kit. Performance tested method 031203.

PubMed

Bapanpally, Chandra; Montier, Laura; Khan, Shah; Kasra, Akif; Brunelle, Sharon L

2014-01-01

The SAS Molecular tests Escherichia coli O157 Detection method, a loop-mediated isothermal amplification method, performed as well as or better than the U.S. Department of Agriculture, Food Safety Inspection Service Microbiology Laboratory Guidebook and the U.S. Food and Drug Administration Bacteriological Analytical Manual reference methods for ground beef, beef trim, bagged mixed lettuce, and fresh spinach. Ground beef (30% fat, 25 g test portion) was validated for 7-8 h enrichment, leafy greens were validated in a 6-7 h enrichment, and ground beef (30% fat, 375 g composite test portion) and beef trim (375 g composite test portion) were validated in a 16-20 h enrichment. The method performance for meat and leafy green matrixes was also shown to be acceptable under conditions of co-enrichment with Salmonella. Thus, after a short co-enrichment step, ground beef, beef trim, lettuce, and spinach can be tested for both Salmonella and E. coli O157. The SAS Molecular tests Salmonella Detection Kit was validated using the same test portions as for the SAS Molecular tests E. coli O157 Detection Kit and those results are presented in a separate report. Inclusivity and exclusivity testing revealed no false negatives and no false positives among the 50 E. coli 0157 strains, including H7 and non-motile strains, and 30 non-E. coli O157 strains examined. Finally, the method was shown to be robust when variations to DNA extract hold time and DNA volume were varied. The method comparison and robustness data suggest a full 7 h enrichment time should be used for 25 g ground beef test portions.

Theory and practice of conventional adventitious virus testing.

PubMed

Gregersen, Jens-Peter

2011-01-01

CONFERENCE PROCEEDING Proceedings of the PDA/FDA Adventitious Viruses in Biologics: Detection and Mitigation Strategies Workshop in Bethesda, MD, USA; December 1-3, 2010 Guest Editors: Arifa Khan (Bethesda, MD), Patricia Hughes (Bethesda, MD) and Michael Wiebe (San Francisco, CA) For decades conventional tests in cell cultures and in laboratory animals have served as standard methods for broad-spectrum screening for adventitious viruses. New virus detection methods based on molecular biology have broadened and improved our knowledge about potential contaminating viruses and about the suitability of the conventional test methods. This paper summarizes and discusses practical aspects of conventional test schemes, such as detectability of various viruses, questionable or false-positive results, animal numbers needed, time and cost of testing, and applicability for rapidly changing starting materials. Strategies to improve the virus safety of biological medicinal products are proposed. The strategies should be based upon a flexible application of existing and new methods along with a scientifically based risk assessment. However, testing alone does not guarantee the absence of adventitious agents and must be accompanied by virus removing or virus inactivating process steps for critical starting materials, raw materials, and for the drug product.

A new multi-scale method to reveal hierarchical modular structures in biological networks.

PubMed

Jiao, Qing-Ju; Huang, Yan; Shen, Hong-Bin

2016-11-15

Biological networks are effective tools for studying molecular interactions. Modular structure, in which genes or proteins may tend to be associated with functional modules or protein complexes, is a remarkable feature of biological networks. Mining modular structure from biological networks enables us to focus on a set of potentially important nodes, which provides a reliable guide to future biological experiments. The first fundamental challenge in mining modular structure from biological networks is that the quality of the observed network data is usually low owing to noise and incompleteness in the obtained networks. The second problem that poses a challenge to existing approaches to the mining of modular structure is that the organization of both functional modules and protein complexes in networks is far more complicated than was ever thought. For instance, the sizes of different modules vary considerably from each other and they often form multi-scale hierarchical structures. To solve these problems, we propose a new multi-scale protocol for mining modular structure (named ISIMB) driven by a node similarity metric, which works in an iteratively converged space to reduce the effects of the low data quality of the observed network data. The multi-scale node similarity metric couples both the local and the global topology of the network with a resolution regulator. By varying this resolution regulator to give different weightings to the local and global terms in the metric, the ISIMB method is able to fit the shape of modules and to detect them on different scales. Experiments on protein-protein interaction and genetic interaction networks show that our method can not only mine functional modules and protein complexes successfully, but can also predict functional modules from specific to general and reveal the hierarchical organization of protein complexes.

Prediction and Testing of Biological Networks Underlying Intestinal Cancer

PubMed Central

Mariadason, John M.; Wang, Donghai; Augenlicht, Leonard H.; Chance, Mark R.

2010-01-01

Colorectal cancer progresses through an accumulation of somatic mutations, some of which reside in so-called “driver” genes that provide a growth advantage to the tumor. To identify points of intersection between driver gene pathways, we implemented a network analysis framework using protein interactions to predict likely connections – both precedented and novel – between key driver genes in cancer. We applied the framework to find significant connections between two genes, Apc and Cdkn1a (p21), known to be synergistic in tumorigenesis in mouse models. We then assessed the functional coherence of the resulting Apc-Cdkn1a network by engineering in vivo single node perturbations of the network: mouse models mutated individually at Apc (Apc1638N+/−) or Cdkn1a (Cdkn1a−/−), followed by measurements of protein and gene expression changes in intestinal epithelial tissue. We hypothesized that if the predicted network is biologically coherent (functional), then the predicted nodes should associate more specifically with dysregulated genes and proteins than stochastically selected genes and proteins. The predicted Apc-Cdkn1a network was significantly perturbed at the mRNA-level by both single gene knockouts, and the predictions were also strongly supported based on physical proximity and mRNA coexpression of proteomic targets. These results support the functional coherence of the proposed Apc-Cdkn1a network and also demonstrate how network-based predictions can be statistically tested using high-throughput biological data. PMID:20824133

In vitro testing of biological control agents on A1 and A2 isolates of Phytophthora ramorum

Treesearch

Marianne Elliott; Simon Shamoun

2008-01-01

Biological control products were tested in vitro with six isolates of Phytophthora ramorum. These isolates were geographically diverse and were selected based on their pathogenicity to detached Rhododendron leaves. In addition to five commercially available biocontrol products, nine species of Trichoderma were tested. The in vitro...

Drinking water test methods in crisis-afflicted areas: comparison of methods under field conditions.

PubMed

Merle, Roswitha; Bleul, Ingo; Schulenburg, Jörg; Kreienbrock, Lothar; Klein, Günter

2011-11-01

To simplify the testing of drinking water in crisis-afflicted areas (as in Kosovo in 2007), rapid test methods were compared with the standard test. For Escherichia coli and coliform pathogens, rapid tests were made available: Colilert(®)-18, P/A test with 4-methylumbelliferyl-β-D-glucoronid, and m-Endo Broth. Biochemical differentiation was carried out by Enterotube™ II. Enterococci were determined following the standard ISO test and by means of Enterolert™. Four hundred ninety-nine water samples were tested for E. coli and coliforms using four methods. Following the standard method, 20.8% (n=104) of the samples contained E. coli, whereas the rapid tests detected between 19.6% (m-Endo Broth, 92.0% concordance) and 20.0% (concordance: 93.6% Colilert-18 and 94.8% P/A-test) positive samples. Regarding coliforms, the percentage of concordant results ranged from 98.4% (P/A-test) to 99.0% (Colilert-18). Colilert-18 and m-Endo Broth detected even more positive samples than the standard method did. Enterococci were detected in 93 of 573 samples by the standard method, but in 92 samples by Enterolert (concordance: 99.5%). Considering the high-quality equipment and time requirements of the standard method, the use of rapid tests in crisis-afflicted areas is sufficiently reliable.

Evaluation of biological methods for a future methodological implementation of the Hazard criterion H14 'ecotoxic' in the European waste list (2000/532/EC).

PubMed

Moser, Heidrun; Roembke, Joerg; Donnevert, Gerhild; Becker, Roland

2011-02-01

The ecotoxicological characterization of waste is part of its assessment as hazardous or non-hazardous according to the European Waste List. For this classification 15 hazard criteria are derived from the Council Directive 91/689/EEC on hazardous waste. Some of the hazard criteria are based on the content of dangerous substances. The criterion H14 'ecotoxic' lacks of an assessment and testing strategy and no specific threshold values have been defined so far. Based on the recommendations of CEN guideline 14735 (2005), an international round robin test (ring test) was organized by the German Federal Environment Agency in order to define suitable test methods for the biological assessment of waste and waste eluates. A basic test battery, consisting of three aquatic and three terrestrial tests, was compiled. In addition, data were submitted for ten additional tests (five aquatic (including a genotoxicity test) and five terrestrial ones). The tests were performed with three representative waste types: an ash from an incineration plant, a soil containing high concentrations of organic contaminants (polycyclic aromatic hydrocarbons) and a preserved wood waste. The results of this ring test confirm that a combination of a battery of biological tests and chemical residual analysis is needed for an ecotoxicological characterization of wastes. With small modifications the basic test battery is considered to be well suitable for the hazard and risk assessment of wastes and waste eluates. All results and documents are accessible via a web-based data bank application.

Biological Concerns on the Selection of Animal Models for Teratogenic Testing.

PubMed

Alves-Pimenta, Sofia; Colaço, Bruno; Oliveira, Paula A; Venâncio, Carlos

2018-01-01

During pregnancy fetus can be exposed to a variety of chemicals which may induce abortion and malformations. Due to the amounts of new substances coming into the market every year, a high demand for a rapid, reliable, and cost-effective method to detect potential toxicity is necessary. Different species have been used as animal models for teratogen screening, most of them sharing similar development processes with humans. However, the application of embryology knowledge to teratology is hampered by the complexity of the reproduction processes.The present chapter outlines the essential development periods in different models, and highlights the similarities and differences between species, advantages and disadvantages of each group, and specific sensitivities for teratogenic tests. These models can be organized into the following categories: (1) invertebrate species such Caenorhabditis elegans and Drosophila melanogaster, which have become ideal for screening simple mechanisms in the early periods of reproductive cycle, allowing for rapid results and minor ethical concerns; (2) vertebrate nonmammalian species such Xenopus laevis and Danio rerio, important models to assess teratogenic potential in later development with fewer ethical requirements; and (3) the mammalian species Mus musculus, Rattus norvegicus, and Oryctolagus cuniculus, phylogenetically more close to humans, essential to assess complex specialized processes, that occur later in development.Rules for development toxicology tests require the use of mammalian species. However, ethical concerns and costs limit their use in large-scale screening. By contrast, invertebrate and vertebrate nonmammalian species are increasing as alternative animal models, as these organisms combine less ethical requirements, low costs and culture conditions compatible with large-scale screening. In contrast to the in vitro techniques, their main advantage is to allow for high-throughput screening in a whole-animal context

Multi-energy method of digital radiography for imaging of biological objects

NASA Astrophysics Data System (ADS)

Ryzhikov, V. D.; Naydenov, S. V.; Opolonin, O. D.; Volkov, V. G.; Smith, C. F.

2016-03-01

This work has been dedicated to the search for a new possibility to use multi-energy digital radiography (MER) for medical applications. Our work has included both theoretical and experimental investigations of 2-energy (2E) and 3- energy (3D) radiography for imaging the structure of biological objects. Using special simulation methods and digital analysis based on the X-ray interaction energy dependence for each element of importance to medical applications in the X-ray range of energy up to 150 keV, we have implemented a quasi-linear approximation for the energy dependence of the X-ray linear mass absorption coefficient μm (E) that permits us to determine the intrinsic structure of the biological objects. Our measurements utilize multiple X-ray tube voltages (50, 100, and 150 kV) with Al and Cu filters of different thicknesses to achieve 3-energy X-ray examination of objects. By doing so, we are able to achieve significantly improved imaging quality of the structure of the subject biological objects. To reconstruct and visualize the final images, we use both two-dimensional (2D) and three-dimensional (3D) palettes of identification. The result is a 2E and/or 3E representation of the object with color coding of each pixel according to the data outputs. Following the experimental measurements and post-processing, we produce a 3D image of the biological object - in the case of our trials, fragments or parts of chicken and turkey.

A review of chromatographic methods for the determination of water- and fat-soluble vitamins in biological fluids.

PubMed

Karaźniewicz-Łada, Marta; Główka, Anna

2016-01-01

Vitamins are an essential element of nutrition and thus contribute to human health. Vitamins catalyze many biochemical reactions and their lack or excess can cause health problems. Therefore, monitoring vitamin concentrations in plasma or other biological fluids may be useful in the diagnosis of various disorders as well as in the treatment process. Several chromatographic methods have been developed for the determination of these compounds in biological samples, including high-performance liquid chromatography with UV and fluorescence detection. Recently, high-performance liquid chromatography with tandem mass spectrometry methods have been widely used for the determination of vitamins in complex matrices because of their high sensitivity and selectivity. This method requires preconditioning of samples for analysis, including protein precipitation and/or various extraction techniques. The choice of method may depend on the desired cost, convenience, turnaround time, specificity, and accuracy of the information to be obtained. This article reviews the recently reported chromatographic methods used for determination of vitamins in biological fluids. Relevant papers published mostly during the last 5 years were identified by an extensive PubMed search using appropriate keywords. Particular attention was given to the preparation steps and extraction techniques. This report may be helpful in the selection of procedures that are appropriate for certain types of biological materials and analytes. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

40 CFR 63.849 - Test methods and procedures.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 11 2014-07-01 2014-07-01 false Test methods and procedures. 63.849... Test methods and procedures. (a) The owner or operator shall use the following reference methods to determine compliance with the applicable emission limits for TF and POM emissions: (1) Method 1 in appendix...

Predicting clinical biological responses to dental materials.

PubMed

Wataha, John C

2012-01-01

Methods used to measure and predict clinical biological responses to dental materials remain controversial, confusing, and to some extent, unsuccessful. The current paper reviews significant issues surrounding how we assess the biological safety of materials, with a historical summary and critical look at the biocompatibility literature. The review frames these issues from a U.S. perspective to some degree, but emphasizes their global nature and universal importance. The PubMed database and information from the U.S. Food and Drug Administration, International Standards Organization, and American National Standards Institute were searched for prominent literature addressing the definition of biocompatibility, types of biological tests employed, regulatory and standardization issues, and how biological tests are used together to establish the biological safety of materials. The search encompassed articles published in English from approximately 1965-2011. The review does not comprehensively review the literature, but highlights significant issues that confront the field. Years ago, tests for biological safety sought to establish material inertness as the measure of safety, a criterion that is now deemed naive; the definition of biocompatibility has broadened along with the roles for materials in patient oral health care. Controversies persist about how in vitro or animal tests should be used to evaluate the biological safety of materials for clinical use. Controlled clinical trials remain the single best measure of the clinical response to materials, but even these tests have significant limitations and are less useful to identify mechanisms that shape material performance. Practice-based research networks and practitioner databases are emerging as important supplements to controlled clinical trials, but their final utility remains to be determined. Today we ask materials to play increasingly sophisticated structural and therapeutic roles in patient treatment. To

Multipath interference test method for distributed amplifiers

NASA Astrophysics Data System (ADS)

Okada, Takahiro; Aida, Kazuo

2005-12-01

A method for testing distributed amplifiers is presented; the multipath interference (MPI) is detected as a beat spectrum between the multipath signal and the direct signal using a binary frequency shifted keying (FSK) test signal. The lightwave source is composed of a DFB-LD that is directly modulated by a pulse stream passing through an equalizer, and emits the FSK signal of the frequency deviation of about 430MHz at repetition rate of 80-100 kHz. The receiver consists of a photo-diode and an electrical spectrum analyzer (ESA). The base-band power spectrum peak appeared at the frequency of the FSK frequency deviation can be converted to amount of MPI using a calibration chart. The test method has improved the minimum detectable MPI as low as -70 dB, compared to that of -50 dB of the conventional test method. The detailed design and performance of the proposed method are discussed, including the MPI simulator for calibration procedure, computer simulations for evaluating the error caused by the FSK repetition rate and the fiber length under test and experiments on singlemode fibers and distributed Raman amplifier.

A robust gene-stacking method utilizing yeast assembly for plant synthetic biology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shih, Patrick M.; Vuu, Khanh; Mansoori, Nasim

The advent and growth of synthetic biology has demonstrated its potential as a promising avenue of research to address many societal needs. But, plant synthetic biology efforts have been hampered by a dearth of DNA part libraries, versatile transformation vectors and efficient assembly strategies. We describe a versatile system (named jStack) utilizing yeast homologous recombination to efficiently assemble DNA into plant transformation vectors. We also demonstrate how this method can facilitate pathway engineering of molecules of pharmaceutical interest, production of potential biofuels and shuffling of disease-resistance traits between crop species. Our approach provides a powerful alternative to conventional strategies formore » stacking genes and traits to address many impending environmental and agricultural challenges.« less

A robust gene-stacking method utilizing yeast assembly for plant synthetic biology

DOE PAGES

Shih, Patrick M.; Vuu, Khanh; Mansoori, Nasim; ...

2016-10-26

The advent and growth of synthetic biology has demonstrated its potential as a promising avenue of research to address many societal needs. But, plant synthetic biology efforts have been hampered by a dearth of DNA part libraries, versatile transformation vectors and efficient assembly strategies. We describe a versatile system (named jStack) utilizing yeast homologous recombination to efficiently assemble DNA into plant transformation vectors. We also demonstrate how this method can facilitate pathway engineering of molecules of pharmaceutical interest, production of potential biofuels and shuffling of disease-resistance traits between crop species. Our approach provides a powerful alternative to conventional strategies formore » stacking genes and traits to address many impending environmental and agricultural challenges.« less

An experimental test of an extended discretion approach for high school biology laboratory investigations

NASA Astrophysics Data System (ADS)

Leonard, William H.; Cavana, Gordon R.; Lowery, Lawrence F.

Discretion-the exercise of independent judgment-was observed to be lacking in most commercially available laboratory investigations for high school biology. An Extended Discretion (ED) laboratory approach was developed and tested experimentally against the BSCS Green Version laboratory program, using ten classes of 10th-grade biology in a suburban California high school. Five teachers were each assigned one experimental and one control group. The primary differences between the two approaches were that the BSCS was more prescriptive and directive than the ED approach and the ED approach increased discretionary demands upon the student over the school year. A treatment verification procedure showed statistically significant differences between the two approaches. The hypothesis under test was that when high school biology students are taught laboratory concepts under comparatively high discretionary demands, they would perform as well as or better than a similar group of students taught with BSCS Green Version investigations. A second hypothesis was that teachers would prefer to use the ED approach over the BSCS approach for their future classes. A t analysis between experimental and control groups for each teacher was employed. There were significant differences in favor of the ED group on laboratory report scores for three teachers and no differences for two teachers. There were significant differences in favor of the ED group on laboratory concepts quiz scores for three teachers, no differences for one teacher, and significant differences in favor of the BSCS group for only one teacher. A t analysis of teacher evaluation of the two approaches showed a significant teacher preference overall for the ED approach. Both experimental hypotheses were accepted. The ED approach was observed to be difficult for students at first, but it was found to be a workable and productive means of teaching laboratory concepts in biology which also required extensive use of individual

An novel frequent probability pattern mining algorithm based on circuit simulation method in uncertain biological networks.

PubMed

He, Jieyue; Wang, Chunyan; Qiu, Kunpu; Zhong, Wei

2014-01-01

Motif mining has always been a hot research topic in bioinformatics. Most of current research on biological networks focuses on exact motif mining. However, due to the inevitable experimental error and noisy data, biological network data represented as the probability model could better reflect the authenticity and biological significance, therefore, it is more biological meaningful to discover probability motif in uncertain biological networks. One of the key steps in probability motif mining is frequent pattern discovery which is usually based on the possible world model having a relatively high computational complexity. In this paper, we present a novel method for detecting frequent probability patterns based on circuit simulation in the uncertain biological networks. First, the partition based efficient search is applied to the non-tree like subgraph mining where the probability of occurrence in random networks is small. Then, an algorithm of probability isomorphic based on circuit simulation is proposed. The probability isomorphic combines the analysis of circuit topology structure with related physical properties of voltage in order to evaluate the probability isomorphism between probability subgraphs. The circuit simulation based probability isomorphic can avoid using traditional possible world model. Finally, based on the algorithm of probability subgraph isomorphism, two-step hierarchical clustering method is used to cluster subgraphs, and discover frequent probability patterns from the clusters. The experiment results on data sets of the Protein-Protein Interaction (PPI) networks and the transcriptional regulatory networks of E. coli and S. cerevisiae show that the proposed method can efficiently discover the frequent probability subgraphs. The discovered subgraphs in our study contain all probability motifs reported in the experiments published in other related papers. The algorithm of probability graph isomorphism evaluation based on circuit simulation

Methods of information geometry in computational system biology (consistency between chemical and biological evolution).

PubMed

Astakhov, Vadim

2009-01-01

Interest in simulation of large-scale metabolic networks, species development, and genesis of various diseases requires new simulation techniques to accommodate the high complexity of realistic biological networks. Information geometry and topological formalisms are proposed to analyze information processes. We analyze the complexity of large-scale biological networks as well as transition of the system functionality due to modification in the system architecture, system environment, and system components. The dynamic core model is developed. The term dynamic core is used to define a set of causally related network functions. Delocalization of dynamic core model provides a mathematical formalism to analyze migration of specific functions in biosystems which undergo structure transition induced by the environment. The term delocalization is used to describe these processes of migration. We constructed a holographic model with self-poetic dynamic cores which preserves functional properties under those transitions. Topological constraints such as Ricci flow and Pfaff dimension were found for statistical manifolds which represent biological networks. These constraints can provide insight on processes of degeneration and recovery which take place in large-scale networks. We would like to suggest that therapies which are able to effectively implement estimated constraints, will successfully adjust biological systems and recover altered functionality. Also, we mathematically formulate the hypothesis that there is a direct consistency between biological and chemical evolution. Any set of causal relations within a biological network has its dual reimplementation in the chemistry of the system environment.

Accelerated Dynamic Corrosion Test Method Development

DTIC Science & Technology

test method has poor correlation to outdoor exposures, particularly for non-chromate primers. As a result, more realistic cyclic environmental...exposures have been developed to more closely resemble actual atmospheric corrosion damage. Several existing tests correlate well with the outdoor performance

Building biological foundries for next-generation synthetic biology.

PubMed

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.

A review of consensus test methods for established medical imaging modalities and their implications for optical coherence tomography

NASA Astrophysics Data System (ADS)

Pfefer, Joshua; Agrawal, Anant

2012-03-01

In recent years there has been increasing interest in development of consensus, tissue-phantom-based approaches for assessment of biophotonic imaging systems, with the primary goal of facilitating clinical translation of novel optical technologies. Well-characterized test methods based on tissue phantoms can provide useful tools for performance assessment, thus enabling standardization and device inter-comparison during preclinical development as well as quality assurance and re-calibration in the clinical setting. In this review, we study the role of phantom-based test methods as described in consensus documents such as international standards for established imaging modalities including X-ray CT, MRI and ultrasound. Specifically, we focus on three image quality characteristics - spatial resolution, spatial measurement accuracy and image uniformity - and summarize the terminology, metrics, phantom design/construction approaches and measurement/analysis procedures used to assess these characteristics. Phantom approaches described are those in routine clinical use and tend to have simplified morphology and biologically-relevant physical parameters. Finally, we discuss the potential for applying knowledge gained from existing consensus documents in the development of standardized, phantom-based test methods for optical coherence tomography.

Biological Stability of Drinking Water: Controlling Factors, Methods, and Challenges.

PubMed

Prest, Emmanuelle I; Hammes, Frederik; van Loosdrecht, Mark C M; Vrouwenvelder, Johannes S

2016-01-01

Biological stability of drinking water refers to the concept of providing consumers with drinking water of same microbial quality at the tap as produced at the water treatment facility. However, uncontrolled growth of bacteria can occur during distribution in water mains and premise plumbing, and can lead to hygienic (e.g., development of opportunistic pathogens), aesthetic (e.g., deterioration of taste, odor, color) or operational (e.g., fouling or biocorrosion of pipes) problems. Drinking water contains diverse microorganisms competing for limited available nutrients for growth. Bacterial growth and interactions are regulated by factors, such as (i) type and concentration of available organic and inorganic nutrients, (ii) type and concentration of residual disinfectant, (iii) presence of predators, such as protozoa and invertebrates, (iv) environmental conditions, such as water temperature, and (v) spatial location of microorganisms (bulk water, sediment, or biofilm). Water treatment and distribution conditions in water mains and premise plumbing affect each of these factors and shape bacterial community characteristics (abundance, composition, viability) in distribution systems. Improved understanding of bacterial interactions in distribution systems and of environmental conditions impact is needed for better control of bacterial communities during drinking water production and distribution. This article reviews (i) existing knowledge on biological stability controlling factors and (ii) how these factors are affected by drinking water production and distribution conditions. In addition, (iii) the concept of biological stability is discussed in light of experience with well-established and new analytical methods, enabling high throughput analysis and in-depth characterization of bacterial communities in drinking water. We discussed, how knowledge gained from novel techniques will improve design and monitoring of water treatment and distribution systems in order

Biological Stability of Drinking Water: Controlling Factors, Methods, and Challenges

PubMed Central

Prest, Emmanuelle I.; Hammes, Frederik; van Loosdrecht, Mark C. M.; Vrouwenvelder, Johannes S.

2016-01-01

Biological stability of drinking water refers to the concept of providing consumers with drinking water of same microbial quality at the tap as produced at the water treatment facility. However, uncontrolled growth of bacteria can occur during distribution in water mains and premise plumbing, and can lead to hygienic (e.g., development of opportunistic pathogens), aesthetic (e.g., deterioration of taste, odor, color) or operational (e.g., fouling or biocorrosion of pipes) problems. Drinking water contains diverse microorganisms competing for limited available nutrients for growth. Bacterial growth and interactions are regulated by factors, such as (i) type and concentration of available organic and inorganic nutrients, (ii) type and concentration of residual disinfectant, (iii) presence of predators, such as protozoa and invertebrates, (iv) environmental conditions, such as water temperature, and (v) spatial location of microorganisms (bulk water, sediment, or biofilm). Water treatment and distribution conditions in water mains and premise plumbing affect each of these factors and shape bacterial community characteristics (abundance, composition, viability) in distribution systems. Improved understanding of bacterial interactions in distribution systems and of environmental conditions impact is needed for better control of bacterial communities during drinking water production and distribution. This article reviews (i) existing knowledge on biological stability controlling factors and (ii) how these factors are affected by drinking water production and distribution conditions. In addition, (iii) the concept of biological stability is discussed in light of experience with well-established and new analytical methods, enabling high throughput analysis and in-depth characterization of bacterial communities in drinking water. We discussed, how knowledge gained from novel techniques will improve design and monitoring of water treatment and distribution systems in order

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

DOEpatents

Gourley, Paul L.; Gourley, Mark F.

1997-01-01

An apparatus and method 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 thereof.

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

DOEpatents

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.

A suite of phantom-based test methods for assessing image quality of photoacoustic tomography systems

NASA Astrophysics Data System (ADS)

Vogt, William C.; Jia, Congxian; Wear, Keith A.; Garra, Brian S.; Pfefer, T. Joshua

2017-03-01

As Photoacoustic Tomography (PAT) matures and undergoes clinical translation, objective performance test methods are needed to facilitate device development, regulatory clearance and clinical quality assurance. For mature medical imaging modalities such as CT, MRI, and ultrasound, tissue-mimicking phantoms are frequently incorporated into consensus standards for performance testing. A well-validated set of phantom-based test methods is needed for evaluating performance characteristics of PAT systems. To this end, we have constructed phantoms using a custom tissue-mimicking material based on PVC plastisol with tunable, biologically-relevant optical and acoustic properties. Each phantom is designed to enable quantitative assessment of one or more image quality characteristics including 3D spatial resolution, spatial measurement accuracy, ultrasound/PAT co-registration, uniformity, penetration depth, geometric distortion, sensitivity, and linearity. Phantoms contained targets including high-intensity point source targets and dye-filled tubes. This suite of phantoms was used to measure the dependence of performance of a custom PAT system (equipped with four interchangeable linear array transducers of varying design) on design parameters (e.g., center frequency, bandwidth, element geometry). Phantoms also allowed comparison of image artifacts, including surface-generated clutter and bandlimited sensing artifacts. Results showed that transducer design parameters create strong variations in performance including a trade-off between resolution and penetration depth, which could be quantified with our method. This study demonstrates the utility of phantom-based image quality testing in device performance assessment, which may guide development of consensus standards for PAT systems.

PE Metrics: Background, Testing Theory, and Methods

ERIC Educational Resources Information Center

Zhu, Weimo; Rink, Judy; Placek, Judith H.; Graber, Kim C.; Fox, Connie; Fisette, Jennifer L.; Dyson, Ben; Park, Youngsik; Avery, Marybell; Franck, Marian; Raynes, De

2011-01-01

New testing theories, concepts, and psychometric methods (e.g., item response theory, test equating, and item bank) developed during the past several decades have many advantages over previous theories and methods. In spite of their introduction to the field, they have not been fully accepted by physical educators. Further, the manner in which…

Dormancy and Recovery Testing for Biological Wastewater Processors

NASA Technical Reports Server (NTRS)

Hummerick, Mary F.; Coutts, Janelle L.; Lunn, Griffin M.; Spencer, LaShelle; Khodadad, Christina L.; Birmele, Michele N.; Frances, Someliz; Wheeler, Raymond

2015-01-01

Resource recovery and recycling waste streams to usable water via biological water processors is a plausible component of an integrated water purification system. Biological processing as a pretreatment can reduce the load of organic carbon and nitrogen compounds entering physiochemical systems downstream. Aerated hollow fiber membrane bioreactors, have been proposed and studied for a number of years as an approach for treating wastewater streams for space exploration.

Ethics and methods for biological rhythm research on animals and human beings.

PubMed

Portaluppi, Francesco; Smolensky, Michael H; Touitou, Yvan

2010-10-01

This article updates the ethical standards and methods for the conduct of high-quality animal and human biological rhythm research, which should be especially useful for new investigators of the rhythms of life. The editors of Chronobiology International adhere to and endorse the Code of Conduct and Best Practice Guidelines of the Committee On Publication Ethics (COPE), which encourages communication of such updates at regular intervals in the journal. The journal accepts papers representing original work, no part of which was previously submitted for publication elsewhere, except as brief abstracts, as well as in-depth reviews. The majority of research papers published in Chronobiology International entails animal and human investigations. The editors and readers of the journal expect authors of submitted manuscripts to have made an important contribution to the research of biological rhythms and related phenomena using ethical methods/procedures and unbiased, accurate, and honest reporting of findings. Authors of scientific papers are required to declare all potential conflicts of interest. The journal and its editors endorse compliance of investigators to the Guide for the Care and Use of Laboratory Animals of the Institute for Laboratory Animal Research of the National Research Council, relating to the conduct of ethical research on laboratory and other animals, and the principles of the Declaration of Helsinki of the World Medical Association, relating to the conduct of ethical research on human beings. The peer review of manuscripts by Chronobiology International thus includes judgment as to whether or not the protocols and methods conform to ethical standards. Authors are expected to show mastery of the basic methods and procedures of biological rhythm research and proper statistical assessment of data, including the appropriate application of time series data analyses, as briefly reviewed in this article. The journal editors strive to consistently achieve

40 CFR 60.133 - Test methods and procedures.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 6 2010-07-01 2010-07-01 false Test methods and procedures. 60.133 Section 60.133 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS... and Bronze Production Plants § 60.133 Test methods and procedures. (a) In conducting performance tests...

40 CFR 60.133 - Test methods and procedures.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 7 2012-07-01 2012-07-01 false Test methods and procedures. 60.133 Section 60.133 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS... and Bronze Production Plants § 60.133 Test methods and procedures. (a) In conducting performance tests...

40 CFR 60.133 - Test methods and procedures.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 6 2011-07-01 2011-07-01 false Test methods and procedures. 60.133 Section 60.133 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS... and Bronze Production Plants § 60.133 Test methods and procedures. (a) In conducting performance tests...

Evaluation of a bioluminescence method, contact angle measurements and topography for testing the cleanability of plastic surfaces under laboratory conditions

NASA Astrophysics Data System (ADS)

Redsven, I.; Kymäläinen, H.-R.; Pesonen-Leinonen, E.; Kuisma, R.; Ojala-Paloposki, T.; Hautala, M.; Sjöberg, A.-M.

2007-04-01

Detection of adenosine triphosphate (ATP) by bioluminescence is used, for instance, in the food industry and in hospitals to assess the hygiene status of surfaces. The aim of this laboratory study was to investigate the feasibility of the ATP method for estimating the cleanability of resilient floor coverings from biological soil. The surfaces were worn using a Soiling and Wearing Drum Tester, and soiled and cleaned with an Erichsen Washability and Scrubbing Resistance Tester. In the laboratory test carried out with the bioluminescence method, most of the new and worn floor coverings that were biologically soiled were cleaned efficiently. According to this study, the semiquantitative ATP screening method can be used for hygiene monitoring of flooring materials. No correlation was found between cleanability and contact angles or surface topography measured using a profilometer. However, by revealing local irregularities and damage on surfaces, scanning electron micrographs appeared useful in explaining differences in cleanability.

Methods for isolation and viability assessment of biological organisms

DOEpatents

Letant, Sonia Edith; Baker, Sarah Elyse; Bond, Tiziana; Chang, Allan Shih-Ping

2015-02-03

Isolation of biological or chemical organisms can be accomplished using a surface enhanced Raman scattering (SERS) system. The SERS system can be a single or a stacked plurality of photonic crystal membranes with noble-metal lined through pores for flowing analyte potentially containing the biological or chemical organisms. The through pores can be adapted to trap individual biological or chemical organisms and emit SERS spectra, which can then be detected by a detector and further analyzed for viability of the biological or chemical organism.

Insects as test systems for assessing the potential role of microgravity in biological development and evolution

NASA Astrophysics Data System (ADS)

Vernós, I.; Carratalá, M.; González-Jurado, J.; Valverde, J. R.; Calleja, M.; Domingo, A.; Vinós, J.; Cervera, M.; Marco, R.

Gravity and radiation are undoubtedly the two major environmental factors altered in space. Gravity is a weak force, which creates a permanent potential field acting on the mass of biological systems and their cellular components, strongly reduced in space flights. Developmental systems, particularly at very early stages, provide the larger cellular compartments known, where the effects of alterations in the size of the gravity vector on living organisms can be more effectively tested. The insects, one of the more highly evolved classes of animals in which early development occurs in a syncytial embryo, are systems particularly well suited to test these effects and the specific developmental mechanisms affected. Furthermore, they share some basic features such as small size, short life cycles, relatively high radio-resistance, etc. and show a diversity of developmental strategies and tempos advantageous in experiments of this type in space. Drosophila melanogaster, the current biological paradigm to study development, with so much genetic and evolutionary background available, is clearly the reference organism for these studies. The current evidence on the effects of the physical parameters altered in space flights on insect development indicate a surprising correlation between effects seen on the fast developing and relatively small Drosophila embryo and the more slowly developing and large Carausius morosus system. In relation to the issue of the importance of developmental and environmental constraints in biological evolution, still the missing link in current evolutionary thinking, insects and space facilities for long-term experiments could provide useful experimental settings where to critically assess how development and evolution may be interconnected. Finally, it has to be pointed out that since there are experimental data indicating a possible synergism between microgravity and space radiation, possible effects of space radiation should be taken into

Insects as test systems for assessing the potential role of microgravity in biological development and evolution.