Sample records for accurately reflect biological

  1. Biology Reflective Assessment Curriculum

    NASA Astrophysics Data System (ADS)

    Bayley, Cheryl Ann

    Often students and educators view assessments as an obligation and finality for a unit. In the current climate of high-stakes testing and accountability, the balance of time, resources and emphasis on students' scores related to assessment have been slanted considerably toward the summative side. This tension between assessment for accountability and assessment to inform teaching strains instruction and educators' ability to use that information to design learning opportunities that help students develop deeper conceptual understanding. A substantive body of research indicates that formative and reflective assessment can significantly improve student learning. Biology Reflective Assessment Curriculum (BRAC) examines support provided for high school science students through assessment practices. This investigation incorporates the usage of reflective assessments as a guiding practice for differentiated instruction and student choice. Reflective assessment is a metacognitive strategy that promotes self-monitoring and evaluation. The goals of the curriculum are to promote self-efficacy and conceptual understanding in students learning biology through developing their metacognitive awareness. BRAC was implemented in a high school biology classroom. Data from assessments, metacognitive surveys, self-efficacy surveys, reflective journals, student work, a culminating task and field notes were used to evaluate the effectiveness of the curriculum. The results suggest that students who develop their metacognitive skills developed a deeper conceptual understanding and improved feelings of self-efficacy when they were engaged in a reflective assessment unit embedded with student choice. BRAC is a tool for teachers to use assessments to assist students in becoming metacognitive and to guide student choice in learning opportunities.

  2. Accurate high-speed liquid handling of very small biological samples.

    PubMed

    Schober, A; Günther, R; Schwienhorst, A; Döring, M; Lindemann, B F

    1993-08-01

    Molecular biology techniques require the accurate pipetting of buffers and solutions with volumes in the microliter range. Traditionally, hand-held pipetting devices are used to fulfill these requirements, but many laboratories have also introduced robotic workstations for the handling of liquids. Piston-operated pumps are commonly used in manually as well as automatically operated pipettors. These devices cannot meet the demands for extremely accurate pipetting of very small volumes at the high speed that would be necessary for certain applications (e.g., in sequencing projects with high throughput). In this paper we describe a technique for the accurate microdispensation of biochemically relevant solutions and suspensions with the aid of a piezoelectric transducer. It is suitable for liquids of a viscosity between 0.5 and 500 milliPascals. The obtainable drop sizes range from 5 picoliters to a few nanoliters with up to 10,000 drops per second. Liquids can be dispensed in single or accumulated drops to handle a wide volume range. The system proved to be excellently suitable for the handling of biological samples. It did not show any detectable negative impact on the biological function of dissolved or suspended molecules or particles.

  3. [Around biological evolution. Reflections of a physicist].

    PubMed

    Sanchez-Palencia, Evariste

    2016-01-01

    This text is the written version of a talk at the Société de Biologie on February 17, 2016. It contains reflections of a non-biologist scientist on general problems of biological evolution, including the kind of causality involved, the ideas emerging from it, in particular the constructive and structuring character of phenomena such as predation, the role of stability and attractors. This leads to a larger reflection on dialectics, the general framework of evolving processes, which overpasses formal logic and instantaneousness. © Société de Biologie, 2016.

  4. Successional stage of biological soil crusts: an accurate indicator of ecohydrological condition

    USGS Publications Warehouse

    Belnap, Jayne; Wilcox, Bradford P.; Van Scoyoc, Matthew V.; Phillips, Susan L.

    2013-01-01

    Biological soil crusts are a key component of many dryland ecosystems. Following disturbance, biological soil crusts will recover in stages. Recently, a simple classification of these stages has been developed, largely on the basis of external features of the crusts, which reflects their level of development (LOD). The classification system has six LOD classes, from low (1) to high (6). To determine whether the LOD of a crust is related to its ecohydrological function, we used rainfall simulation to evaluate differences in infiltration, runoff, and erosion among crusts in the various LODs, across a range of soil depths and with different wetting pre-treatments. We found large differences between the lowest and highest LODs, with runoff and erosion being greatest from the lowest LOD. Under dry antecedent conditions, about 50% of the water applied ran off the lowest LOD plots, whereas less than 10% ran off the plots of the two highest LODs. Similarly, sediment loss was 400 g m-2 from the lowest LOD and almost zero from the higher LODs. We scaled up the results from these simulations using the Rangeland Hydrology and Erosion Model. Modelling results indicate that erosion increases dramatically as slope length and gradient increase, especially beyond the threshold values of 10 m for slope length and 10% for slope gradient. Our findings confirm that the LOD classification is a quick, easy, nondestructive, and accurate index of hydrological condition and should be incorporated in field and modelling assessments of ecosystem health.

  5. Can cancer researchers accurately judge whether preclinical reports will reproduce?

    PubMed Central

    Mandel, David R.; Kimmelman, Jonathan

    2017-01-01

    There is vigorous debate about the reproducibility of research findings in cancer biology. Whether scientists can accurately assess which experiments will reproduce original findings is important to determining the pace at which science self-corrects. We collected forecasts from basic and preclinical cancer researchers on the first 6 replication studies conducted by the Reproducibility Project: Cancer Biology (RP:CB) to assess the accuracy of expert judgments on specific replication outcomes. On average, researchers forecasted a 75% probability of replicating the statistical significance and a 50% probability of replicating the effect size, yet none of these studies successfully replicated on either criterion (for the 5 studies with results reported). Accuracy was related to expertise: experts with higher h-indices were more accurate, whereas experts with more topic-specific expertise were less accurate. Our findings suggest that experts, especially those with specialized knowledge, were overconfident about the RP:CB replicating individual experiments within published reports; researcher optimism likely reflects a combination of overestimating the validity of original studies and underestimating the difficulties of repeating their methodologies. PMID:28662052

  6. Inverse Algorithm Optimization for Determining Optical Properties of Biological Materials from Spatially-Resolved Diffuse Reflectance

    USDA-ARS?s Scientific Manuscript database

    Optical characterization of biological materials is useful in many scientific and industrial applications like biomedical diagnosis and nondestructive quality evaluation of food and agricultural products. However, accurate determination of the optical properties from intact biological materials base...

  7. Total-Internal-Reflection Platforms for Chemical and Biological Sensing Applications

    NASA Astrophysics Data System (ADS)

    Sapsford, Kim E.

    Sensing platforms based on the principle of total internal reflection (TIR) represent a fairly mature yet still expanding and exciting field of research. Sensor development has mainly been driven by the need for rapid, stand-alone, automated devices for application in the fields of clinical diagnosis and screening, food and water safety, environmental monitoring, and chemical and biological warfare agent detection. The technologies highlighted in this chapter are continually evolving, taking advantage of emerging advances in microfabrication, lab-on-a-chip, excitation, and detection techniques. This chapter describes many of the underlying principles of TIR-based sensing platforms and additionally focusses on planar TIR fluorescence (TIRF)-based chemical and biological sensors.

  8. Reflecting on Graphs: Attributes of Graph Choice and Construction Practices in Biology

    PubMed Central

    Angra, Aakanksha; Gardner, Stephanie M.

    2017-01-01

    Undergraduate biology education reform aims to engage students in scientific practices such as experimental design, experimentation, and data analysis and communication. Graphs are ubiquitous in the biological sciences, and creating effective graphical representations involves quantitative and disciplinary concepts and skills. Past studies document student difficulties with graphing within the contexts of classroom or national assessments without evaluating student reasoning. Operating under the metarepresentational competence framework, we conducted think-aloud interviews to reveal differences in reasoning and graph quality between undergraduate biology students, graduate students, and professors in a pen-and-paper graphing task. All professors planned and thought about data before graph construction. When reflecting on their graphs, professors and graduate students focused on the function of graphs and experimental design, while most undergraduate students relied on intuition and data provided in the task. Most undergraduate students meticulously plotted all data with scaled axes, while professors and some graduate students transformed the data, aligned the graph with the research question, and reflected on statistics and sample size. Differences in reasoning and approaches taken in graph choice and construction corroborate and extend previous findings and provide rich targets for undergraduate and graduate instruction. PMID:28821538

  9. Reflecting on Graphs: Attributes of Graph Choice and Construction Practices in Biology.

    PubMed

    Angra, Aakanksha; Gardner, Stephanie M

    2017-01-01

    Undergraduate biology education reform aims to engage students in scientific practices such as experimental design, experimentation, and data analysis and communication. Graphs are ubiquitous in the biological sciences, and creating effective graphical representations involves quantitative and disciplinary concepts and skills. Past studies document student difficulties with graphing within the contexts of classroom or national assessments without evaluating student reasoning. Operating under the metarepresentational competence framework, we conducted think-aloud interviews to reveal differences in reasoning and graph quality between undergraduate biology students, graduate students, and professors in a pen-and-paper graphing task. All professors planned and thought about data before graph construction. When reflecting on their graphs, professors and graduate students focused on the function of graphs and experimental design, while most undergraduate students relied on intuition and data provided in the task. Most undergraduate students meticulously plotted all data with scaled axes, while professors and some graduate students transformed the data, aligned the graph with the research question, and reflected on statistics and sample size. Differences in reasoning and approaches taken in graph choice and construction corroborate and extend previous findings and provide rich targets for undergraduate and graduate instruction. © 2017 A. Angra and S. M. Gardner. CBE—Life Sciences Education © 2017 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).

  10. Improved algorithm for estimating optical properties of food and biological materials using spatially-resolved diffuse reflectance

    USDA-ARS?s Scientific Manuscript database

    In this research, the inverse algorithm for estimating optical properties of food and biological materials from spatially-resolved diffuse reflectance was optimized in terms of data smoothing, normalization and spatial region of reflectance profile for curve fitting. Monte Carlo simulation was used ...

  11. Branch and bound algorithm for accurate estimation of analytical isotropic bidirectional reflectance distribution function models.

    PubMed

    Yu, Chanki; Lee, Sang Wook

    2016-05-20

    We present a reliable and accurate global optimization framework for estimating parameters of isotropic analytical bidirectional reflectance distribution function (BRDF) models. This approach is based on a branch and bound strategy with linear programming and interval analysis. Conventional local optimization is often very inefficient for BRDF estimation since its fitting quality is highly dependent on initial guesses due to the nonlinearity of analytical BRDF models. The algorithm presented in this paper employs L1-norm error minimization to estimate BRDF parameters in a globally optimal way and interval arithmetic to derive our feasibility problem and lower bounding function. Our method is developed for the Cook-Torrance model but with several normal distribution functions such as the Beckmann, Berry, and GGX functions. Experiments have been carried out to validate the presented method using 100 isotropic materials from the MERL BRDF database, and our experimental results demonstrate that the L1-norm minimization provides a more accurate and reliable solution than the L2-norm minimization.

  12. Accurate and fiducial-marker-free correction for three-dimensional chromatic shift in biological fluorescence microscopy.

    PubMed

    Matsuda, Atsushi; Schermelleh, Lothar; Hirano, Yasuhiro; Haraguchi, Tokuko; Hiraoka, Yasushi

    2018-05-15

    Correction of chromatic shift is necessary for precise registration of multicolor fluorescence images of biological specimens. New emerging technologies in fluorescence microscopy with increasing spatial resolution and penetration depth have prompted the need for more accurate methods to correct chromatic aberration. However, the amount of chromatic shift of the region of interest in biological samples often deviates from the theoretical prediction because of unknown dispersion in the biological samples. To measure and correct chromatic shift in biological samples, we developed a quadrisection phase correlation approach to computationally calculate translation, rotation, and magnification from reference images. Furthermore, to account for local chromatic shifts, images are split into smaller elements, for which the phase correlation between channels is measured individually and corrected accordingly. We implemented this method in an easy-to-use open-source software package, called Chromagnon, that is able to correct shifts with a 3D accuracy of approximately 15 nm. Applying this software, we quantified the level of uncertainty in chromatic shift correction, depending on the imaging modality used, and for different existing calibration methods, along with the proposed one. Finally, we provide guidelines to choose the optimal chromatic shift registration method for any given situation.

  13. Covariation of Peptide Abundances Accurately Reflects Protein Concentration Differences*

    PubMed Central

    Pirmoradian, Mohammad

    2017-01-01

    Most implementations of mass spectrometry-based proteomics involve enzymatic digestion of proteins, expanding the analysis to multiple proteolytic peptides for each protein. Currently, there is no consensus of how to summarize peptides' abundances to protein concentrations, and such efforts are complicated by the fact that error control normally is applied to the identification process, and do not directly control errors linking peptide abundance measures to protein concentration. Peptides resulting from suboptimal digestion or being partially modified are not representative of the protein concentration. Without a mechanism to remove such unrepresentative peptides, their abundance adversely impacts the estimation of their protein's concentration. Here, we present a relative quantification approach, Diffacto, that applies factor analysis to extract the covariation of peptides' abundances. The method enables a weighted geometrical average summarization and automatic elimination of incoherent peptides. We demonstrate, based on a set of controlled label-free experiments using standard mixtures of proteins, that the covariation structure extracted by the factor analysis accurately reflects protein concentrations. In the 1% peptide-spectrum match-level FDR data set, as many as 11% of the peptides have abundance differences incoherent with the other peptides attributed to the same protein. If not controlled, such contradicting peptide abundance have a severe impact on protein quantifications. When adding the quantities of each protein's three most abundant peptides, we note as many as 14% of the proteins being estimated as having a negative correlation with their actual concentration differences between samples. Diffacto reduced the amount of such obviously incorrectly quantified proteins to 1.6%. Furthermore, by analyzing clinical data sets from two breast cancer studies, our method revealed the persistent proteomic signatures linked to three subtypes of breast cancer

  14. A novel method for accurate patterning and positioning of biological cells

    NASA Astrophysics Data System (ADS)

    Jing, Gaoshan; Labukas, Joseph P.; Iqbal, Aziz; Perry, Susan Fueshko; Ferguson, Gregory S.; Tatic-Lucic, Svetlana

    2007-05-01

    The ability to anchor cells in predefined patterns on a surface has become very important for the development of cell-based sensors, tissue-engineering applications, and the understanding of basic cell functions. Currently, the most widely used technique to generate micrometer or sub-micrometer-sized patterns for various biological applications is microcontact printing (μCP). However, the fidelity of the final pattern may be compromised by deformation of the PDMS stamps used during printing. A novel technique for accurately patterning and positioning biological cells is presented, which can overcome this obstacle. We have fabricated a chip on a silicon wafer using standard photolithographic and deposition processes consisting of gold patterns on top of PECVD silicon dioxide. A hydrophobic self-assembled monolayer (SAM) derived from 1-hexadecanethiol (HDT) was coated on the gold surface to prevent cell growth, and a hydrophilic SAM derived from (3-trimethoxysilyl propyl)-diethylenetriamine (DETA) was coated on the exposed PECVD silicon dioxide surface to promote cell growth. Immortalized mouse hypothalamic neurons (GT1-7) were cultured in vitro on the chip, and patterned cells were fluorescently stained and visualized by fluorescence microscopy. By our method, hydrophobic and hydrophilic regions can be reliably generated and easily visualized under a microscope prior to cell culturing. Cell growth was precisely controlled and limited to specific areas. The achieved resolution was 2 microns, and it could be improved with high resolution photolithographic methods.

  15. Structural Molecular Biology-A Personal Reflection on the Occasion of John Kendrew's 100th Birthday.

    PubMed

    Cramer, Patrick

    2017-08-18

    Here, I discuss the development and future of structural molecular biology, concentrating on the eukaryotic transcription machinery and reflecting on John Kendrew's legacy from a personal perspective. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. A method of online quantitative interpretation of diffuse reflection profiles of biological tissues

    NASA Astrophysics Data System (ADS)

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

    2013-02-01

    We have developed a method of combined interpretation of spectral and spatial characteristics of diffuse reflection of biological tissues, which makes it possible to determine biophysical parameters of the tissue with a high accuracy in real time under conditions of their general variability. Using the Monte Carlo method, we have modeled a statistical ensemble of profiles of diffuse reflection coefficients of skin, which corresponds to a wave variation of its biophysical parameters. On its basis, we have estimated the retrieval accuracy of biophysical parameters using the developed method and investigated the stability of the method to errors of optical measurements. We have showed that it is possible to determine online the concentrations of melanin, hemoglobin, bilirubin, oxygen saturation of blood, and structural parameters of skin from measurements of its diffuse reflection in the spectral range 450-800 nm at three distances between the radiation source and detector.

  17. How accelerated biological aging can affect solar reflective polymeric based building materials

    NASA Astrophysics Data System (ADS)

    Ferrari, C.; Santunione, G.; Libbra, A.; Muscio, A.; Sgarbi, E.

    2017-11-01

    Among the main issues concerning building materials, in particular outdoor ones, one can identify the colonization by microorganisms referred to as biological aggression. This can affect not only the aesthetical aspect but also the thermal performance of solar reflective materials. In order to improve the reliability of tests aimed to assess the resistance to biological aggression and contextually reduce the test duration, an accelerated test method has been developed. It is based on a lab reproducible setup where specific and controlled environmental and boundary conditions are imposed to accelerate as much as possible biological growth on building materials. Due to their widespread use, polymeric materials have been selected for the present analysis, in the aim of reaching an advanced bio-aged level in a relatively short time (8 weeks or less) and at the same time comparatively evaluate different materials under a given set of ageing conditions. Surface properties before, during and after ageing have been investigated by surface, microstructural and chemical analyses, as well as by examination of time progressive images to assess bacterial and algal growth rate.

  18. Accurate single-shot quantitative phase imaging of biological specimens with telecentric digital holographic microscopy.

    PubMed

    Doblas, Ana; Sánchez-Ortiga, Emilio; Martínez-Corral, Manuel; Saavedra, Genaro; Garcia-Sucerquia, Jorge

    2014-04-01

    The advantages of using a telecentric imaging system in digital holographic microscopy (DHM) to study biological specimens are highlighted. To this end, the performances of nontelecentric DHM and telecentric DHM are evaluated from the quantitative phase imaging (QPI) point of view. The evaluated stability of the microscope allows single-shot QPI in DHM by using telecentric imaging systems. Quantitative phase maps of a section of the head of the drosophila melanogaster fly and of red blood cells are obtained via single-shot DHM with no numerical postprocessing. With these maps we show that the use of telecentric DHM provides larger field of view for a given magnification and permits more accurate QPI measurements with less number of computational operations.

  19. Fully automated laboratory and field-portable goniometer used for performing accurate and precise multiangular reflectance measurements

    NASA Astrophysics Data System (ADS)

    Harms, Justin D.; Bachmann, Charles M.; Ambeau, Brittany L.; Faulring, Jason W.; Ruiz Torres, Andres J.; Badura, Gregory; Myers, Emily

    2017-10-01

    Field-portable goniometers are created for a wide variety of applications. Many of these applications require specific types of instruments and measurement schemes and must operate in challenging environments. Therefore, designs are based on the requirements that are specific to the application. We present a field-portable goniometer that was designed for measuring the hemispherical-conical reflectance factor (HCRF) of various soils and low-growing vegetation in austere coastal and desert environments and biconical reflectance factors in laboratory settings. Unlike some goniometers, this system features a requirement for "target-plane tracking" to ensure that measurements can be collected on sloped surfaces, without compromising angular accuracy. The system also features a second upward-looking spectrometer to measure the spatially dependent incoming illumination, an integrated software package to provide full automation, an automated leveling system to ensure a standard frame of reference, a design that minimizes the obscuration due to self-shading to measure the opposition effect, and the ability to record a digital elevation model of the target region. This fully automated and highly mobile system obtains accurate and precise measurements of HCRF in a wide variety of terrain and in less time than most other systems while not sacrificing consistency or repeatability in laboratory environments.

  20. An accurate bacterial DNA quantification assay for HTS library preparation of human biological samples.

    PubMed

    Seashols-Williams, Sarah; Green, Raquel; Wohlfahrt, Denise; Brand, Angela; Tan-Torres, Antonio Limjuco; Nogales, Francy; Brooks, J Paul; Singh, Baneshwar

    2018-05-17

    Sequencing and classification of microbial taxa within forensically relevant biological fluids has the potential for applications in the forensic science and biomedical fields. The quantity of bacterial DNA from human samples is currently estimated based on quantity of total DNA isolated. This method can miscalculate bacterial DNA quantity due to the mixed nature of the sample, and consequently library preparation is often unreliable. We developed an assay that can accurately and specifically quantify bacterial DNA within a mixed sample for reliable 16S ribosomal DNA (16S rDNA) library preparation and high throughput sequencing (HTS). A qPCR method was optimized using universal 16S rDNA primers, and a commercially available bacterial community DNA standard was used to develop a precise standard curve. Following qPCR optimization, 16S rDNA libraries from saliva, vaginal and menstrual secretions, urine, and fecal matter were amplified and evaluated at various DNA concentrations; successful HTS data were generated with as low as 20 pg of bacterial DNA. Changes in bacterial DNA quantity did not impact observed relative abundances of major bacterial taxa, but relative abundance changes of minor taxa were observed. Accurate quantification of microbial DNA resulted in consistent, successful library preparations for HTS analysis. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Two-dimensional flow nanometry of biological nanoparticles for accurate determination of their size and emission intensity

    NASA Astrophysics Data System (ADS)

    Block, Stephan; Fast, Björn Johansson; Lundgren, Anders; Zhdanov, Vladimir P.; Höök, Fredrik

    2016-09-01

    Biological nanoparticles (BNPs) are of high interest due to their key role in various biological processes and use as biomarkers. BNP size and composition are decisive for their functions, but simultaneous determination of both properties with high accuracy remains challenging. Optical microscopy allows precise determination of fluorescence/scattering intensity, but not the size of individual BNPs. The latter is better determined by tracking their random motion in bulk, but the limited illumination volume for tracking this motion impedes reliable intensity determination. Here, we show that by attaching BNPs to a supported lipid bilayer, subjecting them to hydrodynamic flows and tracking their motion via surface-sensitive optical imaging enable determination of their diffusion coefficients and flow-induced drifts, from which accurate quantification of both BNP size and emission intensity can be made. For vesicles, the accuracy of this approach is demonstrated by resolving the expected radius-squared dependence of their fluorescence intensity for radii down to 15 nm.

  2. Two-Dimensional Standing Wave Total Internal Reflection Fluorescence Microscopy: Superresolution Imaging of Single Molecular and Biological Specimens

    PubMed Central

    Chung, Euiheon; Kim, Daekeun; Cui, Yan; Kim, Yang-Hyo; So, Peter T. C.

    2007-01-01

    The development of high resolution, high speed imaging techniques allows the study of dynamical processes in biological systems. Lateral resolution improvement of up to a factor of 2 has been achieved using structured illumination. In a total internal reflection fluorescence microscope, an evanescence excitation field is formed as light is total internally reflected at an interface between a high and a low index medium. The <100 nm penetration depth of evanescence field ensures a thin excitation region resulting in low background fluorescence. We present even higher resolution wide-field biological imaging by use of standing wave total internal reflection fluorescence (SW-TIRF). Evanescent standing wave (SW) illumination is used to generate a sinusoidal high spatial frequency fringe pattern on specimen for lateral resolution enhancement. To prevent thermal drift of the SW, novel detection and estimation of the SW phase with real-time feedback control is devised for the stabilization and control of the fringe phase. SW-TIRF is a wide-field superresolution technique with resolution better than a fifth of emission wavelength or ∼100 nm lateral resolution. We demonstrate the performance of the SW-TIRF microscopy using one- and two-directional SW illumination with a biological sample of cellular actin cytoskeleton of mouse fibroblast cells as well as single semiconductor nanocrystal molecules. The results confirm the superior resolution of SW-TIRF in addition to the merit of a high signal/background ratio from TIRF microscopy. PMID:17483188

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

    PubMed Central

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

    2013-01-01

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

  4. Fast and Accurate Hybrid Stream PCRTMSOLAR Radiative Transfer Model for Reflected Solar Spectrum Simulation in the Cloudy Atmosphere

    NASA Technical Reports Server (NTRS)

    Yang, Qiguang; Liu, Xu; Wu, Wan; Kizer, Susan; Baize, Rosemary R.

    2016-01-01

    A hybrid stream PCRTM-SOLAR model has been proposed for fast and accurate radiative transfer simulation. It calculates the reflected solar (RS) radiances with a fast coarse way and then, with the help of a pre-saved matrix, transforms the results to obtain the desired high accurate RS spectrum. The methodology has been demonstrated with the hybrid stream discrete ordinate (HSDO) radiative transfer (RT) model. The HSDO method calculates the monochromatic radiances using a 4-stream discrete ordinate method, where only a small number of monochromatic radiances are simulated with both 4-stream and a larger N-stream (N = 16) discrete ordinate RT algorithm. The accuracy of the obtained channel radiance is comparable to the result from N-stream moderate resolution atmospheric transmission version 5 (MODTRAN5). The root-mean-square errors are usually less than 5x10(exp -4) mW/sq cm/sr/cm. The computational speed is three to four-orders of magnitude faster than the medium speed correlated-k option MODTRAN5. This method is very efficient to simulate thousands of RS spectra under multi-layer clouds/aerosols and solar radiation conditions for climate change study and numerical weather prediction applications.

  5. Introductory Biology Students’ Use of Enhanced Answer Keys and Reflection Questions to Engage in Metacognition and Enhance Understanding

    PubMed Central

    Sabel, Jaime L.; Dauer, Joseph T.; Forbes, Cory T.

    2017-01-01

    Providing feedback to students as they learn to integrate individual concepts into complex systems is an important way to help them to develop robust understanding, but it is challenging in large, undergraduate classes for instructors to provide feedback that is frequent and directed enough to help individual students. Various scaffolds can be used to help students engage in self-regulated learning and generate internal feedback to improve their learning. This study examined the use of enhanced answer keys with added reflection questions and instruction as scaffolds for engaging undergraduate students in self-regulated learning within an introductory biology course. Study findings show that both the enhanced answer keys and reflection questions helped students to engage in metacognition and develop greater understanding of biological concepts. Further, students who received additional instruction on the use of the scaffolds changed how they used them and, by the end of the semester, were using the scaffolds in significantly different ways and showed significantly higher learning gains than students who did not receive the instruction. These findings provide evidence for the benefit of designing scaffolds within biology courses that will support students in engaging in metacognition and enhancing their understanding of biological concepts. PMID:28645893

  6. Introductory Biology Students' Use of Enhanced Answer Keys and Reflection Questions to Engage in Metacognition and Enhance Understanding.

    PubMed

    Sabel, Jaime L; Dauer, Joseph T; Forbes, Cory T

    2017-01-01

    Providing feedback to students as they learn to integrate individual concepts into complex systems is an important way to help them to develop robust understanding, but it is challenging in large, undergraduate classes for instructors to provide feedback that is frequent and directed enough to help individual students. Various scaffolds can be used to help students engage in self-regulated learning and generate internal feedback to improve their learning. This study examined the use of enhanced answer keys with added reflection questions and instruction as scaffolds for engaging undergraduate students in self-regulated learning within an introductory biology course. Study findings show that both the enhanced answer keys and reflection questions helped students to engage in metacognition and develop greater understanding of biological concepts. Further, students who received additional instruction on the use of the scaffolds changed how they used them and, by the end of the semester, were using the scaffolds in significantly different ways and showed significantly higher learning gains than students who did not receive the instruction. These findings provide evidence for the benefit of designing scaffolds within biology courses that will support students in engaging in metacognition and enhancing their understanding of biological concepts. © 2017 J. L. Sabel et al. CBE—Life Sciences Education © 2017 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).

  7. Measurement of complex permittivities of biological materials and human skin in vivo in the frequency band

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

    Ghodgaonkar, D.K.

    1987-01-01

    A new method, namely, modified infinite sample method, has been developed which is particularly suitable for millimeter-wave dielectric measurements of biological materials. In this method, an impedance transformer is used which reduces the reflectivity of the biological sample. Because of the effect of introducing impendance transformer, the measured reflection coefficients are more sensitive to the complex permittivities of biological samples. For accurate measurement of reflection coefficients, two automated measurment systems were developed which cover the frequencies range of 26.5-60 GHz. An uncertainty analysis was performed to get an estimate of the errors in the measured complex permittivities. The dielectric propertiesmore » were measured for 10% saline solution, whole human blood, 200 mg/ml bovine serum albumin (BSA) solution and suspension of Saccharomyces cerevisiae cells. The Maxwell-Fricke equation, which is derived from dielectric mixture theory, was used for determination bound water in BSA solution. The results of all biological samples were interpreted by fitting Debye relaxation and Cole-Cole model. It is observed that the dielectric data for the biological materials can be explained on the basis of Debye relaxation of water molecule.« less

  8. Accurate Determination of the Q Quality Factor in Magnetoelastic Resonant Platforms for Advanced Biological Detection

    PubMed Central

    Lopes, Ana Catarina; Sagasti, Ariane; Lasheras, Andoni; Muto, Virginia; Gutiérrez, Jon; Kouzoudis, Dimitris; Barandiarán, José Manuel

    2018-01-01

    The main parameters of magnetoelastic resonators in the detection of chemical (i.e., salts, gases, etc.) or biological (i.e., bacteria, phages, etc.) agents are the sensitivity S (or external agent change magnitude per Hz change in the resonance frequency) and the quality factor Q of the resonance. We present an extensive study on the experimental determination of the Q factor in such magnetoelastic resonant platforms, using three different strategies: (a) analyzing the real and imaginary components of the susceptibility at resonance; (b) numerical fitting of the modulus of the susceptibility; (c) using an exact mathematical expression for the real part of the susceptibility. Q values obtained by the three methods are analyzed and discussed, aiming to establish the most adequate one to accurately determine the quality factor of the magnetoelastic resonance. PMID:29547578

  9. Accurate Determination of the Q Quality Factor in Magnetoelastic Resonant Platforms for Advanced Biological Detection.

    PubMed

    Lopes, Ana Catarina; Sagasti, Ariane; Lasheras, Andoni; Muto, Virginia; Gutiérrez, Jon; Kouzoudis, Dimitris; Barandiarán, José Manuel

    2018-03-16

    The main parameters of magnetoelastic resonators in the detection of chemical (i.e., salts, gases, etc.) or biological (i.e., bacteria, phages, etc.) agents are the sensitivity S (or external agent change magnitude per Hz change in the resonance frequency) and the quality factor Q of the resonance. We present an extensive study on the experimental determination of the Q factor in such magnetoelastic resonant platforms, using three different strategies: (a) analyzing the real and imaginary components of the susceptibility at resonance; (b) numerical fitting of the modulus of the susceptibility; (c) using an exact mathematical expression for the real part of the susceptibility. Q values obtained by the three methods are analyzed and discussed, aiming to establish the most adequate one to accurately determine the quality factor of the magnetoelastic resonance.

  10. Retrieving the optical parameters of biological tissues using diffuse reflectance spectroscopy and Fourier series expansions. I. theory and application.

    PubMed

    Muñoz Morales, Aarón A; Vázquez Y Montiel, Sergio

    2012-10-01

    The determination of optical parameters of biological tissues is essential for the application of optical techniques in the diagnosis and treatment of diseases. Diffuse Reflection Spectroscopy is a widely used technique to analyze the optical characteristics of biological tissues. In this paper we show that by using diffuse reflectance spectra and a new mathematical model we can retrieve the optical parameters by applying an adjustment of the data with nonlinear least squares. In our model we represent the spectra using a Fourier series expansion finding mathematical relations between the polynomial coefficients and the optical parameters. In this first paper we use spectra generated by the Monte Carlo Multilayered Technique to simulate the propagation of photons in turbid media. Using these spectra we determine the behavior of Fourier series coefficients when varying the optical parameters of the medium under study. With this procedure we find mathematical relations between Fourier series coefficients and optical parameters. Finally, the results show that our method can retrieve the optical parameters of biological tissues with accuracy that is adequate for medical applications.

  11. Technique for examining biological materials using diffuse reflectance spectroscopy and the kubelka-munk function

    DOEpatents

    Alfano, Robert R.; Yang, Yuanlong

    2003-09-02

    Method and apparatus for examining biological materials using diffuse reflectance spectroscopy and the Kubelka-Munk function. In one aspect, the method is used to determine whether a tissue sample is cancerous or not and comprises the steps of (a) measuring the diffuse reflectance from the tissue sample at a first wavelength and at a second wavelength, wherein the first wavelength is a wavelength selected from the group consisting of 255-265 nm and wherein the second wavelength is a wavelength selected from the group consisting of 275-285 nm; (b) using the Kubelka-Munk function to transform the diffuse reflectance measurement obtained at the first and second wavelengths; and (c) comparing a ratio or a difference of the transformed Kubelka-Munk measurements at the first and second wavelengths to appropriate standards determine whether or not the tissue sample is cancerous. One can use the spectral profile of KMF between 250 nm to 300 nm to determine whether or not the tissue sample is cancerous or precancerous. According to the value at the first and second wavelengths determine whether or not the malignant tissue is invasive or mixed invasive and in situ or carcinoma in situ.

  12. ARCSTONE: Accurate Calibration of Lunar Spectral Reflectance from space

    NASA Astrophysics Data System (ADS)

    Young, C. L.; Lukashin, C.; Jackson, T.; Cooney, M.; Ryan, N.; Beverly, J.; Davis, W.; Nguyen, T.; Rutherford, G.; Swanson, R.; Kehoe, M.; Kopp, G.; Smith, P.; Woodward, J.; Carvo, J.; Stone, T.

    2017-12-01

    Calibration accuracy and consistency are key on-orbit performance metrics for Earth observing sensors. The accuracy and consistency of measurements across multiple instruments in low Earth and geostationary orbits are directly connected to the scientific understanding of complex systems, such as Earth's weather and climate. Recent studies have demonstrated the quantitative impacts of observational accuracy on the science data products [1] and the ability to detect climate change trends for essential climate variables (e.g., Earth's radiation budget, cloud feedback, and long-term trends in cloud parameters) [2, 3]. It is common for sensors to carry references for calibration at various wavelengths onboard, but these can be subject to degradation and increase mass and risk. The Moon can be considered a natural solar diffuser in space. Establishing the Moon as an on-orbit high-accuracy calibration reference enables broad intercalibration opportunities, as the lunar reflectance is time-invariant and can be directly measured by most Earth-observing instruments. Existing approaches to calibrate sensors against the Moon can achieve stabilities of a tenth of a percent over a decade, as demonstrated by the SeaWIFS. However, the current lunar calibration quality, with 5 - 10% bias, depends on the photometric model of the Moon [4]. Significant improvements in the lunar reference are possible and are necessary for climate-level absolute calibrations using the Moon. The ARCSTONE instrument will provide a reliable reference for high-accuracy on-orbit calibration for reflected solar instruments. An orbiting spectrometer flying on a CubeSat in low Earth orbit will provide lunar spectral reflectance with accuracy < 0.5% (k = 1), sufficient to establish an SI-traceable absolute lunar calibration standard for past, current, and future Earth weather and climate sensors. The ARCSTONE team will present the instrument design status and path forward for development, building, calibration

  13. Reflecting on complexity of biological systems: Kant and beyond?

    PubMed

    Van de Vijver, Gertrudis; Van Speybroeck, Linda; Vandevyvere, Windy

    2003-01-01

    Living organisms are currently most often seen as complex dynamical systems that develop and evolve in relation to complex environments. Reflections on the meaning of the complex dynamical nature of living systems show an overwhelming multiplicity in approaches, descriptions, definitions and methodologies. Instead of sustaining an epistemic pluralism, which often functions as a philosophical armistice in which tolerance and so-called neutrality discharge proponents of the burden to clarify the sources and conditions of agreement and disagreement, this paper aims at analysing: (i) what has been Kant's original conceptualisation of living organisms as natural purposes; (ii) how the current perspectives are to be related to Kant's viewpoint; (iii) what are the main trends in current complexity thinking. One of the basic ideas is that the attention for structure and its epistemological consequences witness to a great extent of Kant's viewpoint, and that the idea of organisational stratification today constitutes a different breeding ground within which complexity issues are raised. The various approaches of complexity in biological systems are captured in terms of two different styles, universalism and (weak and strong) constructivism, between which hybrid forms exist.

  14. Extending Whole Slide Imaging: Color Darkfield Internal Reflection Illumination (DIRI) for Biological Applications

    PubMed Central

    Namiki, Kana; Miyawaki, Atsushi; Ishikawa, Takuji

    2017-01-01

    Whole slide imaging (WSI) is a useful tool for multi-modal imaging, and in our work, we have often combined WSI with darkfield microscopy. However, traditional darkfield microscopy cannot use a single condenser to support high- and low-numerical-aperture objectives, which limits the modality of WSI. To overcome this limitation, we previously developed a darkfield internal reflection illumination (DIRI) microscope using white light-emitting diodes (LEDs). Although the developed DIRI is useful for biological applications, substantial problems remain to be resolved. In this study, we propose a novel illumination technique called color DIRI. The use of three-color LEDs dramatically improves the capability of the system, such that color DIRI (1) enables optimization of the illumination color; (2) can be combined with an oil objective lens; (3) can produce fluorescence excitation illumination; (4) can adjust the wavelength of light to avoid cell damage or reactions; and (5) can be used as a photostimulator. These results clearly illustrate that the proposed color DIRI can significantly extend WSI modalities for biological applications. PMID:28085892

  15. Approaching system equilibrium with accurate or not accurate feedback information in a two-route system

    NASA Astrophysics Data System (ADS)

    Zhao, Xiao-mei; Xie, Dong-fan; Li, Qi

    2015-02-01

    With the development of intelligent transport system, advanced information feedback strategies have been developed to reduce traffic congestion and enhance the capacity. However, previous strategies provide accurate information to travelers and our simulation results show that accurate information brings negative effects, especially in delay case. Because travelers prefer to the best condition route with accurate information, and delayed information cannot reflect current traffic condition but past. Then travelers make wrong routing decisions, causing the decrease of the capacity and the increase of oscillations and the system deviating from the equilibrium. To avoid the negative effect, bounded rationality is taken into account by introducing a boundedly rational threshold BR. When difference between two routes is less than the BR, routes have equal probability to be chosen. The bounded rationality is helpful to improve the efficiency in terms of capacity, oscillation and the gap deviating from the system equilibrium.

  16. Biology and management of ependymomas

    PubMed Central

    Wu, Jing; Armstrong, Terri S.; Gilbert, Mark R.

    2016-01-01

    Ependymomas are rare primary tumors of the central nervous system in children and adults that comprise histologically similar but genetically distinct subgroups. The tumor biology is typically more associated with the site of origin rather than being age-specific. Genetically distinct subgroups have been identified by genomic studies based on locations in classic grade II and III ependymomas. They are supratentorial ependymomas with C11orf95-RELA fusion or YAP1 fusion, infratentorial ependymomas with or without a hypermethylated phenotype (CIMP), and spinal cord ependymomas. Myxopapillary ependymomas and subependymomas have different biology than ependymomas with typical WHO grade II or III histology. Surgery and radiotherapy are the mainstays of treatment, while the role of chemotherapy has not yet been established. An in-depth understanding of tumor biology, developing reliable animal models that accurately reflect tumor molecule features, and high throughput drug screening are essential for developing new therapies. Collaborative efforts between scientists, physicians, and advocacy groups will enhance the translation of laboratory findings into clinical trials. Improvements in disease control underscore the need to incorporate assessment and management of patients' symptoms to ensure that treatment advances translate into improvement in quality of life. PMID:27022130

  17. Reflective array modeling for reflective and directional SAW transducers.

    PubMed

    Morgan, D P

    1998-01-01

    This paper presents a new approximate method for analyzing reflective SAW transducers, with much of the convenience of the coupled-mode (COM) method but with better accuracy. Transduction accuracy is obtained by incorporating the accurate electrostatic solution, giving for example correct harmonics, and allowance for electrode width variation, in a simple manner. Results are shown for a single-electrode transducer, Natural SPUDT and DART SPUDT, each using theoretically derived parameters. In contrast to the COM, the RAM can give accurate results for short or withdrawal-weighted transducers and for wide analysis bandwidth.

  18. Accurate elevation and normal moveout corrections of seismic reflection data on rugged topography

    USGS Publications Warehouse

    Liu, J.; Xia, J.; Chen, C.; Zhang, G.

    2005-01-01

    The application of the seismic reflection method is often limited in areas of complex terrain. The problem is the incorrect correction of time shifts caused by topography. To apply normal moveout (NMO) correction to reflection data correctly, static corrections are necessary to be applied in advance for the compensation of the time distortions of topography and the time delays from near-surface weathered layers. For environment and engineering investigation, weathered layers are our targets, so that the static correction mainly serves the adjustment of time shifts due to an undulating surface. In practice, seismic reflected raypaths are assumed to be almost vertical through the near-surface layers because they have much lower velocities than layers below. This assumption is acceptable in most cases since it results in little residual error for small elevation changes and small offsets in reflection events. Although static algorithms based on choosing a floating datum related to common midpoint gathers or residual surface-consistent functions are available and effective, errors caused by the assumption of vertical raypaths often generate pseudo-indications of structures. This paper presents the comparison of applying corrections based on the vertical raypaths and bias (non-vertical) raypaths. It also provides an approach of combining elevation and NMO corrections. The advantages of the approach are demonstrated by synthetic and real-world examples of multi-coverage seismic reflection surveys on rough topography. ?? The Royal Society of New Zealand 2005.

  19. Some biological reflections on the concept of life.

    PubMed

    Pennazio, Sergio

    2010-01-01

    Life is the natural phenomenon that has always aroused the largest interest of philosophers, theologians and scientists, on which a new science--biology--was founded two century ago just for throwing light on its mechanisms. As the pre-Hellenic culture was not able to separate distinctly philosophy from science, life was interpreted as a spurious flurry of the activity of Nature, in which religion, magic and science were interlaced in an intricate way. The Hippocratic medicine constituted the first attempt to focus attention on life by collecting some biological knowledge in order to maintain man's health. All the subsequent physiologists (from the Hellenic to the Latin period) benefited from the precepts of the Corpus Hippocraticum as long as the Christian religion imposed its theological rules that favoured the question relative to soul ever more closely interlaced with the physiology of body. The concept of life became therefore subjected to a number of opposite theories with strong prevalence of metaphysical conjectures until the 19th century but, in spite of this imposition, splendid successes were achieved by physiologists and naturalists such as Harvey, Descartes, Haller, Malpighi, Spallanzani, Wolff, and others, who laid the foundation of a biology that has Lamarck as promoter. The importance of Lamarck's biology came from the release from metaphysics with the introduction of physical and structural concepts which permeated the experimental biology to come. Three main events characterised the biology of the 19th century: i) the interplay of the new chemistry with biology, ii) the cell theory, iii) the concept of metabolism. These events led biology to the 20th century, the era of biochemistry and molecular genetics. The discoveries relative to metabolism characterised the first half of this century, while the second half was witness to the internal mechanisms regulating the life of cells, perhaps the most advanced success of the biology of all time. Today

  20. Cultural inter-population differences do not reflect biological distances: an example of interdisciplinary analysis of populations from Eastern Adriatic coast.

    PubMed

    Bašić, Željana; Fox, Ayano R; Anterić, Ivana; Jerković, Ivan; Polašek, Ozren; Anđelinović, Šimun; Holland, Mitchell M; Primorac, Dragan

    2015-06-01

    To compare the population group from the Šopot graveyard with population groups from traditional Croatian medieval graveyards by using anthropological, craniometrics, and mitochondrial (mtDNA) analysis and to examine if the cultural differences between population groups reflect biological differences. We determined sex, age at death, pathological, and traumatic changes of skeletal remains from the Šopot graveyard and compared them with a cumulative medieval sample from the same region. We also performed principal component analysis to compare skeletal remains from Šopot with those from Ostrovica and other Central European samples according to 8 cranial measurements. Finally, we compared 46 skeletons from Šopot with medieval (Ostrovica) and contemporary populations using mDNA haplogroup profiling. The remains from Šopot were similar to the cumulative sample in lifestyle and quality of life markers. Principal component analysis showed that they were closely related to Eastern Adriatic coast sites (including Ostrovica and Šopot) in terms of cranial morphology, indicating similar biological makeup. According to mDNA testing, Šopot population showed no significant differences in the haplogroup prevalence from either medieval or contemporary populations. This study shows that the Šopot population does not significantly differ from other medieval populations from this area. Besides similar quality of life markers, these populations also had similar biological markers. Substantial archeological differences can therefore be attributed to apparent cultural influences, which in this case do not reflect biological differences.

  1. Cultural inter-population differences do not reflect biological distances: an example of interdisciplinary analysis of populations from Eastern Adriatic coast

    PubMed Central

    Bašić, Željana; Fox, Ayano R; Anterić, Ivana; Jerković, Ivan; Polašek, Ozren; Anđelinović, Šimun; Holland, Mitchell M; Primorac, Dragan

    2015-01-01

    Aim To compare the population group from the Šopot graveyard with population groups from traditional Croatian medieval graveyards by using anthropological, craniometrics, and mitochondrial (mtDNA) analysis and to examine if the cultural differences between population groups reflect biological differences. Methods We determined sex, age at death, pathological, and traumatic changes of skeletal remains from the Šopot graveyard and compared them with a cumulative medieval sample from the same region. We also performed principal component analysis to compare skeletal remains from Šopot with those from Ostrovica and other Central European samples according to 8 cranial measurements. Finally, we compared 46 skeletons from Šopot with medieval (Ostrovica) and contemporary populations using mDNA haplogroup profiling. Results The remains from Šopot were similar to the cumulative sample in lifestyle and quality of life markers. Principal component analysis showed that they were closely related to Eastern Adriatic coast sites (including Ostrovica and Šopot) in terms of cranial morphology, indicating similar biological makeup. According to mDNA testing, Šopot population showed no significant differences in the haplogroup prevalence from either medieval or contemporary populations. Conclusion This study shows that the Šopot population does not significantly differ from other medieval populations from this area. Besides similar quality of life markers, these populations also had similar biological markers. Substantial archeological differences can therefore be attributed to apparent cultural influences, which in this case do not reflect biological differences. PMID:26088847

  2. Stream biological surveys - self-defense for coal mine operators

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

    Hampton, E.L.; Pennington, W.L.; Lackey, J.L.

    1979-12-01

    According to Section 779.20 of the Permanent Regulatory Program Regulations, Surface Coal Mining and Reclamation Operations, Department of the Interior, office of Surface Mining Reclamation and Enforcement, coal mine operators must provide information on fish and wildlife resources in order to obtain mining permits. Although considered to be a liability by many mine operators, stream biological surveys can, in reality, become a significant asset. When combined with appropriate water quality measurements, stream biological surveys can adequately assess a stream's health. Although initially adding cost, stream biological surveys can actually save money and potential litigation during the mining period. However, streammore » biological surveys must be conducted before any mining activity is initiated and should continue on a periodic basis thereafter. Only in this manner can mine operators be assured that biological measurements made on streams affected by their operation are accurate reflections of pre- and post-mining conditions. Armed with this vital information, mine operators have a basis to defend against any unjustified claims that their operations are having deleterious effects on the stream in question. This paper addresses the purpose, scope, methodology, and interpretation of results of stream biological surveys. Additionally, methods for utilizing information from stream biological surveys will be stressed.« less

  3. Models in biology: ‘accurate descriptions of our pathetic thinking’

    PubMed Central

    2014-01-01

    In this essay I will sketch some ideas for how to think about models in biology. I will begin by trying to dispel the myth that quantitative modeling is somehow foreign to biology. I will then point out the distinction between forward and reverse modeling and focus thereafter on the former. Instead of going into mathematical technicalities about different varieties of models, I will focus on their logical structure, in terms of assumptions and conclusions. A model is a logical machine for deducing the latter from the former. If the model is correct, then, if you believe its assumptions, you must, as a matter of logic, also believe its conclusions. This leads to consideration of the assumptions underlying models. If these are based on fundamental physical laws, then it may be reasonable to treat the model as ‘predictive’, in the sense that it is not subject to falsification and we can rely on its conclusions. However, at the molecular level, models are more often derived from phenomenology and guesswork. In this case, the model is a test of its assumptions and must be falsifiable. I will discuss three models from this perspective, each of which yields biological insights, and this will lead to some guidelines for prospective model builders. PMID:24886484

  4. Penetration depth of photons in biological tissues from hyperspectral imaging in shortwave infrared in transmission and reflection geometries.

    PubMed

    Zhang, Hairong; Salo, Daniel; Kim, David M; Komarov, Sergey; Tai, Yuan-Chuan; Berezin, Mikhail Y

    2016-12-01

    Measurement of photon penetration in biological tissues is a central theme in optical imaging. A great number of endogenous tissue factors such as absorption, scattering, and anisotropy affect the path of photons in tissue, making it difficult to predict the penetration depth at different wavelengths. Traditional studies evaluating photon penetration at different wavelengths are focused on tissue spectroscopy that does not take into account the heterogeneity within the sample. This is especially critical in shortwave infrared where the individual vibration-based absorption properties of the tissue molecules are affected by nearby tissue components. We have explored the depth penetration in biological tissues from 900 to 1650 nm using Monte–Carlo simulation and a hyperspectral imaging system with Michelson spatial contrast as a metric of light penetration. Chromatic aberration-free hyperspectral images in transmission and reflection geometries were collected with a spectral resolution of 5.27 nm and a total acquisition time of 3 min. Relatively short recording time minimized artifacts from sample drying. Results from both transmission and reflection geometries consistently revealed that the highest spatial contrast in the wavelength range for deep tissue lies within 1300 to 1375 nm; however, in heavily pigmented tissue such as the liver, the range 1550 to 1600 nm is also prominent.

  5. Accurate Measurements of Spectral Reflectance in Picasso's Guernica Painting.

    PubMed

    de Luna, Javier Muñoz; Fernandez-Balbuena, Antonio Alvarez; Vázquez, Daniel; Melgosa, Manuel; Durán, Humberto; García, Jorge; Muro, Carmen

    2016-01-01

    The use of non-invasive spectral measurements to control the conservation status is a part of the preventive conservation of artworks which nowadays is becoming increasingly interesting. This paper describes how to use a spectral measuring device and an illumination system specifically designed for such a task in a very large dimension artwork painting (7.8 m wide × 3.5 m high). The system, controlled by a Cartesian robot, allows spectral measurements in a spectral range of 400-780 nm. The measured data array has a total of 2201 circular regions with 5.5 mm spot diameter placed on a square grid. Colorimetric calculations performed from these spectral measurements may be used to characterize color shifts related to reflectance changes in specific areas of the paint. A color shifting from the expected gray has been shown. © The Author(s) 2015.

  6. Streamlined system for purifying and quantifying a diverse library of compounds and the effect of compound concentration measurements on the accurate interpretation of biological assay results.

    PubMed

    Popa-Burke, Ioana G; Issakova, Olga; Arroway, James D; Bernasconi, Paul; Chen, Min; Coudurier, Louis; Galasinski, Scott; Jadhav, Ajit P; Janzen, William P; Lagasca, Dennis; Liu, Darren; Lewis, Roderic S; Mohney, Robert P; Sepetov, Nikolai; Sparkman, Darren A; Hodge, C Nicholas

    2004-12-15

    As part of an overall systems approach to generating highly accurate screening data across large numbers of compounds and biological targets, we have developed and implemented streamlined methods for purifying and quantitating compounds at various stages of the screening process, coupled with automated "traditional" storage methods (DMSO, -20 degrees C). Specifically, all of the compounds in our druglike library are purified by LC/MS/UV and are then controlled for identity and concentration in their respective DMSO stock solutions by chemiluminescent nitrogen detection (CLND)/evaporative light scattering detection (ELSD) and MS/UV. In addition, the compound-buffer solutions used in the various biological assays are quantitated by LC/UV/CLND to determine the concentration of compound actually present during screening. Our results show that LC/UV/CLND/ELSD/MS is a widely applicable method that can be used to purify, quantitate, and identify most small organic molecules from compound libraries. The LC/UV/CLND technique is a simple and sensitive method that can be easily and cost-effectively employed to rapidly determine the concentrations of even small amounts of any N-containing compound in aqueous solution. We present data to establish error limits for concentration determination that are well within the overall variability of the screening process. This study demonstrates that there is a significant difference between the predicted amount of soluble compound from stock DMSO solutions following dilution into assay buffer and the actual amount present in assay buffer solutions, even at the low concentrations employed for the assays. We also demonstrate that knowledge of the concentrations of compounds to which the biological target is exposed is critical for accurate potency determinations. Accurate potency values are in turn particularly important for drug discovery, for understanding structure-activity relationships, and for building useful empirical models of

  7. Standardization of vitrinite reflectance measurements in shale petroleum systems: How accurate are my Ro data?

    USGS Publications Warehouse

    Hackley, Paul C.

    2014-01-01

    Vitrinite reflectance generally is considered the most robust thermal maturity parameter available for application to hydrocarbon exploration and petroleum system evaluation. However, until 2011 there was no standardized methodology available to provide guidelines for vitrinite reflectance measurements in shale. Efforts to correct this deficiency resulted in publication of ASTM D7708-11: Standard test method for microscopical determination of the reflectance of vitrinite dispersed in sedimentary rocks. In 2012-2013, an interlaboratory exercise was conducted to establish precision limits for the measurement technique. Six samples, representing a wide variety of shale, were tested in duplicate by 28 analysts in 22 laboratories from 14 countries. Samples ranged from immature to overmature (Ro 0.31-1.53%), from organic-rich to organic-lean (1-22 wt.% total organic carbon), and contained Type I (lacustrine), Type II (marine), and Type III (terrestrial) kerogens. Repeatability values (difference between repetitive results from same operator, same conditions) ranged from 0.03-0.11% absolute reflectance, whereas reproducibility values (difference between results obtained on same test material by different operators, different laboratories) ranged from 0.12-0.54% absolute reflectance. Repeatability and reproducibility degraded consistently with increasing maturity and decreasing organic content. However, samples with terrestrial kerogens (Type III) fell off this trend, showing improved levels of reproducibility due to higher vitrinite content and improved ease of identification. Operators did not consistently meet the reporting requirements of the test method, indicating that a common reporting template is required to improve data quality. The most difficult problem encountered was the petrographic distinction of solid bitumens and low-reflecting inert macerals from vitrinite when vitrinite occurred with reflectance ranges overlapping the other components. Discussion among

  8. Penetration depth of photons in biological tissues from hyperspectral imaging in shortwave infrared in transmission and reflection geometries

    PubMed Central

    Zhang, Hairong; Salo, Daniel; Kim, David M.; Komarov, Sergey; Tai, Yuan-Chuan; Berezin, Mikhail Y.

    2016-01-01

    Abstract. Measurement of photon penetration in biological tissues is a central theme in optical imaging. A great number of endogenous tissue factors such as absorption, scattering, and anisotropy affect the path of photons in tissue, making it difficult to predict the penetration depth at different wavelengths. Traditional studies evaluating photon penetration at different wavelengths are focused on tissue spectroscopy that does not take into account the heterogeneity within the sample. This is especially critical in shortwave infrared where the individual vibration-based absorption properties of the tissue molecules are affected by nearby tissue components. We have explored the depth penetration in biological tissues from 900 to 1650 nm using Monte–Carlo simulation and a hyperspectral imaging system with Michelson spatial contrast as a metric of light penetration. Chromatic aberration-free hyperspectral images in transmission and reflection geometries were collected with a spectral resolution of 5.27 nm and a total acquisition time of 3 min. Relatively short recording time minimized artifacts from sample drying. Results from both transmission and reflection geometries consistently revealed that the highest spatial contrast in the wavelength range for deep tissue lies within 1300 to 1375 nm; however, in heavily pigmented tissue such as the liver, the range 1550 to 1600 nm is also prominent. PMID:27930773

  9. Intellectual property rights, standards and data exchange in systems biology: Reflections from the IP Expert Meeting at the University of Luxembourg, 8-9 October 2015, ERASysAPP - ERA-Net for Systems Biology Applications.

    PubMed

    van Zimmeren, Esther; Rutz, Berthold; Minssen, Timo

    2016-12-01

    Intellectual property rights (IPRs) have become a key concern for researchers and industry in basically all high-tech sectors. IPRs regularly figure prominently in scientific journals and at scientific conferences and lead to dedicated workshops to increase the awareness and "IPR savviness" of scientists. In 2015, Biotechnology Journal published a report from an expert meeting on "Synthetic Biology & Intellectual Property Rights" organized by the Danish Agency for Science, Technology and Innovation sponsored by the European Research Area Network (ERA-Net) in Synthetic Biology (ERASynBio), in which we provided a number of recommendations for a variety of stakeholders [1]. The current article offers some deeper reflections about the interface between IPRs, standards and data exchange in systems biology (SysBio) resulting from an Expert Meeting funded by another ERA-Net, ERASysAPP. The meeting brought together experts and stakeholders (e.g. scientists, company representatives, officials from public funding organizations) in SysBio from different European countries. Despite the different profiles of the stakeholders at the meeting and the variety of interests, many concerns and opinions were shared. In case particular views were expressed by a specific type of stakeholder, this will be explicitly mentioned in the text. In this article, we explore a number of particularly relevant issues that were discussed at the meeting and offer some recommendations. SysBio involves the study of biological systems at a so-called systems level. This is not a new concept in the life sciences - many former approaches in physiology, enzymology and other scientific disciplines have already taken a systemic view of selected biological subjects. Yet, SysBio has gained strong interest within the past 10 to 15 years. One predominant reason and a critical prerequisite for this success story being that the relevant scientific methodologies and research tools have become far more powerful and

  10. Diffuse reflectance spectroscopy and optical polarization imaging of in-vivo biological tissue

    NASA Astrophysics Data System (ADS)

    Mora-Núñez, A.; Castillejos, Y.; García-Torales, G.; Martínez-Ponce, G.

    2013-11-01

    A number of optical techniques have been reported in the scientific literature as accomplishable methodologies to diagnose diseases in biological tissue, for instance, diffuse reflectance spectroscopy (DRS) and optical polarization imaging (OPI). The skin is the largest organ in the body and consists of three primary layers, namely, the epidermis (the outermost layer exposed to the world), the dermis, and the hypodermis. The epidermis changes from to site to site, mainly because of difference in hydration. A lower water content increase light scattering and reduce the penetration depth of radiation. In this work, two hairless mice have been selected to evaluate their skin features by using DRS and OPI. Four areas of the specimen body were chosen to realize the comparison: back, abdomen, tail, and head. From DRS, it was possible to distinguish the skin nature because of different blood irrigation at dermis. In the other hand, OPI shows pseudo-depolarizing regions in the measured Mueller images related to a spatially varying propagation of the scattered light. This provides information about the cell size in the irradiated skin.

  11. Functional proteomic analysis revealed ground-base ion radiations cannot reflect biological effects of space radiations of rice

    NASA Astrophysics Data System (ADS)

    Wang, Wei; Sun, Yeqing; Zhao, Qian; Han, Lu

    2016-07-01

    Highly ionizing radiation (HZE) in space is considered as main factor causing biological effects. Radiobiological studies during space flights are unrepeatable due to the variable space radiation environment, ground-base ion radiations are usually performed to simulate of the space biological effect. Spaceflights present a low-dose rate (0.1˜~0.3mGy/day) radiation environment inside aerocrafts while ground-base ion radiations present a much higher dose rate (100˜~500mGy/min). Whether ground-base ion radiation can reflect effects of space radiation is worth of evaluation. In this research, we compared the functional proteomic profiles of rice plants between on-ground simulated HZE particle radiation and spaceflight treatments. Three independent ground-base seed ionizing radiation experiments with different cumulative doses (dose range: 2˜~20000mGy) and different liner energy transfer (LET) values (13.3˜~500keV/μμm) and two independent seed spaceflight experiments onboard Chinese 20th satellite and SZ-6 spacecraft were carried out. Alterations in the proteome were analyzed by two-dimensional difference gel electrophoresis (2-D DIGE) with MALDI-TOF/TOF mass spectrometry identifications. 45 and 59 proteins showed significant (p<0.05) and reproducible quantitative differences in ground-base ion radiation and spaceflight experiments respectively. The functions of ground-base radiation and spaceflight proteins were both involved in a wide range of biological processes. Gene Ontology enrichment analysis further revealed that ground-base radiation responsive proteins were mainly involved in removal of superoxide radicals, defense response to stimulus and photosynthesis, while spaceflight responsive proteins mainly participate in nucleoside metabolic process, protein folding and phosphorylation. The results implied that ground-base radiations cannot truly reflect effects of spaceflight radiations, ground-base radiation was a kind of indirect effect to rice causing

  12. Autofluorescence and diffuse reflectance patterns in cervical spectroscopy

    NASA Astrophysics Data System (ADS)

    Marin, Nena Maribel

    Fluorescence and diffuse reflectance spectroscopy are two new optical technologies, which have shown promise to aid in the real time, non-invasive identification of cancers and precancers. Spectral patterns carry a fingerprint of scattering, absorption and fluorescence properties in tissue. Scattering, absorption and fluorescence in tissue are directly affected by biological features that are diagnostically significant, such as nuclear size, micro-vessel density, volume fraction of collagen fibers, tissue oxygenation and cell metabolism. Thus, analysis of spectral patterns can unlock a wealth of information directly related with the onset and progression of disease. Data from a Phase II clinical trial to assess the technical efficacy of fluorescence and diffuse reflectance spectroscopy acquired from 850 women at three clinical locations with two research grade optical devices is calibrated and analyzed. Tools to process and standardize spectra so that data from multiple spectrometers can be combined and analyzed are presented. Methodologies for calibration and quality assurance of optical systems are established to simplify design issues and ensure validity of data for future clinical trials. Empirically based algorithms, using multivariate statistical approaches are applied to spectra and evaluated as a clinical diagnostic tool. Physically based algorithms, using mathematical models of light propagation in tissue are presented. The presented mathematical model combines a diffusion theory in P3 approximation reflectance model and a 2-layer fluorescence model using exponential attenuation and diffusion theory. The resulting adjoint fluorescence and reflectance model extracts twelve optical properties characterizing fluorescence efficiency of cervical epithelium and stroma fluorophores, stromal hemoglobin and collagen absorption, oxygen saturation, and stromal scattering strength and shape. Validations with Monte Carlo simulations show that adjoint model extracted

  13. Secular change in chert distribution: a reflection of evolving biological participation in the silica cycle

    NASA Technical Reports Server (NTRS)

    Maliva, R. G.; Knoll, A. H.; Siever, R.

    1989-01-01

    In the modern oceans, the removal of dissolved silica from sea water is principally a biological process carried out by diatoms, with lesser contributions from radiolaria, silicoflagellates, and sponges. Because such silica in sediments is often redistributed locally during diagenesis to from nodular or bedded chert, stratigraphic changes in the facies distribution of early diagenetic chert provide important insights into the development of biological participation in the silica cycle. The abundance of chert in upper Proterozoic peritidal carbonates suggests that at this time silica was removed from seawater principally by abiological processes operating in part of the margins of the oceans. With the evolution of demosponges near the beginning of the Cambrian Period, subtidal biogenetic cherts became increasingly common, and with the Ordovician rise of radiolaria to ecological and biogeochemical prominence, sedimented skeletons became a principal sink for oceanic silica. Cherts of Silurian to Cretaceous age share many features of facies distribution and petrography but they differ from Cenozoic siliceous deposits. These differences are interpreted to reflect the mid-Cretaceous radiation of diatoms and their subsequent rise to domination of the silica cycle. Biogeochemical cycles provide an important framework for the paleobiological interpretation of the organisms that participate in them.

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

    DOEpatents

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

    1992-12-15

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

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

    DOEpatents

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

    1992-01-01

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

  16. Nursing students' reflections on racism.

    PubMed

    Schaefer, Karen Moore

    2008-01-01

    Racism is the systematic oppression of people of color at personal/interpersonal, institutional, and/or cultural levels. Discussions about racism often become emotional and personal. A discussion related to the accurate labeling of students on the basis of their heritage in an undergraduate professional issues class became emotionally charged. To prevent any further escalation of emotions, the author brought closure by asking students to read and write a reflective response to the Black Prayer. This article is a summary of urban nursing students' reflections and how giving voice to such reflections is a way of opening the door to frank discussions of racism and its effects.

  17. Documentation of pain care processes does not accurately reflect pain management delivered in primary care.

    PubMed

    Krebs, Erin E; Bair, Matthew J; Carey, Timothy S; Weinberger, Morris

    2010-03-01

    Researchers and quality improvement advocates sometimes use review of chart-documented pain care processes to assess the quality of pain management. Studies have found that primary care providers frequently fail to document pain assessment and management. To assess documentation of pain care processes in an academic primary care clinic and evaluate the validity of this documentation as a measure of pain care delivered. Prospective observational study. 237 adult patients at a university-affiliated internal medicine clinic who reported any pain in the last week. Immediately after a visit, we asked patients to report the pain treatment they received. Patients completed the Brief Pain Inventory (BPI) to assess pain severity at baseline and 1 month later. We extracted documentation of pain care processes from the medical record and used kappa statistics to assess agreement between documentation and patient report of pain treatment. Using multivariable linear regression, we modeled whether documented or patient-reported pain care predicted change in pain at 1 month. Participants' mean age was 53.7 years, 66% were female, and 74% had chronic pain. Physicians documented pain assessment for 83% of visits. Patients reported receiving pain treatment more often (67%) than was documented by physicians (54%). Agreement between documentation and patient report was moderate for receiving a new pain medication (k = 0.50) and slight for receiving pain management advice (k = 0.13). In multivariable models, documentation of new pain treatment was not associated with change in pain (p = 0.134). In contrast, patient-reported receipt of new pain treatment predicted pain improvement (p = 0.005). Chart documentation underestimated pain care delivered, compared with patient report. Documented pain care processes had no relationship with pain outcomes at 1 month, but patient report of receiving care predicted clinically significant improvement. Chart review measures may not accurately

  18. Method for accurate growth of vertical-cavity surface-emitting lasers

    DOEpatents

    Chalmers, Scott A.; Killeen, Kevin P.; Lear, Kevin L.

    1995-01-01

    We report a method for accurate growth of vertical-cavity surface-emitting lasers (VCSELs). The method uses a single reflectivity spectrum measurement to determine the structure of the partially completed VCSEL at a critical point of growth. This information, along with the extracted growth rates, allows imprecisions in growth parameters to be compensated for during growth of the remaining structure, which can then be completed with very accurate critical dimensions. Using this method, we can now routinely grow lasing VCSELs with Fabry-Perot cavity resonance wavelengths controlled to within 0.5%.

  19. Method for accurate growth of vertical-cavity surface-emitting lasers

    DOEpatents

    Chalmers, S.A.; Killeen, K.P.; Lear, K.L.

    1995-03-14

    The authors report a method for accurate growth of vertical-cavity surface-emitting lasers (VCSELs). The method uses a single reflectivity spectrum measurement to determine the structure of the partially completed VCSEL at a critical point of growth. This information, along with the extracted growth rates, allows imprecisions in growth parameters to be compensated for during growth of the remaining structure, which can then be completed with very accurate critical dimensions. Using this method, they can now routinely grow lasing VCSELs with Fabry-Perot cavity resonance wavelengths controlled to within 0.5%. 4 figs.

  20. Accurate color synthesis of three-dimensional objects in an image

    NASA Astrophysics Data System (ADS)

    Xin, John H.; Shen, Hui-Liang

    2004-05-01

    Our study deals with color synthesis of a three-dimensional object in an image; i.e., given a single image, a target color can be accurately mapped onto the object such that the color appearance of the synthesized object closely resembles that of the actual one. As it is almost impossible to acquire the complete geometric description of the surfaces of an object in an image, this study attempted to recover the implicit description of geometry for the color synthesis. The description was obtained from either a series of spectral reflectances or the RGB signals at different surface positions on the basis of the dichromatic reflection model. The experimental results showed that this implicit image-based representation is related to the object geometry and is sufficient for accurate color synthesis of three-dimensional objects in an image. The method established is applicable to the color synthesis of both rigid and deformable objects and should contribute to color fidelity in virtual design, manufacturing, and retailing.

  1. Automated selected reaction monitoring software for accurate label-free protein quantification.

    PubMed

    Teleman, Johan; Karlsson, Christofer; Waldemarson, Sofia; Hansson, Karin; James, Peter; Malmström, Johan; Levander, Fredrik

    2012-07-06

    Selected reaction monitoring (SRM) is a mass spectrometry method with documented ability to quantify proteins accurately and reproducibly using labeled reference peptides. However, the use of labeled reference peptides becomes impractical if large numbers of peptides are targeted and when high flexibility is desired when selecting peptides. We have developed a label-free quantitative SRM workflow that relies on a new automated algorithm, Anubis, for accurate peak detection. Anubis efficiently removes interfering signals from contaminating peptides to estimate the true signal of the targeted peptides. We evaluated the algorithm on a published multisite data set and achieved results in line with manual data analysis. In complex peptide mixtures from whole proteome digests of Streptococcus pyogenes we achieved a technical variability across the entire proteome abundance range of 6.5-19.2%, which was considerably below the total variation across biological samples. Our results show that the label-free SRM workflow with automated data analysis is feasible for large-scale biological studies, opening up new possibilities for quantitative proteomics and systems biology.

  2. Identification of Terrestrial Reflectance From Remote Sensing

    NASA Technical Reports Server (NTRS)

    Alter-Gartenberg, Rachel; Nolf, Scott R.; Stacy, Kathryn (Technical Monitor)

    2000-01-01

    Correcting for atmospheric effects is an essential part of surface-reflectance recovery from radiance measurements. Model-based atmospheric correction techniques enable an accurate identification and classification of terrestrial reflectances from multi-spectral imagery. Successful and efficient removal of atmospheric effects from remote-sensing data is a key factor in the success of Earth observation missions. This report assesses the performance, robustness and sensitivity of two atmospheric-correction and reflectance-recovery techniques as part of an end-to-end simulation of hyper-spectral acquisition, identification and classification.

  3. Reflections on Self-Reflection: Contemplating Flawed Self-Judgments in the Clinic, Classroom, and Office Cubicle.

    PubMed

    Dunning, David; Heath, Chip; Suls, Jerry M

    2018-03-01

    We reflect back on our 2004 monograph reviewing the implications of faulty self-judgment for health, education, and the workplace. The review proved popular, no doubt because the importance of accurate self-assessment is best reflected in just how broad the literature is that touches on this topic. We discuss opportunities and challenges to be found in the future study of self-judgment accuracy and error, and suggest that designing interventions aimed at improving self-judgments may prove to be a worthwhile but complex and nuanced task.

  4. Ocean color remote sensing using polarization properties of reflected sunlight

    NASA Technical Reports Server (NTRS)

    Frouin, R.; Pouliquen, E.; Breon, F.-M.

    1994-01-01

    The effects of the atmosphere and surface on sunlight backscattered to space by the ocean may be substantially reduced by using the unpolarized component of reflectance instead of total reflectance. At 450 nm, a wavelength of interest in ocean color remote sensing, and for typical conditions, 45% of the unpolarized reflectance may originate from the water body instead of 20% of the total reflectance, which represents a gain of a factor 2.2 in useful signal for water composition retrieval. The best viewing geometries are adjacent to the glitter region; they correspond to scattering angles around 100 deg, but they may change slightly depending on the polarization characteristics of the aerosols. As aerosol optical thickness increases, the atmosphere becomes less efficient at polarizing sunlight, and the enhancement of the water body contribution to unpolarized reflectance is reduced. Since the perturbing effects are smaller on unpolarized reflectance, at least for some viewing geometries, they may be more easily corrected, leading to a more accurate water-leaving signal and, therefore, more accurate estimates of phytoplankton pigment concentration.

  5. Fast and Accurate Circuit Design Automation through Hierarchical Model Switching.

    PubMed

    Huynh, Linh; Tagkopoulos, Ilias

    2015-08-21

    In computer-aided biological design, the trifecta of characterized part libraries, accurate models and optimal design parameters is crucial for producing reliable designs. As the number of parts and model complexity increase, however, it becomes exponentially more difficult for any optimization method to search the solution space, hence creating a trade-off that hampers efficient design. To address this issue, we present a hierarchical computer-aided design architecture that uses a two-step approach for biological design. First, a simple model of low computational complexity is used to predict circuit behavior and assess candidate circuit branches through branch-and-bound methods. Then, a complex, nonlinear circuit model is used for a fine-grained search of the reduced solution space, thus achieving more accurate results. Evaluation with a benchmark of 11 circuits and a library of 102 experimental designs with known characterization parameters demonstrates a speed-up of 3 orders of magnitude when compared to other design methods that provide optimality guarantees.

  6. The "What Is a System" Reflection Interview as a Knowledge Integration Activity for High School Students' Understanding of Complex Systems in Human Biology

    ERIC Educational Resources Information Center

    Tripto, Jaklin; Ben-Zvi Assaraf, Orit; Snapir, Zohar; Amit, Miriam

    2016-01-01

    This study examined the reflection interview as a tool for assessing and facilitating the use of "systems language" amongst 11th grade students who have recently completed their first year of high school biology. Eighty-three students composed two concept maps in the 10th grade--one at the beginning of the school year and one at its end.…

  7. Discrete ordinates solutions of nongray radiative transfer with diffusely reflecting walls

    NASA Technical Reports Server (NTRS)

    Menart, J. A.; Lee, Haeok S.; Kim, Tae-Kuk

    1993-01-01

    Nongray gas radiation in a plane parallel slab bounded by gray, diffusely reflecting walls is studied using the discrete ordinates method. The spectral equation of transfer is averaged over a narrow wavenumber interval preserving the spectral correlation effect. The governing equations are derived by considering the history of multiple reflections between two reflecting wails. A closure approximation is applied so that only a finite number of reflections have to be explicitly included. The closure solutions express the physics of the problem to a very high degree and show relatively little error. Numerical solutions are obtained by applying a statistical narrow-band model for gas properties and a discrete ordinates code. The net radiative wail heat fluxes and the radiative source distributions are obtained for different temperature profiles. A zeroth-degree formulation, where no wall reflection is handled explicitly, is sufficient to predict the radiative transfer accurately for most cases considered, when compared with increasingly accurate solutions based on explicitly tracing a larger number of wail reflections without any closure approximation applied.

  8. Diffuse reflectance relations based on diffusion dipole theory for large absorption and reduced scattering

    NASA Astrophysics Data System (ADS)

    Bremmer, Rolf H.; van Gemert, Martin J. C.; Faber, Dirk J.; van Leeuwen, Ton G.; Aalders, Maurice C. G.

    2013-08-01

    Diffuse reflectance spectra are used to determine the optical properties of biological samples. In medicine and forensic science, the turbid objects under study often possess large absorption and/or scattering properties. However, data analysis is frequently based on the diffusion approximation to the radiative transfer equation, implying that it is limited to tissues where the reduced scattering coefficient dominates over the absorption coefficient. Nevertheless, up to absorption coefficients of 20 m at reduced scattering coefficients of 1 and 11.5 mm-1, we observed excellent agreement (r2=0.994) between reflectance measurements of phantoms and the diffuse reflectance equation proposed by Zonios et al. [Appl. Opt. 38, 6628-6637 (1999)], derived as an approximation to one of the diffusion dipole equations of Farrell et al. [Med. Phys. 19, 879-888 (1992)]. However, two parameters were fitted to all phantom experiments, including strongly absorbing samples, implying that the reflectance equation differs from diffusion theory. Yet, the exact diffusion dipole approximation at high reduced scattering and absorption also showed agreement with the phantom measurements. The mathematical structure of the diffuse reflectance relation used, derived by Zonios et al. [Appl. Opt. 38, 6628-6637 (1999)], explains this observation. In conclusion, diffuse reflectance relations derived as an approximation to the diffusion dipole theory of Farrell et al. can analyze reflectance ratios accurately, even for much larger absorption than reduced scattering coefficients. This allows calibration of fiber-probe set-ups so that the object's diffuse reflectance can be related to its absorption even when large. These findings will greatly expand the application of diffuse reflection spectroscopy. In medicine, it may allow the use of blue/green wavelengths and measurements on whole blood, and in forensic science, it may allow inclusion of objects such as

  9. Nutritional status in sick children and adolescents is not accurately reflected by BMI-SDS.

    PubMed

    Fusch, Gerhard; Raja, Preeya; Dung, Nguyen Quang; Karaolis-Danckert, Nadina; Barr, Ronald; Fusch, Christoph

    2013-01-01

    Nutritional status provides helpful information of disease severity and treatment effectiveness. Body mass index standard deviation scores (BMI-SDS) provide an approximation of body composition and thus are frequently used to classify nutritional status of sick children and adolescents. However, the accuracy of estimating body composition in this population using BMI-SDS has not been assessed. Thus, this study aims to evaluate the accuracy of nutritional status classification in sick infants and adolescents using BMI-SDS, upon comparison to classification using percentage body fat (%BF) reference charts. BMI-SDS was calculated from anthropometric measurements and %BF was measured using dual-energy x-ray absorptiometry (DXA) for 393 sick children and adolescents (5 months-18 years). Subjects were classified by nutritional status (underweight, normal weight, overweight, and obese), using 2 methods: (1) BMI-SDS, based on age- and gender-specific percentiles, and (2) %BF reference charts (standard). Linear regression and a correlation analysis were conducted to compare agreement between both methods of nutritional status classification. %BF reference value comparisons were also made between 3 independent sources based on German, Canadian, and American study populations. Correlation between nutritional status classification by BMI-SDS and %BF agreed moderately (r (2) = 0.75, 0.76 in boys and girls, respectively). The misclassification of nutritional status in sick children and adolescents using BMI-SDS was 27% when using German %BF references. Similar rates observed when using Canadian and American %BF references (24% and 23%, respectively). Using BMI-SDS to determine nutritional status in a sick population is not considered an appropriate clinical tool for identifying individual underweight or overweight children or adolescents. However, BMI-SDS may be appropriate for longitudinal measurements or for screening purposes in large field studies. When accurate nutritional

  10. Accurate radiative transfer calculations for layered media.

    PubMed

    Selden, Adrian C

    2016-07-01

    Simple yet accurate results for radiative transfer in layered media with discontinuous refractive index are obtained by the method of K-integrals. These are certain weighted integrals applied to the angular intensity distribution at the refracting boundaries. The radiative intensity is expressed as the sum of the asymptotic angular intensity distribution valid in the depth of the scattering medium and a transient term valid near the boundary. Integrated boundary equations are obtained, yielding simple linear equations for the intensity coefficients, enabling the angular emission intensity and the diffuse reflectance (albedo) and transmittance of the scattering layer to be calculated without solving the radiative transfer equation directly. Examples are given of half-space, slab, interface, and double-layer calculations, and extensions to multilayer systems are indicated. The K-integral method is orders of magnitude more accurate than diffusion theory and can be applied to layered scattering media with a wide range of scattering albedos, with potential applications to biomedical and ocean optics.

  11. Biology Curriculum Reform in Venezuela.

    ERIC Educational Resources Information Center

    Rondon, Leonor Mariasole

    2001-01-01

    Describes science in the Venezuelan school system which reflects on the process of development followed to design and validate the Biology Study Programs (BSP) with the emphasis on the relevance of curricular changes proposed in biological science for secondary education. (Contains 19 references.) (ASK)

  12. Effects on biological systems of reflected light from a satellite power system

    NASA Technical Reports Server (NTRS)

    White, M.

    1981-01-01

    Light reflection produced by the satellite power system and the possible effects of that light on the human eye, plants, and animals were studied. For the human eye, two cases of reflected light, might cause eye damage if viewed for too long. These cases are: (1) if, while in low Earth orbit, the orbital transfer vehicle is misaligned to reflect the Sun to Earth there exists a maximum safe fixation time for the naked eye of 42.4 secs; (2) reflection from the aluminum paint on the back of the orbital transfer vehicle, while in or near low Earth orbit, can be safely viewed by the naked eye for 129 sec. For plants and animals the intensity and timing of light are not a major problem. Ways for reducing and/or eliminating the irradiances are proposed.

  13. Reflective-impulsive style and conceptual tempo in a gross motor task.

    PubMed

    Keller, J; Ripoll, H

    2001-06-01

    The reflective-impulsive construct refers to responses made slowly or quickly in a situation with high uncertainty. Children who are labeled "reflective" take a longer time to respond and make few errors, whereas "impulsive" children are fast and inaccurate. Although the validity of the test and the definition of reflective-impulsive style are well accepted, whether such respond fast or slow to all tasks is questioned. Some children do not fit the dichotomy. Two other groups arise, the fast-accurate and the slow-inaccurate. The response styles of 86 boys, ages 5, 7, and 9 years performing a gross motor task, i.e., hitting a ball with a racquet, were studied. Analysis indicated that the slowest children on the Matching Familiar Figures Test can be faster than the fastest ones and remain more accurate. As the definition of the reflective-impulsive style is based on time, the reflective ones might better be viewed as children who can adapt the response time to the context and thus be more efficient at problem-solving.

  14. An improved method to estimate reflectance parameters for high dynamic range imaging

    NASA Astrophysics Data System (ADS)

    Li, Shiying; Deguchi, Koichiro; Li, Renfa; Manabe, Yoshitsugu; Chihara, Kunihiro

    2008-01-01

    Two methods are described to accurately estimate diffuse and specular reflectance parameters for colors, gloss intensity and surface roughness, over the dynamic range of the camera used to capture input images. Neither method needs to segment color areas on an image, or to reconstruct a high dynamic range (HDR) image. The second method improves on the first, bypassing the requirement for specific separation of diffuse and specular reflection components. For the latter method, diffuse and specular reflectance parameters are estimated separately, using the least squares method. Reflection values are initially assumed to be diffuse-only reflection components, and are subjected to the least squares method to estimate diffuse reflectance parameters. Specular reflection components, obtained by subtracting the computed diffuse reflection components from reflection values, are then subjected to a logarithmically transformed equation of the Torrance-Sparrow reflection model, and specular reflectance parameters for gloss intensity and surface roughness are finally estimated using the least squares method. Experiments were carried out using both methods, with simulation data at different saturation levels, generated according to the Lambert and Torrance-Sparrow reflection models, and the second method, with spectral images captured by an imaging spectrograph and a moving light source. Our results show that the second method can estimate the diffuse and specular reflectance parameters for colors, gloss intensity and surface roughness more accurately and faster than the first one, so that colors and gloss can be reproduced more efficiently for HDR imaging.

  15. Do changes in biomarkers from space radiation reflect dose or risk?

    NASA Astrophysics Data System (ADS)

    Brooks, A.

    . Following low-LET radiation exposure, the biological response often does not increase as a linear function of dose. Thus, the RBE and the subsequent risk predicted is dependent on the dose where the two radiation types are compared. To avoid this problem the standard procedure is to use the dose and dose-rate response and compare the linear components of the two r diation exposures. Important riska comparisons are often done at very low doses, where the reference radiation may either increase or decrease as a function of dose. Since the low-LET exposure often does not produce a significant change above the background level of damage, the derived RBE factors can become very large.Studies using micronuclei as biomarkers following exposure to mono-energetic neutrons, x-rays and gamma rays delivered at very low doses (up to 0.10 Gy) demonstrated the differences in the shape of each dose-response relationship and the problems associated with the RBE. These studies show that RBE may not accurately reflect the hazards or risk associated with space radiation exposure. As additional measures of biological change are developed, it may become possible to base risk on biological change and not on changes in radiation doses. Research funded through grants # DE-FG03-99ER62787 from DOE Office of Biological and Environmental Research and RO1 CA74053-01 from NIH/NASA to Washington State University Tri-Cities.

  16. Do Predation Rates on Artificial Nests Accurately Reflect Predation Rates on Natural Bird Nests?

    Treesearch

    David I. King; Richard M. DeGraaf; Curtice R. Griffin; Thomas J. Maier

    1999-01-01

    Artificial nests are widely used in avian field studies. However, it is unclear how well predation rates on artificial nests reflect predation rates on natural nests. Therefore, we compared survival rates of artificial nests (unused natural nests baited with House Sparrow eggs) with survival rates of active bird nests in the same habitat at the same sites. Survival...

  17. An Extrapolation of a Radical Equation More Accurately Predicts Shelf Life of Frozen Biological Matrices.

    PubMed

    De Vore, Karl W; Fatahi, Nadia M; Sass, John E

    2016-08-01

    Arrhenius modeling of analyte recovery at increased temperatures to predict long-term colder storage stability of biological raw materials, reagents, calibrators, and controls is standard practice in the diagnostics industry. Predicting subzero temperature stability using the same practice is frequently criticized but nevertheless heavily relied upon. We compared the ability to predict analyte recovery during frozen storage using 3 separate strategies: traditional accelerated studies with Arrhenius modeling, and extrapolation of recovery at 20% of shelf life using either ordinary least squares or a radical equation y = B1x(0.5) + B0. Computer simulations were performed to establish equivalence of statistical power to discern the expected changes during frozen storage or accelerated stress. This was followed by actual predictive and follow-up confirmatory testing of 12 chemistry and immunoassay analytes. Linear extrapolations tended to be the most conservative in the predicted percent recovery, reducing customer and patient risk. However, the majority of analytes followed a rate of change that slowed over time, which was fit best to a radical equation of the form y = B1x(0.5) + B0. Other evidence strongly suggested that the slowing of the rate was not due to higher-order kinetics, but to changes in the matrix during storage. Predicting shelf life of frozen products through extrapolation of early initial real-time storage analyte recovery should be considered the most accurate method. Although in this study the time required for a prediction was longer than a typical accelerated testing protocol, there are less potential sources of error, reduced costs, and a lower expenditure of resources. © 2016 American Association for Clinical Chemistry.

  18. Accurate Structural Correlations from Maximum Likelihood Superpositions

    PubMed Central

    Theobald, Douglas L; Wuttke, Deborah S

    2008-01-01

    The cores of globular proteins are densely packed, resulting in complicated networks of structural interactions. These interactions in turn give rise to dynamic structural correlations over a wide range of time scales. Accurate analysis of these complex correlations is crucial for understanding biomolecular mechanisms and for relating structure to function. Here we report a highly accurate technique for inferring the major modes of structural correlation in macromolecules using likelihood-based statistical analysis of sets of structures. This method is generally applicable to any ensemble of related molecules, including families of nuclear magnetic resonance (NMR) models, different crystal forms of a protein, and structural alignments of homologous proteins, as well as molecular dynamics trajectories. Dominant modes of structural correlation are determined using principal components analysis (PCA) of the maximum likelihood estimate of the correlation matrix. The correlations we identify are inherently independent of the statistical uncertainty and dynamic heterogeneity associated with the structural coordinates. We additionally present an easily interpretable method (“PCA plots”) for displaying these positional correlations by color-coding them onto a macromolecular structure. Maximum likelihood PCA of structural superpositions, and the structural PCA plots that illustrate the results, will facilitate the accurate determination of dynamic structural correlations analyzed in diverse fields of structural biology. PMID:18282091

  19. Reflectance spectra of subarctic lichens

    NASA Technical Reports Server (NTRS)

    Petzold, Donald E.; Goward, Samuel N.

    1988-01-01

    Lichens constitute a major portion of the ground cover of high latitude environments, but little has been reported concerning their in situ solar spectral reflectance properties. Knowledge of these properties is important for the interpretation of remotely sensed observations from high latitude regions, as well as in studies of high latitude ecology and energy balance climatology. The spectral reflectance of common boreal vascular plants is similar to that of vascular plants of the midlatitudes. The dominant lichens, in contrast, display variable reflectance patterns in visible wavelengths. The relative reflectance peak at 0.55 microns, common to green vegetation, is absent or indistinct in spectra of pervasive boreal forest and tundra lichens, despite the presence of chlorophyll in the inner algal cells. Lichens of the dominant genus, Cladina, display strong absorption of ultraviolet energy and short-wavelength blue light relative to their absorption in other visible wavelengths. Since the Cladinae dominate both the surface vegetation in open woodlands of the boreal forest and the low arctic tundra, their unusual spectral reflectance patterns will enable accurate monitoring of the boreal forest-tundra ecotone and detection of its vigor and movement in the future.

  20. New Tools and New Biology: Recent Miniaturized Systems for Molecular and Cellular Biology

    PubMed Central

    Hamon, Morgan; Hong, Jong Wook

    2013-01-01

    Recent advances in applied physics and chemistry have led to the development of novel microfluidic systems. Microfluidic systems allow minute amounts of reagents to be processed using μm-scale channels and offer several advantages over conventional analytical devices for use in biological sciences: faster, more accurate and more reproducible analytical performance, reduced cell and reagent consumption, portability, and integration of functional components in a single chip. In this review, we introduce how microfluidics has been applied to biological sciences. We first present an overview of the fabrication of microfluidic systems and describe the distinct technologies available for biological research. We then present examples of microsystems used in biological sciences, focusing on applications in molecular and cellular biology. PMID:24305843

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

    PubMed

    Bonham, Kevin S; Stefan, Melanie I

    2017-10-01

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

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

    PubMed Central

    2017-01-01

    While women are generally underrepresented in STEM fields, there are noticeable differences between fields. For instance, the gender ratio in biology is more balanced than in computer science. We were interested in how this difference is reflected in the interdisciplinary field of computational/quantitative biology. To this end, we examined the proportion of female authors in publications from the PubMed and arXiv databases. There are fewer female authors on research papers in computational biology, as compared to biology in general. This is true across authorship position, year, and journal impact factor. A comparison with arXiv shows that quantitative biology papers have a higher ratio of female authors than computer science papers, placing computational biology in between its two parent fields in terms of gender representation. Both in biology and in computational biology, a female last author increases the probability of other authors on the paper being female, pointing to a potential role of female PIs in influencing the gender balance. PMID:29023441

  3. On the renormalisation of the diffusion asymptotics in the problem of reflection of a narrow optical beam from a biological medium

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

    Appanov, A Yu; Barabanenkov, Yu N

    2005-12-31

    An analytic hybrid method is considered for solving the stationary radiation transfer equation in the problem on reflection of a narrow laser beam from biological media such as the 2% aqueous solution of intralipid and erythrocyte suspension with the volume concentration (hematocrit) H=0.41. The method is based on the reciprocity of the Green function in the radiation transfer theory and on the iteration solution of the integral equation for this function. As a result, the ray intensity is represented as a sum of two terms. The first of them describes the contribution of finite-order scattering to the intensity of amore » beam diffusely reflected from the medium. The second term contains the explicit analytic expression for a spatially distributed effective source of diffuse radiation emerging from the deep layers of the medium to the surface. This approach substantially improves the diffusion approximation for the problem under study and allows one to obtain the uniform asymptotics of the reflection coefficient at the specified interval of distances between the radiation source and detector on the medium surface with the relative error within {+-}6% for the 2% intralipid emulsion and erythrocyte suspension (H=0.41). (radiation scattering)« less

  4. Generalized Fokker-Planck theory for electron and photon transport in biological tissues: application to radiotherapy.

    PubMed

    Olbrant, Edgar; Frank, Martin

    2010-12-01

    In this paper, we study a deterministic method for particle transport in biological tissues. The method is specifically developed for dose calculations in cancer therapy and for radiological imaging. Generalized Fokker-Planck (GFP) theory [Leakeas and Larsen, Nucl. Sci. Eng. 137 (2001), pp. 236-250] has been developed to improve the Fokker-Planck (FP) equation in cases where scattering is forward-peaked and where there is a sufficient amount of large-angle scattering. We compare grid-based numerical solutions to FP and GFP in realistic medical applications. First, electron dose calculations in heterogeneous parts of the human body are performed. Therefore, accurate electron scattering cross sections are included and their incorporation into our model is extensively described. Second, we solve GFP approximations of the radiative transport equation to investigate reflectance and transmittance of light in biological tissues. All results are compared with either Monte Carlo or discrete-ordinates transport solutions.

  5. Directional statistics-based reflectance model for isotropic bidirectional reflectance distribution functions.

    PubMed

    Nishino, Ko; Lombardi, Stephen

    2011-01-01

    We introduce a novel parametric bidirectional reflectance distribution function (BRDF) model that can accurately encode a wide variety of real-world isotropic BRDFs with a small number of parameters. The key observation we make is that a BRDF may be viewed as a statistical distribution on a unit hemisphere. We derive a novel directional statistics distribution, which we refer to as the hemispherical exponential power distribution, and model real-world isotropic BRDFs as mixtures of it. We derive a canonical probabilistic method for estimating the parameters, including the number of components, of this novel directional statistics BRDF model. We show that the model captures the full spectrum of real-world isotropic BRDFs with high accuracy, but a small footprint. We also demonstrate the advantages of the novel BRDF model by showing its use for reflection component separation and for exploring the space of isotropic BRDFs.

  6. Biological Feasibility of Measles Eradication

    PubMed Central

    Strebel, Peter

    2011-01-01

    Recent progress in reducing global measles mortality has renewed interest in measles eradication. Three biological criteria are deemed important for disease eradication: (1) humans are the sole pathogen reservoir; (2) accurate diagnostic tests exist; and (3) an effective, practical intervention is available at reasonable cost. Interruption of transmission in large geographical areas for prolonged periods further supports the feasibility of eradication. Measles is thought by many experts to meet these criteria: no nonhuman reservoir is known to exist, accurate diagnostic tests are available, and attenuated measles vaccines are effective and immunogenic. Measles has been eliminated in large geographical areas, including the Americas. Measles eradication is biologically feasible. The challenges for measles eradication will be logistical, political, and financial. PMID:21666201

  7. Mechanism for accurate, protein-assisted DNA annealing by Deinococcus radiodurans DdrB

    PubMed Central

    Sugiman-Marangos, Seiji N.; Weiss, Yoni M.; Junop, Murray S.

    2016-01-01

    Accurate pairing of DNA strands is essential for repair of DNA double-strand breaks (DSBs). How cells achieve accurate annealing when large regions of single-strand DNA are unpaired has remained unclear despite many efforts focused on understanding proteins, which mediate this process. Here we report the crystal structure of a single-strand annealing protein [DdrB (DNA damage response B)] in complex with a partially annealed DNA intermediate to 2.2 Å. This structure and supporting biochemical data reveal a mechanism for accurate annealing involving DdrB-mediated proofreading of strand complementarity. DdrB promotes high-fidelity annealing by constraining specific bases from unauthorized association and only releases annealed duplex when bound strands are fully complementary. To our knowledge, this mechanism provides the first understanding for how cells achieve accurate, protein-assisted strand annealing under biological conditions that would otherwise favor misannealing. PMID:27044084

  8. Global, long-term surface reflectance records from Landsat

    USDA-ARS?s Scientific Manuscript database

    Global, long-term monitoring of changes in Earth’s land surface requires quantitative comparisons of satellite images acquired under widely varying atmospheric conditions. Although physically based estimates of surface reflectance (SR) ultimately provide the most accurate representation of Earth’s s...

  9. Measuring Light Reflectance of BGO Crystal Surfaces

    NASA Astrophysics Data System (ADS)

    Janecek, Martin; Moses, William W.

    2008-10-01

    A scintillating crystal's surface reflectance has to be well understood in order to accurately predict and optimize the crystal's light collection through Monte Carlo simulations. In this paper, we measure the inner surface reflectance properties for BGO. The measurements include BGO crystals with a mechanically polished surface, rough-cut surface, and chemically etched surface, and with various reflectors attached, both air-coupled and with coupling compound. The measurements are performed with a laser aimed at the center of a hemispherical shaped BGO crystal. The hemispherical shape eliminates any non-perpendicular angles for light entering and exiting the crystal. The reflected light is collected with an array of photodiodes. The laser can be set at an arbitrary angle, and the photodiode array is rotated to fully cover 2pi of solid angle. The current produced in the photodiodes is readout with a digital multimeter connected through a multiplexer. The two rows of photodiodes achieve 5-degree by 4-degree resolution, and the current measurement has a dynamic range of 105:1. The acquired data was not described by the commonly assumed linear combination of specular and diffuse (Lambertian) distributions, except for a very few surfaces. Surface roughness proved to be the most important parameter when choosing crystal setup. The reflector choice was of less importance and of almost no consequence for rough-cut surfaces. Pure specular reflection distribution for all incidence angles was measured for polished surfaces with VM2000 film, while the most Lambertian distribution for any surface finish was measured for titanium dioxide paint. The distributions acquired in this paper will be used to create more accurate Monte Carlo models for light reflection distribution within BGO crystals.

  10. Light Field Imaging Based Accurate Image Specular Highlight Removal

    PubMed Central

    Wang, Haoqian; Xu, Chenxue; Wang, Xingzheng; Zhang, Yongbing; Peng, Bo

    2016-01-01

    Specular reflection removal is indispensable to many computer vision tasks. However, most existing methods fail or degrade in complex real scenarios for their individual drawbacks. Benefiting from the light field imaging technology, this paper proposes a novel and accurate approach to remove specularity and improve image quality. We first capture images with specularity by the light field camera (Lytro ILLUM). After accurately estimating the image depth, a simple and concise threshold strategy is adopted to cluster the specular pixels into “unsaturated” and “saturated” category. Finally, a color variance analysis of multiple views and a local color refinement are individually conducted on the two categories to recover diffuse color information. Experimental evaluation by comparison with existed methods based on our light field dataset together with Stanford light field archive verifies the effectiveness of our proposed algorithm. PMID:27253083

  11. Method and apparatus for characterizing reflected ultrasonic pulses

    NASA Technical Reports Server (NTRS)

    Yost, William T. (Inventor); Cantrell, John H., Jr. (Inventor)

    1991-01-01

    The invention is a method of and apparatus for characterizing the amplitudes of a sequence of reflected pulses R1, R2, and R3 by converting them into corresponding electric signals E1, E2, and E3 to substantially the same value during each sequence thereby restoring the reflected pulses R1, R2, and R3 to their initial reflection values by timing means, an exponential generator, and a time gain compensator. Envelope and baseline reject circuits permit the display and accurate location of the time spaced sequence of electric signals having substantially the same amplitude on a measurement scale on a suitable video display or oscilloscope.

  12. Reflecting on Graphs: Attributes of Graph Choice and Construction Practices in Biology

    ERIC Educational Resources Information Center

    Angra, Aakanksha; Gardner, Stephanie M.

    2017-01-01

    Undergraduate biology education reform aims to engage students in scientific practices such as experimental design, experimentation, and data analysis and communication. Graphs are ubiquitous in the biological sciences, and creating effective graphical representations involves quantitative and disciplinary concepts and skills. Past studies…

  13. Monte Carlo simulation of cutaneous absorption and reflectance for clear, matt and dark biological tissue with varicosities: an investigation for dermatological laser

    NASA Astrophysics Data System (ADS)

    Klouch, Nawel; Riane, Houaria; Hamdache, Fatima; Addi, Djamel

    2013-05-01

    We are interested in modeling the interaction between light and biological tissue from the Monte Carlo method which is an approach used to solve modeling problems in different physical domains. Through the Monte Carlo approach we are going to try to interpret the spectral response absorption, reflectance, transmittance of normal human tissue under its three dominant tints in the visible range (350-700) nm. Then we will focus on the spectral response of the human tissue with varicosities in order to determinate the optimal conditions of operating the semiconductor laser for esthetic aim.

  14. Self-reflection, gender and science achievement

    NASA Astrophysics Data System (ADS)

    Shoop, Kathleen A.

    Drawing on socio-cognitive learning theory, this study compared achievement scores of 134 male and female high school biology students randomly assigned to groups which either used self-reflection, used self-reflection and received feedback, or did not self-reflect. Following a pretest, the teacher provided self-reflection strategy instruction to students in the two intervention groups and then subsequently provided in-class self-reflection time for these groups. The posttest concluded the unit; the retention measure was five weeks later. A quasi-experimental 3 x 3 x 2 (time x intervention x gender) factorial repeated-measures control group design was used for this study; a repeated measures ANOVA and several one-way ANOVA's were used to answer the research questions. Results from the repeated-measures ANOVA revealed significant results for Time and Time x Intervention, with the reflection group demonstrating significantly lower gains from pretest to posttest than the other two groups. The ANOVA examining differences between those who reflected and those who reflected and received feedback provided significant results with similar results for the difference between the control group and the reflection group. For teachers and students this study provides several areas of practical significance. Primarily, teachers may find lower student achievement if students regularly self-reflect but do not receive feedback for their reflection.

  15. Dynamic Biological Functioning Important for Simulating and Stabilizing Ocean Biogeochemistry

    NASA Astrophysics Data System (ADS)

    Buchanan, P. J.; Matear, R. J.; Chase, Z.; Phipps, S. J.; Bindoff, N. L.

    2018-04-01

    The biogeochemistry of the ocean exerts a strong influence on the climate by modulating atmospheric greenhouse gases. In turn, ocean biogeochemistry depends on numerous physical and biological processes that change over space and time. Accurately simulating these processes is fundamental for accurately simulating the ocean's role within the climate. However, our simulation of these processes is often simplistic, despite a growing understanding of underlying biological dynamics. Here we explore how new parameterizations of biological processes affect simulated biogeochemical properties in a global ocean model. We combine 6 different physical realizations with 6 different biogeochemical parameterizations (36 unique ocean states). The biogeochemical parameterizations, all previously published, aim to more accurately represent the response of ocean biology to changing physical conditions. We make three major findings. First, oxygen, carbon, alkalinity, and phosphate fields are more sensitive to changes in the ocean's physical state. Only nitrate is more sensitive to changes in biological processes, and we suggest that assessment protocols for ocean biogeochemical models formally include the marine nitrogen cycle to assess their performance. Second, we show that dynamic variations in the production, remineralization, and stoichiometry of organic matter in response to changing environmental conditions benefit the simulation of ocean biogeochemistry. Third, dynamic biological functioning reduces the sensitivity of biogeochemical properties to physical change. Carbon and nitrogen inventories were 50% and 20% less sensitive to physical changes, respectively, in simulations that incorporated dynamic biological functioning. These results highlight the importance of a dynamic biology for ocean properties and climate.

  16. Two years comparative studies on biological effects of environmental UV radiation

    NASA Astrophysics Data System (ADS)

    Grof, P.; Ronto, Gyorgyi; Gaspar, S.; Berces, A.; Szabo, Laszlo D.

    1994-07-01

    A method has been developed for determination of the biologically effective UV dose based on T7 phage as biosensor. In field experiments clockwork driven telescope has been used for determining doses from direct and global (direct plus diffuse) solar radiation. On fine summer days at mid-latitude this arrangement allowed the following comparisons: measured doses from direct and global radiation obtained at the same time and measuring site reflecting the biological importance of diffuse radiation; direct and global radiation obtained at the same time and measuring site reflecting the biological importance of diffuse radiation; direct and global doses obtained at the same time on different measuring sites (downtown, suburb, outside the town) reflecting the differences caused by air quality; direct and global doses obtained on the same measuring place, in summertime of two different years reflecting the importance of the long-term measurements for estimating the biological risk caused by increased UV-B radiation; measured data and model calculations.

  17. A reflection model for eclipsing binary stars

    NASA Technical Reports Server (NTRS)

    Wood, D. B.

    1973-01-01

    A highly accurate reflection model has been developed which emphasizes efficiency of computer calculation. It is assumed that the heating of the irradiated star must depend upon the following properties of the irradiating star: (1) effective temperature; (2) apparent area as seen from a point on the surface of the irradiated star; (3) limb darkening; and (4) zenith distance of the apparent centre as seen from a point on the surface of the irradiated star. The algorithm eliminates the need to integrate over the irradiating star while providing a highly accurate representation of the integrated bolometric flux, even for gravitationally distorted stars.

  18. Scaling in cognitive performance reflects multiplicative multifractal cascade dynamics

    PubMed Central

    Stephen, Damian G.; Anastas, Jason R.; Dixon, James A.

    2012-01-01

    Self-organized criticality purports to build multi-scaled structures out of local interactions. Evidence of scaling in various domains of biology may be more generally understood to reflect multiplicative interactions weaving together many disparate scales. The self-similarity of power-law scaling entails homogeneity: fluctuations distribute themselves similarly across many spatial and temporal scales. However, this apparent homogeneity can be misleading, especially as it spans more scales. Reducing biological processes to one power-law relationship neglects rich cascade dynamics. We review recent research into multifractality in executive-function cognitive tasks and propose that scaling reflects not criticality but instead interactions across multiple scales and among fluctuations of multiple sizes. PMID:22529819

  19. Accurate Phylogenetic Tree Reconstruction from Quartets: A Heuristic Approach

    PubMed Central

    Reaz, Rezwana; Bayzid, Md. Shamsuzzoha; Rahman, M. Sohel

    2014-01-01

    Supertree methods construct trees on a set of taxa (species) combining many smaller trees on the overlapping subsets of the entire set of taxa. A ‘quartet’ is an unrooted tree over taxa, hence the quartet-based supertree methods combine many -taxon unrooted trees into a single and coherent tree over the complete set of taxa. Quartet-based phylogeny reconstruction methods have been receiving considerable attentions in the recent years. An accurate and efficient quartet-based method might be competitive with the current best phylogenetic tree reconstruction methods (such as maximum likelihood or Bayesian MCMC analyses), without being as computationally intensive. In this paper, we present a novel and highly accurate quartet-based phylogenetic tree reconstruction method. We performed an extensive experimental study to evaluate the accuracy and scalability of our approach on both simulated and biological datasets. PMID:25117474

  20. High-Throughput Phenotyping of Maize Leaf Physiological and Biochemical Traits Using Hyperspectral Reflectance1[OPEN

    PubMed Central

    Yendrek, Craig R.; Tomaz, Tiago; Montes, Christopher M.; Cao, Youyuan; Morse, Alison M.; Brown, Patrick J.; McIntyre, Lauren M.; Leakey, Andrew D.B.

    2017-01-01

    High-throughput, noninvasive field phenotyping has revealed genetic variation in crop morphological, developmental, and agronomic traits, but rapid measurements of the underlying physiological and biochemical traits are needed to fully understand genetic variation in plant-environment interactions. This study tested the application of leaf hyperspectral reflectance (λ = 500–2,400 nm) as a high-throughput phenotyping approach for rapid and accurate assessment of leaf photosynthetic and biochemical traits in maize (Zea mays). Leaf traits were measured with standard wet-laboratory and gas-exchange approaches alongside measurements of leaf reflectance. Partial least-squares regression was used to develop a measure of leaf chlorophyll content, nitrogen content, sucrose content, specific leaf area, maximum rate of phosphoenolpyruvate carboxylation, [CO2]-saturated rate of photosynthesis, and leaf oxygen radical absorbance capacity from leaf reflectance spectra. Partial least-squares regression models accurately predicted five out of seven traits and were more accurate than previously used simple spectral indices for leaf chlorophyll, nitrogen content, and specific leaf area. Correlations among leaf traits and statistical inferences about differences among genotypes and treatments were similar for measured and modeled data. The hyperspectral reflectance approach to phenotyping was dramatically faster than traditional measurements, enabling over 1,000 rows to be phenotyped during midday hours over just 2 to 4 d, and offers a nondestructive method to accurately assess physiological and biochemical trait responses to environmental stress. PMID:28049858

  1. The Experience of Addiction as Told by the Addicted: Incorporating Biological Understandings into Self-Story

    PubMed Central

    Hammer, Rachel R; Dingel, Molly J; Ostergren, Jenny E; Nowakowski, Katherine E; Koenig, Barbara A

    2012-01-01

    How do the addicted view addiction against the framework of formal theories that attempt to explain the condition? In this empirical paper, we report on the lived experience of addiction based on 63 semi-structured, open-ended interviews with individuals in treatment for alcohol and nicotine abuse at five sites in Minnesota. Using qualitative analysis, we identified four themes that provide insights into understanding how people who are addicted view their addiction, with particular emphasis on the biological model. More than half of our sample articulated a biological understanding of addiction as a disease. Themes did not cluster by addictive substance used; however, biological understandings of addiction did cluster by treatment center. Biological understandings have the potential to become dominant narratives of addiction in the current era. Though the desire for a “unified theory” of addiction seems curiously seductive to scholars, it lacks utility. Conceptual “disarray” may actually reflect a more accurate representation of the illness as told by those who live with it. For practitioners in the field of addiction, we suggest the practice of narrative medicine with its ethic of negative capability as a useful approach for interpreting and relating to diverse experiences of disease and illness. PMID:23081782

  2. Planar Reflection of Gaseous Detonations

    NASA Astrophysics Data System (ADS)

    Damazo, Jason Scott

    Pipes containing flammable gaseous mixtures may be subjected to internal detonation. When the detonation normally impinges on a closed end, a reflected shock wave is created to bring the flow back to rest. This study built on the work of Karnesky (2010) and examined deformation of thin-walled stainless steel tubes subjected to internal reflected gaseous detonations. A ripple pattern was observed in the tube wall for certain fill pressures, and a criterion was developed that predicted when the ripple pattern would form. A two-dimensional finite element analysis was performed using Johnson-Cook material properties; the pressure loading created by reflected gaseous detonations was accounted for with a previously developed pressure model. The residual plastic strain between experiments and computations was in good agreement. During the examination of detonation-driven deformation, discrepancies were discovered in our understanding of reflected gaseous detonation behavior. Previous models did not accurately describe the nature of the reflected shock wave, which motivated further experiments in a detonation tube with optical access. Pressure sensors and schlieren images were used to examine reflected shock behavior, and it was determined that the discrepancies were related to the reaction zone thickness extant behind the detonation front. During these experiments reflected shock bifurcation did not appear to occur, but the unfocused visualization system made certainty impossible. This prompted construction of a focused schlieren system that investigated possible shock wave-boundary layer interaction, and heat-flux gauges analyzed the boundary layer behind the detonation front. Using these data with an analytical boundary layer solution, it was determined that the strong thermal boundary layer present behind the detonation front inhibits the development of reflected shock wave bifurcation.

  3. Accurate evaluation and analysis of functional genomics data and methods

    PubMed Central

    Greene, Casey S.; Troyanskaya, Olga G.

    2016-01-01

    The development of technology capable of inexpensively performing large-scale measurements of biological systems has generated a wealth of data. Integrative analysis of these data holds the promise of uncovering gene function, regulation, and, in the longer run, understanding complex disease. However, their analysis has proved very challenging, as it is difficult to quickly and effectively assess the relevance and accuracy of these data for individual biological questions. Here, we identify biases that present challenges for the assessment of functional genomics data and methods. We then discuss evaluation methods that, taken together, begin to address these issues. We also argue that the funding of systematic data-driven experiments and of high-quality curation efforts will further improve evaluation metrics so that they more-accurately assess functional genomics data and methods. Such metrics will allow researchers in the field of functional genomics to continue to answer important biological questions in a data-driven manner. PMID:22268703

  4. Reflective terahertz (THz) imaging: system calibration using hydration phantoms

    NASA Astrophysics Data System (ADS)

    Bajwa, Neha; Garritano, James; Lee, Yoon Kyung; Tewari, Priyamvada; Sung, Shijun; Maccabi, Ashkan; Nowroozi, Bryan; Babakhanian, Meghedi; Sanghvi, Sajan; Singh, Rahul; Grundfest, Warren; Taylor, Zachary

    2013-02-01

    Terahertz (THz) hydration sensing continues to gain traction in the medical imaging community due to its unparalleled sensitivity to tissue water content. Rapid and accurate detection of fluid shifts following induction of thermal skin burns as well as remote corneal hydration sensing have been previously demonstrated in vivo using reflective, pulsed THz imaging. The hydration contrast sensing capabilities of this technology were recently confirmed in a parallel 7 Tesla Magnetic Resonance (MR) imaging study, in which burn areas are associated with increases in local mobile water content. Successful clinical translation of THz sensing, however, still requires quantitative assessments of system performance measurements, specifically hydration concentration sensitivity, with tissue substitutes. This research aims to calibrate the sensitivity of a novel, reflective THz system to tissue water content through the use of hydration phantoms for quantitative comparisons of THz hydration imagery.Gelatin phantoms were identified as an appropriate tissue-mimicking model for reflective THz applications, and gel composition, comprising mixtures of water and protein, was varied between 83% to 95% hydration, a physiologically relevant range. A comparison of four series of gelatin phantom studies demonstrated a positive linear relationship between THz reflectivity and water concentration, with statistically significant hydration sensitivities (p < .01) ranging between 0.0209 - 0.038% (reflectivity: %hydration). The THz-phantom interaction is simulated with a three-layer model using the Transfer Matrix Method with agreement in hydration trends. Having demonstrated the ability to accurately and noninvasively measure water content in tissue equivalent targets with high sensitivity, reflective THz imaging is explored as a potential tool for early detection and intervention of corneal pathologies.

  5. Visualizing time-related data in biology, a review

    PubMed Central

    Secrier, Maria; Schneider, Reinhard

    2014-01-01

    Time is of the essence in biology as in so much else. For example, monitoring disease progression or the timing of developmental defects is important for the processes of drug discovery and therapy trials. Furthermore, an understanding of the basic dynamics of biological phenomena that are often strictly time regulated (e.g. circadian rhythms) is needed to make accurate inferences about the evolution of biological processes. Recent advances in technologies have enabled us to measure timing effects more accurately and in more detail. This has driven related advances in visualization and analysis tools that try to effectively exploit this data. Beyond timeline plots, notable attempts at more involved temporal interpretation have been made in recent years, but awareness of the available resources is still limited within the scientific community. Here, we review some advances in biological visualization of time-driven processes and consider how they aid data analysis and interpretation. PMID:23585583

  6. Growth/reflectance model interface for wheat and corresponding model

    NASA Technical Reports Server (NTRS)

    Suits, G. H.; Sieron, R.; Odenweller, J.

    1984-01-01

    The use of modeling to explore the possibility of discovering new and useful crop condition indicators which might be available from the Thematic Mapper and to connect these symptoms to the biological causes in the crop is discussed. A crop growth model was used to predict the day to day growth features of the crop as it responds biologically to the various environmental factors. A reflectance model was used to predict the character of the interaction of daylight with the predicted growth features. An atmospheric path radiance was added to the reflected daylight to simulate the radiance appearing at the sensor. Finally, the digitized data sent to a ground station were calculated. The crop under investigation is wheat.

  7. Biological Races in Humans

    PubMed Central

    Templeton, Alan R.

    2013-01-01

    Races may exist in humans in a cultural sense, but biological concepts of race are needed to access their reality in a non-species-specific manner and to see if cultural categories correspond to biological categories within humans. Modern biological concepts of race can be implemented objectively with molecular genetic data through hypothesis-testing. Genetic data sets are used to see if biological races exist in humans and in our closest evolutionary relative, the chimpanzee. Using the two most commonly used biological concepts of race, chimpanzees are indeed subdivided into races but humans are not. Adaptive traits, such as skin color, have frequently been used to define races in humans, but such adaptive traits reflect the underlying environmental factor to which they are adaptive and not overall genetic differentiation, and different adaptive traits define discordant groups. There are no objective criteria for choosing one adaptive trait over another to define race. As a consequence, adaptive traits do not define races in humans. Much of the recent scientific literature on human evolution portrays human populations as separate branches on an evolutionary tree. A tree-like structure among humans has been falsified whenever tested, so this practice is scientifically indefensible. It is also socially irresponsible as these pictorial representations of human evolution have more impact on the general public than nuanced phrases in the text of a scientific paper. Humans have much genetic diversity, but the vast majority of this diversity reflects individual uniqueness and not race. PMID:23684745

  8. Calculation of vitrinite reflectance from thermal histories: A comparison of some methods

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

    Morrow, D.W.; Issler, D.R.

    1993-04-01

    Vitrinite reflectance values (%R[sub o]) calculated from commonly used methods are compared with respect to time invariant temperatures and constant heating rates. Two monofunctional methods, one involving a time-temperature index to vitrinite reflectance correlation (TTI-%R[sub o]) to depth correlation, yield vitrinite reflectance values that are similar to those calculated by recently published Arrhenius-based methods, such as EASY%R[sub o]. The approximate agreement between these methods supports the perception that the EASY%R[sub o] algorithm is the most accurate method for the prediction of vitrinite reflectances throughout the range of organic maturity normally encountered. However, calibration of these methods against vitrinite reflectance datamore » from two basin sequences with well-documented geologic histories indicates that, although the EASY%R[sub o] method has wide applicability, it slightly overestimates vitrinite reflectances in strata of low to medium maturity up to a %R[sub o] value of 0.9%. The two monofunctional methods may be more accurate for prediction of vitrinite reflectances in similar sequences of low maturity. An older, but previously widely accepted TTI-%R[sub O] correlation consistently overestimates vitrinite reflectances with respect to other methods. Underestimation of paleogeothermal gradients in the original calibration of time-temperature history to vitrinite reflectance may have introduced a systematic bias to the TTI-%R[sub o] correlation used in this method. Also, incorporation of TAI (thermal alteration index) data and its conversion to %R[sub o]-equivalent values may have introduced inaccuracies. 36 refs., 7 figs.« less

  9. 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).

  10. Screening vaccine formulations for biological activity using fresh human whole blood

    PubMed Central

    Brookes, Roger H; Hakimi, Jalil; Ha, Yukyung; Aboutorabian, Sepideh; Ausar, Salvador F; Hasija, Manvi; Smith, Steven G; Todryk, Stephen M; Dockrell, Hazel M; Rahman, Nausheen

    2014-01-01

    Understanding the relevant biological activity of any pharmaceutical formulation destined for human use is crucial. For vaccine-based formulations, activity must reflect the expected immune response, while for non-vaccine therapeutic agents, such as monoclonal antibodies, a lack of immune response to the formulation is desired. During early formulation development, various biochemical and biophysical characteristics can be monitored in a high-throughput screening (HTS) format. However, it remains impractical and arguably unethical to screen samples in this way for immunological functionality in animal models. Furthermore, data for immunological functionality lag formulation design by months, making it cumbersome to relate back to formulations in real-time. It is also likely that animal testing may not accurately reflect the response in humans. For a more effective formulation screen, a human whole blood (hWB) approach can be used to assess immunological functionality. The functional activity relates directly to the human immune response to a complete formulation (adjuvant/antigen) and includes adjuvant response, antigen response, adjuvant-modulated antigen response, stability, and potentially safety. The following commentary discusses the hWB approach as a valuable new tool to de-risk manufacture, formulation design, and clinical progression. PMID:24401565

  11. Screening vaccine formulations for biological activity using fresh human whole blood.

    PubMed

    Brookes, Roger H; Hakimi, Jalil; Ha, Yukyung; Aboutorabian, Sepideh; Ausar, Salvador F; Hasija, Manvi; Smith, Steven G; Todryk, Stephen M; Dockrell, Hazel M; Rahman, Nausheen

    2014-01-01

    Understanding the relevant biological activity of any pharmaceutical formulation destined for human use is crucial. For vaccine-based formulations, activity must reflect the expected immune response, while for non-vaccine therapeutic agents, such as monoclonal antibodies, a lack of immune response to the formulation is desired. During early formulation development, various biochemical and biophysical characteristics can be monitored in a high-throughput screening (HTS) format. However, it remains impractical and arguably unethical to screen samples in this way for immunological functionality in animal models. Furthermore, data for immunological functionality lag formulation design by months, making it cumbersome to relate back to formulations in real-time. It is also likely that animal testing may not accurately reflect the response in humans. For a more effective formulation screen, a human whole blood (hWB) approach can be used to assess immunological functionality. The functional activity relates directly to the human immune response to a complete formulation (adjuvant/antigen) and includes adjuvant response, antigen response, adjuvant-modulated antigen response, stability, and potentially safety. The following commentary discusses the hWB approach as a valuable new tool to de-risk manufacture, formulation design, and clinical progression.

  12. CUFID-query: accurate network querying through random walk based network flow estimation.

    PubMed

    Jeong, Hyundoo; Qian, Xiaoning; Yoon, Byung-Jun

    2017-12-28

    Functional modules in biological networks consist of numerous biomolecules and their complicated interactions. Recent studies have shown that biomolecules in a functional module tend to have similar interaction patterns and that such modules are often conserved across biological networks of different species. As a result, such conserved functional modules can be identified through comparative analysis of biological networks. In this work, we propose a novel network querying algorithm based on the CUFID (Comparative network analysis Using the steady-state network Flow to IDentify orthologous proteins) framework combined with an efficient seed-and-extension approach. The proposed algorithm, CUFID-query, can accurately detect conserved functional modules as small subnetworks in the target network that are expected to perform similar functions to the given query functional module. The CUFID framework was recently developed for probabilistic pairwise global comparison of biological networks, and it has been applied to pairwise global network alignment, where the framework was shown to yield accurate network alignment results. In the proposed CUFID-query algorithm, we adopt the CUFID framework and extend it for local network alignment, specifically to solve network querying problems. First, in the seed selection phase, the proposed method utilizes the CUFID framework to compare the query and the target networks and to predict the probabilistic node-to-node correspondence between the networks. Next, the algorithm selects and greedily extends the seed in the target network by iteratively adding nodes that have frequent interactions with other nodes in the seed network, in a way that the conductance of the extended network is maximally reduced. Finally, CUFID-query removes irrelevant nodes from the querying results based on the personalized PageRank vector for the induced network that includes the fully extended network and its neighboring nodes. Through extensive

  13. pyQms enables universal and accurate quantification of mass spectrometry data.

    PubMed

    Leufken, Johannes; Niehues, Anna; Sarin, L Peter; Wessel, Florian; Hippler, Michael; Leidel, Sebastian A; Fufezan, Christian

    2017-10-01

    Quantitative mass spectrometry (MS) is a key technique in many research areas (1), including proteomics, metabolomics, glycomics, and lipidomics. Because all of the corresponding molecules can be described by chemical formulas, universal quantification tools are highly desirable. Here, we present pyQms, an open-source software for accurate quantification of all types of molecules measurable by MS. pyQms uses isotope pattern matching that offers an accurate quality assessment of all quantifications and the ability to directly incorporate mass spectrometer accuracy. pyQms is, due to its universal design, applicable to every research field, labeling strategy, and acquisition technique. This opens ultimate flexibility for researchers to design experiments employing innovative and hitherto unexplored labeling strategies. Importantly, pyQms performs very well to accurately quantify partially labeled proteomes in large scale and high throughput, the most challenging task for a quantification algorithm. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  14. Hemispherical reflectance model for passive images in an outdoor environment.

    PubMed

    Kim, Charles C; Thai, Bea; Yamaoka, Neil; Aboutalib, Omar

    2015-05-01

    We present a hemispherical reflectance model for simulating passive images in an outdoor environment where illumination is provided by natural sources such as the sun and the clouds. While the bidirectional reflectance distribution function (BRDF) accurately produces radiance from any objects after the illumination, using the BRDF in calculating radiance requires double integration. Replacing the BRDF by hemispherical reflectance under the natural sources transforms the double integration into a multiplication. This reduces both storage space and computation time. We present the formalism for the radiance of the scene using hemispherical reflectance instead of BRDF. This enables us to generate passive images in an outdoor environment taking advantage of the computational and storage efficiencies. We show some examples for illustration.

  15. Premature trial discontinuation often not accurately reflected in registries: comparison of registry records with publications.

    PubMed

    Alturki, Reem; Schandelmaier, Stefan; Olu, Kelechi Kalu; von Niederhäusern, Belinda; Agarwal, Arnav; Frei, Roy; Bhatnagar, Neera; Hooft, Lotty; von Elm, Erik; Briel, Matthias

    2017-01-01

    One quarter of randomized clinical trials (RCTs) are prematurely discontinued and frequently remain unpublished. Trial registries can document whether a trial is ongoing, suspended, discontinued, or completed and therefore represent an important source for trial status information. The accuracy of this information is unclear. To examine the accuracy of completion status and reasons for discontinuation documented in trial registries as compared to corresponding publications of discontinued RCTs and to investigate potential predictors for accurate trial status information in registries. We conducted a cross-sectional study comparing information provided in publications (reference standard) to corresponding registry entries. First, we reviewed publications of RCTs providing information on both discontinuation and registration. We identified eligible publications through systematic searches of MEDLINE and EMBASE (2010-2014) and an international cohort of 1,017 RCTs initiated between 2000 and 2003. Second, pairs of investigators independently and in duplicate extracted data from publications and corresponding registry records. Third, for each discontinued RCT, we compared publication information to registry information. We used multivariable regression to examine whether accurate labeling of trials as discontinued (vs. other status) in the registry was associated with recent initiation of RCT, industry sponsorship, multicenter design, or larger sample size. We identified 173 publications of RCTs that were discontinued due to slow recruitment (55%), harm (16%), futility (11%), benefit (5%), other reasons (3%), or multiple reasons (9%). Trials were registered with clinicaltrials.gov (77%), isrctn.com (14%), or other registries (8%). Of the 173 corresponding registry records, 77 (45%) trials were labeled as discontinued and 57 (33%) provided a reason for discontinuation (of which 53, 93%, provided the same reason as in the publication). Labeling of discontinued trials as

  16. Mass spectrometry-based protein identification with accurate statistical significance assignment.

    PubMed

    Alves, Gelio; Yu, Yi-Kuo

    2015-03-01

    Assigning statistical significance accurately has become increasingly important as metadata of many types, often assembled in hierarchies, are constructed and combined for further biological analyses. Statistical inaccuracy of metadata at any level may propagate to downstream analyses, undermining the validity of scientific conclusions thus drawn. From the perspective of mass spectrometry-based proteomics, even though accurate statistics for peptide identification can now be achieved, accurate protein level statistics remain challenging. We have constructed a protein ID method that combines peptide evidences of a candidate protein based on a rigorous formula derived earlier; in this formula the database P-value of every peptide is weighted, prior to the final combination, according to the number of proteins it maps to. We have also shown that this protein ID method provides accurate protein level E-value, eliminating the need of using empirical post-processing methods for type-I error control. Using a known protein mixture, we find that this protein ID method, when combined with the Sorić formula, yields accurate values for the proportion of false discoveries. In terms of retrieval efficacy, the results from our method are comparable with other methods tested. The source code, implemented in C++ on a linux system, is available for download at ftp://ftp.ncbi.nlm.nih.gov/pub/qmbp/qmbp_ms/RAId/RAId_Linux_64Bit. Published by Oxford University Press 2014. This work is written by US Government employees and is in the public domain in the US.

  17. Whipworm kinomes reflect a unique biology and adaptation to the host animal.

    PubMed

    Stroehlein, Andreas J; Young, Neil D; Korhonen, Pasi K; Chang, Bill C H; Nejsum, Peter; Pozio, Edoardo; La Rosa, Giuseppe; Sternberg, Paul W; Gasser, Robin B

    2017-11-01

    Roundworms belong to a diverse phylum (Nematoda) which is comprised of many parasitic species including whipworms (genus Trichuris). These worms have adapted to a biological niche within the host and exhibit unique morphological characteristics compared with other nematodes. Although these adaptations are known, the underlying molecular mechanisms remain elusive. The availability of genomes and transcriptomes of some whipworms now enables detailed studies of their molecular biology. Here, we defined and curated the full complement of an important class of enzymes, the protein kinases (kinomes) of two species of Trichuris, using an advanced and integrated bioinformatic pipeline. We investigated the transcription of Trichuris suis kinase genes across developmental stages, sexes and tissues, and reveal that selectively transcribed genes can be linked to central roles in developmental and reproductive processes. We also classified and functionally annotated the curated kinomes by integrating evidence from structural modelling and pathway analyses, and compared them with other curated kinomes of phylogenetically diverse nematode species. Our findings suggest unique adaptations in signalling processes governing worm morphology and biology, and provide an important resource that should facilitate experimental investigations of kinases and the biology of signalling pathways in nematodes. Copyright © 2017 Australian Society for Parasitology. Published by Elsevier Ltd. All rights reserved.

  18. Depth-resolved measurements with elliptically polarized reflectance spectroscopy

    PubMed Central

    Bailey, Maria J.; Sokolov, Konstantin

    2016-01-01

    The ability of elliptical polarized reflectance spectroscopy (EPRS) to detect spectroscopic alterations in tissue mimicking phantoms and in biological tissue in situ is demonstrated. It is shown that there is a linear relationship between light penetration depth and ellipticity. This dependence is used to demonstrate the feasibility of a depth-resolved spectroscopic imaging using EPRS. The advantages and drawbacks of EPRS in evaluation of biological tissue are analyzed and discussed. PMID:27446712

  19. Item Construction Using Reflective, Formative, or Rasch Measurement Models: Implications for Group Work

    ERIC Educational Resources Information Center

    Peterson, Christina Hamme; Gischlar, Karen L.; Peterson, N. Andrew

    2017-01-01

    Measures that accurately capture the phenomenon are critical to research and practice in group work. The vast majority of group-related measures were developed using the reflective measurement model rooted in classical test theory (CTT). Depending on the construct definition and the measure's purpose, the reflective model may not always be the…

  20. CellNet: network biology applied to stem cell engineering.

    PubMed

    Cahan, Patrick; Li, Hu; Morris, Samantha A; Lummertz da Rocha, Edroaldo; Daley, George Q; Collins, James J

    2014-08-14

    Somatic cell reprogramming, directed differentiation of pluripotent stem cells, and direct conversions between differentiated cell lineages represent powerful approaches to engineer cells for research and regenerative medicine. We have developed CellNet, a network biology platform that more accurately assesses the fidelity of cellular engineering than existing methodologies and generates hypotheses for improving cell derivations. Analyzing expression data from 56 published reports, we found that cells derived via directed differentiation more closely resemble their in vivo counterparts than products of direct conversion, as reflected by the establishment of target cell-type gene regulatory networks (GRNs). Furthermore, we discovered that directly converted cells fail to adequately silence expression programs of the starting population and that the establishment of unintended GRNs is common to virtually every cellular engineering paradigm. CellNet provides a platform for quantifying how closely engineered cell populations resemble their target cell type and a rational strategy to guide enhanced cellular engineering. Copyright © 2014 Elsevier Inc. All rights reserved.

  1. CellNet: Network Biology Applied to Stem Cell Engineering

    PubMed Central

    Cahan, Patrick; Li, Hu; Morris, Samantha A.; da Rocha, Edroaldo Lummertz; Daley, George Q.; Collins, James J.

    2014-01-01

    SUMMARY Somatic cell reprogramming, directed differentiation of pluripotent stem cells, and direct conversions between differentiated cell lineages represent powerful approaches to engineer cells for research and regenerative medicine. We have developed CellNet, a network biology platform that more accurately assesses the fidelity of cellular engineering than existing methodologies and generates hypotheses for improving cell derivations. Analyzing expression data from 56 published reports, we found that cells derived via directed differentiation more closely resemble their in vivo counterparts than products of direct conversion, as reflected by the establishment of target cell-type gene regulatory networks (GRNs). Furthermore, we discovered that directly converted cells fail to adequately silence expression programs of the starting population, and that the establishment of unintended GRNs is common to virtually every cellular engineering paradigm. CellNet provides a platform for quantifying how closely engineered cell populations resemble their target cell type and a rational strategy to guide enhanced cellular engineering. PMID:25126793

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  3. Designing synthetic biology.

    PubMed

    Agapakis, Christina M

    2014-03-21

    Synthetic biology is frequently defined as the application of engineering design principles to biology. Such principles are intended to streamline the practice of biological engineering, to shorten the time required to design, build, and test synthetic gene networks. This streamlining of iterative design cycles can facilitate the future construction of biological systems for a range of applications in the production of fuels, foods, materials, and medicines. The promise of these potential applications as well as the emphasis on design has prompted critical reflection on synthetic biology from design theorists and practicing designers from many fields, who can bring valuable perspectives to the discipline. While interdisciplinary connections between biologists and engineers have built synthetic biology via the science and the technology of biology, interdisciplinary collaboration with artists, designers, and social theorists can provide insight on the connections between technology and society. Such collaborations can open up new avenues and new principles for research and design, as well as shed new light on the challenging context-dependence-both biological and social-that face living technologies at many scales. This review is inspired by the session titled "Design and Synthetic Biology: Connecting People and Technology" at Synthetic Biology 6.0 and covers a range of literature on design practice in synthetic biology and beyond. Critical engagement with how design is used to shape the discipline opens up new possibilities for how we might design the future of synthetic biology.

  4. Development of accurate potentials to explore the structure of water on 2D materials

    NASA Astrophysics Data System (ADS)

    Bejagam, Karteek; Singh, Samrendra; Deshmukh, Sanket; Deshmkuh Group Team; Samrendra Group Collaboration

    Water play an important role in many biological and non-biological process. Thus structure of water at various interfaces and under confinement has always been the topic of immense interest. 2-D materials have shown great potential in surface coating applications and nanofluidic devices. However, the exact atomic level understanding of the wettability of single layer of these 2-D materials is still lacking mainly due to lack of experimental techniques and computational methodologies including accurate force-field potentials and algorithms to measure the contact angle of water. In the present study, we have developed a new algorithm to measure the accurate contact angle between water and 2-D materials. The algorithm is based on fitting the best sphere to the shape of the droplet. This novel spherical fitting method accounts for every individual molecule of the droplet, rather than those at the surface only. We employ this method of contact angle measurements to develop the accurate non-bonded potentials between water and 2-D materials including graphene and boron nitride (BN) to reproduce the experimentally observed contact angle of water on these 2-D materials. Different water models such as SPC, SPC/Fw, and TIP3P were used to study the structure of water at the interfaces.

  5. Quantitative analysis of binary polymorphs mixtures of fusidic acid by diffuse reflectance FTIR spectroscopy, diffuse reflectance FT-NIR spectroscopy, Raman spectroscopy and multivariate calibration.

    PubMed

    Guo, Canyong; Luo, Xuefang; Zhou, Xiaohua; Shi, Beijia; Wang, Juanjuan; Zhao, Jinqi; Zhang, Xiaoxia

    2017-06-05

    Vibrational spectroscopic techniques such as infrared, near-infrared and Raman spectroscopy have become popular in detecting and quantifying polymorphism of pharmaceutics since they are fast and non-destructive. This study assessed the ability of three vibrational spectroscopy combined with multivariate analysis to quantify a low-content undesired polymorph within a binary polymorphic mixture. Partial least squares (PLS) regression and support vector machine (SVM) regression were employed to build quantitative models. Fusidic acid, a steroidal antibiotic, was used as the model compound. It was found that PLS regression performed slightly better than SVM regression in all the three spectroscopic techniques. Root mean square errors of prediction (RMSEP) were ranging from 0.48% to 1.17% for diffuse reflectance FTIR spectroscopy and 1.60-1.93% for diffuse reflectance FT-NIR spectroscopy and 1.62-2.31% for Raman spectroscopy. The results indicate that diffuse reflectance FTIR spectroscopy offers significant advantages in providing accurate measurement of polymorphic content in the fusidic acid binary mixtures, while Raman spectroscopy is the least accurate technique for quantitative analysis of polymorphs. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Node fingerprinting: an efficient heuristic for aligning biological networks.

    PubMed

    Radu, Alex; Charleston, Michael

    2014-10-01

    With the continuing increase in availability of biological data and improvements to biological models, biological network analysis has become a promising area of research. An emerging technique for the analysis of biological networks is through network alignment. Network alignment has been used to calculate genetic distance, similarities between regulatory structures, and the effect of external forces on gene expression, and to depict conditional activity of expression modules in cancer. Network alignment is algorithmically complex, and therefore we must rely on heuristics, ideally as efficient and accurate as possible. The majority of current techniques for network alignment rely on precomputed information, such as with protein sequence alignment, or on tunable network alignment parameters, which may introduce an increased computational overhead. Our presented algorithm, which we call Node Fingerprinting (NF), is appropriate for performing global pairwise network alignment without precomputation or tuning, can be fully parallelized, and is able to quickly compute an accurate alignment between two biological networks. It has performed as well as or better than existing algorithms on biological and simulated data, and with fewer computational resources. The algorithmic validation performed demonstrates the low computational resource requirements of NF.

  7. Reflective and refractive objects for mixed reality.

    PubMed

    Knecht, Martin; Traxler, Christoph; Winklhofer, Christoph; Wimmer, Michael

    2013-04-01

    In this paper, we present a novel rendering method which integrates reflective or refractive objects into a differential instant radiosity (DIR) framework usable for mixed-reality (MR) applications. This kind of objects are very special from the light interaction point of view, as they reflect and refract incident rays. Therefore they may cause high-frequency lighting effects known as caustics. Using instant-radiosity (IR) methods to approximate these high-frequency lighting effects would require a large amount of virtual point lights (VPLs) and is therefore not desirable due to real-time constraints. Instead, our approach combines differential instant radiosity with three other methods. One method handles more accurate reflections compared to simple cubemaps by using impostors. Another method is able to calculate two refractions in real-time, and the third method uses small quads to create caustic effects. Our proposed method replaces parts in light paths that belong to reflective or refractive objects using these three methods and thus tightly integrates into DIR. In contrast to previous methods which introduce reflective or refractive objects into MR scenarios, our method produces caustics that also emit additional indirect light. The method runs at real-time frame rates, and the results show that reflective and refractive objects with caustics improve the overall impression for MR scenarios.

  8. Tau-independent Phase Analysis: A Novel Method for Accurately Determining Phase Shifts.

    PubMed

    Tackenberg, Michael C; Jones, Jeff R; Page, Terry L; Hughey, Jacob J

    2018-06-01

    Estimations of period and phase are essential in circadian biology. While many techniques exist for estimating period, comparatively few methods are available for estimating phase. Current approaches to analyzing phase often vary between studies and are sensitive to coincident changes in period and the stage of the circadian cycle at which the stimulus occurs. Here we propose a new technique, tau-independent phase analysis (TIPA), for quantifying phase shifts in multiple types of circadian time-course data. Through comprehensive simulations, we show that TIPA is both more accurate and more precise than the standard actogram approach. TIPA is computationally simple and therefore will enable accurate and reproducible quantification of phase shifts across multiple subfields of chronobiology.

  9. Modeling the effect of reflection from metallic walls on spectroscopic measurements.

    PubMed

    Zastrow, K-D; Keatings, S R; Marot, L; O'Mullane, M G; de Temmerman, G

    2008-10-01

    A modification of JET is presently being prepared to bring operational experience with ITER-like first wall (Be) and divertor (W) materials, geometry and plasma parameters. Reflectivity measurements of JET sample tiles have been performed and the data are used within a simplified model of the JET and ITER vessels to predict additional contributions to quantitative spectroscopic measurements. The most general method to characterize reflectivity is the bidirectional reflection distribution function (BRDF). For extended sources however, such as bremsstrahlung and edge emission of fuel and intrinsic impurities, the results obtained in the modeling are almost as accurate if the total reflectivity with ideal Lambertian angular dependence is used. This is in contrast to the experience in other communities, such as optical design, lighting design, or rendering who deal mostly with pointlike light sources. This result is so far based on a very limited set of measurements and will be reassessed when more detailed BRDF measurements of JET tiles have been made. If it is true it offers the possibility of in situ monitoring of the reflectivity of selected parts of the wall during exposure to plasma operation, while remeasurement of the BRDF is performed during interventions. For a closed vessel structure such as ITER, it is important to consider multiple reflections. This makes it more important to represent the whole of the vessel reasonably accurately in the model, which on the other hand is easier to achieve than for the more complex internal structure of JET. In both cases the dominant contribution is from the first reflection, and a detailed model of the areas intersected by lines of sight of diagnostic interest is required.

  10. Pedagogical Reflections by Secondary Science Teachers at Different NOS Implementation Levels

    NASA Astrophysics Data System (ADS)

    Herman, Benjamin C.; Clough, Michael P.; Olson, Joanne K.

    2017-02-01

    This study investigated what 13 secondary science teachers at various nature of science (NOS) instruction implementation levels talked about when they reflected on their teaching. We then determined if differences exist in the quality of those reflections between high, medium, and low NOS implementers. This study sought to answer the following questions: (1) What do teachers talk about when asked general questions about their pedagogy and NOS pedagogy and (2) what qualitative differences, if any, exist within variables across teachers of varying NOS implementation levels? Evidence derived from these teachers' reflections indicated that self-efficacy and perceptions of general importance for NOS instruction were poor indicators of NOS implementation. However, several factors were associated with the extent that these teachers implemented NOS instruction, including the utility value they hold for NOS teaching, considerations of how people learn, understanding of NOS pedagogy, and their ability to accurately and deeply self-reflect about teaching. Notably, those teachers who effectively implemented the NOS at higher levels value NOS instruction for reasons that transcend immediate instructional objectives. That is, they value teaching NOS for achieving compelling ends realized long after formal schooling (e.g., lifelong socioscientific decision-making for civic reasons), and they deeply reflect about how to teach NOS by drawing from research about how people learn. Low NOS implementers' simplistic notions and reflections about teaching and learning appeared to be impeding factors to accurate and consistent NOS implementation. This study has implications for science teacher education efforts that promote NOS instruction.

  11. Derivation of a regional active-optical reflectance sensor corn algorithm

    USDA-ARS?s Scientific Manuscript database

    Active-optical reflectance sensor (AORS) algorithms developed for in-season corn (Zea mays L.) N management have traditionally been derived using sub-regional scale information. However, studies have shown these previously developed AORS algorithms are not consistently accurate when used on a region...

  12. Kubelka-Munk reflectance theory applied to porcelain veneer systems using a colorimeter.

    PubMed

    Davis, B K; Johnston, W M; Saba, R F

    1994-01-01

    The purpose of this study was to demonstrate the ability of Kubelka-Munk reflectance theory to predict color parameters of veneer porcelain on various backings using colorimetric measurements. Tristimulus absorption and scattering coefficients were used to predict the respective tristimulus reflectance values of A1, D3, and translucent porcelain samples after they had been bonded to light and dark substrates using universal, opaque, and untinted shades of bonding resin. Observed and predicted reflectance values exhibited high correlation (r2 > or = 0.93 for each porcelain shade). Kubelka-Munk theory offers an accurate prediction for the resultant colorimetric reflectance parameters of veneer porcelain bonded to variously colored backings.

  13. Light Reflection from Packed Layers of Transparent Spheres: Is Hapke's Photometric Model Accurate Enough to Make Predictions?

    NASA Astrophysics Data System (ADS)

    Zhang, H.; Voss, K. J.

    2011-03-01

    We demonstrate that the diffraction removal procedure outlined by Hapke et al. [Icarus, 199, 210 (2009)] contains an error. By following their intended scheme we found that the Hapke model is not anisotropic enough to describe the reflectance patterns.

  14. The `What is a system' reflection interview as a knowledge integration activity for high school students' understanding of complex systems in human biology

    NASA Astrophysics Data System (ADS)

    Tripto, Jaklin; Ben-Zvi Assaraf, Orit; Snapir, Zohar; Amit, Miriam

    2016-03-01

    This study examined the reflection interview as a tool for assessing and facilitating the use of 'systems language' amongst 11th grade students who have recently completed their first year of high school biology. Eighty-three students composed two concept maps in the 10th grade-one at the beginning of the school year and one at its end. The first part of the interview is dedicated to guiding the students through comparing their two concept maps and by means of both explicit and non-explicit teaching. Our study showed that the explicit guidance in comparing the two concept maps was more effective than the non-explicit, eliciting a variety of different, more specific, types of interactions and patterns (e.g. 'hierarchy', 'dynamism', 'homeostasis') in the students' descriptions of the human body system. The reflection interview as a knowledge integration activity was found to be an effective tool for assessing the subjects' conceptual models of 'system complexity', and for identifying those aspects of a system that are most commonly misunderstood.

  15. The Default Mode Network Differentiates Biological From Non-Biological Motion

    PubMed Central

    Dayan, Eran; Sella, Irit; Mukovskiy, Albert; Douek, Yehonatan; Giese, Martin A.; Malach, Rafael; Flash, Tamar

    2016-01-01

    The default mode network (DMN) has been implicated in an array of social-cognitive functions, including self-referential processing, theory of mind, and mentalizing. Yet, the properties of the external stimuli that elicit DMN activity in relation to these domains remain unknown. Previous studies suggested that motion kinematics is utilized by the brain for social-cognitive processing. Here, we used functional MRI to examine whether the DMN is sensitive to parametric manipulations of observed motion kinematics. Preferential responses within core DMN structures differentiating non-biological from biological kinematics were observed for the motion of a realistically looking, human-like avatar, but not for an abstract object devoid of human form. Differences in connectivity patterns during the observation of biological versus non-biological kinematics were additionally observed. Finally, the results additionally suggest that the DMN is coupled more strongly with key nodes in the action observation network, namely the STS and the SMA, when the observed motion depicts human rather than abstract form. These findings are the first to implicate the DMN in the perception of biological motion. They may reflect the type of information used by the DMN in social-cognitive processing. PMID:25217472

  16. Toward Accurate and Quantitative Comparative Metagenomics

    PubMed Central

    Nayfach, Stephen; Pollard, Katherine S.

    2016-01-01

    Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. PMID:27565341

  17. Information Complexity and Biology

    NASA Astrophysics Data System (ADS)

    Bagnoli, Franco; Bignone, Franco A.; Cecconi, Fabio; Politi, Antonio

    Kolmogorov contributed directly to Biology in essentially three problems: the analysis of population dynamics (Lotka-Volterra equations), the reaction-diffusion formulation of gene spreading (FKPP equation), and some discussions about Mendel's laws. However, the widely recognized importance of his contribution arises from his work on algorithmic complexity. In fact, the limited direct intervention in Biology reflects the generally slow growth of interest of mathematicians towards biological issues. From the early work of Vito Volterra on species competition, to the slow growth of dynamical systems theory, contributions to the study of matter and the physiology of the nervous system, the first 50-60 years have witnessed important contributions, but as scattered pieces apparently uncorrelated, and in branches often far away from Biology. Up to the 40' it is hard to see the initial loose build up of a convergence, for those theories that will become mainstream research by the end of the century, and connected by the study of biological systems per-se.

  18. SNAB: A New Advanced Level Biology Course

    ERIC Educational Resources Information Center

    Reiss, Michael J.

    2005-01-01

    Of all the sciences, biology has probably made the most rapid progress in recent years and the need for this to be reflected in a new Advanced Level biology course has long been recognised in the UK. After wide-ranging consultation and successful piloting in over 50 schools and colleges in England and Wales, the new Salters-Nuffield Advanced…

  19. Reflections on my journey in biomedical research: the art, science, and politics of advocacy.

    PubMed

    Slavkin, H C

    2013-01-01

    Scientific Discovery often reflects the art, science, and advocacy for biomedical research. Here the author reflects on selected highlights of discovery that contributed to several aspects of our understanding of craniofacial biology and craniofacial diseases and disorders.

  20. Fast and Accurate Microplate Method (Biolog MT2) for Detection of Fusarium Fungicides Resistance/Sensitivity.

    PubMed

    Frąc, Magdalena; Gryta, Agata; Oszust, Karolina; Kotowicz, Natalia

    2016-01-01

    The need for finding fungicides against Fusarium is a key step in the chemical plant protection and using appropriate chemical agents. Existing, conventional methods of evaluation of Fusarium isolates resistance to fungicides are costly, time-consuming and potentially environmentally harmful due to usage of high amounts of potentially toxic chemicals. Therefore, the development of fast, accurate and effective detection methods for Fusarium resistance to fungicides is urgently required. MT2 microplates (Biolog(TM)) method is traditionally used for bacteria identification and the evaluation of their ability to utilize different carbon substrates. However, to the best of our knowledge, there is no reports concerning the use of this technical tool to determine fungicides resistance of the Fusarium isolates. For this reason, the objectives of this study are to develop a fast method for Fusarium resistance to fungicides detection and to validate the effectiveness approach between both traditional hole-plate and MT2 microplates assays. In presented study MT2 microplate-based assay was evaluated for potential use as an alternative resistance detection method. This was carried out using three commercially available fungicides, containing following active substances: triazoles (tebuconazole), benzimidazoles (carbendazim) and strobilurins (azoxystrobin), in six concentrations (0, 0.0005, 0.005, 0.05, 0.1, 0.2%), for nine selected Fusarium isolates. In this study, the particular concentrations of each fungicides was loaded into MT2 microplate wells. The wells were inoculated with the Fusarium mycelium suspended in PM4-IF inoculating fluid. Before inoculation the suspension was standardized for each isolates into 75% of transmittance. Traditional hole-plate method was used as a control assay. The fungicides concentrations in control method were the following: 0, 0.0005, 0.005, 0.05, 0.5, 1, 2, 5, 10, 25, and 50%. Strong relationships between MT2 microplate and traditional hole

  1. Fast and Accurate Microplate Method (Biolog MT2) for Detection of Fusarium Fungicides Resistance/Sensitivity

    PubMed Central

    Frąc, Magdalena; Gryta, Agata; Oszust, Karolina; Kotowicz, Natalia

    2016-01-01

    The need for finding fungicides against Fusarium is a key step in the chemical plant protection and using appropriate chemical agents. Existing, conventional methods of evaluation of Fusarium isolates resistance to fungicides are costly, time-consuming and potentially environmentally harmful due to usage of high amounts of potentially toxic chemicals. Therefore, the development of fast, accurate and effective detection methods for Fusarium resistance to fungicides is urgently required. MT2 microplates (BiologTM) method is traditionally used for bacteria identification and the evaluation of their ability to utilize different carbon substrates. However, to the best of our knowledge, there is no reports concerning the use of this technical tool to determine fungicides resistance of the Fusarium isolates. For this reason, the objectives of this study are to develop a fast method for Fusarium resistance to fungicides detection and to validate the effectiveness approach between both traditional hole-plate and MT2 microplates assays. In presented study MT2 microplate-based assay was evaluated for potential use as an alternative resistance detection method. This was carried out using three commercially available fungicides, containing following active substances: triazoles (tebuconazole), benzimidazoles (carbendazim) and strobilurins (azoxystrobin), in six concentrations (0, 0.0005, 0.005, 0.05, 0.1, 0.2%), for nine selected Fusarium isolates. In this study, the particular concentrations of each fungicides was loaded into MT2 microplate wells. The wells were inoculated with the Fusarium mycelium suspended in PM4-IF inoculating fluid. Before inoculation the suspension was standardized for each isolates into 75% of transmittance. Traditional hole-plate method was used as a control assay. The fungicides concentrations in control method were the following: 0, 0.0005, 0.005, 0.05, 0.5, 1, 2, 5, 10, 25, and 50%. Strong relationships between MT2 microplate and traditional hole

  2. Computational Systems Biology

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

    McDermott, Jason E.; Samudrala, Ram; Bumgarner, Roger E.

    2009-05-01

    protein and mRNA) and metabolomics. With such tools, research to consider systems as a whole are being conceived, planned and implemented experimentally on an ever more frequent and wider scale. The other is the growth of computational processing power and tools. Methods to analyze large data sets of this kind are often computationally demanding and, as is the case in other areas, the field has benefited from continuing improvements in computational hardware and methods. The field of computational biology is very much like a telescope with two sequential lenses: one lens represents the biological data and the other represents a computational and/or mathematical model of the data. Both lenses must be properly coordinated to yield an image that reflects biological reality. This means that the design parameters for both lenses must be designed in concert to create a system that yields a model of the organism that provides both predictive and mechanistic information. The chapters in this book describe the construction of subcomponents of such a system. Computational systems biology is a rapidly evolving field and no single group of investigators has yet developed a compete system that integrates both data generation and data analysis in such a way so as to allow full and accurate modeling of any single biological organism. However, the field is rapidly moving in that direction. The chapters in this book represent a snapshot of the current methods being developed and used in the area of computational systems biology. Each method or database described within represents one or more steps on the path to a complete description of a biological system. How these tools will evolve and ultimately be integrated is an area of intense research and interest. We hope that readers of this book will be motivated by the chapters within and become involved in this exciting area of research.« less

  3. Biology. CUNY Panel: Rethinking the Disciplines. Women in the Curriculum Series.

    ERIC Educational Resources Information Center

    Spanier, Bonnie B.; Rosser, Sue V.; Muzio, Joseph N.; Tucker, Edward B.

    This collection of four essays examines the ways in which biology, as a discipline, reflects ongoing scholarship on gender, race, ethnicity, social class, and sexual orientation. In "Natural Sciences: Molecular Biology," Bonnie B. Spanier examines common ideological distortions in biology, including superimposing stereotypical gender attributes…

  4. Non-invasive optoacoustic probing of the density and stiffness of single biological cells

    NASA Astrophysics Data System (ADS)

    Dehoux, T.; Audoin, B.

    2012-12-01

    Recently, the coherent generation of GHz acoustic waves using ultrashort laser pulses has demonstrated the ability to probe the sound velocity in vegetal cells and in cell-mimicking soft micro-objects with micrometer resolution, opening tremendous potentialities for single-cell biology. However, manipulating biological media in physiological conditions is often a technical challenge when using a laser-based setup. In this article, we present a new opto-acoustic bio-transducer composed of a thin metal film sputtered on a transparent heat sink that allows reducing importantly the laser-induced cellular stresses, and offers a wide variety of optical configurations. In particular, by exploiting the acoustic reflection coefficient at the sample-transducer interface and the photoacoustic interaction inside the transparent sample, the density and compressibility of the sample can be probed simultaneously. Using an ad hoc signal analysis based on Hilbert and wavelet transforms, these quantities are measured accurately for a reference fluid. Similar analysis performed in a single vegetal cell also suggests high sensitivity to the state of the transducer-cell interface, and notably to the presence of the plasma membrane that encloses the cell vacuole.

  5. Theory of relativistic radiation reflection from plasmas

    NASA Astrophysics Data System (ADS)

    Gonoskov, Arkady

    2018-01-01

    We consider the reflection of relativistically strong radiation from plasma and identify the physical origin of the electrons' tendency to form a thin sheet, which maintains its localisation throughout its motion. Thereby, we justify the principle of relativistic electronic spring (RES) proposed in [Gonoskov et al., Phys. Rev. E 84, 046403 (2011)]. Using the RES principle, we derive a closed set of differential equations that describe the reflection of radiation with arbitrary variation of polarization and intensity from plasma with an arbitrary density profile for an arbitrary angle of incidence. We confirm with ab initio PIC simulations that the developed theory accurately describes laser-plasma interactions in the regime where the reflection of relativistically strong radiation is accompanied by significant, repeated relocation of plasma electrons. In particular, the theory can be applied for the studies of plasma heating and coherent and incoherent emissions in the RES regime of high-intensity laser-plasma interaction.

  6. Achieving perceptually-accurate aural telepresence

    NASA Astrophysics Data System (ADS)

    Henderson, Paul D.

    Immersive multimedia requires not only realistic visual imagery but also a perceptually-accurate aural experience. A sound field may be presented simultaneously to a listener via a loudspeaker rendering system using the direct sound from acoustic sources as well as a simulation or "auralization" of room acoustics. Beginning with classical Wave-Field Synthesis (WFS), improvements are made to correct for asymmetries in loudspeaker array geometry. Presented is a new Spatially-Equalized WFS (SE-WFS) technique to maintain the energy-time balance of a simulated room by equalizing the reproduced spectrum at the listener for a distribution of possible source angles. Each reproduced source or reflection is filtered according to its incidence angle to the listener. An SE-WFS loudspeaker array of arbitrary geometry reproduces the sound field of a room with correct spectral and temporal balance, compared with classically-processed WFS systems. Localization accuracy of human listeners in SE-WFS sound fields is quantified by psychoacoustical testing. At a loudspeaker spacing of 0.17 m (equivalent to an aliasing cutoff frequency of 1 kHz), SE-WFS exhibits a localization blur of 3 degrees, nearly equal to real point sources. Increasing the loudspeaker spacing to 0.68 m (for a cutoff frequency of 170 Hz) results in a blur of less than 5 degrees. In contrast, stereophonic reproduction is less accurate with a blur of 7 degrees. The ventriloquist effect is psychometrically investigated to determine the effect of an intentional directional incongruence between audio and video stimuli. Subjects were presented with prerecorded full-spectrum speech and motion video of a talker's head as well as broadband noise bursts with a static image. The video image was displaced from the audio stimulus in azimuth by varying amounts, and the perceived auditory location measured. A strong bias was detectable for small angular discrepancies between audio and video stimuli for separations of less than 8

  7. On the role of emotion in biological and robotic autonomy.

    PubMed

    Ziemke, Tom

    2008-02-01

    This paper reviews some of the differences between notions of biological and robotic autonomy, and how these differences have been reflected in discussions of embodiment, grounding and other concepts in AI and autonomous robotics. Furthermore, the relations between homeostasis, emotion and embodied cognition are discussed as well as recent proposals to model their interplay in robots, which reflects a commitment to a multi-tiered affectively/emotionally embodied view of mind that takes organismic embodiment more serious than usually done in biologically inspired robotics.

  8. S-Nitrosothiol measurements in biological systems⋄

    PubMed Central

    Gow, Andrew; Doctor, Allan; Mannick, Joan; Gaston, Benjamin

    2007-01-01

    S-Nitrosothiol (SNO) cysteine modifications are regulated signaling reactions that dramatically affect, and are affected by, protein conformation. The lability of the S-NO bond can make SNO-modified proteins cumbersome to measure accurately. Here, we review methodologies for detecting SNO modifications in biology. There are three caveats. 1) Many assays for biological SNOs are used near the limit of detection: standard curves must be in the biologically relevant concentration range. 2) The assays that are most reliable are those that modify SNO protein or peptide chemistry the least. 3) Each result should be quantitatively validated using more than one assay. Improved assays are needed and are in development. PMID:17379583

  9. [Progress in synthetic biology of "973 Funding Program" in China].

    PubMed

    Chen, Guoqiang; Wang, Ying

    2015-06-01

    This paper reviews progresses made in China from 2011 in areas of "Synthetic Biology" supported by State Basic Research 973 Program. Till the end of 2014, 9 "synthetic biology" projects have been initiated with emphasis on "microbial manufactures" with the 973 Funding Program. Combined with the very recent launch of one project on "mammalian cell synthetic biology" and another on "plant synthetic biology", Chinese "synthetic biology" research reflects its focus on "manufactures" while not giving up efforts on "synthetic biology" of complex systems.

  10. A time-accurate high-resolution TVD scheme for solving the Navier-Stokes equations

    NASA Technical Reports Server (NTRS)

    Kim, Hyun Dae; Liu, Nan-Suey

    1992-01-01

    A total variation diminishing (TVD) scheme has been developed and incorporated into an existing time-accurate high-resolution Navier-Stokes code. The accuracy and the robustness of the resulting solution procedure have been assessed by performing many calculations in four different areas: shock tube flows, regular shock reflection, supersonic boundary layer, and shock boundary layer interactions. These numerical results compare well with corresponding exact solutions or experimental data.

  11. Systems biology for organotypic cell cultures.

    PubMed

    Grego, Sonia; Dougherty, Edward R; Alexander, Francis J; Auerbach, Scott S; Berridge, Brian R; Bittner, Michael L; Casey, Warren; Cooley, Philip C; Dash, Ajit; Ferguson, Stephen S; Fennell, Timothy R; Hawkins, Brian T; Hickey, Anthony J; Kleensang, Andre; Liebman, Michael N J; Martin, Florian; Maull, Elizabeth A; Paragas, Jason; Qiao, Guilin Gary; Ramaiahgari, Sreenivasa; Sumner, Susan J; Yoon, Miyoung

    2017-01-01

    Translating in vitro biological data into actionable information related to human health holds the potential to improve disease treatment and risk assessment of chemical exposures. While genomics has identified regulatory pathways at the cellular level, translation to the organism level requires a multiscale approach accounting for intra-cellular regulation, inter-cellular interaction, and tissue/organ-level effects. Tissue-level effects can now be probed in vitro thanks to recently developed systems of three-dimensional (3D), multicellular, "organotypic" cell cultures, which mimic functional responses of living tissue. However, there remains a knowledge gap regarding interactions across different biological scales, complicating accurate prediction of health outcomes from molecular/genomic data and tissue responses. Systems biology aims at mathematical modeling of complex, non-linear biological systems. We propose to apply a systems biology approach to achieve a computational representation of tissue-level physiological responses by integrating empirical data derived from organotypic culture systems with computational models of intracellular pathways to better predict human responses. Successful implementation of this integrated approach will provide a powerful tool for faster, more accurate and cost-effective screening of potential toxicants and therapeutics. On September 11, 2015, an interdisciplinary group of scientists, engineers, and clinicians gathered for a workshop in Research Triangle Park, North Carolina, to discuss this ambitious goal. Participants represented laboratory-based and computational modeling approaches to pharmacology and toxicology, as well as the pharmaceutical industry, government, non-profits, and academia. Discussions focused on identifying critical system perturbations to model, the computational tools required, and the experimental approaches best suited to generating key data.

  12. Canopy near-infrared reflectance and terrestrial photosynthesis.

    PubMed

    Badgley, Grayson; Field, Christopher B; Berry, Joseph A

    2017-03-01

    Global estimates of terrestrial gross primary production (GPP) remain highly uncertain, despite decades of satellite measurements and intensive in situ monitoring. We report a new approach for quantifying the near-infrared reflectance of terrestrial vegetation (NIR V ). NIR V provides a foundation for a new approach to estimate GPP that consistently untangles the confounding effects of background brightness, leaf area, and the distribution of photosynthetic capacity with depth in canopies using existing moderate spatial and spectral resolution satellite sensors. NIR V is strongly correlated with solar-induced chlorophyll fluorescence, a direct index of photons intercepted by chlorophyll, and with site-level and globally gridded estimates of GPP. NIR V makes it possible to use existing and future reflectance data as a starting point for accurately estimating GPP.

  13. Canopy near-infrared reflectance and terrestrial photosynthesis

    PubMed Central

    Badgley, Grayson; Field, Christopher B.; Berry, Joseph A.

    2017-01-01

    Global estimates of terrestrial gross primary production (GPP) remain highly uncertain, despite decades of satellite measurements and intensive in situ monitoring. We report a new approach for quantifying the near-infrared reflectance of terrestrial vegetation (NIRV). NIRV provides a foundation for a new approach to estimate GPP that consistently untangles the confounding effects of background brightness, leaf area, and the distribution of photosynthetic capacity with depth in canopies using existing moderate spatial and spectral resolution satellite sensors. NIRV is strongly correlated with solar-induced chlorophyll fluorescence, a direct index of photons intercepted by chlorophyll, and with site-level and globally gridded estimates of GPP. NIRV makes it possible to use existing and future reflectance data as a starting point for accurately estimating GPP. PMID:28345046

  14. Acoustic Immittance, Absorbance, and Reflectance in the Human Ear Canal

    PubMed Central

    Rosowski, John J.; Wilber, Laura Ann

    2015-01-01

    Ear canal measurements of acoustic immittance (a term that groups impedance and its inverse, admittance) and the related quantities of acoustic reflectance and power absorbance have been used to assess auditory function and aid in the differential diagnosis of conductive hearing loss for over 50 years. The change in such quantities after stimulation of the acoustic reflex also has been used in diagnosis. In this article, we define these quantities, describe how they are commonly measured, and discuss appropriate calibration procedures and standards necessary for accurate immittance/reflectance measurements. PMID:27516708

  15. Toward Accurate and Quantitative Comparative Metagenomics.

    PubMed

    Nayfach, Stephen; Pollard, Katherine S

    2016-08-25

    Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. The Rényi divergence enables accurate and precise cluster analysis for localisation microscopy.

    PubMed

    Staszowska, Adela D; Fox-Roberts, Patrick; Hirvonen, Liisa M; Peddie, Christopher J; Collinson, Lucy M; Jones, Gareth E; Cox, Susan

    2018-06-01

    Clustering analysis is a key technique for quantitatively characterising structures in localisation microscopy images. To build up accurate information about biological structures, it is critical that the quantification is both accurate (close to the ground truth) and precise (has small scatter and is reproducible). Here we describe how the Rényi divergence can be used for cluster radius measurements in localisation microscopy data. We demonstrate that the Rényi divergence can operate with high levels of background and provides results which are more accurate than Ripley's functions, Voronoi tesselation or DBSCAN. Data supporting this research will be made accessible via a web link. Software codes developed for this work can be accessed via http://coxphysics.com/Renyi_divergence_software.zip. Implemented in C ++. Correspondence and requests for materials can be also addressed to the corresponding author. adela.staszowska@gmail.com or susan.cox@kcl.ac.uk. Supplementary data are available at Bioinformatics online.

  17. A Bayesian spatial model for neuroimaging data based on biologically informed basis functions.

    PubMed

    Huertas, Ismael; Oldehinkel, Marianne; van Oort, Erik S B; Garcia-Solis, David; Mir, Pablo; Beckmann, Christian F; Marquand, Andre F

    2017-11-01

    The dominant approach to neuroimaging data analysis employs the voxel as the unit of computation. While convenient, voxels lack biological meaning and their size is arbitrarily determined by the resolution of the image. Here, we propose a multivariate spatial model in which neuroimaging data are characterised as a linearly weighted combination of multiscale basis functions which map onto underlying brain nuclei or networks or nuclei. In this model, the elementary building blocks are derived to reflect the functional anatomy of the brain during the resting state. This model is estimated using a Bayesian framework which accurately quantifies uncertainty and automatically finds the most accurate and parsimonious combination of basis functions describing the data. We demonstrate the utility of this framework by predicting quantitative SPECT images of striatal dopamine function and we compare a variety of basis sets including generic isotropic functions, anatomical representations of the striatum derived from structural MRI, and two different soft functional parcellations of the striatum derived from resting-state fMRI (rfMRI). We found that a combination of ∼50 multiscale functional basis functions accurately represented the striatal dopamine activity, and that functional basis functions derived from an advanced parcellation technique known as Instantaneous Connectivity Parcellation (ICP) provided the most parsimonious models of dopamine function. Importantly, functional basis functions derived from resting fMRI were more accurate than both structural and generic basis sets in representing dopamine function in the striatum for a fixed model order. We demonstrate the translational validity of our framework by constructing classification models for discriminating parkinsonian disorders and their subtypes. Here, we show that ICP approach is the only basis set that performs well across all comparisons and performs better overall than the classical voxel-based approach

  18. Biological versus electronic adaptive coloration: how can one inform the other?

    PubMed Central

    Kreit, Eric; Mäthger, Lydia M.; Hanlon, Roger T.; Dennis, Patrick B.; Naik, Rajesh R.; Forsythe, Eric; Heikenfeld, Jason

    2013-01-01

    Adaptive reflective surfaces have been a challenge for both electronic paper (e-paper) and biological organisms. Multiple colours, contrast, polarization, reflectance, diffusivity and texture must all be controlled simultaneously without optical losses in order to fully replicate the appearance of natural surfaces and vividly communicate information. This review merges the frontiers of knowledge for both biological adaptive coloration, with a focus on cephalopods, and synthetic reflective e-paper within a consistent framework of scientific metrics. Currently, the highest performance approach for both nature and technology uses colourant transposition. Three outcomes are envisioned from this review: reflective display engineers may gain new insights from millions of years of natural selection and evolution; biologists will benefit from understanding the types of mechanisms, characterization and metrics used in synthetic reflective e-paper; all scientists will gain a clearer picture of the long-term prospects for capabilities such as adaptive concealment and signalling. PMID:23015522

  19. Measuring the complex optical conductivity of graphene by Fabry-Pérot reflectance spectroscopy [Determination of the optical index for few-layer graphene by reflectivity spectroscopy

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

    Ghamsari, Behnood G.; Tosado, Jacob; Yamamoto, Mahito

    Here, we have experimentally studied the optical refractive index of few-layer graphene through reflection spectroscopy at visible wavelengths. A laser scanning microscope (LSM) with a coherent supercontinuum laser source measured the reflectivity of an exfoliated graphene flake on a Si/SiO 2 substrate, containing monolayer, bilayer and trilayer areas, as the wavelength of the laser was varied from 545nm to 710nm. The complex refractive index of few-layer graphene, n-ik, was extracted from the reflectivity contrast to the bare substrate and the Fresnel reflection theory. Since the SiO 2 thickness enters to the modeling as a parameter, it was precisely measured atmore » the location of the sample. It was found that a common constant optical index cannot explain the wavelength-dependent reflectivity data for single-, double- and three-layer graphene simultaneously, but rather each individual few-layer graphene possesses a unique optical index whose complex values were precisely and accurately determined from the experimental data.« less

  20. Measuring the complex optical conductivity of graphene by Fabry-Pérot reflectance spectroscopy [Determination of the optical index for few-layer graphene by reflectivity spectroscopy

    DOE PAGES

    Ghamsari, Behnood G.; Tosado, Jacob; Yamamoto, Mahito; ...

    2016-09-29

    Here, we have experimentally studied the optical refractive index of few-layer graphene through reflection spectroscopy at visible wavelengths. A laser scanning microscope (LSM) with a coherent supercontinuum laser source measured the reflectivity of an exfoliated graphene flake on a Si/SiO 2 substrate, containing monolayer, bilayer and trilayer areas, as the wavelength of the laser was varied from 545nm to 710nm. The complex refractive index of few-layer graphene, n-ik, was extracted from the reflectivity contrast to the bare substrate and the Fresnel reflection theory. Since the SiO 2 thickness enters to the modeling as a parameter, it was precisely measured atmore » the location of the sample. It was found that a common constant optical index cannot explain the wavelength-dependent reflectivity data for single-, double- and three-layer graphene simultaneously, but rather each individual few-layer graphene possesses a unique optical index whose complex values were precisely and accurately determined from the experimental data.« less

  1. Occurrence and Magnitude of High Reflectance Materials on the Moon

    NASA Astrophysics Data System (ADS)

    Nuno, R. G.; Boyd, A. K.; Robinson, M. S.

    2013-12-01

    We utilize a Lunar Reconnaissance Orbiter (LRO) Wide Angle Camera (WAC) 643 nm photometrically normalized (30°, 0°, 30°; i, e, g) reflectance map to investigate the occurrence and origin of high reflectance materials on the Moon. Compositional differences (mainly iron and titanium content) and maturity state (e.g. Copernican crater rays and swirls) are the predominant factors affecting reflectance variations observed on the Moon. Therefore, comparing reflectance values of different regions yields insight into the composition and relative exposure age of lunar materials. But an accurate comparison requires precise reflectance values normalized across every region being investigated. The WAC [1] obtains monthly near-global ground coverage, each month's observations acquired with different lighting conditions. Boyd et al. [2] utilized a geologically homogeneous subset [0°N to 90°N, 146°E to 148°E] of the WAC observations to determine an equation that describes how viewing and lighting angles affect reflectance values. A normalized global reflectance map was generated by applying the local empirical solution globally, with photometric angles derived from the WAC Global Lunar Digital Terrain Model (DTM)(GLD100) [3]. The GLD100 enables accurate correction of reflectance differences caused by local topographic undulations at the scale of 300 meters. We compare reflectance values across the Moon within 80°S to 80°N latitude. The features with the highest reflectance are steep crater walls within Copernican aged craters, such as the walls of Giordano Bruno, which have normalized reflectance values up to 0.35. Near-impact ejecta of some craters have high reflectance values, such as Virtanen (0.22). There are also broad relatively flat features with high reflectance, such as the 900-km Thales-Compton region (0.24) and the 600-km extent of Anaxagoras (Copernican age) ejecta (0.20). Since the interior of Anaxagoras contains occurrences of pure anorthosite [4], the high

  2. Finding Clarity by Fostering Confusion: Reflections on Teaching an Undergraduate Integrated Biological Systems Course

    ERIC Educational Resources Information Center

    Martin, Kirsten H.

    2015-01-01

    Undergraduate biology programs in smaller liberal arts colleges are increasingly becoming focused on health science fields. This narrowing of focus potentially decreases opportunities for these students to explore other sub-fields of biology. This perspectives article highlights how one small university in Connecticut decided to institute a…

  3. The Default Mode Network Differentiates Biological From Non-Biological Motion.

    PubMed

    Dayan, Eran; Sella, Irit; Mukovskiy, Albert; Douek, Yehonatan; Giese, Martin A; Malach, Rafael; Flash, Tamar

    2016-01-01

    The default mode network (DMN) has been implicated in an array of social-cognitive functions, including self-referential processing, theory of mind, and mentalizing. Yet, the properties of the external stimuli that elicit DMN activity in relation to these domains remain unknown. Previous studies suggested that motion kinematics is utilized by the brain for social-cognitive processing. Here, we used functional MRI to examine whether the DMN is sensitive to parametric manipulations of observed motion kinematics. Preferential responses within core DMN structures differentiating non-biological from biological kinematics were observed for the motion of a realistically looking, human-like avatar, but not for an abstract object devoid of human form. Differences in connectivity patterns during the observation of biological versus non-biological kinematics were additionally observed. Finally, the results additionally suggest that the DMN is coupled more strongly with key nodes in the action observation network, namely the STS and the SMA, when the observed motion depicts human rather than abstract form. These findings are the first to implicate the DMN in the perception of biological motion. They may reflect the type of information used by the DMN in social-cognitive processing. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  4. Performance of three reflectance calibration methods for airborne hyperspectral spectrometer data.

    PubMed

    Miura, Tomoaki; Huete, Alfredo R

    2009-01-01

    In this study, the performances and accuracies of three methods for converting airborne hyperspectral spectrometer data to reflectance factors were characterized and compared. The "reflectance mode (RM)" method, which calibrates a spectrometer against a white reference panel prior to mounting on an aircraft, resulted in spectral reflectance retrievals that were biased and distorted. The magnitudes of these bias errors and distortions varied significantly, depending on time of day and length of the flight campaign. The "linear-interpolation (LI)" method, which converts airborne spectrometer data by taking a ratio of linearly-interpolated reference values from the preflight and post-flight reference panel readings, resulted in precise, but inaccurate reflectance retrievals. These reflectance spectra were not distorted, but were subject to bias errors of varying magnitudes dependent on the flight duration length. The "continuous panel (CP)" method uses a multi-band radiometer to obtain continuous measurements over a reference panel throughout the flight campaign, in order to adjust the magnitudes of the linear-interpolated reference values from the preflight and post-flight reference panel readings. Airborne hyperspectral reflectance retrievals obtained using this method were found to be the most accurate and reliable reflectance calibration method. The performances of the CP method in retrieving accurate reflectance factors were consistent throughout time of day and for various flight durations. Based on the dataset analyzed in this study, the uncertainty of the CP method has been estimated to be 0.0025 ± 0.0005 reflectance units for the wavelength regions not affected by atmospheric absorptions. The RM method can produce reasonable results only for a very short-term flight (e.g., < 15 minutes) conducted around a local solar noon. The flight duration should be kept shorter than 30 minutes for the LI method to produce results with reasonable accuracies. An important

  5. Combining observations in the reflective solar and thermal domains for improved mapping of carbon, water and energy fluxes

    USDA-ARS?s Scientific Manuscript database

    The REGularized canopy reFLECtance (REGFLEC) modeling tool integrates leaf optics, canopy reflectance, and atmospheric radiative transfer model components, facilitating accurate retrieval of leaf area index (LAI) and leaf chlorophyll content (Cab) directly from at-sensor radiances in green, red and ...

  6. Surface reflectance retrieval from imaging spectrometer data using three atmospheric codes

    NASA Astrophysics Data System (ADS)

    Staenz, Karl; Williams, Daniel J.; Fedosejevs, Gunar; Teillet, Phil M.

    1994-12-01

    Surface reflectance retrieval from imaging spectrometer data has become important for quantitative information extraction in many application areas. In order to calculate surface reflectance from remotely measured radiance, radiative transfer codes play an important role for removal of the scattering and gaseous absorption effects of the atmosphere. The present study evaluates surface reflectances retrieved from airborne visible/infrared imaging spectrometer (AVIRIS) data using three radiative transfer codes: modified 5S (M5S), 6S, and MODTRAN2. Comparisons of the retrieved surface reflectance with ground-based reflectance were made for different target types such as asphalt, gravel, grass/soil mixture (soccer field), and water (Sooke Lake). The results indicate that the estimation of the atmospheric water vapor content is important for an accurate surface reflectance retrieval regardless of the radiative transfer code used. For the present atmospheric conditions, a difference of 0.1 in aerosol optical depth had little impact on the retrieved surface reflectance. The performance of MODTRAN2 is superior in the gas absorption regions compared to M5S and 6S.

  7. Neuroanatomical correlates of biological motion detection.

    PubMed

    Gilaie-Dotan, Sharon; Kanai, Ryota; Bahrami, Bahador; Rees, Geraint; Saygin, Ayse P

    2013-02-01

    Biological motion detection is both commonplace and important, but there is great inter-individual variability in this ability, the neural basis of which is currently unknown. Here we examined whether the behavioral variability in biological motion detection is reflected in brain anatomy. Perceptual thresholds for detection of biological motion and control conditions (non-biological object motion detection and motion coherence) were determined in a group of healthy human adults (n=31) together with structural magnetic resonance images of the brain. Voxel based morphometry analyzes revealed that gray matter volumes of left posterior superior temporal sulcus (pSTS) and left ventral premotor cortex (vPMC) significantly predicted individual differences in biological motion detection, but showed no significant relationship with performance on the control tasks. Our study reveals a neural basis associated with the inter-individual variability in biological motion detection, reliably linking the neuroanatomical structure of left pSTS and vPMC with biological motion detection performance. Copyright © 2012 Elsevier Ltd. All rights reserved.

  8. Alteration of serum thymus and activation-regulated chemokine level during biologic therapy for psoriasis: Possibility as a marker reflecting favorable response to anti-interleukin-17A agents.

    PubMed

    Shibuya, Takashi; Honma, Masaru; Iinuma, Shin; Iwasaki, Takeshi; Takahashi, Hidetoshi; Ishida-Yamamoto, Akemi

    2018-06-01

    Biologics show great efficacy in treating psoriasis, a chronic inflammatory skin disease. The high cost and side-effects of biologics, dose-reduction, elongation of administration interval and suspension are possible options. However, there has been no reliable biomarker we can use when we consider these moderations in therapy. This study was conducted to test the possibility of using serum thymus and activation-regulated chemokine (TARC) level as an indicator for step down of biologic therapy. Serum TARC level was measured in 70 psoriatic patients at Asahikawa Medical University, and a correlation of TARC and severity of skin lesions was analyzed. Referring to serum TARC level, psoriatic patients can be divided into two groups. One is a population in which serum TARC level is positively correlated with severity of skin lesions, and the other is a population with low psoriatic severity and high TARC level. Serum TARC level was higher in the group that achieved PASI-clear with biologics than in the group which did not achieve PASI-clear. Among biologics, the group treated with secukinumab, an anti-interleukin (IL)-17A agent, showed significantly higher TARC level compared with the group treated with anti-tumor necrosis factor agents. In certain populations achieving PASI-clear, serum TARC level may be a potent marker reflecting better response to IL-17A inhibitors, and in this case step down of treatment for psoriasis is possible. © 2018 Japanese Dermatological Association.

  9. Determining water content of fresh concrete by microwave reflection or transmission measurement.

    DOT National Transportation Integrated Search

    1987-01-01

    In search of a rapid and accurate method for determining the water content of fresh concrete mixes, the microwave reflection and transmission properties of fresh concrete mixes were studied to determine the extent of correlation between each of these...

  10. SWIR calibration of Spectralon reflectance factor

    NASA Astrophysics Data System (ADS)

    Georgiev, Georgi T.; Butler, James J.; Cooksey, Catherine; Ding, Leibo; Thome, Kurtis J.

    2011-11-01

    Satellite instruments operating in the reflective solar wavelength region require accurate and precise determination of the Bidirectional Reflectance Factor (BRF) of laboratory-based diffusers used in their pre-flight and on-orbit radiometric calibrations. BRF measurements are required throughout the reflected-solar spectrum from the ultraviolet through the shortwave infrared. Spectralon diffusers are commonly used as a reflectance standard for bidirectional and hemispherical geometries. The Diffuser Calibration Laboratory (DCaL) at NASA's Goddard Space Flight Center is a secondary calibration facility with reflectance measurements traceable to those made by the Spectral Tri-function Automated Reference Reflectometer (STARR) facility at the National Institute of Standards and Technology (NIST). For more than two decades, the DCaL has provided numerous NASA projects with BRF data in the ultraviolet (UV), visible (VIS) and the Near InfraRed (NIR) spectral regions. Presented in this paper are measurements of BRF from 1475 nm to 1625 nm obtained using an indium gallium arsenide detector and a tunable coherent light source. The sample was a 50.8 mm (2 in) diameter, 99% white Spectralon target. The BRF results are discussed and compared to empirically generated data from a model based on NIST certified values of 6°directional-hemispherical spectral reflectance factors from 900 nm to 2500 nm. Employing a new NIST capability for measuring bidirectional reflectance using a cooled, extended InGaAs detector, BRF calibration measurements of the same sample were also made using NIST's STARR from 1475 nm to 1625 nm at an incident angle of 0° and at viewing angle of 45°. The total combined uncertainty for BRF in this ShortWave Infrared (SWIR) range is less than 1%. This measurement capability will evolve into a BRF calibration service in SWIR region in support of NASA remote sensing missions.

  11. Apparent diffusion coefficient value as a biomarker reflecting morphological and biological features of prostate cancer.

    PubMed

    Bae, Hyeyeol; Yoshida, Soichiro; Matsuoka, Yoh; Nakajima, Hiroshi; Ito, Eisaku; Tanaka, Hiroshi; Oya, Miyako; Nakayama, Takayuki; Takeshita, Hideki; Kijima, Toshiki; Ishioka, Junichiro; Numao, Noboru; Koga, Fumitaka; Saito, Kazutaka; Akashi, Takumi; Fujii, Yasuhisa; Kihara, Kazunori

    2014-03-01

    To assess whether there is an association between the apparent diffusion coefficient (ADC) value and the pathological characteristics of prostate cancer. The study cohort consisted of 29 consecutive patients with prostate cancer treated with radical prostatectomy. All patients underwent diffusion-weighted MRI before the prostate biopsy. In 42 tumor foci, the associations of the ADC values with the clinicopathological characteristics and Ki-67 labeling index (LI) were analyzed. High-grade cancers (Gleason score [GS] ≥ 4 + 3), larger cancers (maximum diameter (MD) ≥ 16 mm), and highly proliferating cancers (Ki-67 LI ≥ 4.43 %) had significantly lower ADC values, respectively (P < .001, P = .008, and P = .044, respectively). There was no significant difference in ADC value according to age, prostate-specific antigen, presence of extra-prostatic extension, and intra-tumoral stroma proportion. Multivariate analysis showed that GS, Ki-67 LI, and MD had independent and significant correlations with ADC value (P < .001, P = .006, and P = .002, respectively). Low ADC tumors (<0.52 × 10(-3) mm(2)/s) are likely to be high-grade cancer foci compared with high ADC tumors (relative risk: 65.2). The sensitivity and specificity of the ADC value to predict high-grade cancer foci are 81.8 and 93.5 %, respectively. A low ADC value reflects the morphological and biological features of prostate cancer. Analyzing the ADC value may make it possible to more precisely predict the cancer aggressiveness of each focus before treatment.

  12. Biological research on burnout-depression overlap: Long-standing limitations and on-going reflections.

    PubMed

    Bianchi, Renzo; Schonfeld, Irvin Sam; Laurent, Eric

    2017-12-01

    In this commentary, we discuss seldom-noticed methodological problems affecting biological research on burnout and depression and make recommendations to overcome the limitations of past studies conducted in this area. First, we suggest that identified subtypes of depression (e.g., depression with melancholic features and depression with atypical features) should be taken into account in future biological research on burnout and depression, given that different subtypes of depression have been associated with distinct autonomic and neuroendocrine profiles. Second, we underline that research on burnout-depression overlap is made difficult by the absence of a consensual conceptualization and operationalization of burnout. In order to resolve this problem, we draw researchers' attention to the urgency of establishing a commonly shared, clinically valid diagnosis for burnout. Finally, we question the possibility of identifying a biological signature for burnout in light of global research on burnout-depression overlap. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. Accurate and facile determination of the index of refraction of organic thin films near the carbon 1s absorption edge.

    PubMed

    Yan, Hongping; Wang, Cheng; McCarn, Allison R; Ade, Harald

    2013-04-26

    A practical and accurate method to obtain the index of refraction, especially the decrement δ, across the carbon 1s absorption edge is demonstrated. The combination of absorption spectra scaled to the Henke atomic scattering factor database, the use of the doubly subtractive Kramers-Kronig relations, and high precision specular reflectivity measurements from thin films allow the notoriously difficult-to-measure δ to be determined with high accuracy. No independent knowledge of the film thickness or density is required. High confidence interpolation between relatively sparse measurements of δ across an absorption edge is achieved. Accurate optical constants determined by this method are expected to greatly improve the simulation and interpretation of resonant soft x-ray scattering and reflectivity data. The method is demonstrated using poly(methyl methacrylate) and should be extendable to all organic materials.

  14. Non-melanoma skin cancer of the head and neck: the aid of reflectance confocal microscopy for the accurate diagnosis and management.

    PubMed

    Ferrari, Barbara; Salgarelli, Attilio C; Mandel, Victor D; Bellini, Pierantonio; Reggiani, Camilla; Farnetani, Francesca; Pellacani, Giovanni; Magnoni, Cristina

    2017-04-01

    Non-melanoma skin cancer (NMSC) represents the most common cutaneous neoplasms of the head and neck. In recent years, novel non-invasive diagnostic tool have been developed, and among these we have the reflectance confocal microscopy (RCM), that offers the evaluation of the skin at real time with cellular resolution. Numerous studies have identified the main confocal features of skin tumours, demonstrating the good correlation of these features with certain dermatoscopic patterns and histologic findings. The aim of this analysis was to provide new insight into the role of RCM in the diagnosis and management of NMSC of the head and neck. Data comes from the most recent literature, taking into account previous essential reported information in this field. The study eligibility criteria were: studies providing update information, focusing on RCM findings in NMSC, without restrictions for age, sex, ethnicity. A search concerning the role of dermoscopy and RCM in the diagnosis of NMSC was performed on Medline. Duplicated studies, single case report and papers with language other than English were excluded from this study. RCM clues were analysed for NMSC in association with clinical, dermoscopic and histopathologic findings. Moreover, some new findings have been described and possible applications for NMSC of the head and neck have been discussed. RCM allows tissue imaging in vivo contributing to a more accurate diagnosis of NMSC of the head and neck, sparing time for the patient and costs for the public health system. RCM can also be used for selection of the biopsy site and it is helpful in defining the surgical safety margins to keep during the excision of skin cancers.

  15. Analytical Measurement of Discrete Hydrogen Sulfide Pools in Biological Specimens

    PubMed Central

    Shen, Xinggui; Peter, Elvis A.; Bir, Shyamal; Wang, Rui; Kevil, Christopher G.

    2015-01-01

    Hydrogen sulfide (H2S) is a ubiquitous gaseous signaling molecule that plays a vital role in numerous cellular functions and has become the focus of many research endeavors including pharmaco-therapeutic manipulation. Amongst the challenges facing the field is the accurate measurement of biologically active H2S. We have recently reported that the typically used methylene blue method and its associated results are invalid and do not measure bonafide H2S. The complexity of analytical H2S measurement reflects the fact that hydrogen sulfide is a volatile gas and exists in the body in different forms, including a free form, an acid labile pool and as bound sulfane sulfur. Here we describe a new protocol to discretely measure specific H2S pools using the monobromobimane method coupled with RP-HPLC. This new protocol involves selective liberation, trapping and derivatization of H2S. Acid-labile H2S is released by incubating the sample in an acidic solution (pH 2.6) of 100 mM phosphate buffer with 0.1 mM DTPA, in an enclosed system to contain volatilized H2S. Volatilized H2S is then trapped in 100 mM Tris-HCl (pH 9.5, 0.1 mM DTPA) and then reacted with excess monobromobimane. In a separate aliquot, the contribution of bound sulfane sulfur pool was measured by incubating the sample with 1 mM TCEP (Tris(2-carboxyethyl)phosphine hydrochloride), a reducing agent to reduce disulfide bonds, in 100 mM phosphate buffer (pH 2.6, 0.1 mM DTPA), and H2S measurement performed in an analogous manner to the one described above. The acid labile pool was determined by subtracting the free hydrogen sulfide value from the value obtained by the acid liberation protocol. The bound sulfane sulfur pool was determined by subtracting the H2S measurement from the acid liberation protocol alone compared to that of TCEP plus acidic conditions. In summary, our new method protocol allows very sensitive and accurate measurement of the three primary biological pools of H2S including free, acid labile

  16. Reflecting Reflective Practice

    ERIC Educational Resources Information Center

    Galea, Simone

    2012-01-01

    This paper demystifies reflective practice on teaching by focusing on the idea of reflection itself and how it has been conceived by two philosophers, Plato and Irigaray. It argues that reflective practice has become a standardized method of defining the teacher in teacher education and teacher accreditation systems. It explores how practices of…

  17. The importance and attainment of accurate absolute radiometric calibration

    NASA Technical Reports Server (NTRS)

    Slater, P. N.

    1984-01-01

    The importance of accurate absolute radiometric calibration is discussed by reference to the needs of those wishing to validate or use models describing the interaction of electromagnetic radiation with the atmosphere and earth surface features. The in-flight calibration methods used for the Landsat Thematic Mapper (TM) and the Systeme Probatoire d'Observation de la Terre, Haute Resolution visible (SPOT/HRV) systems are described and their limitations discussed. The questionable stability of in-flight absolute calibration methods suggests the use of a radiative transfer program to predict the apparent radiance, at the entrance pupil of the sensor, of a ground site of measured reflectance imaged through a well characterized atmosphere. The uncertainties of such a method are discussed.

  18. Reflections on Conceptual Tempo: Relationship Between Cognitive Style and Performance as a Function of Task Characteristics

    ERIC Educational Resources Information Center

    Bush, Ellen S.; Dweck, Carol S.

    1975-01-01

    Children classified as high-anxious reflective in cognitive style were found to perform as well on speeded tasks as low-anxious reflective children and both groups were found to be faster and more accurate than impulsive children. This suggests redefining cognitive style to stress the strategies used rather than predispositions for particular…

  19. 3D shape measurement of automotive glass by using a fringe reflection technique

    NASA Astrophysics Data System (ADS)

    Skydan, O. A.; Lalor, M. J.; Burton, D. R.

    2007-01-01

    In automotive and glass making industries, there is a need for accurately measuring the 3D shapes of reflective surfaces to speed up and ensure product development and manufacturing quality by using non-contact techniques. This paper describes a technique for the measurement of non-full-field reflective surfaces of automotive glass by using a fringe reflection technique. Physical properties of the measurement surfaces do not allow us to apply optical geometries used in existing techniques for surface measurement based upon direct fringe pattern illumination. However, this property of surface reflectivity can be used to implement similar ideas from existing techniques in a new improved method. In other words, the reflective surface can be used as a mirror to reflect illuminated fringe patterns onto a screen behind. It has been found that in the case of implementing the reflective fringe technique, the phase-shift distribution depends not only on the height of the object but also on the slope at each measurement point. This requires the solving of differential equations to find the surface slope and height distributions in the x and y directions and development of the additional height reconstruction algorithms. The main focus has been made on developing a mathematical model of the optical sub-system and discussing ways for its practical implementation including calibration procedures. A number of implemented image processing algorithms for system calibration and data analysis are discussed and two experimental results are given for automotive glass surfaces with different shapes and defects. The proposed technique showed the ability to provide accurate non-destructive measurement of 3D shapes of the reflective automotive glass surfaces and can be used as a key element for a glass shape quality control system on-line or in a laboratory environment.

  20. Systems Biology for Organotypic Cell Cultures

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

    Grego, Sonia; Dougherty, Edward R.; Alexander, Francis J.

    Translating in vitro biological data into actionable information related to human health holds the potential to improve disease treatment and risk assessment of chemical exposures. While genomics has identified regulatory pathways at the cellular level, translation to the organism level requires a multiscale approach accounting for intra-cellular regulation, inter-cellular interaction, and tissue/organ-level effects. Tissue-level effects can now be probed in vitro thanks to recently developed systems of three-dimensional (3D), multicellular, “organotypic” cell cultures, which mimic functional responses of living tissue. However, there remains a knowledge gap regarding interactions across different biological scales, complicating accurate prediction of health outcomes from molecular/genomicmore » data and tissue responses. Systems biology aims at mathematical modeling of complex, non-linear biological systems. We propose to apply a systems biology approach to achieve a computational representation of tissue-level physiological responses by integrating empirical data derived from organotypic culture systems with computational models of intracellular pathways to better predict human responses. Successful implementation of this integrated approach will provide a powerful tool for faster, more accurate and cost-effective screening of potential toxicants and therapeutics. On September 11, 2015, an interdisciplinary group of scientists, engineers, and clinicians gathered for a workshop in Research Triangle Park, North Carolina, to discuss this ambitious goal. Participants represented laboratory-based and computational modeling approaches to pharmacology and toxicology, as well as the pharmaceutical industry, government, non-profits, and academia. Discussions focused on identifying critical system perturbations to model, the computational tools required, and the experimental approaches best suited to generating key data. This consensus report summarizes the

  1. An improved thin film approximation to accurately determine the optical conductivity of graphene from infrared transmittance

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

    Weber, J. W.; Bol, A. A.; Sanden, M. C. M. van de

    2014-07-07

    This work presents an improved thin film approximation to extract the optical conductivity from infrared transmittance in a simple yet accurate way. This approximation takes into account the incoherent reflections from the backside of the substrate. These reflections are shown to have a significant effect on the extracted optical conductivity and hence on derived parameters as carrier mobility and density. By excluding the backside reflections, the error for these parameters for typical chemical vapor deposited (CVD) graphene on a silicon substrate can be as high as 17% and 45% for the carrier mobility and density, respectively. For the mid- andmore » near-infrared, the approximation can be simplified such that the real part of the optical conductivity is extracted without the need for a parameterization of the optical conductivity. This direct extraction is shown for Fourier transform infrared (FTIR) transmittance measurements of CVD graphene on silicon in the photon energy range of 370–7000 cm{sup −1}. From the real part of the optical conductivity, the carrier density, mobility, and number of graphene layers are determined but also residue, originating from the graphene transfer, is detected. FTIR transmittance analyzed with the improved thin film approximation is shown to be a non-invasive, easy, and accurate measurement and analysis method for assessing the quality of graphene and can be used for other 2-D materials.« less

  2. Ecology Content in Introductory Biology Courses: A Comparative Analysis

    ERIC Educational Resources Information Center

    Pool, Richard F.; Turner, Gregory D.; Böttger, S. Anne

    2013-01-01

    In recent years the need for ecological literacy and problem solving has increased, but there is no evidence that this need is reflected by increased ecology coverage at institutions of higher education (IHE) across the United States. Because introductory biology courses may serve to direct student interest toward particular biological categories…

  3. [Monitoring of Crack Propagation in Repaired Structures Based on Characteristics of FBG Sensors Reflecting Spectra].

    PubMed

    Yuan, Shen-fang; Jin, Xin; Qiu, Lei; Huang, Hong-mei

    2015-03-01

    In order to improve the security of aircraft repaired structures, a method of crack propagation monitoring in repaired structures is put forward basing on characteristics of Fiber Bragg Grating (FBG) reflecting spectra in this article. With the cyclic loading effecting on repaired structure, cracks propagate, while non-uniform strain field appears nearby the tip of crack which leads to the FBG sensors' reflecting spectra deformations. The crack propagating can be monitored by extracting the characteristics of FBG sensors' reflecting spectral deformations. A finite element model (FEM) of the specimen is established. Meanwhile, the distributions of strains which are under the action of cracks of different angles and lengths are obtained. The characteristics, such as main peak wavelength shift, area of reflecting spectra, second and third peak value and so on, are extracted from the FBGs' reflecting spectral which are calculated by transfer matrix algorithm. An artificial neural network is built to act as the model between the characteristics of the reflecting spectral and the propagation of crack. As a result, the crack propagation of repaired structures is monitored accurately and the error of crack length is less than 0.5 mm, the error of crack angle is less than 5 degree. The accurately monitoring problem of crack propagation of repaired structures is solved by taking use of this method. It has important significance in aircrafts safety improvement and maintenance cost reducing.

  4. Light distribution modulated diffuse reflectance spectroscopy.

    PubMed

    Huang, Pin-Yuan; Chien, Chun-Yu; Sheu, Chia-Rong; Chen, Yu-Wen; Tseng, Sheng-Hao

    2016-06-01

    Typically, a diffuse reflectance spectroscopy (DRS) system employing a continuous wave light source would need to acquire diffuse reflectances measured at multiple source-detector separations for determining the absorption and reduced scattering coefficients of turbid samples. This results in a multi-fiber probe structure and an indefinite probing depth. Here we present a novel DRS method that can utilize a few diffuse reflectances measured at one source-detector separation for recovering the optical properties of samples. The core of innovation is a liquid crystal (LC) cell whose scattering property can be modulated by the bias voltage. By placing the LC cell between the light source and the sample, the spatial distribution of light in the sample can be varied as the scattering property of the LC cell modulated by the bias voltage, and this would induce intensity variation of the collected diffuse reflectance. From a series of Monte Carlo simulations and phantom measurements, we found that this new light distribution modulated DRS (LDM DRS) system was capable of accurately recover the absorption and scattering coefficients of turbid samples and its probing depth only varied by less than 3% over the full bias voltage variation range. Our results suggest that this LDM DRS platform could be developed to various low-cost, efficient, and compact systems for in-vivo superficial tissue investigation.

  5. Light distribution modulated diffuse reflectance spectroscopy

    PubMed Central

    Huang, Pin-Yuan; Chien, Chun-Yu; Sheu, Chia-Rong; Chen, Yu-Wen; Tseng, Sheng-Hao

    2016-01-01

    Typically, a diffuse reflectance spectroscopy (DRS) system employing a continuous wave light source would need to acquire diffuse reflectances measured at multiple source-detector separations for determining the absorption and reduced scattering coefficients of turbid samples. This results in a multi-fiber probe structure and an indefinite probing depth. Here we present a novel DRS method that can utilize a few diffuse reflectances measured at one source-detector separation for recovering the optical properties of samples. The core of innovation is a liquid crystal (LC) cell whose scattering property can be modulated by the bias voltage. By placing the LC cell between the light source and the sample, the spatial distribution of light in the sample can be varied as the scattering property of the LC cell modulated by the bias voltage, and this would induce intensity variation of the collected diffuse reflectance. From a series of Monte Carlo simulations and phantom measurements, we found that this new light distribution modulated DRS (LDM DRS) system was capable of accurately recover the absorption and scattering coefficients of turbid samples and its probing depth only varied by less than 3% over the full bias voltage variation range. Our results suggest that this LDM DRS platform could be developed to various low-cost, efficient, and compact systems for in-vivo superficial tissue investigation. PMID:27375931

  6. Flash Lamp Integrating Sphere Technique for Measuring the Dynamic Reflectance of Shocked Materials

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

    Stevens, Gerald; La Lone, Brandon; Veeser, Lynn

    2013-07-08

    Accurate reflectance (R) measurements of metals undergoing shock wave compression can benefit high pressure research in several ways. For example, pressure dependent reflectance measurements can be used to deduce electronic band structure, and discrete changes with pressure or temperature may indicate the occurrence of a phase boundary. Additionally, knowledge of the wavelength dependent emissivity (1 -R, for opaque samples) of the metal surface is essential for accurate pyrometric temperature measurement because the radiance is a function of both the temperature and emissivity. We have developed a method for measuring dynamic reflectance in the visible and near IR spectral regions withmore » nanosecond response time and less than 1.5% uncertainty. The method utilizes an integrating sphere fitted with a xenon flash-lamp illumination source. Because of the integrating sphere, the measurements are insensitive to changes in surface curvature or tilt. The in-situ high brightness of the flash-lamp exceeds the sample’s thermal radiance and also enables the use of solid state detectors for recording the reflectance signals with minimal noise. Using the method, we have examined the dynamic reflectance of gallium and tin subjected to shock compression from high explosives. The results suggest significant reflectance changes across phase boundaries for both metals. We have also used the method to determine the spectral emissivity of shock compressed tin at the interface between tin and a LiF window. The results were used to perform emissivity corrections to previous pyrometry data and obtain shock temperatures of the tin/LiF interface with uncertainties of less than 2%.« less

  7. Shedding light on the variability of optical skin properties: finding a path towards more accurate prediction of light propagation in human cutaneous compartments

    PubMed Central

    Mignon, C.; Tobin, D. J.; Zeitouny, M.; Uzunbajakava, N. E.

    2018-01-01

    Finding a path towards a more accurate prediction of light propagation in human skin remains an aspiration of biomedical scientists working on cutaneous applications both for diagnostic and therapeutic reasons. The objective of this study was to investigate variability of the optical properties of human skin compartments reported in literature, to explore the underlying rational of this variability and to propose a dataset of values, to better represent an in vivo case and recommend a solution towards a more accurate prediction of light propagation through cutaneous compartments. To achieve this, we undertook a novel, logical yet simple approach. We first reviewed scientific articles published between 1981 and 2013 that reported on skin optical properties, to reveal the spread in the reported quantitative values. We found variations of up to 100-fold. Then we extracted the most trust-worthy datasets guided by a rule that the spectral properties should reflect the specific biochemical composition of each of the skin layers. This resulted in the narrowing of the spread in the calculated photon densities to 6-fold. We conclude with a recommendation to use the identified most robust datasets when estimating light propagation in human skin using Monte Carlo simulations. Alternatively, otherwise follow our proposed strategy to screen any new datasets to determine their biological relevance. PMID:29552418

  8. Comparison of 5 reflectance meters for capillary blood glucose determination.

    PubMed

    Kolopp, M; Louis, J; Pointel, J P; Kohler, F; Drouin, P; Debry, G

    1983-03-01

    Manufacturing quality, accuracy and users opinion (i.e. medical and nurses staff and patients) were compared among five Destrostix reading reflectance-meters for home-blood-glucose-monitoring. Two machines (dextrometer and glucometer) equipped with microprocessors, integrated circuits and good quality wiring are best made. Reflectance-meter capillary blood glucose measurements were found to be accurate enough for home-blood-glucose-monitoring, compared to a reference method. However, two machines from the same brand were different in blood glucose accuracy. Glucocheck had poorest results. Users prefer small sized, battery powered machines. Glucometer appears to be best suited to home-blood-glucose-monitoring.

  9. Refractive index measurement for biomaterial samples by total internal reflection.

    PubMed

    Jin, Y L; Chen, J Y; Xu, L; Wang, P N

    2006-10-21

    The refractive index of biological tissue is a fundamental parameter in applications of optical diagnosis and laser treatments. In the present work, the refractive indices and thermo-optic coefficients of some basic biomaterials, such as blood plasma, haemoglobin solution and lipid membrane, were studied by the method of total internal reflection at the wavelengths of 532 and 632.8 nm that are the most frequently used laser wavelengths in the biomedical field. The effects of the sample concentration and the temperature on refractive index were measured, and empirical relationships were summarized, accompanied by a theoretical explanation based on molecular polarization theory. The results provide some fundamental data for the refractive indices of these biomaterials under variant conditions, and also demonstrate that the total internal reflection method is a feasible and reliable way to measure the refractive indices of biological samples.

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

    PubMed

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

    2010-10-24

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

  11. Weighted least-square approach for simultaneous measurement of multiple reflective surfaces

    NASA Astrophysics Data System (ADS)

    Tang, Shouhong; Bills, Richard E.; Freischlad, Klaus

    2007-09-01

    Phase shifting interferometry (PSI) is a highly accurate method for measuring the nanometer-scale relative surface height of a semi-reflective test surface. PSI is effectively used in conjunction with Fizeau interferometers for optical testing, hard disk inspection, and semiconductor wafer flatness. However, commonly-used PSI algorithms are unable to produce an accurate phase measurement if more than one reflective surface is present in the Fizeau interferometer test cavity. Examples of test parts that fall into this category include lithography mask blanks and their protective pellicles, and plane parallel optical beam splitters. The plane parallel surfaces of these parts generate multiple interferograms that are superimposed in the recording plane of the Fizeau interferometer. When using wavelength shifting in PSI the phase shifting speed of each interferogram is proportional to the optical path difference (OPD) between the two reflective surfaces. The proposed method is able to differentiate each underlying interferogram from each other in an optimal manner. In this paper, we present a method for simultaneously measuring the multiple test surfaces of all underlying interferograms from these superimposed interferograms through the use of a weighted least-square fitting technique. The theoretical analysis of weighted least-square technique and the measurement results will be described in this paper.

  12. An accurate automated technique for quasi-optics measurement of the microwave diagnostics for fusion plasma

    NASA Astrophysics Data System (ADS)

    Hu, Jianqiang; Liu, Ahdi; Zhou, Chu; Zhang, Xiaohui; Wang, Mingyuan; Zhang, Jin; Feng, Xi; Li, Hong; Xie, Jinlin; Liu, Wandong; Yu, Changxuan

    2017-08-01

    A new integrated technique for fast and accurate measurement of the quasi-optics, especially for the microwave/millimeter wave diagnostic systems of fusion plasma, has been developed. Using the LabVIEW-based comprehensive scanning system, we can realize not only automatic but also fast and accurate measurement, which will help to eliminate the effects of temperature drift and standing wave/multi-reflection. With the Matlab-based asymmetric two-dimensional Gaussian fitting method, all the desired parameters of the microwave beam can be obtained. This technique can be used in the design and testing of microwave diagnostic systems such as reflectometers and the electron cyclotron emission imaging diagnostic systems of the Experimental Advanced Superconducting Tokamak.

  13. Reflectivity Spectra for Commonly Used Reflectors

    NASA Astrophysics Data System (ADS)

    Janecek, Martin

    2012-06-01

    Monte Carlo simulations play an important role in developing and evaluating the performance of radiation detection systems. To accurately model a reflector in an optical Monte Carlo simulation, the reflector's spectral response has to be known. We have measured the reflection coefficient for many commonly used reflectors for wavelengths from 250 nm to 800 nm. The reflectors were also screened for fluorescence and angular distribution changes with wavelength. The reflectors examined in this work include several polytetrafluoroethylene (PTFE) reflectors, Spectralon, GORE diffuse reflector, titanium dioxide paint, magnesium oxide, nitrocellulose filter paper, Tyvek paper, Lumirror, Melinex, ESR films, and aluminum foil. All PTFE films exhibited decreasing reflectivity with longer wavelengths due to transmission. To achieve >;0.95 reflectivity in the 380 to 500 nm range, the PTFE films have to be at least 0.5 mm thick-nitrocellulose is a good alternative if a thin diffuse reflector is needed. Several of the reflectors have sharp declines in reflectivity below a cut-off wavelength, including TiO2 (420 nm), ESR film (395 nm), nitrocellulose (330 nm), Lumirror (325 nm), and Melinex (325 nm). PTFE-like reflectors were the only examined reflectors that had reflectivity above 0.90 for wavelengths below 300 nm. Lumirror, Melinex, and ESR film exhibited fluorescence. Lumirror and Melinex are excited by wavelengths between 320 and 420 nm and have their emission peaks located at 440 nm, while ESR film is excited by wavelengths below 400 nm and the emission peak is located at 430 nm. Lumirror and Melinex also exhibited changing angular distributions with wavelength.

  14. Transforming the Teaching of Science Graduate Students through Reflection

    ERIC Educational Resources Information Center

    Schussler, Elisabeth; Torres, Lisette E.; Rybczynski, Stephen; Gerald, Gary W.; Monroe, Emy; Sarkar, Purbasha; Shahi, Dhan; Osman, Muna A.

    2008-01-01

    This paper presents an assessment of a biology education seminar for science graduate students. It describes how this seminar emphasized pedagogy "and" reflective assignments to help students identify and explore novel instructional strategies, discover who they are as teachers, focus on student learning, and acknowledge the challenges…

  15. jasonSWIR Calibration of Spectralon Reflectance Factor

    NASA Technical Reports Server (NTRS)

    Georgiev, Georgi T.; Butler, James J.; Cooksey, Cahterine; Ding, Leibo; Thome, Kurtis J.

    2011-01-01

    Satellite instruments operating in the reflective solar wavelength region require accurate and precise determination of the Bidirectional Reflectance Factor (BRF) of laboratory-based diffusers used in their pre-flight and on-orbit radiometric calibrations. BRF measurements are required throughout the reflected-solar spectrum from the ultraviolet through the shortwave infrared. Spectralon diffusers are commonly used as a reflectance standard for bidirectional and hemispherical geometries. The Diffuser Calibration Laboratory (DCaL) at NASA's Goddard Space Flight Center is a secondary calibration facility with reflectance measurements traceable to those made by the Spectral Tri-function Automated Reference Reflectometer (STARR) facility at the National Institute of Standards and Technology (NIST). For more than two decades, the DCaL has provided numerous NASA projects with BRF data in the ultraviolet (UV), visible (VIS) and the Near infraRed (NIR) spectral regions. Presented in this paper are measurements of BRF from 1475nm to 1625nm obtained using an indium gallium arsenide detector and a tunable coherent light source. The sample was a 2 inch diameter, 99% white Spectralon target. The BRF results are discussed and compared to empirically generated data from a model based on NIST certified values of 6deg directional/hemispherical spectral reflectance factors from 900nm to 2500nm. Employing a new NIST capability for measuring bidirectional reflectance using a cooled, extended InGaAs detector, BRF calibration measurements of the same sample were also made using NIST's STARR from 1475nm to 1625nm at an incident angle of 0deg and at viewing angles of 40deg, 45deg, and 50deg. The total combined uncertainty for BRF in this ShortWave Infrared (SWIR) range is less than 1%. This measurement capability will evolve into a BRF calibration service in SWIR region in support of NASA remote sensing missions. Keywords: BRF, BRDF, Calibration, Spectralon, Reflectance, Remote Sensing.

  16. Colocalization analysis in fluorescence micrographs: verification of a more accurate calculation of pearson's correlation coefficient.

    PubMed

    Barlow, Andrew L; Macleod, Alasdair; Noppen, Samuel; Sanderson, Jeremy; Guérin, Christopher J

    2010-12-01

    One of the most routine uses of fluorescence microscopy is colocalization, i.e., the demonstration of a relationship between pairs of biological molecules. Frequently this is presented simplistically by the use of overlays of red and green images, with areas of yellow indicating colocalization of the molecules. Colocalization data are rarely quantified and can be misleading. Our results from both synthetic and biological datasets demonstrate that the generation of Pearson's correlation coefficient between pairs of images can overestimate positive correlation and fail to demonstrate negative correlation. We have demonstrated that the calculation of a thresholded Pearson's correlation coefficient using only intensity values over a determined threshold in both channels produces numerical values that more accurately describe both synthetic datasets and biological examples. Its use will bring clarity and accuracy to colocalization studies using fluorescent microscopy.

  17. Techniques for Accurate Sizing of Gold Nanoparticles Using Dynamic Light Scattering with Particular Application to Chemical and Biological Sensing Based on Aggregate Formation.

    PubMed

    Zheng, Tianyu; Bott, Steven; Huo, Qun

    2016-08-24

    Gold nanoparticles (AuNPs) have found broad applications in chemical and biological sensing, catalysis, biomolecular imaging, in vitro diagnostics, cancer therapy, and many other areas. Dynamic light scattering (DLS) is an analytical tool used routinely for nanoparticle size measurement and analysis. Due to its relatively low cost and ease of operation in comparison to other more sophisticated techniques, DLS is the primary choice of instrumentation for analyzing the size and size distribution of nanoparticle suspensions. However, many DLS users are unfamiliar with the principles behind the DLS measurement and are unware of some of the intrinsic limitations as well as the unique capabilities of this technique. The lack of sufficient understanding of DLS often leads to inappropriate experimental design and misinterpretation of the data. In this study, we performed DLS analyses on a series of citrate-stabilized AuNPs with diameters ranging from 10 to 100 nm. Our study shows that the measured hydrodynamic diameters of the AuNPs can vary significantly with concentration and incident laser power. The scattered light intensity of the AuNPs has a nearly sixth order power law increase with diameter, and the enormous scattered light intensity of AuNPs with diameters around or exceeding 80 nm causes a substantial multiple scattering effect in conventional DLS instruments. The effect leads to significant errors in the reported average hydrodynamic diameter of the AuNPs when the measurements are analyzed in the conventional way, without accounting for the multiple scattering. We present here some useful methods to obtain the accurate hydrodynamic size of the AuNPs using DLS. We also demonstrate and explain an extremely powerful aspect of DLS-its exceptional sensitivity in detecting gold nanoparticle aggregate formation, and the use of this unique capability for chemical and biological sensing applications.

  18. Off-axis reflective optical apparatus

    NASA Technical Reports Server (NTRS)

    Ames, Lawrence L. (Inventor); Leary, David F. (Inventor); Mammini, Paul V. (Inventor)

    2005-01-01

    Embodiments of the present invention are directed to a simple apparatus and a convenient and accurate method of mounting the components to form an off-axis reflective optical apparatus such as a collimator. In one embodiment, an off-axis reflective optical apparatus comprises a mounting block having a ferrule holder support surface and an off-axis reflector support surface which is generally perpendicular to the ferrule holder support surface. An optical reflector is mounted on the off-axis reflector support surface and has a reflected beam centerline. The optical reflector has a conic reflective surface and a conic center. A ferrule holder is mounted on the ferrule holder support surface. The ferrule holder provides a ferrule for coupling to an optical fiber and orienting a fiber tip of the optical fiber along a fiber axis toward the optical reflector. The fiber axis is nonparallel to the reflected beam centerline. Prior to mounting the optical reflector to the off-axis reflector support surface and prior to mounting the ferrule holder to the ferrule holder support surface, the optical reflector is movable on the off-axis reflector surface and the ferrule holder is movable on the ferrule holder support surface to align the conic center of the optical reflector with respect to the fiber tip of the optical fiber, and the apparatus has at least one of the following features: (1) the optical reflector is movable on the off-axis reflector support surface to adjust a focus of the fiber tip with respect to the optical reflector, and (2) the ferrule holder is movable on the ferrule holder support surface to adjust the focus of the fiber tip with respect to the optical reflector.

  19. Computational optimization and biological evolution.

    PubMed

    Goryanin, Igor

    2010-10-01

    Modelling and optimization principles become a key concept in many biological areas, especially in biochemistry. Definitions of objective function, fitness and co-evolution, although they differ between biology and mathematics, are similar in a general sense. Although successful in fitting models to experimental data, and some biochemical predictions, optimization and evolutionary computations should be developed further to make more accurate real-life predictions, and deal not only with one organism in isolation, but also with communities of symbiotic and competing organisms. One of the future goals will be to explain and predict evolution not only for organisms in shake flasks or fermenters, but for real competitive multispecies environments.

  20. Accurate artificial boundary conditions for the semi-discretized linear Schrödinger and heat equations on rectangular domains

    NASA Astrophysics Data System (ADS)

    Ji, Songsong; Yang, Yibo; Pang, Gang; Antoine, Xavier

    2018-01-01

    The aim of this paper is to design some accurate artificial boundary conditions for the semi-discretized linear Schrödinger and heat equations in rectangular domains. The Laplace transform in time and discrete Fourier transform in space are applied to get Green's functions of the semi-discretized equations in unbounded domains with single-source. An algorithm is given to compute these Green's functions accurately through some recurrence relations. Furthermore, the finite-difference method is used to discretize the reduced problem with accurate boundary conditions. Numerical simulations are presented to illustrate the accuracy of our method in the case of the linear Schrödinger and heat equations. It is shown that the reflection at the corners is correctly eliminated.

  1. Influence of target reflection on three-dimensional range gated reconstruction.

    PubMed

    Chua, Sing Yee; Wang, Xin; Guo, Ningqun; Tan, Ching Seong

    2016-08-20

    The range gated technique is a promising laser ranging method that is widely used in different fields such as surveillance, industry, and military. In a range gated system, a reflected laser pulse returned from the target scene contains key information for range reconstruction, which directly affects the system performance. Therefore, it is necessary to study the characteristics and effects of the target reflection factor. In this paper, theoretical and experimental analyses are performed to investigate the influence of target reflection on three-dimensional (3D) range gated reconstruction. Based on laser detection and ranging (LADAR) and bidirectional reflection distribution function (BRDF) theory, a 3D range gated reconstruction model is derived and the effect on range accuracy is analyzed from the perspectives of target surface reflectivity and angle of laser incidence. Our theoretical and experimental study shows that the range accuracy is proportional to the target surface reflectivity, but it decreases when the angle of incidence increases to adhere to the BRDF model. The presented findings establish a comprehensive understanding of target reflection in 3D range gated reconstruction, which is of interest to various applications such as target recognition and object modeling. This paper provides a reference for future improvement to perform accurate range compensation or correction.

  2. Integrated three-dimensional shape and reflection properties measurement system.

    PubMed

    Krzesłowski, Jakub; Sitnik, Robert; Maczkowski, Grzegorz

    2011-02-01

    Creating accurate three-dimensional (3D) digitalized models of cultural heritage objects requires that information about surface geometry be integrated with measurements of other material properties like color and reflectance. Up until now, these measurements have been performed in laboratories using manually integrated (subjective) data analyses. We describe an out-of-laboratory bidirectional reflectance distribution function (BRDF) and 3D shape measurement system that implements shape and BRDF measurement in a single setup with BRDF uncertainty evaluation. The setup aligns spatial data with the angular reflectance distribution, yielding a better estimation of the surface's reflective properties by integrating these two modality measurements into one setup using a single detector. This approach provides a better picture of an object's intrinsic material features, which in turn produces a higher-quality digitalized model reconstruction. Furthermore, this system simplifies the data processing by combining structured light projection and photometric stereo. The results of our method of data analysis describe the diffusive and specular attributes corresponding to every measured geometric point and can be used to render intricate 3D models in an arbitrarily illuminated scene.

  3. Polarized Light Reflected and Transmitted by Thick Rayleigh Scattering Atmospheres

    NASA Astrophysics Data System (ADS)

    Natraj, Vijay; Hovenier, J. W.

    2012-03-01

    Accurate values for the intensity and polarization of light reflected and transmitted by optically thick Rayleigh scattering atmospheres with a Lambert surface underneath are presented. A recently reported new method for solving integral equations describing Chandrasekhar's X- and Y-functions is used. The results have been validated using various tests and techniques, including the doubling-adding method, and are accurate to within one unit in the eighth decimal place. Tables are stored electronically and expected to be useful as benchmark results for the (exo)planetary science and astrophysics communities. Asymptotic expressions to obtain Stokes parameters for a thick layer from those of a semi-infinite atmosphere are also provided.

  4. Accurate finite difference methods for time-harmonic wave propagation

    NASA Technical Reports Server (NTRS)

    Harari, Isaac; Turkel, Eli

    1994-01-01

    Finite difference methods for solving problems of time-harmonic acoustics are developed and analyzed. Multidimensional inhomogeneous problems with variable, possibly discontinuous, coefficients are considered, accounting for the effects of employing nonuniform grids. A weighted-average representation is less sensitive to transition in wave resolution (due to variable wave numbers or nonuniform grids) than the standard pointwise representation. Further enhancement in method performance is obtained by basing the stencils on generalizations of Pade approximation, or generalized definitions of the derivative, reducing spurious dispersion, anisotropy and reflection, and by improving the representation of source terms. The resulting schemes have fourth-order accurate local truncation error on uniform grids and third order in the nonuniform case. Guidelines for discretization pertaining to grid orientation and resolution are presented.

  5. INAA Application for Trace Element Determination in Biological Reference Material

    NASA Astrophysics Data System (ADS)

    Atmodjo, D. P. D.; Kurniawati, S.; Lestiani, D. D.; Adventini, N.

    2017-06-01

    Trace element determination in biological samples is often used in the study of health and toxicology. Determination change to its essentiality and toxicity of trace element require an accurate determination method, which implies that a good Quality Control (QC) procedure should be performed. In this study, QC for trace element determination in biological samples was applied by analyzing the Standard Reference Material (SRM) Bovine muscle 8414 NIST using Instrumental Neutron Activation Analysis (INAA). Three selected trace element such as Fe, Zn, and Se were determined. Accuracy of the elements showed as %recovery and precision as %coefficient of variance (%CV). The result showed that %recovery of Fe, Zn, and Se were in the range between 99.4-107%, 92.7-103%, and 91.9-112%, respectively, whereas %CV were 2.92, 3.70, and 5.37%, respectively. These results showed that INAA method is precise and accurate for trace element determination in biological matrices.

  6. HyperART: non-invasive quantification of leaf traits using hyperspectral absorption-reflectance-transmittance imaging.

    PubMed

    Bergsträsser, Sergej; Fanourakis, Dimitrios; Schmittgen, Simone; Cendrero-Mateo, Maria Pilar; Jansen, Marcus; Scharr, Hanno; Rascher, Uwe

    2015-01-01

    Combined assessment of leaf reflectance and transmittance is currently limited to spot (point) measurements. This study introduces a tailor-made hyperspectral absorption-reflectance-transmittance imaging (HyperART) system, yielding a non-invasive determination of both reflectance and transmittance of the whole leaf. We addressed its applicability for analysing plant traits, i.e. assessing Cercospora beticola disease severity or leaf chlorophyll content. To test the accuracy of the obtained data, these were compared with reflectance and transmittance measurements of selected leaves acquired by the point spectroradiometer ASD FieldSpec, equipped with the FluoWat device. The working principle of the HyperART system relies on the upward redirection of transmitted and reflected light (range of 400 to 2500 nm) of a plant sample towards two line scanners. By using both the reflectance and transmittance image, an image of leaf absorption can be calculated. The comparison with the dynamically high-resolution ASD FieldSpec data showed good correlation, underlying the accuracy of the HyperART system. Our experiments showed that variation in both leaf chlorophyll content of four different crop species, due to different fertilization regimes during growth, and fungal symptoms on sugar beet leaves could be accurately estimated and monitored. The use of leaf reflectance and transmittance, as well as their sum (by which the non-absorbed radiation is calculated) obtained by the HyperART system gave considerably improved results in classification of Cercospora leaf spot disease and determination of chlorophyll content. The HyperART system offers the possibility for non-invasive and accurate mapping of leaf transmittance and absorption, significantly expanding the applicability of reflectance, based on mapping spectroscopy, in plant sciences. Therefore, the HyperART system may be readily employed for non-invasive determination of the spatio-temporal dynamics of various plant

  7. [Exposure to biological agents used in Polish enterprises: analysis of data derived from the National Register of Biological Agent].

    PubMed

    Kozajda, Anna; Szadkowska-Stańczyk, Irena

    2011-01-01

    The National Register of Biological Agents at Work and the National Information Centre for Biological Agents Present at Workplaces were established in the Nofer Institute of Occupational Medicine in 2005. The National Information Centre carries out consultation and education activities concerning occupational exposure and risk assessment, development and implementation of preventive programs and accurate registration of reliable information about the use of biological agents. Educational materials on biological exposure are published on the website. The National Register of Biological Agents (database) collects and periodically analyzes the information obtained from employers about the use of biological agents for research, diagnostic or industrial purposes. As of 10 December 2010 there were 240 notifications from companies, which use biological agents for the following purposes: research--69, industrial--30 and diagnostic--321. Near 75% of all notifications were obtained from different diagnostic laboratories (public and private). In total, 3226 workers, including 2967 (92%) women and 256 (8%) men were exposed to biological agents. In general, occupational exposure to 209 biological agents (186 of risk group 2 and 23 of risk group 3, of which 16 are additionally marked by 3**) were registered in the data base.

  8. A pairwise maximum entropy model accurately describes resting-state human brain networks

    PubMed Central

    Watanabe, Takamitsu; Hirose, Satoshi; Wada, Hiroyuki; Imai, Yoshio; Machida, Toru; Shirouzu, Ichiro; Konishi, Seiki; Miyashita, Yasushi; Masuda, Naoki

    2013-01-01

    The resting-state human brain networks underlie fundamental cognitive functions and consist of complex interactions among brain regions. However, the level of complexity of the resting-state networks has not been quantified, which has prevented comprehensive descriptions of the brain activity as an integrative system. Here, we address this issue by demonstrating that a pairwise maximum entropy model, which takes into account region-specific activity rates and pairwise interactions, can be robustly and accurately fitted to resting-state human brain activities obtained by functional magnetic resonance imaging. Furthermore, to validate the approximation of the resting-state networks by the pairwise maximum entropy model, we show that the functional interactions estimated by the pairwise maximum entropy model reflect anatomical connexions more accurately than the conventional functional connectivity method. These findings indicate that a relatively simple statistical model not only captures the structure of the resting-state networks but also provides a possible method to derive physiological information about various large-scale brain networks. PMID:23340410

  9. Status and trends of the nation's biological resources

    USGS Publications Warehouse

    Mac, Michael J.; Opler, Paul A.; Puckett Haecker, Catherine E.; Doran, Peter D.

    1998-01-01

    This report is a comprehensive summary of the status and trends of our nation’s biological resources. The report describes the major processes and factors affecting biological resources, and it treats regional status and trends. Authors of the chapters and boxes in this two-volume report were drawn from federal and state agencies, universities, and private organizations, reflecting the U.S. Geological Survey’s national partnership approach to providing comprehensive, reliable information about our biological resources. Following scientific tradition, each chapter and box was peer-reviewed by anonymous scientific reviewers.

  10. Accurate metacognition for visual sensory memory representations.

    PubMed

    Vandenbroucke, Annelinde R E; Sligte, Ilja G; Barrett, Adam B; Seth, Anil K; Fahrenfort, Johannes J; Lamme, Victor A F

    2014-04-01

    The capacity to attend to multiple objects in the visual field is limited. However, introspectively, people feel that they see the whole visual world at once. Some scholars suggest that this introspective feeling is based on short-lived sensory memory representations, whereas others argue that the feeling of seeing more than can be attended to is illusory. Here, we investigated this phenomenon by combining objective memory performance with subjective confidence ratings during a change-detection task. This allowed us to compute a measure of metacognition--the degree of knowledge that subjects have about the correctness of their decisions--for different stages of memory. We show that subjects store more objects in sensory memory than they can attend to but, at the same time, have similar metacognition for sensory memory and working memory representations. This suggests that these subjective impressions are not an illusion but accurate reflections of the richness of visual perception.

  11. Angular Distribution of the X-ray Reflection in Accretion Disks

    NASA Astrophysics Data System (ADS)

    Garcia, Javier; Dauser, T.; Lohfink, A. M.; Kallman, T. R.; McClintock, J. E.; Steiner, J. F.; Brenneman, L.; Wilms, J.; Reynolds, C. S.; Tombesi, F.

    2014-01-01

    For the study of black holes, it is essential to have an accurate disk-reflection model with a proper treatment of the relativistic effects that occur near strong gravitational fields. These models are used to constrain the properties of the disk, including its inner radius, the degree of ionization of the gas, and the elemental abundances. Importantly, reflection models are the key to measuring black hole spin via the Fe-line method. However, most current reflection models only provide an angle-averaged solution for the flux reflected at the surface of the disk, which can systematically affect the inferred disk emission. We overcome this limitation by exploiting the full capabilities of our reflection code XILLVER. The solution of the reflected intensity of the radiation field is calculated for each photon energy, position in the slab, and viewing angle. We use this information to construct a grid of reflection models in which the inclination of the system is included as a free fitting parameter. Additionally, we directly connect the angle-resolved XILLVER model with the relativistic blurring code RELLINE to produce a self-consistent numerical model for to angular distribution of the reflected X-ray spectra from ionized accretion disks around black holes. The new model, RELCONV_XILL, is provided in the appropriate format to be used in combination with the commonly used fitting packages. An additional version of the new model, RELCONV_LP_XILL, which simulates the reflected spectra in a lampost scenario, is also supplied.

  12. Biologically controlled minerals as potential indicators of life

    NASA Technical Reports Server (NTRS)

    Schwartz, D. E.; Mancinelli, R. L.; Kaneshiro, E.

    1991-01-01

    Minerals can be produced and deposited either by abiotic or biologic means. Regardless of their origin, mineral crystals reflect the environment conditions (e.g., temperature, pressure, chemical composition, and redox potential) present during crystal formation. Biologically-produced mineral crystals are grown or reworked under the control of their host organism and reflect an environment different from the abiotic environment. In addition, minerals of either biologic or abiotic origin have great longevities. For these reasons, biologically produced minerals have been proposed as biomarkers. Biomarkers are key morphological, chemical, and isotopic signatures of living systems that can be used to determine if life processes have occurred. Studies of biologically controlled minerals produced by the protist, Paramecium tetraurelia, were initiated since techniques have already been developed to culture them and isolate their crystalline material, and methods are already in place to analyze this material. Two direct crystalline phases were identified. One phase, whose chemical composition is high in Mg, was identified as struvite. The second phase, whose chemical composition is high in Ca, has not been previously found occurring naturally and may be considered a newly discovered material. Analyses are underway to determine the characteristics of these minerals in order to compare them with characteristics of these minerals in order to compare them with characteristics of minerals formed abiotically, but with the same chemical composition.

  13. Reflection and refraction seismic on the great Ancona landslide

    NASA Astrophysics Data System (ADS)

    Stucchi, E.; Mazzotti, A.

    2003-04-01

    The Adriatic coast in Italy is characterised by the occurrence of several landslide bodies, some of which of huge extension. Here we present the results of seismic refraction and reflection studies recently carried out on the Ancona Landslide, which is located immediately westward of the harbour city of Ancona, and interests an area of about 3.5 km^2 with a landslide front of 2 km. The acquired seismic profile crosses the entire landslide body and was performed employing land and marine sources and receivers. Thus it allows the simultaneous acquisition of marine-marine, marine-land, land-marine and land-land data. The most significant acquisition parameters are: nominal maximum source-receiver offset 600 m, receiver group interval 5 m, single airgun and small explosive charges as energy sources, profile length 1.5 km, average reflection coverage on land 4000% and at sea 20000%. Notwithstanding the significant noise contamination due to intense human activities (road, naval and railway traffic) in the area, the data shows good first breaks and reflections which we use for refraction and reflection processing. The refraction study makes use of GRM and other techniques (Lawton) and it leads to a good definition of the shallower landslide bodies but it is not able to depict the deeper decollement surface. It is also very useful in providing a detailed near surface velocity model that is crucial for the determination of accurate static corrections for the reflection data. High quality subsurface images are achieved by applying different processing sequences to the different sets (marine, land or land-marine) of reflection seismic data. The processing steps that turned out as more effective to the achievement of such a quality were the noise removal by means of FX and SVD filtering, the attenuation of the bubble effect for the marine source data, the ground roll attenuation and the computation of accurate statics. The outcomes of the refraction and reflection

  14. Biological and remote sensing perspectives of pigmentation in coral reef organisms.

    PubMed

    Hedley, John D; Mumby, Peter J

    2002-01-01

    Coral reef communities face unprecedented pressures on local, regional and global scales as a consequence of climate change and anthropogenic disturbance. Optical remote sensing, from satellites or aircraft, is possibly the only means of measuring the effects of such stresses at appropriately large spatial scales (many thousands of square kilometres). To map key variables such as coral community structure, percentages of living coral or percentages of dead coral, a remote sensing instrument must be able to distinguish the reflectance spectra (i.e. "spectral signature", reflected light as a function of wavelength) of each category. For biotic classes, reflectance is a complex function of pigmentation, structure and morphology. Studies of coral "colour" fall into two disparate but potentially complementary types. Firstly, biological studies tend to investigate the structure and significance of pigmentation in reef organisms. These studies often lack details that would be useful from a remote sensing perspective such as intraspecific variation in pigment concentration or the contribution of fluorescence to reflectance. Secondly, remote sensing studies take empirical measurements of spectra and seek wavelengths that discriminate benthic categories. Benthic categories used in remote sensing sometimes consist of species groupings that are biologically or spectrally inappropriate (e.g. merging of algal phyla with distinct pigments). Here, we attempt to bridge the gap between biological and remote sensing perspectives of pigmentation in reef taxa. The aim is to assess the extent to which spectral discrimination can be given a biological foundation, to reduce the ad hoc nature of discriminatory criteria, and to understand the fundamental (biological) limitations in the spectral separability of biotic classes. Sources of pigmentation in reef biota are reviewed together with remote sensing studies where spectral discrimination has been effectively demonstrated between benthic

  15. Student Perceived and Determined Knowledge of Biology Concepts in an Upper-Level Biology Course.

    PubMed

    Ziegler, Brittany; Montplaisir, Lisa

    2014-01-01

    Students who lack metacognitive skills can struggle with the learning process. To be effective learners, students should recognize what they know and what they do not know. This study examines the relationship between students' perception of their knowledge and determined knowledge in an upper-level biology course utilizing a pre/posttest approach. Significant differences in students' perception of their knowledge and their determined knowledge exist at the beginning (pretest) and end (posttest) of the course. Alignment between student perception and determined knowledge was significantly more accurate on the posttest compared with the pretest. Students whose determined knowledge was in the upper quartile had significantly better alignment between their perception and determined knowledge on the pre- and posttest than students in the lower quartile. No difference exists between how students perceived their knowledge between upper- and lower-quartile students. There was a significant difference in alignment of perception and determined knowledge between males and females on the posttest, with females being more accurate in their perception of knowledge. This study provides evidence of discrepancies that exist between what students perceive they know and what they actually know. © 2014 B. Ziegler and L. Montplaisir. CBE—Life Sciences Education © 2014 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).

  16. Bidirectional reflectance distribution function measurements and analysis of retroreflective materials.

    PubMed

    Belcour, Laurent; Pacanowski, Romain; Delahaie, Marion; Laville-Geay, Aude; Eupherte, Laure

    2014-12-01

    We compare the performance of various analytical retroreflecting bidirectional reflectance distribution function (BRDF) models to assess how they reproduce accurately measured data of retroreflecting materials. We introduce a new parametrization, the back vector parametrization, to analyze retroreflecting data, and we show that this parametrization better preserves the isotropy of data. Furthermore, we update existing BRDF models to improve the representation of retroreflective data.

  17. Improved Algorithms for Accurate Retrieval of UV - Visible Diffuse Attenuation Coefficients in Optically Complex, Inshore Waters

    NASA Technical Reports Server (NTRS)

    Cao, Fang; Fichot, Cedric G.; Hooker, Stanford B.; Miller, William L.

    2014-01-01

    Photochemical processes driven by high-energy ultraviolet radiation (UVR) in inshore, estuarine, and coastal waters play an important role in global bio geochemical cycles and biological systems. A key to modeling photochemical processes in these optically complex waters is an accurate description of the vertical distribution of UVR in the water column which can be obtained using the diffuse attenuation coefficients of down welling irradiance (Kd()). The Sea UV Sea UVc algorithms (Fichot et al., 2008) can accurately retrieve Kd ( 320, 340, 380,412, 443 and 490 nm) in oceanic and coastal waters using multispectral remote sensing reflectances (Rrs(), Sea WiFS bands). However, SeaUVSeaUVc algorithms are currently not optimized for use in optically complex, inshore waters, where they tend to severely underestimate Kd(). Here, a new training data set of optical properties collected in optically complex, inshore waters was used to re-parameterize the published SeaUVSeaUVc algorithms, resulting in improved Kd() retrievals for turbid, estuarine waters. Although the updated SeaUVSeaUVc algorithms perform best in optically complex waters, the published SeaUVSeaUVc models still perform well in most coastal and oceanic waters. Therefore, we propose a composite set of SeaUVSeaUVc algorithms, optimized for Kd() retrieval in almost all marine systems, ranging from oceanic to inshore waters. The composite algorithm set can retrieve Kd from ocean color with good accuracy across this wide range of water types (e.g., within 13 mean relative error for Kd(340)). A validation step using three independent, in situ data sets indicates that the composite SeaUVSeaUVc can generate accurate Kd values from 320 490 nm using satellite imagery on a global scale. Taking advantage of the inherent benefits of our statistical methods, we pooled the validation data with the training set, obtaining an optimized composite model for estimating Kd() in UV wavelengths for almost all marine waters. This

  18. Modeling Co-evolution of Speech and Biology.

    PubMed

    de Boer, Bart

    2016-04-01

    Two computer simulations are investigated that model interaction of cultural evolution of language and biological evolution of adaptations to language. Both are agent-based models in which a population of agents imitates each other using realistic vowels. The agents evolve under selective pressure for good imitation. In one model, the evolution of the vocal tract is modeled; in the other, a cognitive mechanism for perceiving speech accurately is modeled. In both cases, biological adaptations to using and learning speech evolve, even though the system of speech sounds itself changes at a more rapid time scale than biological evolution. However, the fact that the available acoustic space is used maximally (a self-organized result of cultural evolution) is constant, and therefore biological evolution does have a stable target. This work shows that when cultural and biological traits are continuous, their co-evolution may lead to cognitive adaptations that are strong enough to detect empirically. Copyright © 2016 Cognitive Science Society, Inc.

  19. Accurate band-to-band registration of AOTF imaging spectrometer using motion detection technology

    NASA Astrophysics Data System (ADS)

    Zhou, Pengwei; Zhao, Huijie; Jin, Shangzhong; Li, Ningchuan

    2016-05-01

    This paper concerns the problem of platform vibration induced band-to-band misregistration with acousto-optic imaging spectrometer in spaceborne application. Registrating images of different bands formed at different time or different position is difficult, especially for hyperspectral images form acousto-optic tunable filter (AOTF) imaging spectrometer. In this study, a motion detection method is presented using the polychromatic undiffracted beam of AOTF. The factors affecting motion detect accuracy are analyzed theoretically, and calculations show that optical distortion is an easily overlooked factor to achieve accurate band-to-band registration. Hence, a reflective dual-path optical system has been proposed for the first time, with reduction of distortion and chromatic aberration, indicating the potential of higher registration accuracy. Consequently, a spectra restoration experiment using additional motion detect channel is presented for the first time, which shows the accurate spectral image registration capability of this technique.

  20. X-ray Reflected Spectra from Accretion Disk Models. III. A Complete Grid of Ionized Reflection Calculations

    NASA Technical Reports Server (NTRS)

    Garcia, J.; Dauser, T.; Reynolds, C. S.; Kallman, T. R.; McClintock, J. E.; Wilms, J.; Ekmann, W.

    2013-01-01

    We present a new and complete library of synthetic spectra for modeling the component of emission that is reflected from an illuminated accretion disk. The spectra were computed using an updated version of our code xillver that incorporates new routines and a richer atomic data base. We offer in the form of a table model an extensive grid of reflection models that cover a wide range of parameters. Each individual model is characterized by the photon index Gamma of the illuminating radiation, the ionization parameter zeta at the surface of the disk (i.e., the ratio of the X-ray flux to the gas density), and the iron abundance A(sub Fe) relative to the solar value. The ranges of the parameters covered are: 1.2 <= Gamma <= 3.4, 1 <= zeta <= 104, and 0.5 <= A(sub Fe) <= 10. These ranges capture the physical conditions typically inferred from observations of active galactic nuclei, and also stellar-mass black holes in the hard state. This library is intended for use when the thermal disk flux is faint compared to the incident power-law flux. The models are expected to provide an accurate description of the Fe K emission line, which is the crucial spectral feature used to measure black hole spin. A total of 720 reflection spectra are provided in a single FITS file suitable for the analysis of X-ray observations via the atable model in xspec. Detailed comparisons with previous reflection models illustrate the improvements incorporated in this version of xillver.

  1. Multispectral near-IR reflectance imaging of simulated early occlusal lesions: Variation of lesion contrast with lesion depth and severity

    PubMed Central

    Simon, Jacob C.; Chan, Kenneth H.; Darling, Cynthia L.; Fried, Daniel

    2014-01-01

    Background and Objectives Early demineralization appears with high contrast at near-IR wavelengths due to a ten to twenty fold difference in the magnitude of light scattering between sound and demineralized enamel. Water absorption in the near-IR has a significant effect on the lesion contrast and the highest contrast has been measured in spectral regions with higher water absorption. The purpose of this study was to determine how the lesion contrast changes with lesion severity and depth for different spectral regions in the near-IR and compare that range of contrast with visible reflectance and fluorescence. Materials and Methods Forty-four human molars were used in this in vitro study. Teeth were painted with an acid-resistant varnish, leaving a 4×4 mm window on the occlusal surface of each tooth exposed for demineralization. Artificial lesions were produced in the unprotected windows after 12–48 hr exposure to a demineralizing solution at pH-4.5. Near-IR reflectance images were acquired over several near-IR spectral distributions, visible light reflectance, and fluorescence with 405-nm excitation and detection at wavelengths greater than 500-nm. Crossed polarizers were used for reflectance measurements to reduce interference from specular reflectance. Cross polarization optical coherence tomography (CP-OCT) was used to non-destructively assess the depth and severity of demineralization in each sample window. Matching two dimensional CP-OCT images of the lesion depth and integrated reflectivity were compared with the reflectance and fluorescence images to determine how accurately the variation in the lesion contrast represents the variation in the lesion severity. Results Artificial lesions appear more uniform on tooth surfaces exposed to an acid challenge at visible wavelengths than they do in the near-IR. Measurements of the lesion depth and severity using CP-OCT show that the lesion severity varies markedly across the sample windows and that the lesion

  2. Journal of Biological Education: A Personal Reflection on Its First 50 Years

    ERIC Educational Resources Information Center

    Reiss, Michael J.

    2016-01-01

    In this commentary, Michael Reiss describes his time with the "Journal of Biology Education" ("JBE") dating back to 1984 when the journal published his first article (Reiss 1984). Over the years, Reiss has authored 31 "JBE" pieces (excluding reviews) including one in honor of the journal's 25th anniversary (Reiss…

  3. Evaluation of several non-reflecting computational boundary conditions for duct acoustics

    NASA Technical Reports Server (NTRS)

    Watson, Willie R.; Zorumski, William E.; Hodge, Steve L.

    1994-01-01

    Several non-reflecting computational boundary conditions that meet certain criteria and have potential applications to duct acoustics are evaluated for their effectiveness. The same interior solution scheme, grid, and order of approximation are used to evaluate each condition. Sparse matrix solution techniques are applied to solve the matrix equation resulting from the discretization. Modal series solutions for the sound attenuation in an infinite duct are used to evaluate the accuracy of each non-reflecting boundary conditions. The evaluations are performed for sound propagation in a softwall duct, for several sources, sound frequencies, and duct lengths. It is shown that a recently developed nonlocal boundary condition leads to sound attenuation predictions considerably more accurate for short ducts. This leads to a substantial reduction in the number of grid points when compared to other non-reflecting conditions.

  4. Predicting perturbation patterns from the topology of biological networks.

    PubMed

    Santolini, Marc; Barabási, Albert-László

    2018-06-20

    High-throughput technologies, offering an unprecedented wealth of quantitative data underlying the makeup of living systems, are changing biology. Notably, the systematic mapping of the relationships between biochemical entities has fueled the rapid development of network biology, offering a suitable framework to describe disease phenotypes and predict potential drug targets. However, our ability to develop accurate dynamical models remains limited, due in part to the limited knowledge of the kinetic parameters underlying these interactions. Here, we explore the degree to which we can make reasonably accurate predictions in the absence of the kinetic parameters. We find that simple dynamically agnostic models are sufficient to recover the strength and sign of the biochemical perturbation patterns observed in 87 biological models for which the underlying kinetics are known. Surprisingly, a simple distance-based model achieves 65% accuracy. We show that this predictive power is robust to topological and kinetic parameter perturbations, and we identify key network properties that can increase up to 80% the recovery rate of the true perturbation patterns. We validate our approach using experimental data on the chemotactic pathway in bacteria, finding that a network model of perturbation spreading predicts with ∼80% accuracy the directionality of gene expression and phenotype changes in knock-out and overproduction experiments. These findings show that the steady advances in mapping out the topology of biochemical interaction networks opens avenues for accurate perturbation spread modeling, with direct implications for medicine and drug development.

  5. Time-driven Activity-based Costing More Accurately Reflects Costs in Arthroplasty Surgery.

    PubMed

    Akhavan, Sina; Ward, Lorrayne; Bozic, Kevin J

    2016-01-01

    categories with the most variability between TA and TDABC estimates were operating room services and room and board. Traditional hospital cost accounting systems overestimate the costs associated with many surgical procedures, including primary TJA. TDABC provides a more accurate measure of true resource use associated with TJAs and can be used to identify high-cost/high-variability processes that can be targeted for process/quality improvement. Level III, therapeutic study.

  6. Tools for Accurate and Efficient Analysis of Complex Evolutionary Mechanisms in Microbial Genomes. Final Report

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

    Nakhleh, Luay

    I proposed to develop computationally efficient tools for accurate detection and reconstruction of microbes' complex evolutionary mechanisms, thus enabling rapid and accurate annotation, analysis and understanding of their genomes. To achieve this goal, I proposed to address three aspects. (1) Mathematical modeling. A major challenge facing the accurate detection of HGT is that of distinguishing between these two events on the one hand and other events that have similar "effects." I proposed to develop a novel mathematical approach for distinguishing among these events. Further, I proposed to develop a set of novel optimization criteria for the evolutionary analysis of microbialmore » genomes in the presence of these complex evolutionary events. (2) Algorithm design. In this aspect of the project, I proposed to develop an array of e cient and accurate algorithms for analyzing microbial genomes based on the formulated optimization criteria. Further, I proposed to test the viability of the criteria and the accuracy of the algorithms in an experimental setting using both synthetic as well as biological data. (3) Software development. I proposed the nal outcome to be a suite of software tools which implements the mathematical models as well as the algorithms developed.« less

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

    PubMed

    Douglass, John K; Wcislo, William T

    2010-08-01

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

  8. Hydrogeologic structure underlying a recharge pond delineated with shear-wave seismic reflection and cone penetrometer data

    USGS Publications Warehouse

    Haines, S.S.; Pidlisecky, Adam; Knight, R.

    2009-01-01

    With the goal of improving the understanding of the subsurface structure beneath the Harkins Slough recharge pond in Pajaro Valley, California, USA, we have undertaken a multimodal approach to develop a robust velocity model to yield an accurate seismic reflection section. Our shear-wave reflection section helps us identify and map an important and previously unknown flow barrier at depth; it also helps us map other relevant structure within the surficial aquifer. Development of an accurate velocity model is essential for depth conversion and interpretation of the reflection section. We incorporate information provided by shear-wave seismic methods along with cone penetrometer testing and seismic cone penetrometer testing measurements. One velocity model is based on reflected and refracted arrivals and provides reliable velocity estimates for the full depth range of interest when anchored on interface depths determined from cone data and borehole drillers' logs. A second velocity model is based on seismic cone penetrometer testing data that provide higher-resolution ID velocity columns with error estimates within the depth range of the cone penetrometer testing. Comparison of the reflection/refraction model with the seismic cone penetrometer testing model also suggests that the mass of the cone truck can influence velocity with the equivalent effect of approximately one metre of extra overburden stress. Together, these velocity models and the depth-converted reflection section result in a better constrained hydrologic model of the subsurface and illustrate the pivotal role that cone data can provide in the reflection processing workflow. ?? 2009 European Association of Geoscientists & Engineers.

  9. A novel reflectometer for relative reflectance measurements of CCDs

    NASA Astrophysics Data System (ADS)

    Hart, Murdock; Barkhouser, Robert H.; Gunn, James E.; Smee, Stephen A.

    2016-07-01

    The high quantum efficiencies (QE) of backside illuminated charge coupled devices (CCD) has ushered in the age of the large scale astronomical survey. The QE of these devices can be greater than 90%, and is dependent upon the operating temperature, device thickness, backside charging mechanisms, and anti-reflection (AR) coatings. But at optical wavelengths the QE is well approximated as one minus the reflectance, thus the measurement of the backside reflectivity of these devices provides a second independent measure of their QE. We have designed and constructed a novel instrument to measure the relative specular reflectance of CCD detectors, with a significant portion of this device being constructed using a 3D fused deposition model (FDM) printer. This device implements both a monitor and measurement photodiode to simultaneously collect in- cident and reflected measurements reducing errors introduced by the relative reflectance calibration process. While most relative reflectometers are highly dependent upon a precisely repeatable target distance for accurate measurements, we have implemented a method of measurement which minimizes these errors. Using the reflectometer we have measured the reflectance of two types of Hamamatsu CCD detectors. The first device is a Hamamatsu 2k x 4k backside illuminated high resistivity p-type silicon detector which has been optimized to operate in the blue from 380 nm - 650 nm. The second detector being a 2k x 4k backside illuminated high resistivity p-type silicon detector optimized for use in the red from 640 nm - 960 nm. We have not only been able to measure the reflectance of these devices as a function of wavelength we have also sampled the reflectance as a function of position on the device, and found a reflection gradient across these devices.

  10. Accurate and precise determination of isotopic ratios by MC-ICP-MS: a review.

    PubMed

    Yang, Lu

    2009-01-01

    For many decades the accurate and precise determination of isotope ratios has remained a very strong interest to many researchers due to its important applications in earth, environmental, biological, archeological, and medical sciences. Traditionally, thermal ionization mass spectrometry (TIMS) has been the technique of choice for achieving the highest accuracy and precision. However, recent developments in multi-collector inductively coupled plasma mass spectrometry (MC-ICP-MS) have brought a new dimension to this field. In addition to its simple and robust sample introduction, high sample throughput, and high mass resolution, the flat-topped peaks generated by this technique provide for accurate and precise determination of isotope ratios with precision reaching 0.001%, comparable to that achieved with TIMS. These features, in combination with the ability of the ICP source to ionize nearly all elements in the periodic table, have resulted in an increased use of MC-ICP-MS for such measurements in various sample matrices. To determine accurate and precise isotope ratios with MC-ICP-MS, utmost care must be exercised during sample preparation, optimization of the instrument, and mass bias corrections. Unfortunately, there are inconsistencies and errors evident in many MC-ICP-MS publications, including errors in mass bias correction models. This review examines "state-of-the-art" methodologies presented in the literature for achievement of precise and accurate determinations of isotope ratios by MC-ICP-MS. Some general rules for such accurate and precise measurements are suggested, and calculations of combined uncertainty of the data using a few common mass bias correction models are outlined.

  11. Dynamic sensing model for accurate delectability of environmental phenomena using event wireless sensor network

    NASA Astrophysics Data System (ADS)

    Missif, Lial Raja; Kadhum, Mohammad M.

    2017-09-01

    Wireless Sensor Network (WSN) has been widely used for monitoring where sensors are deployed to operate independently to sense abnormal phenomena. Most of the proposed environmental monitoring systems are designed based on a predetermined sensing range which does not reflect the sensor reliability, event characteristics, and the environment conditions. Measuring of the capability of a sensor node to accurately detect an event within a sensing field is of great important for monitoring applications. This paper presents an efficient mechanism for even detection based on probabilistic sensing model. Different models have been presented theoretically in this paper to examine their adaptability and applicability to the real environment applications. The numerical results of the experimental evaluation have showed that the probabilistic sensing model provides accurate observation and delectability of an event, and it can be utilized for different environment scenarios.

  12. BOREAS RSS-19 1994 Seasonal Understory Reflectance Data

    NASA Technical Reports Server (NTRS)

    Miller, John R.; Hall, Forrest G. (Editor); Nickerson, Jaime (Editor); White, H. Peter; Peddle, Derek; Freemantle, Jim; Smith, David E. (Technical Monitor)

    2000-01-01

    The BOREAS RSS-19 team collected airborne remotely sensed images and ground reflectance data for characterizing the radiometric properties of the boreal forest landscape. One objective of BOREAS is to further the understanding of the spectral bidirectional reflectance of typical boreal ecosystem stands in the visible/near-infrared regime. An essential input for any canopy BRDF model is an accurate estimate of the average understory reflectance, both for sunlit and shaded conditions. These variables can be expected to vary seasonally because of species-dependent differences in the phenological cycle of foliar display. In response to these requirements, the average understory reflectance for the flux tower sites of both the NSA (Thompson, Manitoba) and the SSA (Candle Lake, Saskatchewan) was observed throughout the year during five field campaigns. This was done by measuring the nadir reflectance (400 to 850 nm) of sunlit and shaded understory (vegetation and snow cover) along a surveyed LAI transect line (Chen, RSS-07) at each site near solar noon and documenting an average site reflectance. Comparisons between sites reveal differences in the green and infrared regions of the spectra, because of the differing species in the understory for each site. Temporal (seasonal) variation for each site was also observed (06-Feb-1994 to 16-Sep-1994), indicating the changing flora mixtures and changing spectral signatures as the understory matures during the growing season. The data are stored in tabular ASCII files. The data files are available on a CD-ROM (see document number 20010000884) or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).

  13. Remote-sensing reflectance of turbid sediment-dominated waters. Reduction of sediment type variations and changing illumination conditions effects by use of reflectance ratios.

    PubMed

    Doxaran, David; Froidefond, Jean-Marie; Castaing, Patrice

    2003-05-20

    Variations of sediment type (grain size and refractive index) and changing illumination conditions affect the reflectance signal of coastal waters and limit the accuracy of sediment-concentration estimations from remote-sensing measurements. These effects are analyzed from numerous in situ remote-sensing measurements carried out in the Gironde and Loire Estuaries and then reduced and partly eliminated when reflectance ratios between the near infrared and the visible are considered. These ratios showed high correlation with the sediment concentration. On the basis of the obtained relationships, performing correspondence functions were established that allow an accurate estimation of suspended sediments in the estuaries from Système Probatoire d'Observation de la Terre, Landsat, and Sea-Viewing Wide Field-of-View Sensor data, independently of the date of acquisition.

  14. Light reflection by the cuticle of C. aurigans scarabs: a biological broadband reflector of left handed circularly polarized light

    NASA Astrophysics Data System (ADS)

    Libby, E.; Azofeifa, D. E.; Hernández-Jiménez, M.; Barboza-Aguilar, C.; Solís, A.; García-Aguilar, I.; Arce-Marenco, L.; Hernández, A.; Vargas, W. E.

    2014-08-01

    Measured reflection spectra from elytra of Chrysina aurigans scarabs are reported. They show a broad reflection band for wavelengths from 0.525 to 1.0 μm with a sequence of maxima and minima reflection values superimposed on a mean value of around 40% for the high reflection band. Different mechanisms contributing to the reflection spectra have been considered, with the dominant effect, reflection of left handed circularly polarized light, being produced by a laminated left handed twisted structure whose pitch changes with depth through the procuticle in a more complex way than that characterizing broad band circular polarizers based on cholesteric liquid crystals.

  15. Methods for biological data integration: perspectives and challenges

    PubMed Central

    Gligorijević, Vladimir; Pržulj, Nataša

    2015-01-01

    Rapid technological advances have led to the production of different types of biological data and enabled construction of complex networks with various types of interactions between diverse biological entities. Standard network data analysis methods were shown to be limited in dealing with such heterogeneous networked data and consequently, new methods for integrative data analyses have been proposed. The integrative methods can collectively mine multiple types of biological data and produce more holistic, systems-level biological insights. We survey recent methods for collective mining (integration) of various types of networked biological data. We compare different state-of-the-art methods for data integration and highlight their advantages and disadvantages in addressing important biological problems. We identify the important computational challenges of these methods and provide a general guideline for which methods are suited for specific biological problems, or specific data types. Moreover, we propose that recent non-negative matrix factorization-based approaches may become the integration methodology of choice, as they are well suited and accurate in dealing with heterogeneous data and have many opportunities for further development. PMID:26490630

  16. Comparison of LANDSAT-2 and field spectrometer reflectance signatures of south Texas rangeland plant communities

    NASA Technical Reports Server (NTRS)

    Richardson, A. J.; Escobar, D. E.; Gausman, H. W.; Everitt, J. H. (Principal Investigator)

    1982-01-01

    The accuracy was assessed for an atmospheric correction method that depends on clear water bodies to infer solar and atmospheric parameters for radiative transfer equations by measuring the reflectance signature of four prominent south Texas rangeland plants with the LANDSAT satellite multispectral scanner (MSS) and a ground based spectroradiometer. The rangeland plant reflectances produced by the two sensors were correlated with no significant deviation of the slope from unity or of the intercept from zero. These results indicated that the atmospheric correction produced LANDSAT MSS estimates of rangeland plant reflectances that are as accurate as the ground based spectroradiometer.

  17. Cardiac vagal flexibility and accurate personality impressions: Examining a physiological correlate of the good judge.

    PubMed

    Human, Lauren J; Mendes, Wendy Berry

    2018-02-23

    Research has long sought to identify which individuals are best at accurately perceiving others' personalities or are good judges, yet consistent predictors of this ability have been difficult to find. In the current studies, we revisit this question by examining a novel physiological correlate of social sensitivity, cardiac vagal flexibility, which reflects dynamic modulation of cardiac vagal control. We examined whether greater cardiac vagal flexibility was associated with forming more accurate personality impressions, defined as viewing targets more in line with their distinctive self-reported profile of traits, in two studies, including a thin-slice video perceptions study (N = 109) and a dyadic interaction study (N = 175). Across studies, we found that individuals higher in vagal flexibility formed significantly more accurate first impressions of others' more observable personality traits (e.g., extraversion, creativity, warmth). These associations held while including a range of relevant covariates, including cardiac vagal tone, sympathetic activation, and gender. In sum, social sensitivity as indexed by cardiac vagal flexibility is linked to forming more accurate impressions of others' observable traits, shedding light on a characteristic that may help to identify the elusive good judge and providing insight into its neurobiological underpinnings. © 2018 Wiley Periodicals, Inc.

  18. A Reflective Look at Reflecting Teams

    ERIC Educational Resources Information Center

    Pender, Rebecca L.; Stinchfield, Tracy

    2012-01-01

    This article reviewed existing literature and research on the reflecting team process. There is a dearth of empirical research that explores the reflecting team process and the outcome of counseling that uses reflecting teams. Implications of using reflecting teams for counselors, counselor educators, and clients will be discussed. A call for…

  19. Time-Accurate, Unstructured-Mesh Navier-Stokes Computations with the Space-Time CESE Method

    NASA Technical Reports Server (NTRS)

    Chang, Chau-Lyan

    2006-01-01

    Application of the newly emerged space-time conservation element solution element (CESE) method to compressible Navier-Stokes equations is studied. In contrast to Euler equations solvers, several issues such as boundary conditions, numerical dissipation, and grid stiffness warrant systematic investigations and validations. Non-reflecting boundary conditions applied at the truncated boundary are also investigated from the stand point of acoustic wave propagation. Validations of the numerical solutions are performed by comparing with exact solutions for steady-state as well as time-accurate viscous flow problems. The test cases cover a broad speed regime for problems ranging from acoustic wave propagation to 3D hypersonic configurations. Model problems pertinent to hypersonic configurations demonstrate the effectiveness of the CESE method in treating flows with shocks, unsteady waves, and separations. Good agreement with exact solutions suggests that the space-time CESE method provides a viable alternative for time-accurate Navier-Stokes calculations of a broad range of problems.

  20. Using Reflectance Measurements to Determine Ecosystem Light Use Efficiency

    NASA Astrophysics Data System (ADS)

    Huemmrich, K. F.; Middleton, E. M.; Hall, F. G.; Knox, R. G.; Walter-Shea, E.; Verma, S. B.

    2006-05-01

    Understanding the dynamics of the global carbon cycle requires an accurate determination of the spatial and temporal distribution of photosynthetic CO2 uptake by terrestrial vegetation. Remote sensing observations may provide the spatially extensive observations required for this type of analysis. A light use efficiency model is one approach to modeling carbon fluxes driven by remotely sensed inputs. Photosynthetic down-regulation has been associated with changes in the apparent spectral reflectance of leaves and these responses may permit the estimation of ecosystem photosynthetic light use efficiency (LUE). At a prairie site in Oklahoma, CO2 flux measurements from an eddy covariance system along with biophysical data were collected through 1998 and 1999. During the growing seasons hyperspectral reflectance measurements were collected in nearby plots at multiple times in a day at approximately monthly intervals. LUE is calculated as the ratio of carbon uptake by the ecosystem and the fraction of photosynthetically active radiation (PAR) absorbed by green leaves. The LUE values are compared with reflectance indexes examining how relationships vary over hours, months, and years. For this system a number of different reflectance indexes have been found to correlate with LUE; including the Photochemical Reflectance Index (PRI) and the Structure Independent Pigment Index (SIPI); as well as spectral first derivatives at 460, 550, and 615nm; and second derivatives at 510 and 620nm. This methodology provides a nondestructive, repeatable, direct comparison between ecosystem carbon fluxes and spectral reflectance at scales relevant to remote sensing.

  1. Characterizing Topology of Probabilistic Biological Networks.

    PubMed

    Todor, Andrei; Dobra, Alin; Kahveci, Tamer

    2013-09-06

    Biological interactions are often uncertain events, that may or may not take place with some probability. Existing studies analyze the degree distribution of biological networks by assuming that all the given interactions take place under all circumstances. This strong and often incorrect assumption can lead to misleading results. Here, we address this problem and develop a sound mathematical basis to characterize networks in the presence of uncertain interactions. We develop a method that accurately describes the degree distribution of such networks. We also extend our method to accurately compute the joint degree distributions of node pairs connected by edges. The number of possible network topologies grows exponentially with the number of uncertain interactions. However, the mathematical model we develop allows us to compute these degree distributions in polynomial time in the number of interactions. It also helps us find an adequate mathematical model using maximum likelihood estimation. Our results demonstrate that power law and log-normal models best describe degree distributions for probabilistic networks. The inverse correlation of degrees of neighboring nodes shows that, in probabilistic networks, nodes with large number of interactions prefer to interact with those with small number of interactions more frequently than expected.

  2. Measurement and Validation of Bidirectional Reflectance of Space Shuttle and Space Station Materials for Computerized Lighting Models

    NASA Technical Reports Server (NTRS)

    Fletcher, Lauren E.; Aldridge, Ann M.; Wheelwright, Charles; Maida, James

    1997-01-01

    Task illumination has a major impact on human performance: What a person can perceive in his environment significantly affects his ability to perform tasks, especially in space's harsh environment. Training for lighting conditions in space has long depended on physical models and simulations to emulate the effect of lighting, but such tests are expensive and time-consuming. To evaluate lighting conditions not easily simulated on Earth, personnel at NASA Johnson Space Center's (JSC) Graphics Research and Analysis Facility (GRAF) have been developing computerized simulations of various illumination conditions using the ray-tracing program, Radiance, developed by Greg Ward at Lawrence Berkeley Laboratory. Because these computer simulations are only as accurate as the data used, accurate information about the reflectance properties of materials and light distributions is needed. JSC's Lighting Environment Test Facility (LETF) personnel gathered material reflectance properties for a large number of paints, metals, and cloths used in the Space Shuttle and Space Station programs, and processed these data into reflectance parameters needed for the computer simulations. They also gathered lamp distribution data for most of the light sources used, and validated the ability to accurately simulate lighting levels by comparing predictions with measurements for several ground-based tests. The result of this study is a database of material reflectance properties for a wide variety of materials, and lighting information for most of the standard light sources used in the Shuttle/Station programs. The combination of the Radiance program and GRAF's graphics capability form a validated computerized lighting simulation capability for NASA.

  3. An overview of surface radiance and biology studies in FIFE

    NASA Astrophysics Data System (ADS)

    Blad, B. L.; Schimel, D. S.

    1992-11-01

    The use of satellite data to study and to understand energy and mass exchanges between the land surface and the atmosphere requires information about various biological processes and how various reflected or emitted spectral radiances are influenced by or manifested in these processes. To obtain such information, studies were conducted by the First ISLSCP Field Experiment (FIFE) surface radiances and biology (SRB) group using surface, near-surface, helicopter, and aircraft measurements. The two primary objectives of this group were to relate radiative fluxes to biophysical parameters and physiological processes and to assess how various management treatments affect important biological processes. This overview paper summarizes the results obtained by various SRB teams working in nine different areas: (1) measurement of bidirectional reflectance and estimation of hemispherical albedo; (2) evaluation of spatial and seasonal variability of spectral reflectance and vegetation indices; (3) determination of surface and radiational factors and their effects on vegetation indices and PAR relationships; (4) use of surface temperatures to estimate sensible heat flux; (5) controls over photosynthesis and respiration at small scales; (6) soil surface CO2 fluxes and grassland carbon budget; (7) landscape variations in controls over gas exchange and energy partitioning; (8) radiometric response of prairie to management and topography; and (9) determination of nitrogen gas exchanges in a tallgrass prairie.

  4. Meaning Making: What Reflective Essays Reveal about Biology Students' Conceptions about Natural Selection

    ERIC Educational Resources Information Center

    Balgopal, Meena M.; Montplaisir, Lisa M.

    2011-01-01

    The process of reflective writing can play a central role in making meaning as learners process new information and connect it to prior knowledge. An examination of the written discourse can therefore be revealing of learners' cognitive understanding and affective (beliefs, feelings, motivation to learn) responses to concepts. Despite reflective…

  5. X-RAY REFLECTED SPECTRA FROM ACCRETION DISK MODELS. III. A COMPLETE GRID OF IONIZED REFLECTION CALCULATIONS

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

    Garcia, J.; McClintock, J. E.; Dauser, T.

    2013-05-10

    We present a new and complete library of synthetic spectra for modeling the component of emission that is reflected from an illuminated accretion disk. The spectra were computed using an updated version of our code XILLVER that incorporates new routines and a richer atomic database. We offer in the form of a table model an extensive grid of reflection models that cover a wide range of parameters. Each individual model is characterized by the photon index {Gamma} of the illuminating radiation, the ionization parameter {xi} at the surface of the disk (i.e., the ratio of the X-ray flux to themore » gas density), and the iron abundance A{sub Fe} relative to the solar value. The ranges of the parameters covered are 1.2 {<=} {Gamma} {<=} 3.4, 1 {<=} {xi} {<=} 10{sup 4}, and 0.5 {<=} A{sub Fe} {<=} 10. These ranges capture the physical conditions typically inferred from observations of active galactic nuclei, and also stellar-mass black holes in the hard state. This library is intended for use when the thermal disk flux is faint compared to the incident power-law flux. The models are expected to provide an accurate description of the Fe K emission line, which is the crucial spectral feature used to measure black hole spin. A total of 720 reflection spectra are provided in a single FITS file (http://hea-www.cfa.harvard.edu/{approx}javier/xillver/) suitable for the analysis of X-ray observations via the atable model in XSPEC. Detailed comparisons with previous reflection models illustrate the improvements incorporated in this version of XILLVER.« less

  6. Nanofibers of Human Tropoelastin-inspired peptides: Structural characterization and biological properties.

    PubMed

    Secchi, Valeria; Franchi, Stefano; Fioramonti, Marco; Polzonetti, Giovanni; Iucci, Giovanna; Bochicchio, Brigida; Battocchio, Chiara

    2017-08-01

    Regenerative medicine is taking great advantage from the use of biomaterials in the treatments of a wide range of diseases and injuries. Among other biomaterials, self-assembling peptides are appealing systems due to their ability to spontaneously form nanostructured hydrogels that can be directly injected into lesions. Indeed, self-assembling peptide scaffolds are expected to behave as biomimetic matrices able to surround cells, to promote specific interactions, and to control and modify cell behavior by mimicking the native environment as well. We selected three pentadecapeptides inspired by Human Tropoelastin, a natural protein of the extracellular matrix, expected to show high biocompatibility. Moreover, the here proposed self-assembling peptides (SAPs) are able to spontaneously aggregate in nanofibers in biological environment, as revealed by AFM (Atomic Force Microscopy). Peptides were characterized by XPS (X-ray Photoelectron Spectroscopy) and IRRAS (Infrared Reflection Absorption Spectroscopy) both as lyophilized (not aggregated) and as aggregated (nanofibers) samples in order to investigate some potential differences in their chemical composition and intermolecular interactions, and to analyze the surface and interface of nanofibers. Finally, an accurate investigation of the biological properties of the SAPs and of their interaction with cells was performed by culturing for the first time human Mesenchymal Stem Cells (hMSCs) in presence of SAPs. The final aim of this work was to assess if Human Tropoelastin-inspired nanostructured fibers could exert a cytotoxic effect and to evaluate their biocompatibility, cellular adhesion and proliferation. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Concurrent chart review provides more accurate documentation and increased calculated case mix index, severity of illness, and risk of mortality.

    PubMed

    Frazee, Richard C; Matejicka, Anthony V; Abernathy, Stephen W; Davis, Matthew; Isbell, Travis S; Regner, Justin L; Smith, Randall W; Jupiter, Daniel C; Papaconstantinou, Harry T

    2015-04-01

    Case mix index (CMI) is calculated to determine the relative value assigned to a Diagnosis-Related Group. Accurate documentation of patient complications and comorbidities and major complications and comorbidities changes CMI and can affect hospital reimbursement and future pay for performance metrics. Starting in 2010, a physician panel concurrently reviewed the documentation of the trauma/acute care surgeons. Clarifications of the Centers for Medicare and Medicaid Services term-specific documentation were made by the panel, and the surgeon could incorporate or decline the clinical queries. A retrospective review of trauma/acute care inpatients was performed. The mean severity of illness, risk of mortality, and CMI from 2009 were compared with the 3 subsequent years. Mean length of stay and mean Injury Severity Score by year were listed as measures of patient acuity. Statistical analysis was performed using ANOVA and t-test, with p < 0.05 for significance. Each year demonstrated an increase in severity of illness, risk of mortality, and CMI compared with baseline values (p < 0.05). Length of stay was not significantly different, reflecting similar patient populations throughout the study. Injury Severity Score decreased in 2011 and 2012 compared with 2009, reflecting a lower level of injury in the trauma population. A concurrent documentation review significantly increases severity of illness, risk of mortality, and CMI scores in a trauma/acute care service compared with pre-program levels. These changes reflect more accurate key word documentation rather than a change in patient acuity. The increased scores might impact hospital reimbursement and more accurately stratify outcomes measures for care providers. Copyright © 2015 American College of Surgeons. Published by Elsevier Inc. All rights reserved.

  8. Workshop Report: Systems Biology for Organotypic Cell Cultures

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

    Grego, Sonia; Dougherty, Edward R.; Alexander, Francis Joseph

    Translating in vitro biological data into actionable information related to human health holds the potential to improve disease treatment and risk assessment of chemical exposures. While genomics has identified regulatory pathways at the cellular level, translation to the organism level requires a multiscale approach accounting for intra-cellular regulation, inter-cellular interaction, and tissue/organ-level effects. Tissue-level effects can now be probed in vitro thanks to recently developed systems of three-dimensional (3D), multicellular, “organotypic” cell cultures, which mimic functional responses of living tissue. However, there remains a knowledge gap regarding interactions across different biological scales, complicating accurate prediction of health outcomes from molecular/genomicmore » data and tissue responses. Systems biology aims at mathematical modeling of complex, non-linear biological systems. We propose to apply a systems biology approach to achieve a computational representation of tissue-level physiological responses by integrating empirical data derived from organotypic culture systems with computational models of intracellular pathways to better predict human responses. Successful implementation of this integrated approach will provide a powerful tool for faster, more accurate and cost-effective screening of potential toxicants and therapeutics. On September 11, 2015, an interdisciplinary group of scientists, engineers, and clinicians gathered for a workshop in Research Triangle Park, North Carolina, to discuss this ambitious goal. Participants represented laboratory-based and computational modeling approaches to pharmacology and toxicology, as well as the pharmaceutical industry, government, non-profits, and academia. Discussions focused on identifying critical system perturbations to model, the computational tools required, and the experimental approaches best suited to generating key data.« less

  9. Workshop Report: Systems Biology for Organotypic Cell Cultures

    DOE PAGES

    Grego, Sonia; Dougherty, Edward R.; Alexander, Francis Joseph; ...

    2016-11-14

    Translating in vitro biological data into actionable information related to human health holds the potential to improve disease treatment and risk assessment of chemical exposures. While genomics has identified regulatory pathways at the cellular level, translation to the organism level requires a multiscale approach accounting for intra-cellular regulation, inter-cellular interaction, and tissue/organ-level effects. Tissue-level effects can now be probed in vitro thanks to recently developed systems of three-dimensional (3D), multicellular, “organotypic” cell cultures, which mimic functional responses of living tissue. However, there remains a knowledge gap regarding interactions across different biological scales, complicating accurate prediction of health outcomes from molecular/genomicmore » data and tissue responses. Systems biology aims at mathematical modeling of complex, non-linear biological systems. We propose to apply a systems biology approach to achieve a computational representation of tissue-level physiological responses by integrating empirical data derived from organotypic culture systems with computational models of intracellular pathways to better predict human responses. Successful implementation of this integrated approach will provide a powerful tool for faster, more accurate and cost-effective screening of potential toxicants and therapeutics. On September 11, 2015, an interdisciplinary group of scientists, engineers, and clinicians gathered for a workshop in Research Triangle Park, North Carolina, to discuss this ambitious goal. Participants represented laboratory-based and computational modeling approaches to pharmacology and toxicology, as well as the pharmaceutical industry, government, non-profits, and academia. Discussions focused on identifying critical system perturbations to model, the computational tools required, and the experimental approaches best suited to generating key data.« less

  10. Improving the performance of active-optical reflectance sensor algorithms using soil and weather information

    USDA-ARS?s Scientific Manuscript database

    Active-optical reflectance sensors (AORS) use corn (Zea mays L.) plant tissue as a bioassay of crop N status to determine future N requirements. However, studies have shown AORS algorithms used for making N fertilizer recommendations are not consistently accurate. Thus, AORS algorithm improvements s...

  11. [Biological characteristics of calliphoridae and its application in forensic medicine].

    PubMed

    Zhao, Boa; Wen, Charn; Qi, Li-Li; Wang, He; Wang, Ji

    2013-12-01

    Diptera Calliphoridae is the first major kind of flies that appears on the decomposed corpses. In forensic entomology, according to the living characteristics of Calliphoridae flies, we could accurately estimate postmortem interval (PMI) in a murder or unidentified case and could provide useful clues to solve the case. This paper introduces the characteristics of the biology and morphology of Diptera Calliphoridae, and reviews the combined application of forensic entomology, molecular biology, mathematical morphology and toxicology.

  12. Rapid and accurate pyrosequencing of angiosperm plastid genomes

    PubMed Central

    Moore, Michael J; Dhingra, Amit; Soltis, Pamela S; Shaw, Regina; Farmerie, William G; Folta, Kevin M; Soltis, Douglas E

    2006-01-01

    Background Plastid genome sequence information is vital to several disciplines in plant biology, including phylogenetics and molecular biology. The past five years have witnessed a dramatic increase in the number of completely sequenced plastid genomes, fuelled largely by advances in conventional Sanger sequencing technology. Here we report a further significant reduction in time and cost for plastid genome sequencing through the successful use of a newly available pyrosequencing platform, the Genome Sequencer 20 (GS 20) System (454 Life Sciences Corporation), to rapidly and accurately sequence the whole plastid genomes of the basal eudicot angiosperms Nandina domestica (Berberidaceae) and Platanus occidentalis (Platanaceae). Results More than 99.75% of each plastid genome was simultaneously obtained during two GS 20 sequence runs, to an average depth of coverage of 24.6× in Nandina and 17.3× in Platanus. The Nandina and Platanus plastid genomes shared essentially identical gene complements and possessed the typical angiosperm plastid structure and gene arrangement. To assess the accuracy of the GS 20 sequence, over 45 kilobases of sequence were generated for each genome using conventional sequencing. Overall error rates of 0.043% and 0.031% were observed in GS 20 sequence for Nandina and Platanus, respectively. More than 97% of all observed errors were associated with homopolymer runs, with ~60% of all errors associated with homopolymer runs of 5 or more nucleotides and ~50% of all errors associated with regions of extensive homopolymer runs. No substitution errors were present in either genome. Error rates were generally higher in the single-copy and noncoding regions of both plastid genomes relative to the inverted repeat and coding regions. Conclusion Highly accurate and essentially complete sequence information was obtained for the Nandina and Platanus plastid genomes using the GS 20 System. More importantly, the high accuracy observed in the GS 20 plastid

  13. Machine Learning of Parameters for Accurate Semiempirical Quantum Chemical Calculations

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

    Dral, Pavlo O.; von Lilienfeld, O. Anatole; Thiel, Walter

    2015-05-12

    We investigate possible improvements in the accuracy of semiempirical quantum chemistry (SQC) methods through the use of machine learning (ML) models for the parameters. For a given class of compounds, ML techniques require sufficiently large training sets to develop ML models that can be used for adapting SQC parameters to reflect changes in molecular composition and geometry. The ML-SQC approach allows the automatic tuning of SQC parameters for individual molecules, thereby improving the accuracy without deteriorating transferability to molecules with molecular descriptors very different from those in the training set. The performance of this approach is demonstrated for the semiempiricalmore » OM2 method using a set of 6095 constitutional isomers C7H10O2, for which accurate ab initio atomization enthalpies are available. The ML-OM2 results show improved average accuracy and a much reduced error range compared with those of standard OM2 results, with mean absolute errors in atomization enthalpies dropping from 6.3 to 1.7 kcal/mol. They are also found to be superior to the results from specific OM2 reparameterizations (rOM2) for the same set of isomers. The ML-SQC approach thus holds promise for fast and reasonably accurate high-throughput screening of materials and molecules.« less

  14. Machine learning of parameters for accurate semiempirical quantum chemical calculations

    DOE PAGES

    Dral, Pavlo O.; von Lilienfeld, O. Anatole; Thiel, Walter

    2015-04-14

    We investigate possible improvements in the accuracy of semiempirical quantum chemistry (SQC) methods through the use of machine learning (ML) models for the parameters. For a given class of compounds, ML techniques require sufficiently large training sets to develop ML models that can be used for adapting SQC parameters to reflect changes in molecular composition and geometry. The ML-SQC approach allows the automatic tuning of SQC parameters for individual molecules, thereby improving the accuracy without deteriorating transferability to molecules with molecular descriptors very different from those in the training set. The performance of this approach is demonstrated for the semiempiricalmore » OM2 method using a set of 6095 constitutional isomers C 7H 10O 2, for which accurate ab initio atomization enthalpies are available. The ML-OM2 results show improved average accuracy and a much reduced error range compared with those of standard OM2 results, with mean absolute errors in atomization enthalpies dropping from 6.3 to 1.7 kcal/mol. They are also found to be superior to the results from specific OM2 reparameterizations (rOM2) for the same set of isomers. The ML-SQC approach thus holds promise for fast and reasonably accurate high-throughput screening of materials and molecules.« less

  15. Experimental and model based investigation of the links between snow bidirectional reflectance and snow microstructure

    NASA Astrophysics Data System (ADS)

    Dumont, M.; Flin, F.; Malinka, A.; Brissaud, O.; Hagenmuller, P.; Dufour, A.; Lapalus, P.; Lesaffre, B.; Calonne, N.; Rolland du Roscoat, S.; Ando, E.

    2017-12-01

    Snow optical properties are unique among Earth surface and crucial for a wide range of applications. The bi-directional reflectance, hereafter BRDF, of snow is sensible to snow microstructure. However the complex interplays between different parameters of snow microstructure namely size parameters and shape parameters on reflectance are challenging to disentangle both theoretically and experimentally. An accurate understanding and modelling of snow BRDF is required to correctly process satellite data. BRDF measurements might also provide means of characterizing snow morphology. This study presents one of the very few dataset that combined bi-directional reflectance measurements over 500-2500 nm and X-ray tomography of the snow microstructure for three different snow samples and two snow types. The dataset is used to evaluate the approach from Malinka, 2014 that relates snow optical properties to the chord length distribution in the snow microstructure. For low and medium absorption, the model accurately reproduces the measurements but tends to slightly overestimate the anisotropy of the reflectance. The model indicates that the deviation of the ice chord length distribution from an exponential distribution, that can be understood as a characterization of snow types, does not impact the reflectance for such absorptions. The simulations are also impacted by the uncertainties in the ice refractive index values. At high absorption and high viewing/incident zenith angle, the simulations and the measurements disagree indicating that some of the assumptions made in the model are not met anymore. The study also indicates that crystal habits might play a significant role for the reflectance under such geometries and wavelengths. However quantitative relationship between crystal habits and reflectance alongside with potential optical methodologies to classify snow morphology would require an extended dataset over more snow types. This extended dataset can likely be obtained

  16. Relation of agronomic and multispectral reflectance characteristics of spring wheat canopies

    NASA Technical Reports Server (NTRS)

    Bauer, M. E. (Principal Investigator); Ahlrichs, J. S.

    1982-01-01

    The relationships between crop canopy variables such as leaf area index (LAI) and their multispectral reflectance properties were investigated along with the potential for estimating canopy variables from remotely sensed reflectance measurements. Reflectance spectra over the 0.4 to 2.5 micron wavelength range were acquired during each of the major development stages of spring wheat canopies at Williston, North Dakota, during three seasons. Treatments included planting date, N fertilization, cultivar, and soil moisture. Agronomic measurements included development stage, biomass, LAI, and percent soil cover. High correlations were found between reflectance and percent cover, LAI, and biomass. A near infrared wavelength band, 0.76 to 0.90 microns, was most important in explaining variation in LAI and percent cover, while a middle infrared band, 2.08 to 2.35 microns, explained the most variation in biomass and plant water content. Transformations, including the near infrared/red reflectance ratio and greenness index, were also highly correlated to canopy variables. The relationship of canopy variables to reflectance decreased as the crop began to ripen. the canopy variables could be accurately predicted using measurements from three to five wavelength bands. The wavelength bands proposed for the thematic mapper sensor were more strongly related to the canopy variables than the LANDSAT MSS bands.

  17. Phase-sensitive terahertz spectroscopy with backward-wave oscillators in reflection mode.

    PubMed

    Pronin, A V; Goncharov, Yu G; Fischer, T; Wosnitza, J

    2009-12-01

    In this article we describe a method which allows accurate measurements of the complex reflection coefficient r = absolute value(r) x exp(i phi(R)) of a solid at frequencies of 1-50 cm(-1) (30 GHz-1.5 THz). Backward-wave oscillators are used as sources for monochromatic coherent radiation tunable in frequency. The amplitude of the complex reflection (the reflectivity) is measured in a standard way, while the phase shift, introduced by the reflection from the sample surface, is measured using a Michelson interferometer. This method is particular useful for nontransparent samples, where phase-sensitive transmission measurements are not possible. The method requires no Kramers-Kronig transformation in order to extract the sample's electrodynamic properties (such as the complex dielectric function or complex conductivity). Another area of application of this method is the study of magnetic materials with complex dynamic permeabilities different from unity at the measurement frequencies (for example, colossal-magnetoresistance materials and metamaterials). Measuring both the phase-sensitive transmission and the phase-sensitive reflection allows for a straightforward model-independent determination of the dielectric permittivity and magnetic permeability of such materials.

  18. Phase-sensitive terahertz spectroscopy with backward-wave oscillators in reflection mode

    NASA Astrophysics Data System (ADS)

    Pronin, A. V.; Goncharov, Yu. G.; Fischer, T.; Wosnitza, J.

    2009-12-01

    In this article we describe a method which allows accurate measurements of the complex reflection coefficient r̂=|r̂|ṡexp(iφR) of a solid at frequencies of 1-50 cm-1 (30 GHz-1.5 THz). Backward-wave oscillators are used as sources for monochromatic coherent radiation tunable in frequency. The amplitude of the complex reflection (the reflectivity) is measured in a standard way, while the phase shift, introduced by the reflection from the sample surface, is measured using a Michelson interferometer. This method is particular useful for nontransparent samples, where phase-sensitive transmission measurements are not possible. The method requires no Kramers-Kronig transformation in order to extract the sample's electrodynamic properties (such as the complex dielectric function or complex conductivity). Another area of application of this method is the study of magnetic materials with complex dynamic permeabilities different from unity at the measurement frequencies (for example, colossal-magnetoresistance materials and metamaterials). Measuring both the phase-sensitive transmission and the phase-sensitive reflection allows for a straightforward model-independent determination of the dielectric permittivity and magnetic permeability of such materials.

  19. Study and reflections on the functional and organizational role of neuromessenger nitric oxide in learning: An artificial and biological approach

    NASA Astrophysics Data System (ADS)

    Suárez Araujo, C. P.

    2000-05-01

    We present in this work a theoretical and conceptual study and some reflections on a fundamental aspect concerning with the structure and brain function: the Cellular Communication. The main interests of our study are the signal transmission mechanisms and the neuronal mechanisms responsible to learning. We propose the consideration of a new kind of communication mechanisms, different to the synaptic transmission, "Diffusion or Volume Transmission." This new alternative is based on a diffusing messenger as nitric oxide (NO). Our study aims towards the design of a conceptual framework, which covers implications of NO in the artificial neural networks (ANNs), both in neural architecture and learning processing. This conceptual frame might be able to provide possible biological support for many aspects of ANNs and to generate new concepts to improve the structure and operation of them. Some of these new concepts are The Fast Diffusion Neural Propagation (FDNP), the Diffuse Neighborhood (DNB), (1), the Diffusive Hybrid Neuromodulation (DHN), the Virtual Weights. Finally we will propose a new mathematical formulation for the Hebb learning law, taking into account the NO effect. Along the same lines, we will reflect on the possibility of a new formal framework for learning processes in ANNs, which consist of slow and fast learning concerning with co-operation between the classical neurotransmission and FDNP. We will develop this work from a computational neuroscience point of view, proposing a global study framework of diffusion messenger NO (GSFNO), using a hybrid natural/artificial approach. Finally it is important to note that we can consider this paper the first paper of a set of scientific work on nitric oxide (NO) and artificial neural networks (ANNs): NO and ANNs Series. We can say that this paper has a character of search and query on both subjects their implications and co-existence.

  20. More on analyzing the reflection of a laser beam by a deformed highly reflective volume Bragg grating using iteration of the beam propagation method.

    PubMed

    Shu, Hong; Mokhov, Sergiy; Zeldovich, Boris Ya; Bass, Michael

    2009-01-01

    A further extension of the iteration method for beam propagation calculation is presented that can be applied for volume Bragg gratings (VBGs) with extremely large grating strength. A reformulation of the beam propagation formulation is presented for analyzing the reflection of a laser beam by a deformed VBG. These methods will be shown to be very accurate and efficient. A VBG with generic z-dependent distortion has been analyzed using these methods.

  1. Spectrodirectional Investigation of a Geometric-Optical Canopy Reflectance Model by Laboratory Simulation

    NASA Astrophysics Data System (ADS)

    Stanford, Adam Christopher

    Canopy reflectance models (CRMs) can accurately estimate vegetation canopy biophysical-structural information such as Leaf Area Index (LAI) inexpensively using satellite imagery. The strict physical basis which geometric-optical CRMs employ to mathematically link canopy bidirectional reflectance and structure allows for the tangible replication of a CRM's geometric abstraction of a canopy in the laboratory, enabling robust CRM validation studies. To this end, the ULGS-2 goniometer was used to obtain multiangle, hyperspectral (Spectrodirectional) measurements of a specially-designed tangible physical model forest, developed based upon the Geometric-Optical Mutual Shadowing (GOMS) CRM, at three different canopy cover densities. GOMS forward-modelled reflectance values had high levels of agreement with ULGS-2 measurements, with obtained reflectance RMSE values ranging from 0.03% to 0.1%. Canopy structure modelled via GOMS Multiple-Forward-Mode (MFM) inversion had varying levels of success. The methods developed in this thesis can potentially be extended to more complex CRMs through the implementation of 3D printing.

  2. Evolution Acceptance and Epistemological Beliefs of College Biology Students

    ERIC Educational Resources Information Center

    Borgerding, Lisa A.; Deniz, Hasan; Anderson, Elizabeth Shevock

    2017-01-01

    Evolutionary theory is central to biology, and scientifically accurate evolution instruction is promoted within national and state standards documents. Previous literature has identified students' epistemological beliefs as potential predictors of evolution acceptance. The present work seeks to explore more directly how student views of evolution…

  3. Reflections on fifty years of publications on the history of general biology and special embryology.

    PubMed

    Oppenheimer, J M

    1975-12-01

    The publications of fifty years (1925-1974) of the histroy of biology and embryology are surveyed. In America, the earliest background for work during this period was provided by the collectors, mainly physicians, of books into extensive private libraries. The collectors, for instance Osler, Cushing, and Fulton in this country and Geoffrey Keynes abroad, became expert technical bibliographers during the early part of the half-century under consideration. High standards for medical, thus biological history, insofar as these fields overlap, were also set earlier by Sudhoff's Institut für Geschichte der Medizin in Leipzig, and American historical studies benefited when Sigerist came from Leipzig to Baltimore in the early 1930's. Textbooks of medical history are omitted from discussion here, but a number of more or less general histories of biology published within the specified period are briefly evaluated. The discussion next turns to histories of embryology, general and special. Recent monographs on the classical embryologists, Wolff and von Baer, are enumerated, as are a number of biographies and autobiographies of important embryologists published here or abroad during our half-century. Then general histories of embryology are discussed, and finally some specialized ones. Needham, Roger, and Adelmann are singled out as the most important contributors to the history of embryology, in the West, during the period covered. Few of the contributors to the history of biology and medicine during the years of 1925 through 1974 were trained as historians while students. It is concluded that the History of Science Society has performed an important contribution in professionalizing the history of biology and embryology, but it is pointed out that a great new challenge faces it in the necessity to counteract anti-historical and anti-intellectual moods and movements of today.

  4. The First Cut Is the Deepest: Reflections on the State of Animal Dissection in Biology Education

    ERIC Educational Resources Information Center

    De Villiers, Rian; Monk, Martin

    2005-01-01

    In biology education, the study of structure has traditionally involved the use of dissection. Animal-rights campaigners have caused biology educators and learners to question the necessity of dissections. This study reviews the research evidence for the efficacy of alternatives to dissection and then turns to research evidence on attitudes to…

  5. Comparison of narrow-band reflectance spectroscopy and tristimulus colorimetry for measurements of skin and hair color in persons of different biological ancestry.

    PubMed

    Shriver, M D; Parra, E J

    2000-05-01

    We have used two modern computerized handheld reflectometers, the Photovolt ColorWalk colorimeter (a tristimulus colorimeter; Photovolt, UMM Electronics, Indianapolis, IN) and the DermaSpectrometer (a specialized narrow-band reflectometer; Cortex Technology, Hadsund, Denmark), to compare two methods for the objective determination of skin and hair color. These instruments both determine color by measuring the intensity of reflected light of particular wavelengths. The Photovolt ColorWalk instrument does so by shining a white light and sensing the intensity of the reflected light with a linear photodiode array. The ColorWalk results can then be expressed in terms of several standard color systems, most importantly, the Commission International d'Eclairage (CIE) Lab system, in which any color can be described by three values: L*, the lightness; a*, the amount of green or red; and b*, the amount of yellow or blue. Instead of a white light and photodiodes, the DermaSpectrometer uses two light-emitting diodes (LEDs), one green and one red, to illuminate a surface, and then it records the intensity of the reflected light. The results of these readings are expressed in terms of erythema (E) and melanin (M) indices. We measured the unexposed skin of the inner upper arm, the exposed skin of the forehead, and the hair, of 80 persons using these two instruments. Since it is important for the application of these measures in anthropology that we understand their relationship across a number of different pigmentation levels, we sampled persons from several different groups, namely, European Americans (n = 55), African Americans (n = 9), South Asians (n = 7), and East Asians (n = 9). In these subjects, there is a very high correlation between L* and the M index for the inner arm (R(2) = 0.928, P < 0.001), the forehead (R(2) = 0.822, P < 0.001), and the hair (R(2) = 0.827, P < 0.001). The relationship between a* and the E index is complex and dependent on the pigmentation level

  6. Infrared reflectance spectra: effects of particle size, provenance and preparation

    NASA Astrophysics Data System (ADS)

    Su, Yin-Fong; Myers, Tanya L.; Brauer, Carolyn S.; Blake, Thomas A.; Forland, Brenda M.; Szecsody, J. E.; Johnson, Timothy J.

    2014-10-01

    We have recently developed methods for making more accurate infrared total and diffuse directional - hemispherical reflectance measurements using an integrating sphere. We have found that reflectance spectra of solids, especially powders, are influenced by a number of factors including the sample preparation method, the particle size and morphology, as well as the sample origin. On a quantitative basis we have investigated some of these parameters and the effects they have on reflectance spectra, particularly in the longwave infrared. In the IR the spectral features may be observed as either maxima or minima: In general, upward-going peaks in the reflectance spectrum result from strong surface scattering, i.e. rays that are reflected from the surface without bulk penetration, whereas downward-going peaks are due to either absorption or volume scattering, i.e. rays that have penetrated or refracted into the sample interior and are not reflected. The light signals reflected from solids usually encompass all such effects, but with strong dependencies on particle size and preparation. This paper measures the reflectance spectra in the 1.3 - 16 micron range for various bulk materials that have a combination of strong and weak absorption bands in order to observe the effects on the spectral features: Bulk materials were ground with a mortar and pestle and sieved to separate the samples into various size fractions between 5 and 500 microns. The median particle size is demonstrated to have large effects on the reflectance spectra. For certain minerals we also observe significant spectral change depending on the geologic origin of the sample. All three such effects (particle size, preparation and provenance) result in substantial change in the reflectance spectra for solid materials; successful identification algorithms will require sufficient flexibility to account for these parameters.

  7. The structural basis for enhanced silver reflectance in Koi fish scale and skin.

    PubMed

    Gur, Dvir; Leshem, Ben; Oron, Dan; Weiner, Steve; Addadi, Lia

    2014-12-10

    Fish have evolved biogenic multilayer reflectors composed of stacks of intracellular anhydrous guanine crystals separated by cytoplasm, to produce the silvery luster of their skin and scales. Here we compare two different variants of the Japanese Koi fish; one of them with enhanced reflectivity. Our aim is to determine how biology modulates reflectivity, and from this to obtain a mechanistic understanding of the structure and properties governing the intensity of silver reflectance. We measured the reflectance of individual scales with a custom-made microscope, and then for each individual scale we characterized the structure of the guanine crystal/cytoplasm layers using high-resolution cryo-SEM. The measured reflectance and the structural-geometrical parameters were used to calculate the reflectance of each scale, and the results were compared to the experimental measurements. We show that enhanced reflectivity is obtained with the same basic guanine crystal/cytoplasm stacks, but the structural arrangement between the stack, inside the stacks, and relative to the scale surface is varied when reflectivity is enhanced. Finally, we propose a model that incorporates the basic building block parameters, the crystal orientation inside the tissue, and the resulting reflectance and explains the mechanistic basis for reflectance enhancement.

  8. Dissecting innate immune responses with the tools of systems biology.

    PubMed

    Smith, Kelly D; Bolouri, Hamid

    2005-02-01

    Systems biology strives to derive accurate predictive descriptions of complex systems such as innate immunity. The innate immune system is essential for host defense, yet the resulting inflammatory response must be tightly regulated. Current understanding indicates that this system is controlled by complex regulatory networks, which maintain homoeostasis while accurately distinguishing pathogenic infections from harmless exposures. Recent studies have used high throughput technologies and computational techniques that presage predictive models and will be the foundation of a systems level understanding of innate immunity.

  9. Carbene footprinting accurately maps binding sites in protein-ligand and protein-protein interactions

    NASA Astrophysics Data System (ADS)

    Manzi, Lucio; Barrow, Andrew S.; Scott, Daniel; Layfield, Robert; Wright, Timothy G.; Moses, John E.; Oldham, Neil J.

    2016-11-01

    Specific interactions between proteins and their binding partners are fundamental to life processes. The ability to detect protein complexes, and map their sites of binding, is crucial to understanding basic biology at the molecular level. Methods that employ sensitive analytical techniques such as mass spectrometry have the potential to provide valuable insights with very little material and on short time scales. Here we present a differential protein footprinting technique employing an efficient photo-activated probe for use with mass spectrometry. Using this methodology the location of a carbohydrate substrate was accurately mapped to the binding cleft of lysozyme, and in a more complex example, the interactions between a 100 kDa, multi-domain deubiquitinating enzyme, USP5 and a diubiquitin substrate were located to different functional domains. The much improved properties of this probe make carbene footprinting a viable method for rapid and accurate identification of protein binding sites utilizing benign, near-UV photoactivation.

  10. Accurate atom-mapping computation for biochemical reactions.

    PubMed

    Latendresse, Mario; Malerich, Jeremiah P; Travers, Mike; Karp, Peter D

    2012-11-26

    The complete atom mapping of a chemical reaction is a bijection of the reactant atoms to the product atoms that specifies the terminus of each reactant atom. Atom mapping of biochemical reactions is useful for many applications of systems biology, in particular for metabolic engineering where synthesizing new biochemical pathways has to take into account for the number of carbon atoms from a source compound that are conserved in the synthesis of a target compound. Rapid, accurate computation of the atom mapping(s) of a biochemical reaction remains elusive despite significant work on this topic. In particular, past researchers did not validate the accuracy of mapping algorithms. We introduce a new method for computing atom mappings called the minimum weighted edit-distance (MWED) metric. The metric is based on bond propensity to react and computes biochemically valid atom mappings for a large percentage of biochemical reactions. MWED models can be formulated efficiently as Mixed-Integer Linear Programs (MILPs). We have demonstrated this approach on 7501 reactions of the MetaCyc database for which 87% of the models could be solved in less than 10 s. For 2.1% of the reactions, we found multiple optimal atom mappings. We show that the error rate is 0.9% (22 reactions) by comparing these atom mappings to 2446 atom mappings of the manually curated Kyoto Encyclopedia of Genes and Genomes (KEGG) RPAIR database. To our knowledge, our computational atom-mapping approach is the most accurate and among the fastest published to date. The atom-mapping data will be available in the MetaCyc database later in 2012; the atom-mapping software will be available within the Pathway Tools software later in 2012.

  11. Accurate wavelength measurements of a putative standard for near-infrared diffuse reflection spectrometry.

    PubMed

    Isaksson, Tomas; Yang, Husheng; Kemeny, Gabor J; Jackson, Richard S; Wang, Qian; Alam, M Kathleen; Griffiths, Peter R

    2003-02-01

    The diffuse reflection (DR) spectrum of a sample consisting of a mixture of rare earth oxides and talc was measured at 2 cm-1 resolution, using five different accessories installed on five different Fourier transform near-infrared (FT-NIR) spectrometers from four manufacturers. Peak positions for 37 peaks were determined using two peak-picking algorithms: center-of-mass and polynomial fitting. The wavenumber of the band center reported by either of these techniques was sensitive to the slope of the baseline, and so the baseline of the spectra was corrected using either a polynomial fit or conversion to the second derivative. Significantly different results were obtained with one combination of spectrometer and accessory than the others. Apparently, the beam path through the interferometer and DR accessory was different for this accessory than for any of the other measurements, causing a severe degradation of the resolution. Spectra measured on this instrument were removed as outliers. For measurements made on FT-NIR spectrometers, it is shown that it is important to check the resolution at which the spectrum has been measured using lines in the vibration-rotation spectrum of atmospheric water vapor and to specify the peak-picking and baseline-correction algorithms that are used to process the measured spectra. The variance between the results given by the four different methods of peak-picking and baseline correction was substantially larger than the variance between the remaining five measurements. Certain bands were found to be more suitable than others for use as wavelength standards. A band at 5943.13 cm-1 (1682.62 nm) was found to be the most stable band between the four methods and the six measurements. A band at 5177.04 cm-1 (1931.61 nm) has the highest precision between different measurements when polynomial baseline correction and polynomial peak-picking algorithms are used.

  12. Improved clinical documentation leads to superior reportable outcomes: An accurate representation of patient's clinical status.

    PubMed

    Elkbuli, Adel; Godelman, Steven; Miller, Ashley; Boneva, Dessy; Bernal, Eileen; Hai, Shaikh; McKenney, Mark

    2018-05-01

    Clinical documentation can be an underappreciated. Trauma Centers (TCs) are now routinely evaluated for quality performance. TCs with poor documentation may not accurately reflect actual injury burden or comorbidities and can impact accuracy of mortality measures. Markers exist to adjust crude death rates for injury severity: observed over expected deaths (O/E) adjust for injury; Case Mix Index (CMI) reflects disease burden, and Severity of Illness (SOI) measures organ dysfunction. We aim to evaluate the impact of implementing a Clinical Documentation Improvement Program (CDIP) on reported outcomes. Review of 2-years of prospectively collected data for trauma patients, during the implementation of CDIP. A two-group prospective observational study design was used to evaluate the pre-implementation and the post-implementation phase of improved clinical documentation. T-test and Chi-Squared were used with significance defined as p < 0.05. In the pre-implementation period, there were 49 deaths out of 1419 (3.45%), while post-implementation period, had 38 deaths out of 1454 (2.61%), (non-significant). There was however, a significant difference between O/E ratios. In the pre-phase, the O/E was 1.36 and 0.70 in the post-phase (p < 0.001). The two groups also differed on CMI with a pre-group mean of 2.48 and a post-group of 2.87 (p < 0.001), indicating higher injury burden in the post-group. SOI started at 2.12 and significantly increased to 2.91, signifying more organ system dysfunction (p < 0.018). Improved clinical documentation results in improved accuracy of measures of mortality, injury severity, and comorbidities and a more accurate reflection in O/E mortality ratios, CMI, and SOI. Copyright © 2018 IJS Publishing Group Ltd. Published by Elsevier Ltd. All rights reserved.

  13. Dopamine Reward Prediction Error Responses Reflect Marginal Utility

    PubMed Central

    Stauffer, William R.; Lak, Armin; Schultz, Wolfram

    2014-01-01

    Summary Background Optimal choices require an accurate neuronal representation of economic value. In economics, utility functions are mathematical representations of subjective value that can be constructed from choices under risk. Utility usually exhibits a nonlinear relationship to physical reward value that corresponds to risk attitudes and reflects the increasing or decreasing marginal utility obtained with each additional unit of reward. Accordingly, neuronal reward responses coding utility should robustly reflect this nonlinearity. Results In two monkeys, we measured utility as a function of physical reward value from meaningful choices under risk (that adhered to first- and second-order stochastic dominance). The resulting nonlinear utility functions predicted the certainty equivalents for new gambles, indicating that the functions’ shapes were meaningful. The monkeys were risk seeking (convex utility function) for low reward and risk avoiding (concave utility function) with higher amounts. Critically, the dopamine prediction error responses at the time of reward itself reflected the nonlinear utility functions measured at the time of choices. In particular, the reward response magnitude depended on the first derivative of the utility function and thus reflected the marginal utility. Furthermore, dopamine responses recorded outside of the task reflected the marginal utility of unpredicted reward. Accordingly, these responses were sufficient to train reinforcement learning models to predict the behaviorally defined expected utility of gambles. Conclusions These data suggest a neuronal manifestation of marginal utility in dopamine neurons and indicate a common neuronal basis for fundamental explanatory constructs in animal learning theory (prediction error) and economic decision theory (marginal utility). PMID:25283778

  14. Dopamine reward prediction error responses reflect marginal utility.

    PubMed

    Stauffer, William R; Lak, Armin; Schultz, Wolfram

    2014-11-03

    Optimal choices require an accurate neuronal representation of economic value. In economics, utility functions are mathematical representations of subjective value that can be constructed from choices under risk. Utility usually exhibits a nonlinear relationship to physical reward value that corresponds to risk attitudes and reflects the increasing or decreasing marginal utility obtained with each additional unit of reward. Accordingly, neuronal reward responses coding utility should robustly reflect this nonlinearity. In two monkeys, we measured utility as a function of physical reward value from meaningful choices under risk (that adhered to first- and second-order stochastic dominance). The resulting nonlinear utility functions predicted the certainty equivalents for new gambles, indicating that the functions' shapes were meaningful. The monkeys were risk seeking (convex utility function) for low reward and risk avoiding (concave utility function) with higher amounts. Critically, the dopamine prediction error responses at the time of reward itself reflected the nonlinear utility functions measured at the time of choices. In particular, the reward response magnitude depended on the first derivative of the utility function and thus reflected the marginal utility. Furthermore, dopamine responses recorded outside of the task reflected the marginal utility of unpredicted reward. Accordingly, these responses were sufficient to train reinforcement learning models to predict the behaviorally defined expected utility of gambles. These data suggest a neuronal manifestation of marginal utility in dopamine neurons and indicate a common neuronal basis for fundamental explanatory constructs in animal learning theory (prediction error) and economic decision theory (marginal utility). Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  15. Accurate and general treatment of electrostatic interaction in Hamiltonian adaptive resolution simulations

    NASA Astrophysics Data System (ADS)

    Heidari, M.; Cortes-Huerto, R.; Donadio, D.; Potestio, R.

    2016-10-01

    In adaptive resolution simulations the same system is concurrently modeled with different resolution in different subdomains of the simulation box, thereby enabling an accurate description in a small but relevant region, while the rest is treated with a computationally parsimonious model. In this framework, electrostatic interaction, whose accurate treatment is a crucial aspect in the realistic modeling of soft matter and biological systems, represents a particularly acute problem due to the intrinsic long-range nature of Coulomb potential. In the present work we propose and validate the usage of a short-range modification of Coulomb potential, the Damped shifted force (DSF) model, in the context of the Hamiltonian adaptive resolution simulation (H-AdResS) scheme. This approach, which is here validated on bulk water, ensures a reliable reproduction of the structural and dynamical properties of the liquid, and enables a seamless embedding in the H-AdResS framework. The resulting dual-resolution setup is implemented in the LAMMPS simulation package, and its customized version employed in the present work is made publicly available.

  16. Totally Implantable Wireless Ultrasonic Doppler Blood Flowmeters: Toward Accurate Miniaturized Chronic Monitors.

    PubMed

    Rothfuss, Michael A; Unadkat, Jignesh V; Gimbel, Michael L; Mickle, Marlin H; Sejdić, Ervin

    2017-03-01

    Totally implantable wireless ultrasonic blood flowmeters provide direct-access chronic vessel monitoring in hard-to-reach places without using wired bedside monitors or imaging equipment. Although wireless implantable Doppler devices are accurate for most applications, device size and implant lifetime remain vastly underdeveloped. We review past and current approaches to miniaturization and implant lifetime extension for wireless implantable Doppler devices and propose approaches to reduce device size and maximize implant lifetime for the next generation of devices. Additionally, we review current and past approaches to accurate blood flow measurements. This review points toward relying on increased levels of monolithic customization and integration to reduce size. Meanwhile, recommendations to maximize implant lifetime should include alternative sources of power, such as transcutaneous wireless power, that stand to extend lifetime indefinitely. Coupling together the results will pave the way for ultra-miniaturized totally implantable wireless blood flow monitors for truly chronic implantation. Copyright © 2016 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

  17. Students Reflecting on Test Performance and Feedback: An On-Line Approach

    ERIC Educational Resources Information Center

    Fyfe, Georgina; Fyfe, Sue; Meyer, Jan; Ziman, Mel; Sanders, Kathy; Hill, Julie

    2014-01-01

    Undergraduate students accessing on-line tests in Human Biology in three Western Australian universities were asked to complete an on-line post-test reflective survey about their perceptions of their test performance in light of automated feedback. The survey allowed pre-determined choices and comment text boxes relating to students' perceptions…

  18. Effect of Process-Oriented Guided-Inquiry Learning on Non-majors Biology Students' Understanding of Biological Classification

    NASA Astrophysics Data System (ADS)

    Wozniak, Breann M.

    The purpose of this study was to examine the effect of process-oriented guided-inquiry learning (POGIL) on non-majors college biology students' understanding of biological classification. This study addressed an area of science instruction, POGIL in the non-majors college biology laboratory, which has yet to be qualitatively and quantitatively researched. A concurrent triangulation mixed methods approach was used. Students' understanding of biological classification was measured in two areas: scores on pre and posttests (consisting of 11 multiple choice questions), and conceptions of classification as elicited in pre and post interviews and instructor reflections. Participants were Minnesota State University, Mankato students enrolled in BIOL 100 Summer Session. One section was taught with the traditional curriculum (n = 6) and the other section in the POGIL curriculum (n = 10) developed by the researcher. Three students from each section were selected to take part in pre and post interviews. There were no significant differences within each teaching method (p < .05). There was a tendency of difference in the means. The POGIL group may have scored higher on the posttest (M = 8.830 +/- .477 vs. M = 7.330 +/- .330; z =-1.729, p = .084) and the traditional group may have scored higher on the pretest than the posttest (M = 8.333 +/- .333 vs M = 7.333 +/- .333; z = -1.650 , p = .099). Two themes emerged after the interviews and instructor reflections: 1) After instruction students had a more extensive understanding of classification in three areas: vocabulary terms, physical characteristics, and types of evidence used to classify. Both groups extended their understanding, but only POGIL students could explain how molecular evidence is used in classification. 2) The challenges preventing students from understanding classification were: familiar animal categories and aquatic habitats, unfamiliar organisms, combining and subdividing initial groupings, and the hierarchical

  19. Shaping biological knowledge: applications in proteomics.

    PubMed

    Lisacek, F; Chichester, C; Gonnet, P; Jaillet, O; Kappus, S; Nikitin, F; Roland, P; Rossier, G; Truong, L; Appel, R

    2004-01-01

    The central dogma of molecular biology has provided a meaningful principle for data integration in the field of genomics. In this context, integration reflects the known transitions from a chromosome to a protein sequence: transcription, intron splicing, exon assembly and translation. There is no such clear principle for integrating proteomics data, since the laws governing protein folding and interactivity are not quite understood. In our effort to bring together independent pieces of information relative to proteins in a biologically meaningful way, we assess the bias of bioinformatics resources and consequent approximations in the framework of small-scale studies. We analyse proteomics data while following both a data-driven (focus on proteins smaller than 10 kDa) and a hypothesis-driven (focus on whole bacterial proteomes) approach. These applications are potentially the source of specialized complements to classical biological ontologies.

  20. Accurate acoustic power measurement for low-intensity focused ultrasound using focal axial vibration velocity

    NASA Astrophysics Data System (ADS)

    Tao, Chenyang; Guo, Gepu; Ma, Qingyu; Tu, Juan; Zhang, Dong; Hu, Jimin

    2017-07-01

    Low-intensity focused ultrasound is a form of therapy that can have reversible acoustothermal effects on biological tissue, depending on the exposure parameters. The acoustic power (AP) should be chosen with caution for the sake of safety. To recover the energy of counteracted radial vibrations at the focal point, an accurate AP measurement method using the focal axial vibration velocity (FAVV) is proposed in explicit formulae and is demonstrated experimentally using a laser vibrometer. The experimental APs for two transducers agree well with theoretical calculations and numerical simulations, showing that AP is proportional to the square of the FAVV, with a fixed power gain determined by the physical parameters of the transducers. The favorable results suggest that the FAVV can be used as a valuable parameter for non-contact AP measurement, providing a new strategy for accurate power control for low-intensity focused ultrasound in biomedical engineering.

  1. The Scientific and Societal Need for Accurate Global Remote Sensing of Marine Suspended Sediments

    NASA Technical Reports Server (NTRS)

    Acker, James G.

    2006-01-01

    Population pressure, commercial development, and climate change are expected to cause continuing alteration of the vital oceanic coastal zone environment. These pressures will influence both the geology and biology of the littoral, nearshore, and continental shelf regions. A pressing need for global observation of coastal change processes is an accurate remotely-sensed data product for marine suspended sediments. The concentration, delivery, transport, and deposition of sediments is strongly relevant to coastal primary production, inland and coastal hydrology, coastal erosion, and loss of fragile wetland and island habitats. Sediment transport and deposition is also related to anthropogenic activities including agriculture, fisheries, aquaculture, harbor and port commerce, and military operations. Because accurate estimation of marine suspended sediment concentrations requires advanced ocean optical analysis, a focused collaborative program of algorithm development and assessment is recommended, following the successful experience of data refinement for remotely-sensed global ocean chlorophyll concentrations.

  2. Analysing Vee Diagram Reflections to Explore Pre-Service Science Teachers' Understanding the Nature of Science in Biology

    ERIC Educational Resources Information Center

    Savran-Gencer, Ayse

    2014-01-01

    Vee diagrams have been a metacognitive tool to help in learning the nature and structure of knowledge by reflecting on the scientific process and making knowledge much more explicit to learners during the practical work. This study aimed to assess pre-service science teachers' understanding some aspects of NOS by analyzing their reflections on the…

  3. EDITORIAL: Physical Biology

    NASA Astrophysics Data System (ADS)

    Roscoe, Jane

    2004-06-01

    Physical Biology is a new peer-reviewed publication from Institute of Physics Publishing. Launched in 2004, the journal will foster the integration of biology with the traditionally more quantitative fields of physics, chemistry, computer science and other math-based disciplines. Its primary aim is to further the understanding of biological systems at all levels of complexity, ranging from the role of structure and dynamics of a single molecule to cellular networks and organisms. The journal encourages the development of a new biology-driven physics based on the extraordinary and increasingly rich data arising in biology, and provides research directions for those involved in the creation of novel bio-engineered systems. Physical Biology will publish a stimulating combination of full length research articles, communications, perspectives, reviews and tutorials from a wide range of disciplines covering topics such as: Single-molecule studies and nanobiotechnology Molecular interactions and protein folding Charge transfer and photobiology Ion channels; structure, function and ion regulation Molecular motors and force generation Subcellular processes Biological networks and neural systems Modeling aspects of molecular and cell biology Cell-cell signaling and interaction Biological patterns and development Evolutionary processes Novel tools and methods in physical biology Experts in the areas encompassed by the journal's scope have been appointed to the Editorial Scientific Committee and the composition of the Committee will be updated regularly to reflect the developments in this new and exciting field. Physical Biology is free online to everyone in 2004; you are invited to take advantage of this offer by visiting the journal homepage at http://physbio.iop.org This special print edition of Physical Biology is a combination of issues 1 and 2 of this electronic-only journal and it brings together an impressive range of articles in the fields covered, including a popular

  4. NASA Space Biology Research Associate Program for the 21st Century

    NASA Technical Reports Server (NTRS)

    Sonnenfeld, Gerald

    2000-01-01

    The Space Biology Research Associate Program for the 21st Century provided a unique opportunity to train individuals to conduct biological research in hypo- and hyper-gravity, and to conduct ground-based research. This grant was developed to maximize the potential for Space Biology as an emerging discipline and to train a cadre of space biologists. The field of gravitational and space biology is rapidly growing at the future of the field is reflected in the quality and education of its personnel. Our chief objective was to train and develop these scientists rapidly and in a cost effective model.

  5. ReflectED: Evaluation Report and Executive Summary

    ERIC Educational Resources Information Center

    Motteram, Gary; Choudry, Sophina; Kalambouka, Afroditi; Hutcheson, Graeme; Barton, Hutcheson

    2016-01-01

    The ReflectED programme was developed by Rosendale Primary School to improve pupils' metacognition--their ability to think about and manage their own learning. This includes the skills of setting and monitoring goals, assessing progress, and identifying personal strengths and challenges. ReflectED consists of 28, weekly, half-hour lessons, which…

  6. Challenging Narcissus, or Reflecting on Reflecting.

    ERIC Educational Resources Information Center

    Achilles, C. M.

    The concept of reflective practice and teaching people to be reflective practitioners is examined. The document begins with a look at professional knowledge according to three prominent professionals in the educational administration field: Schon, Schein, and Achilles. "Reflective" strategies that could be incorporated into courses and…

  7. A Reflection on Reflection.

    ERIC Educational Resources Information Center

    Smith, Pat

    2002-01-01

    Reflects on the articles in this themed issue on reflective practice. Notes that these teacher/authors have been influenced by prior learning, past experience, feelings, attitudes, values, the school constraints on the learning environment, and their own assumptions about teaching. Describes how teachers have formed a learning community to…

  8. Geostatistics and spatial analysis in biological anthropology.

    PubMed

    Relethford, John H

    2008-05-01

    A variety of methods have been used to make evolutionary inferences based on the spatial distribution of biological data, including reconstructing population history and detection of the geographic pattern of natural selection. This article provides an examination of geostatistical analysis, a method used widely in geology but which has not often been applied in biological anthropology. Geostatistical analysis begins with the examination of a variogram, a plot showing the relationship between a biological distance measure and the geographic distance between data points and which provides information on the extent and pattern of spatial correlation. The results of variogram analysis are used for interpolating values of unknown data points in order to construct a contour map, a process known as kriging. The methods of geostatistical analysis and discussion of potential problems are applied to a large data set of anthropometric measures for 197 populations in Ireland. The geostatistical analysis reveals two major sources of spatial variation. One pattern, seen for overall body and craniofacial size, shows an east-west cline most likely reflecting the combined effects of past population dispersal and settlement. The second pattern is seen for craniofacial height and shows an isolation by distance pattern reflecting rapid spatial changes in the midlands region of Ireland, perhaps attributable to the genetic impact of the Vikings. The correspondence of these results with other analyses of these data and the additional insights generated from variogram analysis and kriging illustrate the potential utility of geostatistical analysis in biological anthropology. (c) 2008 Wiley-Liss, Inc.

  9. Biased and unbiased strategies to identify biologically active small molecules.

    PubMed

    Abet, Valentina; Mariani, Angelica; Truscott, Fiona R; Britton, Sébastien; Rodriguez, Raphaël

    2014-08-15

    Small molecules are central players in chemical biology studies. They promote the perturbation of cellular processes underlying diseases and enable the identification of biological targets that can be validated for therapeutic intervention. Small molecules have been shown to accurately tune a single function of pluripotent proteins in a reversible manner with exceptional temporal resolution. The identification of molecular probes and drugs remains a worthy challenge that can be addressed by the use of biased and unbiased strategies. Hypothesis-driven methodologies employs a known biological target to synthesize complementary hits while discovery-driven strategies offer the additional means of identifying previously unanticipated biological targets. This review article provides a general overview of recent synthetic frameworks that gave rise to an impressive arsenal of biologically active small molecules with unprecedented cellular mechanisms. Copyright © 2014. Published by Elsevier Ltd.

  10. Reflectance spectroscopy for noninvasive evaluation of hair follicle stage

    NASA Astrophysics Data System (ADS)

    Liu, Caihua; Guan, Yue; Wang, Jianru; Zhong, Xiewei; Liu, Xiuli; Zhu, Dan

    2015-05-01

    Hair follicle offers an excellent model for systems biology and regenerative medicine. So far, the stages of hair follicle growth have been evaluated by histological examination. In this work, a noninvasive spectroscopy was proposed by measuring the diffuse reflectance of mouse skin and analyzing the melanin value. Results show that the skin diffuse reflectance was relatively high when hair follicles were at the telogen stage and at the beginning of the anagen stage, and decreased with the progression of the anagen stage. When the hair follicle entered into the catagen stage, the diffuse reflectance gradually increased. The changes in the melanin content of skin had contrary dynamics. Substages of the hair follicle cycle could be distinguished by comparing the changes in melanin value with the histological examination. This study provided a new method for noninvasive evaluation of the hair follicle stage, and should be valuable for basic and therapeutic investigations on hair regeneration.

  11. Infrared reflectance spectra: Effects of particle size, provenance and preparation

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

    Su, Yin-Fong; Myers, Tanya L.; Brauer, Carolyn S.

    2014-09-22

    We have recently developed methods for making more accurate infrared total and diffuse directional - hemispherical reflectance measurements using an integrating sphere. We have found that reflectance spectra of solids, especially powders, are influenced by a number of factors including the sample preparation method, the particle size and morphology, as well as the sample origin. On a quantitative basis we have investigated some of these parameters and the effects they have on reflectance spectra, particularly in the longwave infrared. In the IR the spectral features may be observed as either maxima or minima: In general, upward-going peaks in the reflectancemore » spectrum result from strong surface scattering, i.e. rays that are reflected from the surface without bulk penetration, whereas downward-going peaks are due to either absorption or volume scattering, i.e. rays that have penetrated or refracted into the sample interior and are not reflected. The light signals reflected from solids usually encompass all such effects, but with strong dependencies on particle size and preparation. This paper measures the reflectance spectra in the 1.3 – 16 micron range for various bulk materials that have a combination of strong and weak absorption bands in order to observe the effects on the spectral features: Bulk materials were ground with a mortar and pestle and sieved to separate the samples into various size fractions between 5 and 500 microns. The median particle size is demonstrated to have large effects on the reflectance spectra. For certain minerals we also observe significant spectral change depending on the geologic origin of the sample. All three such effects (particle size, preparation and provenance) result in substantial change in the reflectance spectra for solid materials; successful identification algorithms will require sufficient flexibility to account for these parameters.« less

  12. The Fourier analysis of biological transients.

    PubMed

    Harris, C M

    1998-08-31

    With modern computing technology the digital implementation of the Fourier transform is widely available, mostly in the form of the fast Fourier transform (FFT). Although the FFT has become almost synonymous with the Fourier transform, it is a fast numerical technique for computing the discrete Fourier transform (DFT) of a finite sequence of sampled data. The DFT is not directly equivalent to the continuous Fourier transform of the underlying biological signal, which becomes important when analyzing biological transients. Although this distinction is well known by some, for many it leads to confusion in how to interpret the FFT of biological data, and in how to precondition data so as to yield a more accurate Fourier transform using the FFT. We review here the fundamentals of Fourier analysis with emphasis on the analysis of transient signals. As an example of a transient, we consider the human saccade to illustrate the pitfalls and advantages of various Fourier analyses.

  13. Refractory Graft-Versus-Host Disease-Free, Relapse-Free Survival as an Accurate and Easy-to-Calculate Endpoint to Assess the Long-Term Transplant Success.

    PubMed

    Kawamura, Koji; Nakasone, Hideki; Kurosawa, Saiko; Yoshimura, Kazuki; Misaki, Yukiko; Gomyo, Ayumi; Hayakawa, Jin; Tamaki, Masaharu; Akahoshi, Yu; Kusuda, Machiko; Kameda, Kazuaki; Wada, Hidenori; Ishihara, Yuko; Sato, Miki; Terasako-Saito, Kiriko; Kikuchi, Misato; Kimura, Shun-Ichi; Tanihara, Aki; Kako, Shinichi; Kanamori, Heiwa; Mori, Takehiko; Takahashi, Satoshi; Taniguchi, Shuichi; Atsuta, Yoshiko; Kanda, Yoshinobu

    2018-02-21

    The aim of this study was to develop a new composite endpoint that accurately reflects the long-term success of allogeneic hematopoietic stem cell transplantation (allo-HSCT), as the conventional graft-versus-host disease (GVHD)-free, relapse-free survival (GRFS) overestimates the impact of GVHD. First, we validated current GRFS (cGRFS), which recently was proposed as a more accurate endpoint of long-term transplant success. cGRFS was defined as survival without disease relapse/progression or active chronic GVHD at a given time after allo-HSCT, calculated using 2 distinct methods: a linear combination of a Kaplan-Meier estimates approach and a multistate modelling approach. Next, we developed a new composite endpoint, refractory GRFS (rGRFS). rGRFS was calculated similarly to conventional GRFS treating grade III to IV acute GVHD, chronic GVHD requiring systemic treatment, and disease relapse/progression as events, except that GVHD that resolved and did not require systemic treatment at the last evaluation was excluded as an event in rGRFS. The 2 cGRFS curves obtained using 2 different approaches were superimposed and both were superior to that of conventional GRFS, reflecting the proportion of patients with resolved chronic GVHD. Finally, the curves of cGRFS and rGRFS overlapped after the first 2 years of post-transplant follow-up. These results suggest that cGRFS and rGRFS more accurately reflect transplant success than conventional GRFS. Especially, rGRFS can be more easily calculated than cGRFS and analyzed with widely used statistical approaches, whereas cGRFS more accurately represents the burden of GVHD-related morbidity in the first 2 years after transplantation. Copyright © 2018 The American Society for Blood and Marrow Transplantation. Published by Elsevier Inc. All rights reserved.

  14. A spectral reflectance estimation technique using multispectral data from the Viking lander camera

    NASA Technical Reports Server (NTRS)

    Park, S. K.; Huck, F. O.

    1976-01-01

    A technique is formulated for constructing spectral reflectance curve estimates from multispectral data obtained with the Viking lander camera. The multispectral data are limited to six spectral channels in the wavelength range from 0.4 to 1.1 micrometers and most of these channels exhibit appreciable out-of-band response. The output of each channel is expressed as a linear (integral) function of the (known) solar irradiance, atmospheric transmittance, and camera spectral responsivity and the (unknown) spectral responsivity and the (unknown) spectral reflectance. This produces six equations which are used to determine the coefficients in a representation of the spectral reflectance as a linear combination of known basis functions. Natural cubic spline reflectance estimates are produced for a variety of materials that can be reasonably expected to occur on Mars. In each case the dominant reflectance features are accurately reproduced, but small period features are lost due to the limited number of channels. This technique may be a valuable aid in selecting the number of spectral channels and their responsivity shapes when designing a multispectral imaging system.

  15. Prospective Technology Assessment of Synthetic Biology: Fundamental and Propaedeutic Reflections in Order to Enable an Early Assessment.

    PubMed

    Schmidt, Jan Cornelius

    2016-08-01

    Synthetic biology is regarded as one of the key technosciences of the future. The goal of this paper is to present some fundamental considerations to enable procedures of a technology assessment (TA) of synthetic biology. To accomplish such an early "upstream" assessment of a not yet fully developed technology, a special type of TA will be considered: Prospective TA (ProTA). At the center of ProTA are the analysis and the framing of "synthetic biology," including a characterization and assessment of the technological core. The thesis is that if there is any differentia specifica giving substance to the umbrella term "synthetic biology," it is the idea of harnessing self-organization for engineering purposes. To underline that we are likely experiencing an epochal break in the ontology of technoscientific systems, this new type of technology is called "late-modern technology." -I start this paper by analyzing the three most common visions of synthetic biology. Then I argue that one particular vision deserves more attention because it underlies the others: the vision of self-organization. I discuss the inherent limits of this new type of late-modern technology in the attempt to control and monitor possible risk issues. I refer to Hans Jonas' ethics and his early anticipation of the risks of a novel type of technology. I end by drawing conclusions for the approach of ProTA towards an early societal shaping of synthetic biology.

  16. High-resolution reflectometer for monitoring of biological samples

    NASA Astrophysics Data System (ADS)

    Men, Liqiu; Lu, Ping; Chen, Qiying

    2008-06-01

    High-resolution optical low-coherence reflectometry is applied to monitor biological samples. It has been found that the reflectivity of aged cow's milk is significantly lower than that of the fresh milk with a difference of 5.35dB. During the process of heating the fresh milk at a constant temperature of 80°C, the reflectivity of the milk gradually decreases with the increase of the heating duration. The technique is proved to be effective in monitoring the change in the refractive index of the sample.

  17. NNLOPS accurate associated HW production

    NASA Astrophysics Data System (ADS)

    Astill, William; Bizon, Wojciech; Re, Emanuele; Zanderighi, Giulia

    2016-06-01

    We present a next-to-next-to-leading order accurate description of associated HW production consistently matched to a parton shower. The method is based on reweighting events obtained with the HW plus one jet NLO accurate calculation implemented in POWHEG, extended with the MiNLO procedure, to reproduce NNLO accurate Born distributions. Since the Born kinematics is more complex than the cases treated before, we use a parametrization of the Collins-Soper angles to reduce the number of variables required for the reweighting. We present phenomenological results at 13 TeV, with cuts suggested by the Higgs Cross section Working Group.

  18. Second-harmonic patterned polarization-analyzed reflection confocal microscope

    NASA Astrophysics Data System (ADS)

    Okoro, Chukwuemeka; Toussaint, Kimani C.

    2017-08-01

    We introduce the second-harmonic patterned polarization-analyzed reflection confocal (SPPARC) microscope-a multimodal imaging platform that integrates Mueller matrix polarimetry with reflection confocal and second-harmonic generation (SHG) microscopy. SPPARC microscopy provides label-free three-dimensional (3-D), SHG-patterned confocal images that lend themselves to spatially dependent, linear polarimetric analysis for extraction of rich polarization information based on the Mueller calculus. To demonstrate its capabilities, we use SPPARC microscopy to analyze both porcine tendon and ligament samples and find differences in both circular degree-of-polarization and depolarization parameters. Moreover, using the collagen-generated SHG signal as an endogenous counterstain, we show that the technique can be used to provide 3-D polarimetric information of the surrounding extrafibrillar matrix plus cells or EFMC region. The unique characteristics of SPPARC microscopy holds strong potential for it to more accurately and quantitatively describe microstructural changes in collagen-rich samples in three spatial dimensions.

  19. Does the nature of science influence college students' learning of biological evolution?

    NASA Astrophysics Data System (ADS)

    Butler, Wilbert, Jr.

    This quasi-experimental, mixed-methods study assessed the influence of the nature of science (NOS) instruction on college students' learning of biological evolution. In this research, conducted in two introductory biology courses, in each course the same instruction was employed, with one important exception: in the experimental section students were involved in an explicit, reflective treatment of the nature of science (Explicit, reflective NOS), in the traditional treatment section, NOS was implicitly addressed (traditional treatment). In both sections, NOS aspects of science addressed included is tentative, empirically based, subjective, inferential, and based on relationship between scientific theories and laws. Students understanding of evolution, acceptance of evolution, and understanding of the nature of science were assessed before, during and after instruction. Data collection entailed qualitative and quantitative methods including Concept Inventory for Natural Selection (CINS), Measure of Acceptance of the Theory of Evolution (MATE) survey, Views of nature of Science (VNOS-B survey), as well as interviews, classroom observations, and journal writing to address understand students' views of science and understanding and acceptance of evolution. The quantitative data were analyzed via inferential statistics and the qualitative data were analyzed using grounded theory. The data analysis allowed for the construction and support for four assertions: Assertion 1: Students engaged in explicit and reflective NOS specific instruction significantly improved their understanding of the nature of science concepts. Alternatively, students engaged in instruction using an implicit approach to the nature of science did not improve their understanding of the nature of science to the same degree. The VNOS-B results indicated that students in the explicit, reflective NOS class showed the better understanding of the NOS after the course than students in the implicit NOS class

  20. Evidence for an Explanation Advantage in Naïve Biological Reasoning

    PubMed Central

    Legare, Cristine H.; Wellman, Henry M.; Gelman, Susan A.

    2013-01-01

    The present studies compare young children's explanations and predictions for the biological phenomenon of contamination. In Study 1, 36 preschoolers and 24 adults heard vignettes concerning contamination, and were asked either to make a prediction or to provide an explanation. Even 3-year-olds readily supplied contamination-based explanations, and most children mentioned an unseen mechanism (germs, contact through bodily fluids). Moreover, unlike adults who performed at ceiling across both explanation and prediction tasks, children were significantly more accurate with their explanations than their predictions. In Study 2, we varied the strength of cues regarding the desirability of the contaminated substance (N = 24 preschoolers). Although desirability affected responses, for both levels of desirability participants were significantly more accurate on explanation than prediction questions. Altogether, these studies demonstrate a significant “explanation advantage” for children's reasoning in the domain of everyday biology. PMID:18710700

  1. Analyzing Change in Students' Gene-to-Evolution Models in College-Level Introductory Biology

    ERIC Educational Resources Information Center

    Dauer, Joseph T.; Momsen, Jennifer L.; Speth, Elena Bray; Makohon-Moore, Sasha C.; Long, Tammy M.

    2013-01-01

    Research in contemporary biology has become increasingly complex and organized around understanding biological processes in the context of systems. To better reflect the ways of thinking required for learning about systems, we developed and implemented a pedagogical approach using box-and-arrow models (similar to concept maps) as a foundational…

  2. Reflective Teaching

    ERIC Educational Resources Information Center

    Farrell, Thomas S. C.

    2013-01-01

    Thomas Farrell's "Reflective Teaching" outlines four principles that take teachers from just doing reflection to making it a way of being. Using the four principles, Reflective Practice Is Evidence Based, Reflective Practice Involves Dialogue, Reflective Practice Links Beliefs and Practices, and Reflective Practice Is a Way of Life,…

  3. Simulations in Medicine and Biology: Insights and perspectives

    NASA Astrophysics Data System (ADS)

    Spyrou, George M.

    2015-01-01

    Modern medicine and biology have been transformed into quantitative sciences of high complexity, with challenging objectives. The aims of medicine are related to early diagnosis, effective therapy, accurate intervention, real time monitoring, procedures/systems/instruments optimization, error reduction, and knowledge extraction. Concurrently, following the explosive production of biological data concerning DNA, RNA, and protein biomolecules, a plethora of questions has been raised in relation to their structure and function, the interactions between them, their relationships and dependencies, their regulation and expression, their location, and their thermodynamic characteristics. Furthermore, the interplay between medicine and biology gives rise to fields like molecular medicine and systems biology which are further interconnected with physics, mathematics, informatics, and engineering. Modelling and simulation is a powerful tool in the fields of Medicine and Biology. Simulating the phenomena hidden inside a diagnostic or therapeutic medical procedure, we are able to obtain control on the whole system and perform multilevel optimization. Furthermore, modelling and simulation gives insights in the various scales of biological representation, facilitating the understanding of the huge amounts of derived data and the related mechanisms behind them. Several examples, as well as the insights and the perspectives of simulations in biomedicine will be presented.

  4. Highly accurate thickness measurement of multi-layered automotive paints using terahertz technology

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

    Krimi, Soufiene; Beigang, René; Klier, Jens

    2016-07-11

    In this contribution, we present a highly accurate approach for thickness measurements of multi-layered automotive paints using terahertz time domain spectroscopy in reflection geometry. The proposed method combines the benefits of a model-based material parameters extraction method to calibrate the paint coatings, a generalized Rouard's method to simulate the terahertz radiation behavior within arbitrary thin films, and the robustness of a powerful evolutionary optimization algorithm to increase the sensitivity of the minimum thickness measurement limit. Within the framework of this work, a self-calibration model is introduced, which takes into consideration the real industrial challenges such as the effect of wet-on-wetmore » spray in the painting process.« less

  5. Cell biology solves mysteries of reproduction.

    PubMed

    Sutovsky, Peter

    2012-09-01

    Reproduction and fertility have been objects of keen inquiry since the dawn of humanity. Medieval anatomists provided the first accurate depictions of the female reproductive system, and early microscopists were fascinated by the magnified sight of sperm cells. Initial successes were achieved in the in vitro fertilization of frogs and the artificial insemination of dogs. Gamete and embryo research was in the cradle of modern cell biology, providing the first evidence of the multi-cellular composition of living beings and pointing out the importance of chromosomes for heredity. In the 20th century, reproductive research paved the way for the study of the cytoskeleton, cell signaling, and the cell cycle. In the last three decades, the advent of reproductive cell biology has brought us human in vitro fertilization, animal cloning, and human and animal embryonic stem cells. It has contributed to the development of transgenesis, proteomics, genomics, and epigenetics. This Special Issue represents a sample of the various areas of reproductive biology, with emphasis on molecular and cell biological aspects. Advances in spermatology, ovarian function, fertilization, and maternal-fetal interactions are discussed within the framework of fertility and diseases such as endometriosis and diabetes.

  6. Adaptive filtering in biological signal processing.

    PubMed

    Iyer, V K; Ploysongsang, Y; Ramamoorthy, P A

    1990-01-01

    The high dependence of conventional optimal filtering methods on the a priori knowledge of the signal and noise statistics render them ineffective in dealing with signals whose statistics cannot be predetermined accurately. Adaptive filtering methods offer a better alternative, since the a priori knowledge of statistics is less critical, real time processing is possible, and the computations are less expensive for this approach. Adaptive filtering methods compute the filter coefficients "on-line", converging to the optimal values in the least-mean square (LMS) error sense. Adaptive filtering is therefore apt for dealing with the "unknown" statistics situation and has been applied extensively in areas like communication, speech, radar, sonar, seismology, and biological signal processing and analysis for channel equalization, interference and echo canceling, line enhancement, signal detection, system identification, spectral analysis, beamforming, modeling, control, etc. In this review article adaptive filtering in the context of biological signals is reviewed. An intuitive approach to the underlying theory of adaptive filters and its applicability are presented. Applications of the principles in biological signal processing are discussed in a manner that brings out the key ideas involved. Current and potential future directions in adaptive biological signal processing are also discussed.

  7. Diffraction of a shock wave by a compression corner; regular and single Mach reflection

    NASA Technical Reports Server (NTRS)

    Vijayashankar, V. S.; Kutler, P.; Anderson, D.

    1976-01-01

    The two dimensional, time dependent Euler equations which govern the flow field resulting from the injection of a planar shock with a compression corner are solved with initial conditions that result in either regular reflection or single Mach reflection of the incident planar shock. The Euler equations which are hyperbolic are transformed to include the self similarity of the problem. A normalization procedure is employed to align the reflected shock and the Mach stem as computational boundaries to implement the shock fitting procedure. A special floating fitting scheme is developed in conjunction with the method of characteristics to fit the slip surface. The reflected shock, the Mach stem, and the slip surface are all treated as harp discontinuities, thus, resulting in a more accurate description of the inviscid flow field. The resulting numerical solutions are compared with available experimental data and existing first-order, shock-capturing numerical solutions.

  8. Biologically-Derived Photonic Materials for Thermal Protection Systems

    NASA Technical Reports Server (NTRS)

    Johnson, Sylvia M.; Squire, Thomas H.; Lawson, John W.; Gusman, Michael; Lau, K.-H.; Sanjurjo, Angel

    2014-01-01

    Space vehicles entering a planetary atmosphere at high velocity can be subject to substantial radiative heating from the shock layer in addition to the convective heating caused by the flow of hot gas past the vehicle surface. The radiative component can be very high but of a short duration. Approaches to combat this effect include investigation of various materials to reflect the radiation. Photonic materials can be used to reflect radiation. The wavelengths reflected depend on the length scale of the ordered microstructure. Fabricating photonic structures, such as layers, can be time consuming and expensive. We have used a biologically-derived material as the template for forming a high temperature photonic material that could be incorporated into a heatshield thermal protection material.

  9. The aims of systems biology: between molecules and organisms.

    PubMed

    Noble, D

    2011-05-01

    The systems approach to biology has a long history. Its recent rapid resurgence at the turn of the century reflects the problems encountered in interpreting the sequencing of the genome and the failure of that immense achievement to provide rapid and direct solutions to major multi-factorial diseases. This paper argues that systems biology is necessarily multilevel and that there is no privileged level of causality in biological systems. It is an approach rather than a separate discipline. Functionality arises from biological networks that interact with the genome, the environment and the phenotype. This view of biology is very different from the gene-centred views of neo-Darwinism and molecular biology. In neuroscience, the systems approach leads naturally to 2 important conclusions: first, that the idea of 'programs' in the brain is confusing, and second, that the self is better interpreted as a process than as an object. © Georg Thieme Verlag KG Stuttgart · New York.

  10. Susceptibility patterns for amoxicillin/clavulanate tests mimicking the licensed formulations and pharmacokinetic relationships: do the MIC obtained with 2:1 ratio testing accurately reflect activity against beta-lactamase-producing strains of Haemophilus influenzae and Moraxella catarrhalis?

    PubMed

    Pottumarthy, Sudha; Sader, Helio S; Fritsche, Thomas R; Jones, Ronald N

    2005-11-01

    Amoxicillin/clavulanate has recently undergone formulation changes (XR and ES-600) that represent 14:1 and 16:1 ratios of amoxicillin/clavulanate. These ratios greatly differ from the 2:1 ratio used in initial formulations and in vitro susceptibility testing. The objective of this study was to determine if the reference method using a 2:1 ratio accurately reflects the susceptibility to the various clinically used amoxicillin/clavulanate formulations and their respective serum concentration ratios. A collection of 330 Haemophilus influenzae strains (300 beta-lactamase-positive and 30 beta-lactamase-negative) and 40 Moraxella catarrhalis strains (30 beta-lactamase-positive and 10 beta-lactamase-negative) were tested by the broth microdilution method against eight amoxicillin/clavulanate combinations (4:1, 5:1, 7:1, 9:1, 14:1, and 16:1 ratios; 0.5 and 2 microg/mL fixed clavulanate concentrations) and the minimum inhibitory concentration (MIC) results were compared with those obtained with the reference 2:1 ratio testing. For the beta-lactamase-negative strains of both genera, there was no demonstrable change in the MIC values obtained for all ratios analyzed (2:1 to 16:1). For the beta-lactamase-positive strains of H. influenzae and M. catarrhalis, at ratios >or=4:1 there was a shift in the central tendency of the MIC scatterplot compared with the results of testing 2:1 ratio. As a result, there was a 2-fold dilution increase in the MIC(50) and MIC(90) values, most evident for H. influenzae and BRO-1-producing M. catarrhalis strains. For beta-lactamase-positive strains of H. influenzae, the shift resulted in a change in the interpretive result for 3 isolates (1.0%) from susceptible using the reference method (2:1 ratio) to resistant (8/4 microg/mL; very major error) at the 16:1 ratio. In addition, the number of isolates with MIC values at or 1 dilution lower than the breakpoint (4/2 microg/mL) increased from 5% at 2:1 ratio to 32-33% for ratios 14:1 and 16:1. Our

  11. Reconstructing surface wave profiles from reflected acoustic pulses using multiple receivers.

    PubMed

    Walstead, Sean P; Deane, Grant B

    2014-08-01

    Surface wave shapes are determined by analyzing underwater reflected acoustic signals collected at multiple receivers. The transmitted signals are of nominal frequency 300 kHz and are reflected off surface gravity waves that are paddle-generated in a wave tank. An inverse processing algorithm reconstructs 50 surface wave shapes over a length span of 2.10 m. The inverse scheme uses a broadband forward scattering model based on Kirchhoff's diffraction formula to determine wave shapes. The surface reconstruction algorithm is self-starting in that source and receiver geometry and initial estimates of wave shape are determined from the same acoustic signals used in the inverse processing. A high speed camera provides ground-truth measurements of the surface wave field for comparison with the acoustically derived surface waves. Within Fresnel zone regions the statistical confidence of the inversely optimized surface profile exceeds that of the camera profile. Reconstructed surfaces are accurate to a resolution of about a quarter-wavelength of the acoustic pulse only within Fresnel zones associated with each source and receiver pair. Multiple isolated Fresnel zones from multiple receivers extend the spatial extent of accurate surface reconstruction while overlapping Fresnel zones increase confidence in the optimized profiles there.

  12. Algorithms in nature: the convergence of systems biology and computational thinking

    PubMed Central

    Navlakha, Saket; Bar-Joseph, Ziv

    2011-01-01

    Computer science and biology have enjoyed a long and fruitful relationship for decades. Biologists rely on computational methods to analyze and integrate large data sets, while several computational methods were inspired by the high-level design principles of biological systems. Recently, these two directions have been converging. In this review, we argue that thinking computationally about biological processes may lead to more accurate models, which in turn can be used to improve the design of algorithms. We discuss the similar mechanisms and requirements shared by computational and biological processes and then present several recent studies that apply this joint analysis strategy to problems related to coordination, network analysis, and tracking and vision. We also discuss additional biological processes that can be studied in a similar manner and link them to potential computational problems. With the rapid accumulation of data detailing the inner workings of biological systems, we expect this direction of coupling biological and computational studies to greatly expand in the future. PMID:22068329

  13. Heterotypic mouse models of canine osteosarcoma recapitulate tumor heterogeneity and biological behavior

    PubMed Central

    Tomiyasu, Hirotaka; Garbe, John R.; Cornax, Ingrid; Amaya, Clarissa; O'Sullivan, M. Gerard; Subramanian, Subbaya

    2016-01-01

    ABSTRACT Osteosarcoma (OS) is a heterogeneous and rare disease with a disproportionate impact because it mainly affects children and adolescents. Lamentably, more than half of patients with OS succumb to metastatic disease. Clarification of the etiology of the disease, development of better strategies to manage progression, and methods to guide personalized treatments are among the unmet health needs for OS patients. Progress in managing the disease has been hindered by the extreme heterogeneity of OS; thus, better models that accurately recapitulate the natural heterogeneity of the disease are needed. For this study, we used cell lines derived from two spontaneous canine OS tumors with distinctly different biological behavior (OS-1 and OS-2) for heterotypic in vivo modeling that recapitulates the heterogeneous biology and behavior of this disease. Both cell lines demonstrated stability of the transcriptome when grown as orthotopic xenografts in athymic nude mice. Consistent with the behavior of the original tumors, OS-2 xenografts grew more rapidly at the primary site and had greater propensity to disseminate to lung and establish microscopic metastasis. Moreover, OS-2 promoted formation of a different tumor-associated stromal environment than OS-1 xenografts. OS-2-derived tumors comprised a larger percentage of the xenograft tumors than OS-1-derived tumors. In addition, a robust pro-inflammatory population dominated the stromal cell infiltrates in OS-2 xenografts, whereas a mesenchymal population with a gene signature reflecting myogenic signaling dominated those in the OS-1 xenografts. Our studies show that canine OS cell lines maintain intrinsic features of the tumors from which they were derived and recapitulate the heterogeneous biology and behavior of bone cancer in mouse models. This system provides a resource to understand essential interactions between tumor cells and the stromal environment that drive the progression and metastatic propensity of OS. PMID

  14. Heterotypic mouse models of canine osteosarcoma recapitulate tumor heterogeneity and biological behavior.

    PubMed

    Scott, Milcah C; Tomiyasu, Hirotaka; Garbe, John R; Cornax, Ingrid; Amaya, Clarissa; O'Sullivan, M Gerard; Subramanian, Subbaya; Bryan, Brad A; Modiano, Jaime F

    2016-12-01

    Osteosarcoma (OS) is a heterogeneous and rare disease with a disproportionate impact because it mainly affects children and adolescents. Lamentably, more than half of patients with OS succumb to metastatic disease. Clarification of the etiology of the disease, development of better strategies to manage progression, and methods to guide personalized treatments are among the unmet health needs for OS patients. Progress in managing the disease has been hindered by the extreme heterogeneity of OS; thus, better models that accurately recapitulate the natural heterogeneity of the disease are needed. For this study, we used cell lines derived from two spontaneous canine OS tumors with distinctly different biological behavior (OS-1 and OS-2) for heterotypic in vivo modeling that recapitulates the heterogeneous biology and behavior of this disease. Both cell lines demonstrated stability of the transcriptome when grown as orthotopic xenografts in athymic nude mice. Consistent with the behavior of the original tumors, OS-2 xenografts grew more rapidly at the primary site and had greater propensity to disseminate to lung and establish microscopic metastasis. Moreover, OS-2 promoted formation of a different tumor-associated stromal environment than OS-1 xenografts. OS-2-derived tumors comprised a larger percentage of the xenograft tumors than OS-1-derived tumors. In addition, a robust pro-inflammatory population dominated the stromal cell infiltrates in OS-2 xenografts, whereas a mesenchymal population with a gene signature reflecting myogenic signaling dominated those in the OS-1 xenografts. Our studies show that canine OS cell lines maintain intrinsic features of the tumors from which they were derived and recapitulate the heterogeneous biology and behavior of bone cancer in mouse models. This system provides a resource to understand essential interactions between tumor cells and the stromal environment that drive the progression and metastatic propensity of OS. © 2016

  15. Towards physical principles of biological evolution

    NASA Astrophysics Data System (ADS)

    Katsnelson, Mikhail I.; Wolf, Yuri I.; Koonin, Eugene V.

    2018-03-01

    Biological systems reach organizational complexity that far exceeds the complexity of any known inanimate objects. Biological entities undoubtedly obey the laws of quantum physics and statistical mechanics. However, is modern physics sufficient to adequately describe, model and explain the evolution of biological complexity? Detailed parallels have been drawn between statistical thermodynamics and the population-genetic theory of biological evolution. Based on these parallels, we outline new perspectives on biological innovation and major transitions in evolution, and introduce a biological equivalent of thermodynamic potential that reflects the innovation propensity of an evolving population. Deep analogies have been suggested to also exist between the properties of biological entities and processes, and those of frustrated states in physics, such as glasses. Such systems are characterized by frustration whereby local state with minimal free energy conflict with the global minimum, resulting in ‘emergent phenomena’. We extend such analogies by examining frustration-type phenomena, such as conflicts between different levels of selection, in biological evolution. These frustration effects appear to drive the evolution of biological complexity. We further address evolution in multidimensional fitness landscapes from the point of view of percolation theory and suggest that percolation at level above the critical threshold dictates the tree-like evolution of complex organisms. Taken together, these multiple connections between fundamental processes in physics and biology imply that construction of a meaningful physical theory of biological evolution might not be a futile effort. However, it is unrealistic to expect that such a theory can be created in one scoop; if it ever comes to being, this can only happen through integration of multiple physical models of evolutionary processes. Furthermore, the existing framework of theoretical physics is unlikely to suffice

  16. 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.

  17. 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

  18. Accurate Arabic Script Language/Dialect Classification

    DTIC Science & Technology

    2014-01-01

    Army Research Laboratory Accurate Arabic Script Language/Dialect Classification by Stephen C. Tratz ARL-TR-6761 January 2014 Approved for public...1197 ARL-TR-6761 January 2014 Accurate Arabic Script Language/Dialect Classification Stephen C. Tratz Computational and Information Sciences...Include area code) Standard Form 298 (Rev. 8/98) Prescribed by ANSI Std. Z39.18 January 2014 Final Accurate Arabic Script Language/Dialect Classification

  19. Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2.

    PubMed

    Sorokin, Anatoly; Le Novère, Nicolas; Luna, Augustin; Czauderna, Tobias; Demir, Emek; Haw, Robin; Mi, Huaiyu; Moodie, Stuart; Schreiber, Falk; Villéger, Alice

    2015-09-04

    The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Entity Relationship language (ER) represents biological entities and their interactions and relationships within a network. SBGN ER focuses on all potential relationships between entities without considering temporal aspects. The nodes (elements) describe biological entities, such as proteins and complexes. The edges (connections) provide descriptions of interactions and relationships (or influences), e.g., complex formation, stimulation and inhibition. Among all three languages of SBGN, ER is the closest to protein interaction networks in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

  20. Prototype Biology-Based Radiation Risk Module Project

    NASA Technical Reports Server (NTRS)

    Terrier, Douglas; Clayton, Ronald G.; Patel, Zarana; Hu, Shaowen; Huff, Janice

    2015-01-01

    Biological effects of space radiation and risk mitigation are strategic knowledge gaps for the Evolvable Mars Campaign. The current epidemiology-based NASA Space Cancer Risk (NSCR) model contains large uncertainties (HAT #6.5a) due to lack of information on the radiobiology of galactic cosmic rays (GCR) and lack of human data. The use of experimental models that most accurately replicate the response of human tissues is critical for precision in risk projections. Our proposed study will compare DNA damage, histological, and cell kinetic parameters after irradiation in normal 2D human cells versus 3D tissue models, and it will use a multi-scale computational model (CHASTE) to investigate various biological processes that may contribute to carcinogenesis, including radiation-induced cellular signaling pathways. This cross-disciplinary work, with biological validation of an evolvable mathematical computational model, will help reduce uncertainties within NSCR and aid risk mitigation for radiation-induced carcinogenesis.

  1. Growing trend of CE at the omics level: the frontier of systems biology.

    PubMed

    Oh, Eulsik; Hasan, Md Nabiul; Jamshed, Muhammad; Park, Soo Hyun; Hong, Hye-Min; Song, Eun Joo; Yoo, Young Sook

    2010-01-01

    In a novel attempt to comprehend the complexity of life, systems biology has recently emerged as a state-of-the-art approach for biological research in contrast to the reductionist approaches that have been used in molecular cell biology since the 1950s. Because a massive amount of information is required in many systems biology studies of life processes, we have increasingly come to depend on techniques that provide high-throughput omics data. CE and CE coupled to MS have served as powerful analytical tools for providing qualitative and quantitative omics data. Recent systems biology studies have focused strongly on the diagnosis and treatment of diseases. The increasing number of clinical research papers on drug discovery and disease therapies reflects this growing interest among scientists. Since such clinical research reflects one of the ultimate purposes of bioscience, these trends will be sustained for a long time. Thus, this review mainly focuses on the application of CE and CE-MS in diagnosis as well as on the latest CE methods developed. Furthermore, we outline the new challenges that arose in 2008 and later in elucidating the system-level functions of the bioconstituents of living organisms.

  2. Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems

    PubMed Central

    Boué, Stéphanie; Talikka, Marja; Westra, Jurjen Willem; Hayes, William; Di Fabio, Anselmo; Park, Jennifer; Schlage, Walter K.; Sewer, Alain; Fields, Brett; Ansari, Sam; Martin, Florian; Veljkovic, Emilija; Kenney, Renee; Peitsch, Manuel C.; Hoeng, Julia

    2015-01-01

    With the wealth of publications and data available, powerful and transparent computational approaches are required to represent measured data and scientific knowledge in a computable and searchable format. We developed a set of biological network models, scripted in the Biological Expression Language, that reflect causal signaling pathways across a wide range of biological processes, including cell fate, cell stress, cell proliferation, inflammation, tissue repair and angiogenesis in the pulmonary and cardiovascular context. This comprehensive collection of networks is now freely available to the scientific community in a centralized web-based repository, the Causal Biological Network database, which is composed of over 120 manually curated and well annotated biological network models and can be accessed at http://causalbionet.com. The website accesses a MongoDB, which stores all versions of the networks as JSON objects and allows users to search for genes, proteins, biological processes, small molecules and keywords in the network descriptions to retrieve biological networks of interest. The content of the networks can be visualized and browsed. Nodes and edges can be filtered and all supporting evidence for the edges can be browsed and is linked to the original articles in PubMed. Moreover, networks may be downloaded for further visualization and evaluation. Database URL: http://causalbionet.com PMID:25887162

  3. A flexible and accurate digital volume correlation method applicable to high-resolution volumetric images

    NASA Astrophysics Data System (ADS)

    Pan, Bing; Wang, Bo

    2017-10-01

    Digital volume correlation (DVC) is a powerful technique for quantifying interior deformation within solid opaque materials and biological tissues. In the last two decades, great efforts have been made to improve the accuracy and efficiency of the DVC algorithm. However, there is still a lack of a flexible, robust and accurate version that can be efficiently implemented in personal computers with limited RAM. This paper proposes an advanced DVC method that can realize accurate full-field internal deformation measurement applicable to high-resolution volume images with up to billions of voxels. Specifically, a novel layer-wise reliability-guided displacement tracking strategy combined with dynamic data management is presented to guide the DVC computation from slice to slice. The displacements at specified calculation points in each layer are computed using the advanced 3D inverse-compositional Gauss-Newton algorithm with the complete initial guess of the deformation vector accurately predicted from the computed calculation points. Since only limited slices of interest in the reference and deformed volume images rather than the whole volume images are required, the DVC calculation can thus be efficiently implemented on personal computers. The flexibility, accuracy and efficiency of the presented DVC approach are demonstrated by analyzing computer-simulated and experimentally obtained high-resolution volume images.

  4. Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals

    PubMed Central

    Uervirojnangkoorn, Monarin; Zeldin, Oliver B; Lyubimov, Artem Y; Hattne, Johan; Brewster, Aaron S; Sauter, Nicholas K; Brunger, Axel T; Weis, William I

    2015-01-01

    There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as the resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. These developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited. DOI: http://dx.doi.org/10.7554/eLife.05421.001 PMID:25781634

  5. Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals

    DOE PAGES

    Uervirojnangkoorn, Monarin; Zeldin, Oliver B.; Lyubimov, Artem Y.; ...

    2015-03-17

    There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as themore » resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. In conclusion, these developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited.« less

  6. Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals

    DOE PAGES

    Uervirojnangkoorn, Monarin; Zeldin, Oliver B.; Lyubimov, Artem Y.; ...

    2015-03-17

    There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as themore » resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. These developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited.« less

  7. Accurate Satellite-Derived Estimates of Tropospheric Ozone Radiative Forcing

    NASA Technical Reports Server (NTRS)

    Joiner, Joanna; Schoeberl, Mark R.; Vasilkov, Alexander P.; Oreopoulos, Lazaros; Platnick, Steven; Livesey, Nathaniel J.; Levelt, Pieternel F.

    2008-01-01

    Estimates of the radiative forcing due to anthropogenically-produced tropospheric O3 are derived primarily from models. Here, we use tropospheric ozone and cloud data from several instruments in the A-train constellation of satellites as well as information from the GEOS-5 Data Assimilation System to accurately estimate the instantaneous radiative forcing from tropospheric O3 for January and July 2005. We improve upon previous estimates of tropospheric ozone mixing ratios from a residual approach using the NASA Earth Observing System (EOS) Aura Ozone Monitoring Instrument (OMI) and Microwave Limb Sounder (MLS) by incorporating cloud pressure information from OMI. Since we cannot distinguish between natural and anthropogenic sources with the satellite data, our estimates reflect the total forcing due to tropospheric O3. We focus specifically on the magnitude and spatial structure of the cloud effect on both the shortand long-wave radiative forcing. The estimates presented here can be used to validate present day O3 radiative forcing produced by models.

  8. Realized niche shift during a global biological invasion

    PubMed Central

    Tingley, Reid; Vallinoto, Marcelo; Sequeira, Fernando; Kearney, Michael R.

    2014-01-01

    Accurate forecasts of biological invasions are crucial for managing invasion risk but are hampered by niche shifts resulting from evolved environmental tolerances (fundamental niche shifts) or the presence of novel biotic and abiotic conditions in the invaded range (realized niche shifts). Distinguishing between these kinds of niche shifts is impossible with traditional, correlative approaches to invasion forecasts, which exclusively consider the realized niche. Here we overcome this challenge by combining a physiologically mechanistic model of the fundamental niche with correlative models based on the realized niche to study the global invasion of the cane toad Rhinella marina. We find strong evidence that the success of R. marina in Australia reflects a shift in the species’ realized niche, as opposed to evolutionary shifts in range-limiting traits. Our results demonstrate that R. marina does not fill its fundamental niche in its native South American range and that areas of niche unfilling coincide with the presence of a closely related species with which R. marina hybridizes. Conversely, in Australia, where coevolved taxa are absent, R. marina largely fills its fundamental niche in areas behind the invasion front. The general approach taken here of contrasting fundamental and realized niche models provides key insights into the role of biotic interactions in shaping range limits and can inform effective management strategies not only for invasive species but also for assisted colonization under climate change. PMID:24982155

  9. Exploring High School Biology Students' Engagement with More and Less Epistemologically Considerate Texts

    ERIC Educational Resources Information Center

    Kloser, Matthew

    2013-01-01

    Texts play an integral role in science research and science classrooms yet biology textbooks have traditionally failed to reflect the epistemic elements of the discipline such as justification of claims and visual representations of empirical data. This study investigates high school biology students' reading experiences when engaging more…

  10. Phase and Index of Refraction Imaging by Hyperspectral Reflectance Confocal Microscopy.

    PubMed

    Selci, Stefano

    2016-12-16

    A hyperspectral reflectance confocal microscope (HSCM) was realized by CNR-ISC (Consiglio Nazionale delle Ricerche-Istituto dei Sistemi Complessi) a few years ago. The instrument and data have been already presented and discussed. The main activity of this HSCM has been within biology, and reflectance data have shown good matching between spectral signatures and the nature or evolution on many types of cells. Such a relationship has been demonstrated mainly with statistical tools like Principal Component Analysis (PCA), or similar concepts, which represent a very common approach for hyperspectral imaging. However, the point is that reflectance data contains much more useful information and, moreover, there is an obvious interest to go from reflectance, bound to the single experiment, to reflectivity, or other physical quantities, related to the sample alone. To accomplish this aim, we can follow well-established analyses and methods used in reflectance spectroscopy. Therefore, we show methods of calculations for index of refraction n , extinction coefficient k and local thicknesses of frequency starting from phase images by fast Kramers-Kronig (KK) algorithms and the Abeles matrix formalism. Details, limitations and problems of the presented calculations as well as alternative procedures are given for an example of HSCM images of red blood cells (RBC).

  11. Predicting Clear-Sky Reflectance Over Snow/Ice in Polar Regions

    NASA Technical Reports Server (NTRS)

    Chen, Yan; Sun-Mack, Sunny; Arduini, Robert F.; Hong, Gang; Minnis, Patrick

    2015-01-01

    Satellite remote sensing of clouds requires an accurate estimate of the clear-sky radiances for a given scene to detect clouds and aerosols and to retrieve their microphysical properties. Knowing the spatial and angular variability of clear-sky albedo is essential for predicting clear-sky radiance at solar wavelengths. The Clouds and the Earth's Radiant Energy System (CERES) Project uses the nearinfrared (NIR; 1.24, 1.6 or 2.13 micrometers), visible (VIS; 0.63 micrometers) and vegetation (VEG; 0.86 micrometers) channels available on the Terra and Aqua Moderate Resolution Imaging Spectroradiometer (MODIS) to help identify clouds and retrieve their properties in both snow-free and snow-covered conditions. Thus, it is critical to have reliable distributions of clear-sky albedo for all of these channels. In CERES Edition 4 (Ed4), the 1.24-micrometer channel is used to retrieve cloud optical depth over snow/ice-covered surfaces. Thus, it is especially critical to accurately predict the 1.24-micrometer clear-sky albedo alpha and reflectance rho for a given location and time. Snow albedo and reflectance patterns are very complex due to surface texture, particle shapes and sizes, melt water, and vegetation protrusions from the snow surface. To minimize those effects, this study focuses on the permanent snow cover of Antarctica where vegetation is absent and melt water is minimal. Clear-sky albedos are determined as a function of solar zenith angle (SZA) from observations over all scenes determined to be cloud-free to produce a normalized directional albedo model (DRM). The DRM is used to develop alpha(SZA=0 degrees) on 10 foot grid for each season. These values provide the basis for predicting r at any location and set of viewing & illumination conditions. This paper examines the accuracy of this approach for two theoretical snow surface reflectance models.

  12. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate... indispensable in examinations conducted within the Department of Veterans Affairs. Muscle atrophy must also be...

  13. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate... indispensable in examinations conducted within the Department of Veterans Affairs. Muscle atrophy must also be...

  14. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate... indispensable in examinations conducted within the Department of Veterans Affairs. Muscle atrophy must also be...

  15. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate... indispensable in examinations conducted within the Department of Veterans Affairs. Muscle atrophy must also be...

  16. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate... indispensable in examinations conducted within the Department of Veterans Affairs. Muscle atrophy must also be...

  17. Feedback about More Accurate versus Less Accurate Trials: Differential Effects on Self-Confidence and Activation

    ERIC Educational Resources Information Center

    Badami, Rokhsareh; VaezMousavi, Mohammad; Wulf, Gabriele; Namazizadeh, Mahdi

    2012-01-01

    One purpose of the present study was to examine whether self-confidence or anxiety would be differentially affected by feedback from more accurate rather than less accurate trials. The second purpose was to determine whether arousal variations (activation) would predict performance. On Day 1, participants performed a golf putting task under one of…

  18. Fourier Transform Mass Spectrometry and Nuclear Magnetic Resonance Analysis for the Rapid and Accurate Characterization of Hexacosanoylceramide.

    PubMed

    Ross, Charles W; Simonsick, William J; Bogusky, Michael J; Celikay, Recep W; Guare, James P; Newton, Randall C

    2016-06-28

    Ceramides are a central unit of all sphingolipids which have been identified as sites of biological recognition on cellular membranes mediating cell growth and differentiation. Several glycosphingolipids have been isolated, displaying immunomodulatory and anti-tumor activities. These molecules have generated considerable interest as potential vaccine adjuvants in humans. Accurate analyses of these and related sphingosine analogues are important for the characterization of structure, biological function, and metabolism. We report the complementary use of direct laser desorption ionization (DLDI), sheath flow electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) and high-field nuclear magnetic resonance (NMR) analysis for the rapid, accurate identification of hexacosanoylceramide and starting materials. DLDI does not require stringent sample preparation and yields representative ions. Sheath-flow ESI yields ions of the product and byproducts and was significantly better than monospray ESI due to improved compound solubility. Negative ion sheath flow ESI provided data of starting materials and products all in one acquisition as hexacosanoic acid does not ionize efficiently when ceramides are present. NMR provided characterization of these lipid molecules complementing the results obtained from MS analyses. NMR data was able to differentiate straight chain versus branched chain alkyl groups not easily obtained from mass spectrometry.

  19. Seismic reflection imaging, accounting for primary and multiple reflections

    NASA Astrophysics Data System (ADS)

    Wapenaar, Kees; van der Neut, Joost; Thorbecke, Jan; Broggini, Filippo; Slob, Evert; Snieder, Roel

    2015-04-01

    Imaging of seismic reflection data is usually based on the assumption that the seismic response consists of primary reflections only. Multiple reflections, i.e. waves that have reflected more than once, are treated as primaries and are imaged at wrong positions. There are two classes of multiple reflections, which we will call surface-related multiples and internal multiples. Surface-related multiples are those multiples that contain at least one reflection at the earth's surface, whereas internal multiples consist of waves that have reflected only at subsurface interfaces. Surface-related multiples are the strongest, but also relatively easy to deal with because the reflecting boundary (the earth's surface) is known. Internal multiples constitute a much more difficult problem for seismic imaging, because the positions and properties of the reflecting interfaces are not known. We are developing reflection imaging methodology which deals with internal multiples. Starting with the Marchenko equation for 1D inverse scattering problems, we derived 3D Marchenko-type equations, which relate reflection data at the surface to Green's functions between virtual sources anywhere in the subsurface and receivers at the surface. Based on these equations, we derived an iterative scheme by which these Green's functions can be retrieved from the reflection data at the surface. This iterative scheme requires an estimate of the direct wave of the Green's functions in a background medium. Note that this is precisely the same information that is also required by standard reflection imaging schemes. However, unlike in standard imaging, our iterative Marchenko scheme retrieves the multiple reflections of the Green's functions from the reflection data at the surface. For this, no knowledge of the positions and properties of the reflecting interfaces is required. Once the full Green's functions are retrieved, reflection imaging can be carried out by which the primaries and multiples are

  20. [History and biology: possible dialogues, necessary distances].

    PubMed

    Duarte, Regina Horta

    2009-01-01

    Evolution has often been rejected as a theory incompatible with proper historical reflection. While there are undoubtedly insurmountable barriers between biology and the study of man and society, a rigorous analysis of Darwinist theory demonstrates epistemological areas of contact between history and evolutionary biology. The amazing temporal perspective shared by both areas of knowledge points to some bridges of communication, like the importance of the event and of creation processes, the rejection of teleology and the idea of progress, the complexity of events between chance and necessity, and the impossibility of making predictions. This affords an opportunity for a transdisciplinary approach at a moment of various contemporary challenges.

  1. Photonic structures in biology

    NASA Astrophysics Data System (ADS)

    Vukusic, Pete; Sambles, J. Roy

    2003-08-01

    Millions of years before we began to manipulate the flow of light using synthetic structures, biological systems were using nanometre-scale architectures to produce striking optical effects. An astonishing variety of natural photonic structures exists: a species of Brittlestar uses photonic elements composed of calcite to collect light, Morpho butterflies use multiple layers of cuticle and air to produce their striking blue colour and some insects use arrays of elements, known as nipple arrays, to reduce reflectivity in their compound eyes. Natural photonic structures are providing inspiration for technological applications.

  2. Separation and reconstruction of high pressure water-jet reflective sound signal based on ICA

    NASA Astrophysics Data System (ADS)

    Yang, Hongtao; Sun, Yuling; Li, Meng; Zhang, Dongsu; Wu, Tianfeng

    2011-12-01

    The impact of high pressure water-jet on the different materials target will produce different reflective mixed sound. In order to reconstruct the reflective sound signals distribution on the linear detecting line accurately and to separate the environment noise effectively, the mixed sound signals acquired by linear mike array were processed by ICA. The basic principle of ICA and algorithm of FASTICA were described in detail. The emulation experiment was designed. The environment noise signal was simulated by using band-limited white noise and the reflective sound signal was simulated by using pulse signal. The reflective sound signal attenuation produced by the different distance transmission was simulated by weighting the sound signal with different contingencies. The mixed sound signals acquired by linear mike array were synthesized by using the above simulated signals and were whitened and separated by ICA. The final results verified that the environment noise separation and the reconstruction of the detecting-line sound distribution can be realized effectively.

  3. Making Science Real: Photo-Sharing in Biology and Chemistry

    ERIC Educational Resources Information Center

    Waycott, Jenny; Dalgarno, Barney; Kennedy, Gregor; Bishop, Andrea

    2012-01-01

    In this paper, we examine students' reflections about the value of two photo-sharing activities that were implemented in undergraduate Biology and Chemistry subjects. Both activities aimed, broadly, to provide support for authentic and meaningful learning experiences in undergraduate science. Although the activities were similar--both required…

  4. Live cell refractometry using Hilbert phase microscopy and confocal reflectance microscopy.

    PubMed

    Lue, Niyom; Choi, Wonshik; Popescu, Gabriel; Yaqoob, Zahid; Badizadegan, Kamran; Dasari, Ramachandra R; Feld, Michael S

    2009-11-26

    Quantitative chemical analysis has served as a useful tool for understanding cellular metabolisms in biology. Among many physical properties used in chemical analysis, refractive index in particular has provided molecular concentration that is an important indicator for biological activities. In this report, we present a method of extracting full-field refractive index maps of live cells in their native states. We first record full-field optical thickness maps of living cells by Hilbert phase microscopy and then acquire physical thickness maps of the same cells using a custom-built confocal reflectance microscope. Full-field and axially averaged refractive index maps are acquired from the ratio of optical thickness to physical thickness. The accuracy of the axially averaged index measurement is 0.002. This approach can provide novel biological assays of label-free living cells in situ.

  5. Live Cell Refractometry Using Hilbert Phase Microscopy and Confocal Reflectance Microscopy†

    PubMed Central

    Lue, Niyom; Choi, Wonshik; Popescu, Gabriel; Yaqoob, Zahid; Badizadegan, Kamran; Dasari, Ramachandra R.; Feld, Michael S.

    2010-01-01

    Quantitative chemical analysis has served as a useful tool for understanding cellular metabolisms in biology. Among many physical properties used in chemical analysis, refractive index in particular has provided molecular concentration that is an important indicator for biological activities. In this report, we present a method of extracting full-field refractive index maps of live cells in their native states. We first record full-field optical thickness maps of living cells by Hilbert phase microscopy and then acquire physical thickness maps of the same cells using a custom-built confocal reflectance microscope. Full-field and axially averaged refractive index maps are acquired from the ratio of optical thickness to physical thickness. The accuracy of the axially averaged index measurement is 0.002. This approach can provide novel biological assays of label-free living cells in situ. PMID:19803506

  6. Calculating life? Duelling discourses in interdisciplinary systems biology.

    PubMed

    Calvert, Jane; Fujimura, Joan H

    2011-06-01

    A high profile context in which physics and biology meet today is in the new field of systems biology. Systems biology is a fascinating subject for sociological investigation because the demands of interdisciplinary collaboration have brought epistemological issues and debates front and centre in discussions amongst systems biologists in conference settings, in publications, and in laboratory coffee rooms. One could argue that systems biologists are conducting their own philosophy of science. This paper explores the epistemic aspirations of the field by drawing on interviews with scientists working in systems biology, attendance at systems biology conferences and workshops, and visits to systems biology laboratories. It examines the discourses of systems biologists, looking at how they position their work in relation to previous types of biological inquiry, particularly molecular biology. For example, they raise the issue of reductionism to distinguish systems biology from molecular biology. This comparison with molecular biology leads to discussions about the goals and aspirations of systems biology, including epistemic commitments to quantification, rigor and predictability. Some systems biologists aspire to make biology more similar to physics and engineering by making living systems calculable, modelable and ultimately predictable-a research programme that is perhaps taken to its most extreme form in systems biology's sister discipline: synthetic biology. Other systems biologists, however, do not think that the standards of the physical sciences are the standards by which we should measure the achievements of systems biology, and doubt whether such standards will ever be applicable to 'dirty, unruly living systems'. This paper explores these epistemic tensions and reflects on their sociological dimensions and their consequences for future work in the life sciences. Copyright © 2010 Elsevier Ltd. All rights reserved.

  7. Accurate Construction of Photoactivated Localization Microscopy (PALM) Images for Quantitative Measurements

    PubMed Central

    Coltharp, Carla; Kessler, Rene P.; Xiao, Jie

    2012-01-01

    Localization-based superresolution microscopy techniques such as Photoactivated Localization Microscopy (PALM) and Stochastic Optical Reconstruction Microscopy (STORM) have allowed investigations of cellular structures with unprecedented optical resolutions. One major obstacle to interpreting superresolution images, however, is the overcounting of molecule numbers caused by fluorophore photoblinking. Using both experimental and simulated images, we determined the effects of photoblinking on the accurate reconstruction of superresolution images and on quantitative measurements of structural dimension and molecule density made from those images. We found that structural dimension and relative density measurements can be made reliably from images that contain photoblinking-related overcounting, but accurate absolute density measurements, and consequently faithful representations of molecule counts and positions in cellular structures, require the application of a clustering algorithm to group localizations that originate from the same molecule. We analyzed how applying a simple algorithm with different clustering thresholds (tThresh and dThresh) affects the accuracy of reconstructed images, and developed an easy method to select optimal thresholds. We also identified an empirical criterion to evaluate whether an imaging condition is appropriate for accurate superresolution image reconstruction with the clustering algorithm. Both the threshold selection method and imaging condition criterion are easy to implement within existing PALM clustering algorithms and experimental conditions. The main advantage of our method is that it generates a superresolution image and molecule position list that faithfully represents molecule counts and positions within a cellular structure, rather than only summarizing structural properties into ensemble parameters. This feature makes it particularly useful for cellular structures of heterogeneous densities and irregular geometries, and

  8. Modeling thermal infrared (2-14 micrometer) reflectance spectra of frost and snow

    NASA Technical Reports Server (NTRS)

    Wald, Andrew E.

    1994-01-01

    Existing theories of radiative transfer in close-packed media assume that each particle scatters independently of its neighbors. For opaque particles, such as are common in the thermal infrared, this assumption is not valid, and these radiative transfer theories will not be accurate. A new method is proposed, called 'diffraction subtraction', which modifies the scattering cross section of close-packed large, opaque spheres to account for the effect of close packing on the diffraction cross section of a scattering particle. This method predicts the thermal infrared reflectance of coarse (greater than 50 micrometers radius), disaggregated granular snow. However, such coarse snow is typically old and metamorphosed, with adjacent grains welded together. The reflectance of such a welded block can be described as partly Fresnel in nature and cannot be predicted using Mie inputs to radiative transfer theory. Owing to the high absorption coefficient of ice in the thermal infrared, a rough surface reflectance model can be used to calculate reflectance from such a block. For very small (less than 50 micrometers), disaggregated particles, it is incorrect in principle to treat diffraction independently of reflection and refraction, and the theory fails. However, for particles larger than 50 micrometers, independent scattering is a valid assumption, and standard radiative transfer theory works.

  9. Biological inquiry: a new course and assessment plan in response to the call to transform undergraduate biology.

    PubMed

    Goldey, Ellen S; Abercrombie, Clarence L; Ivy, Tracie M; Kusher, Dave I; Moeller, John F; Rayner, Doug A; Smith, Charles F; Spivey, Natalie W

    2012-01-01

    We transformed our first-year curriculum in biology with a new course, Biological Inquiry, in which >50% of all incoming, first-year students enroll. The course replaced a traditional, content-driven course that relied on outdated approaches to teaching and learning. We diversified pedagogical practices by adopting guided inquiry in class and in labs, which are devoted to building authentic research skills through open-ended experiments. Students develop core biological knowledge, from the ecosystem to molecular level, and core skills through regular practice in hypothesis testing, reading primary literature, analyzing data, interpreting results, writing in disciplinary style, and working in teams. Assignments and exams require higher-order cognitive processes, and students build new knowledge and skills through investigation of real-world problems (e.g., malaria), which engages students' interest. Evidence from direct and indirect assessment has guided continuous course revision and has revealed that compared with the course it replaced, Biological Inquiry produces significant learning gains in all targeted areas. It also retains 94% of students (both BA and BS track) compared with 79% in the majors-only course it replaced. The project has had broad impact across the entire college and reflects the input of numerous constituencies and close collaboration among biology professors and students.

  10. Biological Inquiry: A New Course and Assessment Plan in Response to the Call to Transform Undergraduate Biology

    PubMed Central

    Goldey, Ellen S.; Abercrombie, Clarence L.; Ivy, Tracie M.; Kusher, Dave I.; Moeller, John F.; Rayner, Doug A.; Smith, Charles F.; Spivey, Natalie W.

    2012-01-01

    We transformed our first-year curriculum in biology with a new course, Biological Inquiry, in which >50% of all incoming, first-year students enroll. The course replaced a traditional, content-driven course that relied on outdated approaches to teaching and learning. We diversified pedagogical practices by adopting guided inquiry in class and in labs, which are devoted to building authentic research skills through open-ended experiments. Students develop core biological knowledge, from the ecosystem to molecular level, and core skills through regular practice in hypothesis testing, reading primary literature, analyzing data, interpreting results, writing in disciplinary style, and working in teams. Assignments and exams require higher-order cognitive processes, and students build new knowledge and skills through investigation of real-world problems (e.g., malaria), which engages students’ interest. Evidence from direct and indirect assessment has guided continuous course revision and has revealed that compared with the course it replaced, Biological Inquiry produces significant learning gains in all targeted areas. It also retains 94% of students (both BA and BS track) compared with 79% in the majors-only course it replaced. The project has had broad impact across the entire college and reflects the input of numerous constituencies and close collaboration among biology professors and students. PMID:23222831

  11. Correlation between MCAT biology content specifications and topic scope and sequence of general education college biology textbooks.

    PubMed

    Rissing, Steven W

    2013-01-01

    Most American colleges and universities offer gateway biology courses to meet the needs of three undergraduate audiences: biology and related science majors, many of whom will become biomedical researchers; premedical students meeting medical school requirements and preparing for the Medical College Admissions Test (MCAT); and students completing general education (GE) graduation requirements. Biology textbooks for these three audiences present a topic scope and sequence that correlates with the topic scope and importance ratings of the biology content specifications for the MCAT regardless of the intended audience. Texts for "nonmajors," GE courses appear derived directly from their publisher's majors text. Topic scope and sequence of GE texts reflect those of "their" majors text and, indirectly, the MCAT. MCAT term density of GE texts equals or exceeds that of their corresponding majors text. Most American universities require a GE curriculum to promote a core level of academic understanding among their graduates. This includes civic scientific literacy, recognized as an essential competence for the development of public policies in an increasingly scientific and technological world. Deriving GE biology and related science texts from majors texts designed to meet very different learning objectives may defeat the scientific literacy goals of most schools' GE curricula.

  12. Correlation between MCAT Biology Content Specifications and Topic Scope and Sequence of General Education College Biology Textbooks

    PubMed Central

    Rissing, Steven W.

    2013-01-01

    Most American colleges and universities offer gateway biology courses to meet the needs of three undergraduate audiences: biology and related science majors, many of whom will become biomedical researchers; premedical students meeting medical school requirements and preparing for the Medical College Admissions Test (MCAT); and students completing general education (GE) graduation requirements. Biology textbooks for these three audiences present a topic scope and sequence that correlates with the topic scope and importance ratings of the biology content specifications for the MCAT regardless of the intended audience. Texts for “nonmajors,” GE courses appear derived directly from their publisher's majors text. Topic scope and sequence of GE texts reflect those of “their” majors text and, indirectly, the MCAT. MCAT term density of GE texts equals or exceeds that of their corresponding majors text. Most American universities require a GE curriculum to promote a core level of academic understanding among their graduates. This includes civic scientific literacy, recognized as an essential competence for the development of public policies in an increasingly scientific and technological world. Deriving GE biology and related science texts from majors texts designed to meet very different learning objectives may defeat the scientific literacy goals of most schools’ GE curricula. PMID:24006392

  13. Rayleigh Scattering in Planetary Atmospheres: Corrected Tables Through Accurate Computation of X and Y Functions

    NASA Astrophysics Data System (ADS)

    Natraj, Vijay; Li, King-Fai; Yung, Yuk L.

    2009-02-01

    Tables that have been used as a reference for nearly 50 years for the intensity and polarization of reflected and transmitted light in Rayleigh scattering atmospheres have been found to be inaccurate, even to four decimal places. We convert the integral equations describing the X and Y functions into a pair of coupled integro-differential equations that can be efficiently solved numerically. Special care has been taken in evaluating Cauchy principal value integrals and their derivatives that appear in the solution of the Rayleigh scattering problem. The new approach gives results accurate to eight decimal places for the entire range of tabulation (optical thicknesses 0.02-1.0, surface reflectances 0-0.8, solar and viewing zenith angles 0°-88.85°, and relative azimuth angles 0°-180°), including the most difficult case of direct transmission in the direction of the sun. Revised tables have been created and stored electronically for easy reference by the planetary science and astrophysics community.

  14. Exploring Extreme Retro-reflection by Asteroids Using Las Cumbres Observatory Robotic Telescope Observations

    NASA Astrophysics Data System (ADS)

    Goguen, Jay D.; Bauer, James M.

    2017-10-01

    The reflectivity of solar system surfaces ‘spikes’ sharply when the Sun is less than 1 degree from directly behind the observer. The Galileo spacecraft measured the reflectivity of part of Europa’s surface to increase by as much as a factor of 8 as the observer moves from 5 degrees to the exact backscattering direction! One mechanism explains this spike as coherent light scattering that occurs only close to this unique retro-reflection geometry. Due to the tight linear alignment of the target, observer and Sun required to measure the peak brightness of the spike, accurate and complete measurements of the amplitude and decay of the spike exist for only a few targets. We used the unique capabilities of the automated Las Cumbres Observatory global telescope network (LCO) to systematically measure this extreme opposition surge for 60+ asteroids sampling a variety of taxonomic classes in the Bus/DeMeo taxonomy.Each asteroid was observed in the SDSS r’ and g’ filters during the ~8 hour interval when it passes within ~0.1 deg of the point opposite the Sun on the sky. Supporting observations of each asteroid with LCO collected over ~50 days measure asteroid rotation and phase angle brightness changes to enable accurate characterization of the retro-reflection spike. This data set vastly increases the number and variety of the surfaces characterized at such small phase angles compared to existing asteroid data. We examine how the spike characteristics vary with surface composition, albedo, and wavelength providing new constraints on physical models of this ubiquitous yet poorly understood phenomenon.Analysis and modeling of these measurements will advance our understanding of the physical mechanism responsible for this enhanced retro-reflection thereby improving our ability to characterize these surfaces from remote observations. The ability to infer surface physical properties from remote sensing data is a key capability for future asteroid missions, manned

  15. Use of spectral analogy to evaluate canopy reflectance sensitivity to leaf optical property

    NASA Technical Reports Server (NTRS)

    Baret, Frederic; Vanderbilt, Vern C.; Steven, Michael D.; Jacquemoud, Stephane

    1993-01-01

    The spectral variation of canopy reflectance is mostly governed by the absorption properties of the elements, hence the leaves, since their intrinsic scattering properties show very little spectral variation. The relationship between canopy reflectance and leaf reflectance measured at the red edge over sugar beet canopies was used to simulate canopy reflectance from leaf reflectance spectra measured over the whole spectral domain. The results show that the spectral analogies found allows accurate reconstruction of canopy reflectance spectra. Explicit assumptions about the very low spectral variation of leaf intrinsic scattering properties are thus indirectly justified. The sensitivity of canopy reflectance (rho(sub c)) to leaf optical properties can then be investigated from concurrent spectral variations of canopy (delta rho(sub c)/delta lambda) and leaf reflectance (delta rho(sub l)/delta lambda): (delta rho(sub c))/(delta rho(sub l)) = ((delta rho(sub c))/(delta lambda) ((delta rho( sub l))/(delta lambda))(sup -1)). This expression is strictly valid only when the optical properties of the soil background or the other vegetation elements such as bark are either spectrally flat or do not contribute significantly to canopy reflectance. Simulations using the SAIL and PROSPECT models demonstrate that the sensitivity of canopy reflectance to leaf reflectance is significant for large vegetation cover fractions in spectral domains where absorption is low. In these conditions, multiple, scattering enhances the leaf absorption features by a factor that can be greater than 2.0. To override the limitations of the SAIL model for the description of the canopy architecture, we tested the previous findings on experimental data. Concurrent canopy and leaf reflectance spectra were measured for a range of sugar beet canopies. The results show good agreement with the theoretical findings. Conclusions are drawn about the applicability of these findings, with particular attention to

  16. Accurate quantification of microRNA via single strand displacement reaction on DNA origami motif.

    PubMed

    Zhu, Jie; Feng, Xiaolu; Lou, Jingyu; Li, Weidong; Li, Sheng; Zhu, Hongxin; Yang, Lun; Zhang, Aiping; He, Lin; Li, Can

    2013-01-01

    DNA origami is an emerging technology that assembles hundreds of staple strands and one single-strand DNA into certain nanopattern. It has been widely used in various fields including detection of biological molecules such as DNA, RNA and proteins. MicroRNAs (miRNAs) play important roles in post-transcriptional gene repression as well as many other biological processes such as cell growth and differentiation. Alterations of miRNAs' expression contribute to many human diseases. However, it is still a challenge to quantitatively detect miRNAs by origami technology. In this study, we developed a novel approach based on streptavidin and quantum dots binding complex (STV-QDs) labeled single strand displacement reaction on DNA origami to quantitatively detect the concentration of miRNAs. We illustrated a linear relationship between the concentration of an exemplary miRNA as miRNA-133 and the STV-QDs hybridization efficiency; the results demonstrated that it is an accurate nano-scale miRNA quantifier motif. In addition, both symmetrical rectangular motif and asymmetrical China-map motif were tested. With significant linearity in both motifs, our experiments suggested that DNA Origami motif with arbitrary shape can be utilized in this method. Since this DNA origami-based method we developed owns the unique advantages of simple, time-and-material-saving, potentially multi-targets testing in one motif and relatively accurate for certain impurity samples as counted directly by atomic force microscopy rather than fluorescence signal detection, it may be widely used in quantification of miRNAs.

  17. Accurate Quantification of microRNA via Single Strand Displacement Reaction on DNA Origami Motif

    PubMed Central

    Lou, Jingyu; Li, Weidong; Li, Sheng; Zhu, Hongxin; Yang, Lun; Zhang, Aiping; He, Lin; Li, Can

    2013-01-01

    DNA origami is an emerging technology that assembles hundreds of staple strands and one single-strand DNA into certain nanopattern. It has been widely used in various fields including detection of biological molecules such as DNA, RNA and proteins. MicroRNAs (miRNAs) play important roles in post-transcriptional gene repression as well as many other biological processes such as cell growth and differentiation. Alterations of miRNAs' expression contribute to many human diseases. However, it is still a challenge to quantitatively detect miRNAs by origami technology. In this study, we developed a novel approach based on streptavidin and quantum dots binding complex (STV-QDs) labeled single strand displacement reaction on DNA origami to quantitatively detect the concentration of miRNAs. We illustrated a linear relationship between the concentration of an exemplary miRNA as miRNA-133 and the STV-QDs hybridization efficiency; the results demonstrated that it is an accurate nano-scale miRNA quantifier motif. In addition, both symmetrical rectangular motif and asymmetrical China-map motif were tested. With significant linearity in both motifs, our experiments suggested that DNA Origami motif with arbitrary shape can be utilized in this method. Since this DNA origami-based method we developed owns the unique advantages of simple, time-and-material-saving, potentially multi-targets testing in one motif and relatively accurate for certain impurity samples as counted directly by atomic force microscopy rather than fluorescence signal detection, it may be widely used in quantification of miRNAs. PMID:23990889

  18. FIBER AND INTEGRATED OPTICS: Reflection of electromagnetic radiation from a multilayer waveguide structure with an absorbing metal layer

    NASA Astrophysics Data System (ADS)

    Chernushich, A. P.; Shkerdin, G. N.; Shukin, Yu M.

    1992-10-01

    The angular distribution of the reflection coefficient of an asymmetric multilayer planar structure containing a thin metal film and a planar optical waveguide has been found by accurate numerical calculations. There are resonances in the reflection coefficient associated with hybrid modes of the structure. The cases of strong and weak coupling of the surface polariton modes with the waveguide modes are discussed. The results of the numerical analysis agree with solutions of Maxwell's equations for a multilayer planar structure.

  19. Reflection and Non-Reflection of Particle Wavepackets

    ERIC Educational Resources Information Center

    Cox, Timothy; Lekner, John

    2008-01-01

    Exact closed-form solutions of the time-dependent Schrodinger equation are obtained, describing the propagation of wavepackets in the neighbourhood of a potential. Examples given include zero reflection, total reflection and partial reflection of the wavepacket, for the sech[superscript 2]x/a, 1/x[superscript 2] and delta(x) potentials,…

  20. Stereotypes of Age Differences in Personality Traits: Universal and Accurate?

    PubMed Central

    Chan, Wayne; McCrae, Robert R.; De Fruyt, Filip; Jussim, Lee; Löckenhoff, Corinna E.; De Bolle, Marleen; Costa, Paul T.; Sutin, Angelina R.; Realo, Anu; Allik, Jüri; Nakazato, Katsuharu; Shimonaka, Yoshiko; Hřebíčková, Martina; Kourilova, Sylvie; Yik, Michelle; Ficková, Emília; Brunner-Sciarra, Marina; de Figueora, Nora Leibovich; Schmidt, Vanina; Ahn, Chang-kyu; Ahn, Hyun-nie; Aguilar-Vafaie, Maria E.; Siuta, Jerzy; Szmigielska, Barbara; Cain, Thomas R.; Crawford, Jarret T.; Mastor, Khairul Anwar; Rolland, Jean-Pierre; Nansubuga, Florence; Miramontez, Daniel R.; Benet-Martínez, Veronica; Rossier, Jérôme; Bratko, Denis; Halberstadt, Jamin; Yamaguchi, Mami; Knežević, Goran; Martin, Thomas A.; Gheorghiu, Mirona; Smith, Peter B.; Barbaranelli, Claduio; Wang, Lei; Shakespeare-Finch, Jane; Lima, Margarida P.; Klinkosz, Waldemar; Sekowski, Andrzej; Alcalay, Lidia; Simonetti, Franco; Avdeyeva, Tatyana V.; Pramila, V. S.; Terracciano, Antonio

    2012-01-01

    Age trajectories for personality traits are known to be similar across cultures. To address whether stereotypes of age groups reflect these age-related changes in personality, we asked participants in 26 countries (N = 3,323) to rate typical adolescents, adults, and old persons in their own country. Raters across nations tended to share similar beliefs about different age groups; adolescents were seen as impulsive, rebellious, undisciplined, preferring excitement and novelty, whereas old people were consistently considered lower on impulsivity, activity, antagonism, and Openness. These consensual age group stereotypes correlated strongly with published age differences on the five major dimensions of personality and most of 30 specific traits, using as criteria of accuracy both self-reports and observer ratings, different survey methodologies, and data from up to 50 nations. However, personal stereotypes were considerably less accurate, and consensual stereotypes tended to exaggerate differences across age groups. PMID:23088227

  1. Formal reasoning about systems biology using theorem proving

    PubMed Central

    Hasan, Osman; Siddique, Umair; Tahar, Sofiène

    2017-01-01

    System biology provides the basis to understand the behavioral properties of complex biological organisms at different levels of abstraction. Traditionally, analysing systems biology based models of various diseases have been carried out by paper-and-pencil based proofs and simulations. However, these methods cannot provide an accurate analysis, which is a serious drawback for the safety-critical domain of human medicine. In order to overcome these limitations, we propose a framework to formally analyze biological networks and pathways. In particular, we formalize the notion of reaction kinetics in higher-order logic and formally verify some of the commonly used reaction based models of biological networks using the HOL Light theorem prover. Furthermore, we have ported our earlier formalization of Zsyntax, i.e., a deductive language for reasoning about biological networks and pathways, from HOL4 to the HOL Light theorem prover to make it compatible with the above-mentioned formalization of reaction kinetics. To illustrate the usefulness of the proposed framework, we present the formal analysis of three case studies, i.e., the pathway leading to TP53 Phosphorylation, the pathway leading to the death of cancer stem cells and the tumor growth based on cancer stem cells, which is used for the prognosis and future drug designs to treat cancer patients. PMID:28671950

  2. Effect of reflective practice education on self-reflection, insight, and reflective thinking among experienced nurses: a pilot study.

    PubMed

    Asselin, Marilyn E; Fain, James A

    2013-01-01

    A mixed-method study was conducted to determine whether nurses' participation in a reflective practice continuing education program using a structured reflection model makes a difference in nurses' self-reflection, insight, and reflective thinking about clinical practice situations. Findings suggested that use of structured reflection using question cues, written narratives, and peer-facilitated reflection increased nurses' engagement in self-reflection and enhanced reflective thinking in practice. Including reflective practice education in novice orientation and preceptor training may be beneficial.

  3. Terahertz time-domain spectroscopy for non-invasive assessment of water content in biological samples.

    PubMed

    Borovkova, Mariia; Khodzitsky, Mikhail; Demchenko, Petr; Cherkasova, Olga; Popov, Alexey; Meglinski, Igor

    2018-05-01

    We apply terahertz time-domain spectroscopy for the quantitative non-invasive assessment of the water content in biological samples, such as Carpinus caroliniana tree leaves and pork muscles. The developed experimental terahertz time-domain spectroscopy system operates both in transmission and reflection modes. The Landau-Looyenga-Lifshitz-based model is used for the calculation of the water concentration within the samples. The results of the water concentration measurements are compared with the results of the gravimetric measurements. The obtained results show that the water content in biological samples can be measured non-invasively, with a high accuracy, utilizing terahertz waves in transmission and reflection modes.

  4. Anatomy-Based Algorithms for Detecting Oral Cancer Using Reflectance and Fluorescence Spectroscopy

    PubMed Central

    McGee, Sasha; Mardirossian, Vartan; Elackattu, Alphi; Mirkovic, Jelena; Pistey, Robert; Gallagher, George; Kabani, Sadru; Yu, Chung-Chieh; Wang, Zimmern; Badizadegan, Kamran; Grillone, Gregory; Feld, Michael S.

    2010-01-01

    Objectives We used reflectance and fluorescence spectroscopy to noninvasively and quantitatively distinguish benign from dysplastic/malignant oral lesions. We designed diagnostic algorithms to account for differences in the spectral properties among anatomic sites (gingiva, buccal mucosa, etc). Methods In vivo reflectance and fluorescence spectra were collected from 71 patients with oral lesions. The tissue was then biopsied and the specimen evaluated by histopathology. Quantitative parameters related to tissue morphology and biochemistry were extracted from the spectra. Diagnostic algorithms specific for combinations of sites with similar spectral properties were developed. Results Discrimination of benign from dysplastic/malignant lesions was most successful when algorithms were designed for individual sites (area under the receiver operator characteristic curve [ROC-AUC], 0.75 for the lateral surface of the tongue) and was least accurate when all sites were combined (ROC-AUC, 0.60). The combination of sites with similar spectral properties (floor of mouth and lateral surface of the tongue) yielded an ROC-AUC of 0.71. Conclusions Accurate spectroscopic detection of oral disease must account for spectral variations among anatomic sites. Anatomy-based algorithms for single sites or combinations of sites demonstrated good diagnostic performance in distinguishing benign lesions from dysplastic/malignant lesions and consistently performed better than algorithms developed for all sites combined. PMID:19999369

  5. Motor equivalence during multi-finger accurate force production

    PubMed Central

    Mattos, Daniela; Schöner, Gregor; Zatsiorsky, Vladimir M.; Latash, Mark L.

    2014-01-01

    We explored stability of multi-finger cyclical accurate force production action by analysis of responses to small perturbations applied to one of the fingers and inter-cycle analysis of variance. Healthy subjects performed two versions of the cyclical task, with and without an explicit target. The “inverse piano” apparatus was used to lift/lower a finger by 1 cm over 0.5 s; the subjects were always instructed to perform the task as accurate as they could at all times. Deviations in the spaces of finger forces and modes (hypothetical commands to individual fingers) were quantified in directions that did not change total force (motor equivalent) and in directions that changed the total force (non-motor equivalent). Motor equivalent deviations started immediately with the perturbation and increased progressively with time. After a sequence of lifting-lowering perturbations leading to the initial conditions, motor equivalent deviations were dominating. These phenomena were less pronounced for analysis performed with respect to the total moment of force with respect to an axis parallel to the forearm/hand. Analysis of inter-cycle variance showed consistently higher variance in a subspace that did not change the total force as compared to the variance that affected total force. We interpret the results as reflections of task-specific stability of the redundant multi-finger system. Large motor equivalent deviations suggest that reactions of the neuromotor system to a perturbation involve large changes of neural commands that do not affect salient performance variables, even during actions with the purpose to correct those salient variables. Consistency of the analyses of motor equivalence and variance analysis provides additional support for the idea of task-specific stability ensured at a neural level. PMID:25344311

  6. Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems.

    PubMed

    Boué, Stéphanie; Talikka, Marja; Westra, Jurjen Willem; Hayes, William; Di Fabio, Anselmo; Park, Jennifer; Schlage, Walter K; Sewer, Alain; Fields, Brett; Ansari, Sam; Martin, Florian; Veljkovic, Emilija; Kenney, Renee; Peitsch, Manuel C; Hoeng, Julia

    2015-01-01

    With the wealth of publications and data available, powerful and transparent computational approaches are required to represent measured data and scientific knowledge in a computable and searchable format. We developed a set of biological network models, scripted in the Biological Expression Language, that reflect causal signaling pathways across a wide range of biological processes, including cell fate, cell stress, cell proliferation, inflammation, tissue repair and angiogenesis in the pulmonary and cardiovascular context. This comprehensive collection of networks is now freely available to the scientific community in a centralized web-based repository, the Causal Biological Network database, which is composed of over 120 manually curated and well annotated biological network models and can be accessed at http://causalbionet.com. The website accesses a MongoDB, which stores all versions of the networks as JSON objects and allows users to search for genes, proteins, biological processes, small molecules and keywords in the network descriptions to retrieve biological networks of interest. The content of the networks can be visualized and browsed. Nodes and edges can be filtered and all supporting evidence for the edges can be browsed and is linked to the original articles in PubMed. Moreover, networks may be downloaded for further visualization and evaluation. Database URL: http://causalbionet.com © The Author(s) 2015. Published by Oxford University Press.

  7. Reflectance spectroscopy of fresh whole leaves for the estimation of chemical concentration

    NASA Technical Reports Server (NTRS)

    Curran, Paul J.; Dungan, Jennifer L.; Macler, Bruce A.; Plummer, Stephen E.; Peterson, David L.

    1992-01-01

    Remotely sensed plant-canopy data in the visible and near-IR ranges are used to establish relations between the canopy reflectance and the chemical content of the leaves. The mathematical relation is generated by means of stepwise regression based on the derivative reflectance at certain wavelengths. Fourier filtering and sample control are used to minimize instrument noise and spectral overlap respectively, and absorption features are noted that correspond to sugar and protein. The coefficients of determination between estimated and measured concentrations are at least 0.82 for such substances as starch and chlorophyll. It is recommended in the analysis of remotly sensed canopy data that the chemicals with strong spectral overlaps with the chemical of interest be accounted for in order to estimate foliar chemical concentrations accurately.

  8. Hospital blood bank information systems accurately reflect patient transfusion: results of a validation study.

    PubMed

    McQuilten, Zoe K; Schembri, Nikita; Polizzotto, Mark N; Akers, Christine; Wills, Melissa; Cole-Sinclair, Merrole F; Whitehead, Susan; Wood, Erica M; Phillips, Louise E

    2011-05-01

    Hospital transfusion laboratories collect information regarding blood transfusion and some registries gather clinical outcomes data without transfusion information, providing an opportunity to integrate these two sources to explore effects of transfusion on clinical outcomes. However, the use of laboratory information system (LIS) data for this purpose has not been validated previously. Validation of LIS data against individual patient records was undertaken at two major centers. Data regarding all transfusion episodes were analyzed over seven 24-hour periods. Data regarding 596 units were captured including 399 red blood cell (RBC), 95 platelet (PLT), 72 plasma, and 30 cryoprecipitate units. They were issued to: inpatient 221 (37.1%), intensive care 109 (18.3%), outpatient 95 (15.9%), operating theater 45 (7.6%), emergency department 27 (4.5%), and unrecorded 99 (16.6%). All products recorded by LIS as issued were documented as transfused to intended patients. Median time from issue to transfusion initiation could be calculated for 535 (89.8%) components: RBCs 16 minutes (95% confidence interval [CI], 15-18 min; interquartile range [IQR], 7-30 min), PLTs 20 minutes (95% CI, 15-22 min; IQR, 10-37 min), fresh-frozen plasma 33 minutes (95% CI, 14-83 min; IQR, 11-134 min), and cryoprecipitate 3 minutes (95% CI, -10 to 42 min; IQR, -15 to 116 min). Across a range of blood component types and destinations comparison of LIS data with clinical records demonstrated concordance. The difference between LIS timing data and patient clinical records reflects expected time to transport, check, and prepare transfusion but does not affect the validity of linkage for most research purposes. Linkage of clinical registries with LIS data can therefore provide robust information regarding individual patient transfusion. This enables analysis of joint data sets to determine the impact of transfusion on clinical outcomes. © 2010 American Association of Blood Banks.

  9. Synthetic biology: new engineering rules for an emerging discipline

    PubMed Central

    Andrianantoandro, Ernesto; Basu, Subhayu; Karig, David K; Weiss, Ron

    2006-01-01

    Synthetic biologists engineer complex artificial biological systems to investigate natural biological phenomena and for a variety of applications. We outline the basic features of synthetic biology as a new engineering discipline, covering examples from the latest literature and reflecting on the features that make it unique among all other existing engineering fields. We discuss methods for designing and constructing engineered cells with novel functions in a framework of an abstract hierarchy of biological devices, modules, cells, and multicellular systems. The classical engineering strategies of standardization, decoupling, and abstraction will have to be extended to take into account the inherent characteristics of biological devices and modules. To achieve predictability and reliability, strategies for engineering biology must include the notion of cellular context in the functional definition of devices and modules, use rational redesign and directed evolution for system optimization, and focus on accomplishing tasks using cell populations rather than individual cells. The discussion brings to light issues at the heart of designing complex living systems and provides a trajectory for future development. PMID:16738572

  10. Synthetic biology: new engineering rules for an emerging discipline.

    PubMed

    Andrianantoandro, Ernesto; Basu, Subhayu; Karig, David K; Weiss, Ron

    2006-01-01

    Synthetic biologists engineer complex artificial biological systems to investigate natural biological phenomena and for a variety of applications. We outline the basic features of synthetic biology as a new engineering discipline, covering examples from the latest literature and reflecting on the features that make it unique among all other existing engineering fields. We discuss methods for designing and constructing engineered cells with novel functions in a framework of an abstract hierarchy of biological devices, modules, cells, and multicellular systems. The classical engineering strategies of standardization, decoupling, and abstraction will have to be extended to take into account the inherent characteristics of biological devices and modules. To achieve predictability and reliability, strategies for engineering biology must include the notion of cellular context in the functional definition of devices and modules, use rational redesign and directed evolution for system optimization, and focus on accomplishing tasks using cell populations rather than individual cells. The discussion brings to light issues at the heart of designing complex living systems and provides a trajectory for future development.

  11. Bedrock mapping of buried valley networks using seismic reflection and airborne electromagnetic data

    NASA Astrophysics Data System (ADS)

    Oldenborger, G. A.; Logan, C. E.; Hinton, M. J.; Pugin, A. J.-M.; Sapia, V.; Sharpe, D. R.; Russell, H. A. J.

    2016-05-01

    In glaciated terrain, buried valleys often host aquifers that are significant groundwater resources. However, given the range of scales, spatial complexity and depth of burial, buried valleys often remain undetected or insufficiently mapped. Accurate and thorough mapping of bedrock topography is a crucial step in detecting and delineating buried valleys and understanding formative valley processes. We develop a bedrock mapping procedure supported by the combination of seismic reflection data and helicopter time-domain electromagnetic data with water well records for the Spiritwood buried valley aquifer system in Manitoba, Canada. The limited spatial density of water well bedrock observations precludes complete depiction of the buried valley bedrock topography and renders the water well records alone inadequate for accurate hydrogeological model building. Instead, we leverage the complementary strengths of seismic reflection and airborne electromagnetic data for accurate local detection of the sediment-bedrock interface and for spatially extensive coverage, respectively. Seismic reflection data are used to define buried valley morphology in cross-section beneath survey lines distributed over a regional area. A 3D model of electrical conductivity is derived from inversion of the airborne electromagnetic data and used to extrapolate buried valley morphology over the entire survey area. A spatially variable assignment of the electrical conductivity at the bedrock surface is applied to different features of the buried valley morphology identified in the seismic cross-sections. Electrical conductivity is then used to guide construction of buried valley shapes between seismic sections. The 3D locus of points defining each morphological valley feature is constructed using a path optimization routine that utilizes deviation from the assigned electrical conductivities as the cost function. Our resulting map represents a bedrock surface of unprecedented detail with more

  12. Accurate characterisation of hole size and location by projected fringe profilometry

    NASA Astrophysics Data System (ADS)

    Wu, Yuxiang; Dantanarayana, Harshana G.; Yue, Huimin; Huntley, Jonathan M.

    2018-06-01

    The ability to accurately estimate the location and geometry of holes is often required in the field of quality control and automated assembly. Projected fringe profilometry is a potentially attractive technique on account of being non-contacting, of lower cost, and orders of magnitude faster than the traditional coordinate measuring machine. However, we demonstrate in this paper that fringe projection is susceptible to significant (hundreds of µm) measurement artefacts in the neighbourhood of hole edges, which give rise to errors of a similar magnitude in the estimated hole geometry. A mechanism for the phenomenon is identified based on the finite size of the imaging system’s point spread function and the resulting bias produced near to sample discontinuities in geometry and reflectivity. A mathematical model is proposed, from which a post-processing compensation algorithm is developed to suppress such errors around the holes. The algorithm includes a robust and accurate sub-pixel edge detection method based on a Fourier descriptor of the hole contour. The proposed algorithm was found to reduce significantly the measurement artefacts near the hole edges. As a result, the errors in estimated hole radius were reduced by up to one order of magnitude, to a few tens of µm for hole radii in the range 2–15 mm, compared to those from the uncompensated measurements.

  13. Hyperspectral retrieval of surface reflectances: A new scheme

    NASA Astrophysics Data System (ADS)

    Thelen, Jean-Claude; Havemann, Stephan

    2013-05-01

    Here, we present a new prototype algorithm for the simultaneous retrieval of the atmospheric profiles (temperature, humidity, ozone and aerosol) and the surface reflectance from hyperspectral radiance measurements obtained from air/space borne, hyperspectral imagers. The new scheme, proposed here, consists of a fast radiative transfer code, based on empirical orthogonal functions (EOFs), in conjunction with a 1D-Var retrieval scheme. The inclusion of an 'exact' scattering code based on spherical harmonics, allows for an accurate treatment of Rayleigh scattering and scattering by aerosols, water droplets and ice-crystals, thus making it possible to also retrieve cloud and aerosol optical properties, although here we will concentrate on non-cloudy scenes.

  14. Transmission and reflection of terahertz plasmons in two-dimensional plasmonic devices

    DOE PAGES

    Sydoruk, Oleksiy; Choonee, Kaushal; Dyer, Gregory Conrad

    2015-03-10

    We found that plasmons in two-dimensional semiconductor devices will be reflected by discontinuities, notably, junctions between gated and non-gated electron channels. The transmitted and reflected plasmons can form spatially- and frequency-varying signals, and their understanding is important for the design of terahertz detectors, oscillators, and plasmonic crystals. Using mode decomposition, we studied terahertz plasmons incident on a junction between a gated and a nongated channel. The plasmon reflection and transmission coefficients were found numerically and analytically and studied between 0.3 and 1 THz for a range of electron densities. At higher frequencies, we could describe the plasmons by a simplifiedmore » model of channels in homogeneous dielectrics, for which the analytical approximations were accurate. At low frequencies, however, the full geometry and mode spectrum had to be taken into account. Moreover, the results agreed with simulations by the finite-element method. As a result, mode decomposition thus proved to be a powerful method for plasmonic devices, combining the rigor of complete solutions of Maxwell's equations with the convenience of analytical expressions.« less

  15. Exact simulation of polarized light reflectance by particle deposits

    NASA Astrophysics Data System (ADS)

    Ramezan Pour, B.; Mackowski, D. W.

    2015-12-01

    The use of polarimetric light reflection measurements as a means of identifying the physical and chemical characteristics of particulate materials obviously relies on an accurate model of predicting the effects of particle size, shape, concentration, and refractive index on polarized reflection. The research examines two methods for prediction of reflection from plane parallel layers of wavelength—sized particles. The first method is based on an exact superposition solution to Maxwell's time harmonic wave equations for a deposit of spherical particles that are exposed to a plane incident wave. We use a FORTRAN-90 implementation of this solution (the Multiple Sphere T Matrix (MSTM) code), coupled with parallel computational platforms, to directly simulate the reflection from particle layers. The second method examined is based upon the vector radiative transport equation (RTE). Mie theory is used in our RTE model to predict the extinction coefficient, albedo, and scattering phase function of the particles, and the solution of the RTE is obtained from adding—doubling method applied to a plane—parallel configuration. Our results show that the MSTM and RTE predictions of the Mueller matrix elements converge when particle volume fraction in the particle layer decreases below around five percent. At higher volume fractions the RTE can yield results that, depending on the particle size and refractive index, significantly depart from the exact predictions. The particle regimes which lead to dependent scattering effects, and the application of methods to correct the vector RTE for particle interaction, will be discussed.

  16. Analogical reflection as a source for the science of life: Kant and the possibility of the biological sciences.

    PubMed

    Nassar, Dalia

    2016-08-01

    In contrast to the previously widespread view that Kant's work was largely in dialogue with the physical sciences, recent scholarship has highlighted Kant's interest in and contributions to the life sciences. Scholars are now investigating the extent to which Kant appealed to and incorporated insights from the life sciences and considering the ways he may have contributed to a new conception of living beings. The scholarship remains, however, divided in its interest: historians of science are concerned with the content of Kant's claims, and the ways in which they may or may not have contributed to the emerging science of life, while historians of philosophy focus on the systematic justifications for Kant's claims, e.g., the methodological and theoretical underpinnings of Kant's statement that living beings are mechanically inexplicable. My aim in this paper is to bring together these two strands of scholarship into dialogue by showing how Kant's methodological concerns (specifically, his notion of reflective judgment) contributed to his conception of living beings and to the ontological concern with life as a distinctive object of study. I argue that although Kant's explicit statement was that biology could not be a science, his implicit and more fundamental claim was that the study of living beings necessitates a distinctive mode of thought, a mode that is essentially analogical. I consider the implications of this view, and argue that it is by developing a new methodology for grasping organized beings that Kant makes his most important contribution to the new science of life. Copyright © 2016. Published by Elsevier Ltd.

  17. A Reflection on the Fate of Chiral 1,2,4-Triazole Fungicides in Biological Systems

    EPA Science Inventory

    In biological systems, stereoisomers of chiral compounds can exhibit significantly different pharmacokinetics (absorption, distribution, metabolism, and elimination) and pharmacodynamics (physiological effects). Pharmacokinetic processes (i.e., what the body does to the chemical)...

  18. Diffusion Profiling via a Histogram Approach Distinguishes Low-grade from High-grade Meningiomas, Can Reflect the Respective Proliferative Potential and Progesterone Receptor Status.

    PubMed

    Gihr, Georg Alexander; Horvath-Rizea, Diana; Garnov, Nikita; Kohlhof-Meinecke, Patricia; Ganslandt, Oliver; Henkes, Hans; Meyer, Hans Jonas; Hoffmann, Karl-Titus; Surov, Alexey; Schob, Stefan

    2018-02-01

    Presurgical grading, estimation of growth kinetics, and other prognostic factors are becoming increasingly important for selecting the best therapeutic approach for meningioma patients. Diffusion-weighted imaging (DWI) provides microstructural information and reflects tumor biology. A novel DWI approach, histogram profiling of apparent diffusion coefficient (ADC) volumes, provides more distinct information than conventional DWI. Therefore, our study investigated whether ADC histogram profiling distinguishes low-grade from high-grade lesions and reflects Ki-67 expression and progesterone receptor status. Pretreatment ADC volumes of 37 meningioma patients (28 low-grade, 9 high-grade) were used for histogram profiling. WHO grade, Ki-67 expression, and progesterone receptor status were evaluated. Comparative and correlative statistics investigating the association between histogram profiling and neuropathology were performed. The entire ADC profile (p10, p25, p75, p90, mean, median) was significantly lower in high-grade versus low-grade meningiomas. The lower percentiles, mean, and modus showed significant correlations with Ki-67 expression. Skewness and entropy of the ADC volumes were significantly associated with progesterone receptor status and Ki-67 expression. ROC analysis revealed entropy to be the most accurate parameter distinguishing low-grade from high-grade meningiomas. ADC histogram profiling provides a distinct set of parameters, which help differentiate low-grade versus high-grade meningiomas. Also, histogram metrics correlate significantly with histological surrogates of the respective proliferative potential. More specifically, entropy revealed to be the most promising imaging biomarker for presurgical grading. Both, entropy and skewness were significantly associated with progesterone receptor status and Ki-67 expression and therefore should be investigated further as predictors for prognostically relevant tumor biological features. Since absolute ADC

  19. Reflective properties of randomly rough surfaces under large incidence angles.

    PubMed

    Qiu, J; Zhang, W J; Liu, L H; Hsu, P-f; Liu, L J

    2014-06-01

    The reflective properties of randomly rough surfaces at large incidence angles have been reported due to their potential applications in some of the radiative heat transfer research areas. The main purpose of this work is to investigate the formation mechanism of the specular reflection peak of rough surfaces at large incidence angles. The bidirectional reflectance distribution function (BRDF) of rough aluminum surfaces with different roughnesses at different incident angles is measured by a three-axis automated scatterometer. This study used a validated and accurate computational model, the rigorous coupled-wave analysis (RCWA) method, to compare and analyze the measurement BRDF results. It is found that the RCWA results show the same trend of specular peak as the measurement. This paper mainly focuses on the relative roughness at the range of 0.16<σ/λ<5.35. As the relative roughness decreases, the specular peak enhancement dramatically increases and the scattering region significantly reduces, especially under large incidence angles. The RCWA and the Rayleigh criterion results have been compared, showing that the relative error of the total integrated scatter increases as the roughness of the surface increases at large incidence angles. In addition, the zero-order diffractive power calculated by RCWA and the reflectance calculated by Fresnel equations are compared. The comparison shows that the relative error declines sharply when the incident angle is large and the roughness is small.

  20. Philosophy of biology: about the fossilization of disciplines and other embryonic thoughts.

    PubMed

    Van Speybroeck, Linda

    2007-01-01

    This paper focuses on a running dispute between Werner Callebaut's naturalistic view and Filip Kolen and Gertrudis Van de Vijver's transcendentalist view on the nature of philosophy of biology and the relation of this discipline to biological sciences. It is argued that, despite differences in opinion, both positions agree that philosophy of biology's ultimate goal is to 'move' biology or at least be 'meaningful' to it. In order to make this goal clear and effective, more is needed than a polarizing debate which hardly touches upon biology. Therefore, a redirection in discussion is suggested towards a reflection on the possibilities of incorporating philosophy in interdisciplinary research, and on finding concrete research questions which are of interest both to the philosopher and to the biologist.

  1. A protocol for EBT3 radiochromic film dosimetry using reflection scanning

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

    Papaconstadopoulos, Pavlos, E-mail: pavpapac@gmail.com; Hegyi, Gyorgy; Seuntjens, Jan

    2014-12-15

    Purpose: To evaluate the performance of the EBT3 radiochromic film dosimetry system using reflection measurements and to suggest a calibration protocol for precise and accurate reflection film dosimetry. Methods: A set of 14 Gafchromic EBT3 film pieces were irradiated to various doses ranging from 0 to 8 Gy and subsequently scanned using both the reflection and transmission mode. Scanning resolution varied from 50 to 508 dpi (0.5–0.05 mm/pixel). Both the red and green color channels of scanned images were used to relate the film response to the dose. A sensitivity, uncertainty, and accuracy analysis was performed for all scanning modesmore » and color channels. The total uncertainty, along with the fitting and experimental uncertainty components, was identified and analyzed. A microscope resolution target was used to evaluate possible resolution losses under reflection scanning. The calibration range was optimized for reflection scanning in the low (<2 Gy) and high (>2 Gy) dose regions based on the reported results. Results: Reflection scanning using the red channel exhibited the highest sensitivity among all modes, being up to 150% higher than transmission mode in the red channel for the lowest dose level. Furthermore, there was no apparent loss in resolution between the two modes. However, higher uncertainties and reduced accuracy were observed for the red channel under reflection mode, especially at dose levels higher than 2 Gy. These uncertainties were mainly attributed to saturation effects which were translated in poor fitting results. By restricting the calibration to the 0–2 Gy dose range, the situation is reversed and the red reflection mode was superior to the transmission mode. For higher doses, the green channel in reflection mode presented comparable results to the red transmission. Conclusions: A two-color reflection scanning protocol can be suggested for EBT3 radiochromic film dosimetry using the red channel for doses less than 2 Gy and the

  2. Deep learning for computational biology.

    PubMed

    Angermueller, Christof; Pärnamaa, Tanel; Parts, Leopold; Stegle, Oliver

    2016-07-29

    Technological advances in genomics and imaging have led to an explosion of molecular and cellular profiling data from large numbers of samples. This rapid increase in biological data dimension and acquisition rate is challenging conventional analysis strategies. Modern machine learning methods, such as deep learning, promise to leverage very large data sets for finding hidden structure within them, and for making accurate predictions. In this review, we discuss applications of this new breed of analysis approaches in regulatory genomics and cellular imaging. We provide background of what deep learning is, and the settings in which it can be successfully applied to derive biological insights. In addition to presenting specific applications and providing tips for practical use, we also highlight possible pitfalls and limitations to guide computational biologists when and how to make the most use of this new technology. © 2016 The Authors. Published under the terms of the CC BY 4.0 license.

  3. Multiple Replica Repulsion Technique for Efficient Conformational Sampling of Biological Systems

    PubMed Central

    Malevanets, Anatoly; Wodak, Shoshana J.

    2011-01-01

    Here, we propose a technique for sampling complex molecular systems with many degrees of freedom. The technique, termed “multiple replica repulsion” (MRR), does not suffer from poor scaling with the number of degrees of freedom associated with common replica exchange procedures and does not require sampling at high temperatures. The algorithm involves creation of multiple copies (replicas) of the system, which interact with one another through a repulsive potential that can be applied to the system as a whole or to portions of it. The proposed scheme prevents oversampling of the most populated states and provides accurate descriptions of conformational perturbations typically associated with sampling ground-state energy wells. The performance of MRR is illustrated for three systems of increasing complexity. A two-dimensional toy potential surface is used to probe the sampling efficiency as a function of key parameters of the procedure. MRR simulations of the Met-enkephalin pentapeptide, and the 76-residue protein ubiquitin, performed in presence of explicit water molecules and totaling 32 ns each, investigate the ability of MRR to characterize the conformational landscape of the peptide, and the protein native basin, respectively. Results obtained for the enkephalin peptide reflect more closely the extensive conformational flexibility of this peptide than previously reported simulations. Those obtained for ubiquitin show that conformational ensembles sampled by MRR largely encompass structural fluctuations relevant to biological recognition, which occur on the microsecond timescale, or are observed in crystal structures of ubiquitin complexes with other proteins. MRR thus emerges as a very promising simple and versatile technique for modeling the structural plasticity of complex biological systems. PMID:21843487

  4. Determination of optical coefficients of biological tissue from a single integrating-sphere

    NASA Astrophysics Data System (ADS)

    Zhang, Lianshun; Shi, Aijuan; Lu, Hongguang

    2012-01-01

    The detection of interactions between light and tissue can be used to characterize the optical properties of the tissue. The development is described of a method that determines optical coefficients of biological tissue from a single optical reflectance spectrum measured with an integrating-sphere. The experimental system incorporated a DH-2000 deuterium tungsten halogen light source, a USB4000-VIS-NIR miniature fiber optic spectrometer and an integrating-sphere. Fat emulsion and ink were used to mimic the scattering and absorbing properties of tissue in the tested sample. The measured optical reflectance spectrums with different scattering and absorbing properties were used to train a back-propagation neural network (BPNN). Then the neural network (BPNN) was used to determine the optical coefficients of biological tissue from a single optical reflectance spectrum measured with an integrating-sphere. Tests on tissue-simulation phantoms showed the relative errors of this technique to be 7% for the reduced scattering coefficient and 15% for the absorption coefficients. The optical properties of human skin were also measured in vivo.

  5. Dynamic Functional Connectivity States Reflecting Psychotic-like Experiences.

    PubMed

    Barber, Anita D; Lindquist, Martin A; DeRosse, Pamela; Karlsgodt, Katherine H

    2018-05-01

    Psychotic-like experiences (PLEs) are associated with lower social and occupational functioning, and lower executive function. Emerging evidence also suggests that PLEs reflect neural dysfunction resembling that of psychotic disorders. The present study examined dynamic connectivity related to a measure of PLEs derived from the Achenbach Adult Self-Report, in an otherwise-healthy sample of adults from the Human Connectome Project. A total of 76 PLE-endorsing and 153 control participants were included in the final sample. To characterize network dysfunction, dynamic connectivity states were examined across large-scale resting-state networks using dynamic conditional correlation and k-means clustering. Three dynamic states were identified. The PLE-endorsing group spent more time than the control group in state 1, a state reflecting hyperconnectivity within visual regions and hypoconnectivity within the default mode network, and less time in state 2, a state characterized by robust within-network connectivity for all networks and strong default mode network anticorrelations. Within the PLE-endorsing group, worse executive function was associated with more time spent in and more transitions into state 1 and less time spent in and fewer transitions into state 3. PLEs are associated with altered large-scale brain dynamics, which tip the system away from spending more time in states reflecting more "typical" connectivity patterns toward more time in states reflecting visual hyperconnectivity and default mode hypoconnectivity. Copyright © 2017 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

  6. Analysis of biological time-lapse microscopic experiment from the point of view of the information theory.

    PubMed

    Štys, Dalibor; Urban, Jan; Vaněk, Jan; Císař, Petr

    2011-06-01

    We report objective analysis of information in the microscopic image of the cell monolayer. The process of transfer of information about the cell by the microscope is analyzed in terms of the classical Shannon information transfer scheme. The information source is the biological object, the information transfer channel is the whole microscope including the camera chip. The destination is the model of biological system. The information contribution is analyzed as information carried by a point to overall information in the image. Subsequently we obtain information reflection of the biological object. This is transformed in the biological model which, in information terminology, is the destination. This, we propose, should be constructed as state transitions in individual cells modulated by information bonds between the cells. We show examples of detected cell states in multidimensional state space. This space is reflected as colour channel intensity phenomenological state space. We have also observed information bonds and show examples of them.

  7. Analysis of biological time-lapse microscopic experiment from the point of view of the information theory.

    PubMed

    Stys, Dalibor; Urban, Jan; Vanek, Jan; Císar, Petr

    2010-07-01

    We report objective analysis of information in the microscopic image of the cell monolayer. The process of transfer of information about the cell by the microscope is analyzed in terms of the classical Shannon information transfer scheme. The information source is the biological object, the information transfer channel is the whole microscope including the camera chip. The destination is the model of biological system. The information contribution is analyzed as information carried by a point to overall information in the image. Subsequently we obtain information reflection of the biological object. This is transformed in the biological model which, in information terminology, is the destination. This, we propose, should be constructed as state transitions in individual cells modulated by information bonds between the cells. We show examples of detected cell states in multidimensional state space reflected in space an colour channel intensity phenomenological state space. We have also observed information bonds and show examples of them. Copyright 2010 Elsevier Ltd. All rights reserved.

  8. X-ray reflectivity measurements of liquid/solid interfaces under high hydrostatic pressure conditions.

    PubMed

    Wirkert, Florian J; Paulus, Michael; Nase, Julia; Möller, Johannes; Kujawski, Simon; Sternemann, Christian; Tolan, Metin

    2014-01-01

    A high-pressure cell for in situ X-ray reflectivity measurements of liquid/solid interfaces at hydrostatic pressures up to 500 MPa (5 kbar), a pressure regime that is particularly important for the study of protein unfolding, is presented. The original set-up of this hydrostatic high-pressure cell is discussed and its unique properties are demonstrated by the investigation of pressure-induced adsorption of the protein lysozyme onto hydrophobic silicon wafers. The presented results emphasize the enormous potential of X-ray reflectivity studies under high hydrostatic pressure conditions for the in situ investigation of adsorption phenomena in biological systems.

  9. Detection and Analysis of Partial Reflections of HF Waves from the Lower Ionosphere

    NASA Astrophysics Data System (ADS)

    Erdman, A.; Moore, R. C.

    2016-12-01

    On the afternoon of August 27, 2011, the western half of the High Frequency Active Auroral Research Program's (HAARP's) HF transmitter repeatedly broadcast a low-power (1 kW/Tx), 4.5-MHz, X-mode polarized, 10 microsecond pulse. The HF beam was directed vertically, and the inter-pulse period was 20 milliseconds. HF observations were performed at Oasis (62° 23' 30" N, 145° 9' 03" W) using two crossed 90-foot folded dipoles. Observations clearly indicate the detection of a ground wave and multiple reflections from different sources at F-region altitudes, which is consistent with digisonde measurements at 4.5 MHz. Additional reflections were detected at a virtual altitude of 90-110 km, and we interpret these reflections as partial reflections from the rapid conductivity change at the base of the ionosphere. We compare these observations with the predictions of a new finite-difference time-domain (FDTD) plasma model. The model is a one-dimensional, second-order accurate, cold plasma FDTD model of the ionosphere extending from ground through the lower F-region. The model accounts for a spatially varying plasma frequency, cyclotron frequency, and electron-neutral collision frequency. We discuss the possibility to analyze partial reflections from the base of the ionosphere as a function of frequency to characterize the reflecting plasma.

  10. WISB: Warwick Integrative Synthetic Biology Centre

    PubMed Central

    McCarthy, John

    2016-01-01

    Synthetic biology promises to create high-impact solutions to challenges in the areas of biotechnology, human/animal health, the environment, energy, materials and food security. Equally, synthetic biologists create tools and strategies that have the potential to help us answer important fundamental questions in biology. Warwick Integrative Synthetic Biology (WISB) pursues both of these mutually complementary ‘build to apply’ and ‘build to understand’ approaches. This is reflected in our research structure, in which a core theme on predictive biosystems engineering develops underpinning understanding as well as next-generation experimental/theoretical tools, and these are then incorporated into three applied themes in which we engineer biosynthetic pathways, microbial communities and microbial effector systems in plants. WISB takes a comprehensive approach to training, education and outreach. For example, WISB is a partner in the EPSRC/BBSRC-funded U.K. Doctoral Training Centre in synthetic biology, we have developed a new undergraduate module in the subject, and we have established five WISB Research Career Development Fellowships to support young group leaders. Research in Ethical, Legal and Societal Aspects (ELSA) of synthetic biology is embedded in our centre activities. WISB has been highly proactive in building an international research and training network that includes partners in Barcelona, Boston, Copenhagen, Madrid, Marburg, São Paulo, Tartu and Valencia. PMID:27284024

  11. WISB: Warwick Integrative Synthetic Biology Centre.

    PubMed

    McCarthy, John

    2016-06-15

    Synthetic biology promises to create high-impact solutions to challenges in the areas of biotechnology, human/animal health, the environment, energy, materials and food security. Equally, synthetic biologists create tools and strategies that have the potential to help us answer important fundamental questions in biology. Warwick Integrative Synthetic Biology (WISB) pursues both of these mutually complementary 'build to apply' and 'build to understand' approaches. This is reflected in our research structure, in which a core theme on predictive biosystems engineering develops underpinning understanding as well as next-generation experimental/theoretical tools, and these are then incorporated into three applied themes in which we engineer biosynthetic pathways, microbial communities and microbial effector systems in plants. WISB takes a comprehensive approach to training, education and outreach. For example, WISB is a partner in the EPSRC/BBSRC-funded U.K. Doctoral Training Centre in synthetic biology, we have developed a new undergraduate module in the subject, and we have established five WISB Research Career Development Fellowships to support young group leaders. Research in Ethical, Legal and Societal Aspects (ELSA) of synthetic biology is embedded in our centre activities. WISB has been highly proactive in building an international research and training network that includes partners in Barcelona, Boston, Copenhagen, Madrid, Marburg, São Paulo, Tartu and Valencia. © 2016 The Author(s).

  12. The 'Biologically-Inspired Computing' Column

    NASA Technical Reports Server (NTRS)

    Hinchey, Mike

    2006-01-01

    The field of Biology changed dramatically in 1953, with the determination by Francis Crick and James Dewey Watson of the double helix structure of DNA. This discovery changed Biology for ever, allowing the sequencing of the human genome, and the emergence of a "new Biology" focused on DNA, genes, proteins, data, and search. Computational Biology and Bioinformatics heavily rely on computing to facilitate research into life and development. Simultaneously, an understanding of the biology of living organisms indicates a parallel with computing systems: molecules in living cells interact, grow, and transform according to the "program" dictated by DNA. Moreover, paradigms of Computing are emerging based on modelling and developing computer-based systems exploiting ideas that are observed in nature. This includes building into computer systems self-management and self-governance mechanisms that are inspired by the human body's autonomic nervous system, modelling evolutionary systems analogous to colonies of ants or other insects, and developing highly-efficient and highly-complex distributed systems from large numbers of (often quite simple) largely homogeneous components to reflect the behaviour of flocks of birds, swarms of bees, herds of animals, or schools of fish. This new field of "Biologically-Inspired Computing", often known in other incarnations by other names, such as: Autonomic Computing, Pervasive Computing, Organic Computing, Biomimetics, and Artificial Life, amongst others, is poised at the intersection of Computer Science, Engineering, Mathematics, and the Life Sciences. Successes have been reported in the fields of drug discovery, data communications, computer animation, control and command, exploration systems for space, undersea, and harsh environments, to name but a few, and augur much promise for future progress.

  13. Surface Reflectance of Mars Observed by CRISM-MRO: 1. Multi-angle Approach for Retrieval of Surface Reflectance from CRISM Observations (mars-reco)

    NASA Technical Reports Server (NTRS)

    Ceamanos, Xavier; Doute, S.; Fernando, J.; Pinet, P.; Lyapustin, A.

    2013-01-01

    This article addresses the correction for aerosol effects in near-simultaneous multiangle observations acquired by the Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) aboard the Mars Reconnaissance Orbiter. In the targeted mode, CRISM senses the surface of Mars using 11 viewing angles, which allow it to provide unique information on the scattering properties of surface materials. In order to retrieve these data, however, appropriate strategies must be used to compensate the signal sensed by CRISM for aerosol contribution. This correction is particularly challenging as the photometric curve of these suspended particles is often correlated with the also anisotropic photometric curve of materials at the surface. This article puts forward an innovative radiative transfer based method named Multi-angle Approach for Retrieval of Surface Reflectance from CRISM Observations (MARS-ReCO). The proposed method retrieves photometric curves of surface materials in reflectance units after removing aerosol contribution. MARS-ReCO represents a substantial improvement regarding previous techniques as it takes into consideration the anisotropy of the surface, thus providing more realistic surface products. Furthermore, MARS-ReCO is fast and provides error bars on the retrieved surface reflectance. The validity and accuracy of MARS-ReCO is explored in a sensitivity analysis based on realistic synthetic data. According to experiments, MARS-ReCO provides accurate results (up to 10 reflectance error) under favorable acquisition conditions. In the companion article, photometric properties of Martian materials are retrieved using MARS-ReCO and validated using in situ measurements acquired during the Mars Exploration Rovers mission.

  14. Sex-Specific Biology of the Human Malaria Parasite Revealed from the Proteomes of Mature Male and Female Gametocytes.

    PubMed

    Miao, Jun; Chen, Zhao; Wang, Zenglei; Shrestha, Sony; Li, Xiaolian; Li, Runze; Cui, Liwang

    2017-04-01

    The gametocytes of the malaria parasites are obligate for perpetuating the parasite's life cycle through mosquitoes, but the sex-specific biology of gametocytes is poorly understood. We generated a transgenic line in the human malaria parasite Plasmodium falciparum , which allowed us to accurately separate male and female gametocytes by flow cytometry. In-depth analysis of the proteomes by liquid chromatography-tandem mass spectrometry identified 1244 and 1387 proteins in mature male and female gametocytes, respectively. GFP-tagging of nine selected proteins confirmed their sex-partitions to be agreeable with the results from the proteomic analysis. The sex-specific proteomes showed significant differences that are consistent with the divergent functions of the two sexes. Although the male-specific proteome (119 proteins) is enriched in proteins associated with the flagella and genome replication, the female-specific proteome (262 proteins) is more abundant in proteins involved in metabolism, translation and organellar functions. Compared with the Plasmodium berghei sex-specific proteomes, this study revealed both extensive conservation and considerable divergence between these two species, which reflect the disparities between the two species in proteins involved in cytoskeleton, lipid metabolism and protein degradation. Comparison with three sex-specific proteomes allowed us to obtain high-confidence lists of 73 and 89 core male- and female-specific/biased proteins conserved in Plasmodium The identification of sex-specific/biased proteomes in Plasmodium lays a solid foundation for understanding the molecular mechanisms underlying the unique sex-specific biology in this early-branching eukaryote. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  15. Intra-Cavity Total Reflection For High Sensitivity Measurement Of Optical Properties

    DOEpatents

    Pipino, Andrew Charles Rule

    1999-11-16

    An optical cavity resonator device is provided for conducting sensitive murement of optical absorption by matter in any state with diffraction-limited spatial resolution through utilization of total internal reflection within a high-Q (high quality, low loss) optical cavity. Intracavity total reflection generates an evanescent wave that decays exponentially in space at a point external to the cavity, thereby providing a localized region where absorbing materials can be sensitively probed through alteration of the Q-factor of the otherwise isolated cavity. When a laser pulse is injected into the cavity and passes through the evanescent state, an amplitude loss resulting from absorption is incurred that reduces the lifetime of the pulse in the cavity. By monitoring the decay of the injected pulse, the absorption coefficient of manner within the evanescent wave region is accurately obtained from the decay time measurement.

  16. Intra-Cavity Total Reflection For High Sensitivity Measurement Of Optical Properties

    DOEpatents

    Pipino, Andrew C. R.; Hudgens, Jeffrey W.

    1999-08-24

    An optical cavity resonator device is provided for conducting sensitive murement of optical absorption by matter in any state with diffraction-limited spatial resolution through utilization of total internal reflection within a high-Q (high quality, low loss) optical cavity. Intracavity total reflection generates an evanescent wave that decays exponentially in space at a point external to the cavity, thereby providing a localized region where absorbing materials can be sensitively probed through alteration of the Q-factor of the otherwise isolated cavity. When a laser pulse is injected into the cavity and passes through the evanescent state, an amplitude loss resulting from absorption is incurred that reduces the lifetime of the pulse in the cavity. By monitoring the decay of the injected pulse, the absorption coefficient of manner within the evanescent wave region is accurately obtained from the decay time measurement.

  17. Hyperspectral imaging-based spatially-resolved technique for accurate measurement of the optical properties of horticultural products

    NASA Astrophysics Data System (ADS)

    Cen, Haiyan

    Hyperspectral imaging-based spatially-resolved technique is promising for determining the optical properties and quality attributes of horticultural and food products. However, considerable challenges still exist for accurate determination of spectral absorption and scattering properties from intact horticultural products. The objective of this research was, therefore, to develop and optimize hyperspectral imaging-based spatially-resolved technique for accurate measurement of the optical properties of horticultural products. Monte Carlo simulations and experiments for model samples of known optical properties were performed to optimize the inverse algorithm of a single-layer diffusion model and the optical designs, for extracting the absorption (micro a) and reduced scattering (micros') coefficients from spatially-resolved reflectance profiles. The logarithm and integral data transformation and the relative weighting methods were found to greatly improve the parameter estimation accuracy with the relative errors of 10.4%, 10.7%, and 11.4% for micro a, and 6.6%, 7.0%, and 7.1% for micros', respectively. More accurate measurements of optical properties were obtained when the light beam was of Gaussian type with the diameter of less than 1 mm, and the minimum and maximum source-detector distances were 1.5 mm and 10--20 transport mean free paths, respectively. An optical property measuring prototype was built, based on the optimization results, and evaluated for automatic measurement of absorption and reduced scattering coefficients for the wavelengths of 500--1,000 nm. The instrument was used to measure the optical properties, and assess quality/maturity, of 500 'Redstar' peaches and 1039 'Golden Delicious' (GD) and 1040 'Delicious' (RD) apples. A separate study was also conducted on confocal laser scanning and scanning electron microscopic image analysis and compression test of fruit tissue specimens to measure the structural and mechanical properties of 'Golden

  18. Accurate reliability analysis method for quantum-dot cellular automata circuits

    NASA Astrophysics Data System (ADS)

    Cui, Huanqing; Cai, Li; Wang, Sen; Liu, Xiaoqiang; Yang, Xiaokuo

    2015-10-01

    Probabilistic transfer matrix (PTM) is a widely used model in the reliability research of circuits. However, PTM model cannot reflect the impact of input signals on reliability, so it does not completely conform to the mechanism of the novel field-coupled nanoelectronic device which is called quantum-dot cellular automata (QCA). It is difficult to get accurate results when PTM model is used to analyze the reliability of QCA circuits. To solve this problem, we present the fault tree models of QCA fundamental devices according to different input signals. After that, the binary decision diagram (BDD) is used to quantitatively investigate the reliability of two QCA XOR gates depending on the presented models. By employing the fault tree models, the impact of input signals on reliability can be identified clearly and the crucial components of a circuit can be found out precisely based on the importance values (IVs) of components. So this method is contributive to the construction of reliable QCA circuits.

  19. Systems biology for molecular life sciences and its impact in biomedicine.

    PubMed

    Medina, Miguel Ángel

    2013-03-01

    Modern systems biology is already contributing to a radical transformation of molecular life sciences and biomedicine, and it is expected to have a real impact in the clinical setting in the next years. In this review, the emergence of systems biology is contextualized with a historic overview, and its present state is depicted. The present and expected future contribution of systems biology to the development of molecular medicine is underscored. Concerning the present situation, this review includes a reflection on the "inflation" of biological data and the urgent need for tools and procedures to make hidden information emerge. Descriptions of the impact of networks and models and the available resources and tools for applying them in systems biology approaches to molecular medicine are provided as well. The actual current impact of systems biology in molecular medicine is illustrated, reviewing two cases, namely, those of systems pharmacology and cancer systems biology. Finally, some of the expected contributions of systems biology to the immediate future of molecular medicine are commented.

  20. Impact of differences in the solar irradiance spectrum on surface reflectance retrieval with different radiative transfer codes

    NASA Technical Reports Server (NTRS)

    Staenz, K.; Williams, D. J.; Fedosejevs, G.; Teillet, P. M.

    1995-01-01

    Surface reflectance retrieval from imaging spectrometer data as acquired with the Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) has become important for quantitative analysis. In order to calculate surface reflectance from remotely measured radiance, radiative transfer codes such as 5S and MODTRAN2 play an increasing role for removal of scattering and absorption effects of the atmosphere. Accurate knowledge of the exo-atmospheric solar irradiance (E(sub 0)) spectrum at the spectral resolution of the sensor is important for this purpose. The present study investigates the impact of differences in the solar irradiance function, as implemented in a modified version of 5S (M5S), 6S, and MODTRAN2, and as proposed by Green and Gao, on the surface reflectance retrieved from AVIRIS data. Reflectance measured in situ is used as a basis of comparison.

  1. Influence of cost functions and optimization methods on solving the inverse problem in spatially resolved diffuse reflectance spectroscopy

    NASA Astrophysics Data System (ADS)

    Rakotomanga, Prisca; Soussen, Charles; Blondel, Walter C. P. M.

    2017-03-01

    Diffuse reflectance spectroscopy (DRS) has been acknowledged as a valuable optical biopsy tool for in vivo characterizing pathological modifications in epithelial tissues such as cancer. In spatially resolved DRS, accurate and robust estimation of the optical parameters (OP) of biological tissues is a major challenge due to the complexity of the physical models. Solving this inverse problem requires to consider 3 components: the forward model, the cost function, and the optimization algorithm. This paper presents a comparative numerical study of the performances in estimating OP depending on the choice made for each of the latter components. Mono- and bi-layer tissue models are considered. Monowavelength (scalar) absorption and scattering coefficients are estimated. As a forward model, diffusion approximation analytical solutions with and without noise are implemented. Several cost functions are evaluated possibly including normalized data terms. Two local optimization methods, Levenberg-Marquardt and TrustRegion-Reflective, are considered. Because they may be sensitive to the initial setting, a global optimization approach is proposed to improve the estimation accuracy. This algorithm is based on repeated calls to the above-mentioned local methods, with initial parameters randomly sampled. Two global optimization methods, Genetic Algorithm (GA) and Particle Swarm Optimization (PSO), are also implemented. Estimation performances are evaluated in terms of relative errors between the ground truth and the estimated values for each set of unknown OP. The combination between the number of variables to be estimated, the nature of the forward model, the cost function to be minimized and the optimization method are discussed.

  2. National Biological Service Research Supports Watershed Planning

    USGS Publications Warehouse

    Snyder, Craig D.

    1996-01-01

    The National Biological Service's Leetown Science Center is investigating how human impacts on watershed, riparian, and in-stream habitats affect fish communities. The research will provide the basis for a Ridge and Valley model that will allow resource managers to accurately predict and effectively mitigate human impacts on water quality. The study takes place in the Opequon Creek drainage basin of West Virginia. A fourth-order tributary of the Potomac, the basin falls within the Ridge and Valley. The study will identify biological components sensitive to land use patterns and the condition of the riparian zone; the effect of stream size, location, and other characteristics on fish communities; the extent to which remote sensing can reliable measure the riparian zone; and the relationship between the rate of landscape change and the structure of fish communities.

  3. Industrial and Biological Analogies Used Creatively by Business Professionals

    ERIC Educational Resources Information Center

    Kennedy, Emily B.; Miller, Derek J.; Niewiarowski, Peter H.

    2018-01-01

    The objective of this study was to test the effect of far-field industrial (i.e., man-made) versus biological analogies on creativity of business professionals from two organizations engaged in the idea generation phase of new product development. Psychological effects, as reflected in language use, were measured via computerized text analysis of…

  4. High reflectance-low stress Mo-Si multilayer reflective coatings

    DOEpatents

    Montcalm, Claude; Mirkarimi, Paul B.

    2000-01-01

    A high reflectance-low stress Mo-Si multilayer reflective coating particularly useful for the extreme ultraviolet (EUV) wavelength region. While the multilayer reflective coating has particular application for EUV lithography, it has numerous other applications where high reflectance and low stress multilayer coatings are utilized. Multilayer coatings having high near-normal incidence reflectance (R.gtoreq.65%) and low residual stress (.ltoreq.100 MPa) have been produced using thermal and non-thermal approaches. The thermal approach involves heating the multilayer coating to a given temperature for a given time after deposition in order to induce structural changes in the multilayer coating that will have an overall "relaxation" effect without reducing the reflectance significantly.

  5. Accurate Encoding and Decoding by Single Cells: Amplitude Versus Frequency Modulation

    PubMed Central

    Micali, Gabriele; Aquino, Gerardo; Richards, David M.; Endres, Robert G.

    2015-01-01

    Cells sense external concentrations and, via biochemical signaling, respond by regulating the expression of target proteins. Both in signaling networks and gene regulation there are two main mechanisms by which the concentration can be encoded internally: amplitude modulation (AM), where the absolute concentration of an internal signaling molecule encodes the stimulus, and frequency modulation (FM), where the period between successive bursts represents the stimulus. Although both mechanisms have been observed in biological systems, the question of when it is beneficial for cells to use either AM or FM is largely unanswered. Here, we first consider a simple model for a single receptor (or ion channel), which can either signal continuously whenever a ligand is bound, or produce a burst in signaling molecule upon receptor binding. We find that bursty signaling is more accurate than continuous signaling only for sufficiently fast dynamics. This suggests that modulation based on bursts may be more common in signaling networks than in gene regulation. We then extend our model to multiple receptors, where continuous and bursty signaling are equivalent to AM and FM respectively, finding that AM is always more accurate. This implies that the reason some cells use FM is related to factors other than accuracy, such as the ability to coordinate expression of multiple genes or to implement threshold crossing mechanisms. PMID:26030820

  6. Energy stable and high-order-accurate finite difference methods on staggered grids

    NASA Astrophysics Data System (ADS)

    O'Reilly, Ossian; Lundquist, Tomas; Dunham, Eric M.; Nordström, Jan

    2017-10-01

    For wave propagation over distances of many wavelengths, high-order finite difference methods on staggered grids are widely used due to their excellent dispersion properties. However, the enforcement of boundary conditions in a stable manner and treatment of interface problems with discontinuous coefficients usually pose many challenges. In this work, we construct a provably stable and high-order-accurate finite difference method on staggered grids that can be applied to a broad class of boundary and interface problems. The staggered grid difference operators are in summation-by-parts form and when combined with a weak enforcement of the boundary conditions, lead to an energy stable method on multiblock grids. The general applicability of the method is demonstrated by simulating an explosive acoustic source, generating waves reflecting against a free surface and material discontinuity.

  7. Narrowband Angular Reflectance Properties of the Alkali Flats at White Sands, New Mexico

    NASA Technical Reports Server (NTRS)

    Whitlock, Charles H.; LeCroy, Stuart R.; Wheeler, Robert J.

    1994-01-01

    Results from helicopter measurements of the angular properties of surface reflectance for the alkali flats regions of the White Sands Missile Range are presented for the wavelength interval of 0.4 to 0.85 microns. This work was performed to allow accurate radiative transfer calculations over the region. Detailed tables and interpolation equations are given that permit other investigators to perform satellite calibrations over the alkali flats site. The effects of wavelength and soil moisture on narrowband angular reflectance are also investigated. Although there is a spectral variation in surface albedo, there is little spectral effect in Anisotropic Factor except in the forward scattering peak at solar zenith angles greater than 60 deg. The magnitude of the forward-scattering peak is also sensitive to soil moisture, with wet conditions causing a larger peak. The significance of this result is that angular reflectance properties at the center of the alkali flats usually will be different than those at the flats edge because moisture differences typically exist.

  8. Towards accurate modeling of noncovalent interactions for protein rigidity analysis.

    PubMed

    Fox, Naomi; Streinu, Ileana

    2013-01-01

    Protein rigidity analysis is an efficient computational method for extracting flexibility information from static, X-ray crystallography protein data. Atoms and bonds are modeled as a mechanical structure and analyzed with a fast graph-based algorithm, producing a decomposition of the flexible molecule into interconnected rigid clusters. The result depends critically on noncovalent atomic interactions, primarily on how hydrogen bonds and hydrophobic interactions are computed and modeled. Ongoing research points to the stringent need for benchmarking rigidity analysis software systems, towards the goal of increasing their accuracy and validating their results, either against each other and against biologically relevant (functional) parameters. We propose two new methods for modeling hydrogen bonds and hydrophobic interactions that more accurately reflect a mechanical model, without being computationally more intensive. We evaluate them using a novel scoring method, based on the B-cubed score from the information retrieval literature, which measures how well two cluster decompositions match. To evaluate the modeling accuracy of KINARI, our pebble-game rigidity analysis system, we use a benchmark data set of 20 proteins, each with multiple distinct conformations deposited in the Protein Data Bank. Cluster decompositions for them were previously determined with the RigidFinder method from Gerstein's lab and validated against experimental data. When KINARI's default tuning parameters are used, an improvement of the B-cubed score over a crude baseline is observed in 30% of this data. With our new modeling options, improvements were observed in over 70% of the proteins in this data set. We investigate the sensitivity of the cluster decomposition score with case studies on pyruvate phosphate dikinase and calmodulin. To substantially improve the accuracy of protein rigidity analysis systems, thorough benchmarking must be performed on all current systems and future

  9. Towards accurate modeling of noncovalent interactions for protein rigidity analysis

    PubMed Central

    2013-01-01

    Background Protein rigidity analysis is an efficient computational method for extracting flexibility information from static, X-ray crystallography protein data. Atoms and bonds are modeled as a mechanical structure and analyzed with a fast graph-based algorithm, producing a decomposition of the flexible molecule into interconnected rigid clusters. The result depends critically on noncovalent atomic interactions, primarily on how hydrogen bonds and hydrophobic interactions are computed and modeled. Ongoing research points to the stringent need for benchmarking rigidity analysis software systems, towards the goal of increasing their accuracy and validating their results, either against each other and against biologically relevant (functional) parameters. We propose two new methods for modeling hydrogen bonds and hydrophobic interactions that more accurately reflect a mechanical model, without being computationally more intensive. We evaluate them using a novel scoring method, based on the B-cubed score from the information retrieval literature, which measures how well two cluster decompositions match. Results To evaluate the modeling accuracy of KINARI, our pebble-game rigidity analysis system, we use a benchmark data set of 20 proteins, each with multiple distinct conformations deposited in the Protein Data Bank. Cluster decompositions for them were previously determined with the RigidFinder method from Gerstein's lab and validated against experimental data. When KINARI's default tuning parameters are used, an improvement of the B-cubed score over a crude baseline is observed in 30% of this data. With our new modeling options, improvements were observed in over 70% of the proteins in this data set. We investigate the sensitivity of the cluster decomposition score with case studies on pyruvate phosphate dikinase and calmodulin. Conclusion To substantially improve the accuracy of protein rigidity analysis systems, thorough benchmarking must be performed on all

  10. Human cell structure-driven model construction for predicting protein subcellular location from biological images.

    PubMed

    Shao, Wei; Liu, Mingxia; Zhang, Daoqiang

    2016-01-01

    The systematic study of subcellular location pattern is very important for fully characterizing the human proteome. Nowadays, with the great advances in automated microscopic imaging, accurate bioimage-based classification methods to predict protein subcellular locations are highly desired. All existing models were constructed on the independent parallel hypothesis, where the cellular component classes are positioned independently in a multi-class classification engine. The important structural information of cellular compartments is missed. To deal with this problem for developing more accurate models, we proposed a novel cell structure-driven classifier construction approach (SC-PSorter) by employing the prior biological structural information in the learning model. Specifically, the structural relationship among the cellular components is reflected by a new codeword matrix under the error correcting output coding framework. Then, we construct multiple SC-PSorter-based classifiers corresponding to the columns of the error correcting output coding codeword matrix using a multi-kernel support vector machine classification approach. Finally, we perform the classifier ensemble by combining those multiple SC-PSorter-based classifiers via majority voting. We evaluate our method on a collection of 1636 immunohistochemistry images from the Human Protein Atlas database. The experimental results show that our method achieves an overall accuracy of 89.0%, which is 6.4% higher than the state-of-the-art method. The dataset and code can be downloaded from https://github.com/shaoweinuaa/. dqzhang@nuaa.edu.cn 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.

  11. Obtaining Accurate Probabilities Using Classifier Calibration

    ERIC Educational Resources Information Center

    Pakdaman Naeini, Mahdi

    2016-01-01

    Learning probabilistic classification and prediction models that generate accurate probabilities is essential in many prediction and decision-making tasks in machine learning and data mining. One way to achieve this goal is to post-process the output of classification models to obtain more accurate probabilities. These post-processing methods are…

  12. Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3.

    PubMed

    Moodie, Stuart; Le Novère, Nicolas; Demir, Emek; Mi, Huaiyu; Villéger, Alice

    2015-09-04

    The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Process Description language represents biological entities and processes between these entities within a network. SBGN PD focuses on the mechanistic description and temporal dependencies of biological interactions and transformations. The nodes (elements) are split into entity nodes describing, e.g., metabolites, proteins, genes and complexes, and process nodes describing, e.g., reactions and associations. The edges (connections) provide descriptions of relationships (or influences) between the nodes, such as consumption, production, stimulation and inhibition. Among all three languages of SBGN, PD is the closest to metabolic and regulatory pathways in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

  13. Reflection Coefficients.

    ERIC Educational Resources Information Center

    Greenslade, Thomas B., Jr.

    1994-01-01

    Discusses and provides an example of reflectivity approximation to determine whether reflection will occur. Provides a method to show thin-film interference on a projection screen. Also applies the reflectivity concepts to electromagnetic wave systems. (MVL)

  14. Measuring and Modeling the Effect of Surface Moisture on the Spectral Reflectance of Coastal Beach Sand

    PubMed Central

    Nolet, Corjan; Poortinga, Ate; Roosjen, Peter; Bartholomeus, Harm; Ruessink, Gerben

    2014-01-01

    Surface moisture is an important supply limiting factor for aeolian sand transport, which is the primary driver of coastal dune development. As such, it is critical to account for the control of surface moisture on available sand for dune building. Optical remote sensing has the potential to measure surface moisture at a high spatio-temporal resolution. It is based on the principle that wet sand appears darker than dry sand: it is less reflective. The goals of this study are (1) to measure and model reflectance under controlled laboratory conditions as function of wavelength () and surface moisture () over the optical domain of 350–2500 nm, and (2) to explore the implications of our laboratory findings for accurately mapping the distribution of surface moisture under natural conditions. A laboratory spectroscopy experiment was conducted to measure spectral reflectance (1 nm interval) under different surface moisture conditions using beach sand. A non-linear increase of reflectance upon drying was observed over the full range of wavelengths. Two models were developed and tested. The first model is grounded in optics and describes the proportional contribution of scattering and absorption of light by pore water in an unsaturated sand matrix. The second model is grounded in soil physics and links the hydraulic behaviour of pore water in an unsaturated sand matrix to its optical properties. The optical model performed well for volumetric moisture content 24% ( 0.97), but underestimated reflectance for between 24–30% ( 0.92), most notable around the 1940 nm water absorption peak. The soil-physical model performed very well ( 0.99) but is limited to 4% 24%. Results from a field experiment show that a short-wave infrared terrestrial laser scanner ( = 1550 nm) can accurately relate surface moisture to reflectance (standard error 2.6%), demonstrating its potential to derive spatially extensive surface moisture maps of a natural coastal beach. PMID:25383709

  15. RapGene: a fast and accurate strategy for synthetic gene assembly in Escherichia coli

    PubMed Central

    Zampini, Massimiliano; Stevens, Pauline Rees; Pachebat, Justin A.; Kingston-Smith, Alison; Mur, Luis A. J.; Hayes, Finbarr

    2015-01-01

    The ability to assemble DNA sequences de novo through efficient and powerful DNA fabrication methods is one of the foundational technologies of synthetic biology. Gene synthesis, in particular, has been considered the main driver for the emergence of this new scientific discipline. Here we describe RapGene, a rapid gene assembly technique which was successfully tested for the synthesis and cloning of both prokaryotic and eukaryotic genes through a ligation independent approach. The method developed in this study is a complete bacterial gene synthesis platform for the quick, accurate and cost effective fabrication and cloning of gene-length sequences that employ the widely used host Escherichia coli. PMID:26062748

  16. A Parallel Distributed Processing Approach to Behavior and Biology in Schizophrenia

    DTIC Science & Technology

    1989-10-01

    delusions) and the other that reflects dopamine underactivity (negative symptoms - e.g., avolition, amotivation and withdrawal). Several authors have... amotivation . While both may be related to frontal lobe Behavior and Biology in Schizophrenia Cohen and Servan-Schreiber 32 deficits, the models in their

  17. Manipulation of biological samples using micro and nano techniques.

    PubMed

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

    2009-01-01

    The constant interest in handling, integrating and understanding biological systems of interest for the biomedical field, the pharmaceutical industry and the biomaterial researchers demand the use of techniques that allow the manipulation of biological samples causing minimal or no damage to their natural structure. Thanks to the advances in micro- and nanofabrication during the last decades several manipulation techniques offer us the possibility to image, characterize and manipulate biological material in a controlled way. Using these techniques the integration of biomaterials with remarkable properties with physical transducers has been possible, giving rise to new and highly sensitive biosensing devices. This article reviews the different techniques available to manipulate and integrate biological materials in a controlled manner either by sliding them along a surface (2-D manipulation), by grapping them and moving them to a new position (3-D manipulation), or by manipulating and relocating them applying external forces. The advantages and drawbacks are mentioned together with examples that reflect the state of the art of manipulation techniques for biological samples (171 references).

  18. Quantitative computational models of molecular self-assembly in systems biology

    PubMed Central

    Thomas, Marcus; Schwartz, Russell

    2017-01-01

    Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally. PMID:28535149

  19. Quantitative computational models of molecular self-assembly in systems biology.

    PubMed

    Thomas, Marcus; Schwartz, Russell

    2017-05-23

    Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally.

  20. Biological aspects of chondrosarcoma: Leaps and hurdles.

    PubMed

    Mery, Benoîte; Espenel, Sophie; Guy, Jean-Baptiste; Rancoule, Chloé; Vallard, Alexis; Aloy, Marie-Thérèse; Rodriguez-Lafrasse, Claire; Magné, Nicolas

    2018-06-01

    Chondrosarcomas are characterized by their chemo- and radioresistance leading to a therapeutic surgical approach which remains the only available treatment with a 10-year survival between 30% and 80% depending on the grade. Non-surgical treatments are under investigation and rely on an accurate biological understanding of drug resistance mechanisms. Novel targeted therapy which represents a new relevant therapeutic approach will open new treatment options by targeting several pathways responsible for processes of proliferation and invasion. Survival pathways such as PI3K, AKT, mTOR and VEGF have been shown to be involved in proliferation of chondrosarcoma cells and antiapoptotic proteins may also play a relevant role. Other proteins such as p53 or COX2 have been identified as potential new targets. This review provides an insight into the biological substantial treatment challenges of CHS and focuses on improving our understanding of CH biology through an overview of major signaling pathways that could represent targets for new therapeutic approaches. Copyright © 2018 Elsevier B.V. All rights reserved.

  1. General probability-matched relations between radar reflectivity and rain rate

    NASA Technical Reports Server (NTRS)

    Rosenfeld, Daniel; Wolff, David B.; Atlas, David

    1993-01-01

    An improved method for transforming radar-observed reflectivities Ze into rain rate R is presented. The method is based on a formulation of a Ze-R function constrained such that (1) the radar-retrieved pdf of R and all of its moments are identical to those determined from the gauges over a sufficiently large domain, and (2) the fraction of the time that it is raining above a low but still has an accurately measurable rain intensity is identical for both the radar and for simultaneous measurements of collocated gauges on average. Data measured by a 1.65-deg beamwidth C-band radar and 22 gauges located in the vicinity of Darwin, Australia, are used. The resultant Ze-R functions show a strong range dependence, especially for the rain regimes characterized by strong reflectivity gradients and substantial attenuation. The application of these novel Ze-R functions to the radar data produces excellent matches to the gauge measurements without any systematic bias.

  2. Tangible Models and Haptic Representations Aid Learning of Molecular Biology Concepts

    ERIC Educational Resources Information Center

    Johannes, Kristen; Powers, Jacklyn; Couper, Lisa; Silberglitt, Matt; Davenport, Jodi

    2016-01-01

    Can novel 3D models help students develop a deeper understanding of core concepts in molecular biology? We adapted 3D molecular models, developed by scientists, for use in high school science classrooms. The models accurately represent the structural and functional properties of complex DNA and Virus molecules, and provide visual and haptic…

  3. Geometric optimisation of an accurate cosine correcting optic fibre coupler for solar spectral measurement.

    PubMed

    Cahuantzi, Roberto; Buckley, Alastair

    2017-09-01

    Making accurate and reliable measurements of solar irradiance is important for understanding performance in the photovoltaic energy sector. In this paper, we present design details and performance of a number of fibre optic couplers for use in irradiance measurement systems employing remote light sensors applicable for either spectrally resolved or broadband measurement. The angular and spectral characteristics of different coupler designs are characterised and compared with existing state-of-the-art commercial technology. The new coupler designs are fabricated from polytetrafluorethylene (PTFE) rods and operate through forward scattering of incident sunlight on the front surfaces of the structure into an optic fibre located in a cavity to the rear of the structure. The PTFE couplers exhibit up to 4.8% variation in scattered transmission intensity between 425 nm and 700 nm and show minimal specular reflection, making the designs accurate and reliable over the visible region. Through careful geometric optimization near perfect cosine dependence on the angular response of the coupler can be achieved. The PTFE designs represent a significant improvement over the state of the art with less than 0.01% error compared with ideal cosine response for angles of incidence up to 50°.

  4. Sensitivity analysis of dynamic biological systems with time-delays.

    PubMed

    Wu, Wu Hsiung; Wang, Feng Sheng; Chang, Maw Shang

    2010-10-15

    Mathematical modeling has been applied to the study and analysis of complex biological systems for a long time. Some processes in biological systems, such as the gene expression and feedback control in signal transduction networks, involve a time delay. These systems are represented as delay differential equation (DDE) models. Numerical sensitivity analysis of a DDE model by the direct method requires the solutions of model and sensitivity equations with time-delays. The major effort is the computation of Jacobian matrix when computing the solution of sensitivity equations. The computation of partial derivatives of complex equations either by the analytic method or by symbolic manipulation is time consuming, inconvenient, and prone to introduce human errors. To address this problem, an automatic approach to obtain the derivatives of complex functions efficiently and accurately is necessary. We have proposed an efficient algorithm with an adaptive step size control to compute the solution and dynamic sensitivities of biological systems described by ordinal differential equations (ODEs). The adaptive direct-decoupled algorithm is extended to solve the solution and dynamic sensitivities of time-delay systems describing by DDEs. To save the human effort and avoid the human errors in the computation of partial derivatives, an automatic differentiation technique is embedded in the extended algorithm to evaluate the Jacobian matrix. The extended algorithm is implemented and applied to two realistic models with time-delays: the cardiovascular control system and the TNF-α signal transduction network. The results show that the extended algorithm is a good tool for dynamic sensitivity analysis on DDE models with less user intervention. By comparing with direct-coupled methods in theory, the extended algorithm is efficient, accurate, and easy to use for end users without programming background to do dynamic sensitivity analysis on complex biological systems with time-delays.

  5. Effect of mineralogical, geochemical and biological properties on soils reflectance to assess temporal and spatial dynamics of BSCs in Sahelian ecosystems

    NASA Astrophysics Data System (ADS)

    Bourguignon, A.; Cerdan, O.; Desprats, J. F.; Marin, B.; Malam Issa, O.; Valentin, C.; Rajot, J. L.

    2012-04-01

    Land degradation and desertification are among the major environmental problems, resulting in reduced productivity and development of bare surfaces in arid and semi-arid areas of the world. One important factor that acts to increase soil stability and nutrient content, and thus to prevent water and wind erosion and enhance soil productivity of arid environment, is the presence of biological soil crusts (BSCs). They are the dominant ground cover and a key component of arid environments built up mainly by cyanobacteria. They enhance degraded soil quality by providing a stable and water-retaining substratum and increasing fertility by N and C fixations. The BioCrust project, funded by ANR (VMCS 2008), focuses on BSCs in the Sahelian zone of West Africa (Niger), a highly vulnerable zone facing soil degradation due to the harsh climatic conditions, with variable rainfall, and high anthropic pressure on land use. Unlike arid areas of developed countries (USA, Australia and Israel) or China where BSCs have been extensively studied, studies from Sahelian zone (Africa) are limited (neither the inventory of their different form nor the estimation of their spatial extension has been carried out). The form, structure and composition of BSCs vary depending on characteristics related to soils and biological composition. This study focuses on the soils characterisation using ground-based spectroradiometry. An extensive database was built included spectral measurements on BSCs, bare soils and vegetation that occur in the same area, visual criteria, in situ and laboratory measurements on the physical, chemical and biological characteristics of BSCs and their substratum. The work is carried out on geo-statistical processing of data acquired in sites along a north-south climatic gradient and three types of representative land uses. The investigated areas are highly vulnerable zone facing soil degradation due to the harsh climatic conditions, with variable rainfall, and high anthropic

  6. Improved canopy reflectance modeling and scene inference through improved understanding of scene pattern

    NASA Technical Reports Server (NTRS)

    Franklin, Janet; Simonett, David

    1988-01-01

    The Li-Strahler reflectance model, driven by LANDSAT Thematic Mapper (TM) data, provided regional estimates of tree size and density within 20 percent of sampled values in two bioclimatic zones in West Africa. This model exploits tree geometry in an inversion technique to predict average tree size and density from reflectance data using a few simple parameters measured in the field (spatial pattern, shape, and size distribution of trees) and in the imagery (spectral signatures of scene components). Trees are treated as simply shaped objects, and multispectral reflectance of a pixel is assumed to be related only to the proportions of tree crown, shadow, and understory in the pixel. These, in turn, are a direct function of the number and size of trees, the solar illumination angle, and the spectral signatures of crown, shadow and understory. Given the variance in reflectance from pixel to pixel within a homogeneous area of woodland, caused by the variation in the number and size of trees, the model can be inverted to give estimates of average tree size and density. Because the inversion is sensitive to correct determination of component signatures, predictions are not accurate for small areas.

  7. TILDA-V: A full-differential code for proton tracking in biological matter

    DOE PAGES

    Quinto, M. A.; Monti, J. M.; Week, Philippe F.; ...

    2015-09-07

    Understanding the radiation-induced effects at the cellular level is of prime importance for predicting the fate of irradiated biological organisms. Thus, whether it is in radiobiology to identify the DNA critical lesions or in medicine to adapt the radio-therapeutic protocols, an accurate knowledge of the numerous interactions induced by charged particles in living matter is required. Monte-Carlo track-structure simulations represent the most suitable and powerful tools, in particular for modelling the full slowing-down of the ionizing particles in biological matter. Furthermore more of the existing codes are based on semi-empirical cross sections as well as the use of water asmore » surrogate of the biological matter.« less

  8. 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

  9. Accurate Vehicle Location System Using RFID, an Internet of Things Approach.

    PubMed

    Prinsloo, Jaco; Malekian, Reza

    2016-06-04

    Modern infrastructure, such as dense urban areas and underground tunnels, can effectively block all GPS signals, which implies that effective position triangulation will not be achieved. The main problem that is addressed in this project is the design and implementation of an accurate vehicle location system using radio-frequency identification (RFID) technology in combination with GPS and the Global system for Mobile communication (GSM) technology, in order to provide a solution to the limitation discussed above. In essence, autonomous vehicle tracking will be facilitated with the use of RFID technology where GPS signals are non-existent. The design of the system and the results are reflected in this paper. An extensive literature study was done on the field known as the Internet of Things, as well as various topics that covered the integration of independent technology in order to address a specific challenge. The proposed system is then designed and implemented. An RFID transponder was successfully designed and a read range of approximately 31 cm was obtained in the low frequency communication range (125 kHz to 134 kHz). The proposed system was designed, implemented, and field tested and it was found that a vehicle could be accurately located and tracked. It is also found that the antenna size of both the RFID reader unit and RFID transponder plays a critical role in the maximum communication range that can be achieved.

  10. Accurate Vehicle Location System Using RFID, an Internet of Things Approach

    PubMed Central

    Prinsloo, Jaco; Malekian, Reza

    2016-01-01

    Modern infrastructure, such as dense urban areas and underground tunnels, can effectively block all GPS signals, which implies that effective position triangulation will not be achieved. The main problem that is addressed in this project is the design and implementation of an accurate vehicle location system using radio-frequency identification (RFID) technology in combination with GPS and the Global system for Mobile communication (GSM) technology, in order to provide a solution to the limitation discussed above. In essence, autonomous vehicle tracking will be facilitated with the use of RFID technology where GPS signals are non-existent. The design of the system and the results are reflected in this paper. An extensive literature study was done on the field known as the Internet of Things, as well as various topics that covered the integration of independent technology in order to address a specific challenge. The proposed system is then designed and implemented. An RFID transponder was successfully designed and a read range of approximately 31 cm was obtained in the low frequency communication range (125 kHz to 134 kHz). The proposed system was designed, implemented, and field tested and it was found that a vehicle could be accurately located and tracked. It is also found that the antenna size of both the RFID reader unit and RFID transponder plays a critical role in the maximum communication range that can be achieved. PMID:27271638

  11. A customized vision system for tracking humans wearing reflective safety clothing from industrial vehicles and machinery.

    PubMed

    Mosberger, Rafael; Andreasson, Henrik; Lilienthal, Achim J

    2014-09-26

    This article presents a novel approach for vision-based detection and tracking of humans wearing high-visibility clothing with retro-reflective markers. Addressing industrial applications where heavy vehicles operate in the vicinity of humans, we deploy a customized stereo camera setup with active illumination that allows for efficient detection of the reflective patterns created by the worker's safety garments. After segmenting reflective objects from the image background, the interest regions are described with local image feature descriptors and classified in order to discriminate safety garments from other reflective objects in the scene. In a final step, the trajectories of the detected humans are estimated in 3D space relative to the camera. We evaluate our tracking system in two industrial real-world work environments on several challenging video sequences. The experimental results indicate accurate tracking performance and good robustness towards partial occlusions, body pose variation, and a wide range of different illumination conditions.

  12. A Customized Vision System for Tracking Humans Wearing Reflective Safety Clothing from Industrial Vehicles and Machinery

    PubMed Central

    Mosberger, Rafael; Andreasson, Henrik; Lilienthal, Achim J.

    2014-01-01

    This article presents a novel approach for vision-based detection and tracking of humans wearing high-visibility clothing with retro-reflective markers. Addressing industrial applications where heavy vehicles operate in the vicinity of humans, we deploy a customized stereo camera setup with active illumination that allows for efficient detection of the reflective patterns created by the worker's safety garments. After segmenting reflective objects from the image background, the interest regions are described with local image feature descriptors and classified in order to discriminate safety garments from other reflective objects in the scene. In a final step, the trajectories of the detected humans are estimated in 3D space relative to the camera. We evaluate our tracking system in two industrial real-world work environments on several challenging video sequences. The experimental results indicate accurate tracking performance and good robustness towards partial occlusions, body pose variation, and a wide range of different illumination conditions. PMID:25264956

  13. CRISPR editing in biological and biomedical investigation.

    PubMed

    Huang, Jiaojiao; Wang, Yanfang; Zhao, Jianguo

    2018-05-01

    Recently, clustered regularly interspaced short palindromic repeats (CRISPR) based genomic editing technologies have armed researchers with powerful new tools to biological and biomedical investigations. To further improve and expand its functionality, natural, and engineered CRISPR associated nine proteins (Cas9s) have been investigated, various CRISPR delivery strategies have been tested and optimized, and multiple schemes have been developed to ensure precise mammalian genome editing. Benefiting from those in-depth understanding and further development of CRISPR, versatile CRISPR-based platforms for genome editing have been rapidly developed to advance investigations in biology and biomedicine. In biological research area, CRISPR has been widely adopted in both fundamental and applied research fields, such as accurate base editing, transcriptional regulation, and genome-wide screening. In biomedical research area, CRISPR has also shown its extensive applicability in the establishment of animal models for genetic disorders especially those large animals and non-human primates models, and gene therapy to combat virus infectious diseases, to correct monogenic disorders in vivo or in pluripotent cells. In this prospect article, after highlighting recent developments of CRISPR systems, we outline different applications and current limitations of CRISPR use in biological and biomedical investigation. Finally, we provide a perspective for future development and potential risks of this multifunctional technology. © 2017 Wiley Periodicals, Inc.

  14. Characterizing the topology of probabilistic biological networks.

    PubMed

    Todor, Andrei; Dobra, Alin; Kahveci, Tamer

    2013-01-01

    Biological interactions are often uncertain events, that may or may not take place with some probability. This uncertainty leads to a massive number of alternative interaction topologies for each such network. The existing studies analyze the degree distribution of biological networks by assuming that all the given interactions take place under all circumstances. This strong and often incorrect assumption can lead to misleading results. In this paper, we address this problem and develop a sound mathematical basis to characterize networks in the presence of uncertain interactions. Using our mathematical representation, we develop a method that can accurately describe the degree distribution of such networks. We also take one more step and extend our method to accurately compute the joint-degree distributions of node pairs connected by edges. The number of possible network topologies grows exponentially with the number of uncertain interactions. However, the mathematical model we develop allows us to compute these degree distributions in polynomial time in the number of interactions. Our method works quickly even for entire protein-protein interaction (PPI) networks. It also helps us find an adequate mathematical model using MLE. We perform a comparative study of node-degree and joint-degree distributions in two types of biological networks: the classical deterministic networks and the more flexible probabilistic networks. Our results confirm that power-law and log-normal models best describe degree distributions for both probabilistic and deterministic networks. Moreover, the inverse correlation of degrees of neighboring nodes shows that, in probabilistic networks, nodes with large number of interactions prefer to interact with those with small number of interactions more frequently than expected. We also show that probabilistic networks are more robust for node-degree distribution computation than the deterministic ones. all the data sets used, the software

  15. Biological Implications of Dynamical Phases in Non-equilibrium Networks

    NASA Astrophysics Data System (ADS)

    Murugan, Arvind; Vaikuntanathan, Suriyanarayanan

    2016-03-01

    Biology achieves novel functions like error correction, ultra-sensitivity and accurate concentration measurement at the expense of free energy through Maxwell Demon-like mechanisms. The design principles and free energy trade-offs have been studied for a variety of such mechanisms. In this review, we emphasize a perspective based on dynamical phases that can explain commonalities shared by these mechanisms. Dynamical phases are defined by typical trajectories executed by non-equilibrium systems in the space of internal states. We find that coexistence of dynamical phases can have dramatic consequences for function vs free energy cost trade-offs. Dynamical phases can also provide an intuitive picture of the design principles behind such biological Maxwell Demons.

  16. Accurate Quantitative Sensing of Intracellular pH based on Self-ratiometric Upconversion Luminescent Nanoprobe.

    PubMed

    Li, Cuixia; Zuo, Jing; Zhang, Li; Chang, Yulei; Zhang, Youlin; Tu, Langping; Liu, Xiaomin; Xue, Bin; Li, Qiqing; Zhao, Huiying; Zhang, Hong; Kong, Xianggui

    2016-12-09

    Accurate quantitation of intracellular pH (pH i ) is of great importance in revealing the cellular activities and early warning of diseases. A series of fluorescence-based nano-bioprobes composed of different nanoparticles or/and dye pairs have already been developed for pH i sensing. Till now, biological auto-fluorescence background upon UV-Vis excitation and severe photo-bleaching of dyes are the two main factors impeding the accurate quantitative detection of pH i . Herein, we have developed a self-ratiometric luminescence nanoprobe based on förster resonant energy transfer (FRET) for probing pH i , in which pH-sensitive fluorescein isothiocyanate (FITC) and upconversion nanoparticles (UCNPs) were served as energy acceptor and donor, respectively. Under 980 nm excitation, upconversion emission bands at 475 nm and 645 nm of NaYF 4 :Yb 3+ , Tm 3+ UCNPs were used as pH i response and self-ratiometric reference signal, respectively. This direct quantitative sensing approach has circumvented the traditional software-based subsequent processing of images which may lead to relatively large uncertainty of the results. Due to efficient FRET and fluorescence background free, a highly-sensitive and accurate sensing has been achieved, featured by 3.56 per unit change in pH i value 3.0-7.0 with deviation less than 0.43. This approach shall facilitate the researches in pH i related areas and development of the intracellular drug delivery systems.

  17. Accurate Quantitative Sensing of Intracellular pH based on Self-ratiometric Upconversion Luminescent Nanoprobe

    NASA Astrophysics Data System (ADS)

    Li, Cuixia; Zuo, Jing; Zhang, Li; Chang, Yulei; Zhang, Youlin; Tu, Langping; Liu, Xiaomin; Xue, Bin; Li, Qiqing; Zhao, Huiying; Zhang, Hong; Kong, Xianggui

    2016-12-01

    Accurate quantitation of intracellular pH (pHi) is of great importance in revealing the cellular activities and early warning of diseases. A series of fluorescence-based nano-bioprobes composed of different nanoparticles or/and dye pairs have already been developed for pHi sensing. Till now, biological auto-fluorescence background upon UV-Vis excitation and severe photo-bleaching of dyes are the two main factors impeding the accurate quantitative detection of pHi. Herein, we have developed a self-ratiometric luminescence nanoprobe based on förster resonant energy transfer (FRET) for probing pHi, in which pH-sensitive fluorescein isothiocyanate (FITC) and upconversion nanoparticles (UCNPs) were served as energy acceptor and donor, respectively. Under 980 nm excitation, upconversion emission bands at 475 nm and 645 nm of NaYF4:Yb3+, Tm3+ UCNPs were used as pHi response and self-ratiometric reference signal, respectively. This direct quantitative sensing approach has circumvented the traditional software-based subsequent processing of images which may lead to relatively large uncertainty of the results. Due to efficient FRET and fluorescence background free, a highly-sensitive and accurate sensing has been achieved, featured by 3.56 per unit change in pHi value 3.0-7.0 with deviation less than 0.43. This approach shall facilitate the researches in pHi related areas and development of the intracellular drug delivery systems.

  18. Numerical Modeling of Sub-Wavelength Anti-Reflective Structures for Solar Module Applications

    PubMed Central

    Han, Katherine; Chang, Chih-Hung

    2014-01-01

    This paper reviews the current progress in mathematical modeling of anti-reflective subwavelength structures. Methods covered include effective medium theory (EMT), finite-difference time-domain (FDTD), transfer matrix method (TMM), the Fourier modal method (FMM)/rigorous coupled-wave analysis (RCWA) and the finite element method (FEM). Time-based solutions to Maxwell’s equations, such as FDTD, have the benefits of calculating reflectance for multiple wavelengths of light per simulation, but are computationally intensive. Space-discretized methods such as FDTD and FEM output field strength results over the whole geometry and are capable of modeling arbitrary shapes. Frequency-based solutions such as RCWA/FMM and FEM model one wavelength per simulation and are thus able to handle dispersion for regular geometries. Analytical approaches such as TMM are appropriate for very simple thin films. Initial disadvantages such as neglect of dispersion (FDTD), inaccuracy in TM polarization (RCWA), inability to model aperiodic gratings (RCWA), and inaccuracy with metallic materials (FDTD) have been overcome by most modern software. All rigorous numerical methods have accurately predicted the broadband reflection of ideal, graded-index anti-reflective subwavelength structures; ideal structures are tapered nanostructures with periods smaller than the wavelengths of light of interest and lengths that are at least a large portion of the wavelengths considered. PMID:28348287

  19. Optimally designed narrowband guided-mode resonance reflectance filters for mid-infrared spectroscopy

    PubMed Central

    Liu, Jui-Nung; Schulmerich, Matthew V.; Bhargava, Rohit; Cunningham, Brian T.

    2011-01-01

    An alternative to the well-established Fourier transform infrared (FT-IR) spectrometry, termed discrete frequency infrared (DFIR) spectrometry, has recently been proposed. This approach uses narrowband mid-infrared reflectance filters based on guided-mode resonance (GMR) in waveguide gratings, but filters designed and fabricated have not attained the spectral selectivity (≤ 32 cm−1) commonly employed for measurements of condensed matter using FT-IR spectroscopy. With the incorporation of dispersion and optical absorption of materials, we present here optimal design of double-layer surface-relief silicon nitride-based GMR filters in the mid-IR for various narrow bandwidths below 32 cm−1. Both shift of the filter resonance wavelengths arising from the dispersion effect and reduction of peak reflection efficiency and electric field enhancement due to the absorption effect show that the optical characteristics of materials must be taken into consideration rigorously for accurate design of narrowband GMR filters. By incorporating considerations for background reflections, the optimally designed GMR filters can have bandwidth narrower than the designed filter by the antireflection equivalence method based on the same index modulation magnitude, without sacrificing low sideband reflections near resonance. The reported work will enable use of GMR filters-based instrumentation for common measurements of condensed matter, including tissues and polymer samples. PMID:22109445

  20. MULTI-K: accurate classification of microarray subtypes using ensemble k-means clustering

    PubMed Central

    Kim, Eun-Youn; Kim, Seon-Young; Ashlock, Daniel; Nam, Dougu

    2009-01-01

    Background Uncovering subtypes of disease from microarray samples has important clinical implications such as survival time and sensitivity of individual patients to specific therapies. Unsupervised clustering methods have been used to classify this type of data. However, most existing methods focus on clusters with compact shapes and do not reflect the geometric complexity of the high dimensional microarray clusters, which limits their performance. Results We present a cluster-number-based ensemble clustering algorithm, called MULTI-K, for microarray sample classification, which demonstrates remarkable accuracy. The method amalgamates multiple k-means runs by varying the number of clusters and identifies clusters that manifest the most robust co-memberships of elements. In addition to the original algorithm, we newly devised the entropy-plot to control the separation of singletons or small clusters. MULTI-K, unlike the simple k-means or other widely used methods, was able to capture clusters with complex and high-dimensional structures accurately. MULTI-K outperformed other methods including a recently developed ensemble clustering algorithm in tests with five simulated and eight real gene-expression data sets. Conclusion The geometric complexity of clusters should be taken into account for accurate classification of microarray data, and ensemble clustering applied to the number of clusters tackles the problem very well. The C++ code and the data sets tested are available from the authors. PMID:19698124

  1. Biomolecular Deuteration for Neutron Structural Biology and Dynamics.

    PubMed

    Haertlein, Michael; Moulin, Martine; Devos, Juliette M; Laux, Valerie; Dunne, Orla; Forsyth, V Trevor

    2016-01-01

    Neutron scattering studies provide important information in structural biology that is not accessible using other approaches. The uniqueness of the technique, and its complementarity with X-ray scattering, is greatest when full use is made of deuterium labeling. The ability to produce tailor-made deuterium-labeled biological macromolecules allows neutron studies involving solution scattering, crystallography, reflection, and dynamics to be optimized in a manner that has major impact on the scope, quality, and throughput of work in these areas. Deuteration facilities have now been developed at many neutron centres throughout the world; these are having a crucial effect on neutron studies in the life sciences and on biologically related studies in soft matter. This chapter describes methods that have been developed for the efficient production of deuterium-labeled samples for a wide range of neutron scattering applications. Examples are given that illustrate the use of these samples for each of the main techniques. Perspectives for biological deuterium labeling are discussed in relation to developments at current facilities and those that are planned in the future. © 2016 Elsevier Inc. All rights reserved.

  2. Quantitative interpretations of Visible-NIR reflectance spectra of blood.

    PubMed

    Serebrennikova, Yulia M; Smith, Jennifer M; Huffman, Debra E; Leparc, German F; García-Rubio, Luis H

    2008-10-27

    This paper illustrates the implementation of a new theoretical model for rapid quantitative analysis of the Vis-NIR diffuse reflectance spectra of blood cultures. This new model is based on the photon diffusion theory and Mie scattering theory that have been formulated to account for multiple scattering populations and absorptive components. This study stresses the significance of the thorough solution of the scattering and absorption problem in order to accurately resolve for optically relevant parameters of blood culture components. With advantages of being calibration-free and computationally fast, the new model has two basic requirements. First, wavelength-dependent refractive indices of the basic chemical constituents of blood culture components are needed. Second, multi-wavelength measurements or at least the measurements of characteristic wavelengths equal to the degrees of freedom, i.e. number of optically relevant parameters, of blood culture system are required. The blood culture analysis model was tested with a large number of diffuse reflectance spectra of blood culture samples characterized by an extensive range of the relevant parameters.

  3. Analytical model of diffuse reflectance spectrum of skin tissue

    NASA Astrophysics Data System (ADS)

    Lisenko, S. A.; Kugeiko, M. M.; Firago, V. A.; Sobchuk, A. N.

    2014-01-01

    We have derived simple analytical expressions that enable highly accurate calculation of diffusely reflected light signals of skin in the spectral range from 450 to 800 nm at a distance from the region of delivery of exciting radiation. The expressions, taking into account the dependence of the detected signals on the refractive index, transport scattering coefficient, absorption coefficient and anisotropy factor of the medium, have been obtained in the approximation of a two-layer medium model (epidermis and dermis) for the same parameters of light scattering but different absorption coefficients of layers. Numerical experiments on the retrieval of the skin biophysical parameters from the diffuse reflectance spectra simulated by the Monte Carlo method show that commercially available fibre-optic spectrophotometers with a fixed distance between the radiation source and detector can reliably determine the concentration of bilirubin, oxy- and deoxyhaemoglobin in the dermis tissues and the tissue structure parameter characterising the size of its effective scatterers. We present the examples of quantitative analysis of the experimental data, confirming the correctness of estimates of biophysical parameters of skin using the obtained analytical expressions.

  4. Quantification of betaglucans, lipid and protein contents in whole oat groats (Avena sativa L.) using near infrared reflectance spectroscopy

    USDA-ARS?s Scientific Manuscript database

    Whole oat has been described as an important healthy food for humans due to its beneficial nutritional components. Near infrared reflectance spectroscopy (NIRS) is a powerful, fast, accurate and non-destructive analytical tool that can be substituted for some traditional chemical analysis. A total o...

  5. Model for the ultrasound reflection from micro-beads and cells distributed in layers on a uniform surface

    NASA Astrophysics Data System (ADS)

    Couture, O.; Cherin, E.; Foster, F. S.

    2007-07-01

    A model predicting the reflection of ultrasound from multiple layers of small scattering spheres is developed. Predictions of the reflection coefficient, which takes into account the interferences between the different sphere layers, are compared to measurements performed in the 10-80 MHz and 15-35 MHz frequency range with layers of glass beads and spherical acute myeloid leukemia (AML) cells, respectively. For both types of scatterers, the reflection coefficient increases as a function of their density on the surface for less than three superimposed layers, at which point it saturates at 0.38 for glass beads and 0.02 for AML cells. Above three layers, oscillations of the reflection coefficient due to constructive or destructive interference between layers are observed experimentally and are accurately predicted by the model. The use of such a model could lead to a better understanding of the structures observed in layered tissue images.

  6. Subwavelength diffractive acoustics and wavefront manipulation with a reflective acoustic metasurface

    NASA Astrophysics Data System (ADS)

    Wang, Wenqi; Xie, Yangbo; Popa, Bogdan-Ioan; Cummer, Steven A.

    2016-11-01

    Acoustic metasurfaces provide useful wavefront shaping capabilities, such as beam steering, acoustic focusing, and asymmetric transmission, in a compact structure. Most acoustic metasurfaces described in the literature are transmissive devices and focus their performance on steering sound beam of the fundamental diffractive order. In addition, the range of incident angles studied is usually below the critical incidence predicted by generalized Snell's law of reflection. In this work, we comprehensively analyze the wave interaction with a generic periodic phase-modulating structure in order to predict the behavior of all diffractive orders, especially for cases beyond critical incidence. Under the guidance of the presented analysis, a broadband reflective metasurface is designed based on an expanded library of labyrinthine acoustic metamaterials. Various local and nonlocal wavefront shaping properties are experimentally demonstrated, and enhanced absorption of higher order diffractive waves is experimentally shown for the first time. The proposed methodology provides an accurate approach for predicting practical diffracted wave behaviors and opens a new perspective for the study of acoustic periodic structures. The designed metasurface extends the functionalities of acoustic metasurfaces and paves the way for the design of thin planar reflective structures for broadband acoustic wave manipulation and extraordinary absorption.

  7. Integration of Network Biology and Imaging to Study Cancer Phenotypes and Responses.

    PubMed

    Tian, Ye; Wang, Sean S; Zhang, Zhen; Rodriguez, Olga C; Petricoin, Emanuel; Shih, Ie-Ming; Chan, Daniel; Avantaggiati, Maria; Yu, Guoqiang; Ye, Shaozhen; Clarke, Robert; Wang, Chao; Zhang, Bai; Wang, Yue; Albanese, Chris

    2014-01-01

    Ever growing "omics" data and continuously accumulated biological knowledge provide an unprecedented opportunity to identify molecular biomarkers and their interactions that are responsible for cancer phenotypes that can be accurately defined by clinical measurements such as in vivo imaging. Since signaling or regulatory networks are dynamic and context-specific, systematic efforts to characterize such structural alterations must effectively distinguish significant network rewiring from random background fluctuations. Here we introduced a novel integration of network biology and imaging to study cancer phenotypes and responses to treatments at the molecular systems level. Specifically, Differential Dependence Network (DDN) analysis was used to detect statistically significant topological rewiring in molecular networks between two phenotypic conditions, and in vivo Magnetic Resonance Imaging (MRI) was used to more accurately define phenotypic sample groups for such differential analysis. We applied DDN to analyze two distinct phenotypic groups of breast cancer and study how genomic instability affects the molecular network topologies in high-grade ovarian cancer. Further, FDA-approved arsenic trioxide (ATO) and the ND2-SmoA1 mouse model of Medulloblastoma (MB) were used to extend our analyses of combined MRI and Reverse Phase Protein Microarray (RPMA) data to assess tumor responses to ATO and to uncover the complexity of therapeutic molecular biology.

  8. FReD: the floral reflectance database--a web portal for analyses of flower colour.

    PubMed

    Arnold, Sarah E J; Faruq, Samia; Savolainen, Vincent; McOwan, Peter W; Chittka, Lars

    2010-12-10

    Flower colour is of great importance in various fields relating to floral biology and pollinator behaviour. However, subjective human judgements of flower colour may be inaccurate and are irrelevant to the ecology and vision of the flower's pollinators. For precise, detailed information about the colours of flowers, a full reflectance spectrum for the flower of interest should be used rather than relying on such human assessments. The Floral Reflectance Database (FReD) has been developed to make an extensive collection of such data available to researchers. It is freely available at http://www.reflectance.co.uk. The database allows users to download spectral reflectance data for flower species collected from all over the world. These could, for example, be used in modelling interactions between pollinator vision and plant signals, or analyses of flower colours in various habitats. The database contains functions for calculating flower colour loci according to widely-used models of bee colour space, reflectance graphs of the spectra and an option to search for flowers with similar colours in bee colour space. The Floral Reflectance Database is a valuable new tool for researchers interested in the colours of flowers and their association with pollinator colour vision, containing raw spectral reflectance data for a large number of flower species.

  9. A biological phantom for evaluation of CT image reconstruction algorithms

    NASA Astrophysics Data System (ADS)

    Cammin, J.; Fung, G. S. K.; Fishman, E. K.; Siewerdsen, J. H.; Stayman, J. W.; Taguchi, K.

    2014-03-01

    In recent years, iterative algorithms have become popular in diagnostic CT imaging to reduce noise or radiation dose to the patient. The non-linear nature of these algorithms leads to non-linearities in the imaging chain. However, the methods to assess the performance of CT imaging systems were developed assuming the linear process of filtered backprojection (FBP). Those methods may not be suitable any longer when applied to non-linear systems. In order to evaluate the imaging performance, a phantom is typically scanned and the image quality is measured using various indices. For reasons of practicality, cost, and durability, those phantoms often consist of simple water containers with uniform cylinder inserts. However, these phantoms do not represent the rich structure and patterns of real tissue accurately. As a result, the measured image quality or detectability performance for lesions may not reflect the performance on clinical images. The discrepancy between estimated and real performance may be even larger for iterative methods which sometimes produce "plastic-like", patchy images with homogeneous patterns. Consequently, more realistic phantoms should be used to assess the performance of iterative algorithms. We designed and constructed a biological phantom consisting of porcine organs and tissue that models a human abdomen, including liver lesions. We scanned the phantom on a clinical CT scanner and compared basic image quality indices between filtered backprojection and an iterative reconstruction algorithm.

  10. Towards a minimal stochastic model for a large class of diffusion-reactions on biological membranes.

    PubMed

    Chevalier, Michael W; El-Samad, Hana

    2012-08-28

    Diffusion of biological molecules on 2D biological membranes can play an important role in the behavior of stochastic biochemical reaction systems. Yet, we still lack a fundamental understanding of circumstances where explicit accounting of the diffusion and spatial coordinates of molecules is necessary. In this work, we illustrate how time-dependent, non-exponential reaction probabilities naturally arise when explicitly accounting for the diffusion of molecules. We use the analytical expression of these probabilities to derive a novel algorithm which, while ignoring the exact position of the molecules, can still accurately capture diffusion effects. We investigate the regions of validity of the algorithm and show that for most parameter regimes, it constitutes an accurate framework for studying these systems. We also document scenarios where large spatial fluctuation effects mandate explicit consideration of all the molecules and their positions. Taken together, our results derive a fundamental understanding of the role of diffusion and spatial fluctuations in these systems. Simultaneously, they provide a general computational methodology for analyzing a broad class of biological networks whose behavior is influenced by diffusion on membranes.

  11. 3D Cloud Radiative Effects on Polarized Reflectances

    NASA Astrophysics Data System (ADS)

    Cornet, C.; Matar, C.; C-Labonnote, L.; Szczap, F.; Waquet, F.; Parol, F.; Riedi, J.

    2017-12-01

    As recognized in the last IPCC report, clouds have a major importance in the climate budget and need to be better characterized. Remote sensing observations are a way to obtain either global observations of cloud from satellites or a very fine description of clouds from airborne measurements. An increasing numbers of radiometers plan to measure polarized reflectances in addition to total reflectances, since this information is very helpful to obtain aerosol or cloud properties. In a near future, for example, the Multi-viewing, Multi-channel, Multi-polarization Imager (3MI) will be part the EPS-SG Eumetsat-ESA mission. It will achieve multi-angular polarimetric measurements from visible to shortwave infrared wavelengths. An airborne prototype, OSIRIS (Observing System Including Polarization in the Solar Infrared Spectrum), is also presently developed at the Laboratoire d'Optique Atmospherique and had already participated to several measurements campaigns. In order to analyze suitably the measured signal, it it necessary to have realistic and accurate models able to simulate polarized reflectances. The 3DCLOUD model (Szczap et al., 2014) was used to generate three-dimensional synthetic cloud and the 3D radiative transfer model, 3DMCPOL (Cornet et al., 2010) to compute realistic polarized reflectances. From these simulations, we investigate the effects of 3D cloud structures and heterogeneity on the polarized angular signature often used to retrieve cloud or aerosol properties. We show that 3D effects are weak for flat clouds but become quite significant for fractional clouds above ocean. The 3D effects are quite different according to the observation scale. For the airborne scale (few tens of meter), solar illumination effects can lead to polarized cloud reflectance values higher than the saturation limit predicted by the homogeneous cloud assumption. In the cloud gaps, corresponding to shadowed areas of the total reflectances, polarized signal can also be enhanced

  12. Modelling biochemical reaction systems by stochastic differential equations with reflection.

    PubMed

    Niu, Yuanling; Burrage, Kevin; Chen, Luonan

    2016-05-07

    In this paper, we gave a new framework for modelling and simulating biochemical reaction systems by stochastic differential equations with reflection not in a heuristic way but in a mathematical way. The model is computationally efficient compared with the discrete-state Markov chain approach, and it ensures that both analytic and numerical solutions remain in a biologically plausible region. Specifically, our model mathematically ensures that species numbers lie in the domain D, which is a physical constraint for biochemical reactions, in contrast to the previous models. The domain D is actually obtained according to the structure of the corresponding chemical Langevin equations, i.e., the boundary is inherent in the biochemical reaction system. A variant of projection method was employed to solve the reflected stochastic differential equation model, and it includes three simple steps, i.e., Euler-Maruyama method was applied to the equations first, and then check whether or not the point lies within the domain D, and if not perform an orthogonal projection. It is found that the projection onto the closure D¯ is the solution to a convex quadratic programming problem. Thus, existing methods for the convex quadratic programming problem can be employed for the orthogonal projection map. Numerical tests on several important problems in biological systems confirmed the efficiency and accuracy of this approach. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. Macro-/micro-environment-sensitive chemosensing and biological imaging.

    PubMed

    Yang, Zhigang; Cao, Jianfang; He, Yanxia; Yang, Jung Ho; Kim, Taeyoung; Peng, Xiaojun; Kim, Jong Seung

    2014-07-07

    Environment-related parameters, including viscosity, polarity, temperature, hypoxia, and pH, play pivotal roles in controlling the physical or chemical behaviors of local molecules. In particular, in a biological environment, such factors predominantly determine the biological properties of the local environment or reflect corresponding status alterations. Abnormal changes in these factors would cause cellular malfunction or become a hallmark of the occurrence of severe diseases. Therefore, in recent years, they have increasingly attracted research interest from the fields of chemistry and biological chemistry. With the emergence of fluorescence sensing and imaging technology, several fluorescent chemosensors have been designed to respond to such parameters and to further map their distributions and variations in vitro/in vivo. In this work, we have reviewed a number of various environment-responsive chemosensors related to fluorescent recognition of viscosity, polarity, temperature, hypoxia, and pH that have been reported thus far.

  14. Monaural Sound Localization Based on Reflective Structure and Homomorphic Deconvolution

    PubMed Central

    Park, Yeonseok; Choi, Anthony

    2017-01-01

    The asymmetric structure around the receiver provides a particular time delay for the specific incoming propagation. This paper designs a monaural sound localization system based on the reflective structure around the microphone. The reflective plates are placed to present the direction-wise time delay, which is naturally processed by convolutional operation with a sound source. The received signal is separated for estimating the dominant time delay by using homomorphic deconvolution, which utilizes the real cepstrum and inverse cepstrum sequentially to derive the propagation response’s autocorrelation. Once the localization system accurately estimates the information, the time delay model computes the corresponding reflection for localization. Because of the structure limitation, two stages of the localization process perform the estimation procedure as range and angle. The software toolchain from propagation physics and algorithm simulation realizes the optimal 3D-printed structure. The acoustic experiments in the anechoic chamber denote that 79.0% of the study range data from the isotropic signal is properly detected by the response value, and 87.5% of the specific direction data from the study range signal is properly estimated by the response time. The product of both rates shows the overall hit rate to be 69.1%. PMID:28946625

  15. Estimation of the remote-sensing reflectance from above-surface measurements.

    PubMed

    Mobley, C D

    1999-12-20

    The remote-sensing reflectance R(rs) is not directly measurable, and various methodologies have been employed in its estimation. I review the radiative transfer foundations of several commonly used methods for estimating R(rs), and errors associated with estimating R(rs) by removal of surface-reflected sky radiance are evaluated using the Hydrolight radiative transfer numerical model. The dependence of the sea surface reflectance factor rho, which is not an inherent optical property of the surface, on sky conditions, wind speed, solar zenith angle, and viewing geometry is examined. If rho is not estimated accurately, significant errors can occur in the estimated R(rs) for near-zenith Sun positions and for high wind speeds, both of which can give considerable Sun glitter effects. The numerical simulations suggest that a viewing direction of 40 deg from the nadir and 135 deg from the Sun is a reasonable compromise among conflicting requirements. For this viewing direction, a value of rho approximately 0.028 is acceptable only for wind speeds less than 5 m s(-1). For higher wind speeds, curves are presented for the determination of rho as a function of solar zenith angle and wind speed. If the sky is overcast, a value of rho approximately 0.028 is used at all wind speeds.

  16. 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

  17. CLARREO Approach for Reference Intercalibration of Reflected Solar Sensors: On-Orbit Data Matching and Sampling

    NASA Technical Reports Server (NTRS)

    Roithmayr, Carlos; Lukashin, Constantine; Speth, Paul W.; Kopp, Gregg; Thome, Kurt; Wielicki, Bruce A.; Young, David F.

    2014-01-01

    The implementation of the Climate Absolute Radiance and Refractivity Observatory (CLARREO) mission was recommended by the National Research Council in 2007 to provide an on-orbit intercalibration standard with accuracy of 0.3% (k = 2) for relevant Earth observing sensors. The goal of reference intercalibration, as established in the Decadal Survey, is to enable rigorous high-accuracy observations of critical climate change parameters, including reflected broadband radiation [Clouds and Earth's Radiant Energy System (CERES)], cloud properties [Visible Infrared Imaging Radiometer Suite (VIIRS)], and changes in surface albedo, including snow and ice albedo feedback. In this paper, we describe the CLARREO approach for performing intercalibration on orbit in the reflected solar (RS) wavelength domain. It is based on providing highly accurate spectral reflectance and reflected radiance measurements from the CLARREO Reflected Solar Spectrometer (RSS) to establish an on-orbit reference for existing sensors, namely, CERES and VIIRS on Joint Polar Satellite System satellites, Advanced Very High Resolution Radiometer and follow-on imagers on MetOp, Landsat imagers, and imagers on geostationary platforms. One of two fundamental CLARREO mission goals is to provide sufficient sampling of high-accuracy observations that are matched in time, space, and viewing angles with measurements made by existing instruments, to a degree that overcomes the random error sources from imperfect data matching and instrument noise. The data matching is achieved through CLARREO RSS pointing operations on orbit that align its line of sight with the intercalibrated sensor. These operations must be planned in advance; therefore, intercalibration events must be predicted by orbital modeling. If two competing opportunities are identified, one target sensor must be given priority over the other. The intercalibration method is to monitor changes in targeted sensor response function parameters: effective

  18. Visible and near-infrared spectroscopic analysis of raw milk for cow health monitoring: reflectance or transmittance?

    PubMed

    Aernouts, B; Polshin, E; Lammertyn, J; Saeys, W

    2011-11-01

    The composition of produced milk has great value for the dairy farmer. It determines the economic value of the milk and provides valuable information about the metabolism of the corresponding cow. Therefore, online measurement of milk components during milking 2 or more times per day would provide knowledge about the current health and nutritional status of each cow individually. This information provides a solid basis for optimizing cow management. The potential of visible and near-infrared (Vis/NIR) spectroscopy for predicting the fat, crude protein, lactose, and urea content of raw milk online during milking was, therefore, investigated in this study. Two measurement modes (reflectance and transmittance) and different wavelength ranges for Vis/NIR spectroscopy were evaluated and their ability to measure the milk composition online was compared. The Vis/NIR reflectance measurements allowed for very accurate monitoring of the fat and crude protein content in raw milk (R(2)>0.95), but resulted in poor lactose predictions (R(2)<0.75). In contrast, Vis/NIR transmittance spectra of the milk samples gave accurate fat and crude protein predictions (R(2)>0.90) and useful lactose predictions (R(2)=0.88). Neither Vis/NIR reflectance nor transmittance spectroscopy lead to an acceptable prediction of the milk urea content. Transmittance spectroscopy can thus be used to predict the 3 major milk components, but with lower accuracy for fat and crude protein than the reflectance mode. Moreover, the small sample thickness (1mm) required for NIR transmittance measurement considerably complicates its online use. Copyright © 2011 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  19. Measuring Practicum Student Teachers' Reflectivity: The Reflective Pedagogical Thinking Scale

    ERIC Educational Resources Information Center

    Seng, Toh Wah

    2004-01-01

    The purpose of the original study was to investigate practicum student teachers' reflectivity. This paper describes the use of a revised version of the Reflective Pedagogical Thinking Scale (Sparks-Langer, et al., 1990) to measure reflectivity. The original scale was used by the developers to assess reflectivity through a structured interview. The…

  20. RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA

    PubMed Central

    Wright, Imogen A.; Travers, Simon A.

    2014-01-01

    The challenge presented by high-throughput sequencing necessitates the development of novel tools for accurate alignment of reads to reference sequences. Current approaches focus on using heuristics to map reads quickly to large genomes, rather than generating highly accurate alignments in coding regions. Such approaches are, thus, unsuited for applications such as amplicon-based analysis and the realignment phase of exome sequencing and RNA-seq, where accurate and biologically relevant alignment of coding regions is critical. To facilitate such analyses, we have developed a novel tool, RAMICS, that is tailored to mapping large numbers of sequence reads to short lengths (<10 000 bp) of coding DNA. RAMICS utilizes profile hidden Markov models to discover the open reading frame of each sequence and aligns to the reference sequence in a biologically relevant manner, distinguishing between genuine codon-sized indels and frameshift mutations. This approach facilitates the generation of highly accurate alignments, accounting for the error biases of the sequencing machine used to generate reads, particularly at homopolymer regions. Performance improvements are gained through the use of graphics processing units, which increase the speed of mapping through parallelization. RAMICS substantially outperforms all other mapping approaches tested in terms of alignment quality while maintaining highly competitive speed performance. PMID:24861618

  1. An Overview of Biological Macromolecule Crystallization

    PubMed Central

    Krauss, Irene Russo; Merlino, Antonello; Vergara, Alessandro; Sica, Filomena

    2013-01-01

    The elucidation of the three dimensional structure of biological macromolecules has provided an important contribution to our current understanding of many basic mechanisms involved in life processes. This enormous impact largely results from the ability of X-ray crystallography to provide accurate structural details at atomic resolution that are a prerequisite for a deeper insight on the way in which bio-macromolecules interact with each other to build up supramolecular nano-machines capable of performing specialized biological functions. With the advent of high-energy synchrotron sources and the development of sophisticated software to solve X-ray and neutron crystal structures of large molecules, the crystallization step has become even more the bottleneck of a successful structure determination. This review introduces the general aspects of protein crystallization, summarizes conventional and innovative crystallization methods and focuses on the new strategies utilized to improve the success rate of experiments and increase crystal diffraction quality. PMID:23727935

  2. 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

  3. Comparing Resident Self-Report to Chart Audits for Quality Improvement Projects: Accurate Reflection or Cherry-Picking?

    PubMed Central

    Kuperman, Ethan F.; Tobin, Kristen; Kraschnewski, Jennifer L.

    2014-01-01

    Background Resident engagement in quality improvement is a requirement for graduate medical education, but the optimal means of instruction and evaluation of resident progress remain unknown. Objective To determine the accuracy of self-reported chart audits in measuring resident adherence to primary care clinical practice guidelines. Methods During the 2010–2011 academic year, second- and third-year internal medicine residents at a single, university hospital–based program performed chart audits on 10 patients from their primary care clinic to determine adherence to 16 US Preventive Services Task Force primary care guidelines. We compared residents' responses to independent audits of randomly selected patient charts by a single external reviewer. Results Self-reported data were collected by 18 second-year and 15 third-year residents for 330 patients. Independently, 70 patient charts were randomly selected for review by an external auditor. Overall guideline compliance was significantly higher on self-reported audits compared to external audits (82% versus 68%, P < .001). Of 16 guidelines, external audits found significantly lower rates of adherence for 5 (tetanus vaccination, osteoporosis screening, colon cancer screening, cholesterol screening, and obesity screening). Chlamydia screening was more common in audited charts than in self-reported data. Although third-year residents self-reported higher guideline adherence than second-year residents (86% versus 78%, P < .001), external audits for third-year residents found lower overall adherence (64% versus 72%, P  =  .040). Conclusions Residents' self-reported chart audits may significantly overestimate guideline adherence. Increased supervision and independent review appear necessary to accurately evaluate resident performance. PMID:26140117

  4. Comparing Resident Self-Report to Chart Audits for Quality Improvement Projects: Accurate Reflection or Cherry-Picking?

    PubMed

    Kuperman, Ethan F; Tobin, Kristen; Kraschnewski, Jennifer L

    2014-12-01

    Resident engagement in quality improvement is a requirement for graduate medical education, but the optimal means of instruction and evaluation of resident progress remain unknown. To determine the accuracy of self-reported chart audits in measuring resident adherence to primary care clinical practice guidelines. During the 2010-2011 academic year, second- and third-year internal medicine residents at a single, university hospital-based program performed chart audits on 10 patients from their primary care clinic to determine adherence to 16 US Preventive Services Task Force primary care guidelines. We compared residents' responses to independent audits of randomly selected patient charts by a single external reviewer. Self-reported data were collected by 18 second-year and 15 third-year residents for 330 patients. Independently, 70 patient charts were randomly selected for review by an external auditor. Overall guideline compliance was significantly higher on self-reported audits compared to external audits (82% versus 68%, P < .001). Of 16 guidelines, external audits found significantly lower rates of adherence for 5 (tetanus vaccination, osteoporosis screening, colon cancer screening, cholesterol screening, and obesity screening). Chlamydia screening was more common in audited charts than in self-reported data. Although third-year residents self-reported higher guideline adherence than second-year residents (86% versus 78%, P < .001), external audits for third-year residents found lower overall adherence (64% versus 72%, P  =  .040). Residents' self-reported chart audits may significantly overestimate guideline adherence. Increased supervision and independent review appear necessary to accurately evaluate resident performance.

  5. Retrieval of background surface reflectance with BRD components from pre-running BRDF

    NASA Astrophysics Data System (ADS)

    Choi, Sungwon; Lee, Kyeong-Sang; Jin, Donghyun; Lee, Darae; Han, Kyung-Soo

    2016-10-01

    comparing BSR with VGT-S1, bias is from 0.0116 to 0.0158 and RMSE is from 0.0459 to 0.0545. They are very reasonable results, so we confirm that BSR is similar to VGT-S1. And weakness of this study is missing pixel in BSR which are observed less time to retrieve BRD components. If missing pixels are filled, BSR is better to retrieve surface products with more accuracy. And we think that after filling the missing pixel and being more accurate, it can be useful data to retrieve surface product which made by surface reflectance like cloud masking and retrieving aerosol.

  6. Predicting spillover risk to non-target plants pre-release: Bikasha collaris a potential biological control agent of Chinese tallowtree (Triadica sebifera)

    USDA-ARS?s Scientific Manuscript database

    Quarantine host range tests accurately predict direct risk of biological control agents to non-target species. However, a well-known indirect effect of biological control of weeds releases is spillover damage to non-target species. Spillover damage may occur when the population of agents achieves ou...

  7. Reflections on being therapeutic and reflection.

    PubMed

    Elcock, K

    1997-01-01

    This article offers a reflective account of an incident that occurred between a nurse tutor and a patient on a cardiology ward. It highlights the importance of interpersonal skills in creating a therapeutic relationship, in particular those of self-awareness, empathy and intuition. The author's difficulties in running reflective practice sessions for pre-registration students are discussed and insights are offered into why these difficulties arose.

  8. Chapter 7: Total internal reflection fluorescence microscopy.

    PubMed

    Axelrod, Daniel

    2008-01-01

    Total internal reflection fluorescence microscopy (TIRFM), also known as evanescent wave microscopy, is used in a wide range of applications, particularly to view single molecules attached to planar surfaces and to study the position and dynamics of molecules and organelles in living culture cells near the contact regions with the glass coverslip. TIRFM selectively illuminates fluorophores only in a very thin (less than 100 nm deep) layer near the substrate, thereby avoiding excitation of fluorophores outside this subresolution optical section. This chapter reviews the history, current applications in cell biology and biochemistry, basic optical theory, combinations with numerous other optical and spectroscopic approaches, and a range of setup methods, both commercial and custom.

  9. Student Perceived and Determined Knowledge of Biology Concepts in an Upper-Level Biology Course

    PubMed Central

    Montplaisir, Lisa

    2014-01-01

    Students who lack metacognitive skills can struggle with the learning process. To be effective learners, students should recognize what they know and what they do not know. This study examines the relationship between students’ perception of their knowledge and determined knowledge in an upper-level biology course utilizing a pre/posttest approach. Significant differences in students’ perception of their knowledge and their determined knowledge exist at the beginning (pretest) and end (posttest) of the course. Alignment between student perception and determined knowledge was significantly more accurate on the posttest compared with the pretest. Students whose determined knowledge was in the upper quartile had significantly better alignment between their perception and determined knowledge on the pre- and posttest than students in the lower quartile. No difference exists between how students perceived their knowledge between upper- and lower-quartile students. There was a significant difference in alignment of perception and determined knowledge between males and females on the posttest, with females being more accurate in their perception of knowledge. This study provides evidence of discrepancies that exist between what students perceive they know and what they actually know. PMID:26086662

  10. Accurate prediction of protein–protein interactions from sequence alignments using a Bayesian method

    PubMed Central

    Burger, Lukas; van Nimwegen, Erik

    2008-01-01

    Accurate and large-scale prediction of protein–protein interactions directly from amino-acid sequences is one of the great challenges in computational biology. Here we present a new Bayesian network method that predicts interaction partners using only multiple alignments of amino-acid sequences of interacting protein domains, without tunable parameters, and without the need for any training examples. We first apply the method to bacterial two-component systems and comprehensively reconstruct two-component signaling networks across all sequenced bacteria. Comparisons of our predictions with known interactions show that our method infers interaction partners genome-wide with high accuracy. To demonstrate the general applicability of our method we show that it also accurately predicts interaction partners in a recent dataset of polyketide synthases. Analysis of the predicted genome-wide two-component signaling networks shows that cognates (interacting kinase/regulator pairs, which lie adjacent on the genome) and orphans (which lie isolated) form two relatively independent components of the signaling network in each genome. In addition, while most genes are predicted to have only a small number of interaction partners, we find that 10% of orphans form a separate class of ‘hub' nodes that distribute and integrate signals to and from up to tens of different interaction partners. PMID:18277381

  11. Utility of biological sensor tags in animal conservation.

    PubMed

    Wilson, A D M; Wikelski, M; Wilson, R P; Cooke, S J

    2015-08-01

    Electronic tags (both biotelemetry and biologging platforms) have informed conservation and resource management policy and practice by providing vital information on the spatial ecology of animals and their environments. However, the extent of the contribution of biological sensors (within electronic tags) that measure an animal's state (e.g., heart rate, body temperature, and details of locomotion and energetics) is less clear. A literature review revealed that, despite a growing number of commercially available state sensor tags and enormous application potential for such devices in animal biology, there are relatively few examples of their application to conservation. Existing applications fell under 4 main themes: quantifying disturbance (e.g., ecotourism, vehicular and aircraft traffic), examining the effects of environmental change (e.g., climate change), understanding the consequences of habitat use and selection, and estimating energy expenditure. We also identified several other ways in which sensor tags could benefit conservation, such as determining the potential efficacy of management interventions. With increasing sensor diversity of commercially available platforms, less invasive attachment techniques, smaller device sizes, and more researchers embracing such technology, we suggest that biological sensor tags be considered a part of the necessary toolbox for conservation. This approach can measure (in real time) the state of free-ranging animals and thus provide managers with objective, timely, relevant, and accurate data to inform policy and decision making. © 2015 Society for Conservation Biology.

  12. Implementing Recommendations for Introductory Biology by Writing a New Textbook

    PubMed Central

    Barsoum, Mark J.; Sellers, Patrick J.; Campbell, A. Malcolm; Heyer, Laurie J.; Paradise, Christopher J.

    2013-01-01

    We redesigned the undergraduate introductory biology course by writing a new textbook (Integrating Concepts in Biology [ICB]) that follows first principles of learning. Our approach emphasizes primary data interpretation and the utility of mathematics in biology, while de-emphasizing memorization. This redesign divides biology into five big ideas (information, evolution, cells, emergent properties, homeostasis), addressing each at five levels of organization (molecules, cells, organisms, populations, ecological systems). We compared our course outcomes with two sections that used a traditional textbook and were taught by different instructors. On data interpretation assessments administered periodically during the semester, our students performed better than students in the traditional sections (p = 0.046) and exhibited greater improvement over the course of the semester (p = 0.015). On factual content assessments, our students performed similarly to students in the other sections (p = 0.737). Pre- and postsemester assessment of disciplinary perceptions and self-appraisal indicate that our students acquired a more accurate perception of biology as a discipline and may have developed a more realistic evaluation of their scientific abilities than did the control students (p < 0.05). We conclude that ICB improves critical thinking, metacognition, and disciplinary perceptions without compromising content knowledge in introductory biology. PMID:23463233

  13. Implementing recommendations for introductory biology by writing a new textbook.

    PubMed

    Barsoum, Mark J; Sellers, Patrick J; Campbell, A Malcolm; Heyer, Laurie J; Paradise, Christopher J

    2013-01-01

    We redesigned the undergraduate introductory biology course by writing a new textbook (Integrating Concepts in Biology [ICB]) that follows first principles of learning. Our approach emphasizes primary data interpretation and the utility of mathematics in biology, while de-emphasizing memorization. This redesign divides biology into five big ideas (information, evolution, cells, emergent properties, homeostasis), addressing each at five levels of organization (molecules, cells, organisms, populations, ecological systems). We compared our course outcomes with two sections that used a traditional textbook and were taught by different instructors. On data interpretation assessments administered periodically during the semester, our students performed better than students in the traditional sections (p = 0.046) and exhibited greater improvement over the course of the semester (p = 0.015). On factual content assessments, our students performed similarly to students in the other sections (p = 0.737). Pre- and postsemester assessment of disciplinary perceptions and self-appraisal indicate that our students acquired a more accurate perception of biology as a discipline and may have developed a more realistic evaluation of their scientific abilities than did the control students (p < 0.05). We conclude that ICB improves critical thinking, metacognition, and disciplinary perceptions without compromising content knowledge in introductory biology.

  14. Near-Infrared Spectroscopy: More Accurate Than Heart Rate for Monitoring Intensity in Running in Hilly Terrain.

    PubMed

    Born, Dennis-Peter; Stöggl, Thomas; Swarén, Mikael; Björklund, Glenn

    2017-04-01

    To investigate the cardiorespiratory and metabolic response of trail running and evaluate whether heart rate (HR) adequately reflects the exercise intensity or if the tissue-saturation index (TSI) could provide a more accurate measure during running in hilly terrain. Seventeen competitive runners (4 women, V̇O 2 max, 55 ± 6 mL · kg -1 · min -1 ; 13 men, V̇O 2 max, 68 ± 6 mL · kg -1 · min -1 ) performed a time trial on an off-road trail course. The course was made up of 2 laps covering a total distance of 7 km and included 6 steep uphill and downhill sections with an elevation gain of 486 m. All runners were equipped with a portable breath-by-breath gas analyzer, HR belt, global positioning system receiver, and near-infrared spectroscopy (NIRS) device to measure the TSI. During the trail run, the exercise intensity in the uphill and downhill sections was 94% ± 2% and 91% ± 3% of maximal heart rate, respectively, and 84% ± 8% and 68% ± 7% of V̇O 2 max, respectively. The oxygen uptake (V̇O 2 ) increased in the uphill sections and decreased in the downhill sections (P < .01). Although HR was unaffected by the altering slope conditions, the TSI was inversely correlated to the changes in V̇O 2 (r = -.70, P < .05). HR was unaffected by the continuously changing exercise intensity; however, TSI reflected the alternations in V̇O 2 . Recently used exclusively for scientific purposes, this NIRS-based variable may offer a more accurate alternative than HR to monitor running intensity in the future, especially for training and competition in hilly terrain.

  15. Biology and Medicine Division annual report, 1987

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

    Not Available

    Modern biology is characterized by rapid change. The development of new tools and the results derived from their application to various biological systems require significant shifts in our concepts and the strategies that are adopted to analyze and elucidate mechanisms. In parallel with exciting new scientific developments our organizational structure and programmatic emphases have altered. These changes and developments have enabled the life sciences at LBL to be better positioned to create and respond to new opportunities. The work summarized in this annual report reflects a vital multifaceted research program that is in the vanguard of the areas represented. Wemore » are committed to justifying the confidence expressed by LBL through the new mission statement and reorganizational changes designed to give greater prominence to the life sciences.« less

  16. Ensemble of sparse classifiers for high-dimensional biological data.

    PubMed

    Kim, Sunghan; Scalzo, Fabien; Telesca, Donatello; Hu, Xiao

    2015-01-01

    Biological data are often high in dimension while the number of samples is small. In such cases, the performance of classification can be improved by reducing the dimension of data, which is referred to as feature selection. Recently, a novel feature selection method has been proposed utilising the sparsity of high-dimensional biological data where a small subset of features accounts for most variance of the dataset. In this study we propose a new classification method for high-dimensional biological data, which performs both feature selection and classification within a single framework. Our proposed method utilises a sparse linear solution technique and the bootstrap aggregating algorithm. We tested its performance on four public mass spectrometry cancer datasets along with two other conventional classification techniques such as Support Vector Machines and Adaptive Boosting. The results demonstrate that our proposed method performs more accurate classification across various cancer datasets than those conventional classification techniques.

  17. GlycoDeNovo - an Efficient Algorithm for Accurate de novo Glycan Topology Reconstruction from Tandem Mass Spectra

    NASA Astrophysics Data System (ADS)

    Hong, Pengyu; Sun, Hui; Sha, Long; Pu, Yi; Khatri, Kshitij; Yu, Xiang; Tang, Yang; Lin, Cheng

    2017-08-01

    A major challenge in glycomics is the characterization of complex glycan structures that are essential for understanding their diverse roles in many biological processes. We present a novel efficient computational approach, named GlycoDeNovo, for accurate elucidation of the glycan topologies from their tandem mass spectra. Given a spectrum, GlycoDeNovo first builds an interpretation-graph specifying how to interpret each peak using preceding interpreted peaks. It then reconstructs the topologies of peaks that contribute to interpreting the precursor ion. We theoretically prove that GlycoDeNovo is highly efficient. A major innovative feature added to GlycoDeNovo is a data-driven IonClassifier which can be used to effectively rank candidate topologies. IonClassifier is automatically learned from experimental spectra of known glycans to distinguish B- and C-type ions from all other ion types. Our results showed that GlycoDeNovo is robust and accurate for topology reconstruction of glycans from their tandem mass spectra. [Figure not available: see fulltext.

  18. Variability of the reflectance coefficient of skylight from the ocean surface and its implications to ocean color.

    PubMed

    Gilerson, Alexander; Carrizo, Carlos; Foster, Robert; Harmel, Tristan

    2018-04-16

    The value and spectral dependence of the reflectance coefficient (ρ) of skylight from wind-roughened ocean surfaces is critical for determining accurate water leaving radiance and remote sensing reflectances from shipborne, AERONET-Ocean Color and satellite observations. Using a vector radiative transfer code, spectra of the reflectance coefficient and corresponding radiances near the ocean surface and at the top of the atmosphere (TOA) are simulated for a broad range of parameters including flat and windy ocean surfaces with wind speeds up to 15 m/s, aerosol optical thicknesses of 0-1 at 440nm, wavelengths of 400-900 nm, and variable Sun and viewing zenith angles. Results revealed a profound impact of the aerosol load and type on the spectral values of ρ. Such impacts, not included yet in standard processing, may produce significant inaccuracies in the reflectance spectra retrieved from above-water radiometry and satellite observations. Implications for satellite cal/val activities as well as potential changes in measurement and data processing schemes are discussed.

  19. Preparing Biology Teachers to Teach Evolution in a Project-Based Approach

    ERIC Educational Resources Information Center

    Cook, Kristin; Buck, Gayle; Park Rogers, Meredith

    2012-01-01

    This study investigates a project-based learning (PBL) approach to teaching evolution to inform efforts in teacher preparation. Data analysis of a secondary biology educator teaching evolution through a PBL approach illuminated: (1) active student voice, which allowed students to reflect on their positioning on evolution and consider multiple…

  20. Optical reflectance of solution processed quasi-superlattice ZnO and Al-doped ZnO (AZO) channel materials

    NASA Astrophysics Data System (ADS)

    Buckley, Darragh; McCormack, Robert; O'Dwyer, Colm

    2017-04-01

    The angle-resolved reflectance of high crystalline quality, c-axis oriented ZnO and AZO single and periodic quasi-superlattice (QSL) spin-coated TFT channels materials are presented. The data is analysed using an adapted model to accurately determine the spectral region for optical thickness and corresponding reflectance. The optical thickness agrees very well with measured thickness of 1-20 layered QSL thin films determined by transmission electron microscopy if the reflectance from lowest interference order is used. Directional reflectance for single layers or homogeneous QSLs of ZnO and AZO channel materials exhibit a consistent degree of anti-reflection characteristics from 30 to 60° (~10-12% reflection) for thickness ranging from ~40 nm to 500 nm. The reflectance of AZO single layer thin films is  <10% from 30 to 75° at 514.5 nm, and  <6% at 632.8 nm from 30-60°. The data show that ZnO and AZO with granular or periodic substructure behave optically as dispersive, continuous thin films of similar thickness, and angle-resolved spectral mapping provides a design rule for transparency or refractive index determination as a function of film thickness, substructure (dispersion) and viewing angle.

  1. From bricolage to BioBricks™: Synthetic biology and rational design.

    PubMed

    Lewens, Tim

    2013-12-01

    Synthetic biology is often described as a project that applies rational design methods to the organic world. Although humans have influenced organic lineages in many ways, it is nonetheless reasonable to place synthetic biology towards one end of a continuum between purely 'blind' processes of organic modification at one extreme, and wholly rational, design-led processes at the other. An example from evolutionary electronics illustrates some of the constraints imposed by the rational design methodology itself. These constraints reinforce the limitations of the synthetic biology ideal, limitations that are often freely acknowledged by synthetic biology's own practitioners. The synthetic biology methodology reflects a series of constraints imposed on finite human designers who wish, as far as is practicable, to communicate with each other and to intervene in nature in reasonably targeted and well-understood ways. This is better understood as indicative of an underlying awareness of human limitations, rather than as expressive of an objectionable impulse to mastery over nature. Copyright © 2013 Elsevier Ltd. All rights reserved.

  2. Biological effectiveness of neutrons: Research needs

    NASA Astrophysics Data System (ADS)

    Casarett, G. W.; Braby, L. A.; Broerse, J. J.; Elkind, M. M.; Goodhead, D. T.; Oleinick, N. L.

    1994-02-01

    The goal of this report was to provide a conceptual plan for a research program that would provide a basis for determining more precisely the biological effectiveness of neutron radiation with emphasis on endpoints relevant to the protection of human health. This report presents the findings of the experts for seven particular categories of scientific information on neutron biological effectiveness. Chapter 2 examines the radiobiological mechanisms underlying the assumptions used to estimate human risk from neutrons and other radiations. Chapter 3 discusses the qualitative and quantitative models used to organize and evaluate experimental observations and to provide extrapolations where direct observations cannot be made. Chapter 4 discusses the physical principles governing the interaction of radiation with biological systems and the importance of accurate dosimetry in evaluating radiation risk and reducing the uncertainty in the biological data. Chapter 5 deals with the chemical and molecular changes underlying cellular responses and the LET dependence of these changes. Chapter 6, in turn, discusses those cellular and genetic changes which lead to mutation or neoplastic transformation. Chapters 7 and 8 examine deterministic and stochastic effects, respectively, and the data required for the prediction of such effects at different organizational levels and for the extrapolation from experimental results in animals to risks for man. Gaps and uncertainties in this data are examined relative to data required for establishing radiation protection standards for neutrons and procedures for the effective and safe use of neutron and other high-LET radiation therapy.

  3. How to achieve more accurate comparisons in organ donation activity: time to effectiveness indicators.

    PubMed

    Deulofeu, R; Bodí, M A; Twose, J; López, P

    2010-06-01

    We are used to comparisons of activity using donation or transplantation population (pmp) rates between regions or countries, without a further evaluation of the process. But crude pmp rates do not clearly reflect real transplantation capacity, because organ procurement does not finish with the donation step; it is also necessary to know the utilization of the obtained organs. The objective of this study was to present methods and indicators deemed necessary to evaluate the effectiveness of the process. We have proposed the use of simple definitions and indicators to more accurately measure and compare the effectiveness of the total organ procurement process. To illustrate the use and performance of these indicators, we have presented the donation and transplantation activity in Catalonia from 2002 to 2007.

  4. Accurate simulations of helium pick-up experiments using a rejection-free Monte Carlo method

    NASA Astrophysics Data System (ADS)

    Dutra, Matthew; Hinde, Robert

    2018-04-01

    In this paper, we present Monte Carlo simulations of helium droplet pick-up experiments with the intention of developing a robust and accurate theoretical approach for interpreting experimental helium droplet calorimetry data. Our approach is capable of capturing the evaporative behavior of helium droplets following dopant acquisition, allowing for a more realistic description of the pick-up process. Furthermore, we circumvent the traditional assumption of bulk helium behavior by utilizing density functional calculations of the size-dependent helium droplet chemical potential. The results of this new Monte Carlo technique are compared to commonly used Poisson pick-up statistics for simulations that reflect a broad range of experimental parameters. We conclude by offering an assessment of both of these theoretical approaches in the context of our observed results.

  5. System biology of gene regulation.

    PubMed

    Baitaluk, Michael

    2009-01-01

    A famous joke story that exhibits the traditionally awkward alliance between theory and experiment and showing the differences between experimental biologists and theoretical modelers is when a University sends a biologist, a mathematician, a physicist, and a computer scientist to a walking trip in an attempt to stimulate interdisciplinary research. During a break, they watch a cow in a field nearby and the leader of the group asks, "I wonder how one could decide on the size of a cow?" Since a cow is a biological object, the biologist responded first: "I have seen many cows in this area and know it is a big cow." The mathematician argued, "The true volume is determined by integrating the mathematical function that describes the outer surface of the cow's body." The physicist suggested: "Let's assume the cow is a sphere...." Finally the computer scientist became nervous and said that he didn't bring his computer because there is no Internet connection up there on the hill. In this humorous but explanatory story suggestions proposed by theorists can be taken to reflect the view of many experimental biologists that computer scientists and theorists are too far removed from biological reality and therefore their theories and approaches are not of much immediate usefulness. Conversely, the statement of the biologist mirrors the view of many traditional theoretical and computational scientists that biological experiments are for the most part simply descriptive, lack rigor, and that much of the resulting biological data are of questionable functional relevance. One of the goals of current biology as a multidisciplinary science is to bring people from different scientific areas together on the same "hill" and teach them to speak the same "language." In fact, of course, when presenting their data, most experimentalist biologists do provide an interpretation and explanation for the results, and many theorists/computer scientists aim to answer (or at least to fully describe

  6. Profitable capitation requires accurate costing.

    PubMed

    West, D A; Hicks, L L; Balas, E A; West, T D

    1996-01-01

    In the name of costing accuracy, nurses are asked to track inventory use on per treatment basis when more significant costs, such as general overhead and nursing salaries, are usually allocated to patients or treatments on an average cost basis. Accurate treatment costing and financial viability require analysis of all resources actually consumed in treatment delivery, including nursing services and inventory. More precise costing information enables more profitable decisions as is demonstrated by comparing the ratio-of-cost-to-treatment method (aggregate costing) with alternative activity-based costing methods (ABC). Nurses must participate in this costing process to assure that capitation bids are based upon accurate costs rather than simple averages.

  7. Do case-generic measures of queue performance for bypass surgery accurately reflect the waiting-list experiences of those most urgent?

    PubMed

    Burstein, Jason; Lee, Douglas S; Alter, David A

    2006-02-01

    Queue performance is typically assessed using generic measures, which capture the queue in aggregate. The objective of this study was to examine whether case-generic measures of queue performance appropriately reflected the waiting-list experiences of those patients with greatest disease severity. We examined the queue for isolated coronary artery bypass grafting (CABG) in Ontario between April 1993 and March 2000 using data obtained from the Cardiac Care Network. Our primary measure of queue performance was the proportion of patients who received their bypass surgery within their recommended maximum waiting times (%RMWTs) in any given month. We compared case-generic measures of queue performance to case-specific measures of queue performance stratified by urgency level. The queue was largely comprised of elective cases ranging from 73% (1993) to 57%(1999). Urgent patients comprised the minority of the queue ranging from 14% (1993) to 20% (1999). Case-generic month-to-month variations in the percentage of cases completed within RMWTs (an aggregated waiting list measure encompassing the characteristics of all patients in the queue) closely resembled the experiences of elective patients (R2 = 0.81), but conversely, bore little relationship to the waiting-list experiences of those most urgent (R2 = 0.15). Case-generic measures of queue performance for bypass surgery in Ontario were not reflective of the waiting-list experiences of those most urgent. Our results reinforce the concept that urgency-specific waiting list monitoring systems are required to best evaluate and appropriately respond to fluctuations in queue performance.

  8. The Learning-Focused Transformation of Biology and Physics Core Courses at the U.S. Air Force Academy

    ERIC Educational Resources Information Center

    Sagendorf, Kenneth; Noyd, Robert K.; Morris, D. Brent

    2009-01-01

    An institution-wide focus on deep learning has made significant changes in the biology and physics core course curriculum at the U.S. Air Force Academy. The biology course director has reworked course objectives to reflect the learning-focused approach to teaching, while the physics curriculum has adopted new learning outcomes and ways to…

  9. [Medical and biological consequences of nuclear disasters].

    PubMed

    Stalpers, Lukas J A; van Dullemen, Simon; Franken, N A P Klaas

    2012-01-01

    Medical risks of radiation exaggerated; psychological risks underestimated. The discussion about atomic energy has become topical again following the nuclear accident in Fukushima. There is some argument about the gravity of medical and biological consequences of prolonged exposure to radiation. The risk of cancer following a low dose of radiation is usually estimated by linear extrapolation of the incidence of cancer among survivors of the atomic bombs dropped on Hiroshima and Nagasaki in 1945. The radiobiological linear-quadratic model (LQ-model) gives a more accurate description of observed data, is radiobiologically more plausible and is better supported by experimental and clinical data. On the basis of this model there is less risk of cancer being induced following radiation exposure. The gravest consequence of Chernobyl and Fukushima is not the medical and biological damage, but the psychological and economical impact on rescue workers and former inhabitants.

  10. Defined daily doses (DDD) do not accurately reflect opioid doses used in contemporary chronic pain treatment.

    PubMed

    Nielsen, Suzanne; Gisev, Natasa; Bruno, Raimondo; Hall, Wayne; Cohen, Milton; Larance, Briony; Campbell, Gabrielle; Shanahan, Marian; Blyth, Fiona; Lintzeris, Nicholas; Pearson, Sallie; Mattick, Richard; Degenhardt, Louisa

    2017-05-01

    To assess how well the defined daily dose (DDD) metric reflects opioid utilisation among chronic non-cancer pain patients. Descriptive, cross-sectional study, utilising a 7-day medication diary. Community-based treatment settings, Australia. A sample of 1101 people prescribed opioids for chronic non-cancer pain. Opioid dose data was collected via a self-completed 7-day medication diary capturing names, strengths and doses of each medication taken in the past week. Median daily dose was calculated for each opioid. Comparisons were made to the World Health Organization's (WHO) DDD metric. WHO DDDs ranged from 0.6 to 7.1 times the median opioid doses used by the sample. For transdermal fentanyl and oral hydromorphone, the median dose was comparable with the DDD. The DDD for methadone was 0.6 times lower than the median doses used by this sample of chronic pain patients. In contrast, the DDD for oxycodone and transdermal buprenorphine, the most commonly used strong opioids for chronic pain in Australia, was two to seven times higher than actual doses used. For many opioids, there are key differences between the actual doses used in clinical practice and the WHO's DDDs. The interpretation of opioid utilisation studies using population-level DDDs may be limited, and a recalibration of the DDD for many opioids or the reporting of opioid utilisation in oral morphine equivalent doses is recommended. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  11. Monitoring biological heterogeneity in a northern mixed prairie using hierarchical remote sensing methods

    NASA Astrophysics Data System (ADS)

    Zhang, Chunhua

    Heterogeneity, the degree of dissimilarity, is one of the most important and widely applicable concepts in ecology. It is highly related to ecosystem conditions and features wildlife habitat. Grasslands have been described as inherently heterogeneous because their composition and productivity are highly variable across multiple scales. Therefore, biological heterogeneity can be an indicator of ecosystem health. The mixed prairie in Canada, characterized by its semiarid environment, sparse canopy, and plant litter, offers a challenging region for environmental research using remote sensing techniques. This thesis dwells with the plant canopy heterogeneity of the mixed prairie ecosystem in the Grasslands National Park (GNP) and surrounding pastures by combining field biological parameters (e.g., grass cover, leaf area index, and biomass), field collected hyperspectral data, and hierarchical resolution satellite imagery. The thesis scrutinized four aspects of heterogeneity study: the importance of scale in grassland research, relationships between biological parameters and remotely collected data, methodology of measuring biological heterogeneity, and the influence of climatic variation on grasslands biological heterogeneity. First, the importance of scale is examined by applying the semivariogram analysis on field collected hyperspectral and biophysical data. Results indicate that 15 - 20 m should be the appropriate resolution when variations of biological parameters and canopy reflectance are sampled. Therefore, it is reasonable to use RADARSAT 1, Landsat TM, and SPOT images, whose resolutions are around 20 m, to assess the variation of biological heterogeneity. Second, the efficiency of vegetation indices derived from SPOT 4 and Landsat 5 TM images in monitoring the northern mixed prairie health was examined using Pearson's correlation and stepwise regression analyses. Results show that the spectral curve of the grass canopy is similar to that of the bare soil with

  12. Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome.

    PubMed

    Li, Fuyi; Li, Chen; Marquez-Lago, Tatiana T; Leier, André; Akutsu, Tatsuya; Purcell, Anthony W; Smith, A Ian; Lithgow, Trevor; Daly, Roger J; Song, Jiangning; Chou, Kuo-Chen

    2018-06-27

    Kinase-regulated phosphorylation is a ubiquitous type of post-translational modification (PTM) in both eukaryotic and prokaryotic cells. Phosphorylation plays fundamental roles in many signalling pathways and biological processes, such as protein degradation and protein-protein interactions. Experimental studies have revealed that signalling defects caused by aberrant phosphorylation are highly associated with a variety of human diseases, especially cancers. In light of this, a number of computational methods aiming to accurately predict protein kinase family-specific or kinase-specific phosphorylation sites have been established, thereby facilitating phosphoproteomic data analysis. In this work, we present Quokka, a novel bioinformatics tool that allows users to rapidly and accurately identify human kinase family-regulated phosphorylation sites. Quokka was developed by using a variety of sequence scoring functions combined with an optimized logistic regression algorithm. We evaluated Quokka based on well-prepared up-to-date benchmark and independent test datasets, curated from the Phospho.ELM and UniProt databases, respectively. The independent test demonstrates that Quokka improves the prediction performance compared with state-of-the-art computational tools for phosphorylation prediction. In summary, our tool provides users with high-quality predicted human phosphorylation sites for hypothesis generation and biological validation. The Quokka webserver and datasets are freely available at http://quokka.erc.monash.edu/. Supplementary data are available at Bioinformatics online.

  13. Diffracting Reflection: A Move beyond Reflective Practice

    ERIC Educational Resources Information Center

    Mitchell, Veronica Ann

    2017-01-01

    Reflective practice has become a core component in higher education studies. In the health sciences, reflective tasks are required throughout the undergraduate programmes, yet many students struggle to find value in these tasks for their present and future professional practice. Benefits that can be derived from the process are undermined by this…

  14. Lessons from a phenotyping center revealed by the genome-guided mapping of powdery mildew resistance loci

    USDA-ARS?s Scientific Manuscript database

    The genomics era brought unprecedented tools for genetic analysis of host resistance, but careful attention is needed on obtaining accurate and reproducible phenotypes so that genomic results appropriately reflect biology. Phenotyping host resistance by natural infection in the field can produce var...

  15. Correlative imaging across microscopy platforms using the fast and accurate relocation of microscopic experimental regions (FARMER) method

    NASA Astrophysics Data System (ADS)

    Huynh, Toan; Daddysman, Matthew K.; Bao, Ying; Selewa, Alan; Kuznetsov, Andrey; Philipson, Louis H.; Scherer, Norbert F.

    2017-05-01

    Imaging specific regions of interest (ROIs) of nanomaterials or biological samples with different imaging modalities (e.g., light and electron microscopy) or at subsequent time points (e.g., before and after off-microscope procedures) requires relocating the ROIs. Unfortunately, relocation is typically difficult and very time consuming to achieve. Previously developed techniques involve the fabrication of arrays of features, the procedures for which are complex, and the added features can interfere with imaging the ROIs. We report the Fast and Accurate Relocation of Microscopic Experimental Regions (FARMER) method, which only requires determining the coordinates of 3 (or more) conspicuous reference points (REFs) and employs an algorithm based on geometric operators to relocate ROIs in subsequent imaging sessions. The 3 REFs can be quickly added to various regions of a sample using simple tools (e.g., permanent markers or conductive pens) and do not interfere with the ROIs. The coordinates of the REFs and the ROIs are obtained in the first imaging session (on a particular microscope platform) using an accurate and precise encoded motorized stage. In subsequent imaging sessions, the FARMER algorithm finds the new coordinates of the ROIs (on the same or different platforms), using the coordinates of the manually located REFs and the previously recorded coordinates. FARMER is convenient, fast (3-15 min/session, at least 10-fold faster than manual searches), accurate (4.4 μm average error on a microscope with a 100x objective), and precise (almost all errors are <8 μm), even with deliberate rotating and tilting of the sample well beyond normal repositioning accuracy. We demonstrate this versatility by imaging and re-imaging a diverse set of samples and imaging methods: live mammalian cells at different time points; fixed bacterial cells on two microscopes with different imaging modalities; and nanostructures on optical and electron microscopes. FARMER can be readily

  16. Nano-biosensors in cellular and molecular biology.

    PubMed

    Moradi, Sajad; Khaledian, Salar; Abdoli, Mohadese; Shahlaei, Mohsen; Kahrizi, Danial

    2018-04-30

    Detection and quantification of various biological and non-biological species today is one of the most important pillars of all experimental sciences, especially sciences related to human health. This may apply to a chemical in the factory wastewater or to identify a cancer cell in a person's body, it may be apply to trace a useful industrial microorganism or human or plant pathogenic microorganisms. In this regard, scientists from various sciences have always striven to design and provide tools and techniques for identifying and quantifying as accurately as possible to trace various analyte types with greater precision and specificity. Nano science, which has flourished in recent years and is nowadays widely used in all fields of science, also has a unique place in the design and manufacture of sensors and this, in addition to the new and special characteristics of nanoparticles, is due to the ability of nano-devices to penetrate into very tiny places to track the species. On the other hand, due to the high specificity of biological molecules in identifying and connecting to their receptors that have evolved over millions of years, Scientists are now trying to design hybrid devices using nano science and biology, called Nano-biosensors So that they can trace and quantify target molecules in very small amounts and in inaccessible places, such as within the organs and even the cells.

  17. Converting differential-equation models of biological systems to membrane computing.

    PubMed

    Muniyandi, Ravie Chandren; Zin, Abdullah Mohd; Sanders, J W

    2013-12-01

    This paper presents a method to convert the deterministic, continuous representation of a biological system by ordinary differential equations into a non-deterministic, discrete membrane computation. The dynamics of the membrane computation is governed by rewrite rules operating at certain rates. That has the advantage of applying accurately to small systems, and to expressing rates of change that are determined locally, by region, but not necessary globally. Such spatial information augments the standard differentiable approach to provide a more realistic model. A biological case study of the ligand-receptor network of protein TGF-β is used to validate the effectiveness of the conversion method. It demonstrates the sense in which the behaviours and properties of the system are better preserved in the membrane computing model, suggesting that the proposed conversion method may prove useful for biological systems in particular. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  18. Estimating a structured covariance matrix from multi-lab measurements in high-throughput biology.

    PubMed

    Franks, Alexander M; Csárdi, Gábor; Drummond, D Allan; Airoldi, Edoardo M

    2015-03-01

    We consider the problem of quantifying the degree of coordination between transcription and translation, in yeast. Several studies have reported a surprising lack of coordination over the years, in organisms as different as yeast and human, using diverse technologies. However, a close look at this literature suggests that the lack of reported correlation may not reflect the biology of regulation. These reports do not control for between-study biases and structure in the measurement errors, ignore key aspects of how the data connect to the estimand, and systematically underestimate the correlation as a consequence. Here, we design a careful meta-analysis of 27 yeast data sets, supported by a multilevel model, full uncertainty quantification, a suite of sensitivity analyses and novel theory, to produce a more accurate estimate of the correlation between mRNA and protein levels-a proxy for coordination. From a statistical perspective, this problem motivates new theory on the impact of noise, model mis-specifications and non-ignorable missing data on estimates of the correlation between high dimensional responses. We find that the correlation between mRNA and protein levels is quite high under the studied conditions, in yeast, suggesting that post-transcriptional regulation plays a less prominent role than previously thought.

  19. Estimating a structured covariance matrix from multi-lab measurements in high-throughput biology

    PubMed Central

    Franks, Alexander M.; Csárdi, Gábor; Drummond, D. Allan; Airoldi, Edoardo M.

    2015-01-01

    We consider the problem of quantifying the degree of coordination between transcription and translation, in yeast. Several studies have reported a surprising lack of coordination over the years, in organisms as different as yeast and human, using diverse technologies. However, a close look at this literature suggests that the lack of reported correlation may not reflect the biology of regulation. These reports do not control for between-study biases and structure in the measurement errors, ignore key aspects of how the data connect to the estimand, and systematically underestimate the correlation as a consequence. Here, we design a careful meta-analysis of 27 yeast data sets, supported by a multilevel model, full uncertainty quantification, a suite of sensitivity analyses and novel theory, to produce a more accurate estimate of the correlation between mRNA and protein levels—a proxy for coordination. From a statistical perspective, this problem motivates new theory on the impact of noise, model mis-specifications and non-ignorable missing data on estimates of the correlation between high dimensional responses. We find that the correlation between mRNA and protein levels is quite high under the studied conditions, in yeast, suggesting that post-transcriptional regulation plays a less prominent role than previously thought. PMID:25954056

  20. Case studies of community college non-science majors: Effects of self-regulatory interventions on biology self-efficacy and biological literacy

    NASA Astrophysics Data System (ADS)

    Maurer, Matthew J.

    Science literacy has been at the heart of current reform efforts in science education. The focus on developing essential skills needed for individual ability to be literate in science has been at the forefront of most K--12 science curricula. Reform efforts have begun to stretch into the postsecondary arena as well, with an ever increasing dialogue regarding the need for attention to science literacy by college students, especially non-science majors. This study set out to investigate how the use of self-regulatory interventions (specifically, goal setting, concept mapping, and reflective writing) affected student biology self-efficacy and biological literacy. This study employed a qualitative research design, analyzing three case studies. Participants in the study received ten self-regulatory interventions as a set of portfolio assignments. Portfolio work was qualitatively analyzed and coded for self-efficacy, as well as evidence of biological literacy. A biology self-efficacy survey was administered pre- and post- to provide a means of self-efficacy data triangulation. Literacy data was supported via a biological literacy rubric, constructed specifically for this study. Results indicated that mastery experiences were the source of biology self-efficacy. Self-efficacy for specific tasks increased over time, and changes in self-efficacy were corroborated by the self-efficacy survey. Students were found to express biological literacy at nominal, functional, or conceptual levels depending on the specific task. This was supported by data from the biological literacy rubric scores. Final conclusions and implications for the study indicated the need for further research with more samples of students in similar and different contexts. Given the fact that the literature in this area is sparse, the results obtained here have only begun to delve into this area of research. Generalization to other biology courses or contexts outside of the one presented in this study was